Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 2 of 344
Found at i:482000 original size:20 final size:20
Alignment explanation
Indices: 481975--482038 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
481965 TTAAAAACAT
481975 TACATAAATCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
*** *
481995 TACAT-AAT-TAAAAAT-AT
1 TACATAAATCTTTGAATCAC
*
482012 TACATAAGTCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
482032 TACATAA
1 TACATAA
482039 TTAAAAATAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 6 0.19
18 6 0.19
19 7 0.22
20 13 0.41
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (20 bp):
TACATAAATCTTTGAATCAC
Found at i:482058 original size:37 final size:37
Alignment explanation
Indices: 481952--482064 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
481942 ACCCGAATTA
* *
481952 AATCACTACATAATTAAAAACATTACATAAATCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
481989 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
*
482026 AATCACTACATAATTAAAAATATTACACAAGTC-TTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
482062 AAT
1 AAT
482065 TAAAACATAA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 6 0.08
37 67 0.92
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (37 bp):
AATCACTACATAATTAAAAATATTACATAAGTCTTTG
Found at i:482132 original size:24 final size:24
Alignment explanation
Indices: 482105--482163 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
482095 ATTCTCCATT
*
482105 TATATCCATTTCATCTTTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
482129 TATATTCATTTCATCTCTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
482153 TATCTCCATTT
1 TATATCCATTT
482164 GCATTAAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (24 bp):
TATATCCATTTCATCTCTCCAAAA
Found at i:485246 original size:16 final size:16
Alignment explanation
Indices: 485225--485258 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
485215 TTTTTTTTCT
*
485225 TACATTAATTATAATA
1 TACATTAATTACAATA
485241 TACATTAATTACAATA
1 TACATTAATTACAATA
485257 TA
1 TA
485259 TTTAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
TACATTAATTACAATA
Found at i:486181 original size:16 final size:17
Alignment explanation
Indices: 486160--486200 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
486150 GCCTAAGAGA
486160 AAATTGGGCT-GGATTT
1 AAATTGGGCTGGGATTT
*
486176 AAATTGGGCTGGGTTTT
1 AAATTGGGCTGGGATTT
486193 AAATTGGG
1 AAATTGGG
486201 AGGGAGTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.24, C:0.05, G:0.34, T:0.37
Consensus pattern (17 bp):
AAATTGGGCTGGGATTT
Found at i:498341 original size:15 final size:15
Alignment explanation
Indices: 498293--498342 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
498283 TTTATCAAAT
498293 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* * *
498308 TCATTTTGATTGAAT
1 TTATATTGATTGAAA
498323 TTATATTGATTGAAA
1 TTATATTGATTGAAA
498338 TTATA
1 TTATA
498343 ATATATATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:498868 original size:23 final size:23
Alignment explanation
Indices: 498829--498918 Score: 126
Period size: 23 Copynumber: 3.9 Consensus size: 23
498819 GAGGATTTAT
*
498829 AATATTCCGAGTGTGTTTGGGTTG
1 AATATT-CGGGTGTGTTTGGGTTG
498853 AATATTCGGGTGTGTTTGGGTTG
1 AATATTCGGGTGTGTTTGGGTTG
* *
498876 GATATTCTGGTGTGTTTGGGTTG
1 AATATTCGGGTGTGTTTGGGTTG
* *
498899 GATATTCTGGTGTGTTTGGG
1 AATATTCGGGTGTGTTTGGG
498919 AGGAATCCAC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
23 57 0.90
24 6 0.10
ACGTcount: A:0.12, C:0.06, G:0.38, T:0.44
Consensus pattern (23 bp):
AATATTCGGGTGTGTTTGGGTTG
Found at i:498898 original size:46 final size:47
Alignment explanation
Indices: 498830--498918 Score: 144
Period size: 46 Copynumber: 1.9 Consensus size: 47
498820 AGGATTTATA
498830 ATATTCCGAGTGTGTTTGGGTTGAATATTCGGGTGTGTTTGGGTTGG
1 ATATTCCGAGTGTGTTTGGGTTGAATATTCGGGTGTGTTTGGGTTGG
* * *
498877 ATATTCTG-GTGTGTTTGGGTTGGATATTCTGGTGTGTTTGGG
1 ATATTCCGAGTGTGTTTGGGTTGAATATTCGGGTGTGTTTGGG
498919 AGGAATCCAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 32 0.82
47 7 0.18
ACGTcount: A:0.11, C:0.06, G:0.38, T:0.45
Consensus pattern (47 bp):
ATATTCCGAGTGTGTTTGGGTTGAATATTCGGGTGTGTTTGGGTTGG
Found at i:499045 original size:18 final size:19
Alignment explanation
Indices: 499024--499064 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
499014 AATGAAATGA
499024 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
499042 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
499061 GAAA
1 GAAA
499065 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:507393 original size:17 final size:17
Alignment explanation
Indices: 507371--507405 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
507361 CAAATATTAA
507371 ATTATTTA-TATAGTTTT
1 ATTATTTATTATA-TTTT
507388 ATTATTTATTATATTTT
1 ATTATTTATTATATTTT
507405 A
1 A
507406 AAATTTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
ATTATTTATTATATTTT
Found at i:509363 original size:41 final size:40
Alignment explanation
Indices: 509302--509387 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 40
509292 TTTCCATTAA
509302 TTAATTATTGCAGTTAGATGACGGTTAACTAGCTGCATCAG
1 TTAATTATTGCAGTTAGATGACGGTTAACTAGCTG-ATCAG
* * *
509343 TTAATTATTGCAGTTGGATGATGGTTAACTAGCTGATGAG
1 TTAATTATTGCAGTTAGATGACGGTTAACTAGCTGATCAG
509383 TTAAT
1 TTAAT
509388 GACTGTCCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 9 0.21
41 33 0.79
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.37
Consensus pattern (40 bp):
TTAATTATTGCAGTTAGATGACGGTTAACTAGCTGATCAG
Found at i:509863 original size:29 final size:27
Alignment explanation
Indices: 509821--509879 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
509811 CTCTACTGTA
509821 AAAGTCAAGTCA-TTTCTATAATTAATTTT
1 AAAGTCAAGTCATTTTC-ATAATT--TTTT
*
509850 AAAGTTAAGTCATTTTCATAATTTTTT
1 AAAGTCAAGTCATTTTCATAATTTTTT
509877 AAA
1 AAA
509880 CTTAGAGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 7 0.25
29 17 0.61
30 4 0.14
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (27 bp):
AAAGTCAAGTCATTTTCATAATTTTTT
Found at i:517678 original size:17 final size:17
Alignment explanation
Indices: 517644--517707 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
517634 GCTTAGAATT
* * *
517644 TATTTTTATCATATTAA
1 TATTTTTTTTATAGTAA
517661 TATTTTTTTTATAGTAA
1 TATTTTTTTTATAGTAA
517678 T-TCATTTTTTTA-AGTAA
1 TAT--TTTTTTTATAGTAA
* *
517695 AATTTTTTATATA
1 TATTTTTTTTATA
517708 AATTTATAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 8 0.21
17 21 0.55
18 9 0.24
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (17 bp):
TATTTTTTTTATAGTAA
Found at i:522148 original size:51 final size:51
Alignment explanation
Indices: 522088--522184 Score: 185
Period size: 51 Copynumber: 1.9 Consensus size: 51
522078 ATTTTATAGG
522088 AAACTTAAATACATTAGAGAAGCTACCTATCCTATTAGCCCCTAGTCTATA
1 AAACTTAAATACATTAGAGAAGCTACCTATCCTATTAGCCCCTAGTCTATA
*
522139 AAACTTAAATACATTTGAGAAGCTACCTATCCTATTAGCCCCTAGT
1 AAACTTAAATACATTAGAGAAGCTACCTATCCTATTAGCCCCTAGT
522185 TTGAATTTGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (51 bp):
AAACTTAAATACATTAGAGAAGCTACCTATCCTATTAGCCCCTAGTCTATA
Found at i:527769 original size:30 final size:30
Alignment explanation
Indices: 527733--527794 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
527723 AGGGGGAGGC
*
527733 GGCATTCCAGGGCGTGGGGGTGGTGGAGCA
1 GGCATTCCAGGGCGTGGGGGTGGTGGACCA
*
527763 GGCATTCCAGGGCGTGGTGGTGGTGGACCA
1 GGCATTCCAGGGCGTGGGGGTGGTGGACCA
527793 GG
1 GG
527795 AGGTCCTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.13, C:0.18, G:0.52, T:0.18
Consensus pattern (30 bp):
GGCATTCCAGGGCGTGGGGGTGGTGGACCA
Found at i:529822 original size:5 final size:5
Alignment explanation
Indices: 529812--529840 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
529802 TATAAGATAT
529812 ATAAA ATAAA AT-AA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
529841 TATAGTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:529829 original size:14 final size:14
Alignment explanation
Indices: 529812--529842 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
529802 TATAAGATAT
529812 ATAAAATAAAATAA
1 ATAAAATAAAATAA
529826 ATAAAATAAAATAA
1 ATAAAATAAAATAA
529840 ATA
1 ATA
529843 TAGTTATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
ATAAAATAAAATAA
Found at i:529842 original size:9 final size:10
Alignment explanation
Indices: 529812--529840 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
529802 TATAAGATAT
529812 ATAAAATAAA
1 ATAAAATAAA
529822 AT-AAATAAA
1 ATAAAATAAA
529831 ATAAAATAAA
1 ATAAAATAAA
529841 TATAGTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
ATAAAATAAA
Found at i:535274 original size:31 final size:31
Alignment explanation
Indices: 535232--535305 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
535222 AAAAAATAAC
* *
535232 AAATTGGCTCTTTTAAAAAGGTCGATGGTTA
1 AAATTGACTCTTTTAAAAAGGTCGATGGTCA
* * *
535263 AAATTGACTCTTTTTAAAATGTTGATGGTCA
1 AAATTGACTCTTTTAAAAAGGTCGATGGTCA
*
535294 AAATGGACTCTT
1 AAATTGACTCTT
535306 CGTAAAAGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (31 bp):
AAATTGACTCTTTTAAAAAGGTCGATGGTCA
Found at i:541123 original size:21 final size:21
Alignment explanation
Indices: 541088--541135 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 21
541078 AGGTCTAAAT
541088 TATTTATACAATATG-TGCACATA
1 TATTTATA-AATATGAT-CA-ATA
541111 TATTTAT-AATATGATCAATA
1 TATTTATAAATATGATCAATA
541131 TATTT
1 TATTT
541136 TAGAAATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 8 0.33
21 8 0.33
22 1 0.04
23 7 0.29
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (21 bp):
TATTTATAAATATGATCAATA
Found at i:545389 original size:22 final size:23
Alignment explanation
Indices: 545364--545408 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
545354 ATTTTTCTTG
*
545364 AAATTGAAT-TATAATTTTTTAA
1 AAATTAAATATATAATTTTTTAA
*
545386 AAATTAAATATATATTTTTTTAA
1 AAATTAAATATATAATTTTTTAA
545409 TTTTGAGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
AAATTAAATATATAATTTTTTAA
Found at i:547642 original size:12 final size:12
Alignment explanation
Indices: 547625--547655 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
547615 AATTCTCATA
547625 AATTATTAATAT
1 AATTATTAATAT
547637 AATTATTAATAT
1 AATTATTAATAT
547649 AA-TATTA
1 AATTATTA
547656 TTTTATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTATTAATAT
Found at i:571503 original size:29 final size:27
Alignment explanation
Indices: 571470--571536 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 27
571460 ATTATTAATA
*
571470 TATATATATTTGAACTACAATTAAAATT
1 TATATATATTTGAA-TAAAATTAAAATT
* *
571498 TCATATACATAATTGCATAAAATTAAAATT
1 T-ATAT--ATATTTGAATAAAATTAAAATT
571528 TATATATAT
1 TATATATAT
571537 CAAATTGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
27 3 0.09
28 1 0.03
29 8 0.25
30 13 0.41
31 7 0.22
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (27 bp):
TATATATATTTGAATAAAATTAAAATT
Found at i:574316 original size:14 final size:15
Alignment explanation
Indices: 574285--574319 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
574275 AAATTTTAAG
574285 AAAAATGAATATTGT
1 AAAAATGAATATTGT
*
574300 AAAAATGGATATT-T
1 AAAAATGAATATTGT
574314 AAAAAT
1 AAAAAT
574320 TTTAATTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.31
Consensus pattern (15 bp):
AAAAATGAATATTGT
Found at i:581555 original size:29 final size:30
Alignment explanation
Indices: 581502--581573 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 30
581492 TTAACAGCTC
* *
581502 AGTGACTAAAATGTTATAATACAAA-AAAA
1 AGTGACTAAAATGTGACAATACAAATAAAA
* * *
581531 AGTGACTAAAATGTGACATTTCAAATATAA
1 AGTGACTAAAATGTGACAATACAAATAAAA
581561 A-TGACTAAAATGT
1 AGTGACTAAAATGT
581574 AACCTGAGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 33 0.89
30 4 0.11
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.28
Consensus pattern (30 bp):
AGTGACTAAAATGTGACAATACAAATAAAA
Found at i:582200 original size:22 final size:23
Alignment explanation
Indices: 582174--582222 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
582164 ATTAAAAAGA
* *
582174 TAAAA-TTATATTTTTATTATCG
1 TAAAAGTTACATTTTTACTATCG
582196 TAAAAGTTACATTTTTACTATCG
1 TAAAAGTTACATTTTTACTATCG
582219 TAAA
1 TAAA
582223 GTTTGCAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (23 bp):
TAAAAGTTACATTTTTACTATCG
Found at i:598434 original size:3 final size:3
Alignment explanation
Indices: 598426--598465 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
598416 TTATTGCTTT
598426 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
598466 ATTCATGATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:599120 original size:3 final size:3
Alignment explanation
Indices: 599112--599144 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
599102 AAGACAACCA
*
599112 TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
599145 CCATGCATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:606900 original size:6 final size:6
Alignment explanation
Indices: 606891--606953 Score: 58
Period size: 6 Copynumber: 10.5 Consensus size: 6
606881 CCTCCTTATA
* * *
606891 TCTATC TCTATGC -CTA-C TCCTATC TCTGTC CCTATC TCTATC CCTATC
1 TCTATC TCTAT-C TCTATC T-CTATC TCTATC TCTATC TCTATC TCTATC
*
606939 CCTATC TCTATC TCT
1 TCTATC TCTATC TCT
606954 GTCCCTCTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
4 1 0.02
6 43 0.91
7 3 0.06
ACGTcount: A:0.14, C:0.40, G:0.03, T:0.43
Consensus pattern (6 bp):
TCTATC
Found at i:606915 original size:18 final size:18
Alignment explanation
Indices: 606891--606983 Score: 95
Period size: 18 Copynumber: 5.3 Consensus size: 18
606881 CCTCCTTATA
*
606891 TCTATCTCTATGCCTA-C
1 TCTATCTCTATCCCTATC
*
606908 TCCTATCTCTGTCCCTATC
1 T-CTATCTCTATCCCTATC
*
606927 TCTATCCCTATCCCTATC
1 TCTATCTCTATCCCTATC
*
606945 TCTATCTCTGTCCC--TC
1 TCTATCTCTATCCCTATC
*
606961 T-TATCCCTATCCCTATC
1 TCTATCTCTATCCCTATC
*
606978 CCTATC
1 TCTATC
606984 CTTATCCTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
15 10 0.16
16 3 0.05
17 3 0.05
18 44 0.71
19 2 0.03
ACGTcount: A:0.14, C:0.42, G:0.03, T:0.41
Consensus pattern (18 bp):
TCTATCTCTATCCCTATC
Found at i:606924 original size:12 final size:12
Alignment explanation
Indices: 606909--606983 Score: 84
Period size: 12 Copynumber: 6.5 Consensus size: 12
606899 TATGCCTACT
*
606909 CCTATCTCTGTC
1 CCTATCTCTATC
606921 CCTATCTCTATC
1 CCTATCTCTATC
*
606933 CCTATCCCTATC
1 CCTATCTCTATC
* *
606945 TCTATCTCTGTC
1 CCTATCTCTATC
606957 CC--TCT-TATC
1 CCTATCTCTATC
*
606966 CCTATCCCTATC
1 CCTATCTCTATC
606978 CCTATC
1 CCTATC
606984 CTTATCCTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
9 5 0.10
10 3 0.06
11 2 0.04
12 42 0.81
ACGTcount: A:0.13, C:0.44, G:0.03, T:0.40
Consensus pattern (12 bp):
CCTATCTCTATC
Found at i:606970 original size:21 final size:21
Alignment explanation
Indices: 606923--606980 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
606913 TCTCTGTCCC
*
606923 TATCTCTATCCCTAT-CC-C-
1 TATCCCTATCCCTATCCCTCT
* * *
606941 TATCTCTATCTCTGTCCCTCT
1 TATCCCTATCCCTATCCCTCT
606962 TATCCCTATCCCTATCCCT
1 TATCCCTATCCCTATCCCT
606981 ATCCTTATCC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 13 0.41
19 2 0.06
20 1 0.03
21 16 0.50
ACGTcount: A:0.14, C:0.43, G:0.02, T:0.41
Consensus pattern (21 bp):
TATCCCTATCCCTATCCCTCT
Found at i:606992 original size:6 final size:6
Alignment explanation
Indices: 606909--606990 Score: 74
Period size: 6 Copynumber: 13.2 Consensus size: 6
606899 TATGCCTACT
* * * * * *
606909 CCTATC TCTGTC CCTATC TCTATC CCTATC CCTATC TCTATC TCTGTCC
1 CCTATC CCTATC CCTATC CCTATC CCTATC CCTATC CCTATC CCTAT-C
*
606958 CTCTTATC CCTATC CCTATC CCTATC CTTATC C
1 C-C-TATC CCTATC CCTATC CCTATC CCTATC C
606991 TTCCTATCTC
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
6 55 0.89
7 2 0.03
8 3 0.05
9 2 0.03
ACGTcount: A:0.13, C:0.44, G:0.02, T:0.40
Consensus pattern (6 bp):
CCTATC
Found at i:609050 original size:29 final size:30
Alignment explanation
Indices: 608978--609059 Score: 96
Period size: 29 Copynumber: 2.7 Consensus size: 30
608968 TTTTTGAGAT
608978 TTTATTAAAATAATATAAAAGATAAAATTAA
1 TTTATTAAAATAATAT-AAAGATAAAATTAA
* * *
609009 TTTTTTTAAATAATAT-AAGTTATAAATT-A
1 TTTATTAAAATAATATAAAGATA-AAATTAA
609038 TTTATTAAAATAATATGAAAGA
1 TTTATTAAAATAATAT-AAAGA
609060 ACAATAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
29 20 0.48
30 5 0.12
31 17 0.40
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (30 bp):
TTTATTAAAATAATATAAAGATAAAATTAA
Found at i:609069 original size:29 final size:28
Alignment explanation
Indices: 608978--609069 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 28
608968 TTTTTGAGAT
608978 TTTATTAAAATAATATAAAAGATAAAATTAA
1 TTTATTAAAATAATAT-AAAGAT-AAA-TAA
* * *
609009 TTTTTTTAAATAATAT-AAGTTATAAATTA
1 TTTATTAAAATAATATAAAG--ATAAATAA
609038 TTTATTAAAATAATATGAAAGA-ACAATAA
1 TTTATTAAAATAATAT-AAAGATA-AATAA
609067 TTT
1 TTT
609070 TAGGTGTCGC
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
28 1 0.02
29 27 0.54
30 3 0.06
31 19 0.38
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.41
Consensus pattern (28 bp):
TTTATTAAAATAATATAAAGATAAATAA
Found at i:620426 original size:30 final size:29
Alignment explanation
Indices: 620368--620426 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
620358 AATATCAAAA
* *
620368 TTATACATGAATTTTGTTTTTATACAATT
1 TTATACATGAATTTTGATTTGATACAATT
* *
620397 TTATATATGAAATTTTGATTTGATCCAATT
1 TTATACATG-AATTTTGATTTGATACAATT
620427 CTCACAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.32, C:0.07, G:0.08, T:0.53
Consensus pattern (29 bp):
TTATACATGAATTTTGATTTGATACAATT
Found at i:622618 original size:15 final size:15
Alignment explanation
Indices: 622595--622626 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
622585 AATTTACATT
*
622595 AAAATTTAATATTTA
1 AAAACTTAATATTTA
622610 AAAACTTAATATTTA
1 AAAACTTAATATTTA
622625 AA
1 AA
622627 TACTCAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAACTTAATATTTA
Found at i:627326 original size:13 final size:14
Alignment explanation
Indices: 627302--627335 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
627292 AAACAGCATT
*
627302 AGAAGGTTTATGGA
1 AGAAGATTTATGGA
627316 A-AAGATTTATGGA
1 AGAAGATTTATGGA
627329 AGAAGAT
1 AGAAGAT
627336 ACTCCGCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.26
Consensus pattern (14 bp):
AGAAGATTTATGGA
Found at i:634160 original size:4 final size:4
Alignment explanation
Indices: 634151--634180 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
634141 AATGATGAAA
634151 TCCC TCCC TCCC TCCC TCCC TCCC TCCC TC
1 TCCC TCCC TCCC TCCC TCCC TCCC TCCC TC
634181 TCTCTCTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.73, G:0.00, T:0.27
Consensus pattern (4 bp):
TCCC
Found at i:635462 original size:84 final size:84
Alignment explanation
Indices: 635352--635700 Score: 376
Period size: 84 Copynumber: 4.2 Consensus size: 84
635342 ACTTTGGGCC
*
635352 CTTCAACAGCCTTCTT-AT--TTTCTTCTGCAATCTTCCTTTGC-TCTTCTGCTTTAGCCATCT-
1 CTTCAACAGCCTTCTTCATAGTTTCTTCTGCAATCTTCCTCTGCTTC-TCTGCTTTAGCCATCTC
**
635412 CAATATCAGCTTGTTTTCTTA
65 CAA-ATCAGCACGTTTTCTTA
* * * *
635433 CTTCAACCGCCTTCTTCAT-GTTTTCTTCTGCAATCTTCCTTTGCTTCACTGCTTCAGCCATCTC
1 CTTCAACAGCCTTCTTCATAG-TTTCTTCTGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCTC
*
635497 TAAATCAGCACGTTTTC-TA
65 CAAATCAGCACGTTTTCTTA
*
635516 TCTTCAACAGCCTTCTTCTTAGTTTCTT-TAGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCT
1 -CTTCAACAGCCTTCTTCATAGTTTCTTCT-GCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCT
* *
635580 CCAAATCAGCACATTTTCTTT
64 CCAAATCAGCACGTTTTCTTA
* * * * ** *
635601 CATCAACAGCCTTTTTCTTAGTTTCTTCTGCACTCTTCCTCAAC-TCGCTTGCTTTAGCCATCTC
1 CTTCAACAGCCTTCTTCATAGTTTCTTCTGCAATCTTCCTCTGCTTCTC-TGCTTTAGCCATCTC
* *
635665 CAAATC-GACAAGTTTTCTTT
65 CAAATCAG-CACGTTTTCTTA
*
635685 CTTCAACTGCCTTCTT
1 CTTCAACAGCCTTCTT
635701 TTTCTCTTCT
Statistics
Matches: 231, Mismatches: 25, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
81 15 0.06
82 2 0.01
83 7 0.03
84 200 0.87
85 7 0.03
ACGTcount: A:0.17, C:0.31, G:0.09, T:0.43
Consensus pattern (84 bp):
CTTCAACAGCCTTCTTCATAGTTTCTTCTGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCTCC
AAATCAGCACGTTTTCTTA
Found at i:645078 original size:22 final size:23
Alignment explanation
Indices: 645051--645094 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
645041 AAAAAAATTA
*
645051 TAAAATTATTA-TTGAATTATTT
1 TAAAATTATTATTTAAATTATTT
*
645073 TAAAATTTTTATTTAAATTATT
1 TAAAATTATTATTTAAATTATT
645095 AAAATTCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TAAAATTATTATTTAAATTATTT
Found at i:645355 original size:30 final size:31
Alignment explanation
Indices: 645318--645392 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
645308 AATAACCTAT
* * *
645318 ATTTTTATAATTTTTTAAAATATTAAAT-TA
1 ATTTTTATTATTTTTTAAAAAATTAAATAAA
* *
645348 TTTTTTATTA-GTTTTAAAAAATTAAATAAA
1 ATTTTTATTATTTTTTAAAAAATTAAATAAA
645378 ATTTTTATTATTTTT
1 ATTTTTATTATTTTT
645393 AGGGTCAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 15 0.42
30 18 0.50
31 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (31 bp):
ATTTTTATTATTTTTTAAAAAATTAAATAAA
Found at i:645362 original size:29 final size:30
Alignment explanation
Indices: 645330--645393 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
645320 TTTTATAATT
* * *
645330 TTTTAAAATATTAAAT-TATTTTTTATTAG
1 TTTTAAAAAATTAAATAAAATTTTTATTAG
*
645359 TTTTAAAAAATTAAATAAAATTTTTATTAT
1 TTTTAAAAAATTAAATAAAATTTTTATTAG
645389 TTTTA
1 TTTTA
645394 GGGTCAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
TTTTAAAAAATTAAATAAAATTTTTATTAG
Found at i:667609 original size:4 final size:4
Alignment explanation
Indices: 667600--667630 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
667590 TCAATACGTG
667600 CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CAT
667631 GCATGTATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:669063 original size:31 final size:30
Alignment explanation
Indices: 668981--669065 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
668971 TTTGGTATAT
* * *
668981 AAACTTTGATTT-ACTGTAATTATACATATA
1 AAACTTTGATTTGA-TTTAATTGTACACATA
*
669011 AAACTTTGATTTGGTTTAATTGTACACATA
1 AAACTTTGATTTGATTTAATTGTACACATA
*
669041 AAATTTTGATCTTGATTTAATTGTA
1 AAACTTTGAT-TTGATTTAATTGTA
669066 AACAATTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 34 0.72
31 13 0.28
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (30 bp):
AAACTTTGATTTGATTTAATTGTACACATA
Found at i:673394 original size:28 final size:28
Alignment explanation
Indices: 673354--673412 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
673344 ATAACTCATT
673354 CTTAATCCTTAAATAAAAGGATAATACG
1 CTTAATCCTTAAATAAAAGGATAATACG
* *
673382 CTTAATTCTTAAATAAAAGGATAATATG
1 CTTAATCCTTAAATAAAAGGATAATACG
673410 CTT
1 CTT
673413 CCTCGCAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (28 bp):
CTTAATCCTTAAATAAAAGGATAATACG
Found at i:675679 original size:11 final size:11
Alignment explanation
Indices: 675654--675742 Score: 66
Period size: 11 Copynumber: 8.7 Consensus size: 11
675644 AAAGAAGCCG
675654 AGAAGCCGA-A
1 AGAAGCCGAGA
*
675664 AGAAGCTGAGA
1 AGAAGCCGAGA
675675 AGAAGCCG-GA
1 AGAAGCCGAGA
* *
675685 A-AAACCCA-A
1 AGAAGCCGAGA
*
675694 AGAAGCTGAGA
1 AGAAGCCGAGA
675705 AGAAGCCG-GA
1 AGAAGCCGAGA
* *
675715 A-AAACCCA-A
1 AGAAGCCGAGA
*
675724 AGAAGCTGAGA
1 AGAAGCCGAGA
675735 AGAAGCCG
1 AGAAGCCG
675743 GAAAAACCCA
Statistics
Matches: 58, Mismatches: 14, Indels: 13
0.68 0.16 0.15
Matches are distributed among these distances:
9 12 0.21
10 22 0.38
11 24 0.41
ACGTcount: A:0.48, C:0.19, G:0.29, T:0.03
Consensus pattern (11 bp):
AGAAGCCGAGA
Found at i:675698 original size:30 final size:30
Alignment explanation
Indices: 675645--675757 Score: 192
Period size: 30 Copynumber: 3.8 Consensus size: 30
675635 GACAAACCTA
* * *
675645 AAGAAGCC-GAGAAGCCGAAAGAAGCTGAG
1 AAGAAGCCGGAAAAACCCAAAGAAGCTGAG
675674 AAGAAGCCGGAAAAACCCAAAGAAGCTGAG
1 AAGAAGCCGGAAAAACCCAAAGAAGCTGAG
675704 AAGAAGCCGGAAAAACCCAAAGAAGCTGAG
1 AAGAAGCCGGAAAAACCCAAAGAAGCTGAG
675734 AAGAAGCCGGAAAAACCCAAAGAA
1 AAGAAGCCGGAAAAACCCAAAGAA
675758 CCGGAAAAAC
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 8 0.10
30 72 0.90
ACGTcount: A:0.50, C:0.19, G:0.27, T:0.03
Consensus pattern (30 bp):
AAGAAGCCGGAAAAACCCAAAGAAGCTGAG
Found at i:675766 original size:19 final size:19
Alignment explanation
Indices: 675734--675773 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
675724 AGAAGCTGAG
675734 AAGAAGCCGGAAAAACCCA
1 AAGAAGCCGGAAAAACCCA
675753 AAGAA-CCGGAAAAACCCA
1 AAGAAGCCGGAAAAACCCA
675771 AAG
1 AAG
675774 CACCTGCTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.55, C:0.25, G:0.20, T:0.00
Consensus pattern (19 bp):
AAGAAGCCGGAAAAACCCA
Found at i:678633 original size:24 final size:23
Alignment explanation
Indices: 678595--678644 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
678585 TTAATATATG
* *
678595 AAATATAAATTTTAAATATTTTT
1 AAATATAAATATTAAATATTTAT
*
678618 AAATAATAAATATTAATTATTTAT
1 AAAT-ATAAATATTAAATATTTAT
678642 AAA
1 AAA
678645 ATTTAAAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATATAAATATTAAATATTTAT
Found at i:678698 original size:21 final size:21
Alignment explanation
Indices: 678672--678711 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
678662 AAACTATATT
678672 TTAAATATTTA-AATATAATCA
1 TTAAATATTTATAAT-TAATCA
678693 TTAAATATTTATAATTAAT
1 TTAAATATTTATAATTAAT
678712 ATTTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAAATATTTATAATTAATCA
Found at i:678717 original size:14 final size:14
Alignment explanation
Indices: 678696--678744 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 14
678686 ATAATCATTA
678696 AATA-TTTATAATT
1 AATATTTTATAATT
*
678709 AATATTTTA-AA-A
1 AATATTTTATAATT
*
678721 AATATTTTTTAATT
1 AATATTTTATAATT
678735 AATAATTTTA
1 AAT-ATTTTA
678745 ATAAATTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
12 8 0.29
13 8 0.29
14 7 0.25
15 5 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATATTTTATAATT
Found at i:678733 original size:26 final size:26
Alignment explanation
Indices: 678695--678750 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
678685 TATAATCATT
678695 AAATATTTATAATTAAT-ATTTTAAA
1 AAATATTTATAATTAATAATTTTAAA
* *
678720 AAATATTTTTTAATTAATAATTTTAAT
1 AAATA-TTTATAATTAATAATTTTAAA
678747 AAAT
1 AAAT
678751 TTGTACTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 5 0.19
26 11 0.41
27 11 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
AAATATTTATAATTAATAATTTTAAA
Found at i:685763 original size:243 final size:243
Alignment explanation
Indices: 685335--685824 Score: 872
Period size: 243 Copynumber: 2.0 Consensus size: 243
685325 CAACAGACGA
*
685335 AGCAGGAACACTCCTGCCCATCTTGTCCTGGTCTTCTCTGATGGCCTTGTCAGGTGCCCTCCTCT
1 AGCAGGAACACTCCTGCCCATCTTGTCCTGGTCTTCTCTGATGGCCTTGTCAGGTGCCCTCCTAT
* *
685400 CAGCTTGAGCCTGTTCAAAATTACAATTCATAGGTGCTGCAGGAACACCCTTTTCCTTCCTTACA
66 CAGCTTGAGCCCGTTCAAAATTACAATTCATAGATGCTGCAGGAACACCCTTTTCCTTCCTTACA
*
685465 TCCCCTTCAGCACCTTCAGTACTTAAACTTTTAGCTGCTGCCATGAAAGATACTAATCTCTCAGC
131 TCCCCTTCAGCACCTTCAGCACTTAAACTTTTAGCTGCTGCCATGAAAGATACTAATCTCTCAGC
*
685530 AACTTCTAAGGCTTTAGGGAGGGAATCAGCAACAGTAGCTGTCAAATC
196 AACTTCTAAGGCTTTAGGGAGGGAATCAGCAACAGAAGCTGTCAAATC
** *
685578 AGCAGGAACACTCCTGTTCATCTTGTCCTGGTCTTCTCTGATGGCCTTGTCAGGTTCCCTCCTAT
1 AGCAGGAACACTCCTGCCCATCTTGTCCTGGTCTTCTCTGATGGCCTTGTCAGGTGCCCTCCTAT
685643 CAGCTTGAGCCCGTTCAAAATTACAATTCATAGATGCTGCAGGAACACCCTTTTCCTTCCTTACA
66 CAGCTTGAGCCCGTTCAAAATTACAATTCATAGATGCTGCAGGAACACCCTTTTCCTTCCTTACA
* *
685708 TCCCCTTCAGCACCTTCAGCACTTGAACTTTTAGCTGCTTCCATGAAAGATACTAATCTCTCAGC
131 TCCCCTTCAGCACCTTCAGCACTTAAACTTTTAGCTGCTGCCATGAAAGATACTAATCTCTCAGC
* *
685773 AACTTCTAAGGCTTTAGGGAGGGGATCAGTAACAGAAGCTGTCAAATC
196 AACTTCTAAGGCTTTAGGGAGGGAATCAGCAACAGAAGCTGTCAAATC
685821 AGCA
1 AGCA
685825 ACACTTGATG
Statistics
Matches: 235, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
243 235 1.00
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.29
Consensus pattern (243 bp):
AGCAGGAACACTCCTGCCCATCTTGTCCTGGTCTTCTCTGATGGCCTTGTCAGGTGCCCTCCTAT
CAGCTTGAGCCCGTTCAAAATTACAATTCATAGATGCTGCAGGAACACCCTTTTCCTTCCTTACA
TCCCCTTCAGCACCTTCAGCACTTAAACTTTTAGCTGCTGCCATGAAAGATACTAATCTCTCAGC
AACTTCTAAGGCTTTAGGGAGGGAATCAGCAACAGAAGCTGTCAAATC
Found at i:687347 original size:3 final size:3
Alignment explanation
Indices: 687341--687367 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
687331 AATGAAAAAA
687341 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
687368 CGAAGGGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:693098 original size:21 final size:21
Alignment explanation
Indices: 693072--693112 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
693062 ATCTGCTCAA
* *
693072 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
693093 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
693113 TTGCTCATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:731589 original size:30 final size:29
Alignment explanation
Indices: 731568--731625 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
731558 CAAAAATTGT
731568 AAGGGGTTTAATGAGAATTTCAAAAAAAA
1 AAGGGGTTTAATGAGAATTTCAAAAAAAA
**
731597 AATTGGTTTAATGAGAATTTCAAAAAAAA
1 AAGGGGTTTAATGAGAATTTCAAAAAAAA
731626 TTGAGGAAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.17, T:0.28
Consensus pattern (29 bp):
AAGGGGTTTAATGAGAATTTCAAAAAAAA
Found at i:731661 original size:33 final size:33
Alignment explanation
Indices: 731614--731705 Score: 100
Period size: 33 Copynumber: 2.8 Consensus size: 33
731604 TTAATGAGAA
* *
731614 TTTCAAAAAAAATTGAGGAAGCTTAATT-GAATT
1 TTTCAAAAAAAATTGAGG-AGCCTAATTAAAATT
*
731647 TTTCAAAAAGAATTGAGGAGCCTAATTAAAATT
1 TTTCAAAAAAAATTGAGGAGCCTAATTAAAATT
*
731680 TTT-AGAAAAAAAGTT-AAGAGCCTAAT
1 TTTCA-AAAAAAA-TTGAGGAGCCTAAT
731706 GAGTTTATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
32 9 0.18
33 40 0.78
34 2 0.04
ACGTcount: A:0.47, C:0.08, G:0.15, T:0.30
Consensus pattern (33 bp):
TTTCAAAAAAAATTGAGGAGCCTAATTAAAATT
Found at i:738326 original size:143 final size:143
Alignment explanation
Indices: 738167--738512 Score: 426
Period size: 143 Copynumber: 2.4 Consensus size: 143
738157 TAAATGGGGT
* * *
738167 AAAATACAATCTTACTCCTAATCTAAGGGCATCCATGGTACTTTTACCAATTAAAGGTGTATATA
1 AAAATGCAATCATACTCCTAATCTAAGGGCATCTATGGTACTTTTACCAATTAAAGGTGTATATA
* ** * *
738232 TATATA-TTCAAACACCTTTAATTGCTCTTTGATATAATGTATAATA-ACTAATTTGAACATTTT
66 TATATACTT-AAACACCTTTAATTGCCCTTTGATATAAAATACAA-AGACTAATTTAAACATTTT
*
738295 TTTAATAGATTGGTC
129 TTTAATAGATTGGCC
* * * * * *
738310 AAAATGCAATCCTACTCCTACTCTAAAGGTATCTATGGTACTTTTACCAATTAGAGGTATATATA
1 AAAATGCAATCATACTCCTAATCTAAGGGCATCTATGGTACTTTTACCAATTAAAGGTGTATATA
* * * * **
738375 TATATACTTACACACTTTTAATTGCCCTTTTATTTAAAATACAAAGGTTAATTTAAACATTTTTT
66 TATATACTTAAACACCTTTAATTGCCCTTTGATATAAAATACAAAGACTAATTTAAACATTTTTT
738440 TAATAGATTGGCC
131 TAATAGATTGGCC
* * * * *
738453 AAAATGCAATAATGCTCCTAATTTAAGGGCAGCTATGGTACTTTTACCAATTAAACGTGT
1 AAAATGCAATCATACTCCTAATCTAAGGGCATCTATGGTACTTTTACCAATTAAAGGTGT
738513 GTGAATACAT
Statistics
Matches: 170, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
142 1 0.01
143 167 0.98
144 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (143 bp):
AAAATGCAATCATACTCCTAATCTAAGGGCATCTATGGTACTTTTACCAATTAAAGGTGTATATA
TATATACTTAAACACCTTTAATTGCCCTTTGATATAAAATACAAAGACTAATTTAAACATTTTTT
TAATAGATTGGCC
Found at i:748102 original size:182 final size:181
Alignment explanation
Indices: 747469--748186 Score: 812
Period size: 182 Copynumber: 4.0 Consensus size: 181
747459 TTCCATTACT
* * * * * * * *
747469 TTTCTCCTTTACTGACACAAACAAATACATAAATAGATTACTTTCATCAACTTAACCTGATTTTT
1 TTTCTCCTTT-CTGAGACAAATATATACATAAATGGACTATTTTCATCAATTTAACCTGAATTTT
* *
747534 AACACTCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGGTTAATTGCAGTTTGCTTCT
65 AACACTCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTTCT
* * * * *
747599 AAAAAAGAAACTTAACTGACTGAAGCCTGATTATAACATGTAATACTTCAAC
130 AAGAAAGAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTTCAAC
* *
747651 TTTCTCCTTTTCTGAGACAAATATATACATGAATGGACTATTTTCATCAAATTAACCTGACA-TT
1 TTTCTCC-TTTCTGAGACAAATATATACATAAATGGACTATTTTCATCAATTTAACCTGA-ATTT
* * *
747715 TAAC-CTTCCATTAAGCTTAATA-TAGCTGCAATTCGCAGCTTCTTGATTAATAGCAA-TTGGTC
64 TAACAC-TCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCT-
* * * * *
747777 ACT-GGAAAAGAAACTAAACTGACCGAAGCCTGGTTACAACATTTGATACTTGAA-
127 TCTAAG-AAAGAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTTCAAC
* * *
747831 -TCCT-C-TTCTGAGACAAATATGA-ACATAAATGGACTATTTTCATCAATTTAATCTGACTTTT
1 TTTCTCCTTTCTGAGACAAATAT-ATACATAAATGGACTATTTTCATCAATTTAACCTGAATTTT
* **
747892 AACACTCCATTGAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTGGTTGCAATTTGCTTCT
65 AACACTCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTTCT
* * *
747957 AAGAAAGAAACTAAACTGACTGAAGCCTGATGACAACATGTGATACATCAAC
130 AAGAAAGAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTTCAAC
* * * ** *
748009 TTTCTCCTTTCCTAAGACAAATATATACATAAACGGATTATTTTTGTCAATTTAA-CTCAATTTC
1 TTTCTCCTTT-CTGAGACAAATATATACATAAATGGACTATTTTCATCAATTTAACCTGAATTT-
* ** * * * *
748073 TAACACTCCATCAAGCTTAATATTAGCTGCAATTTGCATCTTCTTGATGAATTTCAAATTGCTTC
64 TAACACTCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTT-
* * *
748138 CTAA-AAAGAAACTAAACTAACCGAAGACTGATTACAACACGTGATACTT
128 CTAAGAAAGAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTT
748187 AATCCATAAT
Statistics
Matches: 450, Mismatches: 67, Indels: 38
0.81 0.12 0.07
Matches are distributed among these distances:
176 67 0.15
177 76 0.17
178 6 0.01
179 6 0.01
180 5 0.01
181 83 0.18
182 200 0.44
183 7 0.02
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.34
Consensus pattern (181 bp):
TTTCTCCTTTCTGAGACAAATATATACATAAATGGACTATTTTCATCAATTTAACCTGAATTTTA
ACACTCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTTCTA
AGAAAGAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTTCAAC
Found at i:748841 original size:16 final size:16
Alignment explanation
Indices: 748797--748846 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
748787 ATTAAAATGG
748797 TAAAATTTT-AATTTA
1 TAAAATTTTAAATTTA
**
748812 -AGTATTTTATAATTTA
1 TAAAATTTTA-AATTTA
*
748828 TAAAATTTTAAATTAA
1 TAAAATTTTAAATTTA
748844 TAA
1 TAA
748847 TAATAAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 6 0.22
16 14 0.52
17 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TAAAATTTTAAATTTA
Found at i:748865 original size:22 final size:23
Alignment explanation
Indices: 748814--748866 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
748804 TTAATTTAAG
* *
748814 TATTTT-ATAATTTATAAAATTT
1 TATTTTAATAATTAATAAAATTA
**
748836 TAAATTAATAA-TAATAAAATTA
1 TATTTTAATAATTAATAAAATTA
748858 TATTTTAAT
1 TATTTTAAT
748867 TTTTTTAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTTAATAATTAATAAAATTA
Found at i:748873 original size:53 final size:53
Alignment explanation
Indices: 748797--748897 Score: 121
Period size: 53 Copynumber: 1.9 Consensus size: 53
748787 ATTAAAATGG
* * * * *
748797 TAAAATTTTAATTTAAGTATTTTATAATTTATAAAATTTTAAATTAATAATAA
1 TAAAATTATAATTTAAGTATTTTAAAAATAATAAAAATTTAAATTAATAATAA
* * * *
748850 TAAAATTATATTTTAATTTTTTTAAAAATAATAAAAATTTAATTTAAT
1 TAAAATTATAATTTAAGTATTTTAAAAATAATAAAAATTTAAATTAAT
748898 CATTTAAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
53 39 1.00
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (53 bp):
TAAAATTATAATTTAAGTATTTTAAAAATAATAAAAATTTAAATTAATAATAA
Found at i:748896 original size:31 final size:31
Alignment explanation
Indices: 748840--748914 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
748830 AAATTTTAAA
* * **
748840 TTAATAATAAT-AAAATTATATTTTAATTTTT
1 TTAAAAATAATAAAAATTATAATTTAA-TCAT
748871 TTAAAAATAATAAAAATT-TAATTTAATCAT
1 TTAAAAATAATAAAAATTATAATTTAATCAT
*
748901 TTAAAAATTATAAA
1 TTAAAAATAATAAA
748915 TATATAAACT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 15 0.39
31 17 0.45
32 6 0.16
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (31 bp):
TTAAAAATAATAAAAATTATAATTTAATCAT
Found at i:755842 original size:2 final size:2
Alignment explanation
Indices: 755835--755875 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
755825 CTCTTTTTGT
755835 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
755876 TTGGATTGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:769882 original size:27 final size:28
Alignment explanation
Indices: 769852--769913 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
769842 AATTATTTGA
* *
769852 AAATTTTTATTTAA-TCATTAAACTTTT
1 AAATTTTTATTTAAGTCACTAAACTGTT
*
769879 AAA-TTTTATTTAAGTCACTGAACTGTT
1 AAATTTTTATTTAAGTCACTAAACTGTT
769906 AAATTTTT
1 AAATTTTT
769914 TCTTTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 10 0.33
27 16 0.53
28 4 0.13
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (28 bp):
AAATTTTTATTTAAGTCACTAAACTGTT
Found at i:773588 original size:12 final size:12
Alignment explanation
Indices: 773571--773601 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
773561 AATAGTGTTT
773571 TATTTATAAATA
1 TATTTATAAATA
773583 TATTTATAAATA
1 TATTTATAAATA
773595 TATTTAT
1 TATTTAT
773602 TGTTAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTTATAAATA
Found at i:774432 original size:20 final size:20
Alignment explanation
Indices: 774396--774435 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
774386 TTAATATATA
*
774396 TAATGAATTTAATTTTAAAT
1 TAATGAATTTAAGTTTAAAT
774416 TAATCGAATTT-AGTTTAAAT
1 TAAT-GAATTTAAGTTTAAAT
774436 AGTTAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (20 bp):
TAATGAATTTAAGTTTAAAT
Found at i:775514 original size:26 final size:26
Alignment explanation
Indices: 775485--775540 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
775475 TTTGAATCAA
*
775485 ATTTGAA-TAAAATTTAACATTTTAAC
1 ATTTGAAGTAAAACTTAA-ATTTTAAC
* *
775511 ATTTTAAGTTAAACTTAAATTTTAAC
1 ATTTGAAGTAAAACTTAAATTTTAAC
775537 ATTT
1 ATTT
775541 TTATCTGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (26 bp):
ATTTGAAGTAAAACTTAAATTTTAAC
Found at i:784457 original size:38 final size:37
Alignment explanation
Indices: 784398--784501 Score: 97
Period size: 37 Copynumber: 2.8 Consensus size: 37
784388 CATTTTTAAG
*
784398 AATAT-AAAGAATATATATAAGTATGTATATGATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATATAAT-TAGA
* * *
784435 AATATGCATAAATATATGTAAGTATATA-ATAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATATAATTA-GA
* *
784473 AATGTGAAAAATATATTTAAGTATGTATA
1 AATATGAAAAATATATATAAGTATGTATA
784502 AGTACGTATA
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
36 2 0.04
37 27 0.50
38 23 0.43
39 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (37 bp):
AATATGAAAAATATATATAAGTATGTATATAATTAGA
Found at i:794769 original size:138 final size:137
Alignment explanation
Indices: 794367--794759 Score: 355
Period size: 136 Copynumber: 2.9 Consensus size: 137
794357 CCTTGTAGTC
* * * * * * * * * *
794367 TGACTTACTATTACACTCAATTGCTATATGTCCGTTTTATGGTCCACGAAGAGTAATTTTTTC-A
1 TGACATACCATTACACCCAATTACTCTATATCCATTTTACGGTCCACGAAGAGAAATCTTTTCGA
* * ** * *
794431 AGGTTATGATTGTTTCTCTCTACAATATTATATACAAGTTTGAACTTGAGGTCACTCCTCGAAAG
66 AGGTTATGATTGTTTCTCTCAACAATATTATATGCAAGTTTGAACAAGAGTTCACTCCTCGAGAG
*
794496 TATTACG
131 TATAACG
** * * * *
794503 TGAGTTACCATTACATCCAATTGCTCTATGTCCA--TTACAGTCCACGAAGA-ATAATCTTTTTC
1 TGACATACCATTACACCCAATTACTCTATATCCATTTTACGGTCCACGAAGAGA-AATC-TTTTC
* * * * * * * *
794565 GAGGGTTATGATTGTTTCTCTCAACTATATTATCTGCAAGGTTTAAATAAGATTTCCCTCGTCGA
64 GAAGGTTATGATTGTTTCTCTCAACAATATTATATGCAA-GTTTGAACAAGAGTTCACTCCTCGA
* *
794630 GAGTGTAATG
128 GAGTATAACG
* **
794640 TGACATACTATTACACCCAATTACTCTATATTTATTTTACGGTCCACGAAGAGAAATCTTTTCGA
1 TGACATACCATTACACCCAATTACTCTATATCCATTTTACGGTCCACGAAGAGAAATCTTTTCGA
* * *
794705 AGGTTATAGA-TGTTTTTCCCAACAATATTATATGCAATGTTTGAACCAGAGTTCA
66 AGGTTAT-GATTGTTTCTCTCAACAATATTATATGCAA-GTTTGAACAAGAGTTCA
794760 TTTTTCGAGA
Statistics
Matches: 202, Mismatches: 47, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
134 17 0.08
135 5 0.02
136 61 0.30
137 49 0.24
138 48 0.24
139 21 0.10
140 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (137 bp):
TGACATACCATTACACCCAATTACTCTATATCCATTTTACGGTCCACGAAGAGAAATCTTTTCGA
AGGTTATGATTGTTTCTCTCAACAATATTATATGCAAGTTTGAACAAGAGTTCACTCCTCGAGAG
TATAACG
Found at i:794939 original size:36 final size:36
Alignment explanation
Indices: 794892--794970 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
794882 AATATATGAT
*
794892 TTGTGATTATAGTACTTGTTGTCAATGCATCATACC
1 TTGTGATTATAGTACTTATTGTCAATGCATCATACC
794928 TTGTGATTATAGTACTTATTGTCAATGCATCATACC
1 TTGTGATTATAGTACTTATTGTCAATGCATCATACC
*
794964 ATGTGAT
1 TTGTGAT
794971 CTCTTATATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (36 bp):
TTGTGATTATAGTACTTATTGTCAATGCATCATACC
Found at i:797069 original size:20 final size:21
Alignment explanation
Indices: 797044--797085 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
797034 AATTTTTTAA
797044 TTATTTTAAAT-ATAAAATAT
1 TTATTTTAAATCATAAAATAT
*
797064 TTATTTTATATCATAAAATAT
1 TTATTTTAAATCATAAAATAT
797085 T
1 T
797086 AAAATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATTTTAAATCATAAAATAT
Found at i:802028 original size:6 final size:7
Alignment explanation
Indices: 801977--802028 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
801967 TAATATCTAG
801977 ATTT-AA
1 ATTTAAA
*
801983 ATTGAAA
1 ATTTAAA
*
801990 TTTTAAA
1 ATTTAAA
801997 ATTTAAA
1 ATTTAAA
802004 ATTTAAA
1 ATTTAAA
*
802011 AGTATAAA
1 A-TTTAAA
*
802019 AATTAAA
1 ATTTAAA
802026 ATT
1 ATT
802029 GATCAATTCG
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
6 3 0.08
7 27 0.75
8 6 0.17
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (7 bp):
ATTTAAA
Found at i:810006 original size:26 final size:27
Alignment explanation
Indices: 809956--810009 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
809946 CTGGAAACCA
809956 ACACAGAAGAAGAATGAACACTAAAATC
1 ACACAGAAGAAGAA-GAACACTAAAATC
809984 ACACAGAAGAAGAA-AATCA-TAAAATC
1 ACACAGAAGAAGAAGAA-CACTAAAATC
810010 TCTATTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 9 0.36
27 2 0.08
28 14 0.56
ACGTcount: A:0.59, C:0.17, G:0.13, T:0.11
Consensus pattern (27 bp):
ACACAGAAGAAGAAGAACACTAAAATC
Found at i:811024 original size:17 final size:17
Alignment explanation
Indices: 810998--811052 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
810988 ATATCAAATA
*
810998 TAATAAAAATATAATTT
1 TAATATAAATATAATTT
*
811015 TAATATAAATATTTAATTA
1 TAATATAAATA--TAATTT
811034 T-AT-TAAATATAAATTT
1 TAATATAAATAT-AATTT
811050 TAA
1 TAA
811053 ATAGATTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 1 0.03
16 5 0.16
17 17 0.55
18 2 0.06
19 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATATAAATATAATTT
Found at i:811060 original size:22 final size:24
Alignment explanation
Indices: 811015--811098 Score: 73
Period size: 26 Copynumber: 3.4 Consensus size: 24
811005 AATATAATTT
* *
811015 TAATATAAATATTTAATTATATTA
1 TAATATAAATATTTAAATAGATTA
811039 -AATATAAAT-TTTAAATAGATTA
1 TAATATAAATATTTAAATAGATTA
* **
811061 TAAAATAAAAATAAGTAAATAAGAGTTA
1 T--AATATAAATATTTAAAT-AGA-TTA
811089 TAATATAAAT
1 TAATATAAAT
811099 TTATCACTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
22 11 0.23
23 9 0.19
25 8 0.17
26 13 0.27
27 3 0.06
28 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (24 bp):
TAATATAAATATTTAAATAGATTA
Found at i:811068 original size:23 final size:23
Alignment explanation
Indices: 811019--811069 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
811009 TAATTTTAAT
* * *
811019 ATAAATATTTAATTATATTAAAT
1 ATAAATATTTAAATAGATTAAAA
811042 ATAAAT-TTTAAATAGATTATAAA
1 ATAAATATTTAAATAGATTA-AAA
811065 ATAAA
1 ATAAA
811070 AATAAGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
ATAAATATTTAAATAGATTAAAA
Found at i:814257 original size:2 final size:2
Alignment explanation
Indices: 814252--814295 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
814242 AGCGTATATA
*
814252 TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
814294 TG
1 TG
814296 ATATACTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.02, C:0.00, G:0.48, T:0.50
Consensus pattern (2 bp):
TG
Found at i:819319 original size:11 final size:13
Alignment explanation
Indices: 819292--819323 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
819282 TTCAACAATT
819292 AATTTTTAGTCTC
1 AATTTTTAGTCTC
819305 AATTTTTA-T-TC
1 AATTTTTAGTCTC
819316 AATTTTTA
1 AATTTTTA
819324 AATAGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.53
12 1 0.05
13 8 0.42
ACGTcount: A:0.28, C:0.09, G:0.03, T:0.59
Consensus pattern (13 bp):
AATTTTTAGTCTC
Found at i:831013 original size:142 final size:143
Alignment explanation
Indices: 830752--831042 Score: 496
Period size: 142 Copynumber: 2.0 Consensus size: 143
830742 CCAGATAAAT
* *
830752 TAATTATAACTAATAGTTAATTATTGTGGTTTGCTTGTATATGGAACCTAATGAACTTGGTTACG
1 TAATAATAACTAATAGTTAATTATTGTGGTTTGATTGTATATGGAACCTAATGAACTTGGTTACG
*
830817 TGGTTTAATGTTTGTTTGAATACTTAAGTTTCATTAATGATTAATTGTTTGATCTC-TAAGGAGC
66 TGGTTTAATGTTTGTTTGAATACTTAACTTTCATTAATGATTAATTGTTTGATCTCTTAAGGAGC
*
830881 TCTTTGAGTTCTC
131 TCTTTGAGTTCCC
* *
830894 TAATAATAACTAATAAG-TAATTATTGTGGTTTGATTGTATGTGGAACCTAATGAACTTGGTTAT
1 TAATAATAACTAAT-AGTTAATTATTGTGGTTTGATTGTATATGGAACCTAATGAACTTGGTTAC
*
830958 GTGGTTTAATGTTTGTTTGAATACTTAACTTTCATTAGTGATTAATTGTTTGATCTCTTAAGGAG
65 GTGGTTTAATGTTTGTTTGAATACTTAACTTTCATTAATGATTAATTGTTTGATCTCTTAAGGAG
831023 CTCTTTGAGTTCCC
130 CTCTTTGAGTTCCC
831037 TAATAA
1 TAATAA
831043 GTGTAGTTGA
Statistics
Matches: 140, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
142 112 0.80
143 28 0.20
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (143 bp):
TAATAATAACTAATAGTTAATTATTGTGGTTTGATTGTATATGGAACCTAATGAACTTGGTTACG
TGGTTTAATGTTTGTTTGAATACTTAACTTTCATTAATGATTAATTGTTTGATCTCTTAAGGAGC
TCTTTGAGTTCCC
Found at i:835781 original size:15 final size:15
Alignment explanation
Indices: 835761--835791 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
835751 TCGTTTGCTT
835761 AACACGATTTTAAGA
1 AACACGATTTTAAGA
835776 AACACGATTTTAAGA
1 AACACGATTTTAAGA
835791 A
1 A
835792 TAAGATCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (15 bp):
AACACGATTTTAAGA
Found at i:837073 original size:34 final size:33
Alignment explanation
Indices: 837030--837129 Score: 107
Period size: 34 Copynumber: 3.0 Consensus size: 33
837020 TGTTATTTTC
**
837030 AAAATATATATAATTTTTATTTGTATAATAATTT
1 AAAA-ATATATAAAATTTATTTGTATAATAATTT
*
837064 AACAAATATATAAAATTTATTAT-TATAAAAATTAT
1 AA-AAATATATAAAATTTATT-TGTATAATAATT-T
*
837099 AAAAATA-A-AAAATTTATTCGTATAATAATTT
1 AAAAATATATAAAATTTATTTGTATAATAATTT
837130 TTATTATAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
31 1 0.02
32 19 0.33
33 1 0.02
34 30 0.53
35 6 0.11
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (33 bp):
AAAAATATATAAAATTTATTTGTATAATAATTT
Found at i:841925 original size:17 final size:17
Alignment explanation
Indices: 841903--841936 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
841893 AGTCTCAATG
841903 ATAAACATATTCTTAGT
1 ATAAACATATTCTTAGT
841920 ATAAACATATTCTTAGT
1 ATAAACATATTCTTAGT
841937 CCTTAGTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (17 bp):
ATAAACATATTCTTAGT
Found at i:842058 original size:24 final size:24
Alignment explanation
Indices: 842021--842067 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
842011 ACAAATCGAC
842021 TTTTAATATGTATAAAT-TTTAAT
1 TTTTAATATGTATAAATATTTAAT
* *
842044 TTTTAAATATTTATATATATTTAA
1 TTTT-AATATGTATAAATATTTAA
842068 ATATTGGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 11 0.55
25 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTTAATATGTATAAATATTTAAT
Found at i:843856 original size:43 final size:43
Alignment explanation
Indices: 843780--843861 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
843770 CTCTATCCTC
* *
843780 CATTTTAATTTAATCAAACTTTAAATATTCTCACTAATTGTTT
1 CATTTTAATTTAATCAAACTTTAAACATGCTCACTAATTGTTT
843823 CATTTTAATTTAATC-AACTTTATAACATGCTCACTAATT
1 CATTTTAATTTAATCAAACTTTA-AACATGCTCACTAATT
843862 TGTCTTCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 7 0.19
43 29 0.81
ACGTcount: A:0.35, C:0.16, G:0.02, T:0.46
Consensus pattern (43 bp):
CATTTTAATTTAATCAAACTTTAAACATGCTCACTAATTGTTT
Found at i:843873 original size:43 final size:42
Alignment explanation
Indices: 843783--843874 Score: 116
Period size: 43 Copynumber: 2.1 Consensus size: 42
843773 TATCCTCCAT
* *
843783 TTTAATTTAATCAAACTTTAAATATTCTCACTAATTGTTTCA
1 TTTAATTTAATCAAACTTTAAACATGCTCACTAATTGTTTCA
843825 TTTTAATTTAATC-AACTTTATAACATGCTCACTAATTTGTCTTC-
1 -TTTAATTTAATCAAACTTTA-AACATGCTCACTAA-TTGT-TTCA
843869 TTTAAT
1 TTTAAT
843875 AGGTTTGTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
42 7 0.16
43 30 0.68
44 4 0.09
45 3 0.07
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.49
Consensus pattern (42 bp):
TTTAATTTAATCAAACTTTAAACATGCTCACTAATTGTTTCA
Found at i:849431 original size:29 final size:30
Alignment explanation
Indices: 849384--849448 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
849374 TGGCCCAAGA
* *
849384 GTAAATACTCAAAATTTGAAGGATTAAAGT
1 GTAAATACTCAAAAGTTGAAGGACTAAAGT
*
849414 GTAAATA-TGAAAAGTTGAAGGACTAAAGT
1 GTAAATACTCAAAAGTTGAAGGACTAAAGT
849443 GTAAAT
1 GTAAAT
849449 TTGATGGATC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 25 0.78
30 7 0.22
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.28
Consensus pattern (30 bp):
GTAAATACTCAAAAGTTGAAGGACTAAAGT
Found at i:849805 original size:46 final size:46
Alignment explanation
Indices: 849753--849934 Score: 276
Period size: 46 Copynumber: 4.0 Consensus size: 46
849743 AGTGTGCTCT
* *
849753 CTGATATGAAATGTGTAAGACCATGGTTGAATGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
849799 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
849845 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
849891 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
849935 TCATGTCAAA
Statistics
Matches: 127, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 1 0.01
46 126 0.99
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:856898 original size:21 final size:21
Alignment explanation
Indices: 856872--856912 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
856862 ATCTGCTCAA
* *
856872 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
856893 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
856913 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:872123 original size:22 final size:22
Alignment explanation
Indices: 872065--872124 Score: 54
Period size: 25 Copynumber: 2.7 Consensus size: 22
872055 ATTAAATAGT
872065 AAATTAA-TTA-TT-TTATTAA
1 AAATTAATTTATTTATTATTAA
* *
872084 AAAATATTTTTATTTTTATTATTAA
1 AAATTA-ATTTA--TTTATTATTAA
872109 AAATTAATTTATTTAT
1 AAATTAATTTATTTAT
872125 ATCAAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
19 5 0.16
21 3 0.10
22 5 0.16
24 6 0.19
25 12 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AAATTAATTTATTTATTATTAA
Found at i:873099 original size:24 final size:26
Alignment explanation
Indices: 873069--873117 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
873059 ATTTTAAATT
873069 TTTTAAAATTA-AATTTAAA-CAAAA
1 TTTTAAAATTAGAATTTAAATCAAAA
* *
873093 TTTTAAATTTAGATTTTAAATCAAA
1 TTTTAAAATTAGAATTTAAATCAAA
873118 TTAAATCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
25 7 0.33
26 4 0.19
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (26 bp):
TTTTAAAATTAGAATTTAAATCAAAA
Found at i:873467 original size:29 final size:31
Alignment explanation
Indices: 873423--873487 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
873413 TATAGTTTAT
*
873423 ATTTTTATAATTTTTAAAAAATTAAATTA-A
1 ATTTTTATAATTTTTAAAAAATTAAAGTATA
* *
873453 ATTTTTATAA-TTTTAAGATATTAAAGTATA
1 ATTTTTATAATTTTTAAAAAATTAAAGTATA
873483 ATTTT
1 ATTTT
873488 ATCTTTACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (31 bp):
ATTTTTATAATTTTTAAAAAATTAAAGTATA
Found at i:876441 original size:5 final size:6
Alignment explanation
Indices: 876411--876438 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
876401 TTGAATGTTT
876411 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
876439 ATTGTCGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:876998 original size:38 final size:38
Alignment explanation
Indices: 876943--877020 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
876933 TGTAATCAAA
*
876943 CTTTTAGTATAAAGGTCTCCATGGTACTTTTACCATAT
1 CTTTTAGTATAAAGGTCTCCATCGTACTTTTACCATAT
*
876981 CTTTTAGTATAAGGGTCTCCATCGTACTTTTACCATAT
1 CTTTTAGTATAAAGGTCTCCATCGTACTTTTACCATAT
877019 CT
1 CT
877021 ACATGTTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (38 bp):
CTTTTAGTATAAAGGTCTCCATCGTACTTTTACCATAT
Found at i:878123 original size:15 final size:16
Alignment explanation
Indices: 878103--878138 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
878093 AATAAAAAGA
878103 AATAAATGTTATTTT-
1 AATAAATGTTATTTTC
878118 AATAAATGTTATTTTC
1 AATAAATGTTATTTTC
878134 AATAA
1 AATAA
878139 GAGAGTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (16 bp):
AATAAATGTTATTTTC
Found at i:885649 original size:67 final size:67
Alignment explanation
Indices: 885567--885697 Score: 226
Period size: 67 Copynumber: 2.0 Consensus size: 67
885557 CAAACATGCT
* *
885567 ATGACTCACTGAAAAAAACTTAAAACTAGTCTTTAAAATAACTCTAAACCTTAAAATGATCGAAG
1 ATGACTCACTAAAAAAAACTTAAAACTAGTCTTCAAAATAACTCTAAACCTTAAAATGATCGAAG
885632 CC
66 CC
* *
885634 ATGACTCACTAAAAAAAACTTAAAGCTAGTCTTCAAAATAACTCTAAATCTTAAAATGATCGAA
1 ATGACTCACTAAAAAAAACTTAAAACTAGTCTTCAAAATAACTCTAAACCTTAAAATGATCGAA
885698 ATACGTAATA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.26
Consensus pattern (67 bp):
ATGACTCACTAAAAAAAACTTAAAACTAGTCTTCAAAATAACTCTAAACCTTAAAATGATCGAAG
CC
Found at i:889960 original size:20 final size:20
Alignment explanation
Indices: 889931--889970 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
889921 TTGGTTGAGT
*
889931 ATTGATTTTTTTTTGTTTAA
1 ATTGAGTTTTTTTTGTTTAA
*
889951 ATTGAGTTTTTTTTTTTTAA
1 ATTGAGTTTTTTTTGTTTAA
889971 TTTTAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (20 bp):
ATTGAGTTTTTTTTGTTTAA
Found at i:890781 original size:3 final size:3
Alignment explanation
Indices: 890773--890800 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
890763 CTTTCATCAC
890773 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
890801 ATCACCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:892256 original size:24 final size:27
Alignment explanation
Indices: 892228--892281 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 27
892218 CATATTCCCA
892228 AATTTCACCCAA-TT-TTAAATT-GAT
1 AATTTCACCCAATTTATTAAATTAGAT
**
892252 AATTTCATTCAATTTATTAAATTAGAT
1 AATTTCACCCAATTTATTAAATTAGAT
892279 AAT
1 AAT
892282 AAAACAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.40
25 2 0.08
26 7 0.28
27 6 0.24
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (27 bp):
AATTTCACCCAATTTATTAAATTAGAT
Found at i:896274 original size:31 final size:31
Alignment explanation
Indices: 896239--896299 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
896229 TTATATTTTA
896239 ATTTGATCAAATTTAGTCAT-TGTACTTTTCT
1 ATTTGATCAAATTTAGT-ATATGTACTTTTCT
* *
896270 ATTTGATCAATTTTAGTTTATGTACTTTTC
1 ATTTGATCAAATTTAGTATATGTACTTTTC
896300 AAATTTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.25, C:0.11, G:0.10, T:0.54
Consensus pattern (31 bp):
ATTTGATCAAATTTAGTATATGTACTTTTCT
Found at i:903021 original size:8 final size:8
Alignment explanation
Indices: 903010--903059 Score: 82
Period size: 8 Copynumber: 6.2 Consensus size: 8
903000 TGTATGCATG
903010 CATGCACA
1 CATGCACA
903018 CATGCACA
1 CATGCACA
903026 CATGCACA
1 CATGCACA
903034 CATGCACA
1 CATGCACA
*
903042 CATGCACG
1 CATGCACA
*
903050 CACGCACA
1 CATGCACA
903058 CA
1 CA
903060 CTAATACATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 39 1.00
ACGTcount: A:0.36, C:0.40, G:0.14, T:0.10
Consensus pattern (8 bp):
CATGCACA
Found at i:906049 original size:14 final size:15
Alignment explanation
Indices: 906030--906058 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
906020 ATATTATATT
906030 AAATTAAA-TTAAAA
1 AAATTAAATTTAAAA
906044 AAATTAAATTTAAAA
1 AAATTAAATTTAAAA
906059 TTTAAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATTAAATTTAAAA
Found at i:906904 original size:19 final size:19
Alignment explanation
Indices: 906875--906921 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
906865 AGAGATTTGA
*
906875 ATAACTTAAAATAACGTATT
1 ATAA-TTAAAATAACGAATT
**
906895 ATAATTAAAATCTCGAATT
1 ATAATTAAAATAACGAATT
906914 ATAATTAA
1 ATAATTAA
906922 TAAGTAAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (19 bp):
ATAATTAAAATAACGAATT
Found at i:922970 original size:7 final size:7
Alignment explanation
Indices: 922958--922986 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
922948 TATAATTTGT
922958 ATTATTA
1 ATTATTA
922965 ATTATTA
1 ATTATTA
922972 ATTATTA
1 ATTATTA
922979 ATTATTA
1 ATTATTA
922986 A
1 A
922987 GTTCAGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
ATTATTA
Found at i:923678 original size:16 final size:16
Alignment explanation
Indices: 923659--923699 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
923649 CTTAAACCCG
*
923659 AAATAATCAAAACTTA
1 AAATAATCAAAACTCA
923675 AAATAAGT-AAAACTCA
1 AAATAA-TCAAAACTCA
923691 AAATAATCA
1 AAATAATCA
923700 GAATCTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.63, C:0.12, G:0.02, T:0.22
Consensus pattern (16 bp):
AAATAATCAAAACTCA
Found at i:926272 original size:135 final size:133
Alignment explanation
Indices: 926025--926447 Score: 436
Period size: 135 Copynumber: 3.1 Consensus size: 133
926015 GGCTACCGTG
** * * ** * ** * *
926025 TTTATGAACATTAAAAAGCGGAGCAAACGTAGAAATTTGGACAGTAAGATGACCGAAAGAATCCC
1 TTTATGAACATTAAAGCGCAGAGCAAGCACAGAAACTTGGACAGTGCGATGACAGAAAGAAGCCC
* * *
926090 TCAGGAGAATAAGAAGGATGCAATGAGTGAAAGAAGCTCTGAAGAGACTAAGAAGGAAAACTGCG
66 TCAGGAGAATAAGAAGGATGCAATGA-TGAAAGAAGCCCTCAGGAGACTAAGAAGGAAAACTGCG
926155 ATCGT
130 ATC-T
* * * * ***
926160 TTTATGAACGTTAAAGTGCGGAGCAAAG-GCAGAAACTTGGTTGGTGCGATGACAGAAAGAAGCC
1 TTTATGAACATTAAAGCGCAGAGC-AAGCACAGAAACTTGGACAGTGCGATGACAGAAAGAAGCC
* * * * *
926224 CTCAGGAGAGTGAGGAGGATGCAATGACTGAAAGTAGCCCTCAGGAGACTAAGAAGGAAAACTGT
65 CTCAGGAGAATAAGAAGGATGCAATGA-TGAAAGAAGCCCTCAGGAGACTAAGAAGGAAAACTGC
926289 GATCTT
129 GATC-T
* * * *
926295 TTTGTGAACATTAAAGCGCAGAGCAAGCACAGGAATTTGGACAGTGCTATGA-ATGAAAGAAGCC
1 TTTATGAACATTAAAGCGCAGAGCAAGCACAGAAACTTGGACAGTGCGATGACA-GAAAGAAGCC
** * * *
926359 CTTGGGAGACTAAGAAGGATGCAATGATCGAAAGAAGCCCTCAGGAGACTAAAAAGGAAAATTGC
65 CTCAGGAGAATAAGAAGGATGCAATGAT-GAAAGAAGCCCTCAGGAGACTAAGAAGGAAAACTGC
*
926424 TATCT
129 GATCT
926429 TTCTATGAACATTAAAGCG
1 TT-TATGAACATTAAAGCG
926448 AATCTGGACA
Statistics
Matches: 238, Mismatches: 45, Indels: 10
0.81 0.15 0.03
Matches are distributed among these distances:
134 8 0.03
135 228 0.96
136 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.19
Consensus pattern (133 bp):
TTTATGAACATTAAAGCGCAGAGCAAGCACAGAAACTTGGACAGTGCGATGACAGAAAGAAGCCC
TCAGGAGAATAAGAAGGATGCAATGATGAAAGAAGCCCTCAGGAGACTAAGAAGGAAAACTGCGA
TCT
Found at i:926666 original size:96 final size:95
Alignment explanation
Indices: 926448--926669 Score: 248
Period size: 96 Copynumber: 2.3 Consensus size: 95
926438 CATTAAAGCG
* * * *
926448 AATCTGGACAGTGCTATGACTGAAAGAAGCCAGCAGGAGACTAAGAAGGAAAACTGCGCTCTTTT
1 AATCTGGACAGTGCAATGACTGAAAGAAGCCAG-AGGAGACTAAGAAGAAAAACTGCGATCTTTC
* *
926513 TATGAACATTAAAGCACGGAGCAAACGTAGA
65 TATAAACATTAAAGCACGGAGCAAACGCAGA
* ** ** * * *
926544 AATCTGGACAGTGCGACAACCAAAAGAAGTCCTTG-TGAGACTAAGAAGAAAAACTGTGATCTTT
1 AATCTGGACAGTGCAATGACTGAAAGAAG-CC-AGAGGAGACTAAGAAGAAAAACTGCGATCTTT
** *
926608 CTATAAACATTAAAGGGCGGAGCAAAGGCAGA
64 CTATAAACATTAAAGCACGGAGCAAACGCAGA
*
926640 AATTTGGACAGTGCAATGACTGAAAGAAGC
1 AATCTGGACAGTGCAATGACTGAAAGAAGC
926670 GGCAATGATA
Statistics
Matches: 102, Mismatches: 22, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
95 1 0.01
96 98 0.96
97 2 0.02
98 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.19
Consensus pattern (95 bp):
AATCTGGACAGTGCAATGACTGAAAGAAGCCAGAGGAGACTAAGAAGAAAAACTGCGATCTTTCT
ATAAACATTAAAGCACGGAGCAAACGCAGA
Found at i:930436 original size:83 final size:84
Alignment explanation
Indices: 930342--930501 Score: 241
Period size: 84 Copynumber: 1.9 Consensus size: 84
930332 TCGCTCGGAC
* * * *
930342 AATTGTCAGAGA-TATCCGGGCTGGGAATTTCTTTACTTTTCCCCGGGGTATAGCTTGACCTTTT
1 AATTGTCAGAGACCATCCGGGATGGGAATTTATTTACTTTTCCCCGGGGTATAACTTGACCTTTT
930406 TGTATGCAACTTCATTTGG
66 TGTATGCAACTTCATTTGG
* * * *
930425 AATTGTTAGAGACCATCCGTGATGGGAATTTATTTATTTTTCCCCGGGGTCTAACTTGACCTTTT
1 AATTGTCAGAGACCATCCGGGATGGGAATTTATTTACTTTTCCCCGGGGTATAACTTGACCTTTT
930490 TGTATGCAACTT
66 TGTATGCAACTT
930502 TTGGAGCACA
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
83 11 0.16
84 57 0.84
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (84 bp):
AATTGTCAGAGACCATCCGGGATGGGAATTTATTTACTTTTCCCCGGGGTATAACTTGACCTTTT
TGTATGCAACTTCATTTGG
Found at i:931256 original size:14 final size:14
Alignment explanation
Indices: 931222--931256 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
931212 CCTCTGTTTT
931222 AAAAAAATAATTAA
1 AAAAAAATAATTAA
* *
931236 AACAAAATTATTAA
1 AAAAAAATAATTAA
931250 AAAAAAA
1 AAAAAAA
931257 AAGACAACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAAAAATAATTAA
Found at i:941518 original size:57 final size:56
Alignment explanation
Indices: 941428--941534 Score: 142
Period size: 57 Copynumber: 1.9 Consensus size: 56
941418 GTTGGGGACT
** **
941428 TAATTAAAATTTTTAAAAAATTTAAAATTTTAATGATTTTTTTTTAAATTTAGGTTC
1 TAATTAAAATTTTTAAAAAATTTAAAAGATTAATGA-TAATTTTTAAATTTAGGTTC
* **
941485 TAATTAAAATTTTTAAAAATTTTATGAGATTAATGATAATTTTTAAATTT
1 TAATTAAAATTTTTAAAAAATTTAAAAGATTAATGATAATTTTTAAATTT
941535 TAAGAGAACT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
56 12 0.28
57 31 0.72
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (56 bp):
TAATTAAAATTTTTAAAAAATTTAAAAGATTAATGATAATTTTTAAATTTAGGTTC
Found at i:941557 original size:30 final size:29
Alignment explanation
Indices: 941485--941563 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 29
941475 ATTTAGGTTC
* *
941485 TAATTAAAATTTTTAAAAATTTTATGAGAT
1 TAATTAATATTTTTAAA-ATTTTAAGAGAT
*
941515 TAA-TGATAATTTTT-AAATTTTAAGAGAACT
1 TAATTAAT-ATTTTTAAAATTTTAAGAG-A-T
941545 TAATTAATATTTTTGAAAA
1 TAATTAATATTTTT-AAAA
941564 ACAGAAAGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
28 9 0.23
29 5 0.13
30 19 0.49
31 3 0.08
32 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.46
Consensus pattern (29 bp):
TAATTAATATTTTTAAAATTTTAAGAGAT
Found at i:946208 original size:24 final size:23
Alignment explanation
Indices: 946164--946208 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
946154 GATAAATAAA
*
946164 TGAATAAATAAGTTTAGAGGGAT
1 TGAATAAATAAGTTTAAAGGGAT
946187 TGAATATAAGTAA-TTTAAAGGG
1 TGAATA-AA-TAAGTTTAAAGGG
946209 TACAGAGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 6 0.32
24 10 0.53
25 3 0.16
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.31
Consensus pattern (23 bp):
TGAATAAATAAGTTTAAAGGGAT
Found at i:949470 original size:23 final size:23
Alignment explanation
Indices: 949426--949473 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
949416 AAATCACGAT
949426 TATAATCAAATAATAATTATTCA
1 TATAATCAAATAATAATTATTCA
* *
949449 TATAAT-AAATTATATTTAATTCA
1 TATAATCAAATAATAATT-ATTCA
949472 TA
1 TA
949474 ATACTTGGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (23 bp):
TATAATCAAATAATAATTATTCA
Found at i:960712 original size:15 final size:15
Alignment explanation
Indices: 960663--960714 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
960653 TTTAAAATAT
960663 ATTTATATTGTT-TTA
1 ATTTATATT-TTATTA
* *
960678 ATTTAATATTTAATAA
1 ATTT-ATATTTTATTA
*
960694 ATTTATATTTTATTT
1 ATTTATATTTTATTA
960709 ATTTAT
1 ATTTAT
960715 TAAAATTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 19 0.63
16 11 0.37
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
ATTTATATTTTATTA
Found at i:962796 original size:18 final size:18
Alignment explanation
Indices: 962773--962808 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
962763 TTGGTCCTCC
962773 ATTTTCTTTTTAATTTTT
1 ATTTTCTTTTTAATTTTT
962791 ATTTTCTTTTTAATTTTT
1 ATTTTCTTTTTAATTTTT
962809 CGTATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (18 bp):
ATTTTCTTTTTAATTTTT
Found at i:963169 original size:77 final size:77
Alignment explanation
Indices: 963074--963216 Score: 225
Period size: 77 Copynumber: 1.9 Consensus size: 77
963064 TGAGCTGACG
* * * *
963074 TGAGGATTAGGATCTAGTATGGAGTTT-GAAGAAATATATTGTTATTGAACTTTGTTTCTTCTTA
1 TGAGGATGAGGATATAGTAT-GAATTTCGAAGAAATATATAGTTATTGAACTTTGTTTCTTCTTA
963138 GTTGTAACTAGCT
65 GTTGTAACTAGCT
*
963151 TGAGGATGAGGATATAGTATGAATTTCGAAGAAATATATAGTTGTTGAACTTTGTTTCTTCTTAG
1 TGAGGATGAGGATATAGTATGAATTTCGAAGAAATATATAGTTATTGAACTTTGTTTCTTCTTAG
963216 T
66 T
963217 GCTAACAAGC
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
76 5 0.08
77 55 0.92
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (77 bp):
TGAGGATGAGGATATAGTATGAATTTCGAAGAAATATATAGTTATTGAACTTTGTTTCTTCTTAG
TTGTAACTAGCT
Found at i:967766 original size:15 final size:15
Alignment explanation
Indices: 967748--967779 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
967738 TCTTTTTGCC
967748 TTTTTAGAAAGAACA
1 TTTTTAGAAAGAACA
967763 TTTTTAGAAAGAACA
1 TTTTTAGAAAGAACA
967778 TT
1 TT
967780 GTAACTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (15 bp):
TTTTTAGAAAGAACA
Found at i:967853 original size:40 final size:40
Alignment explanation
Indices: 967807--967911 Score: 165
Period size: 42 Copynumber: 2.6 Consensus size: 40
967797 TCTAGGATAT
967807 CTACGTGTTTATTTATAAGCTTTTCCTTTAAGATATATGC
1 CTACGTGTTTATTTATAAGCTTTTCCTTTAAGATATATGC
*
967847 CTACGTGTATTTATTTATAAGCTTTTCCTTTAAGATATATGT
1 CTACGTG--TTTATTTATAAGCTTTTCCTTTAAGATATATGC
* *
967889 CTACGTGTTTGTTCATAAGCTTT
1 CTACGTGTTTATTTATAAGCTTT
967912 ATATCTACGT
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
40 21 0.35
42 39 0.65
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.49
Consensus pattern (40 bp):
CTACGTGTTTATTTATAAGCTTTTCCTTTAAGATATATGC
Found at i:971908 original size:42 final size:42
Alignment explanation
Indices: 971861--971946 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
971851 GAGTGCGTTC
971861 ATTTGTGTGTGGTTGATGACGCGGTTAAGAATGATGAGATCT
1 ATTTGTGTGTGGTTGATGACGCGGTTAAGAATGATGAGATCT
971903 ATTTGTGTGTGGTTGATGACGCGGTTAAGAATGATGAGATCT
1 ATTTGTGTGTGGTTGATGACGCGGTTAAGAATGATGAGATCT
971945 AT
1 AT
971947 GAATATCCGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.24, C:0.07, G:0.33, T:0.36
Consensus pattern (42 bp):
ATTTGTGTGTGGTTGATGACGCGGTTAAGAATGATGAGATCT
Done.