Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold142
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1252394
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.30
Warning! 144568 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:1046156 original size:2 final size:2
Alignment explanation
Indices: 1046149--1046186 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1046139 TCGCCTCATT
1046149 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1046187 AGCAACAACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1046590 original size:17 final size:17
Alignment explanation
Indices: 1046568--1046616 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
1046558 CTACCAATTT
1046568 AGAATATTAGCTACACA
1 AGAATATTAGCTACACA
* *
1046585 AGAATATCAGCTACACT
1 AGAATATTAGCTACACA
1046602 AGAATATTAGCTACA
1 AGAATATTAGCTACA
1046617 TTCTAGCTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.24
Consensus pattern (17 bp):
AGAATATTAGCTACACA
Found at i:1047107 original size:2 final size:2
Alignment explanation
Indices: 1047100--1047186 Score: 149
Period size: 2 Copynumber: 43.5 Consensus size: 2
1047090 GTATTAAAAC
*
1047100 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GTA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G-A GA GA GA
1047143 GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1047184 GA G
1 GA G
1047187 TTTAACATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.01
2 79 0.98
3 1 0.01
ACGTcount: A:0.47, C:0.00, G:0.52, T:0.01
Consensus pattern (2 bp):
GA
Found at i:1051882 original size:2 final size:2
Alignment explanation
Indices: 1051841--1051867 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1051831 TATTAAAATA
1051841 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1051868 TATTCAGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1057172 original size:2 final size:2
Alignment explanation
Indices: 1057167--1057203 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1057157 GTACAAACCT
*
1057167 AC AC AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1057204 TAAAATTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:1065889 original size:2 final size:2
Alignment explanation
Indices: 1065884--1065927 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1065874 CTCTTAATTT
1065884 GA GA GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1065925 GA G
1 GA G
1065928 GGTTTTAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1071493 original size:2 final size:2
Alignment explanation
Indices: 1071486--1071515 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1071476 NNNNNNNNNN
1071486 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1071516 GCATTCACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1075625 original size:2 final size:2
Alignment explanation
Indices: 1075620--1075648 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1075610 AAAATGATAT
1075620 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1075649 GGAGGGGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1082375 original size:93 final size:94
Alignment explanation
Indices: 1082145--1082385 Score: 330
Period size: 94 Copynumber: 2.6 Consensus size: 94
1082135 AGTATGACAT
*
1082145 TGAAGAAATACAATCAACTA---GATTTTTTCGTAAATGTCCATTTTGTCTTATATCCCTTCCTT
1 TGAAGAAATACAATCAACTAGTTGATTTTTTC-TGAATGTCCATTTTGTCTTATAT-CC-TCCTT
*
1082207 CCTTTATATCCTTTTTTCGCTTTCTGTTGGTG
63 CCGTTATATCCTTTTTTCGCTTTCTGTTGGTG
* ** *
1082239 AGAAGAAATACAATCAACTAGTTTGGGTTTTTCTGATTGTCCATTTTGTCTTATAT-C-CCTTCC
1 TGAAGAAATACAATCAACTAG-TTGATTTTTTCTGAATGTCCATTTTGTCTTATATCCTCCTTCC
1082302 GTTATATCCATTTTTTCGCTTTCTGTTGGTG
65 GTTATATCC-TTTTTTCGCTTTCTGTTGGTG
* *
1082333 TGAAGAAATACAATCAATTAGTTGTTTTTTTCTGAATGTCCATTTTGTCTTAT
1 TGAAGAAATACAATCAACTAGTTGATTTTTTCTGAATGTCCATTTTGTCTTAT
1082386 GTCCATTTTG
Statistics
Matches: 131, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
93 43 0.33
94 59 0.45
95 1 0.01
97 21 0.16
98 7 0.05
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.46
Consensus pattern (94 bp):
TGAAGAAATACAATCAACTAGTTGATTTTTTCTGAATGTCCATTTTGTCTTATATCCTCCTTCCG
TTATATCCTTTTTTCGCTTTCTGTTGGTG
Found at i:1082387 original size:16 final size:16
Alignment explanation
Indices: 1082368--1082401 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1082358 TTTTTTCTGA
1082368 ATGTCCATTTTGTCTT
1 ATGTCCATTTTGTCTT
1082384 ATGTCCATTTTGTCTT
1 ATGTCCATTTTGTCTT
1082400 AT
1 AT
1082402 ATCCCTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.12, T:0.56
Consensus pattern (16 bp):
ATGTCCATTTTGTCTT
Found at i:1083574 original size:22 final size:22
Alignment explanation
Indices: 1083542--1083583 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1083532 AATCCCAACA
1083542 AAAAAAATATA-AAACAAACCGG
1 AAAAAAATATATAAA-AAACCGG
*
1083564 AAAAAAGTATATAAAAAACC
1 AAAAAAATATATAAAAAACC
1083584 CAACTTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.69, C:0.12, G:0.07, T:0.12
Consensus pattern (22 bp):
AAAAAAATATATAAAAAACCGG
Found at i:1086990 original size:12 final size:12
Alignment explanation
Indices: 1086969--1087006 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1086959 TTGTATTCAA
*
1086969 TTGTTGTTTTTT
1 TTGTTTTTTTTT
1086981 TTGTTTTTTTTT
1 TTGTTTTTTTTT
1086993 TT-TTATTTTTTT
1 TTGTT-TTTTTTT
1087005 TT
1 TT
1087007 AGAAATACGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 2 0.08
12 22 0.92
ACGTcount: A:0.03, C:0.00, G:0.08, T:0.89
Consensus pattern (12 bp):
TTGTTTTTTTTT
Found at i:1086994 original size:14 final size:14
Alignment explanation
Indices: 1086975--1087006 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1086965 TCAATTGTTG
*
1086975 TTTTTTTTGTTTTT
1 TTTTTTTTATTTTT
1086989 TTTTTTTTATTTTT
1 TTTTTTTTATTTTT
1087003 TTTT
1 TTTT
1087007 AGAAATACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.03, C:0.00, G:0.03, T:0.94
Consensus pattern (14 bp):
TTTTTTTTATTTTT
Found at i:1091034 original size:44 final size:44
Alignment explanation
Indices: 1090971--1091181 Score: 248
Period size: 44 Copynumber: 5.1 Consensus size: 44
1090961 GCGTCCAACG
* * *
1090971 GCATCTTCGCTAGCCAAGGGTGTACGATCCTCTCTGCTCCTCTA
1 GCATCTTCGCTAGTCAAGGGTTTACGATCCACTCTGCTCCTCTA
* *
1091015 GCATCTTCGCTAGTCAAGGGTTTACGATCCACCCTGTTCCTCTA
1 GCATCTTCGCTAGTCAAGGGTTTACGATCCACTCTGCTCCTCTA
* * *
1091059 GCATCTTCGATAGCCAAGGGTTTACGATCCTCTCTGCTCCTCTA
1 GCATCTTCGCTAGTCAAGGGTTTACGATCCACTCTGCTCCTCTA
*
1091103 GCA---T--C---T----GGTTTACGATCCAGTCTGCTCCTCTA
1 GCATCTTCGCTAGTCAAGGGTTTACGATCCACTCTGCTCCTCTA
*
1091135 GCATCTTCGCTAGTCAAGGGTTTACGATCCAGTCTGCTCCTCTA
1 GCATCTTCGCTAGTCAAGGGTTTACGATCCACTCTGCTCCTCTA
1091179 GCA
1 GCA
1091182 GAGTGGATCG
Statistics
Matches: 141, Mismatches: 14, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
32 27 0.19
35 1 0.01
37 1 0.01
40 1 0.01
41 1 0.01
44 110 0.78
ACGTcount: A:0.18, C:0.32, G:0.19, T:0.31
Consensus pattern (44 bp):
GCATCTTCGCTAGTCAAGGGTTTACGATCCACTCTGCTCCTCTA
Found at i:1091114 original size:32 final size:32
Alignment explanation
Indices: 1091077--1091140 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
1091067 GATAGCCAAG
*
1091077 GGTTTACGATCCTCTCTGCTCCTCTAGCATCT
1 GGTTTACGATCCACTCTGCTCCTCTAGCATCT
*
1091109 GGTTTACGATCCAGTCTGCTCCTCTAGCATCT
1 GGTTTACGATCCACTCTGCTCCTCTAGCATCT
1091141 TCGCTAGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.14, C:0.33, G:0.17, T:0.36
Consensus pattern (32 bp):
GGTTTACGATCCACTCTGCTCCTCTAGCATCT
Found at i:1091132 original size:76 final size:76
Alignment explanation
Indices: 1091033--1091181 Score: 235
Period size: 76 Copynumber: 2.0 Consensus size: 76
1091023 GCTAGTCAAG
* *
1091033 GGTTTACGATCCACCCTGTTCCTCTAGCATCTTCGATAGCCAAGGGTTTACGATCCTCTCTGCTC
1 GGTTTACGATCCACCCTGCTCCTCTAGCATCTTCGATAGCCAAGGGTTTACGATCCACTCTGCTC
1091098 CTCTAGCATCT
66 CTCTAGCATCT
** * * *
1091109 GGTTTACGATCCAGTCTGCTCCTCTAGCATCTTCGCTAGTCAAGGGTTTACGATCCAGTCTGCTC
1 GGTTTACGATCCACCCTGCTCCTCTAGCATCTTCGATAGCCAAGGGTTTACGATCCACTCTGCTC
1091174 CTCTAGCA
66 CTCTAGCA
1091182 GAGTGGATCG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 66 1.00
ACGTcount: A:0.17, C:0.32, G:0.19, T:0.32
Consensus pattern (76 bp):
GGTTTACGATCCACCCTGCTCCTCTAGCATCTTCGATAGCCAAGGGTTTACGATCCACTCTGCTC
CTCTAGCATCT
Found at i:1091819 original size:2 final size:2
Alignment explanation
Indices: 1091814--1091849 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1091804 AGATAAAAAA
* *
1091814 TC TC TC TC TC TC TC TC TC TT TT TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1091850 CAAAACTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:1107335 original size:17 final size:17
Alignment explanation
Indices: 1107310--1107342 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1107300 ATACTGCATG
1107310 CATGGTTACTACTTAAC
1 CATGGTTACTACTTAAC
*
1107327 CATGTTTACTACTTAA
1 CATGGTTACTACTTAA
1107343 GGAAGGTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (17 bp):
CATGGTTACTACTTAAC
Found at i:1107448 original size:2 final size:2
Alignment explanation
Indices: 1107443--1107469 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1107433 TTCAATTTTT
1107443 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1107470 TTAAATCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1109867 original size:12 final size:12
Alignment explanation
Indices: 1109850--1109875 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1109840 ATGTATAGTA
1109850 TATATACGTCCC
1 TATATACGTCCC
1109862 TATATACGTCCC
1 TATATACGTCCC
1109874 TA
1 TA
1109876 ACCCGATCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.35
Consensus pattern (12 bp):
TATATACGTCCC
Found at i:1113048 original size:21 final size:21
Alignment explanation
Indices: 1113018--1113364 Score: 480
Period size: 21 Copynumber: 16.5 Consensus size: 21
1113008 NNNNNNNNNN
1113018 GACTTTTTATCTCGTTATAAC
1 GACTTTTTATCTCGTTATAAC
*
1113039 GACATTTTATCTCGTTATAAC
1 GACTTTTTATCTCGTTATAAC
* *
1113060 GACTTTTTATCTCGTAATAAT
1 GACTTTTTATCTCGTTATAAC
1113081 GACTTTTTATCTCGTTATAAC
1 GACTTTTTATCTCGTTATAAC
*
1113102 GACATTTTATCTCGTTATAAC
1 GACTTTTTATCTCGTTATAAC
*
1113123 GACATTTTATCTCGTTATAAC
1 GACTTTTTATCTCGTTATAAC
* *
1113144 GACTTTTAAACTCGTTATAAC
1 GACTTTTTATCTCGTTATAAC
* ** *
1113165 GACTTTTAAAAGTCGTAATAAC
1 GACTTTT-TATCTCGTTATAAC
1113187 GACTTTTTATCTCGTTATAAC
1 GACTTTTTATCTCGTTATAAC
*
1113208 GACATTTTATCTCGTTATAAC
1 GACTTTTTATCTCGTTATAAC
*
1113229 GACTTTTTATCTCGTAATAAC
1 GACTTTTTATCTCGTTATAAC
*** ** *
1113250 GACTTAAAAAAGTCGTAATAAC
1 GACTT-TTTATCTCGTTATAAC
1113272 GACTTTTTATCTCGTTATAAC
1 GACTTTTTATCTCGTTATAAC
*
1113293 GACCTTTTATCTCGTTATAAC
1 GACTTTTTATCTCGTTATAAC
1113314 GACTTTTTATCTCGTTATAAC
1 GACTTTTTATCTCGTTATAAC
1113335 GAC-TTTTATCTCGTTATAAC
1 GACTTTTTATCTCGTTATAAC
*
1113355 GACATTTTAT
1 GACTTTTTAT
1113365 TATTTTTTTT
Statistics
Matches: 291, Mismatches: 32, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
20 20 0.07
21 236 0.81
22 35 0.12
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.43
Consensus pattern (21 bp):
GACTTTTTATCTCGTTATAAC
Found at i:1113234 original size:85 final size:85
Alignment explanation
Indices: 1113018--1113342 Score: 526
Period size: 85 Copynumber: 3.8 Consensus size: 85
1113008 NNNNNNNNNN
*
1113018 GACTTTTTATCTCGTTATAACGACATTTTATCTCGTTATAACGACTTTTTATCTCGTAATAATGA
1 GACTTTTTATCTCGTTATAACGACATTTTATCTCGTTATAACGACTTTTTATCTCGTAATAACGA
* ** *
1113083 CTTTT-TATCTCGTTATAAC
66 CTTTTAAAAGTCGTAATAAC
* * * *
1113102 GACATTTTATCTCGTTATAACGACATTTTATCTCGTTATAACGACTTTTAAACTCGTTATAACGA
1 GACTTTTTATCTCGTTATAACGACATTTTATCTCGTTATAACGACTTTTTATCTCGTAATAACGA
1113167 CTTTTAAAAGTCGTAATAAC
66 CTTTTAAAAGTCGTAATAAC
1113187 GACTTTTTATCTCGTTATAACGACATTTTATCTCGTTATAACGACTTTTTATCTCGTAATAACGA
1 GACTTTTTATCTCGTTATAACGACATTTTATCTCGTTATAACGACTTTTTATCTCGTAATAACGA
**
1113252 CTTAAAAAAGTCGTAATAAC
66 CTTTTAAAAGTCGTAATAAC
* *
1113272 GACTTTTTATCTCGTTATAACGACCTTTTATCTCGTTATAACGACTTTTTATCTCGTTATAACGA
1 GACTTTTTATCTCGTTATAACGACATTTTATCTCGTTATAACGACTTTTTATCTCGTAATAACGA
1113337 CTTTTA
66 CTTTTA
1113343 TCTCGTTATA
Statistics
Matches: 221, Mismatches: 19, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
84 65 0.29
85 156 0.71
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.42
Consensus pattern (85 bp):
GACTTTTTATCTCGTTATAACGACATTTTATCTCGTTATAACGACTTTTTATCTCGTAATAACGA
CTTTTAAAAGTCGTAATAAC
Found at i:1114466 original size:16 final size:17
Alignment explanation
Indices: 1114438--1114469 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1114428 ATAAAATGAC
1114438 TGAAAAGAAAAGAAAAT
1 TGAAAAGAAAAGAAAAT
1114455 TGAAAA-AAAAGAAAA
1 TGAAAAGAAAAGAAAA
1114470 CCTCATCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (17 bp):
TGAAAAGAAAAGAAAAT
Found at i:1122362 original size:59 final size:61
Alignment explanation
Indices: 1122213--1122378 Score: 255
Period size: 59 Copynumber: 2.7 Consensus size: 61
1122203 CAATGATACT
*
1122213 ATGTACTGATTGTTGTAGCTACTATATCGTTGAGCCTTGTCCCCCAGTACATGTATAATGATTCG
1 ATGTACTGATTGTTGTAGCTACTATATCGTTGAGCTTTGT-CCCC---ACATGTATAATGATTCG
1122278 ATGTACTGATTGTTGTAGCTACTATATCGTTGAGCTTTGTCCCC-CA-GTATAATGATTCG
1 ATGTACTGATTGTTGTAGCTACTATATCGTTGAGCTTTGTCCCCACATGTATAATGATTCG
* *
1122337 ATGTACTGATTGTTGTAGCTTCTATATCGGTGAGCTTTGTCC
1 ATGTACTGATTGTTGTAGCTACTATATCGTTGAGCTTTGTCC
1122379 ACTGGTCGGA
Statistics
Matches: 98, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
59 53 0.54
60 2 0.02
64 4 0.04
65 39 0.40
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (61 bp):
ATGTACTGATTGTTGTAGCTACTATATCGTTGAGCTTTGTCCCCACATGTATAATGATTCG
Found at i:1135966 original size:92 final size:92
Alignment explanation
Indices: 1135795--1135995 Score: 214
Period size: 92 Copynumber: 2.2 Consensus size: 92
1135785 AAGGAGGTCC
* *
1135795 TATTTAATTTGGTTACAATAGTTACAGCTATATTCTGTGGGTGACAAAAGGTAACACATGTGAAA
1 TATTTAATTTGGTTACAATAGTTACAGCTATATTCTATGGGTGACAAAAGGGAACACATGTGAAA
* *
1135860 AGCCTTTTTCTG-TTTAGCAGAGAGTCT
66 AGCCATTTTCTGTTTTA-CAGAGAGCCT
* * *
1135887 TATTTCATTTGGTTACAATAGTTACCGCTATATTCTCAT-GGTGAC-ATAGGGAA-ACAGTGGTG
1 TATTTAATTTGGTTACAATAGTTACAGCTATATTCT-ATGGGTGACAAAAGGGAACACA-T-GTG
* * * *
1135949 -ACAGTCATTTTCATGTTTTACAGGGGGCCT
63 AAAAGCCATTTTC-TGTTTTACAGAGAGCCT
*
1135979 TATTTTATTTGGTTACA
1 TATTTAATTTGGTTACA
1135996 TCGGATACAA
Statistics
Matches: 92, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
90 3 0.03
91 16 0.17
92 68 0.74
93 5 0.05
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (92 bp):
TATTTAATTTGGTTACAATAGTTACAGCTATATTCTATGGGTGACAAAAGGGAACACATGTGAAA
AGCCATTTTCTGTTTTACAGAGAGCCT
Found at i:1139582 original size:1 final size:1
Alignment explanation
Indices: 1139578--1139607 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
1139568 ATTGGGGGCA
*
1139578 GGGGGAGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1139608 AGTGGTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:1142114 original size:16 final size:16
Alignment explanation
Indices: 1142093--1142124 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1142083 ATGGTTTTAC
1142093 TTCATTATATCCATAA
1 TTCATTATATCCATAA
*
1142109 TTCATTCTATCCATAA
1 TTCATTATATCCATAA
1142125 AACATATTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.44
Consensus pattern (16 bp):
TTCATTATATCCATAA
Found at i:1161497 original size:14 final size:14
Alignment explanation
Indices: 1161460--1161498 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1161450 CTTCTTAACA
*
1161460 TAATTATTTCAGCT
1 TAATTATTTTAGCT
* *
1161474 TAATCATTTTAGGT
1 TAATTATTTTAGCT
1161488 TAATTATTTTA
1 TAATTATTTTA
1161499 TTTGTGCACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (14 bp):
TAATTATTTTAGCT
Found at i:1174139 original size:32 final size:32
Alignment explanation
Indices: 1174088--1174166 Score: 140
Period size: 32 Copynumber: 2.4 Consensus size: 32
1174078 TATAGTCAGC
1174088 TTTCCGTGGGGGAAAAACTGCTATATAGCCATT
1 TTTCCG-GGGGGAAAAACTGCTATATAGCCATT
*
1174121 TTTCCGGGGGGAAGAACTGCTATATAGCCATT
1 TTTCCGGGGGGAAAAACTGCTATATAGCCATT
1174153 TTTCCGGGGGGAAA
1 TTTCCGGGGGGAAA
1174167 GATGGCTAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 38 0.86
33 6 0.14
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (32 bp):
TTTCCGGGGGGAAAAACTGCTATATAGCCATT
Found at i:1174220 original size:11 final size:11
Alignment explanation
Indices: 1174204--1174232 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1174194 AGCAGGCACA
1174204 TCAACGTTGAT
1 TCAACGTTGAT
1174215 TCAACGTTGAT
1 TCAACGTTGAT
1174226 TCAACGT
1 TCAACGT
1174233 CACATTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (11 bp):
TCAACGTTGAT
Found at i:1174301 original size:13 final size:13
Alignment explanation
Indices: 1174283--1174307 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1174273 TTGTTAATTG
1174283 ATCTGACGTTGAA
1 ATCTGACGTTGAA
1174296 ATCTGACGTTGA
1 ATCTGACGTTGA
1174308 TTCAACGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (13 bp):
ATCTGACGTTGAA
Found at i:1176167 original size:39 final size:39
Alignment explanation
Indices: 1176124--1176302 Score: 340
Period size: 39 Copynumber: 4.6 Consensus size: 39
1176114 GGACCATGCA
* *
1176124 GTTGCAGGTGACCTTGATCTTTGGTCGGATCTATTGGAT
1 GTTGCTGGTGACCTTGATCTTTGGCCGGATCTATTGGAT
1176163 GTTGCTGGTGACCTTGATCTTTGGCCGGATCTATTGGAT
1 GTTGCTGGTGACCTTGATCTTTGGCCGGATCTATTGGAT
1176202 GTTGCTGGTGACCTTGATCTTTGGCCGGATCTATTGGAT
1 GTTGCTGGTGACCTTGATCTTTGGCCGGATCTATTGGAT
1176241 GTTGCTGGTGACCTTGATCTTTGGCCGGATCTATTGGAT
1 GTTGCTGGTGACCTTGATCTTTGGCCGGATCTATTGGAT
1176280 GTTGCTGGTGACCTTGATCTTTG
1 GTTGCTGGTGACCTTGATCTTTG
1176303 TTCAGATGTG
Statistics
Matches: 138, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 138 1.00
ACGTcount: A:0.13, C:0.17, G:0.31, T:0.39
Consensus pattern (39 bp):
GTTGCTGGTGACCTTGATCTTTGGCCGGATCTATTGGAT
Found at i:1176337 original size:78 final size:78
Alignment explanation
Indices: 1176124--1176341 Score: 258
Period size: 78 Copynumber: 2.8 Consensus size: 78
1176114 GGACCATGCA
* * * * * * * *
1176124 GTTGCAGGTGACCTTGATCTTTGGTCGGATCTATTGGATGTTGCTGGTGACCTTGATCTTTGGCC
1 GTTGCTGGTGACCTTGATCTTTGGCCAGATCTATTCGATCTTGATGATGAACTTGATCTTTGGCC
1176189 GGATCTATTGGAT
66 GGATCTATTGGAT
* * * * * *
1176202 GTTGCTGGTGACCTTGATCTTTGGCCGGATCTATTGGATGTTGCTGGTGACCTTGATCTTTGGCC
1 GTTGCTGGTGACCTTGATCTTTGGCCAGATCTATTCGATCTTGATGATGAACTTGATCTTTGGCC
1176267 GGATCTATTGGAT
66 GGATCTATTGGAT
** * *
1176280 GTTGCTGGTGACCTTGATCTTTGTTCAGATGTGTTCGATCTTGATGATGAAAC-TGATCTTTG
1 GTTGCTGGTGACCTTGATCTTTGGCCAGATCTATTCGATCTTGATGATG-AACTTGATCTTTG
1176342 ATTGGATCTG
Statistics
Matches: 127, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
78 125 0.98
79 2 0.02
ACGTcount: A:0.15, C:0.17, G:0.29, T:0.39
Consensus pattern (78 bp):
GTTGCTGGTGACCTTGATCTTTGGCCAGATCTATTCGATCTTGATGATGAACTTGATCTTTGGCC
GGATCTATTGGAT
Found at i:1176337 original size:117 final size:117
Alignment explanation
Indices: 1176124--1176341 Score: 312
Period size: 117 Copynumber: 1.9 Consensus size: 117
1176114 GGACCATGCA
*
1176124 GTTGCAGGTGACCTTGATCTTTGGTCGGATCTATTGGATGTTGCTGGTGACCTTGATCTTTGGCC
1 GTTGCAGGTGACCTTGATCTTTGGCCGGATCTATTGGATGTTGCTGGTGACCTTGATCTTTGGCC
* * * * * *
1176189 GGATCTATTGGATGTTGCTGGTGACCTTGATCTTTGGCCGGATCTATTGGAT
66 AGATCTATTCGATCTTGATGATGAACTTGATCTTTGGCCGGATCTATTGGAT
* **
1176241 GTTGCTGGTGACCTTGATCTTTGGCCGGATCTATTGGATGTTGCTGGTGACCTTGATCTTTGTTC
1 GTTGCAGGTGACCTTGATCTTTGGCCGGATCTATTGGATGTTGCTGGTGACCTTGATCTTTGGCC
* *
1176306 AGATGTGTTCGATCTTGATGATGAAAC-TGATCTTTG
66 AGATCTATTCGATCTTGATGATG-AACTTGATCTTTG
1176342 ATTGGATCTG
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
117 86 0.98
118 2 0.02
ACGTcount: A:0.15, C:0.17, G:0.29, T:0.39
Consensus pattern (117 bp):
GTTGCAGGTGACCTTGATCTTTGGCCGGATCTATTGGATGTTGCTGGTGACCTTGATCTTTGGCC
AGATCTATTCGATCTTGATGATGAACTTGATCTTTGGCCGGATCTATTGGAT
Found at i:1176380 original size:117 final size:117
Alignment explanation
Indices: 1176126--1176380 Score: 271
Period size: 117 Copynumber: 2.2 Consensus size: 117
1176116 ACCATGCAGT
* * * *
1176126 TGCAGGTGACCTTGATCTTTGGTCGGATCTATTGGATGTTGCTGGTGACCTTGATCTTTGGCCGG
1 TGCAGGAGACCTTGACCTTTGGCCGGATCTATTGGATGTTGCTGGTGACCTTGATCTTTGGCCAG
* * * * * * *
1176191 ATCTATTGGATGTTGCTGGTGACCTTGATCTTTGGCCGGATCTATTGGATGT
66 ATCTATTCGATCTTGATGATGAACTTGATCTTTGACCGGATCTATTGGATGA
* * * **
1176243 TGCTGGTGACCTTGATCTTTGGCCGGATCTATTGGATGTTGCTGGTGACCTTGATCTTTGTTCAG
1 TGCAGGAGACCTTGACCTTTGGCCGGATCTATTGGATGTTGCTGGTGACCTTGATCTTTGGCCAG
* * ** * * *
1176308 ATGTGTTCGATCTTGATGATGAAAC-TGATCTTTGATTGGATCTGTTTGTTGA
66 ATCTATTCGATCTTGATGATG-AACTTGATCTTTGACCGGATCTATTGGATGA
1176360 TGCAGGAGA-CTGTGACCTTTG
1 TGCAGGAGACCT-TGACCTTTG
1176381 ATGAACTATG
Statistics
Matches: 114, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
116 2 0.02
117 110 0.96
118 2 0.02
ACGTcount: A:0.15, C:0.16, G:0.29, T:0.39
Consensus pattern (117 bp):
TGCAGGAGACCTTGACCTTTGGCCGGATCTATTGGATGTTGCTGGTGACCTTGATCTTTGGCCAG
ATCTATTCGATCTTGATGATGAACTTGATCTTTGACCGGATCTATTGGATGA
Found at i:1181464 original size:2 final size:2
Alignment explanation
Indices: 1181457--1181487 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1181447 NNNNNNNNNN
1181457 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1181488 CTGATTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1181822 original size:11 final size:11
Alignment explanation
Indices: 1181806--1181837 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1181796 ACGACCAAAT
1181806 ATCAACGTTGA
1 ATCAACGTTGA
1181817 ATCAACGTTGA
1 ATCAACGTTGA
*
1181828 AACAACGTTG
1 ATCAACGTTG
1181838 CGTGCCTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (11 bp):
ATCAACGTTGA
Found at i:1186051 original size:16 final size:17
Alignment explanation
Indices: 1186024--1186056 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1186014 TGCTAAAACG
1186024 CGGAACGGAAAACGGAA
1 CGGAACGGAAAACGGAA
1186041 CGGAA-GGAAAACGGAA
1 CGGAACGGAAAACGGAA
1186057 AATCTTATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.48, C:0.15, G:0.36, T:0.00
Consensus pattern (17 bp):
CGGAACGGAAAACGGAA
Found at i:1186694 original size:16 final size:16
Alignment explanation
Indices: 1186673--1186707 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1186663 TTGCTAAAAA
1186673 TACTAGTTTCACAAAT
1 TACTAGTTTCACAAAT
1186689 TACTAGTTTCACAAAT
1 TACTAGTTTCACAAAT
1186705 TAC
1 TAC
1186708 CGGGTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (16 bp):
TACTAGTTTCACAAAT
Found at i:1196740 original size:15 final size:15
Alignment explanation
Indices: 1196720--1196749 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1196710 TTATGGAAAC
1196720 AAATAGAAAAACAGG
1 AAATAGAAAAACAGG
1196735 AAATAGAAAAACAGG
1 AAATAGAAAAACAGG
1196750 CCCCTTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.20, T:0.07
Consensus pattern (15 bp):
AAATAGAAAAACAGG
Found at i:1198646 original size:35 final size:34
Alignment explanation
Indices: 1198591--1198688 Score: 130
Period size: 33 Copynumber: 2.9 Consensus size: 34
1198581 CTTGACCTCT
* *
1198591 GGTGACCTGACATTGGCCTCATTTATCAAG-CTTC
1 GGTGACCTGACCTTGACCTCATTTATCAAGTC-TC
1198625 AGGTGACCTGACCTTGACCTCATTTATCAAAGTCTC
1 -GGTGACCTGACCTTGACCTCATTTATC-AAGTCTC
1198661 --TGACCTGACCTTGACCTCATTTATCAAG
1 GGTGACCTGACCTTGACCTCATTTATCAAG
1198689 GTCATTGGCT
Statistics
Matches: 59, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
32 3 0.05
33 25 0.42
35 25 0.42
36 5 0.08
37 1 0.02
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (34 bp):
GGTGACCTGACCTTGACCTCATTTATCAAGTCTC
Found at i:1199742 original size:2 final size:2
Alignment explanation
Indices: 1199735--1199764 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1199725 TTAAGGCATA
1199735 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1199765 ATATTTTGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1204998 original size:24 final size:24
Alignment explanation
Indices: 1204966--1205013 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1204956 GATGAATTGC
1204966 AATTGATTTATAGTTCCACTGCCG
1 AATTGATTTATAGTTCCACTGCCG
*
1204990 AATTGATTTATAGTTCTACTGCCG
1 AATTGATTTATAGTTCCACTGCCG
1205014 TGAATGCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.40
Consensus pattern (24 bp):
AATTGATTTATAGTTCCACTGCCG
Found at i:1205333 original size:13 final size:13
Alignment explanation
Indices: 1205315--1205339 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1205305 CTAAACCCCG
1205315 GGTTTACTTTTTC
1 GGTTTACTTTTTC
1205328 GGTTTACTTTTT
1 GGTTTACTTTTT
1205340 GAAAACTTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.12, G:0.16, T:0.64
Consensus pattern (13 bp):
GGTTTACTTTTTC
Found at i:1217667 original size:18 final size:18
Alignment explanation
Indices: 1217636--1217677 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1217626 AGTTAATAAG
1217636 TAATGTTTTGTTTCATATT
1 TAAT-TTTTGTTTCATATT
* *
1217655 TAATTTTTTTTTCTTATT
1 TAATTTTTGTTTCATATT
1217673 TAATT
1 TAATT
1217678 AAGTTATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (18 bp):
TAATTTTTGTTTCATATT
Found at i:1228386 original size:17 final size:17
Alignment explanation
Indices: 1228360--1228399 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1228350 ACAACAGTAC
1228360 ATAT-CAAGTACCGTAT
1 ATATGCAAGTACCGTAT
1228376 ATATGCAAGTACCGTAT
1 ATATGCAAGTACCGTAT
1228393 ATATGCA
1 ATATGCA
1228400 CAATGACTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (17 bp):
ATATGCAAGTACCGTAT
Found at i:1230433 original size:16 final size:16
Alignment explanation
Indices: 1230411--1230449 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1230401 GCCGGGCGTC
*
1230411 CGTCCGTGTGTCTGTG
1 CGTCCGTGTGTCCGTG
*
1230427 GGTCCGTGTGTCCGTG
1 CGTCCGTGTGTCCGTG
1230443 CGTCCGT
1 CGTCCGT
1230450 CCGTCACACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.00, C:0.28, G:0.38, T:0.33
Consensus pattern (16 bp):
CGTCCGTGTGTCCGTG
Found at i:1230749 original size:172 final size:172
Alignment explanation
Indices: 1230463--1230915 Score: 784
Period size: 172 Copynumber: 2.6 Consensus size: 172
1230453 TCACACTTTT
1230463 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
* *
1230528 CCACTATTACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
66 CCACTAATACCTTGGTCAAGTTCTAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
*
1230593 CTTTGACAACAATAATGACTCTGTTTTATCCCAAAA-TCGACC
131 CTTTGACAACAATAATGACTCCGTTTTA-CCCAAAAGTCGACC
*
1230635 TTGTAAGCGCTCTCATGCCTACAAATTTGGACGGATTTTCATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
*
1230700 CCACTAATACCTTGGTCAAGTTCTAAAATCAGCATTGGTTGATACTTTTTGTTGGAGTTATGGGA
66 CCACTAATACCTTGGTCAAGTTCTAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
* *
1230765 CTTTGACCACAATAATGACTCCGTTTTACCCAAAAGTTGACC
131 CTTTGACAACAATAATGACTCCGTTTTACCCAAAAGTCGACC
*
1230807 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTAATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
* *
1230872 CCACTAATATCTTGGTCAAGTTCCT-AAATCAGCCTTGGTCGATA
66 CCACTAATACCTTGGTCAAGTT-CTAAAATCAGCATTGGTCGATA
1230916 GACTCGATAC
Statistics
Matches: 267, Mismatches: 12, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
171 7 0.03
172 258 0.97
173 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.36
Consensus pattern (172 bp):
TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
CCACTAATACCTTGGTCAAGTTCTAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
CTTTGACAACAATAATGACTCCGTTTTACCCAAAAGTCGACC
Found at i:1234680 original size:2 final size:2
Alignment explanation
Indices: 1234675--1234728 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1234665 TTAAATATGC
1234675 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1234717 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1234729 TTTATATTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1235031 original size:31 final size:31
Alignment explanation
Indices: 1234996--1235059 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
1234986 CCAACATCTC
1234996 GTACTTCGATATCACTGACCCTCCACAAAAA
1 GTACTTCGATATCACTGACCCTCCACAAAAA
1235027 GTACTTCGATATCACTGACCCTCCACAAAAA
1 GTACTTCGATATCACTGACCCTCCACAAAAA
1235058 GT
1 GT
1235060 GAAAACACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.31, G:0.11, T:0.23
Consensus pattern (31 bp):
GTACTTCGATATCACTGACCCTCCACAAAAA
Found at i:1235075 original size:20 final size:21
Alignment explanation
Indices: 1235050--1235097 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
1235040 ACTGACCCTC
1235050 CACAAAAAGTGAAAACACTG-
1 CACAAAAAGTGAAAACACTGT
**
1235070 CACAAATTGTGAAAACACTGT
1 CACAAAAAGTGAAAACACTGT
1235091 CACAAAA
1 CACAAAA
1235098 CACCTTCGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.52, C:0.21, G:0.12, T:0.15
Consensus pattern (21 bp):
CACAAAAAGTGAAAACACTGT
Found at i:1236936 original size:15 final size:15
Alignment explanation
Indices: 1236914--1236950 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
1236904 AAATTTATTC
1236914 ATAT-TTTTTTTAAT
1 ATATATTTTTTTAAT
1236928 ATATA--TTTTTAAT
1 ATATATTTTTTTAAT
1236941 ATATATTTTT
1 ATATATTTTT
1236951 CCCACATCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
13 13 0.65
14 4 0.20
15 3 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATATATTTTTTTAAT
Found at i:1236938 original size:13 final size:13
Alignment explanation
Indices: 1236920--1236950 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1236910 ATTCATATTT
1236920 TTTTTAATATATA
1 TTTTTAATATATA
1236933 TTTTTAATATATA
1 TTTTTAATATATA
1236946 TTTTT
1 TTTTT
1236951 CCCACATCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTAATATATA
Found at i:1238513 original size:20 final size:19
Alignment explanation
Indices: 1238490--1238575 Score: 59
Period size: 20 Copynumber: 4.3 Consensus size: 19
1238480 TATAGAGTAT
*
1238490 TTCAGCAATATTTAGAATAG
1 TTCAG-AATATTCAGAATAG
* *
1238510 TTCAGACTGTTTCAGCAATA-
1 TTCAGAAT-ATTCAG-AATAG
* *
1238530 TTCAGAACAGTTCAGACT-G
1 TTCAGAATA-TTCAGAATAG
1238549 TTTCAGCAATATTCAGAATAG
1 -TTCAG-AATATTCAGAATAG
1238570 TTCAGA
1 TTCAGA
1238576 CTGTTTTAGC
Statistics
Matches: 50, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
19 5 0.10
20 37 0.74
21 8 0.16
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (19 bp):
TTCAGAATATTCAGAATAG
Found at i:1238523 original size:30 final size:30
Alignment explanation
Indices: 1238489--1238616 Score: 177
Period size: 30 Copynumber: 4.2 Consensus size: 30
1238479 ATATAGAGTA
*
1238489 TTTCAGCAATATTTAGAATAGTTCAGACTG
1 TTTCAGCAATATTCAGAATAGTTCAGACTG
*
1238519 TTTCAGCAATATTCAGAACAGTTCAGACTG
1 TTTCAGCAATATTCAGAATAGTTCAGACTG
1238549 TTTCAGCAATATTCAGAATAGTTCAGACTG
1 TTTCAGCAATATTCAGAATAGTTCAGACTG
* * **
1238579 TTTTAGCACTACACAG-ATCGAGTTCAGACTG
1 TTTCAGCAATATTCAGAAT--AGTTCAGACTG
1238610 TTTCAGC
1 TTTCAGC
1238617 TATGTTCAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
29 2 0.02
30 69 0.78
31 17 0.19
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (30 bp):
TTTCAGCAATATTCAGAATAGTTCAGACTG
Found at i:1239675 original size:51 final size:51
Alignment explanation
Indices: 1239599--1239736 Score: 249
Period size: 51 Copynumber: 2.7 Consensus size: 51
1239589 ACTGAGGGTT
**
1239599 CGGAAAACCATATGACGTCATGTGGGTGGGGTCTGGATCGTGACAGTATAC
1 CGGAAAACCCCATGACGTCATGTGGGTGGGGTCTGGATCGTGACAGTATAC
1239650 CGGAAAACCCCATGACGTCATGTGGGTGGGGTCTGGATCGTGACAGTATAC
1 CGGAAAACCCCATGACGTCATGTGGGTGGGGTCTGGATCGTGACAGTATAC
*
1239701 CGGAAAACCCCATGACGTCATGTTGGTGGGGTCTGG
1 CGGAAAACCCCATGACGTCATGTGGGTGGGGTCTGG
1239737 TGTCATCGTG
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 84 1.00
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.22
Consensus pattern (51 bp):
CGGAAAACCCCATGACGTCATGTGGGTGGGGTCTGGATCGTGACAGTATAC
Found at i:1239850 original size:58 final size:58
Alignment explanation
Indices: 1239776--1239949 Score: 312
Period size: 58 Copynumber: 3.0 Consensus size: 58
1239766 ACTGTGTCAA
*
1239776 GACTTGACCCCAATTATGACCTATGTGGATGGGGTCCGGAAAACCCCATGACGTCATC
1 GACTTGACCTCAATTATGACCTATGTGGATGGGGTCCGGAAAACCCCATGACGTCATC
*
1239834 GACTTGACCTCAATTATGACCTATGTGGGTGGGGTCCGGAAAACCCCATGACGTCATC
1 GACTTGACCTCAATTATGACCTATGTGGATGGGGTCCGGAAAACCCCATGACGTCATC
* *
1239892 GACTTGGCCTCAAATATGACCTATGTGGATGGGGTCCGGAAAACCCCATGACGTCATC
1 GACTTGACCTCAATTATGACCTATGTGGATGGGGTCCGGAAAACCCCATGACGTCATC
1239950 ATGACTGTAT
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 111 1.00
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.23
Consensus pattern (58 bp):
GACTTGACCTCAATTATGACCTATGTGGATGGGGTCCGGAAAACCCCATGACGTCATC
Found at i:1240273 original size:58 final size:58
Alignment explanation
Indices: 1240199--1240372 Score: 312
Period size: 58 Copynumber: 3.0 Consensus size: 58
1240189 ACTGTGTCAA
*
1240199 GACTTGACCCCAATTATGACCTATGTGGATGGGGTCCGGAAAACCCCATGACGTCATC
1 GACTTGACCTCAATTATGACCTATGTGGATGGGGTCCGGAAAACCCCATGACGTCATC
*
1240257 GACTTGACCTCAATTATGACCTATGTGGGTGGGGTCCGGAAAACCCCATGACGTCATC
1 GACTTGACCTCAATTATGACCTATGTGGATGGGGTCCGGAAAACCCCATGACGTCATC
* *
1240315 GACTTGGCCTCAAATATGACCTATGTGGATGGGGTCCGGAAAACCCCATGACGTCATC
1 GACTTGACCTCAATTATGACCTATGTGGATGGGGTCCGGAAAACCCCATGACGTCATC
1240373 ATGACTGTAT
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 111 1.00
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.23
Consensus pattern (58 bp):
GACTTGACCTCAATTATGACCTATGTGGATGGGGTCCGGAAAACCCCATGACGTCATC
Found at i:1240457 original size:423 final size:422
Alignment explanation
Indices: 1239671--1240515 Score: 1681
Period size: 423 Copynumber: 2.0 Consensus size: 422
1239661 ATGACGTCAT
1239671 GTGGGTGGGGTCTGGATCGTGACAGTATACCGGAAAACCCCATGACGTCATGTTGGTGGGGTCTG
1 GTGGGTGGGGTCTGGATCGTGACAGTATACCGGAAAACCCCATGACGTCATGTTGGTGGGGTCTG
1239736 GTGTCATCGTGAATGTGTACTCACCCCTTGACTGTGTCAAGACTTGACCCCAATTATGACCTATG
66 GTGTCATCGTGAATGTGTACTCACCCCTTGACTGTGTCAAGACTTGACCCCAATTATGACCTATG
1239801 TGGATGGGGTCCGGAAAACCCCATGACGTCATCGACTTGACCTCAATTATGACCTATGTGGGTGG
131 TGGATGGGGTCCGGAAAACCCCATGACGTCATCGACTTGACCTCAATTATGACCTATGTGGGTGG
1239866 GGTCCGGAAAACCCCATGACGTCATCGACTTGGCCTCAAATATGACCTATGTGGATGGGGTCCGG
196 GGTCCGGAAAACCCCATGACGTCATCGACTTGGCCTCAAATATGACCTATGTGGATGGGGTCCGG
1239931 AAAACCCCATGACGTCATCATGACTGTATACTGACTGCGTACTGTCCCCCTTACTACTGATGGCG
261 AAAACCCCATGACGTCATCATGACTGTATACTGACTGCGTACTGTCCCCCTTACTACTGATGGCG
1239996 GAAGAATTTCTTAACATGTAAGTTTGTATCATTGTTTATTATAAAAAGGAAAAATATCCAGTCAT
326 GAAGAATTTCTTAACATGTAAGTTTGTATCATTGTTTATTATAAAAAGGAAAAATATCCAGTCAT
1240061 ATTTGGAATGCCTTAACAATAATAAATATTAA
391 ATTTGGAATGCCTTAACAATAATAAATATTAA
1240093 NGTGGGTGGGGTCTGGATCGTGACAGTATACCGGAAAACCCCATGACGTCATGTTGGTGGGGTCT
1 -GTGGGTGGGGTCTGGATCGTGACAGTATACCGGAAAACCCCATGACGTCATGTTGGTGGGGTCT
1240158 GGTGTCATCGTGAATGTGTACTCACCCCTTGACTGTGTCAAGACTTGACCCCAATTATGACCTAT
65 GGTGTCATCGTGAATGTGTACTCACCCCTTGACTGTGTCAAGACTTGACCCCAATTATGACCTAT
1240223 GTGGATGGGGTCCGGAAAACCCCATGACGTCATCGACTTGACCTCAATTATGACCTATGTGGGTG
130 GTGGATGGGGTCCGGAAAACCCCATGACGTCATCGACTTGACCTCAATTATGACCTATGTGGGTG
1240288 GGGTCCGGAAAACCCCATGACGTCATCGACTTGGCCTCAAATATGACCTATGTGGATGGGGTCCG
195 GGGTCCGGAAAACCCCATGACGTCATCGACTTGGCCTCAAATATGACCTATGTGGATGGGGTCCG
1240353 GAAAACCCCATGACGTCATCATGACTGTATACTGACTGCGTACTGTCCCCCTTACTACTGATGGC
260 GAAAACCCCATGACGTCATCATGACTGTATACTGACTGCGTACTGTCCCCCTTACTACTGATGGC
1240418 GGAAGAATTTCTTAACATGTAAGTTTGTATCATTGTTTATTATAAAAAGGAAAAATATCCAGTCA
325 GGAAGAATTTCTTAACATGTAAGTTTGTATCATTGTTTATTATAAAAAGGAAAAATATCCAGTCA
1240483 TATTTGGAATGCCTTAACAATAATAAATATTAA
390 TATTTGGAATGCCTTAACAATAATAAATATTAA
1240516 AGAATCGAAT
Statistics
Matches: 422, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
423 422 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (422 bp):
GTGGGTGGGGTCTGGATCGTGACAGTATACCGGAAAACCCCATGACGTCATGTTGGTGGGGTCTG
GTGTCATCGTGAATGTGTACTCACCCCTTGACTGTGTCAAGACTTGACCCCAATTATGACCTATG
TGGATGGGGTCCGGAAAACCCCATGACGTCATCGACTTGACCTCAATTATGACCTATGTGGGTGG
GGTCCGGAAAACCCCATGACGTCATCGACTTGGCCTCAAATATGACCTATGTGGATGGGGTCCGG
AAAACCCCATGACGTCATCATGACTGTATACTGACTGCGTACTGTCCCCCTTACTACTGATGGCG
GAAGAATTTCTTAACATGTAAGTTTGTATCATTGTTTATTATAAAAAGGAAAAATATCCAGTCAT
ATTTGGAATGCCTTAACAATAATAAATATTAA
Found at i:1251239 original size:9 final size:9
Alignment explanation
Indices: 1251225--1251258 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
1251215 TTAAGTCAAA
1251225 GTTAAGTTT
1 GTTAAGTTT
1251234 GTTAAGTTT
1 GTTAAGTTT
*
1251243 GTTAAGATT
1 GTTAAGTTT
1251252 GTTAAGT
1 GTTAAGT
1251259 AAAGGTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (9 bp):
GTTAAGTTT
Done.