Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold187
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: 870467
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 27366 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:656237 original size:13 final size:13
Alignment explanation
Indices: 656219--656243 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
656209 TTTACAAGAG
656219 TTTATAATTAGAT
1 TTTATAATTAGAT
656232 TTTATAATTAGA
1 TTTATAATTAGA
656244 AACATTTTCT
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTATAATTAGAT
Found at i:663653 original size:19 final size:19
Alignment explanation
Indices: 663631--663667 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
663621 ACCACTGTCA
*
663631 CCCAACGTAATCAAATTTG
1 CCCAACATAATCAAATTTG
*
663650 CCCACCATAATCAAATTT
1 CCCAACATAATCAAATTT
663668 ATTATTAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.30, G:0.05, T:0.27
Consensus pattern (19 bp):
CCCAACATAATCAAATTTG
Found at i:665345 original size:22 final size:22
Alignment explanation
Indices: 665285--665345 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
665275 GCACTAATGA
*
665285 ACAGAGAGCACTAAAGTGCTAT
1 ACAGAGAGCACTAATGTGCTAT
665307 ACAGAGAGCAC-ATATGTGCTA-
1 ACAGAGAGCACTA-ATGTGCTAT
*
665328 ATCGGAGAGCACTAATGT
1 A-CAGAGAGCACTAATGT
665346 TTTAATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 2 0.06
22 31 0.91
23 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.20
Consensus pattern (22 bp):
ACAGAGAGCACTAATGTGCTAT
Found at i:674939 original size:41 final size:41
Alignment explanation
Indices: 674879--674974 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
674869 ACAGGGGCCT
* * * *
674879 GTATGTGCAATTTAGGGGTACCGAAGTACAATCAGGGGCAC
1 GTATGTACAATTCAAGGGTACCGAAGTACAATCAGGGACAC
* * *
674920 GTATGTATAATTCAAGGGTATCGGAGTACAATCAGGGACAC
1 GTATGTACAATTCAAGGGTACCGAAGTACAATCAGGGACAC
674961 GTATGTACAATTCA
1 GTATGTACAATTCA
674975 GGGAATAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (41 bp):
GTATGTACAATTCAAGGGTACCGAAGTACAATCAGGGACAC
Found at i:674970 original size:20 final size:21
Alignment explanation
Indices: 674904--674978 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
674894 GGGTACCGAA
*
674904 GTACAA-TCAGGGGCACGTAT
1 GTACAATTCAGGGACACGTAT
* * *
674924 GTATAATTCAAGGGTA-TCGGA-
1 GTACAATTC-AGGG-ACACGTAT
674945 GTACAA-TCAGGGACACGTAT
1 GTACAATTCAGGGACACGTAT
674965 GTACAATTCAGGGA
1 GTACAATTCAGGGA
674979 ATAATTAACT
Statistics
Matches: 42, Mismatches: 7, Indels: 11
0.70 0.12 0.18
Matches are distributed among these distances:
18 1 0.02
19 7 0.17
20 13 0.31
21 14 0.33
22 7 0.17
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (21 bp):
GTACAATTCAGGGACACGTAT
Found at i:678898 original size:18 final size:19
Alignment explanation
Indices: 678875--678913 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
678865 ATTTTTAAAT
678875 ATTTAAT-ATTTTATTTAA
1 ATTTAATGATTTTATTTAA
*
678893 ATTTAATGTTTTTATTTAA
1 ATTTAATGATTTTATTTAA
678912 AT
1 AT
678914 AAACTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
ATTTAATGATTTTATTTAA
Found at i:681563 original size:14 final size:14
Alignment explanation
Indices: 681544--681570 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
681534 CATGATAAAA
681544 TAAAATACAAGTGG
1 TAAAATACAAGTGG
681558 TAAAATACAAGTG
1 TAAAATACAAGTG
681571 TGCAAGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (14 bp):
TAAAATACAAGTGG
Found at i:711457 original size:63 final size:63
Alignment explanation
Indices: 711379--711504 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
711369 TTGTATATAA
711379 TTGTTTGTGTATATGTGTTTAATAAACATTGTTGATAAAGATAAGATATAAATGTGATCAAAG
1 TTGTTTGTGTATATGTGTTTAATAAACATTGTTGATAAAGATAAGATATAAATGTGATCAAAG
711442 TTGTTTGTGTATATGTGTTTAATAAACATTGTTGATAAAGATAAGATATAAATGTGATCAAAG
1 TTGTTTGTGTATATGTGTTTAATAAACATTGTTGATAAAGATAAGATATAAATGTGATCAAAG
711505 ACTTGAATGG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.40
Consensus pattern (63 bp):
TTGTTTGTGTATATGTGTTTAATAAACATTGTTGATAAAGATAAGATATAAATGTGATCAAAG
Found at i:716050 original size:2 final size:2
Alignment explanation
Indices: 716043--716071 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
716033 CCTGACAATG
716043 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
716072 GTGCAGGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:717613 original size:12 final size:12
Alignment explanation
Indices: 717598--717625 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
717588 TGAGTCTCTT
717598 TCTCTCTCTCCC
1 TCTCTCTCTCCC
717610 TCTCTCTCTCCC
1 TCTCTCTCTCCC
717622 TCTC
1 TCTC
717626 ATCCCCACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (12 bp):
TCTCTCTCTCCC
Found at i:719098 original size:9 final size:9
Alignment explanation
Indices: 719084--719109 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
719074 GAGTGCAATA
719084 CTAAATTGC
1 CTAAATTGC
719093 CTAAATTGC
1 CTAAATTGC
719102 CTAAATTG
1 CTAAATTG
719110 AAGAAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (9 bp):
CTAAATTGC
Found at i:722314 original size:18 final size:18
Alignment explanation
Indices: 722291--722325 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
722281 TTTCAGTACT
722291 TTGTTCATTTCATGCACC
1 TTGTTCATTTCATGCACC
*
722309 TTGTTCTTTTCATGCAC
1 TTGTTCATTTCATGCAC
722326 ACTATTAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.26, G:0.11, T:0.49
Consensus pattern (18 bp):
TTGTTCATTTCATGCACC
Found at i:723992 original size:12 final size:12
Alignment explanation
Indices: 723975--723999 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
723965 GACACTTTAT
723975 TTCACTTGGAAA
1 TTCACTTGGAAA
723987 TTCACTTGGAAA
1 TTCACTTGGAAA
723999 T
1 T
724000 CAAAGGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TTCACTTGGAAA
Found at i:725685 original size:2 final size:2
Alignment explanation
Indices: 725678--725709 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
725668 ATTGGTTGAG
*
725678 AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
725710 TTTGGTTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:725756 original size:23 final size:23
Alignment explanation
Indices: 725729--725778 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
725719 TTGATTACAT
725729 TTTCTAGGTTGCTTTTGGTGCTA
1 TTTCTAGGTTGCTTTTGGTGCTA
** *
725752 TTTCTTTGTTGCTTTTGGTGTTA
1 TTTCTAGGTTGCTTTTGGTGCTA
725775 TTTC
1 TTTC
725779 ATTGTTGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.06, C:0.12, G:0.22, T:0.60
Consensus pattern (23 bp):
TTTCTAGGTTGCTTTTGGTGCTA
Found at i:725783 original size:23 final size:23
Alignment explanation
Indices: 725736--725814 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
725726 CATTTTCTAG
*
725736 GTTGCTTTTGGTGCTATTTCTTT
1 GTTGCTTTTGGTGCTATTTCATT
*
725759 GTTGCTTTTGGTGTTATTTCATT
1 GTTGCTTTTGGTGCTATTTCATT
* *
725782 GTTGTTTTTTTGTGCTATTTCATT
1 GTTG-CTTTTGGTGCTATTTCATT
* *
725806 ATTGTTTTT
1 GTTGCTTTT
725815 AATGTTGTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
23 30 0.61
24 19 0.39
ACGTcount: A:0.08, C:0.09, G:0.19, T:0.65
Consensus pattern (23 bp):
GTTGCTTTTGGTGCTATTTCATT
Found at i:725800 original size:24 final size:24
Alignment explanation
Indices: 725741--725814 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
725731 TCTAGGTTGC
* *
725741 TTTTGGTGCTATTTCTTTGTTG-C
1 TTTTGGTGCTATTTCATTGTTGTT
*
725764 TTTTGGTGTTATTTCATTGTTGTT
1 TTTTGGTGCTATTTCATTGTTGTT
* *
725788 TTTTTGTGCTATTTCATTATTGTT
1 TTTTGGTGCTATTTCATTGTTGTT
725812 TTT
1 TTT
725815 AATGTTGTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 20 0.45
24 24 0.55
ACGTcount: A:0.08, C:0.08, G:0.18, T:0.66
Consensus pattern (24 bp):
TTTTGGTGCTATTTCATTGTTGTT
Found at i:732446 original size:30 final size:30
Alignment explanation
Indices: 732410--732469 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
732400 TAACATGTAT
*
732410 ATGCCTCTAAAATAATAATAAAATTAACAA
1 ATGCCTCTAAAATAATAACAAAATTAACAA
732440 ATGCCTCTAAAATAATAACAAAATTAACAA
1 ATGCCTCTAAAATAATAACAAAATTAACAA
732470 TAAAAAAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.57, C:0.15, G:0.03, T:0.25
Consensus pattern (30 bp):
ATGCCTCTAAAATAATAACAAAATTAACAA
Found at i:735465 original size:18 final size:19
Alignment explanation
Indices: 735442--735490 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
735432 AATCGTGTAG
*
735442 TTCATTTTCAAAAT-ATTA
1 TTCATTTTCAAAATCACTA
*
735460 TTCATTTAC-AAATCACTA
1 TTCATTTTCAAAATCACTA
*
735478 TTCAATTTCAAAA
1 TTCATTTTCAAAA
735491 CATTTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 4 0.16
18 18 0.72
19 3 0.12
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (19 bp):
TTCATTTTCAAAATCACTA
Found at i:745729 original size:40 final size:40
Alignment explanation
Indices: 745674--745795 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
745664 AAGCATGTTC
745674 ACATGCCACTAATTCTGTTAATTGAAAGTATGCAAGGCAT
1 ACATGCCACTAATTCTGTTAATTGAAAGTATGCAAGGCAT
745714 ACATGCCACTAATTCTGTTAATTGAAAGTATGCAAGGCAT
1 ACATGCCACTAATTCTGTTAATTGAAAGTATGCAAGGCAT
745754 ACATGCCACTAATTCTGTTAATTGAAAGTATGCAAGGCAT
1 ACATGCCACTAATTCTGTTAATTGAAAGTATGCAAGGCAT
745794 AC
1 AC
745796 CCCGATAATG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (40 bp):
ACATGCCACTAATTCTGTTAATTGAAAGTATGCAAGGCAT
Found at i:747408 original size:32 final size:32
Alignment explanation
Indices: 747360--747427 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
747350 CCATTACCTA
* * *
747360 TTATATGTGGATGCCTTTGTGGCTATCTGATG
1 TTATATATGGACGCCTTTGTGGCTATCTAATG
*
747392 TTATATATGGACGCCTTTGTGGCTATTTAATG
1 TTATATATGGACGCCTTTGTGGCTATCTAATG
747424 TTAT
1 TTAT
747428 GGATGCCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.46
Consensus pattern (32 bp):
TTATATATGGACGCCTTTGTGGCTATCTAATG
Found at i:747441 original size:28 final size:29
Alignment explanation
Indices: 747397--747453 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
747387 TGATGTTATA
*
747397 TATGGACGCCTTTGTGGCTA-TTTAATGT
1 TATGGACGCCTTCGTGGCTACTTTAATGT
* *
747425 TATGGATGCCTTCGTGGCTACTTTTATGT
1 TATGGACGCCTTCGTGGCTACTTTAATGT
747454 ATAGACTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.16, C:0.16, G:0.25, T:0.44
Consensus pattern (29 bp):
TATGGACGCCTTCGTGGCTACTTTAATGT
Found at i:775997 original size:48 final size:50
Alignment explanation
Indices: 775937--776033 Score: 135
Period size: 51 Copynumber: 2.0 Consensus size: 50
775927 TAAGCTAAAT
775937 TAAATTACAT-A-AACAACCAAAATTGATAATTAATTCCAAGCATAATTC
1 TAAATTACATAACAACAACCAAAATTGATAATTAATTCCAAGCATAATTC
* * * *
775985 TAAATTATATAAACAACAACCAAAATTGGTCATTAGTTCCAAGCATAAT
1 TAAATTACAT-AACAACAACCAAAATTGATAATTAATTCCAAGCATAAT
776034 GTATATCAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
48 9 0.21
50 1 0.02
51 32 0.76
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.29
Consensus pattern (50 bp):
TAAATTACATAACAACAACCAAAATTGATAATTAATTCCAAGCATAATTC
Found at i:776528 original size:15 final size:15
Alignment explanation
Indices: 776508--776538 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
776498 AACAAACCCC
776508 AAATCATCCAAATTG
1 AAATCATCCAAATTG
776523 AAATCATCCAAATTG
1 AAATCATCCAAATTG
776538 A
1 A
776539 CAACAAAAAA
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:0.19, G:0.06, T:0.26
Consensus pattern (15 bp):
AAATCATCCAAATTG
Found at i:781492 original size:14 final size:15
Alignment explanation
Indices: 781473--781501 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
781463 ATTCCACATA
781473 CAAAAA-CATATTTC
1 CAAAAAGCATATTTC
781487 CAAAAAGCATATTTC
1 CAAAAAGCATATTTC
781502 TTAAAACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.28
Consensus pattern (15 bp):
CAAAAAGCATATTTC
Found at i:798946 original size:26 final size:25
Alignment explanation
Indices: 798915--798968 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
798905 TATGATTTTA
*
798915 ATTGTGTCTTAAATATGTCTTAGTTT
1 ATTGTGTCTTAAACATGTCTT-GTTT
* *
798941 ATTGTGTTTTTAACATGTCTTGTTT
1 ATTGTGTCTTAAACATGTCTTGTTT
798966 ATT
1 ATT
798969 ATATTTTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.20, C:0.07, G:0.15, T:0.57
Consensus pattern (25 bp):
ATTGTGTCTTAAACATGTCTTGTTT
Found at i:808227 original size:57 final size:59
Alignment explanation
Indices: 808117--808264 Score: 185
Period size: 57 Copynumber: 2.5 Consensus size: 59
808107 ATTGACGGTA
*
808117 AAAAGGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTG
1 AAAATGATCTAGCCCGGACGGGTGATCC-AT-CTGATATAGCCCTCCCGAAGAATATGTG-G
*
808179 AAAATGATCTAGCCCGGATGGGTGAT-C-T-TGATATAGCCCTCCCGAAGAATATGTGG
1 AAAATGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
* ** *
808235 AAAATGGATTTAGCCCAAACGGGTAATCCA
1 AAAAT-GATCTAGCCCGGACGGGTGATCCA
808265 AATTAGGGTC
Statistics
Matches: 76, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
56 6 0.08
57 43 0.57
58 1 0.01
59 1 0.01
61 1 0.01
62 24 0.32
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (59 bp):
AAAATGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:808493 original size:67 final size:67
Alignment explanation
Indices: 808385--808516 Score: 219
Period size: 67 Copynumber: 2.0 Consensus size: 67
808375 GTTTATATTA
* * *
808385 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCACTATAAGAAATGAGGTTCGCAGGAGTGTGCTCTCT
808450 TG
66 TG
* *
808452 CAGGGGATTTAGCCTGGATTGGTAATCCCACTATAAGAAATGAGGTTTGCAGGAGTGTGCTCTCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCACTATAAGAAATGAGGTTCGCAGGAGTGTGCTCTCT
808517 GAATTGGAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (67 bp):
CAGGGGATTTAGCCTGGACTGGTAATCCCACTATAAGAAATGAGGTTCGCAGGAGTGTGCTCTCT
TG
Found at i:808707 original size:26 final size:27
Alignment explanation
Indices: 808644--808707 Score: 62
Period size: 26 Copynumber: 2.4 Consensus size: 27
808634 GATAAGTACT
808644 TAAAATAATGAAATTAAACTTGAAATACA
1 TAAAAT-ATGAAATT-AACTTGAAATACA
* *
808673 TAGAA-ATGATAATT-ACTTGATATAC-
1 TAAAATATGA-AATTAACTTGAAATACA
808698 TAAAATATGA
1 TAAAATATGA
808708 CATGGAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
25 4 0.13
26 14 0.47
27 4 0.13
28 4 0.13
29 4 0.13
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.31
Consensus pattern (27 bp):
TAAAATATGAAATTAACTTGAAATACA
Found at i:811866 original size:20 final size:20
Alignment explanation
Indices: 811841--811879 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
811831 TACTTTCTTC
811841 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
811861 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
811880 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:812197 original size:50 final size:50
Alignment explanation
Indices: 812081--812266 Score: 177
Period size: 50 Copynumber: 3.7 Consensus size: 50
812071 GATAATAACA
* *
812081 TGCCAAAT-CCATGTCCCAGACATGGTCTTACATGGGATGTT-TCCTGTAC--
1 TGCC-AATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGG
* * *
812130 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
** *
812180 TGCCAATGCCATGTCCCAGACATGGTCTT--ATGGAGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-G-GGAGTTCTCATATCGG
* * * *
812230 TGTCAACGCCATGTCCTAGACATGGTCTTACGTGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
812267 CCTATCATAA
Statistics
Matches: 114, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
48 9 0.08
49 35 0.31
50 68 0.60
51 1 0.01
52 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
Found at i:812268 original size:50 final size:50
Alignment explanation
Indices: 812089--812322 Score: 168
Period size: 50 Copynumber: 4.6 Consensus size: 50
812079 CATGCCAAAT
* ** * * * *
812089 CCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTAC--TGCCAATG
1 CCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATAT-CGGTGCCAACG
* * * * ** *
812138 CCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCGGTGCCAACG
* * *
812188 CCATGTCCCAGACATGGTCTTATG-GAGGACCTCTCATCTCGGTGTCAACG
1 CCATGTCCCAGACATGGTCTTACGTG-GGACCTCTCATATCGGTGCCAACG
* * ** * *
812238 CCATGTCCTAGACATGGTCTTACGTGGGACCTATCATAACCTCAATAATTCCAATG
1 CCATGTCCCAGACATGGTCTTACGTGGGACCTCTCAT-A--TC---GGTGCCAACG
812294 CCATGTCCCAGACATGGTCTTACGTGGGA
1 CCATGTCCCAGACATGGTCTTACGTGGGA
812323 TCTCATTCCT
Statistics
Matches: 147, Mismatches: 28, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
48 1 0.01
49 32 0.22
50 78 0.53
51 1 0.01
53 2 0.01
56 33 0.22
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCGGTGCCAACG
Found at i:823250 original size:28 final size:28
Alignment explanation
Indices: 823210--823266 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
823200 ACTTTGAATT
823210 AAACCAAAGAATAACAATCAAAATAATC
1 AAACCAAAGAATAACAATCAAAATAATC
823238 AAACCAAAGAATAACAATCAAAATAATC
1 AAACCAAAGAATAACAATCAAAATAATC
823266 A
1 A
823267 TTCATGTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.65, C:0.18, G:0.04, T:0.14
Consensus pattern (28 bp):
AAACCAAAGAATAACAATCAAAATAATC
Found at i:823756 original size:34 final size:32
Alignment explanation
Indices: 823695--823768 Score: 85
Period size: 34 Copynumber: 2.2 Consensus size: 32
823685 GACTCCTTTA
* * *
823695 TAATTTATAAAACTTTAAACTATTAATAATAAAAT
1 TAATTT-T-AAACCTTAAAATAATAAT-ATAAAAT
823730 TACATTTTAAACCTTAAAATAATAATATAAAAT
1 TA-ATTTTAAACCTTAAAATAATAATATAAAAT
823763 TAATTT
1 TAATTT
823769 ATTTCTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
32 4 0.11
33 9 0.26
34 15 0.43
35 3 0.09
36 4 0.11
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.41
Consensus pattern (32 bp):
TAATTTTAAACCTTAAAATAATAATATAAAAT
Found at i:830043 original size:20 final size:22
Alignment explanation
Indices: 830005--830044 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
829995 AATAATTATC
830005 ATTTCTATGTATTTCAAGTATA
1 ATTTCTATGTATTTCAAGTATA
*
830027 ATTTC-ATG-ATTTTAAGTA
1 ATTTCTATGTATTTCAAGTA
830045 CTTATCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 3 0.18
22 5 0.29
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (22 bp):
ATTTCTATGTATTTCAAGTATA
Found at i:832271 original size:8 final size:8
Alignment explanation
Indices: 832258--832282 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
832248 ATATATACTA
832258 AATAAAAT
1 AATAAAAT
832266 AATAAAAT
1 AATAAAAT
832274 AATAAAAT
1 AATAAAAT
832282 A
1 A
832283 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:832690 original size:8 final size:8
Alignment explanation
Indices: 832677--832701 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
832667 ATATATACTA
832677 AATAAAAT
1 AATAAAAT
832685 AATAAAAT
1 AATAAAAT
832693 AATAAAAT
1 AATAAAAT
832701 A
1 A
832702 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:832878 original size:419 final size:419
Alignment explanation
Indices: 832100--832938 Score: 1678
Period size: 419 Copynumber: 2.0 Consensus size: 419
832090 TTCATGGATA
832100 TAGAAATTCTTTTGATTTCTAGATGAAAATAGTAATTTTTTGGTGAAAGGACCAAATTGTAAAGA
1 TAGAAATTCTTTTGATTTCTAGATGAAAATAGTAATTTTTTGGTGAAAGGACCAAATTGTAAAGA
832165 AAAGAAAGTTTCTTTCTTTCTTTCCTCTTCATACGTTGGAACGCATGGGAGAAGAGGATGATTCT
66 AAAGAAAGTTTCTTTCTTTCTTTCCTCTTCATACGTTGGAACGCATGGGAGAAGAGGATGATTCT
832230 TCATCTTTCCTTCCATATATATATACTAAATAAAATAATAAAATAATAAAATATTATTTAAAAAT
131 TCATCTTTCCTTCCATATATATATACTAAATAAAATAATAAAATAATAAAATATTATTTAAAAAT
832295 CAAATTAAAATATTAATAAACTAATATTTGTTTAATTAATCTAAAATATCTCCAATATCATCATT
196 CAAATTAAAATATTAATAAACTAATATTTGTTTAATTAATCTAAAATATCTCCAATATCATCATT
832360 ATCTTCTAGATTTCTCTCTTCTAATTGACCATTTTGCCCTTTATGATCTTTTAAAATTCTATCAT
261 ATCTTCTAGATTTCTCTCTTCTAATTGACCATTTTGCCCTTTATGATCTTTTAAAATTCTATCAT
832425 GGAGTCATCACTTAATTTTGTAAAATTACAATTTAATCCCCTAAAATTCTTCACCTTTTTCAATT
326 GGAGTCATCACTTAATTTTGTAAAATTACAATTTAATCCCCTAAAATTCTTCACCTTTTTCAATT
832490 TGGTCCTAATCCATCCATTTTCCTTAGTT
391 TGGTCCTAATCCATCCATTTTCCTTAGTT
832519 TAGAAATTCTTTTGATTTCTAGATGAAAATAGTAATTTTTTGGTGAAAGGACCAAATTGTAAAGA
1 TAGAAATTCTTTTGATTTCTAGATGAAAATAGTAATTTTTTGGTGAAAGGACCAAATTGTAAAGA
832584 AAAGAAAGTTTCTTTCTTTCTTTCCTCTTCATACGTTGGAACGCATGGGAGAAGAGGATGATTCT
66 AAAGAAAGTTTCTTTCTTTCTTTCCTCTTCATACGTTGGAACGCATGGGAGAAGAGGATGATTCT
832649 TCATCTTTCCTTCCATATATATATACTAAATAAAATAATAAAATAATAAAATATTATTTAAAAAT
131 TCATCTTTCCTTCCATATATATATACTAAATAAAATAATAAAATAATAAAATATTATTTAAAAAT
832714 CAAATTAAAATATTAATAAACTAATATTTGTTTAATTAATCTAAAATATCTCCAATATCATCATT
196 CAAATTAAAATATTAATAAACTAATATTTGTTTAATTAATCTAAAATATCTCCAATATCATCATT
832779 ATCTTCTAGATTTCTCTCTTCTAATTGACCATTTTGCCCTTTATGATCTTTTAAAATTCTATCAT
261 ATCTTCTAGATTTCTCTCTTCTAATTGACCATTTTGCCCTTTATGATCTTTTAAAATTCTATCAT
832844 GGAGTCATCACTTAATTTTGTAAAATTACAATTTAATCCCCTAAAATTCTTCACCTTTTTCAATT
326 GGAGTCATCACTTAATTTTGTAAAATTACAATTTAATCCCCTAAAATTCTTCACCTTTTTCAATT
832909 TGGTCCTAATCCATCCATTTTCCTTAGTT
391 TGGTCCTAATCCATCCATTTTCCTTAGTT
832938 T
1 T
832939 CTAGATCATT
Statistics
Matches: 420, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
419 420 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (419 bp):
TAGAAATTCTTTTGATTTCTAGATGAAAATAGTAATTTTTTGGTGAAAGGACCAAATTGTAAAGA
AAAGAAAGTTTCTTTCTTTCTTTCCTCTTCATACGTTGGAACGCATGGGAGAAGAGGATGATTCT
TCATCTTTCCTTCCATATATATATACTAAATAAAATAATAAAATAATAAAATATTATTTAAAAAT
CAAATTAAAATATTAATAAACTAATATTTGTTTAATTAATCTAAAATATCTCCAATATCATCATT
ATCTTCTAGATTTCTCTCTTCTAATTGACCATTTTGCCCTTTATGATCTTTTAAAATTCTATCAT
GGAGTCATCACTTAATTTTGTAAAATTACAATTTAATCCCCTAAAATTCTTCACCTTTTTCAATT
TGGTCCTAATCCATCCATTTTCCTTAGTT
Found at i:846200 original size:76 final size:76
Alignment explanation
Indices: 845923--846204 Score: 318
Period size: 76 Copynumber: 3.7 Consensus size: 76
845913 TGACATTAGA
* * * * ** *
845923 TGTGCCCTGCACTAGTCGAATAAATTGACAAAGACTTGCA-CAAAATGATAGTCAGATTAACTGA
1 TGTGCCCAGCACTAGTCGAATAAATCGACAAAGATTTGCATC-TAGCGCTAGTCAGATTAACTGA
845987 CAATATTAATTG
65 CAATATTAATTG
* * * ** *
845999 TGTGCCCAACACTAGTCGAATAAATTGACAAAGATTT--ATGCCTAGCACTACACATATTAACTG
1 TGTGCCCAGCACTAGTCGAATAAATCGACAAAGATTTGCAT--CTAGCGCTAGTCAGATTAACTG
** *
846062 ATGATATTAATTA
64 ACAATATTAATTG
* * *
846075 TGTGCCCAGCACTAGTCGAATAAATGGACAAAGATTTGCACCTAACGCTAGTCAGATTAACTGAC
1 TGTGCCCAGCACTAGTCGAATAAATCGACAAAGATTTGCATCTAGCGCTAGTCAGATTAACTGAC
846140 AATATTAATTG
66 AATATTAATTG
** *
846151 TGTGCCCAGCTGTAGTTGAATAAATCGACAAAGATTTGCATCTAGCGCTAGTCA
1 TGTGCCCAGCACTAGTCGAATAAATCGACAAAGATTTGCATCTAGCGCTAGTCA
846205 TATAAACCAA
Statistics
Matches: 170, Mismatches: 31, Indels: 10
0.81 0.15 0.05
Matches are distributed among these distances:
74 1 0.01
76 167 0.98
77 1 0.01
78 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (76 bp):
TGTGCCCAGCACTAGTCGAATAAATCGACAAAGATTTGCATCTAGCGCTAGTCAGATTAACTGAC
AATATTAATTG
Found at i:856698 original size:5 final size:5
Alignment explanation
Indices: 856688--856733 Score: 60
Period size: 5 Copynumber: 9.2 Consensus size: 5
856678 TCCTTACTTA
856688 TATTT TATTT T-TGTT TA-TT TATTT TATTT TATGTT TATTT TATTT T
1 TATTT TATTT TAT-TT TATTT TATTT TATTT TAT-TT TATTT TATTT T
856734 TAGTCCTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
4 5 0.14
5 27 0.73
6 5 0.14
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:856724 original size:20 final size:20
Alignment explanation
Indices: 856688--856733 Score: 76
Period size: 19 Copynumber: 2.3 Consensus size: 20
856678 TCCTTACTTA
856688 TATTTTATTTTTGTTTA-TT
1 TATTTTATTTTTGTTTATTT
856707 TATTTTATTTTATGTTTATTT
1 TATTTTATTTT-TGTTTATTT
856728 TATTTT
1 TATTTT
856734 TAGTCCTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 11 0.44
20 6 0.24
21 8 0.32
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.78
Consensus pattern (20 bp):
TATTTTATTTTTGTTTATTT
Found at i:856726 original size:11 final size:11
Alignment explanation
Indices: 856691--856735 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
856681 TTACTTATAT
856691 TTTATTTT-TG
1 TTTATTTTATG
856701 TTTA-TTTAT-
1 TTTATTTTATG
856710 TTTATTTTATG
1 TTTATTTTATG
*
856721 TTTATTTTATT
1 TTTATTTTATG
856732 TTTA
1 TTTA
856736 GTCCTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
9 7 0.23
10 10 0.32
11 14 0.45
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (11 bp):
TTTATTTTATG
Found at i:858888 original size:47 final size:46
Alignment explanation
Indices: 858819--858908 Score: 171
Period size: 47 Copynumber: 1.9 Consensus size: 46
858809 AAATGAGGTT
858819 TTAGTTTACTCTTATTCTTATTATTTAGTAAAAAAATAAAAAAAAAG
1 TTAGTTTACTCTTATTCTTATTATTTAGT-AAAAAATAAAAAAAAAG
858866 TTAGTTTACTCTTATTCTTATTATTTAGTAAAAAATAAAAAAA
1 TTAGTTTACTCTTATTCTTATTATTTAGTAAAAAATAAAAAAA
858909 TAATGTGATT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 14 0.33
47 29 0.67
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.42
Consensus pattern (46 bp):
TTAGTTTACTCTTATTCTTATTATTTAGTAAAAAATAAAAAAAAAG
Found at i:866088 original size:21 final size:21
Alignment explanation
Indices: 866059--866114 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
866049 GAATGACAAA
*
866059 TCAGATTTTTCTTCTTAATTT
1 TCAGCTTTTTCTTCTTAATTT
*
866080 TCAGCTTTTTCTTCTTGATTT
1 TCAGCTTTTTCTTCTTAATTT
866101 TCAGCTTTTTCTTC
1 TCAGCTTTTTCTTC
866115 CTAAAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.12, C:0.20, G:0.07, T:0.61
Consensus pattern (21 bp):
TCAGCTTTTTCTTCTTAATTT
Done.