Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1318
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: 97761
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:4878 original size:2 final size:2
Alignment explanation
Indices: 4871--4906 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4861 ATGTCCATGC
4871 AT AT AT AT AT AT AT AT AT 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 AT AT
4907 CTTTTCTCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8805 original size:2 final size:2
Alignment explanation
Indices: 8798--8828 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8788 ATAACTTAAT
8798 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
8829 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:8833 original size:2 final size:2
Alignment explanation
Indices: 8828--8864 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
8818 TCTCTCTCTC
8828 TA TA TA TA 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 TA TA TA TA T
8865 TAAAATATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12098 original size:3 final size:3
Alignment explanation
Indices: 12090--12134 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
12080 TTATACTTTC
12090 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12135 TTTAATGTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12780 original size:18 final size:17
Alignment explanation
Indices: 12759--12794 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
12749 TGAAACAAAA
*
12759 ATAAATGAATAAACATAT
1 ATAAATAAATAAA-ATAT
12777 ATAAATAAATAAAATAT
1 ATAAATAAATAAAATAT
12794 A
1 A
12795 ATTTGCAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (17 bp):
ATAAATAAATAAAATAT
Found at i:18068 original size:3 final size:3
Alignment explanation
Indices: 18060--18100 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
18050 GTCATAGTAA
18060 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
18101 ATTTGTGATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:24842 original size:17 final size:18
Alignment explanation
Indices: 24822--24862 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
24812 AATTAAAATT
24822 ATTTATTTATTAT-TTTA
1 ATTTATTTATTATATTTA
*
24839 ATTT-TTTTTTATATTTA
1 ATTTATTTATTATATTTA
*
24856 ATATATT
1 ATTTATT
24863 ATATAGGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 7 0.35
17 11 0.55
18 2 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTATTTATTATATTTA
Found at i:37511 original size:165 final size:165
Alignment explanation
Indices: 37310--37631 Score: 556
Period size: 165 Copynumber: 2.0 Consensus size: 165
37300 GAACTCCTAG
* * *
37310 AAGCAGTTGGATTTTTAACTAAAAAAATTTGAGATGAAGGATTTGAGAAAAATAAAATTTTATCT
1 AAGCAGTTAGATTTTTAACTAAAAAAACTTGAGATGAAAGATTTGAGAAAAATAAAATTTTATCT
* * *
37375 TGATCTGCAAATTAAGCATTTGACAAAAGAGATATTTGCTCATCAATTAACTTATATAGAAAATA
66 TGATCTACAAATTAAGCATTTGACAAAAGAGATATTTACTCATCAATTAACTCATATAGAAAA-A
37440 TATTAAAGAGATTTAATATGAATAAAACATATGCAT
130 TATTAAAGAGATTTAATATGAATAAAACATATGCAT
*
37476 AAGCAGTTAGATTTTTAGC-AAAAAAACTTGAGATGAAAGATTTGAGAAAAATAAAATTTTATCT
1 AAGCAGTTAGATTTTTAACTAAAAAAACTTGAGATGAAAGATTTGAGAAAAATAAAATTTTATCT
*
37540 TGATCTACAAATTAAGCATTTGACAAAAGGGATATTTACTCATCAATTAACTCATATAGAAAAAT
66 TGATCTACAAATTAAGCATTTGACAAAAGAGATATTTACTCATCAATTAACTCATATAGAAAAAT
37605 ATTAAAGAGATTTAATATGAATAAAAC
131 ATTAAAGAGATTTAATATGAATAAAAC
37632 TTAACTTGCA
Statistics
Matches: 148, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
164 29 0.20
165 102 0.69
166 17 0.11
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.32
Consensus pattern (165 bp):
AAGCAGTTAGATTTTTAACTAAAAAAACTTGAGATGAAAGATTTGAGAAAAATAAAATTTTATCT
TGATCTACAAATTAAGCATTTGACAAAAGAGATATTTACTCATCAATTAACTCATATAGAAAAAT
ATTAAAGAGATTTAATATGAATAAAACATATGCAT
Found at i:42197 original size:20 final size:21
Alignment explanation
Indices: 42172--42225 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
42162 CATTTTAGGC
42172 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCACTAT
*
42192 ATGTATCGATACATTTACTAT
1 ATGTATCGATACATTCACTAT
* *
42213 TTATATCGATACA
1 ATGTATCGATACA
42226 AATCGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATTCACTAT
Found at i:42602 original size:16 final size:15
Alignment explanation
Indices: 42573--42607 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
42563 ATTTATTTTC
42573 TATTTAAGGAAAATA
1 TATTTAAGGAAAATA
*
42588 TATTTCAAGGCAAATA
1 TATTT-AAGGAAAATA
42604 TATT
1 TATT
42608 GAAGAATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (15 bp):
TATTTAAGGAAAATA
Found at i:43214 original size:16 final size:16
Alignment explanation
Indices: 43193--43240 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
43183 ATTAAAAATA
43193 ATAATTAATTATTAAT
1 ATAATTAATTATTAAT
*
43209 ATAATTAATAATT-AT
1 ATAATTAATTATTAAT
*
43224 ATTAATT-ATTTTTAAT
1 A-TAATTAATTATTAAT
43240 A
1 A
43241 GTGGAAACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 7 0.26
16 20 0.74
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATAATTAATTATTAAT
Found at i:43215 original size:12 final size:11
Alignment explanation
Indices: 43191--43229 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
43181 TAATTAAAAA
43191 TAATAATTAAT
1 TAATAATTAAT
*
43202 TATTAATATAAT
1 TAATAAT-TAAT
43214 TAATAATTATAT
1 TAATAATTA-AT
43226 TAAT
1 TAAT
43230 TATTTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TAATAATTAAT
Found at i:45102 original size:21 final size:21
Alignment explanation
Indices: 45076--45118 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
45066 AAATTTTCAC
*
45076 TCTCTCTCTACACTCTAAAAT
1 TCTCTCACTACACTCTAAAAT
* *
45097 TCTCTCACTTCTCTCTAAAAT
1 TCTCTCACTACACTCTAAAAT
45118 T
1 T
45119 TTATAAATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.42
Consensus pattern (21 bp):
TCTCTCACTACACTCTAAAAT
Found at i:45221 original size:29 final size:27
Alignment explanation
Indices: 45176--45240 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
45166 TTAATATTTA
* *
45176 TTTTTTAGCCGTTAAATTGTATTATTATT
1 TTTTTTAGCCGTTAAATT-T-TAACTATT
*
45205 TTTTTTAG-TGTTAAAATTTTAACTATT
1 TTTTTTAGCCGTT-AAATTTTAACTATT
45232 TTTTTTAGC
1 TTTTTTAGC
45241 AGTAAATCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 14 0.45
28 4 0.13
29 13 0.42
ACGTcount: A:0.25, C:0.06, G:0.09, T:0.60
Consensus pattern (27 bp):
TTTTTTAGCCGTTAAATTTTAACTATT
Found at i:45579 original size:21 final size:21
Alignment explanation
Indices: 45546--45586 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
45536 CTAAGTAAAA
45546 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
45567 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
45587 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:45650 original size:21 final size:20
Alignment explanation
Indices: 45620--45697 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
45610 GTCAAAACCC
*
45620 TGAAAAGTATCGATACACATTT
1 TGAATAGTATCGATACACA--T
*
45642 TGAAT-GTATCGATACAGAT
1 TGAATAGTATCGATACACAT
*
45661 TGCATAGTATCGATACACA-
1 TGAATAGTATCGATACACAT
**
45680 CAAATATGTATCGATACA
1 TGAATA-GTATCGATACA
45698 GGACATTGGC
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 8 0.17
20 23 0.49
21 12 0.26
22 4 0.09
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (20 bp):
TGAATAGTATCGATACACAT
Found at i:45749 original size:53 final size:53
Alignment explanation
Indices: 45668--45803 Score: 227
Period size: 53 Copynumber: 2.5 Consensus size: 53
45658 GATTGCATAG
*
45668 TATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTTC
1 TATCGATACACAC-AATATGTATCGATACAGGACACTGGCAGTAGCCAAATTTC
* *
45722 TATCGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCCAAATTTG
1 TATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTTC
*
45775 TATCGATACACAAAATATGTATCGATACA
1 TATCGATACACACAATATGTATCGATACA
45804 TTGGTAGTAG
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 65 0.83
54 13 0.17
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (53 bp):
TATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTTC
Found at i:45846 original size:10 final size:10
Alignment explanation
Indices: 45827--45857 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
45817 AATCTCATTT
45827 TCACTGTTCA
1 TCACTGTTCA
*
45837 TCACTATTCA
1 TCACTGTTCA
45847 TCACTGTTCA
1 TCACTGTTCA
45857 T
1 T
45858 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:45879 original size:21 final size:22
Alignment explanation
Indices: 45845--45900 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
45835 CATCACTATT
45845 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
45867 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
45888 CATCACTGTTCAT
1 CATCACTGTTCAT
45901 AGATCACTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:52307 original size:39 final size:39
Alignment explanation
Indices: 52264--52384 Score: 115
Period size: 39 Copynumber: 3.2 Consensus size: 39
52254 GCAGAAACAT
*
52264 TTGTTGATTGTAGTTATCATGCAAATTATCTCGGATTAG
1 TTGTTGATTGTAGTTATCGTGCAAATTATCTCGGATTAG
* * ** * * * *
52303 TTGTTAATAGTAGCAAT-GTG-AAA-TATC-AGAAATAT
1 TTGTTGATTGTAGTTATCGTGCAAATTATCTCGGATTAG
*
52338 TTGTTGATTTTAGTTATCGTGCAAATTATCTCGGATTAG
1 TTGTTGATTGTAGTTATCGTGCAAATTATCTCGGATTAG
*
52377 TTTTTGAT
1 TTGTTGAT
52385 AGTAATATTG
Statistics
Matches: 59, Mismatches: 19, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
35 16 0.27
36 7 0.12
37 6 0.10
38 6 0.10
39 24 0.41
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (39 bp):
TTGTTGATTGTAGTTATCGTGCAAATTATCTCGGATTAG
Found at i:52369 original size:74 final size:75
Alignment explanation
Indices: 52213--52450 Score: 352
Period size: 75 Copynumber: 3.2 Consensus size: 75
52203 GAAATATGAG
*
52213 ATTATCTCGGATTAATTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATTGTAGT
1 ATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATTGTAGT
52278 TATCATGCAA
66 TATCATGCAA
* * * *
52288 ATTATCTCGGATTAGTTGTTAATAGTAGCAATGTGAAATAT-CAGAAATATTTGTTGATTTTAGT
1 ATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATTGTAGT
*
52352 TATCGTGCAA
66 TATCATGCAA
* * * * *
52362 ATTATCTCGGATTAGTTTTTGATAGTAATATTGTGAAATATGCTGAAACATTTGTTGATTGTAAT
1 ATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATTGTAGT
* *
52427 TATCATACAG
66 TATCATGCAA
52437 ATTATCTCGGATTA
1 ATTATCTCGGATTA
52451 TCATTTCATC
Statistics
Matches: 144, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
74 66 0.46
75 78 0.54
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.41
Consensus pattern (75 bp):
ATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATTGTAGT
TATCATGCAA
Found at i:52761 original size:47 final size:47
Alignment explanation
Indices: 52692--52792 Score: 202
Period size: 47 Copynumber: 2.1 Consensus size: 47
52682 CAGAACGCGA
52692 ATCCTACGTGGATGCGCTAAACACAGCGCTTTCACGTAGGATTCGCT
1 ATCCTACGTGGATGCGCTAAACACAGCGCTTTCACGTAGGATTCGCT
52739 ATCCTACGTGGATGCGCTAAACACAGCGCTTTCACGTAGGATTCGCT
1 ATCCTACGTGGATGCGCTAAACACAGCGCTTTCACGTAGGATTCGCT
52786 ATCCTAC
1 ATCCTAC
52793 ATGGCGTTGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.26
Consensus pattern (47 bp):
ATCCTACGTGGATGCGCTAAACACAGCGCTTTCACGTAGGATTCGCT
Found at i:55550 original size:22 final size:22
Alignment explanation
Indices: 55490--55562 Score: 87
Period size: 21 Copynumber: 3.4 Consensus size: 22
55480 GAAAGATAAG
*
55490 ATATCAATACTTTCA-CTTAAA
1 ATATCAATACTTTTATCTTAAA
* *
55511 ATTTCAATA-TTTTCTCTTAAA
1 ATATCAATACTTTTATCTTAAA
*
55532 ATATCAATACTTTTATCTTGAA
1 ATATCAATACTTTTATCTTAAA
*
55554 ATATGAATA
1 ATATCAATA
55563 ATTTCTTGCC
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 3 0.07
21 22 0.51
22 18 0.42
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.44
Consensus pattern (22 bp):
ATATCAATACTTTTATCTTAAA
Found at i:55684 original size:90 final size:90
Alignment explanation
Indices: 55514--55685 Score: 240
Period size: 90 Copynumber: 1.9 Consensus size: 90
55504 ACTTAAAATT
* *
55514 TCAATATTTTCTCTTAAAATATCAATACTTTTATCTTGAAATATGAATAATTTCTTGCCTTCAAA
1 TCAATACTTTCTCCTAAAATATCAATACTTTTATCTTGAAATATGAATAATTTCTTGCCTTCAAA
* * *
55579 AATATGACCATTGAAAAGTAAAGTA
66 AAAATAACCAGTGAAAAGTAAAGTA
* *
55604 TCAATACTTTCTCCTAAAATATCAATA-TTTTATCTTGAATTTTGAATAATTTCTTGCCTT-AAA
1 TCAATACTTTCTCCTAAAATATCAATACTTTTATCTTGAAATATGAATAATTTCTTGCCTTCAAA
*
55667 AACAACTAACTAGTGAAAA
66 AA-AA-TAACCAGTGAAAA
55686 CTTTGTATCC
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
88 5 0.07
89 32 0.44
90 35 0.49
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.39
Consensus pattern (90 bp):
TCAATACTTTCTCCTAAAATATCAATACTTTTATCTTGAAATATGAATAATTTCTTGCCTTCAAA
AAAATAACCAGTGAAAAGTAAAGTA
Found at i:57418 original size:22 final size:21
Alignment explanation
Indices: 57387--57444 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
57377 AATTAAAAAT
*
57387 AATTACTTTTAATTAATT-TTAA
1 AATTATTTTTAATT-ATTATT-A
57409 AATTATTTTTAATTATTATTA
1 AATTATTTTTAATTATTATTA
*
57430 AGTTATATTTTAATT
1 AATTAT-TTTTAATT
57445 TAAGTATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 9 0.28
22 23 0.72
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
AATTATTTTTAATTATTATTA
Found at i:57981 original size:17 final size:18
Alignment explanation
Indices: 57946--57981 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
57936 TAACTTAATA
*
57946 GTAATTAAAGATAATTTT
1 GTAATTAAAAATAATTTT
57964 GTAATTAAAAAT-ATTTT
1 GTAATTAAAAATAATTTT
57981 G
1 G
57982 AGTAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (18 bp):
GTAATTAAAAATAATTTT
Found at i:58242 original size:16 final size:16
Alignment explanation
Indices: 58204--58253 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
58194 AATTATCATA
58204 TATTTTATTTATTTAT
1 TATTTTATTTATTTAT
58220 T-TATTTATTTATTTAT
1 TAT-TTTATTTATTTAT
**
58236 TATTTTAAATATTTAT
1 TATTTTATTTATTTAT
58252 TA
1 TA
58254 AAGATAAGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 1 0.03
16 28 0.93
17 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTTATTTATTTAT
Found at i:58252 original size:4 final size:4
Alignment explanation
Indices: 58207--58240 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
58197 TATCATATAT
58207 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
58241 TAAATATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:59008 original size:28 final size:28
Alignment explanation
Indices: 58976--59035 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
58966 TATTGTTTTG
* * *
58976 TTAAATAATGATAAGTTTATTTATTATA
1 TTAAATAATAATAAATTTATTTATTAAA
59004 TTAAATAATAATAAATTTATTTATTAAA
1 TTAAATAATAATAAATTTATTTATTAAA
59032 TTAA
1 TTAA
59036 GTTATCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (28 bp):
TTAAATAATAATAAATTTATTTATTAAA
Found at i:59417 original size:17 final size:18
Alignment explanation
Indices: 59379--59423 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
59369 AATTTATTCA
*
59379 ATTTAATT-AAAATTATT
1 ATTTAATTAAAAAATATT
59396 ATTTAATTAAAAAATATT
1 ATTTAATTAAAAAATATT
*
59414 -TTTATTTAAA
1 ATTTAATTAAA
59424 TTTAATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTAATTAAAAAATATT
Found at i:61220 original size:40 final size:40
Alignment explanation
Indices: 61161--61241 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
61151 TCAAACTGTG
*
61161 ATTATCTACATGTGCAATATTACAAAGTAAAACAAATACT
1 ATTATCTACATATGCAATATTACAAAGTAAAACAAATACT
*
61201 ATTATCTACATATGTAATATTACAAAGTAAAACAAATACT
1 ATTATCTACATATGCAATATTACAAAGTAAAACAAATACT
61241 A
1 A
61242 AAAAAGTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (40 bp):
ATTATCTACATATGCAATATTACAAAGTAAAACAAATACT
Found at i:61850 original size:30 final size:30
Alignment explanation
Indices: 61808--61875 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
61798 TGTTGTGATT
** *
61808 TATTTACTTGTAATATTATGTGTACAACATA
1 TATTTA-TTGTAATATTAAATATACAACATA
61839 TATTTATTGTAATATTAAATATACAACATA
1 TATTTATTGTAATATTAAATATACAACATA
61869 TATTTAT
1 TATTTAT
61876 GGCATATAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 28 0.82
31 6 0.18
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (30 bp):
TATTTATTGTAATATTAAATATACAACATA
Found at i:62420 original size:8 final size:8
Alignment explanation
Indices: 62395--62428 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
62385 AGTATTCGAA
62395 TTTAAGAAT
1 TTTAA-AAT
62404 TTTAGAAAT
1 TTTA-AAAT
62413 TTTAAAAT
1 TTTAAAAT
62421 TTTAAAAT
1 TTTAAAAT
62429 ATATGCTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 12 0.50
9 11 0.46
10 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (8 bp):
TTTAAAAT
Found at i:62421 original size:17 final size:17
Alignment explanation
Indices: 62395--62428 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
62385 AGTATTCGAA
62395 TTTAAGAATTTTAGAAAT
1 TTTAAGAATTTTA-AAAT
62413 TTTAA-AATTTTAAAAT
1 TTTAAGAATTTTAAAAT
62429 ATATGCTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
TTTAAGAATTTTAAAAT
Found at i:64781 original size:18 final size:18
Alignment explanation
Indices: 64735--64786 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
64725 TTGATAATTT
*
64735 TAAAAATAATAAATATAAA
1 TAAAAAT-ATAAAAATAAA
**
64754 T-ATTATATAAAAATAAA
1 TAAAAATATAAAAATAAA
64771 TAAAAATATAAAAATA
1 TAAAAATATAAAAATA
64787 TATTAATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 11 0.41
18 15 0.56
19 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAATATAAAAATAAA
Found at i:64794 original size:26 final size:29
Alignment explanation
Indices: 64734--64794 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
64724 TTTGATAATT
64734 TTAA-AAATAATAAATATAAATATTATATA
1 TTAATAAATAATAAATATAAATA-TATATA
**
64763 AAAATAAATAA-AAATATAAA-A-ATATA
1 TTAATAAATAATAAATATAAATATATATA
64789 TTAATA
1 TTAATA
64795 TTTATATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
26 9 0.33
28 1 0.04
29 11 0.41
30 6 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (29 bp):
TTAATAAATAATAAATATAAATATATATA
Found at i:64819 original size:33 final size:36
Alignment explanation
Indices: 64766--64857 Score: 113
Period size: 33 Copynumber: 2.7 Consensus size: 36
64756 TTATATAAAA
* *
64766 ATAAATA-AAAATATA-AAAATATATTAATATTTAT
1 ATAAATATAAAATATATTAAATATATTAAAATTTAT
*
64800 AT-TATAT-AAAT-TATTAAATATATTAAAATTTAT
1 ATAAATATAAAATATATTAAATATATTAAAATTTAT
*
64833 ATAAATATAAAATATTTTAAATATA
1 ATAAATATAAAATATATTAAATATA
64858 GTTATAACAT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
32 2 0.04
33 26 0.54
34 6 0.12
35 4 0.08
36 10 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (36 bp):
ATAAATATAAAATATATTAAATATATTAAAATTTAT
Found at i:64822 original size:27 final size:27
Alignment explanation
Indices: 64792--64879 Score: 90
Period size: 27 Copynumber: 3.2 Consensus size: 27
64782 AAATATATTA
* *
64792 ATATTTATA-TTATATAAATTATTAAAT
1 ATATTTAAATTTATATAAA-TATAAAAT
*
64819 ATATTAAAATTTATATAAATATAAAAT
1 ATATTTAAATTTATATAAATATAAAAT
*
64846 AT-TTTAAATATAGTTATAACATATAAAAT
1 ATATTTAAATTTA--TATAA-ATATAAAAT
64875 ATATT
1 ATATT
64880 AATAAAATGT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
26 8 0.16
27 16 0.31
28 14 0.27
29 11 0.22
30 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (27 bp):
ATATTTAAATTTATATAAATATAAAAT
Found at i:64823 original size:9 final size:9
Alignment explanation
Indices: 64782--64881 Score: 68
Period size: 9 Copynumber: 11.2 Consensus size: 9
64772 AAAAATATAA
64782 AAATATATT
1 AAATATATT
64791 -AATAT-TT
1 AAATATATT
*
64798 ATAT-TATAT
1 AAATATAT-T
64807 AAAT-TATT
1 AAATATATT
64815 AAATATATT
1 AAATATATT
*
64824 AAAATTTATAT
1 -AAATATAT-T
64835 AAATATA--
1 AAATATATT
*
64842 AAATATTTT
1 AAATATATT
64851 AAATATAGTT
1 AAATATA-TT
* *
64861 ATAACATATA
1 A-AATATATT
64871 AAATATATT
1 AAATATATT
64880 AA
1 AA
64882 TAAAATGTCA
Statistics
Matches: 71, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
7 9 0.13
8 13 0.18
9 25 0.35
10 18 0.25
11 6 0.08
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (9 bp):
AAATATATT
Found at i:64847 original size:7 final size:8
Alignment explanation
Indices: 64738--64857 Score: 58
Period size: 8 Copynumber: 14.9 Consensus size: 8
64728 ATAATTTTAA
64738 AAATA-AT
1 AAATATAT
64745 AAATATA-
1 AAATATAT
64752 AATATTATAT
1 AA-A-TATAT
64762 AAA-A-AT
1 AAATATAT
64768 AAATA-A-
1 AAATATAT
*
64774 AAATATAA
1 AAATATAT
64782 AAATATAT
1 AAATATAT
* *
64790 TAATATTT
1 AAATATAT
*
64798 ATATTATAT
1 A-AATATAT
64807 AAAT-TATT
1 AAATATA-T
64815 AAATATATT
1 AAATATA-T
64824 AAAATTTATAT
1 -AAA--TATAT
64835 AAATATA-
1 AAATATAT
*
64842 AAATATTTT
1 AAATA-TAT
64851 AAATATA
1 AAATATA
64858 GTTATAACAT
Statistics
Matches: 89, Mismatches: 9, Indels: 29
0.70 0.07 0.23
Matches are distributed among these distances:
6 10 0.11
7 18 0.20
8 28 0.31
9 20 0.22
10 8 0.09
11 1 0.01
12 4 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
AAATATAT
Found at i:70311 original size:57 final size:57
Alignment explanation
Indices: 70250--70362 Score: 208
Period size: 57 Copynumber: 2.0 Consensus size: 57
70240 ATAATAAAAA
* *
70250 AATTCCACATTCGTAAAAAGTTTACAAAAAACCTTTATGGAGGAAAAATTCATACTG
1 AATTCCACACTCGTAAAAAGTTTACAAAAAACCTTTATAGAGGAAAAATTCATACTG
70307 AATTCCACACTCGTAAAAAGTTTACAAAAAACCTTTATAGAGGAAAAATTCATACT
1 AATTCCACACTCGTAAAAAGTTTACAAAAAACCTTTATAGAGGAAAAATTCATACT
70363 CAAGAGAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (57 bp):
AATTCCACACTCGTAAAAAGTTTACAAAAAACCTTTATAGAGGAAAAATTCATACTG
Found at i:73035 original size:20 final size:18
Alignment explanation
Indices: 72999--73037 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
72989 TTTTTTAATT
*
72999 TTTAATTAAAAGTTAAAA
1 TTTAATTAAAAGGTAAAA
73017 TTTAATTATATAAGGTAAAA
1 TTTAATTA-A-AAGGTAAAA
73037 T
1 T
73038 AATATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 1 0.06
20 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (18 bp):
TTTAATTAAAAGGTAAAA
Found at i:73584 original size:11 final size:11
Alignment explanation
Indices: 73568--73612 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
73558 AGAAAATACA
*
73568 TATATTTGTAT
1 TATATTTATAT
73579 TATATTTATAT
1 TATATTTATAT
*
73590 TATTTTTATAT
1 TATATTTATAT
*
73601 TATAATTATAT
1 TATATTTATAT
73612 T
1 T
73613 TAAAATATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:74437 original size:85 final size:84
Alignment explanation
Indices: 74284--74438 Score: 211
Period size: 85 Copynumber: 1.8 Consensus size: 84
74274 AAACAAGAAT
* * * * * ** *
74284 ACATATTATTTTTACAAATTGAATCACTATTATAAATTATATAAAATATGTGATAAATTAAGATA
1 ACATATAATTTTTAAAAATTGAATCACGATGATAAATAATATAAAATATAAGATAAATTAAGAGA
74349 TAACAGAAATATGATATAA
66 TAACAGAAATATGATATAA
* *
74368 ACATATAATTTTTTAAAAATTGAATCACGATGATAAATAATATAAAATATAAGATGAATTTAGAG
1 ACATATAA-TTTTTAAAAATTGAATCACGATGATAAATAATATAAAATATAAGATAAATTAAGAG
74433 ATAACA
65 ATAACA
74439 CGAACACAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
84 7 0.12
85 53 0.88
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (84 bp):
ACATATAATTTTTAAAAATTGAATCACGATGATAAATAATATAAAATATAAGATAAATTAAGAGA
TAACAGAAATATGATATAA
Found at i:74675 original size:23 final size:24
Alignment explanation
Indices: 74631--74675 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
74621 CTTCTTTTTT
* *
74631 TTCTTTCATTTTCTTGCTTCTCTC
1 TTCTTTCATTTTCTTCCATCTCTC
74655 TTCTTTC-TTTTCTTCCATCTC
1 TTCTTTCATTTTCTTCCATCTC
74676 CAGAAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.04, C:0.31, G:0.02, T:0.62
Consensus pattern (24 bp):
TTCTTTCATTTTCTTCCATCTCTC
Found at i:76243 original size:4 final size:4
Alignment explanation
Indices: 76215--76276 Score: 88
Period size: 4 Copynumber: 15.5 Consensus size: 4
76205 TCTTTCATCT
* * * *
76215 TATA CATA TATA CATA CATA CATA TATA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
76263 TATA TATA TATA TA
1 TATA TATA TATA TA
76277 AGATTTAACT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (4 bp):
TATA
Found at i:80311 original size:2 final size:2
Alignment explanation
Indices: 80296--80331 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
80286 TAGTCCATTA
* *
80296 AC AC AC AT AG AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
80332 GCAAATCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.50, C:0.44, G:0.03, T:0.03
Consensus pattern (2 bp):
AC
Found at i:82096 original size:4 final size:4
Alignment explanation
Indices: 82087--82120 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
82077 GCTTAAATGG
82087 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
82121 GAGGCTTGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:82732 original size:22 final size:22
Alignment explanation
Indices: 82704--82746 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
82694 GATGATAGCA
*
82704 TTTTAAGAGTCTA-AATATTTCC
1 TTTTAAGAATC-AGAATATTTCC
82726 TTTTAAGAATCAGAATATTTC
1 TTTTAAGAATCAGAATATTTC
82747 TTTCATGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (22 bp):
TTTTAAGAATCAGAATATTTCC
Found at i:82800 original size:15 final size:14
Alignment explanation
Indices: 82779--82821 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
82769 TCATTTCTAA
82779 AATAATATTTTATG
1 AATAATATTTTATG
*
82793 ATATAATATGTTATG
1 A-ATAATATTTTATG
*
82808 AATGAATTTTTTAT
1 AAT-AATATTTTAT
82822 AATTATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 3 0.12
15 21 0.88
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (14 bp):
AATAATATTTTATG
Found at i:87250 original size:20 final size:20
Alignment explanation
Indices: 87225--87299 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
87215 CACAATTCAA
87225 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
87245 GTATCGATACAATGAAAAAAGAT
1 GTATCGATAC-ATG-TTGCA-AT
87268 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
87288 GTATCGATACAT
1 GTATCGATACAT
87300 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 24 0.55
21 4 0.09
22 4 0.09
23 12 0.27
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:87316 original size:41 final size:43
Alignment explanation
Indices: 87225--87320 Score: 178
Period size: 43 Copynumber: 2.3 Consensus size: 43
87215 CACAATTCAA
87225 GTATCGATACATGTTGCAATGTATCGATACAATGAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACAATGAAAAAAGAT
87268 GTATCGATACATGTTGCAATGTATCGATAC-AT-AAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACAATGAAAAAAGAT
87309 GTATCGATACAT
1 GTATCGATACAT
87321 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 21 0.40
42 2 0.04
43 30 0.57
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (43 bp):
GTATCGATACATGTTGCAATGTATCGATACAATGAAAAAAGAT
Found at i:87377 original size:13 final size:13
Alignment explanation
Indices: 87359--87384 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
87349 TACAGCAAGT
87359 ATGTATCGATACA
1 ATGTATCGATACA
87372 ATGTATCGATACA
1 ATGTATCGATACA
87385 CAAAAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:87382 original size:32 final size:32
Alignment explanation
Indices: 87341--87403 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
87331 TAGCCAAACT
**
87341 TGTATCGATACAGCAAGTA-TGTATCGATACAA
1 TGTATCGATACA-CAAAAATTGTATCGATACAA
87373 TGTATCGATACACAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAATTGTATCGATACA
87404 TTGGCTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAAATTGTATCGATACAA
Found at i:91468 original size:15 final size:15
Alignment explanation
Indices: 91448--91478 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
91438 ATAAAATGTC
*
91448 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
91463 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
91478 C
1 C
91479 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:93580 original size:20 final size:21
Alignment explanation
Indices: 93501--93579 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
93491 AATGTCCAAA
*
93501 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
93521 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
93546 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
93566 TTGTATCGATACAT
1 ATGTATCGATACAT
93580 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:93584 original size:13 final size:13
Alignment explanation
Indices: 93566--93604 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
93556 ACATTTTTCT
93566 TTGTATCGATACA
1 TTGTATCGATACA
93579 TTGTATCGATACA
1 TTGTATCGATACA
*
93592 CTGTATCGATACA
1 TTGTATCGATACA
93605 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:96070 original size:20 final size:20
Alignment explanation
Indices: 96047--96119 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
96037 ACAATTCAAA
96047 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
96067 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
96088 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
96108 GTATCGATACAT
1 GTATCGATACAT
96120 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:96091 original size:21 final size:21
Alignment explanation
Indices: 96065--96140 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
96055 ACATGTTGCA
96065 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
96086 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
96106 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
96127 ATGTATCGATACAT
1 ATGTATCGATACAT
96141 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:96098 original size:41 final size:41
Alignment explanation
Indices: 96047--96140 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
96037 ACAATTCAAA
*
96047 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
96088 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
96129 GTATCGATACAT
1 GTATCGATACAT
96141 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:96198 original size:13 final size:13
Alignment explanation
Indices: 96180--96205 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
96170 TACAGCAAGT
96180 ATGTATCGATACA
1 ATGTATCGATACA
96193 ATGTATCGATACA
1 ATGTATCGATACA
96206 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Done.