Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold867
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: 1160077
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.29
Warning! 150854 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:1041519 original size:107 final size:107
Alignment explanation
Indices: 1041333--1041527 Score: 372
Period size: 107 Copynumber: 1.8 Consensus size: 107
1041323 TAGCTATTCG
*
1041333 TCAGTACACTCTCTGTGTTCTGTCAGCTATCCTTCACTAGACTCTTTTTGTTCTGTCAACTATTT
1 TCAGTACACTCTCCGTGTTCTGTCAGCTATCCTTCACTAGACTCTTTTTGTTCTGTCAACTATTT
*
1041398 GCCAGTACACACTATGTGNTCTCTGTGTTCTGTCAGCTACCA
66 GCCAGTACACACTATGTGTTCTCTGTGTTCTGTCAGCTACCA
1041440 TCAGTACACTCTCCGTGTTCTGTCAGCTATCCTTCACTAGACTCTTTTTGTTCTGTCAACTATTT
1 TCAGTACACTCTCCGTGTTCTGTCAGCTATCCTTCACTAGACTCTTTTTGTTCTGTCAACTATTT
1041505 GCCAGTACACACTATGTGTTCTC
66 GCCAGTACACACTATGTGTTCTC
1041528 CAATCCATTA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 86 1.00
ACGTcount: A:0.18, C:0.28, G:0.14, T:0.39
Consensus pattern (107 bp):
TCAGTACACTCTCCGTGTTCTGTCAGCTATCCTTCACTAGACTCTTTTTGTTCTGTCAACTATTT
GCCAGTACACACTATGTGTTCTCTGTGTTCTGTCAGCTACCA
Found at i:1046436 original size:19 final size:20
Alignment explanation
Indices: 1046396--1046432 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1046386 ACCTTGAAAT
1046396 AAAATTTTTAGGTCAAGGTC
1 AAAATTTTTAGGTCAAGGTC
1046416 AAAATTTTT-GGT-AAGGT
1 AAAATTTTTAGGTCAAGGT
1046433 TCAACTAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (20 bp):
AAAATTTTTAGGTCAAGGTC
Found at i:1047171 original size:440 final size:439
Alignment explanation
Indices: 1046209--1047529 Score: 2121
Period size: 440 Copynumber: 3.0 Consensus size: 439
1046199 ATGTTACCCA
* * *
1046209 GACCCAGACAAAATTTTATTATCTTTTTCTTAATTTGACCTTGAGTAAAACATGGTCAAGGTCAT
1 GACCCAGACAAAATTTTATTATTTTTTTCTTAATTTGACCTTGAGTAAAACAAGGTCAAGGTCAA
* *
1046274 ATATAAATCAATAGTACACCTAAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTCT
66 ATATTATTCAATAGTACACCTAAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTCT
* * *
1046339 GTCAAAGTATATTCAGGAGTTGAACAATGAAGTTTTTTTCTAATTTGACCTTGAAATAAAATTTT
131 GTCAAAGTATATTCAGGAGTTGAACAATGAAG-TTTTTTCTAATATGACCTTGAAATAAAAATTC
* * * * *
1046404 TAGGTCAAGGTCAAAATTTTTGGTAAGGTTCAACTAGATTATATACCAACTATCCATGATACAAG
195 TAGGTCAAGGTCAAAAATGTTGGTAAGGTTCAACTAGGTTATATACCATCTATCTATGATACAAG
* * **
1046469 GTAAAAGTCTGTATGTTAAAGGAGTCTTGTGTTATGGTCCGGACAATATTTTTTGTGAAAAGCCA
260 TTAAAAGTCTGTATGTTAAAGGAGTCTTGTGTTATGGTCC-GACAATATTTTTTATGAAAAGCTT
* * * ** *
1046534 GACCTTTAAAAGCAAAATAGGTCAAGATCAAAACTTTTGGTGAGGTGCACTCCTTCTCATTACCA
324 GACCTTGAAGAGCAAAATAGGTCAAGGTCAAAAAATTTGGTG-GGTGCACTCCTTCTCAATACCA
*
1046599 TCTACCTATGTTCTAAGTTTGAAGTCTTAATGTCAAAGGGTATTAAAGTTAT
388 TCTACCTATGTTCCAAGTTTGAAGTCTTAATGTCAAAGGGTATTAAAGTTAT
* * *
1046651 GATCCAGACAAAA--TT-TTATTTTTTTCTTAATTTGACATTGAGTAAACCAAGGTCAAGGTCAA
1 GACCCAGACAAAATTTTATTATTTTTTTCTTAATTTGACCTTGAGTAAAACAAGGTCAAGGTC-A
*
1046713 ATATATTTTTCAATAGTACACCTAAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTT
65 A-ATATTATTCAATAGTACACCTAAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTT
* *
1046778 CTGTCAAAGTATTTTCAGGAGTTGAACAATGAAGATTTTTCTAATATGACCTTGAAATAAAAATT
129 CTGTCAAAGTATATTCAGGAGTTGAACAATGAAGTTTTTTCTAATATGACCTTGAAATAAAAATT
1046843 CTAGGTCAAGGTCAAAAATGTTGGTAAGGTTCAACTAGGTTATATACCATCTATCTATGATACAA
194 CTAGGTCAAGGTCAAAAATGTTGGTAAGGTTCAACTAGGTTATATACCATCTATCTATGATACAA
* *
1046908 GTTAAAAGTCTGTATGTTAAAGGAGTCTTGTG-TATGGTCCAGACAATATTTTTAATTAAAAGCT
259 GTTAAAAGTCTGTATGTTAAAGGAGTCTTGTGTTATGGTCC-GACAATATTTTTTATGAAAAGCT
* *
1046972 TGACCTTGAAGAGCAAAATAAGTCAAGGTCAAAAAATTTGGTGGTGTGCACTCCTTCCCAATACC
323 TGACCTTGAAGAGCAAAATAGGTCAAGGTCAAAAAATTTGGTGG-GTGCACTCCTTCTCAATACC
*
1047037 ATCTACCTATGTTCCAAGTTTGAAGTCTTAATGTCAAAGGGCATTAAAGTTAT
387 ATCTACCTATGTTCCAAGTTTGAAGTCTTAATGTCAAAGGGTATTAAAGTTAT
1047090 GACCCAGACAAAATTTTATTATTTTTTTCTTAATTTGACCTTGAGTAAAACAAGGTCAAGGTCAA
1 GACCCAGACAAAATTTTATTATTTTTTTCTTAATTTGACCTTGAGTAAAACAAGGTCAAGGTCAA
*
1047155 ATATTATTCAATAGTACACCTAAGTGTATTATTAGTGTTCTTTGTTTAAAGTTTGAAGTCCTTCT
66 ATATTATTCAATAGTACACCTAAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTCT
* *
1047220 GTCAAAGTATATTCAGAAGTTGAACAATGAAGTTTTTTCTAATATGACCTTGAAATACAAATTCT
131 GTCAAAGTATATTCAGGAGTTGAACAATGAAGTTTTTTCTAATATGACCTTGAAATAAAAATTCT
*
1047285 AGGTCAAGGTCAAAAATGTTGGTAAGGTTCAACTAGGTTATATACCATCTATCTATGGTACAAGT
196 AGGTCAAGGTCAAAAATGTTGGTAAGGTTCAACTAGGTTATATACCATCTATCTATGATACAAGT
1047350 TAAAAGTCTGTATGTTAAAGGAGTCTTGTGTTATGGTCCGAACAATATTTTTTATGAAAAGCTTG
261 TAAAAGTCTGTATGTTAAAGGAGTCTTGTGTTATGGTCCG-ACAATATTTTTTATGAAAAGCTTG
* * *
1047415 ACCTTGAAGAACAAAATAGGTCAAGGTC-AAAACTTTCGGTGGCGTGCACTCCTTTTCAATACCA
325 ACCTTGAAGAGCAAAATAGGTCAAGGTCAAAAAATTT-GGTGG-GTGCACTCCTTCTCAATACCA
* *
1047479 TCTACCTATGTTCCAAGTTTGAACTCTTAATGTCAAAGGGTATTTAAGTTA
388 TCTACCTATGTTCCAAGTTTGAAGTCTTAATGTCAAAGGGTATTAAAGTTA
1047530 CGGCCTGGAC
Statistics
Matches: 813, Mismatches: 57, Indels: 19
0.91 0.06 0.02
Matches are distributed among these distances:
438 1 0.00
439 185 0.23
440 347 0.43
441 225 0.28
442 55 0.07
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (439 bp):
GACCCAGACAAAATTTTATTATTTTTTTCTTAATTTGACCTTGAGTAAAACAAGGTCAAGGTCAA
ATATTATTCAATAGTACACCTAAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTCT
GTCAAAGTATATTCAGGAGTTGAACAATGAAGTTTTTTCTAATATGACCTTGAAATAAAAATTCT
AGGTCAAGGTCAAAAATGTTGGTAAGGTTCAACTAGGTTATATACCATCTATCTATGATACAAGT
TAAAAGTCTGTATGTTAAAGGAGTCTTGTGTTATGGTCCGACAATATTTTTTATGAAAAGCTTGA
CCTTGAAGAGCAAAATAGGTCAAGGTCAAAAAATTTGGTGGGTGCACTCCTTCTCAATACCATCT
ACCTATGTTCCAAGTTTGAAGTCTTAATGTCAAAGGGTATTAAAGTTAT
Found at i:1054876 original size:25 final size:25
Alignment explanation
Indices: 1053620--1054875 Score: 1679
Period size: 25 Copynumber: 50.6 Consensus size: 25
1053610 TACTTCAAAT
*
1053620 ATGTAGTGGGTGTATTTCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* *
1053645 ATGTAGTGAGTGTATTTCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
1053670 ATGTAGTGGGTGTATATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
1053695 ATGTAGTGGGTGT-TATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
1053719 ATGTAGTGGGTGTATATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* * *
1053744 ATGAAGTGAGTGTATTTCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
1053769 ATGTAGTGGGTGTATATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* * *
1053794 ATGAAGTGAGTGTATTTCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* *
1053819 ATGTAGTGAGTGTATTTCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
** *
1053844 ATGTAGTTAGTGTATGTCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
*
1053869 ATGTAGTGGGTGTATATCTTCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* *
1053894 ATGTTGTGGATGTATATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* *
1053919 ATGTAGTGGGTGTATTTCTCCCAAC
1 ATGTAGTGGGTGTATATCTCCCTAC
1053944 ATGTAGTGGGTGTATATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* * *
1053969 ATGTTGTTGATGTATATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
*
1053994 ATGTAGTGGGTGTATTTCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
1054019 ATGTAGTGGGTGTATATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* * *
1054044 ATGAAGTGAGTGTATTTCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
1054069 ATGTAGTGGGTGTATATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* * *
1054094 ATGAAGTGAGTGTATTTCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
1054119 ATGTAGTGGGTGTATATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* *
1054144 ATGTAGTGGATGTATTTCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
1054169 ATGTAGTGGGTGT-TATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
1054193 ATGTAGTGGGTGTATATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* * *
1054218 ATGTTGTTGATGTATATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
1054243 ATGTAGTGGGTGTATATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* *
1054268 ATGTAGTGGATGTATTTCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
1054293 ATGTAGTGGGTGT-TATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
*
1054317 ATGTAGTGGGTGTATTTCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
*
1054342 ATGTTA-TGGGTGTATTTCTCCCTAC
1 ATG-TAGTGGGTGTATATCTCCCTAC
*
1054367 ATGTAGTGGGTGTATATCTCCCTAT
1 ATGTAGTGGGTGTATATCTCCCTAC
* * *
1054392 ATGTAGTGGGTGTTTATTTCCCTAA
1 ATGTAGTGGGTGTATATCTCCCTAC
*
1054417 ATGTAGTGGGTGTATTTCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
*
1054442 ATGTAATGGGTGTATATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* *
1054467 ATGTAGTGGGTGTTTTTCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
*
1054492 ATGTAGTGGGTGTATTTCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
*
1054517 ATGTTA-TGGGTGTATATCTCCATAC
1 ATG-TAGTGGGTGTATATCTCCCTAC
* *
1054542 AAGAAGTGGGTGT-TATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* *
1054566 ATGTTGTGGGTGT-TATTTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* *
1054590 ATGTAGTGGGTGTATTTCTCCTTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* * * *
1054615 ATGTTGTGGGAGTTTTTC-CCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
*
1054639 ATGTAATGGGTGTATATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* *
1054664 ATGTAGTGGGTGTATTTCTCCTTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
*
1054689 ATGTAGTGGGTGTATTTCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* * *
1054714 AAGAAGTGGGTGT-TATCTCCTTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* **
1054738 ATGTAGTGGGTGTAT-TCCTACCTTT
1 ATGTAGTGGGTGTATAT-CTCCCTAC
* ** *
1054763 ATGTTGTGGGAATAT-TTTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
*
1054787 ATGTTGTGGGTGTATATCTCCCTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
** * * *
1054812 ATGTAGTGTTTGTTTTTCTCCATAC
1 ATGTAGTGGGTGTATATCTCCCTAC
* *
1054837 ATGTAGTGGGTGTACATCTCCTTAC
1 ATGTAGTGGGTGTATATCTCCCTAC
*
1054862 ATGAAGTGGGTGTA
1 ATGTAGTGGGTGTA
1054876 CCAGGTATTT
Statistics
Matches: 1082, Mismatches: 137, Indels: 24
0.87 0.11 0.02
Matches are distributed among these distances:
24 171 0.16
25 907 0.84
26 4 0.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (25 bp):
ATGTAGTGGGTGTATATCTCCCTAC
Found at i:1056514 original size:145 final size:145
Alignment explanation
Indices: 1056248--1056666 Score: 578
Period size: 146 Copynumber: 2.9 Consensus size: 145
1056238 TTTTTAACAA
* * *
1056248 TGACCTTGAACTT-CCTCAATTGACCTTGGGTCAAGGTCATGACACA-CCTTCAGGTTATAAGCA
1 TGACCTTGACCTTGCC-CAAATGACCTTGGGTCAAGGTCATGACACACCCTT-AGGTCATAAGCA
* * * * * * *
1056311 ATC-TTGATGTAAATTAAGAACTTCCGATATTTGTCCATTAA-AAAGATATGAACTGGACATGAA
64 ATCTTTG-TGTGAAGTAAGAACTTCCAATGTTTCTCCA-TAAGAAAGATATG-ACCGGACACGAA
*
1056374 TTTTGCAC-TTTTCTGCCAG
126 TTTTGAACTTTTTCTGCCAG
* * * *
1056393 TGACCTTTACTTTGCCCAAATGATCTTGGGTCAAGGTCATGACACACCCTTATGTCATAAGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* *
1056458 CTTTGTGTGAAGAAAGAACTTCCAATGTTTCTCCATAAGAAAGATATAGACCGGACACAAATTTT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATAT-GACCGGACACGAATTTT
1056523 GAACTTTTTCTGCCAG
130 GAACTTTTTCTGCCAG
*
1056539 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGATACACCCTTAGGTCATAAGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
1056604 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATAT-GACCGGACACGAATT
1056667 AAACAAACAG
Statistics
Matches: 243, Mismatches: 25, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
144 3 0.01
145 99 0.41
146 141 0.58
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (145 bp):
TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGACCGGACACGAATTTTG
AACTTTTTCTGCCAG
Found at i:1057364 original size:28 final size:30
Alignment explanation
Indices: 1057303--1057359 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
1057293 TCCTAACATG
1057303 TATGTACAATGTACACACAGAATATGAATT
1 TATGTACAATGTACACACAGAATATGAATT
*
1057333 TATGTACAATGTACACAGAGAATATGA
1 TATGTACAATGTACACACAGAATATGA
1057360 TTATGACAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (30 bp):
TATGTACAATGTACACACAGAATATGAATT
Found at i:1064314 original size:18 final size:18
Alignment explanation
Indices: 1064287--1064333 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1064277 GAAACCTTTC
*
1064287 CATCTCCTTCCACATC-T
1 CATCTTCTTCCACATCAT
* *
1064304 ACATCTTCTTCCTCTTCAT
1 -CATCTTCTTCCACATCAT
1064323 CATCTTCTTCC
1 CATCTTCTTCC
1064334 TCCTCCTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 24 0.96
19 1 0.04
ACGTcount: A:0.15, C:0.43, G:0.00, T:0.43
Consensus pattern (18 bp):
CATCTTCTTCCACATCAT
Found at i:1064343 original size:18 final size:18
Alignment explanation
Indices: 1064305--1064344 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1064295 TCCACATCTA
*
1064305 CATCTTCTTCCTCTTCAT
1 CATCTTCTTCCTCCTCAT
*
1064323 CATCTTCTTCCTCCTCCT
1 CATCTTCTTCCTCCTCAT
1064341 CATC
1 CATC
1064345 CATCTCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.10, C:0.45, G:0.00, T:0.45
Consensus pattern (18 bp):
CATCTTCTTCCTCCTCAT
Found at i:1072049 original size:1 final size:1
Alignment explanation
Indices: 1071962--1072032 Score: 97
Period size: 1 Copynumber: 71.0 Consensus size: 1
1071952 TTTGAGAAGG
* * * * *
1071962 TTTTTTTTTCTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTGTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1072027 TTTTTT
1 TTTTTT
1072033 GCTTGTCAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.00, C:0.03, G:0.04, T:0.93
Consensus pattern (1 bp):
T
Found at i:1076626 original size:15 final size:15
Alignment explanation
Indices: 1076606--1076640 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1076596 AACGCATAAT
1076606 CGCTAACACACAACA
1 CGCTAACACACAACA
* *
1076621 CGCTAACATACAGCA
1 CGCTAACACACAACA
1076636 CGCTA
1 CGCTA
1076641 GATCACGCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.37, G:0.11, T:0.11
Consensus pattern (15 bp):
CGCTAACACACAACA
Found at i:1076753 original size:2 final size:2
Alignment explanation
Indices: 1076746--1076784 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1076736 GTGTATTTAC
1076746 GA GA GA GA GA 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 GA GA GA GA GA G
1076785 CGTTATATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1078329 original size:38 final size:34
Alignment explanation
Indices: 1078258--1078610 Score: 544
Period size: 34 Copynumber: 10.0 Consensus size: 34
1078248 CCGTCCTGTC
*
1078258 CCGAGGGTCAGGTAAACACTTACAGACAGACAGA
1 CCGAGGGTCAGGTCAACACTTACAGACAGACAGA
1078292 CCGAGGGTCAGGTCAACACTTATATACAGACAGACAGA
1 CCGAGGGTCAGGTCAACAC---T-TACAGACAGACAGA
1078330 CCGAGGGTCAGGTCAACACTTACAGACAGACAGA
1 CCGAGGGTCAGGTCAACACTTACAGACAGACAGA
* *
1078364 CAGAGGGTCAGGTAAACACTTACAGACAGACAGACAGA
1 CCGAGGGTCAGGTCAACACTT----ACAGACAGACAGA
1078402 CCGAGGGTCAGGTCAACACTTACAGACAGACAGACAGA
1 CCGAGGGTCAGGTCAACACTT----ACAGACAGACAGA
1078440 CCGAGGGTCAGGTCAACACTTACAGACAGACAGA
1 CCGAGGGTCAGGTCAACACTTACAGACAGACAGA
1078474 CCGAGGGTCAGGTCAACACTTACAGACAGACAGA
1 CCGAGGGTCAGGTCAACACTTACAGACAGACAGA
* *
1078508 CCGAGGGTCAGGTAAACACTTACAGACAGACAGG
1 CCGAGGGTCAGGTCAACACTTACAGACAGACAGA
*
1078542 CCGAGGGTCAGGTCAACACTTACAGACAGACAGG
1 CCGAGGGTCAGGTCAACACTTACAGACAGACAGA
1078576 CCGAGGGTCAGGTCAACACTTACAGACAGACAGA
1 CCGAGGGTCAGGTCAACACTTACAGACAGACAGA
1078610 C
1 C
1078611 AGACAGACGG
Statistics
Matches: 302, Mismatches: 9, Indels: 16
0.92 0.03 0.05
Matches are distributed among these distances:
34 197 0.65
35 1 0.00
37 1 0.00
38 103 0.34
ACGTcount: A:0.36, C:0.25, G:0.27, T:0.12
Consensus pattern (34 bp):
CCGAGGGTCAGGTCAACACTTACAGACAGACAGA
Found at i:1078375 original size:72 final size:72
Alignment explanation
Indices: 1078258--1078614 Score: 532
Period size: 72 Copynumber: 5.0 Consensus size: 72
1078248 CCGTCCTGTC
*
1078258 CCGAGGGTCAGGTAAACACTTACAGACAGACAGACCGAGGGTCAGGTCAACACTTATATACAGAC
1 CCGAGGGTCAGGTCAACACTTACAGACAGACAGACCGAGGGTCAGGTCAACACTTATATACAGAC
1078323 AGACAGA
66 AGACAGA
* * * *
1078330 CCGAGGGTCAGGTCAACACTTACAGACAGACAGACAGAGGGTCAGGTAAACACTTACAGACAGAC
1 CCGAGGGTCAGGTCAACACTTACAGACAGACAGACCGAGGGTCAGGTCAACACTTATATACAGAC
1078395 AGACAGA
66 AGACAGA
1078402 CCGAGGGTCAGGTCAACACTTACAGACAGACAGACAGACCGAGGGTCAGGTCAACAC---T-TAC
1 CCGAGGGTCAGGTCAACACTT----ACAGACAGACAGACCGAGGGTCAGGTCAACACTTATATAC
1078463 AGACAGACAGA
62 AGACAGACAGA
*
1078474 CCGAGGGTCAGGTCAACACTTACAGACAGACAGACCGAGGGTCAGGTAAACAC---T-TACAGAC
1 CCGAGGGTCAGGTCAACACTTACAGACAGACAGACCGAGGGTCAGGTCAACACTTATATACAGAC
*
1078535 AGACAGG
66 AGACAGA
* * *
1078542 CCGAGGGTCAGGTCAACACTTACAGACAGACAGGCCGAGGGTCAGGTCAACACTTACAGACAGAC
1 CCGAGGGTCAGGTCAACACTTACAGACAGACAGACCGAGGGTCAGGTCAACACTTATATACAGAC
1078607 AGACAGA
66 AGACAGA
1078614 C
1 C
1078615 AGACGGACAG
Statistics
Matches: 261, Mismatches: 16, Indels: 16
0.89 0.05 0.05
Matches are distributed among these distances:
68 96 0.37
72 135 0.52
76 30 0.11
ACGTcount: A:0.36, C:0.25, G:0.27, T:0.12
Consensus pattern (72 bp):
CCGAGGGTCAGGTCAACACTTACAGACAGACAGACCGAGGGTCAGGTCAACACTTATATACAGAC
AGACAGA
Found at i:1078606 original size:4 final size:4
Alignment explanation
Indices: 1078597--1078626 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1078587 GTCAACACTT
*
1078597 ACAG ACAG ACAG ACAG ACAG ACGG ACAG AC
1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG AC
1078627 CGAGGGTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.47, C:0.27, G:0.27, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:1078657 original size:50 final size:50
Alignment explanation
Indices: 1078563--1078659 Score: 151
Period size: 50 Copynumber: 1.9 Consensus size: 50
1078553 GTCAACACTT
* *
1078563 ACAGACAGACAGGCCGAGGGTCAGGTCAACACTTACAGACAGACAGACAG
1 ACAGACAGACAGACCGAGGGTCAGGTCAACACTTACAGAAAGACAGACAG
*
1078613 ACAGACGGACAGACCGAGGGTCAGGTCAACACTTACA-ATAAGACAGA
1 ACAGACAGACAGACCGAGGGTCAGGTCAACACTTACAGA-AAGACAGA
1078660 TGAGGGTGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 1 0.02
50 42 0.98
ACGTcount: A:0.39, C:0.25, G:0.27, T:0.09
Consensus pattern (50 bp):
ACAGACAGACAGACCGAGGGTCAGGTCAACACTTACAGAAAGACAGACAG
Found at i:1081361 original size:2 final size:2
Alignment explanation
Indices: 1081354--1081404 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1081344 TACAAAAGTG
1081354 GA GA 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 GA GA
1081396 GA GA GA GA G
1 GA GA GA GA G
1081405 CATTGTTGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1091388 original size:12 final size:12
Alignment explanation
Indices: 1091371--1091396 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1091361 CTTTAAGAAT
1091371 AAAATAGTACAC
1 AAAATAGTACAC
1091383 AAAATAGTACAC
1 AAAATAGTACAC
1091395 AA
1 AA
1091397 CTGATAACAA
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:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAATAGTACAC
Found at i:1120665 original size:45 final size:45
Alignment explanation
Indices: 1120582--1120677 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 45
1120572 ATCAACATTG
*
1120582 CGATGTCGACCATGTAAACAGGAAAGAAGGCACGCGATGTAGACA
1 CGATGTCGACCATGTAAACAGGAAAGAAGGCACACGATGTAGACA
* * * * *
1120627 CGATGTCGACGATGTAAACAGGATATAAGAG-ATACGATGTAGTCA
1 CGATGTCGACCATGTAAACAGGAAAGAAG-GCACACGATGTAGACA
1120672 CGATGT
1 CGATGT
1120678 TAACTCGATG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
45 43 0.98
46 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (45 bp):
CGATGTCGACCATGTAAACAGGAAAGAAGGCACACGATGTAGACA
Found at i:1121051 original size:9 final size:9
Alignment explanation
Indices: 1121039--1121065 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1121029 TTGCGATATC
1121039 GACGATGTA
1 GACGATGTA
1121048 GACGATGTA
1 GACGATGTA
1121057 GACGATGTA
1 GACGATGTA
1121066 AACAGGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.22
Consensus pattern (9 bp):
GACGATGTA
Found at i:1121143 original size:166 final size:157
Alignment explanation
Indices: 1120791--1121206 Score: 415
Period size: 166 Copynumber: 2.6 Consensus size: 157
1120781 CTCGATGTCA
* * * * **
1120791 ATCAACATTGCGATTTCGACGATG-AATAAAGGCAAGAAGGAACACGATGTAGACACGATGTCGA
1 ATCAACATTGCGATGTCGACGATGTAA-ACAGGAAAGAAGGCACACGATGTAGACACGACATCGA
* * * * *
1120855 CTCGATGTTGGTCAACATTGTGATATCGACAAAGTCGATGGTGTAAACAGGTTATAAGAGGTACG
65 CTCGATGTCGATCAACATTGCGATATCGACAAAGACGATGGTGTAAACAGGATATAAGAGGTACG
* *
1120920 AAGTAGACACGAAGTCTACATGATATTG
130 AAGTAGACACGAAGTCGACACGATATTG
* * * * * *
1120948 ATCAACACTGCAATGCCGACGGTGTAAACAGAAAAGAAGGCACACGATGTATACACGACATCGAC
1 ATCAACATTGCGATGTCGACGATGTAAACAGGAAAGAAGGCACACGATGTAGACACGACATCGAC
*
1121013 TCGATGTCGATCAACATTGCGATATCGACGATGTAGACGATGTAGACGATGTAAACAGGATATAA
66 TCGATGTCGATCAACATTGCGATATCGAC-A--AAGACGA--T-G--G-TGTAAACAGGATATAA
* *
1121078 GAGGTAC-AATGTAGACACGATGTCGACCCGATATTG
122 GAGGTACGAA-GTAGACACGAAGTCGACACGATATTG
* * * * * * ** *
1121114 ATCAACTTTGCGATGTCGACGATGTAAACAGGAAACAAGACACACGATGTGGACTCAATGTGGAC
1 ATCAACATTGCGATGTCGACGATGTAAACAGGAAAGAAGGCACACGATGTAGACACGACATCGAC
*
1121179 TCGATGTTTG-TCAACATTGCGATATCGA
66 TCGATG-TCGATCAACATTGCGATATCGA
1121207 AAATGTACAC
Statistics
Matches: 209, Mismatches: 38, Indels: 15
0.80 0.15 0.06
Matches are distributed among these distances:
157 76 0.36
158 3 0.01
160 5 0.02
162 1 0.00
163 1 0.00
165 3 0.01
166 118 0.56
167 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (157 bp):
ATCAACATTGCGATGTCGACGATGTAAACAGGAAAGAAGGCACACGATGTAGACACGACATCGAC
TCGATGTCGATCAACATTGCGATATCGACAAAGACGATGGTGTAAACAGGATATAAGAGGTACGA
AGTAGACACGAAGTCGACACGATATTG
Found at i:1136982 original size:2 final size:2
Alignment explanation
Indices: 1136975--1137004 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1136965 AAAATTGGTG
*
1136975 TA TA TA TA TA GA 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
1137005 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1140151 original size:2 final size:2
Alignment explanation
Indices: 1140144--1140175 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1140134 ATCTTATGCT
1140144 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
1140176 TTAGGAGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1143860 original size:22 final size:22
Alignment explanation
Indices: 1143835--1143884 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1143825 TCGCTCTGTT
1143835 GCCTTTGCAA-CTTCGCACTCTC
1 GCCTTTG-AATCTTCGCACTCTC
* * *
1143857 GCCTTCGAATCTTCGCGCTTTC
1 GCCTTTGAATCTTCGCACTCTC
1143879 GCCTTT
1 GCCTTT
1143885 TTAGCTCACC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.10, C:0.38, G:0.16, T:0.36
Consensus pattern (22 bp):
GCCTTTGAATCTTCGCACTCTC
Found at i:1144872 original size:15 final size:15
Alignment explanation
Indices: 1144803--1144886 Score: 55
Period size: 15 Copynumber: 5.5 Consensus size: 15
1144793 ATTATATCAA
*
1144803 ATGAAATTGTA-AAT
1 ATGATATTGTATAAT
1144817 ATGATATTGTAATATCAT
1 ATGATATTGT-ATA--AT
** * *
1144835 AAAATATCGTATCAT
1 ATGATATTGTATAAT
*
1144850 ACGATATTGTATAAT
1 ATGATATTGTATAAT
*
1144865 ATGATATTGGT-TTAT
1 ATGATATT-GTATAAT
1144880 ATGATAT
1 ATGATAT
1144887 ATTATCATAT
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
14 9 0.17
15 31 0.57
16 3 0.06
17 2 0.04
18 9 0.17
ACGTcount: A:0.40, C:0.05, G:0.13, T:0.42
Consensus pattern (15 bp):
ATGATATTGTATAAT
Found at i:1146908 original size:13 final size:13
Alignment explanation
Indices: 1146890--1146914 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1146880 AATTACACTT
1146890 AATTACCATTACA
1 AATTACCATTACA
1146903 AATTACCATTAC
1 AATTACCATTAC
1146915 CCCATCCCTG
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:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (13 bp):
AATTACCATTACA
Found at i:1147386 original size:22 final size:22
Alignment explanation
Indices: 1147358--1147408 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1147348 ATCAAAAAAG
*
1147358 GCGAAGGCGAAAGTGCGAAGAT
1 GCGAAGGCCAAAGTGCGAAGAT
* *
1147380 GCGAAGGCCAGAGTGCGAAGTT
1 GCGAAGGCCAAAGTGCGAAGAT
*
1147402 GGGAAGG
1 GCGAAGG
1147409 AGCGATAGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.14, G:0.45, T:0.10
Consensus pattern (22 bp):
GCGAAGGCCAAAGTGCGAAGAT
Found at i:1148444 original size:22 final size:20
Alignment explanation
Indices: 1148397--1148458 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 20
1148387 GTGGTCGCAT
1148397 CTTCGCACTTTCGCTCCTTCGC
1 CTTCGCAC-TTCGC-CCTTCGC
1148419 CTTCGCACTATCGCCCTT-GC
1 CTTCGCACT-TCGCCCTTCGC
1148439 AACTTCGCATCTTCGCCCTT
1 --CTTCGCA-CTTCGCCCTT
1148459 TATTAAGGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
20 2 0.06
21 5 0.14
22 27 0.75
23 2 0.06
ACGTcount: A:0.10, C:0.44, G:0.13, T:0.34
Consensus pattern (20 bp):
CTTCGCACTTCGCCCTTCGC
Found at i:1151184 original size:1 final size:1
Alignment explanation
Indices: 1151180--1151207 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1151170 GTTTTTTTTT
1151180 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1151208 CCAAAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1155380 original size:20 final size:20
Alignment explanation
Indices: 1155355--1155414 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
1155345 CAGACAGTAC
1155355 ACACTAAATCATTAGTCTGT
1 ACACTAAATCATTAGTCTGT
** *
1155375 ACACTAAGCCAGTA--C---
1 ACACTAAATCATTAGTCTGT
1155390 ACACTAAATCATTAGTCTGT
1 ACACTAAATCATTAGTCTGT
1155410 ACACT
1 ACACT
1155415 CAGCCAGTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
15 11 0.38
17 1 0.03
18 1 0.03
20 16 0.55
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (20 bp):
ACACTAAATCATTAGTCTGT
Found at i:1156240 original size:35 final size:35
Alignment explanation
Indices: 1154300--1156224 Score: 2357
Period size: 35 Copynumber: 55.2 Consensus size: 35
1154290 GTACTCAACA
* * * * * *
1154300 AGTACATACTAAATTATAAATCAGTACACGCAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1154335 AGTGCACACTAAATCATTAGTCTGTACACTTAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* * * * *
1154370 AGTGCACAATAAATCATAAGTCTGTACACTTAGAC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
1154405 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* * * * *
1154440 AGTACACACTAAATAATAAGTATGTACACTCAACT
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
*
1154475 AGTACACACTAAATAATTAGTCTGTACACTCAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
*
1154510 AGTACACACTAAATAATTAGTCTGTACACTCAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1154545 AGTACACACTAAATCATAAGTGTGTACACTCAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* * *
1154580 AGTACACACTAAATAATTGGTCTGTACACTTAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* * * * *
1154615 AGTACACATTAACTCATAAGTGTGTACACTCAGCA
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
*
1154650 AGTACACACTAAATAATTAGTCTGTACACTCAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
*
1154685 AGTACACACTAAATAATTAGTCTGTACACTCAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
*
1154720 AGTACACACTAAATC-TTAAGTGTGTACACTCAGCC
1 AGTACACACTAAATCATT-AGTCTGTACACTCAGCC
* * *
1154755 AGTACATACTAAATAATTAGTCTGTACACTTAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* ** * *
1154790 AGTACACACTAACTCAAAAGTGTGTACACTCAGCA
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
*
1154825 AGTACACACTAAATCATTAGTCTGTACACTCAGTC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1154860 AGCT-CCCACTAAATCATTAGTCTGTACACTCAGTC
1 AG-TACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1154895 AGCT-CCCACTGAATCATTAGTCTGTACACTCAGCC
1 AG-TACACACTAAATCATTAGTCTGTACACTCAGCC
*
1154930 AGTACACACTAAATAATTAGTCTGTACACTCAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* * * * *
1154965 AGTCCACACTAAATCATAAGTGTGTATACTCATCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* * *
1155000 ACTACACACTAAATCATTAGTATGTACACTCAGGC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* * * *
1155035 AGTTCCCACTAAATCGTTAGTCTGTACACTCAGCT
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* * * **
1155070 AGTACACACTAAATAATTAGTCTGAACACTTATTC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* * * * *
1155105 AGTGCCCACTAGATCATTAGTGTGTACACTCAGCT
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1155140 AGTACACACTAAATAATTAGTCTGTACACTCAGTC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1155175 AGTTCCCACTAAATCATCT-GTCTGTACACTCAGCC
1 AGTACACACTAAATCAT-TAGTCTGTACACTCAGCC
*
1155210 AGTACACACTAAATCACTAGTCTGTACACTCAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1155245 AGTACACACTAAATAATTAGTCTGTACACTCAGAC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* * *
1155280 AGTACACACTAAATAATTAGTCAGTACACTCAGCT
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* * *
1155315 AGTACACACTAAATCATGAGTCTGTACAGTCAGAC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
*
1155350 AGTACACACTAAATCATTAGTCTGTACACTAAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
1155385 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1155420 AGTACACACTAAATCATCAGTCTGTACACTCAGCT
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1155455 AGTACACACTAAATCATTAGTTTGTACACTCTGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* * * ** *
1155490 AGTACACACTTAATAATTAGTCAGTACACGAAACC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* * * ** *
1155525 AGTTCACACTAAATCATTCGTTTGTTTACTCAGCT
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* * ** *
1155560 AGTAAACACCAAATCAGCAGTCTGTACACTCAGCT
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1155595 AGTACACACTAAATCATCAGTCTGTACACTCAGCT
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
1155630 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* * *
1155665 AGTTCACACAAAATCATTAGTCTGTACACTCAGAC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1155700 AGTACACACTAAATCATAAGTCTGTACACTCAGCT
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
** * * *
1155735 AGTACACACCCAATTATCAGTCTGTACACTCAGGC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1155770 AGTACACACTAAATAATTAGTCTGTACACTCAGGC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1155805 AGTACACACTAAATCATAAGTGTGTACACTCAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1155840 A--ACACA-T--A-CATTAGTTTGTACACTCAGCT
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1155869 AGTACACA-TAAATAATTAGTCTGTACACTCAGTC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* * *
1155903 AGTTC-CAACTAAATCATTAGTCTGTACACGCAGCT
1 AGTACAC-ACTAAATCATTAGTCTGTACACTCAGCC
* *
1155938 AGTACACA-TAAAATAATTAGTCTGTACACTCAGTC
1 AGTACACACT-AAATCATTAGTCTGTACACTCAGCC
* * *
1155973 AGCT-CCCACTTAATCATTAGTCTGTACACTCAGAC
1 AG-TACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1156008 AGTACACACTAAATAATTAGTCTGTACACTCAGAC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
*
1156043 AGTACACACTAAATCATTAGTCTGTACACTCAGAC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1156078 AGTGCACACTAAATAATTAGTCTGTACACTCAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
** * *
1156113 AGTACACACCCAATTATAAGTCTGTACACTCAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* * * * *
1156148 GGTACACACTAAATGATTAGTCAGTACAATAAGCC
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
* *
1156183 AGTACACACTTAATCATTAGTCTGTACACTCAGCT
1 AGTACACACTAAATCATTAGTCTGTACACTCAGCC
1156218 AGTACAC
1 AGTACAC
1156225 GCCTAATTAT
Statistics
Matches: 1619, Mismatches: 253, Indels: 36
0.85 0.13 0.02
Matches are distributed among these distances:
29 19 0.01
30 1 0.00
31 6 0.00
32 1 0.00
33 7 0.00
34 28 0.02
35 1550 0.96
36 7 0.00
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.26
Consensus pattern (35 bp):
AGTACACACTAAATCATTAGTCTGTACACTCAGCC
Found at i:1157975 original size:50 final size:53
Alignment explanation
Indices: 1157915--1158022 Score: 168
Period size: 50 Copynumber: 2.1 Consensus size: 53
1157905 GTGCAAGCAA
*
1157915 TTTGATCTTTTGTTATATACTGTTTTAGA-TTTACTTTACTGACTA-A-CCTG
1 TTTGATCTTTTGTTATATACTGTTATAGAGTTTACTTTACTGACTACAGCCTG
* *
1157965 TTTGATCTTTTGTTATATACTGTTATAGAGTTTGCTTTGCTGACTACAGCCTG
1 TTTGATCTTTTGTTATATACTGTTATAGAGTTTACTTTACTGACTACAGCCTG
1158018 TTTGA
1 TTTGA
1158023 GCTCATAGGT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
50 28 0.54
51 14 0.27
52 1 0.02
53 9 0.17
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.50
Consensus pattern (53 bp):
TTTGATCTTTTGTTATATACTGTTATAGAGTTTACTTTACTGACTACAGCCTG
Found at i:1158451 original size:52 final size:52
Alignment explanation
Indices: 1158341--1158456 Score: 137
Period size: 52 Copynumber: 2.2 Consensus size: 52
1158331 TTTGCTGACC
* **
1158341 AACCTGTTTGATCTTTATGTATATTCTCTTTTAGGTTTGCTTTGTTGATAAA
1 AACCTGTTTGATCTTTATGTATATTCTCTTATAGGTTTGCTTTGCCGATAAA
* * *
1158393 AACCTGTTTGATCTTTTAT-TATATAT-TGTTATAGGTTTGCTTTGCCGATTAG
1 AACCTGTTTGATC-TTTATGTATAT-TCTCTTATAGGTTTGCTTTGCCGATAAA
*
1158445 AGCCTGTTTGAT
1 AACCTGTTTGAT
1158457 TTCTTGTTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
52 49 0.89
53 6 0.11
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (52 bp):
AACCTGTTTGATCTTTATGTATATTCTCTTATAGGTTTGCTTTGCCGATAAA
Done.