Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold121
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: 1176681
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.32
Warning! 78447 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:534031 original size:17 final size:19
Alignment explanation
Indices: 534009--534050 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
533999 TATAGGGCAG
534009 TCTTTTGGGT-TTCT-TTT
1 TCTTTTGGGTCTTCTGTTT
534026 TCTTTT--GTCTTCTGTTT
1 TCTTTTGGGTCTTCTGTTT
534043 TCTTTTGG
1 TCTTTTGG
534051 TTTTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
15 2 0.10
16 4 0.19
17 15 0.71
ACGTcount: A:0.00, C:0.14, G:0.17, T:0.69
Consensus pattern (19 bp):
TCTTTTGGGTCTTCTGTTT
Found at i:535170 original size:31 final size:32
Alignment explanation
Indices: 535105--535172 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
535095 AAACAACAAC
* * *
535105 AATTTGACCTTTTTCTGAAAGATTGATAGTTA
1 AATTTGACCTTTTTCTAAAAGATTAATAGCTA
535137 AATTTGA-CTCTTTT-TAAAAGATTAATAGCTA
1 AATTTGACCT-TTTTCTAAAAGATTAATAGCTA
535168 AATTT
1 AATTT
535173 ATCTCAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 21 0.66
32 11 0.34
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (32 bp):
AATTTGACCTTTTTCTAAAAGATTAATAGCTA
Found at i:538058 original size:29 final size:28
Alignment explanation
Indices: 538016--538090 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
538006 TGGACCTTGG
* * *
538016 ACTTTGAACGTTAGACCCCAGACCCCTAA
1 ACTTTAAACCTTAGACCCCA-AACCCTAA
538045 ACTTTAAACCTTAGACCCCAAACCCTAA
1 ACTTTAAACCTTAGACCCCAAACCCTAA
* *
538073 A-TCCTAGACCTTAGACCC
1 ACT-TTAAACCTTAGACCC
538091 TCGACCCTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
27 1 0.03
28 21 0.52
29 18 0.45
ACGTcount: A:0.33, C:0.36, G:0.09, T:0.21
Consensus pattern (28 bp):
ACTTTAAACCTTAGACCCCAAACCCTAA
Found at i:538073 original size:21 final size:22
Alignment explanation
Indices: 538035--538082 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
538025 GTTAGACCCC
**
538035 AGACCCCTAAACTTTAAA-CCTT
1 AGACCCCTAAACCCTAAATCC-T
538057 AGACCCC-AAACCCTAAATCCT
1 AGACCCCTAAACCCTAAATCCT
538078 AGACC
1 AGACC
538083 TTAGACCCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.38, C:0.38, G:0.06, T:0.19
Consensus pattern (22 bp):
AGACCCCTAAACCCTAAATCCT
Found at i:540696 original size:33 final size:34
Alignment explanation
Indices: 540633--540702 Score: 88
Period size: 33 Copynumber: 2.0 Consensus size: 34
540623 ATTATATCAT
540633 AAGTGTAGAAATCACGTATTTAGTACGATCAAACATA
1 AAGTGTAGAAATCAC---TTTAGTACGATCAAACATA
* *
540670 AAGTGTAGAAATCAC-TTAGTATGATCAGACATA
1 AAGTGTAGAAATCACTTTAGTACGATCAAACATA
540703 TAGTAAGGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 16 0.52
37 15 0.48
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (34 bp):
AAGTGTAGAAATCACTTTAGTACGATCAAACATA
Found at i:552872 original size:125 final size:125
Alignment explanation
Indices: 552586--552969 Score: 525
Period size: 125 Copynumber: 3.0 Consensus size: 125
552576 GTGTACGTAC
* * *
552586 ACAATTGAACCTTGTGTGGAACGCTTGTTGTAGTTTATGTAGAACTTGTAATGTTGATCGATAGT
1 ACAATTGAACCTTGTGTGGAACTCTTGTTGTAGTTTATATAGAACTTGTAATGTTGATAGATAGT
*
552651 AATGTTCTACTATGTTACTTGGACCAGGACTGAGGACTCAAGTGTATGTGTGGATACGAGTATGT
66 AATGCTCTACTATGTTACTT-G---A--ACT-AGGACTCAAGTGTATGTGTGGATACGAGTATGT
552716 AA
124 AA
* * * *
552718 ACAATTGAACCTTGTGTTGAACTCTTGTTGTAGTTTATACAGAACTGGTAATGTTGATAGATACT
1 ACAATTGAACCTTGTGTGGAACTCTTGTTGTAGTTTATATAGAACTTGTAATGTTGATAGATAGT
*
552783 AATGCTCTACTATGTTACTTGAACTAGGACTCAAGTGTATGTGTGGATATGAGTATGTAA
66 AATGCTCTACTATGTTACTTGAACTAGGACTCAAGTGTATGTGTGGATACGAGTATGTAA
* *
552843 ACAATTGAACCTTGTGTGGAATTCTTGTTGTAGTTTATATAGAACTTGTAATGTTAATAGATAGT
1 ACAATTGAACCTTGTGTGGAACTCTTGTTGTAGTTTATATAGAACTTGTAATGTTGATAG--A-T
* * * * *
552908 AGTAATGCTCTACTATCTTACTTGGACTAGGACTCCAGTGTATGTGTGAATACCGAGCATGT
63 AGTAATGCTCTACTATGTTACTTGAACTAGGACTCAAGTGTATGTGTGGATA-CGAGTATGT
552970 GTCCAACATG
Statistics
Matches: 227, Mismatches: 21, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
125 89 0.39
126 3 0.01
127 1 0.00
128 49 0.22
129 7 0.03
131 1 0.00
132 77 0.34
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.36
Consensus pattern (125 bp):
ACAATTGAACCTTGTGTGGAACTCTTGTTGTAGTTTATATAGAACTTGTAATGTTGATAGATAGT
AATGCTCTACTATGTTACTTGAACTAGGACTCAAGTGTATGTGTGGATACGAGTATGTAA
Found at i:553758 original size:19 final size:20
Alignment explanation
Indices: 553734--553771 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
553724 TGCTTTTCTT
553734 TTTTTTTCCTTTTG-AATAC
1 TTTTTTTCCTTTTGTAATAC
*
553753 TTTTTTTTCTTTTGTAATA
1 TTTTTTTCCTTTTGTAATA
553772 ACCATATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.16, C:0.11, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTTTTCCTTTTGTAATAC
Found at i:553758 original size:20 final size:20
Alignment explanation
Indices: 553733--553771 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
553723 TTGCTTTTCT
553733 TTTTTTTTCCTTTTG-AATAC
1 TTTTTTTT-CTTTTGTAATAC
553753 TTTTTTTTCTTTTGTAATA
1 TTTTTTTTCTTTTGTAATA
553772 ACCATATGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTTTTTTCTTTTGTAATAC
Found at i:554378 original size:24 final size:23
Alignment explanation
Indices: 554341--554388 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
554331 TTTATGTTTG
* *
554341 TATATTACATATATATAAATAAT
1 TATATTACAAATATAAAAATAAT
554364 TATATTTACAAATATAAAAATAAT
1 TATA-TTACAAATATAAAAATAAT
554388 T
1 T
554389 TGATATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
TATATTACAAATATAAAAATAAT
Found at i:557983 original size:18 final size:17
Alignment explanation
Indices: 557950--557988 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
557940 TTTTATAAAT
557950 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
557968 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
557985 TGTG
1 TGTG
557989 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:561429 original size:45 final size:45
Alignment explanation
Indices: 561380--561521 Score: 146
Period size: 45 Copynumber: 3.2 Consensus size: 45
561370 TTAAATTTTA
561380 TTTTAAATAAATCATTTTTTTAATATTTTGCTTATTTAAATTAAC
1 TTTTAAATAAATCATTTTTTTAATATTTTGCTTATTTAAATTAAC
* * * * * * ** **
561425 TTTTAAAGTTAAATTAGTTATATTATTA-CTAGGGT-TTTAAATT-TT
1 TTTTAAA--TAAATCA-TTTTTTTAATATTTTGCTTATTTAAATTAAC
561470 TTTTAAATAAATCATTTTTTTAATATTTTGCTTATTTAAATTAAC
1 TTTTAAATAAATCATTTTTTTAATATTTTGCTTATTTAAATTAAC
561515 TTTTAAA
1 TTTTAAA
561522 GTTAAATAAG
Statistics
Matches: 71, Mismatches: 20, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
42 8 0.11
43 9 0.13
44 8 0.11
45 21 0.30
46 8 0.11
47 9 0.13
48 8 0.11
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (45 bp):
TTTTAAATAAATCATTTTTTTAATATTTTGCTTATTTAAATTAAC
Found at i:561490 original size:90 final size:91
Alignment explanation
Indices: 561369--561551 Score: 350
Period size: 90 Copynumber: 2.0 Consensus size: 91
561359 ATATATTAAA
561369 TTTAAATTTTATTTTAAATAAATCATTTTTTTAATATTTTGCTTATTTAAATTAACTTTTAAAGT
1 TTTAAATTTTATTTTAAATAAATCATTTTTTTAATATTTTGCTTATTTAAATTAACTTTTAAAGT
*
561434 TAAATTAGTTATATTATTACTAGGGT
66 TAAATAAGTTATATTATTACTAGGGT
561460 TTTAAATTTT-TTTTAAATAAATCATTTTTTTAATATTTTGCTTATTTAAATTAACTTTTAAAGT
1 TTTAAATTTTATTTTAAATAAATCATTTTTTTAATATTTTGCTTATTTAAATTAACTTTTAAAGT
561524 TAAATAAGTTATATTATTACTAGGGT
66 TAAATAAGTTATATTATTACTAGGGT
561550 TT
1 TT
561552 CTTTATTTTT
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
90 81 0.89
91 10 0.11
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (91 bp):
TTTAAATTTTATTTTAAATAAATCATTTTTTTAATATTTTGCTTATTTAAATTAACTTTTAAAGT
TAAATAAGTTATATTATTACTAGGGT
Found at i:568279 original size:87 final size:87
Alignment explanation
Indices: 568133--568307 Score: 332
Period size: 87 Copynumber: 2.0 Consensus size: 87
568123 TTTATGCCAT
568133 TGGGTATGAGTTGTAAGGATCGACTTGTGATATATGCACTGCAATAGTTTGTTCGAACCGATAAT
1 TGGGTATGAGTTGTAAGGATCGACTTGTGATATATGCACTGCAATAGTTTGTTCGAACCGATAAT
568198 ATGTGAAATGTATATATTCTTA
66 ATGTGAAATGTATATATTCTTA
* *
568220 TGGGTTTGAGTTGTAAGGATCGACTTTTGATATATGCACTGCAATAGTTTGTTCGAACCGATAAT
1 TGGGTATGAGTTGTAAGGATCGACTTGTGATATATGCACTGCAATAGTTTGTTCGAACCGATAAT
568285 ATGTGAAATGTATATATTCTTA
66 ATGTGAAATGTATATATTCTTA
568307 T
1 T
568308 CTTTCATGTG
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.38
Consensus pattern (87 bp):
TGGGTATGAGTTGTAAGGATCGACTTGTGATATATGCACTGCAATAGTTTGTTCGAACCGATAAT
ATGTGAAATGTATATATTCTTA
Found at i:568574 original size:12 final size:11
Alignment explanation
Indices: 568542--568570 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
568532 TTGAATTGTC
568542 AAAATATTATA
1 AAAATATTATA
568553 AAAA-ATTATA
1 AAAATATTATA
568563 AAAATATT
1 AAAATATT
568571 TATATATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAATATTATA
Found at i:574447 original size:31 final size:31
Alignment explanation
Indices: 574392--574469 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
574382 TTTTCCTTAA
* *
574392 TGGCTTGGATAAGCCTT--GATGCAATTGAGT
1 TGGCTT-GAGAAGCCTTGAGATGCAATTGAAT
*
574422 TGGCTTGAGTAGCCTTGAGATGCAATTGAAT
1 TGGCTTGAGAAGCCTTGAGATGCAATTGAAT
574453 TGGCTTGAGAAGCCTTG
1 TGGCTTGAGAAGCCTTG
574470 TGGAAAACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 8 0.19
30 6 0.14
31 28 0.67
ACGTcount: A:0.23, C:0.14, G:0.31, T:0.32
Consensus pattern (31 bp):
TGGCTTGAGAAGCCTTGAGATGCAATTGAAT
Found at i:575260 original size:26 final size:26
Alignment explanation
Indices: 575230--575280 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
575220 AGCCATGAGT
575230 TTGAG-TCGAGATGAGTCGGAGGACCC
1 TTGAGTTCGAGATG-GTCGGAGGACCC
* *
575256 TTGAGTTTGAGTTGGTCGGAGGACC
1 TTGAGTTCGAGATGGTCGGAGGACC
575281 ATAAGCGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.20, C:0.16, G:0.39, T:0.25
Consensus pattern (26 bp):
TTGAGTTCGAGATGGTCGGAGGACCC
Found at i:576743 original size:164 final size:165
Alignment explanation
Indices: 576458--576776 Score: 419
Period size: 164 Copynumber: 1.9 Consensus size: 165
576448 TTGCTGGCTA
* * ** **
576458 TGTTAACATTCTCATAATTGCATTAGTGTACAAGTTTGTTGCTTGTGGGGAGTTTTTAACATAAT
1 TGTTAACA-TCTCATAATTGCATTAGAGTACAAATCAGTTGCTTGTGGGGAGTTCATAACATAAT
* * * *
576523 TATTTAGTTGTTGAAATTGCGAGTATTAGGCTTTTGAAGAAGATTGACTTATGTTTCTGGATTTA
65 TATGTAGTTATTGAAAATGCGAATATTAGGCTTTTGAAGAAGATTGACTTATGTTTCTGGATTTA
* *
576588 CCGATGTATCCGGCTGAGAAATTCTCAACTGGAATC
130 CCAATGTATCCGACTGAGAAATTCTCAACTGGAATC
* *
576624 TGTTAAC-TCTCTTAATTGCATTAGAGTACAAATCAGTTGCTTGTGGGGAG-TCATAACATGCA-
1 TGTTAACATCTCATAATTGCATTAGAGTACAAATCAGTTGCTTGTGGGGAGTTCATAACAT-AAT
* *
576686 TATGTAGTTATTGAAAATGCTGAATATTAGGCTTTTGAAGAATATTGACTTATGTTTCTTGATTT
65 TATGTAGTTATTGAAAATGC-GAATATTAGGCTTTTGAAGAAGATTGACTTATGTTTCTGGATTT
* * *
576751 ACTAATGTGTCTGACTGAGAAATTCT
129 ACCAATGTATCCGACTGAGAAATTCT
576777 AAACCAAAAT
Statistics
Matches: 132, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
163 24 0.18
164 101 0.77
166 7 0.05
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (165 bp):
TGTTAACATCTCATAATTGCATTAGAGTACAAATCAGTTGCTTGTGGGGAGTTCATAACATAATT
ATGTAGTTATTGAAAATGCGAATATTAGGCTTTTGAAGAAGATTGACTTATGTTTCTGGATTTAC
CAATGTATCCGACTGAGAAATTCTCAACTGGAATC
Found at i:590475 original size:17 final size:18
Alignment explanation
Indices: 590455--590488 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
590445 TTTTTGCTTT
590455 TATTTTTATTT-TTTATA
1 TATTTTTATTTATTTATA
*
590472 TATTTTTGTTTATTTAT
1 TATTTTTATTTATTTAT
590489 TTCTGATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (18 bp):
TATTTTTATTTATTTATA
Found at i:591058 original size:23 final size:22
Alignment explanation
Indices: 591032--591075 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
591022 ATATTTAATT
591032 TTATCATTTTAAT-TGAAACTTTA
1 TTAT-ATTTTAATAT-AAACTTTA
*
591055 TTATTTTTTAATATAAACTTT
1 TTATATTTTAATATAAACTTT
591076 TATAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
TTATATTTTAATATAAACTTTA
Found at i:591749 original size:175 final size:176
Alignment explanation
Indices: 591543--591895 Score: 699
Period size: 175 Copynumber: 2.0 Consensus size: 176
591533 TTTTTATTAA
591543 TAGTTGATATTATATTAATTTACTAATTTTAAGTATTAAATTAAAAATATTAATTTTTATTAAAT
1 TAGTTGATATTATATTAATTTACTAATTTTAAGTATTAAATTAAAAATATTAATTTTTATTAAAT
591608 TTGTCTTCTAAATGTATTAAATTGAAATTGCATAGTGAAATTCAATAAAAATCAAATTTTAGTGA
66 TTGTCTTCTAAATGTATTAAATTGAAATTGCATAGTGAAATTCAATAAAAATCAAATTTTAGTGA
591673 TAAAGTTCAATCAAACAAAAGTGAAGTGACAAAATTTAAGATAAAT
131 TAAAGTTCAATCAAACAAAAGTGAAGTGACAAAATTTAAGATAAAT
591719 TAGTTGATATTA-ATTAATTTACTAATTTTAAGTATTAAATTAAAAATATTAATTTTTATTAAAT
1 TAGTTGATATTATATTAATTTACTAATTTTAAGTATTAAATTAAAAATATTAATTTTTATTAAAT
591783 TTGTCTTCTAAATGTATTAAATTGAAATTGCATAGTGAAATTCAATAAAAATCAAATTTTAGTGA
66 TTGTCTTCTAAATGTATTAAATTGAAATTGCATAGTGAAATTCAATAAAAATCAAATTTTAGTGA
591848 TAAAGTTCAATCAAACAAAAGTGAAGTGACAAAATTTAAGATAAAT
131 TAAAGTTCAATCAAACAAAAGTGAAGTGACAAAATTTAAGATAAAT
591894 TA
1 TA
591896 AAATATAATA
Statistics
Matches: 177, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
175 165 0.93
176 12 0.07
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.39
Consensus pattern (176 bp):
TAGTTGATATTATATTAATTTACTAATTTTAAGTATTAAATTAAAAATATTAATTTTTATTAAAT
TTGTCTTCTAAATGTATTAAATTGAAATTGCATAGTGAAATTCAATAAAAATCAAATTTTAGTGA
TAAAGTTCAATCAAACAAAAGTGAAGTGACAAAATTTAAGATAAAT
Found at i:600255 original size:22 final size:20
Alignment explanation
Indices: 600214--600273 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
600204 CAATTCAATA
* * *
600214 TAAAGTATAGATATATATAT
1 TAAAATATAAATATAGATAT
600234 TAAAATTATAAAATATAGATAT
1 TAAAA-TAT-AAATATAGATAT
*
600256 TAAAATATAGATATAGAT
1 TAAAATATAAATATAGAT
600274 TTGGTTTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 13 0.38
21 6 0.18
22 15 0.44
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (20 bp):
TAAAATATAAATATAGATAT
Found at i:600261 original size:14 final size:14
Alignment explanation
Indices: 600242--600269 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
600232 ATTAAAATTA
600242 TAAAATATAGATAT
1 TAAAATATAGATAT
600256 TAAAATATAGATAT
1 TAAAATATAGATAT
600270 AGATTTGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
TAAAATATAGATAT
Found at i:602435 original size:30 final size:30
Alignment explanation
Indices: 602401--602480 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
602391 AATTGAATCA
602401 AAATCAAAGTTCTATGTATAGAATTGCAC-T
1 AAATCAAAGTTCTATGTATA-AATTGCACAT
* * *
602431 AAATCAAAATTCGTATAT-TATATTGCACATT
1 AAATCAAAGTTC-TATGTATAAATTGCACA-T
*
602462 AAATCCAAGTTC-ATGTATA
1 AAATCAAAGTTCTATGTATA
602481 CTTTTGAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
29 10 0.25
30 15 0.38
31 15 0.38
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (30 bp):
AAATCAAAGTTCTATGTATAAATTGCACAT
Found at i:605255 original size:23 final size:24
Alignment explanation
Indices: 605203--605251 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
605193 ATTTTTACCC
605203 CAAA-TTAGCCCTATAAAATTTTA
1 CAAATTTAGCCCTATAAAATTTTA
*
605226 CAAATTTAGCCCT-TAACA-TTTA
1 CAAATTTAGCCCTATAAAATTTTA
605248 CAAA
1 CAAA
605252 ATTTGTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 8 0.33
23 8 0.33
24 8 0.33
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33
Consensus pattern (24 bp):
CAAATTTAGCCCTATAAAATTTTA
Found at i:607715 original size:30 final size:32
Alignment explanation
Indices: 607668--607733 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
607658 GTCCTAAAGG
*
607668 TTTTAAATGTCGTCAGTT-TTGAGCCATTTT-A
1 TTTTAAATGTCGTCAGTTAGTGAG-CATTTTAA
*
607699 TTTTAAAT-TTGTCAGTTAGTGAGCATTTTAA
1 TTTTAAATGTCGTCAGTTAGTGAGCATTTTAA
607730 TTTT
1 TTTT
607734 GGTGTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 14 0.45
31 17 0.55
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (32 bp):
TTTTAAATGTCGTCAGTTAGTGAGCATTTTAA
Found at i:628103 original size:68 final size:67
Alignment explanation
Indices: 628031--628186 Score: 163
Period size: 67 Copynumber: 2.3 Consensus size: 67
628021 CATAGCCCCA
* * *
628031 CTATGGTCTTACACAATATGAACTCATGTTTAACG-TCTTGGCGGACTCCCTTTATTACCATAG-
1 CTATGGTCTTACACAGTATGAACACATG-TTAACGTTC-TAGCGGACTCCCTTTATTACCATAGC
628094 TCGAG
64 T-GAG
* * * * * * *
628099 CTATGGGCTTACATAGTAGGAACACATGTTAACGTTCTAGCGGGCTCCTTTTGTTGCCATAGCTG
1 CTATGGTCTTACACAGTATGAACACATGTTAACGTTCTAGCGGACTCCCTTTATTACCATAGCTG
628164 AG
66 AG
* *
628166 TTATGGTCTTAGACAGTATGA
1 CTATGGTCTTACACAGTATGA
628187 CATCTTTTGA
Statistics
Matches: 71, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
67 45 0.63
68 26 0.37
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (67 bp):
CTATGGTCTTACACAGTATGAACACATGTTAACGTTCTAGCGGACTCCCTTTATTACCATAGCTG
AG
Found at i:629717 original size:14 final size:14
Alignment explanation
Indices: 629700--629728 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
629690 TTGAGCATGG
629700 GTCGTTGCAATGAA
1 GTCGTTGCAATGAA
629714 GTCGTTGCAATGAA
1 GTCGTTGCAATGAA
629728 G
1 G
629729 AGCCAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.28
Consensus pattern (14 bp):
GTCGTTGCAATGAA
Found at i:632385 original size:74 final size:74
Alignment explanation
Indices: 632296--632446 Score: 293
Period size: 74 Copynumber: 2.0 Consensus size: 74
632286 ATCTCTCTTG
632296 TAAATGCTTATTATGAACAAGATAAATACATGACCATATTAGTGCTAAAAACAAACGACCTCTGA
1 TAAATGCTTATTATGAACAAGATAAATACATGACCATATTAGTGCTAAAAACAAACGACCTCTGA
632361 CAGAAAAAT
66 CAGAAAAAT
*
632370 TAAATGCTTATTATGAACAAGATAAATACATGACGATATTAGTGCTAAAAACAAACGACCTCTGA
1 TAAATGCTTATTATGAACAAGATAAATACATGACCATATTAGTGCTAAAAACAAACGACCTCTGA
632435 CAGAAAAAT
66 CAGAAAAAT
632444 TAA
1 TAA
632447 TGAATATTAT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.25
Consensus pattern (74 bp):
TAAATGCTTATTATGAACAAGATAAATACATGACCATATTAGTGCTAAAAACAAACGACCTCTGA
CAGAAAAAT
Found at i:637434 original size:160 final size:160
Alignment explanation
Indices: 637260--637581 Score: 635
Period size: 160 Copynumber: 2.0 Consensus size: 160
637250 TTTTTATTAT
637260 TTAAATTTGATTTTTATTTTATATATTCAGTGAAAAAATTTACTAAAAAATTCTTATTTTTTAGA
1 TTAAATTTGATTTTTATTTTATATATTCAGTGAAAAAATTTACTAAAAAATTCTTATTTTTTAGA
637325 AAATAATAAATATTATTTTAAAAATAATTTTAATTTTCATATAATTTTTTTAAAAATTACATAAA
66 AAATAATAAATATTATTTTAAAAATAATTTTAATTTTCATATAATTTTTTTAAAAATTACATAAA
637390 ATATTATAATTTTTAAAAACTCACTTTACA
131 ATATTATAATTTTTAAAAACTCACTTTACA
637420 TTAAATTTGATTTTTATTTTATATATTCAGTGAAAAAATTTACTAAAAAATTCTTATTTTTTAGA
1 TTAAATTTGATTTTTATTTTATATATTCAGTGAAAAAATTTACTAAAAAATTCTTATTTTTTAGA
637485 AAATAATAAATATTATTTTAAAAATAATTTTAATTTTCATATAATTTTTTTAAAAATTACATAAA
66 AAATAATAAATATTATTTTAAAAATAATTTTAATTTTCATATAATTTTTTTAAAAATTACATAAA
*
637550 ATATTATAATTTTTAACAACTCACTTTACA
131 ATATTATAATTTTTAAAAACTCACTTTACA
637580 TT
1 TT
637582 CCAACCAAAA
Statistics
Matches: 161, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 161 1.00
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (160 bp):
TTAAATTTGATTTTTATTTTATATATTCAGTGAAAAAATTTACTAAAAAATTCTTATTTTTTAGA
AAATAATAAATATTATTTTAAAAATAATTTTAATTTTCATATAATTTTTTTAAAAATTACATAAA
ATATTATAATTTTTAAAAACTCACTTTACA
Found at i:639619 original size:2 final size:2
Alignment explanation
Indices: 639612--639636 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
639602 NNNNNNNNNN
639612 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 T
639637 TACAGTAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:640453 original size:214 final size:216
Alignment explanation
Indices: 640073--640633 Score: 623
Period size: 214 Copynumber: 2.6 Consensus size: 216
640063 AGCCCTGTGG
* * * * *
640073 CTGTTATTGTATCGAAGTTGCCGATATGCTCTTTCTTTTGGGAATTCTTTTTTATGATTATATGA
1 CTGTTATTGCATCTAAGCTGCCGATATGCTCTTTCTTTTGGGACTT-TTTTTT-TGGTTATATGA
* * *
640138 TATAATGATCTTTGGTTTCATTTTTTCTTTGCATATATCTGGATATAACTCTATTTGAGCCATGC
64 TATAATGATCTTTGGATTCAGTTTTTCTTTGCAGATATCTGGATATAACTCTATTTGAGCCATGC
* * * *
640203 TTACCACGATCAAATACAGTTGTTCGGGGTAGCTTAATAGATGATATTTCTGTTTT-GGTACGGT
129 TTACCACGATAAAATACAGTTGTTCGGGGAAGCTTAATAGATGATATTTCTATTTTCCGTACGGT
*
640267 TTTGCCATGCCA-TGGTATTAAC
194 TTTGCCATGCAATTGGTATTAAC
*
640289 TCTGTTATTGCATCTAAGCTGCTGATATGCTCTTTCTTTTGGGACTTTTTTTTTGGTTATATGAT
1 -CTGTTATTGCATCTAAGCTGCCGATATGCTCTTTCTTTTGGGACTTTTTTTTTGGTTATATGAT
* *
640354 ATAATGATCTTTGGATTC-GTTTTTCTTTGCGGAT-TGCTGGATATAACTCTATTTGAGCCTTGC
65 ATAATGATCTTTGGATTCAGTTTTTCTTTGCAGATAT-CTGGATATAACTCTATTTGAGCCATGC
** * ** * * * *
640417 TTATTACTATAAAATATTGTTGTTTGGGGAAGCTTAATTGATGATCTTTTTATTTTCCGTACGGT
129 TTACCACGATAAAATACAGTTGTTCGGGGAAGCTTAATAGATGATATTTCTATTTTCCGTACGGT
640482 TTTGCCATGCAATGGTTTTGGTATTAAC
194 TTTGCCATGCAA-----TTGGTATTAAC
* * *
640510 CTTGTTATTGCAT-TGAAGCTTCCGATATGCTCTTTCTTTTAGGAC-TTTTTTATGGTTGACTAT
1 C-TGTTATTGCATCT-AAGCTGCCGATATGCTCTTTCTTTTGGGACTTTTTTTTTGGTT-A-TAT
* * ** * ** * *
640573 GATATAATGATCTATGGGTTCTCTTTTT-TATGCCTATATCTAGATATTACTCTATTTGAGC
62 GATATAATGATCTTTGGATTCAGTTTTTCTTTGCAGATATCTGGATATAACTCTATTTGAGC
640634 TATTCTTATT
Statistics
Matches: 293, Mismatches: 37, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
213 1 0.00
214 83 0.28
215 46 0.16
216 6 0.02
217 41 0.14
220 13 0.04
221 49 0.17
222 48 0.16
223 6 0.02
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.46
Consensus pattern (216 bp):
CTGTTATTGCATCTAAGCTGCCGATATGCTCTTTCTTTTGGGACTTTTTTTTTGGTTATATGATA
TAATGATCTTTGGATTCAGTTTTTCTTTGCAGATATCTGGATATAACTCTATTTGAGCCATGCTT
ACCACGATAAAATACAGTTGTTCGGGGAAGCTTAATAGATGATATTTCTATTTTCCGTACGGTTT
TGCCATGCAATTGGTATTAAC
Found at i:640675 original size:222 final size:220
Alignment explanation
Indices: 639927--640696 Score: 760
Period size: 222 Copynumber: 3.5 Consensus size: 220
639917 ACATGATCAG
* *
639927 TTTTTCTTTGCCTATATCTGCATATATAACTCTATTTGAGCCATGCTTATTACTATCGAATACTG
1 TTTTT-TTTGCCTATATCTG--GATATAACTCTATTTGAGCCATGCTTATTACTATCAAATACTG
* * * * * *
639992 TTGTT-CAGGATAGCTTAATGGGTGATATTTCTGTTTTCGGTACGATTTTTCCATACAATGGTTT
63 TTGTTCCAGG-TAGCTTAATAGATGATATTTCTGTTTTCCGTACGGTTTTGCCATGCAATGGTTT
* * *
640056 TGGTATTAGCCCTGTGGCTGTTATTGTATCGAAG-TTGCCGATATGCTCTTTCTTTTGGGAATTC
127 TGGTATTA-ACC--T--CTGTTATTGCATTGAAGCTT-CCGATATGCTCTTTCTTTTGGG-A--C
* *
640120 TTTTTTATGATTATATGATATAATGATCTTTGGTTTCA
183 TTTTTTATGGTTATATGATATAATGATCTTTGGATTCA
* ** * *
640158 TTTTTTCTTTGCATATATCTGGATATAACTCTATTTGAGCCATGCTTACCACGATCAAATACAGT
1 -TTTTT-TTTGCCTATATCTGGATATAACTCTATTTGAGCCATGCTTATTACTATCAAATACTGT
** * *
640223 TGTTCGGGGTAGCTTAATAGATGATATTTCTGTTTT-GGTACGGTTTTGCCATGCCA------TG
64 TGTTCCAGGTAGCTTAATAGATGATATTTCTGTTTTCCGTACGGTTTTGCCATGCAATGGTTTTG
* * *
640281 GTATTAA-CTCTGTTATTGCATCT-AAGCTGCTGATATGCTCTTTCTTTTGGGACTTTTTTTTTG
129 GTATTAACCTCTGTTATTGCAT-TGAAGCTTCCGATATGCTCTTTCTTTTGGGAC-TTTTTTATG
*
640344 GTTATATGATATAATGATCTTTGGATTCG
192 GTTATATGATATAATGATCTTTGGATTCA
** * * *
640373 TTTTTCTTTGCGGAT-TGCTGGATATAACTCTATTTGAGCCTTGCTTATTACTATAAAATATTGT
1 TTTTT-TTTGCCTATAT-CTGGATATAACTCTATTTGAGCCATGCTTATTACTATCAAATACTGT
*** * * * * *
640437 TGTTTGGGGAAGCTTAATTGATGATCTTTTTATTTTCCGTACGGTTTTGCCATGCAATGGTTTTG
64 TGTTCCAGGTAGCTTAATAGATGATATTTCTGTTTTCCGTACGGTTTTGCCATGCAATGGTTTTG
*
640502 GTATTAACCT-TGTTATTGCATTGAAGCTTCCGATATGCTCTTTCTTTTAGGACTTTTTTATGGT
129 GTATTAACCTCTGTTATTGCATTGAAGCTTCCGATATGCTCTTTCTTTTGGGACTTTTTTATGGT
* *
640566 TGACTATGATATAATGATCTATGGGTTC-
194 T-A-TATGATATAATGATCTTTGGATTCA
* * * * **
640594 TCTTTTTTATGCCTATATCTAGATATTACTCTATTTGAGCTATTCTTATTA-TGATCAAATTTTG
1 T-TTTTTT-TGCCTATATCTGGATATAACTCTATTTGAGCCATGCTTATTACT-ATCAAATACTG
* * *
640658 TTGTTCCAGGTAGCTTAATCGATGATTTTTGTGTTTTCC
63 TTGTTCCAGGTAGCTTAATAGATGATATTTCTGTTTTCC
640697 ATGTGGTTTT
Statistics
Matches: 454, Mismatches: 64, Indels: 50
0.80 0.11 0.09
Matches are distributed among these distances:
213 1 0.00
214 84 0.19
215 52 0.11
216 1 0.00
217 35 0.08
218 1 0.00
219 1 0.00
220 12 0.03
221 53 0.12
222 101 0.22
223 9 0.02
229 16 0.04
230 67 0.15
231 2 0.00
232 19 0.04
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (220 bp):
TTTTTTTTGCCTATATCTGGATATAACTCTATTTGAGCCATGCTTATTACTATCAAATACTGTTG
TTCCAGGTAGCTTAATAGATGATATTTCTGTTTTCCGTACGGTTTTGCCATGCAATGGTTTTGGT
ATTAACCTCTGTTATTGCATTGAAGCTTCCGATATGCTCTTTCTTTTGGGACTTTTTTATGGTTA
TATGATATAATGATCTTTGGATTCA
Found at i:643616 original size:29 final size:30
Alignment explanation
Indices: 643583--643642 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
643573 GTATTCTTCG
* *
643583 TTTTATTTTGATTACTCAAT-TATTAATAT
1 TTTTATTTTAATCACTCAATATATTAATAT
*
643612 TTTTATTTTAATCACTCAATATTTTAATAT
1 TTTTATTTTAATCACTCAATATATTAATAT
643642 T
1 T
643643 AAATATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (30 bp):
TTTTATTTTAATCACTCAATATATTAATAT
Found at i:643649 original size:15 final size:16
Alignment explanation
Indices: 643615--643655 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
643605 TTAATATTTT
*
643615 TATTTTAATCACTCAA
1 TATTTTAATCACTAAA
*
643631 TATTTTAAT-ATTAAA
1 TATTTTAATCACTAAA
643646 TATTTTAATC
1 TATTTTAATC
643656 GCTTTTCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTTTAATCACTAAA
Found at i:648099 original size:58 final size:59
Alignment explanation
Indices: 648030--648166 Score: 163
Period size: 58 Copynumber: 2.3 Consensus size: 59
648020 TTTACATCTT
* * *
648030 GGTACTTGAACTCGGCTTTAAGGTTTAAATTG-TCACCTAAAGCTTTA-TT-GTCCAATTA
1 GGTACTTGAACTTGGCTTTAAGATTCAAATTGAT-ACCTAAAG-TTTATTTGGTCCAATTA
* * *
648088 GGTACTTGAACTTGACTTTAATATTCAATTTGATACCTAAAGTTTATTTTGGTCCAATTA
1 GGTACTTGAACTTGGCTTTAAGATTCAAATTGATACCTAAAGTTTA-TTTGGTCCAATTA
*
648148 GGTACTTAAACTTGGCTTT
1 GGTACTTGAACTTGGCTTT
648167 TTGGTTCAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
57 4 0.06
58 34 0.51
59 3 0.04
60 26 0.39
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (59 bp):
GGTACTTGAACTTGGCTTTAAGATTCAAATTGATACCTAAAGTTTATTTGGTCCAATTA
Found at i:658991 original size:30 final size:30
Alignment explanation
Indices: 658957--659018 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
658947 CATTTTACTT
*
658957 TTAGGTACAGTTTGGAAAA-CTATTTAGTAA
1 TTAGGTACAGTTTGGAAAATC-ATTTAATAA
*
658987 TTAGGTACTGTTTGGAAAATCATTTAATAA
1 TTAGGTACAGTTTGGAAAATCATTTAATAA
659017 TT
1 TT
659019 GAATTTGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.40
Consensus pattern (30 bp):
TTAGGTACAGTTTGGAAAATCATTTAATAA
Found at i:663074 original size:9 final size:9
Alignment explanation
Indices: 663060--663085 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
663050 TTTGTTAATT
663060 TAGAAACCC
1 TAGAAACCC
663069 TAGAAACCC
1 TAGAAACCC
663078 TAGAAACC
1 TAGAAACC
663086 AAGAGTGCTA
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:0.46, C:0.31, G:0.12, T:0.12
Consensus pattern (9 bp):
TAGAAACCC
Found at i:668719 original size:10 final size:11
Alignment explanation
Indices: 668687--668729 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
668677 TTTGGGTTTA
*
668687 GGTTTTTATTT
1 GGTTTTGATTT
* *
668698 TGTTTTGGTTT
1 GGTTTTGATTT
668709 GGTTTT-ATTT
1 GGTTTTGATTT
668719 GGTTTTGATTT
1 GGTTTTGATTT
668730 CAGATTTGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.07, C:0.00, G:0.23, T:0.70
Consensus pattern (11 bp):
GGTTTTGATTT
Found at i:669582 original size:3 final size:3
Alignment explanation
Indices: 669574--669601 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
669564 TATTTAGTCT
669574 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
669602 AAAACAACTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:677858 original size:15 final size:15
Alignment explanation
Indices: 677838--677867 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
677828 ATTGATGGTT
*
677838 AATATTTTTCTGAAA
1 AATATTTGTCTGAAA
677853 AATATTTGTCTGAAA
1 AATATTTGTCTGAAA
677868 TTCTGCTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (15 bp):
AATATTTGTCTGAAA
Found at i:681094 original size:23 final size:23
Alignment explanation
Indices: 681047--681097 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
681037 GGATTTAAAC
*
681047 AAATATTCATATTTATATAATTA
1 AAATATTCATATTTATATAAATA
*
681070 AAATATTCATATTT-TGTAACATA
1 AAATATTCATATTTATATAA-ATA
681093 AAATA
1 AAATA
681098 ATAATTACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (23 bp):
AAATATTCATATTTATATAAATA
Found at i:681595 original size:19 final size:19
Alignment explanation
Indices: 681557--681595 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
681547 TGACTAGTAC
* *
681557 ATTATTTTTCATTAATCAA
1 ATTATTTTTCATGAAACAA
*
681576 ATTATTTTTCGTGAAACAA
1 ATTATTTTTCATGAAACAA
681595 A
1 A
681596 CATATAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.46
Consensus pattern (19 bp):
ATTATTTTTCATGAAACAA
Found at i:685512 original size:62 final size:59
Alignment explanation
Indices: 685443--685556 Score: 147
Period size: 62 Copynumber: 1.9 Consensus size: 59
685433 AACGATTATC
* * *
685443 TTAATATTAAATTAAATTTAATGTTTATCTTGTAGATAAATATTCTATTAATTTAATAAGAT
1 TTAATATTAAATTAAATCTAATATTTATC-T-T-GATAAATATTATATTAATTTAATAAGAT
* * *
685505 TTAATATTCAATTTAATCTAATATTTATCTTGATAATTATTATATTAATTTA
1 TTAATATTAAATTAAATCTAATATTTATCTTGATAAATATTATATTAATTTA
685557 TTATTAAAGT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 19 0.41
60 1 0.02
61 1 0.02
62 25 0.54
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (59 bp):
TTAATATTAAATTAAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAAGAT
Found at i:686189 original size:322 final size:322
Alignment explanation
Indices: 685604--686248 Score: 1263
Period size: 322 Copynumber: 2.0 Consensus size: 322
685594 TTAAACTCTC
685604 CTTATATAAAGAGAGCTTTGGGTCATTATTTTCCACACTTGAATTTAAGAGAAAGTTGTAGAGAG
1 CTTATATAAAGAGAGCTTTGGGTCATTATTTTCCACACTTGAATTTAAGAGAAAGTTGTAGAGAG
* * *
685669 AAAATTCTCTGAAGAGATTATTTCAGAAAATTTCTAGAGATATTTTTCTTATTTACAACTTTGTC
66 AAAATTCTCTGAAGAGATTATTTAAGAAAAATTCTAAAGATATTTTTCTTATTTACAACTTTGTC
685734 TAAATTTTAGTGAAATTACAAAATTACCCCACTAGTAATTTTTGTGAATTTTTTATTTTATTTTA
131 TAAATTTTAGTGAAATTACAAAATTACCCCACTAGTAATTTTTGTGAATTTTTTATTTTATTTTA
685799 AGCGAGTCCACACTCGAGAGACATGAGCTTGAGGATAGCGAAAAAGACTACTCGGTTGAAGCGTT
196 AGCGAGTCCACACTCGAGAGACATGAGCTTGAGGATAGCGAAAAAGACTACTCGGTTGAAGCGTT
685864 CATCCTAGACAAATCGAGAAAGTACAATTTTGATTAAATGTTTATTACTTTAGATATTACAA
261 CATCCTAGACAAATCGAGAAAGTACAATTTTGATTAAATGTTTATTACTTTAGATATTACAA
685926 CTTATATAAAGAGAGCTTTGGGTCATTATTTTCCACACTTGAATTTAAGAGAAAGTTGTAGAGAG
1 CTTATATAAAGAGAGCTTTGGGTCATTATTTTCCACACTTGAATTTAAGAGAAAGTTGTAGAGAG
685991 AAAATTCTCTGAAGAGATTATTTAAGAAAAATTCTAAAGATATTTTTCTTATTTACAACTTTGTC
66 AAAATTCTCTGAAGAGATTATTTAAGAAAAATTCTAAAGATATTTTTCTTATTTACAACTTTGTC
686056 TAAATTTTAGTGAAATTACAAAATTACCCCACTAGTAATTTTTGTGAATTTTTTATTTTATTTTA
131 TAAATTTTAGTGAAATTACAAAATTACCCCACTAGTAATTTTTGTGAATTTTTTATTTTATTTTA
686121 AGCGAGTCCACACTCGAGAGACATGAGCTTGAGGATAGCGAAAAAGACTACTCGGTTGAAGCGTT
196 AGCGAGTCCACACTCGAGAGACATGAGCTTGAGGATAGCGAAAAAGACTACTCGGTTGAAGCGTT
686186 CATCCTAGACAAATCGAGAAAGTACAATTTTGATTAAATGTTTATTACTTTAGATATTACAA
261 CATCCTAGACAAATCGAGAAAGTACAATTTTGATTAAATGTTTATTACTTTAGATATTACAA
686248 C
1 C
686249 CAAGTTCTTG
Statistics
Matches: 320, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
322 320 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (322 bp):
CTTATATAAAGAGAGCTTTGGGTCATTATTTTCCACACTTGAATTTAAGAGAAAGTTGTAGAGAG
AAAATTCTCTGAAGAGATTATTTAAGAAAAATTCTAAAGATATTTTTCTTATTTACAACTTTGTC
TAAATTTTAGTGAAATTACAAAATTACCCCACTAGTAATTTTTGTGAATTTTTTATTTTATTTTA
AGCGAGTCCACACTCGAGAGACATGAGCTTGAGGATAGCGAAAAAGACTACTCGGTTGAAGCGTT
CATCCTAGACAAATCGAGAAAGTACAATTTTGATTAAATGTTTATTACTTTAGATATTACAA
Found at i:692996 original size:29 final size:30
Alignment explanation
Indices: 692934--693009 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
692924 TACTTATACT
**
692934 CTTTTAACA-TTT-AAAATTTAGTCTCTTTA
1 CTTTTAA-ATTTTAAAAATTTAGTCTCTCAA
* * *
692963 -TTTTTATTTTTAAAAATTTAGTTTCTCAA
1 CTTTTAAATTTTAAAAATTTAGTCTCTCAA
692992 CTTTTAAATTTTAAAAAT
1 CTTTTAAATTTTAAAAAT
693010 ATAAATTCCA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 8 0.22
29 14 0.38
30 15 0.41
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.54
Consensus pattern (30 bp):
CTTTTAAATTTTAAAAATTTAGTCTCTCAA
Found at i:696203 original size:17 final size:17
Alignment explanation
Indices: 696165--696206 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
696155 TTATATATAT
*
696165 TATA-ATTTAAAAATAA
1 TATATATTTAAAAAGAA
*
696181 TATATATTTAAAAAGAT
1 TATATATTTAAAAAGAA
*
696198 TCTATATTT
1 TATATATTT
696207 TTATAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TATATATTTAAAAAGAA
Found at i:697077 original size:28 final size:27
Alignment explanation
Indices: 697046--697099 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
697036 AACATTTTAT
* *
697046 CTATATCGGTTAATTTTTCTTAAAAGAA
1 CTATATCAGTTAATTTAT-TTAAAAGAA
*
697074 CTATATTAGTTAATTTATTTAAAAGA
1 CTATATCAGTTAATTTATTTAAAAGA
697100 TAAATATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.44
Consensus pattern (27 bp):
CTATATCAGTTAATTTATTTAAAAGAA
Found at i:697106 original size:27 final size:28
Alignment explanation
Indices: 697054--697108 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
697044 ATCTATATCG
* *
697054 GTTAATTTTTCTTAAAAGAACTATATTA
1 GTTAATTTATCTTAAAAGAACAATATTA
697082 GTTAATTTAT-TTAAAAGATA-AATATTA
1 GTTAATTTATCTTAAAAGA-ACAATATTA
697109 AAACTATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (28 bp):
GTTAATTTATCTTAAAAGAACAATATTA
Found at i:699782 original size:21 final size:21
Alignment explanation
Indices: 699756--699802 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
699746 ATTTTTACAT
*
699756 TTTTTACCTTATGCAATTATA
1 TTTTTACCTAATGCAATTATA
* *
699777 TTTTTACCTAATGGAGTTATA
1 TTTTTACCTAATGCAATTATA
699798 TTTTT
1 TTTTT
699803 TTGTCTTGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.55
Consensus pattern (21 bp):
TTTTTACCTAATGCAATTATA
Found at i:705772 original size:21 final size:21
Alignment explanation
Indices: 705742--705783 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
705732 GGAGTGAGCA
*
705742 GTACTTCGCAGCAGGTGGAGT
1 GTACTCCGCAGCAGGTGGAGT
*
705763 GTACTCCGCAGTAGGTGGAGT
1 GTACTCCGCAGCAGGTGGAGT
705784 TTGAGCAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.24
Consensus pattern (21 bp):
GTACTCCGCAGCAGGTGGAGT
Found at i:711220 original size:29 final size:30
Alignment explanation
Indices: 711177--711257 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
711167 GAATTGGATC
711177 AAATCAAAATTTCATGTATAAAATTACACA-
1 AAATCAAAA-TTCATGTATAAAATTACACAT
* *
711207 AAATCAAAATTCATGTATACAATTGCACATT
1 AAATCAAAATTCATGTATAAAATTACACA-T
* *
711238 AAACCATAATTCATGTATAA
1 AAATCAAAATTCATGTATAA
711258 TTTTAAGATT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 18 0.41
30 9 0.20
31 17 0.39
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTCATGTATAAAATTACACAT
Found at i:714512 original size:109 final size:109
Alignment explanation
Indices: 714319--714536 Score: 427
Period size: 109 Copynumber: 2.0 Consensus size: 109
714309 TTACAACTAA
714319 CGGGAAAGAATTTGTCCTTCCCTCACCAAATCAGTAATTAGATGTTGGGCTAGCCAAATTTGCCA
1 CGGGAAAGAATTTGTCCTTCCCTCACCAAATCAGTAATTAGATGTTGGGCTAGCCAAATTTGCCA
*
714384 AACAGCTTTAACTGTTGGCTGGGGTTAGATCACTAGGCTAGGAT
66 AACAGCTTTAACTGCTGGCTGGGGTTAGATCACTAGGCTAGGAT
714428 CGGGAAAGAATTTGTCCTTCCCTCACCAAATCAGTAATTAGATGTTGGGCTAGCCAAATTTGCCA
1 CGGGAAAGAATTTGTCCTTCCCTCACCAAATCAGTAATTAGATGTTGGGCTAGCCAAATTTGCCA
714493 AACAGCTTTAACTGCTGGCTGGGGTTAGATCACTAGGCTAGGAT
66 AACAGCTTTAACTGCTGGCTGGGGTTAGATCACTAGGCTAGGAT
714537 ATCTCTTTTT
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (109 bp):
CGGGAAAGAATTTGTCCTTCCCTCACCAAATCAGTAATTAGATGTTGGGCTAGCCAAATTTGCCA
AACAGCTTTAACTGCTGGCTGGGGTTAGATCACTAGGCTAGGAT
Found at i:718015 original size:24 final size:24
Alignment explanation
Indices: 717983--718070 Score: 151
Period size: 24 Copynumber: 3.7 Consensus size: 24
717973 GAATTTGGTA
717983 GTACTCCTTCCTTC-TTAGGCGTTG
1 GTACTCCTTCC-TCGTTAGGCGTTG
718007 GTACTCCTTCCTCGTTAGGCGTTG
1 GTACTCCTTCCTCGTTAGGCGTTG
718031 GTACTCCTTCCTCGTTAGGCGTTG
1 GTACTCCTTCCTCGTTAGGCGTTG
*
718055 GTACTCTTTCCTCGTT
1 GTACTCCTTCCTCGTT
718071 GATTTATTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
23 2 0.03
24 60 0.97
ACGTcount: A:0.08, C:0.30, G:0.22, T:0.41
Consensus pattern (24 bp):
GTACTCCTTCCTCGTTAGGCGTTG
Found at i:718527 original size:18 final size:17
Alignment explanation
Indices: 718504--718556 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
718494 TTTATGAACT
* *
718504 TTTTTTGAAATTTGTTGA
1 TTTTTTAAAATTTATT-A
718522 TTTTTTAAATATTTATTA
1 TTTTTTAAA-ATTTATTA
*
718540 TTTTTTTAAATTT-TTA
1 TTTTTTAAAATTTATTA
718556 T
1 T
718557 GAATTATTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 4 0.13
17 4 0.13
18 17 0.55
19 6 0.19
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
TTTTTTAAAATTTATTA
Found at i:718527 original size:19 final size:17
Alignment explanation
Indices: 718503--718556 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 17
718493 TTTTATGAAC
*
718503 TTTTTTTGAAATTTGTTGA
1 TTTTTTT-AAATTTATT-A
*
718522 TTTTTTAAATATTTATTA
1 TTTTTTTAA-ATTTATTA
718540 TTTTTTTAAATTT-TTA
1 TTTTTTTAAATTTATTA
718556 T
1 T
718557 GAATTATTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 4 0.13
17 4 0.13
18 11 0.35
19 12 0.39
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (17 bp):
TTTTTTTAAATTTATTA
Found at i:721056 original size:5 final size:5
Alignment explanation
Indices: 721046--721081 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
721036 CTCGAAAGTT
721046 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
721082 CGAATGCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:724590 original size:2 final size:2
Alignment explanation
Indices: 724585--724615 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
724575 TACACCCTTG
*
724585 TA TA TA TA TA TG 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 TA T
724616 GATGTGTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:728318 original size:29 final size:29
Alignment explanation
Indices: 728276--728334 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
728266 AACCCTAACA
728276 CTGGTCCTTGATTGATAGGTAGATAAAAG
1 CTGGTCCTTGATTGATAGGTAGATAAAAG
728305 CTGGTCCTTGATTGATAGGTAGATAAAAG
1 CTGGTCCTTGATTGATAGGTAGATAAAAG
728334 C
1 C
728335 AAAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (29 bp):
CTGGTCCTTGATTGATAGGTAGATAAAAG
Found at i:731700 original size:44 final size:43
Alignment explanation
Indices: 731556--731717 Score: 209
Period size: 43 Copynumber: 3.7 Consensus size: 43
731546 TTGCCGCAAA
* * *
731556 CTTTTGCGGCGCTTTTACCACAAACGCCGCTATAGATCAGGAT
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTATAGATCAAGAC
* *
731599 CTTTAGCGGCGCTTTT-CTAACAAACGCCGCTATAGCTCAAGAC
1 CTTTAGCGGCGCTTTTAC-CACAAACGCCGCTATAGATCAAGAC
*
731642 CTTTAGCGGCGCTTTTACCACAAACGCCACTATAGATCAAAGAC
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTATAGATC-AAGAC
* * **
731686 CTTTAGCGACGCTTTGATTACAAACGCCGCTA
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTA
731718 AAAACACCAT
Statistics
Matches: 103, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
42 1 0.01
43 69 0.67
44 33 0.32
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.26
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTACCACAAACGCCGCTATAGATCAAGAC
Found at i:731810 original size:16 final size:16
Alignment explanation
Indices: 731789--731822 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
731779 AAATATTAAA
*
731789 TATTAAAATCAAACAT
1 TATTAAAATCAAAAAT
*
731805 TATTAATATCAAAAAT
1 TATTAAAATCAAAAAT
731821 TA
1 TA
731823 ATTAGTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTAAAATCAAAAAT
Found at i:732079 original size:15 final size:15
Alignment explanation
Indices: 732059--732088 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
732049 TGGATCATCT
732059 TCATCTTCATCTTCA
1 TCATCTTCATCTTCA
*
732074 TCATCTTCTTCTTCA
1 TCATCTTCATCTTCA
732089 CTTTCAACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (15 bp):
TCATCTTCATCTTCA
Found at i:737265 original size:47 final size:47
Alignment explanation
Indices: 737012--737239 Score: 447
Period size: 47 Copynumber: 4.9 Consensus size: 47
737002 ATACATAGGT
*
737012 TTTTTTAAGTTATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
737059 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
737106 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
737153 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
737200 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAA
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAA
737240 GTTTAATGTT
Statistics
Matches: 180, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 180 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (47 bp):
TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
Found at i:737684 original size:8 final size:7
Alignment explanation
Indices: 737627--737686 Score: 54
Period size: 7 Copynumber: 8.6 Consensus size: 7
737617 AATAAAAAAT
737627 CTAAACC
1 CTAAACC
*
737634 CAAAACC
1 CTAAACC
737641 CT-AACC
1 CTAAACC
*
737647 C--GACC
1 CTAAACC
737652 CTTAAAACC
1 C-T-AAACC
737661 CTAAACC
1 CTAAACC
737668 CTAAACC
1 CTAAACC
737675 CTAAATCC
1 CTAAA-CC
737683 CTAA
1 CTAA
737687 CTCTTAACCA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
5 4 0.09
6 5 0.11
7 24 0.55
8 7 0.16
9 4 0.09
ACGTcount: A:0.42, C:0.42, G:0.02, T:0.15
Consensus pattern (7 bp):
CTAAACC
Found at i:737725 original size:15 final size:15
Alignment explanation
Indices: 737666--737736 Score: 60
Period size: 14 Copynumber: 4.9 Consensus size: 15
737656 AAACCCTAAA
* * *
737666 CCCTAAACCCTAAAT
1 CCCTAAACTCTTAAC
737681 CCCT-AACTCTTAAC
1 CCCTAAACTCTTAAC
**
737695 CAAT-AACGTC-TAAC
1 CCCTAAAC-TCTTAAC
737709 CCCTAAACTCTTAAC
1 CCCTAAACTCTTAAC
737724 CCCTAAAC-CTTAA
1 CCCTAAACTCTTAA
737737 ATCTCGACCA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
14 25 0.54
15 21 0.46
ACGTcount: A:0.37, C:0.38, G:0.01, T:0.24
Consensus pattern (15 bp):
CCCTAAACTCTTAAC
Found at i:737794 original size:15 final size:15
Alignment explanation
Indices: 737759--737796 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
737749 ATCCCTTAAT
737759 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
737773 T-AATCCATAATCCC
1 TAAATCCATAATCCC
737787 TAAATCCATA
1 TAAATCCATA
737797 TATATACTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 12 0.55
15 8 0.36
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:738573 original size:73 final size:73
Alignment explanation
Indices: 738419--738637 Score: 276
Period size: 73 Copynumber: 3.0 Consensus size: 73
738409 AAACATCGCT
* * * * * * *
738419 AAATCCCTGAAAGCGCAAAAAAAGGTGTAGTTTTGGCTTAGGTTTTTTTGCGGCGCTTCCTTAAA
1 AAATCCCCGAAAGCGCACAAAACGGAGTCGTTTTGGCTTAGG-TTTTTTGCGGCGCTTTCTAAAA
* *
738484 AACGCTGCT
65 AACGCCGCA
* * *
738493 AAATCCCCGAAAGCGCACAAAACGGAGTCGTTTTGCCTTATGTTTTTTGCGGTGCTTTCTAAAAA
1 AAATCCCCGAAAGCGCACAAAACGGAGTCGTTTTGGCTTAGGTTTTTTGCGGCGCTTTCTAAAAA
738558 ACGCCGCA
66 ACGCCGCA
* * * **
738566 AAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGATTAGGTTTTTTGCGGCGCTTTCCCAAAA
1 AAATCCCCGAAAGCGCACAAAACGGAGTCGTTTTGGCTTAGGTTTTTTGCGGCGCTTTCTAAAAA
738631 ACGCCGC
66 ACGCCGC
738638 TAAAGCCCTG
Statistics
Matches: 125, Mismatches: 20, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
73 90 0.72
74 35 0.28
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (73 bp):
AAATCCCCGAAAGCGCACAAAACGGAGTCGTTTTGGCTTAGGTTTTTTGCGGCGCTTTCTAAAAA
ACGCCGCA
Found at i:738672 original size:114 final size:114
Alignment explanation
Indices: 738541--738869 Score: 482
Period size: 115 Copynumber: 2.9 Consensus size: 114
738531 TATGTTTTTT
* * * *
738541 GCGGTGCTTTCTAAAAAACGCCGCAAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGATTA
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACTGCGTCGTTTTGGATTA
*
738606 GGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTA
66 GGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* ** *
738655 GCGGCGCTTTCTTAAAAACGCCGCTAAACCCCCGAAAGCTCACAAAAACTGCGAGGTTTTACG-T
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAC-AAAACTGCGTCGTTTT-GGAT
* *
738719 TAGGTTTTTTGCGGCGCTATCTCAAAAACGCCGCTAAAGCCGTGAGCATTA
64 TAGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* ** * *
738770 GCGGCGCTTCCTTAAAAATACCGCTAAATCCAC-AAAGCTCACAAAACTGCATCGTTTTGGATTA
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACTGCGTCGTTTTGGATTA
738834 GGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAA
66 GGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAA
738870 TCCACAAAGC
Statistics
Matches: 191, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
112 1 0.01
113 51 0.27
114 48 0.25
115 90 0.47
116 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.25
Consensus pattern (114 bp):
GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACTGCGTCGTTTTGGATTA
GGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:738887 original size:72 final size:72
Alignment explanation
Indices: 738770--738941 Score: 299
Period size: 72 Copynumber: 2.4 Consensus size: 72
738760 GTGAGCATTA
* * *
738770 GCGGCGCTTCCTTAAAAATACCGCTAAATCCACAAAGCTCACAAAACTGCATCGTTTTGGATTAG
1 GCGGCGCTTTCTCAAAAATGCCGCTAAATCCACAAAGCTCACAAAACTGCATCGTTTTGGATTAG
738835 GTTTTTT
66 GTTTTTT
* *
738842 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCACAAAGCTCACAAAACTGCGTCGTTTTGGATTAG
1 GCGGCGCTTTCTCAAAAATGCCGCTAAATCCACAAAGCTCACAAAACTGCATCGTTTTGGATTAG
738907 GTTTTTT
66 GTTTTTT
738914 GCGGCGCTTTCTCAAAAATGCCGCTAAA
1 GCGGCGCTTTCTCAAAAATGCCGCTAAA
738942 GCCCTAAGCA
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 94 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (72 bp):
GCGGCGCTTTCTCAAAAATGCCGCTAAATCCACAAAGCTCACAAAACTGCATCGTTTTGGATTAG
GTTTTTT
Found at i:738920 original size:185 final size:187
Alignment explanation
Indices: 738655--739048 Score: 605
Period size: 185 Copynumber: 2.1 Consensus size: 187
738645 CTGAGCATTA
* * *
738655 GCGGCGCTTTCTTAAAAACGCCGCTAAACCCCCGAAAGCTCACAAAAACTGCGAGGTTTTACGTT
1 GCGGCGCTTTCTAAAAAACGCCGCTAAACCCACGAAAGCTCACAAAAACTGCGACGTTTTACGTT
* *
738720 AGGTTTTTTGCGGCGCTATCTCAAAAACGCCGCTAAAGCCGTGAGCATTAGCGGCGCTTCCTTAA
66 AGGTTTTTTGCGGCGCTATCTCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCCTTAA
*
738785 AAATACCGCTAAATCCACAAAGCTCACAAAACTGCATCGTTTTGGATTAGGTTTTTT
131 AAACACCGCTAAATCCACAAAGCTCACAAAACTGCATCGTTTTGGATTAGGTTTTTT
* * * *
738842 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCAC-AAAGCTCAC-AAAACTGCGTCGTTTT-GGAT
1 GCGGCGCTTTCTAAAAAACGCCGCTAAACCCACGAAAGCTCACAAAAACTGCGACGTTTTACG-T
* *
738904 TAGGTTTTTTGCGGCGCTTTCTCAAAAATGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCCTTA
65 TAGGTTTTTTGCGGCGCTATCTCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCCTTA
** * *
738969 AAAACGTCGCTAAATCCACAAAGCTCACAAAACTGCGTCGTTTTGGATTCGGTTTTTT
130 AAAACACCGCTAAATCCACAAAGCTCACAAAACTGCATCGTTTTGGATTAGGTTTTTT
*
739027 GCGGCGCTTTTTAAAAAACGCC
1 GCGGCGCTTTCTAAAAAACGCC
739049 ACTATTGCTT
Statistics
Matches: 189, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
184 1 0.01
185 149 0.79
186 9 0.05
187 30 0.16
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (187 bp):
GCGGCGCTTTCTAAAAAACGCCGCTAAACCCACGAAAGCTCACAAAAACTGCGACGTTTTACGTT
AGGTTTTTTGCGGCGCTATCTCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCCTTAA
AAACACCGCTAAATCCACAAAGCTCACAAAACTGCATCGTTTTGGATTAGGTTTTTT
Found at i:739139 original size:12 final size:12
Alignment explanation
Indices: 739122--739147 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
739112 TTTTTTATTC
739122 AAACGCCGCTAA
1 AAACGCCGCTAA
739134 AAACGCCGCTAA
1 AAACGCCGCTAA
739146 AA
1 AA
739148 GCCGGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:743000 original size:21 final size:21
Alignment explanation
Indices: 742961--743027 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
742951 CAATATTCAT
742961 TTCAAT-TCAAATAATCAATATA
1 TTCAATAT-AAAT-ATCAATATA
*
742983 TTCAATATATATATCAAT-TCA
1 TTCAATATAAATATCAATAT-A
* *
743004 ATCAATATAAAT-TCAATAAA
1 TTCAATATAAATATCAATATA
743024 TTCA
1 TTCA
743028 TCACATACTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
20 10 0.27
21 17 0.46
22 9 0.24
23 1 0.03
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.37
Consensus pattern (21 bp):
TTCAATATAAATATCAATATA
Found at i:743043 original size:24 final size:24
Alignment explanation
Indices: 742998--743044 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
742988 TATATATATC
742998 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
743022 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
743045 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:743719 original size:11 final size:11
Alignment explanation
Indices: 743688--743779 Score: 51
Period size: 11 Copynumber: 7.9 Consensus size: 11
743678 AAGCCCTTAA
743688 CTTTTGTCTTTC
1 CTTTT-TCTTTC
*
743700 TCCTTTTCTTTC
1 -CTTTTTCTTTC
743712 CTTTTTC-TTC
1 CTTTTTCTTTC
*
743722 CTTTTTTTTTC
1 CTTTTTCTTTC
* * *
743733 CCTTGTGTTTC
1 CTTTTTCTTTC
*
743744 GTTTGTTCTTTC
1 CTTT-TTCTTTC
* *
743756 TTTCTTTTCTATTT
1 -CT-TTTTCT-TTC
743770 CTTTTTCTTT
1 CTTTTTCTTT
743780 TATTTTATTA
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
10 9 0.15
11 21 0.34
12 17 0.28
13 10 0.16
14 4 0.07
ACGTcount: A:0.01, C:0.23, G:0.05, T:0.71
Consensus pattern (11 bp):
CTTTTTCTTTC
Found at i:747214 original size:21 final size:21
Alignment explanation
Indices: 747158--747226 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 21
747148 ATTATAAATG
*
747158 TTTTATAATATTA-TTTTT-AA
1 TTTTA-AATATAATTTTTTAAA
*
747178 TTTTAAATA-GATTTTTTAAA
1 TTTTAAATATAATTTTTTAAA
747198 TTTTAAATATAATTTTTTAATA
1 TTTTAAATATAATTTTTTAA-A
*
747220 TTATAAA
1 TTTTAAA
747227 ACATTTAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 1 0.02
19 9 0.21
20 16 0.38
21 9 0.21
22 7 0.17
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (21 bp):
TTTTAAATATAATTTTTTAAA
Found at i:747232 original size:20 final size:20
Alignment explanation
Indices: 747171--747226 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
747161 TATAATATTA
*
747171 TTTTTAAT-TTTAAATAGAT
1 TTTTTAATATTTAAATAAAT
747190 TTTTTAA-ATTTTAAATATAAT
1 TTTTTAATA-TTTAAATA-AAT
747211 TTTTTAATATTATAAA
1 TTTTTAATATT-TAAA
747227 ACATTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 7 0.23
20 8 0.26
21 11 0.35
22 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTTAATATTTAAATAAAT
Found at i:747655 original size:22 final size:22
Alignment explanation
Indices: 747623--747687 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 22
747613 NNNATTTAAA
*
747623 ATTAAAAAATAATATTATAAAAT
1 ATTATAAAATAA-ATTATAAAAT
747646 ATT-TAAAATATACATT-TAAAAT
1 ATTATAAAATA-A-ATTATAAAAT
*
747668 ATTATAAAATAAATAATAAA
1 ATTATAAAATAAATTATAAA
747688 CAAACAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.06
22 20 0.56
23 14 0.39
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
ATTATAAAATAAATTATAAAAT
Found at i:747675 original size:23 final size:22
Alignment explanation
Indices: 747616--747679 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
747606 NNNNNNNNNN
* *
747616 ATTT-AAA-ATTAAAAAATAAT
1 ATTTAAAATATTATAAAATAAC
747636 ATTATAAAATATT-TAAAATATAC
1 ATT-TAAAATATTATAAAATA-AC
747659 ATTTAAAATATTATAAAATAA
1 ATTTAAAATATTATAAAATAA
747680 ATAATAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 3 0.08
21 1 0.03
22 19 0.51
23 14 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTTAAAATATTATAAAATAAC
Found at i:747723 original size:14 final size:15
Alignment explanation
Indices: 747673--747733 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 15
747663 AAAATATTAT
747673 AAAATAAATAATA-AA
1 AAAATAAATAA-AGAA
* *
747688 CAAACAAATAAA-AA
1 AAAATAAATAAAGAA
*
747702 AAAATAAA-AATGAA
1 AAAATAAATAAAGAA
*
747716 AAAGTAAATAAAGAA
1 AAAATAAATAAAGAA
747731 AAA
1 AAA
747734 CAAATAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
13 2 0.05
14 18 0.49
15 17 0.46
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (15 bp):
AAAATAAATAAAGAA
Found at i:747724 original size:18 final size:17
Alignment explanation
Indices: 747693--747775 Score: 81
Period size: 16 Copynumber: 5.2 Consensus size: 17
747683 ATAAACAAAC
*
747693 AAAT-AAAAAAAAATAA
1 AAATGAAAAACAAATAA
*
747709 AAATGAAAAAGTAAAT--
1 AAATGAAAAA-CAAATAA
747725 AAA-GAAAAACAAAT-A
1 AAATGAAAAACAAATAA
747740 AAATGAAAAA-AACA-AA
1 AAATGAAAAACAA-ATAA
747756 AAATGAAAAACAAATAA
1 AAATGAAAAACAAATAA
747773 AAA
1 AAA
747776 AATCAGAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
14 4 0.07
15 11 0.19
16 26 0.46
17 12 0.21
18 4 0.07
ACGTcount: A:0.80, C:0.04, G:0.06, T:0.11
Consensus pattern (17 bp):
AAATGAAAAACAAATAA
Found at i:747725 original size:47 final size:46
Alignment explanation
Indices: 747674--747777 Score: 124
Period size: 47 Copynumber: 2.3 Consensus size: 46
747664 AAATATTATA
* * *
747674 AAATAAATAATAAACAAA-CAAAT-AAAAAAAAATAAAAATGAAAAAGT
1 AAATAAAGAA-AAACAAATAAAATGAAAAAAAAA-AAAAATGAAAAA-C
*
747721 AAATAAAGAAAAACAAATAAAATGAAAAAAACAAAAAATGAAAAAC
1 AAATAAAGAAAAACAAATAAAATGAAAAAAAAAAAAAATGAAAAAC
747767 AAATAAA-AAAA
1 AAATAAAGAAAA
747778 TCAGAAAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
45 4 0.08
46 14 0.27
47 25 0.49
48 8 0.16
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.12
Consensus pattern (46 bp):
AAATAAAGAAAAACAAATAAAATGAAAAAAAAAAAAAATGAAAAAC
Found at i:747738 original size:14 final size:14
Alignment explanation
Indices: 747689--747777 Score: 67
Period size: 14 Copynumber: 6.1 Consensus size: 14
747679 AATAATAAAC
*
747689 AAACAAATAAAAAA
1 AAACAAATAAAGAA
* *
747703 AAATAAA-AATGAA
1 AAACAAATAAAGAA
*
747716 AAAGTAAATAAAGAA
1 AAA-CAAATAAAGAA
747731 AAACAAATAAAATGAAAA
1 AAACAAAT-AAA-G--AA
747749 AAACAAA-AAATGAA
1 AAACAAATAAA-GAA
747763 AAACAAATAAA-AA
1 AAACAAATAAAGAA
747776 AA
1 AA
747778 TCAGAAAAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
13 11 0.17
14 23 0.37
15 14 0.22
16 6 0.10
18 9 0.14
ACGTcount: A:0.80, C:0.04, G:0.06, T:0.10
Consensus pattern (14 bp):
AAACAAATAAAGAA
Found at i:747739 original size:32 final size:33
Alignment explanation
Indices: 747685--747775 Score: 109
Period size: 32 Copynumber: 2.8 Consensus size: 33
747675 AATAAATAAT
*
747685 AAACAAACAAAT-AAAAAAAAATAAAAATGAAAA
1 AAACAAA-AAATGAAAAACAAATAAAAATGAAAA
* *
747718 AGTA-AATAAA-GAAAAACAAAT-AAAATGAAAA
1 A-AACAAAAAATGAAAAACAAATAAAAATGAAAA
747749 AAACAAAAAATGAAAAACAAATAAAAA
1 AAACAAAAAATGAAAAACAAATAAAAA
747776 AATCAGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
30 1 0.02
31 16 0.33
32 23 0.48
33 7 0.15
34 1 0.02
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.10
Consensus pattern (33 bp):
AAACAAAAAATGAAAAACAAATAAAAATGAAAA
Found at i:748380 original size:6 final size:6
Alignment explanation
Indices: 748346--748378 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
748336 ATCGTCTTTT
*
748346 TATTTA TATTTA TATTTA TATTTA TATATA TAT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TAT
748379 ATTTTGTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
TATTTA
Found at i:748872 original size:24 final size:23
Alignment explanation
Indices: 748843--748889 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
748833 ATGTACATTC
* *
748843 GCATATTTTATATGTCATATATAT
1 GCATATTTAATATAT-ATATATAT
748867 GCATATTTAATATATATATATAT
1 GCATATTTAATATATATATATAT
748890 ATATTAAGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.49
Consensus pattern (23 bp):
GCATATTTAATATATATATATAT
Found at i:751278 original size:29 final size:28
Alignment explanation
Indices: 751235--751297 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
751225 TTTGTTGAGC
* *
751235 TCTGGCTGTATATTTGCAATTACTAGAGT
1 TCTGGCGGTAAATTTGCAATTAC-AGAGT
* *
751264 TCTGGCGGTAAATTTGCAATTTCGGAGT
1 TCTGGCGGTAAATTTGCAATTACAGAGT
751292 TCTGGC
1 TCTGGC
751298 AATTTGTTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 10 0.33
29 20 0.67
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (28 bp):
TCTGGCGGTAAATTTGCAATTACAGAGT
Found at i:754034 original size:9 final size:9
Alignment explanation
Indices: 754014--754082 Score: 93
Period size: 9 Copynumber: 7.7 Consensus size: 9
754004 TTTAATTAAA
*
754014 AATTAACTG
1 AATTAACCG
*
754023 AATTACCCG
1 AATTAACCG
754032 AATTAACCG
1 AATTAACCG
*
754041 AATTAACCA
1 AATTAACCG
754050 AATTAACCG
1 AATTAACCG
* *
754059 GATTACCCG
1 AATTAACCG
754068 AATTAACCG
1 AATTAACCG
754077 AATTAA
1 AATTAA
754083 ATCACTACAT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:757978 original size:72 final size:71
Alignment explanation
Indices: 757777--757978 Score: 262
Period size: 72 Copynumber: 2.8 Consensus size: 71
757767 CACTGCATAA
* * *
757777 CCCATGACATGGGCTTGAAGTACTTGCCACCCAGGGGATTGTACTGGAGCTGGTGAATACTGCAA
1 CCCATGACATGGGC-TGAAGTGCTTGCCACCCAGGGGATTGTACAGGAGCTGATGAATACTGCAA
**
757842 GCCTTGC
65 GCCAGGC
* * *
757849 CCCATGACATGGGCTCGAACTGCTTGCCACCCAGGGGATTGTACAGGCGC-CAGTGAATACTGCA
1 CCCATGACATGGGCT-GAAGTGCTTGCCACCCAGGGGATTGTACAGGAGCTGA-TGAATACTGCA
757913 AGCCAGGC
64 AGCCAGGC
* * *
757921 CCCGTGACATGGGCATGAAGTGCTTGCCACCCCGGGGATTGTGCAGGAGCTGATGAAT
1 CCCATGACATGGGC-TGAAGTGCTTGCCACCCAGGGGATTGTACAGGAGCTGATGAAT
757979 GGGTTGCTAC
Statistics
Matches: 112, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
71 1 0.01
72 109 0.97
73 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.31, T:0.20
Consensus pattern (71 bp):
CCCATGACATGGGCTGAAGTGCTTGCCACCCAGGGGATTGTACAGGAGCTGATGAATACTGCAAG
CCAGGC
Found at i:759908 original size:159 final size:159
Alignment explanation
Indices: 759611--760092 Score: 660
Period size: 159 Copynumber: 3.0 Consensus size: 159
759601 GAAATTCTCT
* * * *
759611 TGCGATCAACATGCTTTTGAGATTCTTTACCATTTCCATTATTTCTTCTTTCCCCATAATTGTTT
1 TGCGACCACCATGTTTTTGAGATTCTTTACCATTTCCATTATTTCTTCTTTCCCCATAACTGTTT
* ** *
759676 CCTGAATCCCTTTCATCACTTGC-TCCACTAAATCCAGATCTCTCAGTGCTGCGTTGTTCATAGA
66 CCTGAATCTCTTTCATCAC-TGCTTCCACTAAATCCAGATCTCTCAACGCTGCGTTGTTCAAAGA
* * *
759740 TATCTGAAGAAAGCATTTTATGAAGGCCAC
130 TTTCTGAAGAAAGCATTCTGTGAAGGCCAC
* ** * * * * * **
759770 TGCGATCACTGTGTTTTTGAGATTTTTTAACATTTCCAATATTTCTCCTTTCACCATAACCATTT
1 TGCGACCACCATGTTTTTGAGATTCTTTACCATTTCCATTATTTCTTCTTTCCCCATAACTGTTT
* *
759835 CCTGAATCTCTTTCATCACTGCTTCCACTAAATCCAGATTTCTCAACACTGCGTTGTTCAAAGAT
66 CCTGAATCTCTTTCATCACTGCTTCCACTAAATCCAGATCTCTCAACGCTGCGTTGTTCAAAGAT
*
759900 TTCAGAAGAAAGCATTCTGTGAAGGCCAC
131 TTCTGAAGAAAGCATTCTGTGAAGGCCAC
* * * *
759929 CGTGACCACCATGTTTTTCAGATTCTTTACCATTTCCATTATTTCTTCTTTCCCCATAACTGCTT
1 TGCGACCACCATGTTTTTGAGATTCTTTACCATTTCCATTATTTCTTCTTTCCCCATAACTGTTT
* **
759994 CCTGAATCTCTTTCATCACTTCTTCCAGAAAATCCAGATCTCTCAACGCTGCGTTGTTCAAAGAT
66 CCTGAATCTCTTTCATCACTGCTTCCACTAAATCCAGATCTCTCAACGCTGCGTTGTTCAAAGAT
*
760059 TTCTGAAGAAAGTATTCTGTGAAGGCCAC
131 TTCTGAAGAAAGCATTCTGTGAAGGCCAC
760088 TGCGA
1 TGCGA
760093 GGAGTAAAAG
Statistics
Matches: 277, Mismatches: 45, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
158 3 0.01
159 274 0.99
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.37
Consensus pattern (159 bp):
TGCGACCACCATGTTTTTGAGATTCTTTACCATTTCCATTATTTCTTCTTTCCCCATAACTGTTT
CCTGAATCTCTTTCATCACTGCTTCCACTAAATCCAGATCTCTCAACGCTGCGTTGTTCAAAGAT
TTCTGAAGAAAGCATTCTGTGAAGGCCAC
Found at i:761213 original size:4 final size:4
Alignment explanation
Indices: 761204--761262 Score: 118
Period size: 4 Copynumber: 14.8 Consensus size: 4
761194 TAGCCATTGC
761204 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
761252 ACAT ACAT ACA
1 ACAT ACAT ACA
761263 ATAAGAAACA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:777975 original size:103 final size:98
Alignment explanation
Indices: 777781--778007 Score: 260
Period size: 103 Copynumber: 2.3 Consensus size: 98
777771 AGTTCATGTG
* *
777781 AATAGTTGCAGATTAAATTTTCCAACAACAATAATAACAATCATAAAACAAAATTGAGCAGCAAA
1 AATAATTGCAGATTAGATTTTCCAACAACAATAATAACAATCATAAAACAAAATTGAGCAGCAAA
*
777846 CTTACTTCGCACATCAAAACACTAAGTTCATACA
66 CTTACTTCGCACACCAAAACACTAAGTTCATA-A
* *
777880 AATAATTGCAAATTAGATTTTCCAACAATC-ATAATAAACAAATACATAAAA-AGGCAATTGAGC
1 AATAATTGCAGATTAGATTTTCCAACAA-CAATAAT-AAC-AAT-CATAAAACA--AAATTGAGC
* * * * *
777943 AGCAAACTTGCTTTGCACACCGAACCGCTAAGTTCATAA
60 AGCAAACTTACTTCGCACACCAAAACACTAAGTTCATAA
* *
777982 AAAAGATTGCAGATTAGATTTCCCAA
1 AATA-ATTGCAGATTAGATTTTCCAA
778008 AAACGATTTT
Statistics
Matches: 108, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
99 30 0.28
100 4 0.04
101 4 0.04
102 11 0.10
103 59 0.55
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.25
Consensus pattern (98 bp):
AATAATTGCAGATTAGATTTTCCAACAACAATAATAACAATCATAAAACAAAATTGAGCAGCAAA
CTTACTTCGCACACCAAAACACTAAGTTCATAA
Found at i:778691 original size:7 final size:7
Alignment explanation
Indices: 778675--778711 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
778665 GACAGAGAGT
778675 AATC-GC
1 AATCGGC
778681 AATCGGC
1 AATCGGC
778688 AATCGGC
1 AATCGGC
778695 AATCGGC
1 AATCGGC
778702 AATCGGC
1 AATCGGC
778709 AAT
1 AAT
778712 TCAAGTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.13
7 26 0.87
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.16
Consensus pattern (7 bp):
AATCGGC
Found at i:779016 original size:78 final size:79
Alignment explanation
Indices: 778911--779060 Score: 223
Period size: 78 Copynumber: 1.9 Consensus size: 79
778901 AATTCTCCTA
**
778911 CTTTTTCAATTTAAAAATCATACTCCAATCATTATCGTTGTTGGTAGA-TTTTGTTAAAATTTAT
1 CTTTTTCAATTTAAAAATCATACTCCAATCATTATCGTCATTGGTA-ATTTTTGTTAAAATTTAT
778975 CAACTTAATATGTTT
65 CAACTTAATATGTTT
* * *
778990 CTTTTT-AATTTAAAAATCCTAGTCCAATCATTATTGTCATTGGTAATTTTTGTTAAAATTTATC
1 CTTTTTCAATTTAAAAATCATACTCCAATCATTATCGTCATTGGTAATTTTTGTTAAAATTTATC
*
779054 AATTTAA
66 AACTTAA
779061 CATATTTATT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
77 1 0.02
78 57 0.89
79 6 0.09
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (79 bp):
CTTTTTCAATTTAAAAATCATACTCCAATCATTATCGTCATTGGTAATTTTTGTTAAAATTTATC
AACTTAATATGTTT
Found at i:779476 original size:14 final size:14
Alignment explanation
Indices: 779457--779504 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
779447 TAAATGATAT
779457 TTTTTTTTACATAA
1 TTTTTTTTACATAA
* * *
779471 TTTTTTTAATAAAA
1 TTTTTTTTACATAA
**
779485 TTACTTTTACATAA
1 TTTTTTTTACATAA
779499 TTTTTT
1 TTTTTT
779505 CTCACTTATG
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTTTTTACATAA
Found at i:779529 original size:86 final size:87
Alignment explanation
Indices: 779428--779600 Score: 339
Period size: 86 Copynumber: 2.0 Consensus size: 87
779418 GAGTTACTAA
779428 TTTTTAATTCACATTCATTTAAATGATATTTTTTTTTACATAATTTTTTTAATAAAATTACTTTT
1 TTTTTAATTCACATTCATTTAAATGATATTTTTTTTTACATAATTTTTTTAATAAAATTACTTTT
779493 ACATAATTTTTTCTCACTTATG
66 ACATAATTTTTTCTCACTTATG
779515 TTTTTAATTC-CATTCATTTAAATGATATTTTTTTTTACATAATTTTTTTAATAAAATTACTTTT
1 TTTTTAATTCACATTCATTTAAATGATATTTTTTTTTACATAATTTTTTTAATAAAATTACTTTT
779579 ACATAATTTTTTCTCACTTATG
66 ACATAATTTTTTCTCACTTATG
779601 GGTATAACAT
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
86 76 0.88
87 10 0.12
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.57
Consensus pattern (87 bp):
TTTTTAATTCACATTCATTTAAATGATATTTTTTTTTACATAATTTTTTTAATAAAATTACTTTT
ACATAATTTTTTCTCACTTATG
Found at i:779562 original size:14 final size:14
Alignment explanation
Indices: 779543--779590 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
779533 TAAATGATAT
779543 TTTTTTTTACATAA
1 TTTTTTTTACATAA
* * *
779557 TTTTTTTAATAAAA
1 TTTTTTTTACATAA
**
779571 TTACTTTTACATAA
1 TTTTTTTTACATAA
779585 TTTTTT
1 TTTTTT
779591 CTCACTTATG
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTTTTTACATAA
Found at i:780087 original size:12 final size:12
Alignment explanation
Indices: 780064--780100 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
780054 TTTTTGCAAC
780064 TATTTTTGTTGT
1 TATTTTTGTTGT
*
780076 TATTTTTATTGT
1 TATTTTTGTTGT
*
780088 TGTTTTTGTTGT
1 TATTTTTGTTGT
780100 T
1 T
780101 TGGCAGTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.08, C:0.00, G:0.16, T:0.76
Consensus pattern (12 bp):
TATTTTTGTTGT
Found at i:780101 original size:56 final size:56
Alignment explanation
Indices: 780018--780150 Score: 135
Period size: 56 Copynumber: 2.4 Consensus size: 56
780008 AAAATTATCT
* * * * *
780018 TGTTGTTTTGTTGTTGTTATTGGTGTTTTGG-TGTT-ATTTTTGCAACTATTTTTGT
1 TGTTTTTTTATTGTTGTTTTTGGTG-TTTGGCAGTTGATTTTTGCAACTATTTTTGA
* * * *
780073 TGTTATTTTTATTGTTGTTTTTGTTGTTTGGCAGTTGTTTTTTGCTACTGTTTTTGA
1 TGTT-TTTTTATTGTTGTTTTTGGTGTTTGGCAGTTGATTTTTGCAACTATTTTTGA
* *
780130 TGTTTTTTCATTGTCGTTTTT
1 TGTTTTTTTATTGTTGTTTTT
780151 AATATTATTT
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
55 9 0.14
56 35 0.55
57 20 0.31
ACGTcount: A:0.08, C:0.05, G:0.21, T:0.65
Consensus pattern (56 bp):
TGTTTTTTTATTGTTGTTTTTGGTGTTTGGCAGTTGATTTTTGCAACTATTTTTGA
Found at i:780586 original size:30 final size:30
Alignment explanation
Indices: 780541--780603 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
780531 ACTTAACAAG
*
780541 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTTAAAAATAATAACAAAATTAA
*
780571 CAAATGTCTTAAAAATAATAACAAAATTAA
1 CAAATGCCTTAAAAATAATAACAAAATTAA
780601 CAA
1 CAA
780604 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.59, C:0.13, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTTAAAAATAATAACAAAATTAA
Found at i:785157 original size:3 final size:3
Alignment explanation
Indices: 785149--785177 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
785139 TTTGATCTAT
785149 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
785178 CTGGGGGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:786990 original size:21 final size:19
Alignment explanation
Indices: 786962--787001 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
786952 TTGTGTTTGG
*
786962 TAAAT-ATATTAACCTTTT
1 TAAATAATATAAACCTTTT
786980 TAAATAATATAAACCTTTT
1 TAAATAATATAAACCTTTT
786999 TAA
1 TAA
787002 GTGTTTGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAATAATATAAACCTTTT
Found at i:787812 original size:14 final size:14
Alignment explanation
Indices: 787793--787840 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
787783 TAAGTAAAAA
787793 ATAATATAAATTTT
1 ATAATATAAATTTT
*
787807 ATAATATATAACCTTT
1 ATAATATA-AA-TTTT
787823 ATAA-ATAAGATTTT
1 ATAATATAA-ATTTT
787837 ATAA
1 ATAA
787841 ATTGTCCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 16 0.55
15 6 0.21
16 7 0.24
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (14 bp):
ATAATATAAATTTT
Found at i:787817 original size:16 final size:15
Alignment explanation
Indices: 787795--787842 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 15
787785 AGTAAAAAAT
787795 AATATAAATTTTATA
1 AATATAAATTTTATA
**
787810 ATATATAACCTTTATA
1 A-ATATAAATTTTATA
*
787826 AATA-AGATTTTATA
1 AATATAAATTTTATA
787840 AAT
1 AAT
787843 TGTCCAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 10 0.37
15 4 0.15
16 13 0.48
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (15 bp):
AATATAAATTTTATA
Found at i:789973 original size:17 final size:17
Alignment explanation
Indices: 789938--789997 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 17
789928 GAAAACGTTT
* *
789938 AATATTGTT-TCTAAAA
1 AATATTTTTATCTCAAA
789954 AATATTTTTATCTCAAA
1 AATATTTTTATCTCAAA
* ***
789971 AATACTTTTAAGACAAA
1 AATATTTTTATCTCAAA
789988 AATATTTTTA
1 AATATTTTTA
789998 AATAAGTTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
16 8 0.22
17 28 0.78
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (17 bp):
AATATTTTTATCTCAAA
Found at i:789998 original size:17 final size:17
Alignment explanation
Indices: 789951--789998 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
789941 ATTGTTTCTA
* *
789951 AAAAATATTTTTATCTC
1 AAAAATATTTTTAACAC
* *
789968 AAAAATACTTTTAAGAC
1 AAAAATATTTTTAACAC
789985 AAAAATATTTTTAA
1 AAAAATATTTTTAA
789999 ATAAGTTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (17 bp):
AAAAATATTTTTAACAC
Found at i:791721 original size:21 final size:20
Alignment explanation
Indices: 791683--791721 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
791673 TATAATTCGA
**
791683 ATTTAAATTAATTTTAAATT
1 ATTTAAATTAATCATAAATT
791703 ATTTAAATTTAATCATAAA
1 ATTTAAA-TTAATCATAAA
791722 AATAACAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTAAATTAATCATAAATT
Found at i:810704 original size:29 final size:30
Alignment explanation
Indices: 810626--810710 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 30
810616 GATTAAATCA
* * *
810626 AAATTGAAGTTTCAAGTATATATTTGAACC
1 AAATTAAAGTTTCAAGTATACAATTGAACC
* * *
810656 ATAATTAGAGTTTCACGTATACAATTGCACC
1 A-AATTAAAGTTTCAAGTATACAATTGAACC
*
810687 AAATTAAAG-TTCATGTATACAATT
1 AAATTAAAGTTTCAAGTATACAATT
810711 ACACATTGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 14 0.30
30 8 0.17
31 24 0.52
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATACAATTGAACC
Found at i:814884 original size:15 final size:14
Alignment explanation
Indices: 814861--814891 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
814851 AGAGATAACT
814861 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
814875 AAAAAGGAAAAAAAG
1 AAAAA-GAAAAAAAG
814890 AA
1 AA
814892 TAAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:821116 original size:30 final size:29
Alignment explanation
Indices: 821038--821116 Score: 72
Period size: 30 Copynumber: 2.7 Consensus size: 29
821028 TTAATTTTTC
* *
821038 TTTTTAAAAACTTTAATTAGACCCACAATT
1 TTTTTAAAAA-TTTAATTAAACCCACAATA
* *
821068 TTTTTAAAAAATTCATTAAACTCCTA-AA-A
1 TTTTTAAAAATTTAATTAAAC-CC-ACAATA
821097 TTTTTAAAAATTTTAATTAA
1 TTTTTAAAAA-TTTAATTAA
821117 CCCGAAAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
29 18 0.45
30 21 0.52
31 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.01, T:0.43
Consensus pattern (29 bp):
TTTTTAAAAATTTAATTAAACCCACAATA
Found at i:822207 original size:59 final size:60
Alignment explanation
Indices: 822103--822276 Score: 242
Period size: 59 Copynumber: 2.9 Consensus size: 60
822093 TTAATATAAT
* * *
822103 ATTTAGTACCTGAATTTGACACTTTTTCTTAATTTGGTACTTAAACTTTTTTT-GGCCCA
1 ATTTGGTACCTGAATTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGGGCCCA
* * *
822162 ATTTGGTACTTGAATTTGACACTTTTTCCTAATTTGATACCTAAACTTTTTTTGGGCTCA
1 ATTTGGTACCTGAATTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGGGCCCA
* * *
822222 ATTTGGTACCTGAACTTGACATTTTTTTCCCTAATTTGGTACCTAAGCTTTTTTT
1 ATTTGGTACCTGAATTTGACA-CTTTTT-CCTAATTTGGTACCTAAACTTTTTTT
822277 TTAGGTTCAA
Statistics
Matches: 101, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
59 48 0.48
60 24 0.24
61 5 0.05
62 24 0.24
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.48
Consensus pattern (60 bp):
ATTTGGTACCTGAATTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGGGCCCA
Found at i:826709 original size:21 final size:18
Alignment explanation
Indices: 826656--826715 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
826646 ATGGCTTTTA
*
826656 AATAATTTTTTAAATTAAGT
1 AATAATATTTT-AA-TAAGT
826676 AATAATATTTTAATAAGT
1 AATAATATTTTAATAAGT
* *
826694 AATAATATTTTATTAATT
1 AATAATATTTTAATAAGT
826712 AATA
1 AATA
826716 TTATAAAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 25 0.68
19 2 0.05
20 10 0.27
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (18 bp):
AATAATATTTTAATAAGT
Found at i:830141 original size:37 final size:37
Alignment explanation
Indices: 830091--830166 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
830081 GATGTATTAA
*
830091 TTCAAGAAAGGACTAAATTGTAAAAGTGAGAAAAGTT
1 TTCAAAAAAGGACTAAATTGTAAAAGTGAGAAAAGTT
830128 TTCAAAAAAGGACTAAATTGTAAAAGTGAGAAAAGTT
1 TTCAAAAAAGGACTAAATTGTAAAAGTGAGAAAAGTT
830165 TT
1 TT
830167 ATGGTCCAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.26
Consensus pattern (37 bp):
TTCAAAAAAGGACTAAATTGTAAAAGTGAGAAAAGTT
Found at i:832003 original size:25 final size:25
Alignment explanation
Indices: 831947--832003 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
831937 CCTTAGCGCA
*
831947 CTCTCTGATTATTAGCACGTTAGTG
1 CTCTCTGATTATTAGCACATTAGTG
*
831972 CTATCTGATTATTAGCACATTAGTG
1 CTCTCTGATTATTAGCACATTAGTG
*
831997 TTCTCTG
1 CTCTCTG
832004 TTCAATAGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (25 bp):
CTCTCTGATTATTAGCACATTAGTG
Found at i:839100 original size:17 final size:18
Alignment explanation
Indices: 839078--839112 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
839068 TTACATTTTG
*
839078 GTTATTTAATT-TTAAAA
1 GTTATTAAATTGTTAAAA
839095 GTTATTAAATTGTTAAAA
1 GTTATTAAATTGTTAAAA
839113 TTGTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (18 bp):
GTTATTAAATTGTTAAAA
Found at i:839448 original size:31 final size:31
Alignment explanation
Indices: 839408--839475 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
839398 CTTAATAGCC
* * *
839408 CAATGACTTAAATAAAAACTTTCAAATAGTT
1 CAATTACTTAAATAAAAACATTCAAATAATT
** *
839439 CAATTACTTAAATGTAAACATTCGAATAATT
1 CAATTACTTAAATAAAAACATTCAAATAATT
839470 CAATTA
1 CAATTA
839476 TCATTTTGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (31 bp):
CAATTACTTAAATAAAAACATTCAAATAATT
Found at i:844425 original size:17 final size:17
Alignment explanation
Indices: 844391--844425 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
844381 GCATATCCTG
* *
844391 ATTCGAAATTCAAAAAA
1 ATTCAAAATTAAAAAAA
844408 ATTCAAAATTAAAAAAA
1 ATTCAAAATTAAAAAAA
844425 A
1 A
844426 AAGAGATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.09, G:0.03, T:0.23
Consensus pattern (17 bp):
ATTCAAAATTAAAAAAA
Found at i:844446 original size:27 final size:30
Alignment explanation
Indices: 844407--844466 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 30
844397 AATTCAAAAA
*
844407 AATTCAAAATTAAA-AAA-AAA-AGAGATG
1 AATTCAAAATTAAATAAAGAAACAAAGATG
* *
844434 AATTCATATTTAAATAAAGAAACAAAGATG
1 AATTCAAAATTAAATAAAGAAACAAAGATG
844464 AAT
1 AAT
844467 GAATTAAGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 12 0.44
28 3 0.11
29 3 0.11
30 9 0.33
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (30 bp):
AATTCAAAATTAAATAAAGAAACAAAGATG
Found at i:846880 original size:49 final size:49
Alignment explanation
Indices: 846808--846911 Score: 145
Period size: 49 Copynumber: 2.1 Consensus size: 49
846798 GAAAAAAAAC
* * ** * *
846808 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
*
846857 AAATTAAAATTGAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
1 AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
846906 AAATTA
1 AAATTA
846912 TAACACATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.31
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
Found at i:852770 original size:17 final size:17
Alignment explanation
Indices: 852736--852770 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
852726 GCATATCCTG
* *
852736 ATTCGAAATTCAAAAAA
1 ATTCAAAATTAAAAAAA
852753 ATTCAAAATTAAAAAAA
1 ATTCAAAATTAAAAAAA
852770 A
1 A
852771 AAGAGATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.09, G:0.03, T:0.23
Consensus pattern (17 bp):
ATTCAAAATTAAAAAAA
Found at i:852791 original size:27 final size:30
Alignment explanation
Indices: 852752--852811 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 30
852742 AATTCAAAAA
*
852752 AATTCAAAATTAAA-AAA-AAA-AGAGATG
1 AATTCAAAATTAAATAAAGAAACAAAGATG
* *
852779 AATTCATATTTAAATAAAGAAACAAAGATG
1 AATTCAAAATTAAATAAAGAAACAAAGATG
852809 AAT
1 AAT
852812 GAATTAAGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 12 0.44
28 3 0.11
29 3 0.11
30 9 0.33
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (30 bp):
AATTCAAAATTAAATAAAGAAACAAAGATG
Found at i:854893 original size:292 final size:293
Alignment explanation
Indices: 854358--854942 Score: 1163
Period size: 292 Copynumber: 2.0 Consensus size: 293
854348 AAATTTATTG
854358 AGAAACATTTATTTTAATGTTTTTAATATATTATATATTTTAATTTTTATATAAAAATAAAATAA
1 AGAAACATTTATTTTAATGTTTTTAATATATTATATATTTTAATTTTTATATAAAAATAAAATAA
854423 AATATTTTTAATACGATCCGAGTCGGGCCTAAATTTAGCATCTATAACTCAAATTTTGACAAAAA
66 AATATTTTTAATACGATCCGAGTCGGGCCTAAATTTAGCATCTATAACTCAAATTTTGACAAAAA
854488 TTTAAATCCACTTTTCGAATTGAGCCAAGCTCTAACCTAAAATTTTGTTAGGCTTAAACAACTTA
131 TTTAAATCCACTTTTCGAATTGAGCCAAGCTCTAACCTAAAATTTTGTTAGGCTTAAACAACTTA
854553 TGAACAAGTTTATACCGGATGCATTTAGTAATGTTTTGGGTTGGTAGTTGGCTCATAGTATATAT
196 TGAACAAGTTTATACCGGATGCATTTAGTAATGTTTTGGGTTGGTAGTTGGCTCATAGTATATAT
854618 TACGGGTCGGATCAGAAAGCCCAATAAGGCTTC
261 TACGGGTCGGATCAGAAAGCCCAATAAGGCTTC
854651 AGAAACATTT-TTTTAATGTTTTTAATATATTATATATTTTAATTTTTATATAAAAATAAAATAA
1 AGAAACATTTATTTTAATGTTTTTAATATATTATATATTTTAATTTTTATATAAAAATAAAATAA
854715 AATATTTTTAATACGATCCGAGTCGGGCCTAAATTTAGCATCTATAACTCAAATTTTGACAAAAA
66 AATATTTTTAATACGATCCGAGTCGGGCCTAAATTTAGCATCTATAACTCAAATTTTGACAAAAA
854780 TTTAAATCCACTTTTCGAATTGAGCCAAGCTCTAACCTAAAATTTTGTTAGGCTTAAACAACTTA
131 TTTAAATCCACTTTTCGAATTGAGCCAAGCTCTAACCTAAAATTTTGTTAGGCTTAAACAACTTA
854845 TGAACAAGTTTATACCGGATGCATTTAGTAATGTTTTGGGTTGGTAGTTGGCTCATAGTATATAT
196 TGAACAAGTTTATACCGGATGCATTTAGTAATGTTTTGGGTTGGTAGTTGGCTCATAGTATATAT
854910 TACGGGTCGGATCAGAAAGCCCAATAAGGCTTC
261 TACGGGTCGGATCAGAAAGCCCAATAAGGCTTC
854943 TCTTTGTTTC
Statistics
Matches: 292, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
292 282 0.97
293 10 0.03
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37
Consensus pattern (293 bp):
AGAAACATTTATTTTAATGTTTTTAATATATTATATATTTTAATTTTTATATAAAAATAAAATAA
AATATTTTTAATACGATCCGAGTCGGGCCTAAATTTAGCATCTATAACTCAAATTTTGACAAAAA
TTTAAATCCACTTTTCGAATTGAGCCAAGCTCTAACCTAAAATTTTGTTAGGCTTAAACAACTTA
TGAACAAGTTTATACCGGATGCATTTAGTAATGTTTTGGGTTGGTAGTTGGCTCATAGTATATAT
TACGGGTCGGATCAGAAAGCCCAATAAGGCTTC
Done.