Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold226
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: 1071921
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.31
Warning! 95108 characters in sequence are not A, C, G, or T
File 4 of 3
Found at i:962011 original size:18 final size:19
Alignment explanation
Indices: 961988--962026 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
961978 ACACTGTCAC
961988 TACTCTGTTAAAAT-AATA
1 TACTCTGTTAAAATAAATA
962006 TACTCTGTTAAAATAAATA
1 TACTCTGTTAAAATAAATA
962025 TA
1 TA
962027 TATATTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.38
Consensus pattern (19 bp):
TACTCTGTTAAAATAAATA
Found at i:967703 original size:2 final size:2
Alignment explanation
Indices: 967691--967733 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
967681 AAATTTCCAG
967691 CT CT ACT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT -CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
967734 GTGCACAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:975809 original size:12 final size:12
Alignment explanation
Indices: 975792--975817 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
975782 TTTGTAAGTT
975792 TACAAAATAATG
1 TACAAAATAATG
975804 TACAAAATAATG
1 TACAAAATAATG
975816 TA
1 TA
975818 AATCATTATT
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:0.58, C:0.08, G:0.08, T:0.27
Consensus pattern (12 bp):
TACAAAATAATG
Found at i:998971 original size:24 final size:24
Alignment explanation
Indices: 998939--998992 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
998929 AAATCCATGT
* *
998939 TAAAATCACATTTGTTTGCATTTG
1 TAAAGTCACATTTGGTTGCATTTG
998963 TAAAGTCACATTTGGTTGCATTTG
1 TAAAGTCACATTTGGTTGCATTTG
998987 TAAAGT
1 TAAAGT
998993 ATTTCTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.43
Consensus pattern (24 bp):
TAAAGTCACATTTGGTTGCATTTG
Found at i:1011331 original size:17 final size:17
Alignment explanation
Indices: 1011311--1011343 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1011301 AAACAATTCA
1011311 ATGCTTT-AAACTTAAAT
1 ATGCTTTCAAA-TTAAAT
1011328 ATGCTTTCAAATTAAA
1 ATGCTTTCAAATTAAA
1011344 CTCTGTATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (17 bp):
ATGCTTTCAAATTAAAT
Found at i:1018967 original size:16 final size:17
Alignment explanation
Indices: 1018946--1018978 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1018936 TCTTTGACAC
1018946 ATGAAT-GCTGTAAAAA
1 ATGAATAGCTGTAAAAA
*
1018962 ATGAATATCTGTAAAAA
1 ATGAATAGCTGTAAAAA
1018979 TAAATTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (17 bp):
ATGAATAGCTGTAAAAA
Found at i:1025663 original size:1 final size:1
Alignment explanation
Indices: 1025659--1025684 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1025649 TTGAATGTGT
1025659 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
1025685 GCCATTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1034824 original size:13 final size:14
Alignment explanation
Indices: 1034794--1034826 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1034784 TCTTTGCCCA
1034794 AAAAAAAAAAAATG
1 AAAAAAAAAAAATG
1034808 AAAAAAAAAAAAT-
1 AAAAAAAAAAAATG
1034821 AAAAAA
1 AAAAAA
1034827 TAAACCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.91, C:0.00, G:0.03, T:0.06
Consensus pattern (14 bp):
AAAAAAAAAAAATG
Found at i:1034836 original size:19 final size:20
Alignment explanation
Indices: 1034791--1034844 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
1034781 CTCTCTTTGC
*
1034791 CCAAAAAAAAAAAAATGAAAA
1 CCAAAAAATAAAAAAT-AAAA
**
1034812 AAAAAAAATAAAAAAT-AAA
1 CCAAAAAATAAAAAATAAAA
1034831 CCAAAAAATAAAAA
1 CCAAAAAATAAAAA
1034845 CAAATAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 15 0.54
21 13 0.46
ACGTcount: A:0.83, C:0.07, G:0.02, T:0.07
Consensus pattern (20 bp):
CCAAAAAATAAAAAATAAAA
Found at i:1034837 original size:13 final size:12
Alignment explanation
Indices: 1034809--1034856 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1034799 AAAAAAATGA
* *
1034809 AAAAAAAAAAAT
1 AAAAAATAAAAC
*
1034821 AAAAAATAAACC
1 AAAAAATAAAAC
1034833 AAAAAATAAAAAC
1 AAAAAAT-AAAAC
1034846 AAATAAATAAA
1 AAA-AAATAAA
1034857 TTGGGGGGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 16 0.53
13 10 0.33
14 4 0.13
ACGTcount: A:0.83, C:0.06, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAAAATAAAAC
Found at i:1034844 original size:7 final size:7
Alignment explanation
Indices: 1034793--1034830 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
1034783 CTCTTTGCCC
*
1034793 AAAAAAA
1 AAAAAAT
1034800 AAAAAAT
1 AAAAAAT
1034807 GAAAAAA-
1 -AAAAAAT
1034814 AAAAAAT
1 AAAAAAT
1034821 AAAAAAT
1 AAAAAAT
1034828 AAA
1 AAA
1034831 CCAAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 6 0.21
7 16 0.57
8 6 0.21
ACGTcount: A:0.89, C:0.00, G:0.03, T:0.08
Consensus pattern (7 bp):
AAAAAAT
Found at i:1034845 original size:14 final size:13
Alignment explanation
Indices: 1034794--1034856 Score: 56
Period size: 14 Copynumber: 4.8 Consensus size: 13
1034784 TCTTTGCCCA
* *
1034794 AAAAAAAAAAAATG
1 AAAAAATAAAAA-C
* *
1034808 AAAAAAAAAAAAT
1 AAAAAATAAAAAC
*
1034821 AAAAAAT-AAACC
1 AAAAAATAAAAAC
1034833 AAAAAATAAAAAC
1 AAAAAATAAAAAC
1034846 AAATAAATAAA
1 AAA-AAATAAA
1034857 TTGGGGGGTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
12 10 0.24
13 13 0.31
14 19 0.45
ACGTcount: A:0.84, C:0.05, G:0.02, T:0.10
Consensus pattern (13 bp):
AAAAAATAAAAAC
Found at i:1034853 original size:26 final size:25
Alignment explanation
Indices: 1034808--1034856 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1034798 AAAAAAAATG
*
1034808 AAAAAAAAAAAATAAAAAATAAACC
1 AAAAAAAAAAAACAAAAAATAAACC
*
1034833 AAAAAATAAAAACAAATAAATAAA
1 AAAAAAAAAAAACAAA-AAATAAA
1034857 TTGGGGGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.84, C:0.06, G:0.00, T:0.10
Consensus pattern (25 bp):
AAAAAAAAAAAACAAAAAATAAACC
Found at i:1038509 original size:64 final size:64
Alignment explanation
Indices: 1038332--1039735 Score: 719
Period size: 66 Copynumber: 21.1 Consensus size: 64
1038322 AATATCATGG
* *** *
1038332 CCTCTAATTTTCGTTGCTATTGGAGAGGGGGTTCAAAATATTATGGTTGCAATATTTTGAACCC
1 CCTCTAATTTTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTGAACCC
* * * * *
1038396 CTCTCCT-ATTTCCATTTCCTTTTGGAGAGGGGGTTCAAAATATTATGGCCATTG-TATTTCGAA
1 C-CT-CTAATTTTCA-TTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCA-CGATATTTTGAA
1038459 CCC
62 CCC
* * *
1038462 CATCTAATATTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTAAACCC
1 CCTCTAATTTTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTGAACCC
* * * * ** * *
1038526 CCTCTAATTTTCAGTGCTAATGCTACTGGAGAGGAGGTTTAAGATATTATGGCTGCAATATTTTA
1 CCTCTAATTTTCA----T--TGCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTG
1038591 AATCCC
60 AA-CCC
* * * * * *
1038597 CTTCCT-CTTTTCAATTCCCATTGGAGAGGGGGTTCAAAATATTATGGCCACGACATATTGAACC
1 CCT-CTAATTTTC-ATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTGAA-C
1038661 CC
63 CC
* * ** *
1038663 CCTCTATTTTTCATTGCTATTGGAGAGGGGGTTC-AAATATCATGGCTGCGATATATTGATACCC
1 CCTCTAATTTTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTGA-ACCC
* * * * ** * * *
1038727 TCTCCT-ATTTCCAATTCCCATTGGAGAGCAGGTTCACAATATTATAGCCATGATATTTTGAACC
1 CCT-CTAATTTTC-ATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTGAA-C
1038791 CC
63 CC
* ** * * *** *
1038793 CCTCTTATTTTCATTGCTATTGGAGA-CAGGTTAAAAATATCATGGTTGCGATATATTGAACCC
1 CCTCTAATTTTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTGAACCC
* * * * * *
1038856 CTATCCT-ATTTCCAATTCCCATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTCAAC
1 C-CT-CTAATTTTC-ATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTGAAC
1038920 CC
63 CC
* **
1038922 CCTCTAATATTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCTGCGATATTTTGAACCCC
1 CCTCTAATTTTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTGAA--CC
1038987 C
64 C
* * * * * ** *
1038988 CCTCTAATTTTCAGTGCTATTGCTACTGGAGAGGGGTTTAAGATATTATTGCTGCAATATTTTGA
1 CCTCTAATTTTCATTGCTATTG-GA---GAG-GGGGTTCAAAATATTATGGCCACGATATTTTGA
1039053 ACCC
61 ACCC
* * * * * * *
1039057 CCTTCCTACCGGTACTTCCAATTTTCT-TTGGAGACGGGGTTCCAAATAATATGGCCGCGATATT
1 CC-T-CTA-----ATTTTC-A-TTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATT
1039121 TTGAACCC
57 TTGAACCC
* ** * * * **
1039129 CACTTTTTTTTTCTTTACTTATT-GAGAGAGGGTTCAAAATATTATGGCTGCGATATTTTGATAC
1 C-CTCTAATTTTCATTGC-TATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTGA-AC
1039193 CC
63 CC
* * * * ** *
1039195 TCTCCT-ATTTCCAATTCCCT-TTGGAGAGGGGGTTCACAATATTATGGCTGCAATATTTTGAAC
1 CCT-CTAATTTTC-ATT-GCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTGAAC
1039258 CC
63 CC
* * ** *
1039260 CCTTCCCCCCTAATTTTCTTTGCTATTGGAGAGGGGGTTCACAATATTATGGCCGGGATAATTTG
1 CC-T-----CTAATTTTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTG
1039325 AACCTC
60 AACC-C
* * * * * *
1039331 CCTTTTAA-TTTCATTGTTATTGGA-AAGGGGTATCAAAATATTATGGTCGCGATATATTGAACC
1 CC-TCTAATTTTCATTGCTATTGGAGAGGGGGT-TCAAAATATTATGGCCACGATATTTTGAACC
1039394 C
64 C
* * ** *
1039395 CTTTCCT--TTTTCCAATTCCCT-TTGGAGA-GGGGTTCACTATATTATGGCCGCGATATACAGT
1 C-CT-CTAATTTT-C-ATT-GCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATAT----T
*
1039456 ATTAAACTCC
57 -TTGAAC-CC
* * * * * * *
1039466 CCTCCT-ATTTCCAGTT-C-ACTTTGAGAGGGGGTTCAAAATATTATGGCCGCAATATATGGAAA
1 CCT-CTAATTTTCA-TTGCTA-TTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTGAAC
**
1039528 TA
63 CC
** * * * ** ** * *
1039530 GGTAGACT-ATTTCCAATTCCCATTGGAGAGTCGGTTCAAAATATTATGGCTGCAATATTTGGAA
1 CCT---CTAATTTTC-ATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTGAA
1039594 CCCC
62 -CCC
* * * * *
1039598 CCTCTAACTTTCATTGCTATTGGAGAGGGGGTTCAAAATATAATTGCCATGATATTTTGACCCCC
1 CCTCTAATTTTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTGA---AC
1039663 CC
63 CC
* * * * ***
1039665 TCCTCGTACTTTTGATTCCCT-TTGGAGAGGGGGTTCACAATATTATGGCTGTGATATTTTGAAC
1 -CCTC-TAATTTTCATT-GCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTGAAC
1039729 CC
63 CC
1039731 CCTCT
1 CCTCT
1039736 CCAATGGGAA
Statistics
Matches: 1037, Mismatches: 212, Indels: 182
0.72 0.15 0.13
Matches are distributed among these distances:
63 5 0.00
64 183 0.18
65 245 0.24
66 253 0.24
67 46 0.04
68 9 0.01
69 58 0.06
70 128 0.12
71 60 0.06
72 35 0.03
73 3 0.00
76 5 0.00
77 4 0.00
78 3 0.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (64 bp):
CCTCTAATTTTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTGAACCC
Found at i:1038690 original size:65 final size:65
Alignment explanation
Indices: 1038332--1039732 Score: 765
Period size: 65 Copynumber: 21.0 Consensus size: 65
1038322 AATATCATGG
* * ** *
1038332 CCTCTAATTTTCGTTGCTATTGGAGAGGGGGTTCAAAATATTATGGTTGCAATATTTTGAACCCC
1 CCTCTATTTTTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCC
* * * * ** *
1038397 TCTCCTA-TTTCCATTTCCTTTTGGAGAGGGGGTTCAAAATATTATGGCCATTG-TATTTCGAA-
1 CCT-CTATTTTTCA-TTGCTATTGGAGAGGGGGTTCAAAATATTATGGCC-GCGATATTTTGAAC
1038459 CCC
63 CCC
* * * * *
1038462 CATCTAATATTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTT-AAACCC
1 CCTCTATTTTTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCC
* * * * * * * *
1038526 CCTCTAATTTTCAGTGCTAATGCTACTGGAGAGGAGGTTTAAGATATTATGGCTGCAATATTTTA
1 CCTCT-ATTTT---T-C-ATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTG
*
1038591 AATCCC
60 AACCCC
* * * * * * *
1038597 CTTCCT-CTTTTCAATTCCCATTGGAGAGGGGGTTCAAAATATTATGGCCACGACATATTGAACC
1 CCT-CTATTTTTC-ATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTGAACC
1038661 CC
64 CC
* * *
1038663 CCTCTATTTTTCATTGCTATTGGAGAGGGGGTTC-AAATATCATGGCTGCGATATATTGATA-CC
1 CCTCTATTTTTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTGA-ACCC
1038726 C
65 C
* * * * ** * * **
1038727 TCTCCTA-TTTCCAATTCCCATTGGAGAGCAGGTTCACAATATTATAGCCATGATATTTTGAACC
1 CCT-CTATTTTTC-ATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTGAACC
1038791 CC
64 CC
** * * ** *
1038793 CCTCT-TATTTTCATTGCTATTGGAGA-CAGGTTAAAAATATCATGGTTGCGATATATTGAACCC
1 CCTCTAT-TTTTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTGAACCC
1038856 C
65 C
** * * * *
1038857 TATCCTA-TTTCCAATTCCCATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTCAA-C
1 CCT-CTATTTTTC-ATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTGAACC
1038920 CC
64 CC
* * *
1038922 CCTCTAATATTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCTGCGATATTTTGAACCCC
1 CCTCTATTTTTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTGAA-CCC
1038987 C
65 C
* * * * * *
1038988 CCTCTAATTTTCAGTGCTATTGCTACTGGAGA-GGGGTTTAAGATATTATTGCTGCAATATTTTG
1 CCTCT-ATTTT---T-C-ATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTG
1039052 AACCCC
60 AACCCC
* * * * * * *
1039058 CTTCCTACCGGTACTTCCAATTTTCT-TTGGAGACGGGGTTCCAAATAATATGGCCGCGATATTT
1 CCT-CTA----T-TTTTC-A-TTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTT
1039122 TGAACCCC
58 TGAACCCC
* * * * * * *
1039130 ACTTTTTTTTTCTTTACTTATT-GAGAGAGGGTTCAAAATATTATGGCTGCGATATTTTGATA-C
1 CCTCTATTTTTCATTGC-TATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTGA-ACC
1039193 CC
64 CC
* * * * * *
1039195 TCTCCTA-TTTCCAATTCCCT-TTGGAGAGGGGGTTCACAATATTATGGCTGCAATATTTTGAAC
1 CCT-CTATTTTTC-ATT-GCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTGAA-
1039258 CCCCTTCC
62 --CC--CC
* * * * * * *
1039266 CCCCTAATTTTCTTTGCTATTGGAGAGGGGGTTCACAATATTATGGCCGGGATAATTTGAACCTC
1 CCTCTATTTTTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCC
* * * *
1039331 CCT-T-TTAATTTCATTGTTATTGGA-AAGGGGTATCAAAATATTATGGTCGCGATATATTGAAC
1 CCTCTATT--TTTCATTGCTATTGGAGAGGGGGT-TCAAAATATTATGGCCGCGATATTTTGAAC
1039393 CCC
63 CCC
** * * **
1039396 TTTCCT-TTTTCCAATTCCCT-TTGGAGA-GGGGTTCACTATATTATGGCCGCGATATACAGTAT
1 CCT-CTATTTTTC-ATT-GCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATAT----T-T
* *
1039458 TAAACTCC
58 TGAACCCC
* * * * *
1039466 CCTCCTA-TTTCCAGTT-C-ACTTTGAGAGGGGGTTCAAAATATTATGGCCGCAATATATGGAA-
1 CCT-CTATTTTTCA-TTGCTA-TTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTGAAC
***
1039527 ATA
63 CCC
** * * * ** * * *
1039530 GGTAGACTA-TTTCCAATTCCCATTGGAGAGTCGGTTCAAAATATTATGGCTGCAATATTTGGAA
1 CCT---CTATTTTTC-ATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTGAA
1039594 CCCC
62 CCCC
** * * ** *
1039598 CCTCTAACTTTCATTGCTATTGGAGAGGGGGTTCAAAATATAATTGCCATGATATTTTGACCCCC
1 CCTCTATTTTTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTGA--ACC
1039663 CC
64 CC
* * * * * *
1039665 TCCTCGTACTTTTGATTCCCT-TTGGAGAGGGGGTTCACAATATTATGGCTGTGATATTTTGAAC
1 -CCTC-TATTTTTCATT-GCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTGAAC
1039729 CCC
63 CCC
1039732 C
1 C
1039733 TCTCCAATGG
Statistics
Matches: 1021, Mismatches: 227, Indels: 175
0.72 0.16 0.12
Matches are distributed among these distances:
63 4 0.00
64 171 0.17
65 254 0.25
66 222 0.22
67 60 0.06
68 8 0.01
69 55 0.05
70 137 0.13
71 56 0.05
72 51 0.05
74 1 0.00
75 2 0.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (65 bp):
CCTCTATTTTTCATTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCC
Found at i:1039369 original size:201 final size:198
Alignment explanation
Indices: 1038349--1039442 Score: 647
Period size: 201 Copynumber: 5.5 Consensus size: 198
1038339 TTTTCGTTGC
* * * *
1038349 TATTGGAGAGGGGGTTCAAAATATTATGGTTGCAATATTTTGAACCCCTCTCCTATTTCCATTTC
1 TATTGGA-AAGGGGTTCAAAATATTATGGCTGCGATATTTTGAA-CCCTCTCCTATTTCCAATTC
* * * * * * *
1038414 CTTTTGGAGAGGGGGTTCAAAATATTATGGC--CATTGTATTTCGAA-CCCCATCTA---ATA-T
64 CCTTTGGAGA-GGGGTTCACAATATTATGGCTGCA--ATATTTTGAACCCCCTTCCACCCCTACT
* * * *
1038472 T-CA-TTGCTATTGGAGAGGGGGTTCAAAATATTATGGCCACGATATTTTAAACCCCC-TCTAAT
126 TCCATTTGCTATTGGAGAGGGGGTTCACAATATTATGGCCGCGATATTTTGAACCCCCTTTTAA-
*
1038534 TTTCAGTGCTAATGC
190 TTTCA----T--TGT
* * * * * * * *
1038549 TACTGGAGAGGAGGTTTAAGATATTATGGCTGCAATATTTTAAATCCC-CTTCCTCTTTTCAATT
1 TATTGGAAAGG-GGTTCAAAATATTATGGCTGCGATATTTTGAA-CCCTC-TCCTATTTCCAATT
* * ** * * * * * *
1038613 CCCATTGGAGAGGGGGTTCAAAATATTATGGCCACGACATATTGAACCCCCCTCTA----T-TTT
63 CCCTTTGGAGA-GGGGTTCACAATATTATGGCTGCAATATTTTGAACCCCCTTCCACCCCTACTT
* * * * * **
1038673 TCA-TTGCTATTGGAGAGGGGGTTCA-AATATCATGGCTGCGATATATTGATACCCTCTCCT-AT
127 CCATTTGCTATTGGAGAGGGGGTTCACAATATTATGGCCGCGATATTTTGA-ACCCCCTTTTAAT
**
1038735 TTCCAATTCC
191 TT-C-ATTGT
* * * * * *** * * *
1038745 CATTGGAGAGCAGGTTCACAATATTATAGCCATGATATTTTGAACCCCCCTCTTATTTTC-ATT-
1 TATTGGAAAG-GGGTTCAAAATATTATGGCTGCGATATTTTGAA-CCCTCTCCTATTTCCAATTC
* ** * * * * * * * *
1038808 GCTATTGGAGACAGGTTAAAAATATCATGGTTGCGATATATTGAA-CCCC-T--A-TCCTATTTC
64 CCT-TTGGAGAGGGGTTCACAATATTATGGCTGCAATATTTTGAACCCCCTTCCACCCCTACTTC
* * * * * *
1038868 CAATTCCCATTGGAGAGGGGGTTCAAAATATTATGGCCGCGATATTTTCAACCCCC-TCTAATAT
128 CATTTGCTATTGGAGAGGGGGTTCACAATATTATGGCCGCGATATTTTGAACCCCCTTTTAAT-T
*
1038932 TCATTGC
192 TCATTGT
* * *
1038939 TATTGGAGAGGGGGTTCAAAATATTATGGCTGCGATATTTTGAACCCCCCCTCTAATTTTCAGTG
1 TATTGGA-AAGGGGTTCAAAATATTATGGCTGCGATATTTTGAACCCTCTC-CT-A-TTTC----
* * * * *
1039004 CTATT-GCTACTGGAGAGGGGTTTA-AGATATTATTGCTGCAATATTTTGAACCCCCTTCCTACC
58 CAATTCCCT-TTGGAGAGGGGTTCACA-ATATTATGGCTGCAATATTTTGAACCCCCTTCC-ACC
** * * *
1039067 GGTACTTCCAATTTTCT-TTGGAGACGGGGTTC-CAAATAATATGGCCGCGATATTTTGAACCCC
120 CCTACTTCC-ATTTGCTATTGGAGAGGGGGTTCAC-AATATTATGGCCGCGATATTTTGAACCCC
** * *
1039130 ACTTTTTTTTTCTTTACT
183 -CTTTTAATTTCATT-GT
*
1039148 TATT-GAGAGAGGGTTCAAAATATTATGGCTGCGATATTTTGATACCCTCTCCTATTTCCAATTC
1 TATTGGAAAG-GGGTTCAAAATATTATGGCTGCGATATTTTGA-ACCCTCTCCTATTTCCAATTC
*
1039212 CCTTTGGAGAGGGGGTTCACAATATTATGGCTGCAATATTTTGAACCCCCTTCC-CCCCTAATTT
64 CCTTTGGAGA-GGGGTTCACAATATTATGGCTGCAATATTTTGAACCCCCTTCCACCCCT-ACTT
* * *
1039276 TC-TTTGCTATTGGAGAGGGGGTTCACAATATTATGGCCGGGATAATTTGAACCTCCCTTTTAAT
127 CCATTTGCTATTGGAGAGGGGGTTCACAATATTATGGCCGCGATATTTTGAACC-CCCTTTTAAT
1039340 TTCATTGT
191 TTCATTGT
* * *
1039348 TATTGGAAAGGGGTATCAAAATATTATGG-TCGCGATATATTGAACCCCTTTCCTTTTTCCAATT
1 TATTGGAAAGGGGT-TCAAAATATTATGGCT-GCGATATTTTGAA-CCCTCTCCTATTTCCAATT
*
1039412 CCCTTTGGAGAGGGGTTCACTATATTATGGC
63 CCCTTTGGAGAGGGGTTCACAATATTATGGC
1039443 CGCGATATAC
Statistics
Matches: 711, Mismatches: 127, Indels: 112
0.75 0.13 0.12
Matches are distributed among these distances:
190 1 0.00
192 1 0.00
193 11 0.02
194 72 0.10
195 40 0.06
196 69 0.10
197 1 0.00
198 1 0.00
199 3 0.00
200 146 0.21
201 185 0.26
202 25 0.04
203 42 0.06
204 1 0.00
206 5 0.01
207 49 0.07
208 46 0.06
209 13 0.02
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.35
Consensus pattern (198 bp):
TATTGGAAAGGGGTTCAAAATATTATGGCTGCGATATTTTGAACCCTCTCCTATTTCCAATTCCC
TTTGGAGAGGGGTTCACAATATTATGGCTGCAATATTTTGAACCCCCTTCCACCCCTACTTCCAT
TTGCTATTGGAGAGGGGGTTCACAATATTATGGCCGCGATATTTTGAACCCCCTTTTAATTTCAT
TGT
Found at i:1039788 original size:66 final size:66
Alignment explanation
Indices: 1039718--1040133 Score: 423
Period size: 66 Copynumber: 6.3 Consensus size: 66
1039708 TATGGCTGTG
1039718 ATATTTTGAACCCCCTCTCCAATGGGAATTGGAAAATAGAGGGGGGTTCAAAATATCGCAGCCAT
1 ATATTTTGAACCCCCTCTCCAATGGGAATTGGAAAATAGAGGGGGGTTCAAAATATCGCAGCCAT
1039783 A
66 A
* *
1039784 ATATTTTAAACCCCCTCTCCAAT-GGAAGTTGGAAAA-AG-GTAGGGGGTTCAATATATCGCAGC
1 ATATTTTGAACCCCCTCTCCAATGGGAA-TTGGAAAATAGAG--GGGGGTTCAAAATATCGCAGC
1039846 CATA
63 CATA
* * * * *
1039850 ATATTTTGAACCCCCTCTCCAATAGCAA-T-GAAAAAATGAGGGGGGTTCCAAATATCGCGGCC-
1 ATATTTTGAACCCCCTCTCCAATGGGAATTGGAAAATA-GAGGGGGGTTCAAAATATCGCAGCCA
1039912 --
65 TA
*
1039912 ATATTTTGAACCCCCTCTCCAATGGGAATTGG-AAATAG-GTAGTGGGTTCAATACATATATCGC
1 ATATTTTGAACCCCCTCTCCAATGGGAATTGGAAAATAGAG--GGGGGTTC-A-A-A-ATATCGC
1039975 AGCCATA
60 AGCCATA
** * * * * * * *
1039982 ATATTTT-ATACCCCCTCTCCAAAAGCAA-TGAAAAAT-GA-GGGGGCTCCAAATTTTGCGGCCA
1 ATATTTTGA-ACCCCCTCTCCAATGGGAATTGGAAAATAGAGGGGGGTTCAAAATATCGCAGCCA
1040043 TA
65 TA
* * *
1040045 ATATTTTGAACCCCCTCTCCAATGGAAATTAG-AAATATGTA-GGGGGTTCAATATATCGCAGCC
1 ATATTTTGAACCCCCTCTCCAATGGGAATTGGAAAATA-G-AGGGGGGTTCAAAATATCGCAGCC
1040108 ATA
64 ATA
1040111 ATATTTTGAACCCCCTCTCCAAT
1 ATATTTTGAACCCCCTCTCCAAT
1040134 AGCAATGAAA
Statistics
Matches: 290, Mismatches: 34, Indels: 52
0.77 0.09 0.14
Matches are distributed among these distances:
61 1 0.00
62 27 0.09
63 50 0.17
64 10 0.03
65 30 0.10
66 121 0.42
67 20 0.07
69 4 0.01
70 27 0.09
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (66 bp):
ATATTTTGAACCCCCTCTCCAATGGGAATTGGAAAATAGAGGGGGGTTCAAAATATCGCAGCCAT
A
Found at i:1039871 original size:132 final size:130
Alignment explanation
Indices: 1039718--1040140 Score: 572
Period size: 132 Copynumber: 3.2 Consensus size: 130
1039708 TATGGCTGTG
* * * *
1039718 ATATTTTGAACCCCCTCTCCAATGGGAATTGGAAAATAGAGGGGGGTTCAAAATATCGCAGCCAT
1 ATATTTTGAACCCCCTCTCCAATAGCAA-TGGAAAATAGAGGGGGGTTCCAAATATCGCGGCCAT
* *
1039783 AATATTTTAAACCCCCTCTCCAATGGAAGTTGGAAAAAGGTAGGGGGTTCAATATATCGCAGCCA
65 AATATTTTGAACCCCCTCTCCAATGGAA-TTGGAAATAGGTAGGGGGTTCAATATATCGCAGCCA
1039848 TA
129 TA
*
1039850 ATATTTTGAACCCCCTCTCCAATAGCAAT-GAAAAAATGAGGGGGGTTCCAAATATCGCGGCC--
1 ATATTTTGAACCCCCTCTCCAATAGCAATGGAAAATA-GAGGGGGGTTCCAAATATCGCGGCCAT
*
1039912 -ATATTTTGAACCCCCTCTCCAATGGGAATTGGAAATAGGTAGTGGGTTCAATACATATATCGCA
65 AATATTTTGAACCCCCTCTCCAAT-GGAATTGGAAATAGGTAGGGGGTTC---A-ATATATCGCA
1039976 GCCATA
125 GCCATA
* * * * *
1039982 ATATTTT-ATACCCCCTCTCCAAAAGCAATGAAAAAT-GA-GGGGGCTCCAAATTTTGCGGCCAT
1 ATATTTTGA-ACCCCCTCTCCAATAGCAATGGAAAATAGAGGGGGGTTCCAAATATCGCGGCCAT
* *
1040044 AATATTTTGAACCCCCTCTCCAATGGAAATTAGAAATATGTAGGGGGTTCAATATATCGCAGCCA
65 AATATTTTGAACCCCCTCTCCAATGG-AATTGGAAATAGGTAGGGGGTTCAATATATCGCAGCCA
1040109 TA
129 TA
1040111 ATATTTTGAACCCCCTCTCCAATAGCAATG
1 ATATTTTGAACCCCCTCTCCAATAGCAATG
1040141 AAACAAGAGG
Statistics
Matches: 260, Mismatches: 18, Indels: 29
0.85 0.06 0.09
Matches are distributed among these distances:
128 41 0.16
129 47 0.18
130 27 0.10
131 28 0.11
132 70 0.27
133 47 0.18
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (130 bp):
ATATTTTGAACCCCCTCTCCAATAGCAATGGAAAATAGAGGGGGGTTCCAAATATCGCGGCCATA
ATATTTTGAACCCCCTCTCCAATGGAATTGGAAATAGGTAGGGGGTTCAATATATCGCAGCCATA
Found at i:1040779 original size:166 final size:165
Alignment explanation
Indices: 1040482--1041010 Score: 778
Period size: 166 Copynumber: 3.2 Consensus size: 165
1040472 AAAGAATCAT
* *
1040482 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCTTATGTAAAACT
1 CTGGCTGATAAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
*
1040547 TTGACCCCCATTGTGGCCCCACCTTACCCCCAGG-GGTCATGATTTTCACAACTTTGAATCTACA
66 TCGACCCCCATTGTGGCCCCACCTTACCCCC-GGTGGTCATGATTTTCACAACTTTGAATCTACA
*
1040611 CTACTTGAGGATGCTTCCACACAAGTTTCAGCTTTC
130 CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
*
1040647 CTGGCTGATAAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATAAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* *
1040712 TCGAGCCCCCATTGTGGCCCCACCCTACCCCCGGTGGTCATGATTTTCACAACTTGGAATCTACA
66 TCGA-CCCCCATTGTGGCCCCACCTTACCCCCGGTGGTCATGATTTTCACAACTTTGAATCTACA
*
1040777 CTACCTAAGGATGCTTCCACACAAGTTTCAGCTTTC
130 CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* * **
1040813 CTGGCAGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCCCTATATTCCTATGTAAAACT
1 CTGGCTGATAAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * * *
1040878 TCGACCCCCCCATTGTGGCCCCACCTTACCCTCGGAT-GTCATGAATTTCACAACTTTGAACCTG
66 TCGA--CCCCCATTGTGGCCCCACCTTACCCCCGG-TGGTCATGATTTTCACAACTTTGAATCTA
* *
1040942 CACTACCTGAGGATGTTTCCACACAA-ATTCAGCTTTC
128 CACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* * * *
1040979 CTGGCT-TTATGGTTCTTAAGAAGAAGATTTTT
1 CTGGCTGATAAGTTTC-TGAGAAGAAGATTTTT
1041011 GAAAATTACT
Statistics
Matches: 330, Mismatches: 29, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
165 72 0.22
166 183 0.55
167 74 0.22
168 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.33
Consensus pattern (165 bp):
CTGGCTGATAAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
TCGACCCCCATTGTGGCCCCACCTTACCCCCGGTGGTCATGATTTTCACAACTTTGAATCTACAC
TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
Found at i:1054444 original size:15 final size:17
Alignment explanation
Indices: 1054416--1054464 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 17
1054406 TTTGCAAAAT
*
1054416 TTTACGGTTATAACGAA
1 TTTACGGATATAACGAA
*
1054433 -TT-CGGATATAACAAA
1 TTTACGGATATAACGAA
*
1054448 TTTACGGATATAGCGAA
1 TTTACGGATATAACGAA
1054465 CTCATTTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 11 0.42
16 4 0.15
17 11 0.42
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (17 bp):
TTTACGGATATAACGAA
Found at i:1056764 original size:11 final size:11
Alignment explanation
Indices: 1056748--1056779 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1056738 CGGGGAAAAC
1056748 AAGTCCCACGT
1 AAGTCCCACGT
1056759 AAGTCCCACGT
1 AAGTCCCACGT
1056770 AAGTCCCACG
1 AAGTCCCACG
1056780 GCAAATGCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.38, G:0.19, T:0.16
Consensus pattern (11 bp):
AAGTCCCACGT
Found at i:1059439 original size:18 final size:19
Alignment explanation
Indices: 1059405--1059441 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1059395 AAATTATACC
1059405 ATTATTTATGAAGAAATGA
1 ATTATTTATGAAGAAATGA
*
1059424 ATTATTTTTG-AGAAATGA
1 ATTATTTATGAAGAAATGA
1059442 TACTAAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (19 bp):
ATTATTTATGAAGAAATGA
Done.