Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold679
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: 81274
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1167 original size:20 final size:20
Alignment explanation
Indices: 1142--1237 Score: 88
Period size: 20 Copynumber: 4.7 Consensus size: 20
1132 TTTTAACTAG
1142 ATGTATCGATACATTGAGCA
1 ATGTATCGATACATTGAGCA
*
1162 ATGTATTGATACATATAGATAG-A
1 ATGTATCGATACAT-T-G--AGCA
* *
1185 ATGTATCGATACATTCATC-
1 ATGTATCGATACATTGAGCA
**
1204 ATGTATCGATACATTGATAA
1 ATGTATCGATACATTGAGCA
*
1224 ATGTATCGGTACAT
1 ATGTATCGATACAT
1238 CTAGGTAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
19 18 0.29
20 26 0.41
21 1 0.02
22 2 0.03
23 14 0.22
24 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTGAGCA
Found at i:2471 original size:95 final size:94
Alignment explanation
Indices: 2372--2594 Score: 201
Period size: 95 Copynumber: 2.4 Consensus size: 94
2362 TATTTTTAAA
2372 TATTTTAATTTATTTAAATTTAAATAAATTAATAAAAAT-GACA-TCAAATAGGAAAAGTTTATT
1 TATTTTAATTTATTTAAATTTAAATAAATTAATAAAAATAGACATTCAAATA--AAAAGTTTATT
* *
2435 AATTTTAAAGTCG-TTTAATATCATGTGGAA-TG
64 AA-TTTAAAGTAGATTT-ATATCATGT-GAACTC
* * * * *
2467 TA-TTTACATATT-TGTT-AATATAAATAAATTAA-AAAAATATATATTTAAATAAAAATTTTAT
1 TATTTTA-AT-TTAT-TTAAATTTAAATAAATTAATAAAAATAGACATTCAAATAAAAAGTTTAT
* *
2528 TAATTTAAATTAGATTTATATTATGTGAACTC
63 TAATTTAAAGTAGATTTATATCATGTGAACTC
* *
2560 TATTTTTATATATTTATTAATTTAAATAAATTAAT
1 TATTTTAATTTATTTA--AATTTAAATAAATTAAT
2595 TAAATTATAT
Statistics
Matches: 103, Mismatches: 12, Indels: 25
0.74 0.09 0.18
Matches are distributed among these distances:
92 6 0.06
93 22 0.21
94 28 0.27
95 37 0.36
96 10 0.10
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (94 bp):
TATTTTAATTTATTTAAATTTAAATAAATTAATAAAAATAGACATTCAAATAAAAAGTTTATTAA
TTTAAAGTAGATTTATATCATGTGAACTC
Found at i:2554 original size:93 final size:96
Alignment explanation
Indices: 2424--2631 Score: 219
Period size: 95 Copynumber: 2.2 Consensus size: 96
2414 ATCAAATAGG
* * * *
2424 AAAAGTTTATTAATTTTAAAGTCGTTTAATATCATGTGGAA-TGTA-TTTACATATTTGTTAATA
1 AAAATTTTATTAA-TTTAAAGTAGTTTAATATCATGT-GAACTCTATTTTACATATTTATTAATA
*
2487 TAAATAAATTAA-AAAAATATATATTTAAA-TA
64 TAAATAAATTAATAAAAATATATAATTAAATTA
* * * *
2518 AAAATTTTATTAATTTAAATTAGATTT-ATATTATGTGAACTCTATTTTTATATATTTATTAATT
1 AAAATTTTATTAATTTAAAGTAG-TTTAATATCATGTGAACTCTA-TTTTACATATTTATTAATA
* * *
2582 TAAATAAATTAATTAAATTATATAATTAAATTT
64 TAAATAAATTAATAAAAATATATAATTAAATTA
*
2615 AATATCTTTATTAATTT
1 AAAAT-TTTATTAATTT
2632 TAAAATTTTA
Statistics
Matches: 94, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
92 3 0.03
93 19 0.20
94 15 0.16
95 27 0.29
96 14 0.15
97 5 0.05
98 11 0.12
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (96 bp):
AAAATTTTATTAATTTAAAGTAGTTTAATATCATGTGAACTCTATTTTACATATTTATTAATATA
AATAAATTAATAAAAATATATAATTAAATTA
Found at i:3060 original size:21 final size:21
Alignment explanation
Indices: 3022--3069 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
3012 TTTTTATTGA
*
3022 TTAATTTTTCCAAGTGATCAGT
1 TTAATTTTT-CAAGTGATCACT
*
3044 TTAATTTTT-AAGCTGATTACT
1 TTAATTTTTCAAG-TGATCACT
3065 TTAAT
1 TTAAT
3070 CCGCTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 3 0.13
21 11 0.48
22 9 0.39
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
TTAATTTTTCAAGTGATCACT
Found at i:3747 original size:21 final size:21
Alignment explanation
Indices: 3723--3763 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3713 TTTGAATAAG
3723 TTATGT-CTATATAAATAGATA
1 TTATGTGCT-TATAAATAGATA
*
3744 TTATTTGCTTATAAATAGAT
1 TTATGTGCTTATAAATAGAT
3764 CCTTTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (21 bp):
TTATGTGCTTATAAATAGATA
Found at i:5917 original size:21 final size:21
Alignment explanation
Indices: 5891--5931 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5881 TATATTTATC
5891 TTATCTTCATTTTTCTCTTTA
1 TTATCTTCATTTTTCTCTTTA
* *
5912 TTATCTTCTTTTTTTTCTTT
1 TTATCTTCATTTTTCTCTTT
5932 TTTCTTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (21 bp):
TTATCTTCATTTTTCTCTTTA
Found at i:5949 original size:16 final size:16
Alignment explanation
Indices: 5917--6009 Score: 70
Period size: 16 Copynumber: 5.8 Consensus size: 16
5907 CTTTATTATC
5917 TTCTTTT-TTTTCTTTT
1 TTCTTTTCTTTTC-TTT
5933 TTCTTTTCTTTTCTTT
1 TTCTTTTCTTTTCTTT
*
5949 TCCCTTTTCCTTTT-TTAT
1 T-TCTTTT-CTTTTCTT-T
5967 TTC-TTTCTTTAT-TTCT
1 TTCTTTTCTTT-TCTT-T
*
5983 TTCTCTT-TTTTCTTT
1 TTCTTTTCTTTTCTTT
*
5998 TTCTTCTCTTTT
1 TTCTTTTCTTTT
6010 TTCTTCATCT
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
15 11 0.17
16 30 0.48
17 15 0.24
18 7 0.11
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCTTTTCTTTTCTTT
Found at i:5999 original size:66 final size:65
Alignment explanation
Indices: 5917--6147 Score: 193
Period size: 74 Copynumber: 3.4 Consensus size: 65
5907 CTTTATTATC
*
5917 TTCTTTTTTTTCTTTTTTCTTTTCTTTTCTTTTCCCTTTTCCTTT-TTTATTTCTTTCTTTATTT
1 TTCTCTTTTTTCTTTTTTCTTTTCTTTTCTTTTCCCTTTTCCTTTCTTT-TTTCTTTCTTT-TTT
5981 CT
64 CT
* *
5983 TTCTCTTTTTTCTTTTTCTTCTCTTTTTTCTTCATCTTTCTACCATTTCCTTTCTTTTTTCTTTC
1 TTCTCTTTTTTC-TTTT-TTCT-TTTCTT-TTC-T-TTTC--CCTTTTCCTTTCTTTTTTCTTTC
6048 TTTTTTCCT
58 TTTTTT-CT
* * * *
6057 TTCTCTCTTTTCCTCTTTTTT-TCTTCTTTTCTTCATCTCTTGTT-CTTTCTTTTTTC-TCCTTT
1 TTCTCT-TTTT--TCTTTTTTCTTTTCTTTTCTT-TTCCCTT-TTCCTTTCTTTTTTCTTTCTTT
*
6119 TTTTT
61 TTTCT
*
6124 TTCATC-TTTTTCTTTTTTTTTTTC
1 TTC-TCTTTTTTCTTTTTTCTTTTC
6148 ACTAGTTTAC
Statistics
Matches: 137, Mismatches: 11, Indels: 35
0.75 0.06 0.19
Matches are distributed among these distances:
64 8 0.06
65 4 0.03
66 15 0.11
67 8 0.06
68 14 0.10
69 19 0.14
70 6 0.04
71 4 0.03
72 7 0.05
73 7 0.05
74 30 0.22
75 9 0.07
76 4 0.03
77 2 0.01
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (65 bp):
TTCTCTTTTTTCTTTTTTCTTTTCTTTTCTTTTCCCTTTTCCTTTCTTTTTTCTTTCTTTTTTCT
Found at i:6004 original size:18 final size:18
Alignment explanation
Indices: 5917--6014 Score: 67
Period size: 18 Copynumber: 5.3 Consensus size: 18
5907 CTTTATTATC
5917 TTCTTTTT-TT-TCTTTT
1 TTCTTTTTCTTCTCTTTT
*
5933 TTC-TTTTCTTTTCTTTT
1 TTCTTTTTCTTCTCTTTT
** * * *
5950 CCCTTTTCCTTTTTTATTTCT
1 TTCTTTT--TCTTCTCTTT-T
5971 TTCTTTATTTCTTTCTCTTTT
1 TTC-TT-TTTC-TTCTCTTTT
5992 TTCTTTTTCTTCTCTTTT
1 TTCTTTTTCTTCTCTTTT
6010 TTCTT
1 TTCTT
6015 CATCTTTCTA
Statistics
Matches: 64, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
15 4 0.06
16 5 0.08
17 7 0.11
18 17 0.27
19 4 0.06
20 10 0.16
21 7 0.11
22 8 0.12
23 2 0.03
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (18 bp):
TTCTTTTTCTTCTCTTTT
Found at i:6020 original size:18 final size:18
Alignment explanation
Indices: 5983--6020 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5973 CTTTATTTCT
**
5983 TTCTCTTTTTTCTTTTTC
1 TTCTCTTTTTTCTTCATC
6001 TTCTCTTTTTTCTTCATC
1 TTCTCTTTTTTCTTCATC
6019 TT
1 TT
6021 TCTACCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (18 bp):
TTCTCTTTTTTCTTCATC
Found at i:6044 original size:74 final size:74
Alignment explanation
Indices: 5929--6094 Score: 202
Period size: 74 Copynumber: 2.3 Consensus size: 74
5919 CTTTTTTTTC
* * *
5929 TTTT-TTCTTTTCTT-TTCTTT-TCCCTTTTCCTTTTTTATTTCTTTCTTTATTT-CTTTCTCT-
1 TTTTCTTCTTTTCTTCATCTTTCTACCATTTCCTTTTTTATTTCTTTCTTT-TTTCCTTTCTCTC
5989 TTTT-TCTTT
65 TTTTCTCTTT
*
5998 TTCTTCTCTTTTTTCTTCATCTTTCTACCATTTCCTTTCTTT-TTTCTTTCTTTTTTCCTTTCTC
1 TT-TTCT-TCTTTTCTTCATCTTTCTACCATTTCCTTT-TTTATTTCTTTCTTTTTTCCTTTCTC
6062 TCTTTTCCTCTTT
63 TCTTTT-CTCTTT
6075 TTTTCTTCTTTTCTTCATCT
1 TTTTCTTCTTTTCTTCATCT
6095 CTTGTTCTTT
Statistics
Matches: 82, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
69 2 0.02
70 2 0.02
71 1 0.01
72 8 0.10
73 8 0.10
74 30 0.37
75 20 0.24
76 4 0.05
77 7 0.09
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.72
Consensus pattern (74 bp):
TTTTCTTCTTTTCTTCATCTTTCTACCATTTCCTTTTTTATTTCTTTCTTTTTTCCTTTCTCTCT
TTTCTCTTT
Found at i:6108 original size:34 final size:32
Alignment explanation
Indices: 6033--6147 Score: 103
Period size: 32 Copynumber: 3.5 Consensus size: 32
6023 TACCATTTCC
*
6033 TTTCTTT-TTTCTTTCTTTTTTCCTTTC-TCTCT
1 TTTCTTTCTTTTTTTCTTTTTT-C-TTCATCTCT
*
6065 TTTC-CTCTTTTTTTCTTCTTTTCTTCATCTCT
1 TTTCTTTCTTTTTTTCTT-TTTTCTTCATCTCT
*
6097 TGTTCTTTCTTTTTTCTCCTTTTTTTTTTCATCT-T
1 T-TTCTTTCTTTTTT-T-C-TTTTTTCTTCATCTCT
*
6132 TTTCTTTTTTTTTTTC
1 TTTCTTTCTTTTTTTC
6148 ACTAGTTTAC
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
31 4 0.06
32 21 0.30
33 8 0.11
34 20 0.29
35 3 0.04
36 12 0.17
37 2 0.03
ACGTcount: A:0.02, C:0.23, G:0.01, T:0.75
Consensus pattern (32 bp):
TTTCTTTCTTTTTTTCTTTTTTCTTCATCTCT
Found at i:6134 original size:15 final size:15
Alignment explanation
Indices: 6102--6141 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
6092 TCTCTTGTTC
6102 TTTCTTTTTTCTCCT
1 TTTCTTTTTTCTCCT
*
6117 TTT-TTTTTTCATCTT
1 TTTCTTTTTTC-TCCT
6132 TTTCTTTTTT
1 TTTCTTTTTT
6142 TTTTTCACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 7 0.32
15 9 0.41
16 6 0.27
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTCTTTTTTCTCCT
Found at i:6147 original size:21 final size:22
Alignment explanation
Indices: 6107--6148 Score: 68
Period size: 21 Copynumber: 1.9 Consensus size: 22
6097 TGTTCTTTCT
6107 TTTTTCTCCTTTTTTTTTTCATC
1 TTTTTCT-CTTTTTTTTTTCATC
6130 TTTTTCT-TTTTTTTTTTCA
1 TTTTTCTCTTTTTTTTTTCA
6149 CTAGTTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTCTCTTTTTTTTTTCATC
Found at i:7875 original size:2 final size:2
Alignment explanation
Indices: 7868--7894 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7858 TTGTTTTTAC
7868 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 T
7895 TGTTTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7880 original size:22 final size:22
Alignment explanation
Indices: 7833--7880 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
7823 TAAGCCAAAA
* *
7833 ATATTATTTTTATTATATGTAC
1 ATATTATTTTTACTATATATAC
* *
7855 ATATTGTTTTTACTATATATAT
1 ATATTATTTTTACTATATATAC
7877 ATAT
1 ATAT
7881 ATATATATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (22 bp):
ATATTATTTTTACTATATATAC
Found at i:9267 original size:21 final size:22
Alignment explanation
Indices: 9236--9277 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
9226 TAGTAATGTA
9236 ATAATAAAATTTATGTACATTC
1 ATAATAAAATTTATGTACATTC
9258 ATAA-AAAATTTATGTACATT
1 ATAATAAAATTTATGTACATT
9278 TTATATTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (22 bp):
ATAATAAAATTTATGTACATTC
Found at i:9434 original size:21 final size:21
Alignment explanation
Indices: 9410--9460 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
9400 AGTATAACAG
*
9410 TATGTAAA-TATAACTTAATTA
1 TATGTAAATTA-AACTTAACTA
*
9431 TATGTAAATTAAACTTAACTG
1 TATGTAAATTAAACTTAACTA
9452 TATGTAAAT
1 TATGTAAAT
9461 CTTTTTTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (21 bp):
TATGTAAATTAAACTTAACTA
Found at i:10480 original size:55 final size:55
Alignment explanation
Indices: 10419--10619 Score: 205
Period size: 55 Copynumber: 3.6 Consensus size: 55
10409 ATATATAGGC
*
10419 TTTTCAATTAAACTCTTTATATATAGAATTTTTAATTAAAATTTCACATAT-AAA
1 TTTTCAATTAAACTCTTTATATATAGAATTTTTAATTAAAATTTCACATGTAAAA
** * * *
10473 TTATTCAATTAAACT-TTGTGCATATTGAATTTTTAATTAAACTTTCATATGTAAAA
1 TT-TTCAATTAAACTCTT-TATATATAGAATTTTTAATTAAAATTTCACATGTAAAA
* * **
10529 TTTTCAATTAAAC-CTTTTGTATATA-AATTTTTTAATT-AAAGTTCTACATGTGCAA
1 TTTTCAATTAAACTC-TTTATATATAGAA-TTTTTAATTAAAATTTC-ACATGTAAAA
* *
10584 TTTTAAATTAAACTTTCTTATATATAGAATTTTTAA
1 TTTTCAATTAAACTCT-TTATATATAGAATTTTTAA
10620 CTTTTTCTTA
Statistics
Matches: 121, Mismatches: 16, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
54 11 0.09
55 86 0.71
56 22 0.18
57 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (55 bp):
TTTTCAATTAAACTCTTTATATATAGAATTTTTAATTAAAATTTCACATGTAAAA
Found at i:10593 original size:110 final size:109
Alignment explanation
Indices: 10393--10599 Score: 251
Period size: 110 Copynumber: 1.9 Consensus size: 109
10383 TTAATTAAAC
* ***
10393 TTTTTATTAAATTTTCATATATAGGCTTTTCAATTAAACTCTTTATATATAGAATTTTTAATTAA
1 TTTTTATTAAACTTTCATATATAAAATTTTCAATTAAACTCTTTATATATAGAATTTTTAATTAA
*
10458 AATTTCACATATAAATTATTCAATTAAACTTTGTGCATATTGAA
66 AATTTCACATATAAATTATTAAATTAAACTTTGTGCATATTGAA
* *
10502 TTTTTAATTAAACTTTCATATGTAAAATTTTCAATTAAAC-CTTTTGTATATA-AATTTTTTAAT
1 TTTTT-ATTAAACTTTCATATATAAAATTTTCAATTAAACTC-TTTATATATAGAA-TTTTTAAT
* * *
10565 T-AAAGTTCTACATGTGCAATT-TTAAATTAAACTTT
63 TAAAATTTC-ACATAT-AAATTATTAAATTAAACTTT
10600 CTTATATATA
Statistics
Matches: 83, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
109 14 0.17
110 65 0.78
111 4 0.05
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.48
Consensus pattern (109 bp):
TTTTTATTAAACTTTCATATATAAAATTTTCAATTAAACTCTTTATATATAGAATTTTTAATTAA
AATTTCACATATAAATTATTAAATTAAACTTTGTGCATATTGAA
Found at i:10764 original size:28 final size:28
Alignment explanation
Indices: 10380--11024 Score: 256
Period size: 28 Copynumber: 23.0 Consensus size: 28
10370 ACATATATAA
*
10380 TTTTTA-AT-TAAACTTTTT-ATTAAA-
1 TTTTTATATATAAAATTTTTAATTAAAC
* *** *
10404 TTTTCATATATAGGCTTTTCAATTAAAC
1 TTTTTATATATAAAATTTTTAATTAAAC
* *
10432 TCTTTATATATAGAATTTTTAATTAAA-
1 TTTTTATATATAAAATTTTTAATTAAAC
* * * *
10459 ATTTCACATAT-AAATTATTCAATTAAAC
1 TTTTTATATATAAAATT-TTTAATTAAAC
* ** **
10487 TTTGTGCATATTGAATTTTTAATTAAAC
1 TTTTTATATATAAAATTTTTAATTAAAC
* * *
10515 -TTTCATATGTAAAATTTTCAATTAAAC
1 TTTTTATATATAAAATTTTTAATTAAAC
* * *
10542 CTTTTGTATATAAATTTTTTAATTAAA-
1 TTTTTATATATAAAATTTTTAATTAAAC
* * * * ** *
10569 GTTCTACATGTGCAATTTTAAATTAAAC
1 TTTTTATATATAAAATTTTTAATTAAAC
* **
10597 TTTCTTATATATAGAATTTTTAACTTTTTCTTAC
1 TTT-TTATATATAAAATTTTTAA----TT-AAAC
* * *
10631 TTTTTATATATGAACTTTTTAATTAGAC
1 TTTTTATATATAAAATTTTTAATTAAAC
* * *
10659 TTTTTTTGTACATATGAAATTTTTAATTGAAC
1 ---TTTT-TATATATAAAATTTTTAATTAAAC
* * * * * * *
10691 CTTTTACAAATAGAATTCTTGA-TAAAA
1 TTTTTATATATAAAATTTTTAATTAAAC
*
10718 TTTTTATAAACATAAAATTTTTAATTAAAC
1 TTTTTAT--ATATAAAATTTTTAATTAAAC
* * *
10748 TTTTTATGTATAAAA-TTTTAGTCAAAC
1 TTTTTATATATAAAATTTTTAATTAAAC
* * * * *
10775 TCTTTATACATAGAGTTTTTAATTAATC
1 TTTTTATATATAAAATTTTTAATTAAAC
** * * * * *
10803 CATTTACATATAGAACTTTTAACTGAAC
1 TTTTTATATATAAAATTTTTAATTAAAC
* * *
10831 ATTTTAAATAGAAAATTTTTAATTAAAC
1 TTTTTATATATAAAATTTTTAATTAAAC
* * * **
10859 TTTTTACACATAGAATTTTTAATTAGGC
1 TTTTTATATATAAAATTTTTAATTAAAC
* ** * ** *
10887 TCTTTGCATGTGGAATTTCTAATTAAAC
1 TTTTTATATATAAAATTTTTAATTAAAC
* * *
10915 -TTCT-TACATGAAATTTTTAATTAAAC
1 TTTTTATATATAAAATTTTTAATTAAAC
* * *
10941 TTTTTAGATGTAAAAAATTTTAATTAAAC
1 TTTTTATATAT-AAAATTTTTAATTAAAC
* * * * *
10970 TTTTTACATGTAGAATTTATAATTAGAC
1 TTTTTATATATAAAATTTTTAATTAAAC
*
10998 -TTTTACT-TATTAAATTTTTAATTAAAC
1 TTTTTA-TATATAAAATTTTTAATTAAAC
11025 CCTCACACAT
Statistics
Matches: 450, Mismatches: 144, Indels: 51
0.70 0.22 0.08
Matches are distributed among these distances:
24 5 0.01
25 2 0.00
26 28 0.06
27 112 0.25
28 187 0.42
29 58 0.13
30 11 0.02
31 4 0.01
32 20 0.04
33 18 0.04
34 5 0.01
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (28 bp):
TTTTTATATATAAAATTTTTAATTAAAC
Found at i:10774 original size:27 final size:28
Alignment explanation
Indices: 10729--10781 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
10719 TTTTATAAAC
* *
10729 ATAAAATTTTTAATTAAACTTTTTATGT
1 ATAAAATTTTTAATCAAACTCTTTATGT
*
10757 ATAAAA-TTTTAGTCAAACTCTTTAT
1 ATAAAATTTTTAATCAAACTCTTTAT
10782 ACATAGAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.49
Consensus pattern (28 bp):
ATAAAATTTTTAATCAAACTCTTTATGT
Found at i:10961 original size:30 final size:29
Alignment explanation
Indices: 10900--10981 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
10890 TTGCATGTGG
*
10900 AATTTCTAATTAAACTTCTTACATG---AA
1 AATTT-TAATTAAACTTTTTACATGTAAAA
* *
10927 ATTTTTAATTAAACTTTTTAGATGTAAAA
1 AATTTTAATTAAACTTTTTACATGTAAAA
10956 AATTTTAATTAAACTTTTTACATGTA
1 AATTTTAATTAAACTTTTTACATGTA
10982 GAATTTATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 17 0.36
27 4 0.09
29 26 0.55
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (29 bp):
AATTTTAATTAAACTTTTTACATGTAAAA
Found at i:10993 original size:83 final size:82
Alignment explanation
Indices: 10843--11024 Score: 213
Period size: 83 Copynumber: 2.2 Consensus size: 82
10833 TTTAAATAGA
* * ** * * *
10843 AAATTTTTAATTAAACTTTTTACACATAGAATTTTTAATTAGGCTCTTTGCATGTGGAATTTCTA
1 AAATTTTTAATTAAACTTTTTACACATAAAAATTTTAATTAAACTCTTTACATGTAGAATTTATA
10908 ATTAAACTTCTTAC-ATG
66 ATTAAACTT-TTACTATG
* ** *
10925 AAATTTTTAATTAAACTTTTTAGATGTAAAAAATTTTAATTAAACTTTTTACATGTAGAATTTAT
1 AAATTTTTAATTAAACTTTTTACACAT-AAAAATTTTAATTAAACTCTTTACATGTAGAATTTAT
* *
10990 AATTAGACTTTTACTTATT
65 AATTAAACTTTTAC-TATG
11009 AAATTTTTAATTAAAC
1 AAATTTTTAATTAAAC
11025 CCTCACACAT
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
82 28 0.33
83 38 0.45
84 18 0.21
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (82 bp):
AAATTTTTAATTAAACTTTTTACACATAAAAATTTTAATTAAACTCTTTACATGTAGAATTTATA
ATTAAACTTTTACTATG
Found at i:11495 original size:6 final size:6
Alignment explanation
Indices: 11477--11520 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
11467 TCCACTTCTT
* *
11477 GAAAAA AAAAAA GAGAAA GAAAGAAA GAAAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA G-AA-AAA GAAAAA GAAAAA GAAAAA
11521 AAATGTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 25 0.78
7 3 0.09
8 4 0.12
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:12918 original size:39 final size:39
Alignment explanation
Indices: 12857--13002 Score: 123
Period size: 39 Copynumber: 3.7 Consensus size: 39
12847 TATTTTGTGA
* * *
12857 TCATATTAGTATTTTTATGTCAAAATTAAACCTTAAAAG
1 TCATTTTAATATTTTTATGTCAAAATTAAACCTTAAGAG
* ***
12896 TCATTTTAATATTTTTATGTCAAAATCCATTTCTTAAGA-
1 TCATTTTAATATTTTTATGTCAAAAT-TAAACCTTAAGAG
* * * * * *
12935 TCGTGTTAGTATTTTCATGTCAAAATTAAACATTTAGAG
1 TCATTTTAATATTTTTATGTCAAAATTAAACCTTAAGAG
* * * *
12974 TCATTTTTATAATTTTATATTAAAATTAA
1 TCATTTTAATATTTTTATGTCAAAATTAA
13003 GTCTTTAAAA
Statistics
Matches: 80, Mismatches: 25, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
38 6 0.08
39 67 0.84
40 7 0.09
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.46
Consensus pattern (39 bp):
TCATTTTAATATTTTTATGTCAAAATTAAACCTTAAGAG
Found at i:12959 original size:78 final size:78
Alignment explanation
Indices: 12818--12991 Score: 208
Period size: 78 Copynumber: 2.2 Consensus size: 78
12808 CTTTAAGGTT
** *
12818 ATTTTAATATTTTTTATGTCAAAACCAGATATTTTGTGATCATATTAGTATTTTTATGTCAAAAT
1 ATTTTAATA-TTTTTATGTCAAAACCA-ATATTTTAAGATCATATTAGTATTTTCATGTCAAAAT
*
12883 TAAACCTTAAAAGTC
64 TAAACATTAAAAGTC
* *
12898 ATTTTAATATTTTTATGTCAAAATCC-AT-TTCTTAAGATCGTGTTAGTATTTTCATGTCAAAAT
1 ATTTTAATATTTTTATGTCAAAA-CCAATATT-TTAAGATCATATTAGTATTTTCATGTCAAAAT
* *
12961 TAAACATTTAGAGTC
64 TAAACATTAAAAGTC
* *
12976 ATTTTTATAATTTTAT
1 ATTTTAATATTTTTAT
12992 ATTAAAATTA
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
77 2 0.02
78 55 0.67
79 14 0.17
80 11 0.13
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (78 bp):
ATTTTAATATTTTTATGTCAAAACCAATATTTTAAGATCATATTAGTATTTTCATGTCAAAATTA
AACATTAAAAGTC
Found at i:16290 original size:2 final size:2
Alignment explanation
Indices: 16257--16281 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16247 TAAATAGGTT
16257 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
16282 GCATATATAA
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:16408 original size:72 final size:69
Alignment explanation
Indices: 16284--16418 Score: 157
Period size: 72 Copynumber: 1.9 Consensus size: 69
16274 ATATATATGC
*
16284 ATATATAAAAAATAATTAAATTGATCTCTCAAAAATTTTAAAAAATTTTTATTATATATTTTTAT
1 ATATATAAAAAATAATTAAATTGATCTCTCAAAAA--TTAAAAAATATTTATT-T-TATTTTTAT
16349 ATCTATTT
62 ATCTATTT
* **
16357 ATATAT-AAAAATAATTAAATTGATCCTTTCAAAAA-TAAATTTTATATTTATTTTATTTTTAT
1 ATATATAAAAAATAATTAAATTGAT-CTCTCAAAAATTAAA--AAATATTTATTTTATTTTTAT
16419 TTATAACTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
70 13 0.24
71 1 0.02
72 26 0.47
73 15 0.27
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.49
Consensus pattern (69 bp):
ATATATAAAAAATAATTAAATTGATCTCTCAAAAATTAAAAAATATTTATTTTATTTTTATATCT
ATTT
Found at i:21751 original size:17 final size:16
Alignment explanation
Indices: 21723--21763 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
21713 AAAAAACCAA
21723 TTTTTTAA-TTTTAAT
1 TTTTTTAACTTTTAAT
21738 TTTTTTAACTTTTTAAT
1 TTTTTTAAC-TTTTAAT
*
21755 TATTTTAAC
1 TTTTTTAAC
21764 GTCGTTGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.35
17 15 0.65
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTTAACTTTTAAT
Found at i:23039 original size:2 final size:2
Alignment explanation
Indices: 23032--23065 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
23022 GATTTTCGGT
*
23032 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23066 AAAGGTCGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:25973 original size:15 final size:15
Alignment explanation
Indices: 25938--26005 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
25928 CATTTATCAT
*
25938 AATAGATATATAAAA
1 AATAAATATATAAAA
**
25953 TGTAAATATATAAAA
1 AATAAATATATAAAA
25968 AATAAATA-A-AATACA
1 AATAAATATATAA-A-A
* *
25983 ACTAAATATATTAAA
1 AATAAATATATAAAA
25998 AATAAATA
1 AATAAATA
26006 AAATTGTAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
13 2 0.05
14 2 0.05
15 34 0.83
16 2 0.05
17 1 0.02
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (15 bp):
AATAAATATATAAAA
Found at i:30441 original size:28 final size:28
Alignment explanation
Indices: 30369--30759 Score: 379
Period size: 28 Copynumber: 13.6 Consensus size: 28
30359 CACCAACTTG
* *
30369 TGTGGGCTTTAGAGAAAGTTGCCACTAACTT
1 TGTGGGCTTT-GA-AAAGATGCCACTGAC-T
*
30400 GTGTGGGCTTTGAAACGATGCCACTGACT
1 -TGTGGGCTTTGAAAAGATGCCACTGACT
* *
30429 TGTGAGCTTTGAAAAGATGCCATTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * *
30457 TGTGGGTTTTGAAATGATGCCATTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
*
30485 TGTGGGCTTTGAAAAGATGCCACTGATT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * * *
30513 TGTGGGCTTTGAAAGGATGCAACTAACA
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * *
30541 TGTGGGCTTTGAGAAGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* *
30569 TGTGGGTTTTGAAAAGATGCCATTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * *
30597 TATGGGCTTTGAAAAGGGTTGCCACTAACT
1 TGTGGGCTTTGAAAA--GATGCCACTGACT
* *
30627 TGTGCGCTTTGAAGAGATGCCA-TCGACT
1 TGTGGGCTTTGAAAAGATGCCACT-GACT
* *
30655 TGTGGGCTTTGAAAAAATGCCACTAACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * *
30683 TATGGGCTTTGAAAAAGGTTGCCACTGATT
1 TGTGGGCTTTG-AAAA-GATGCCACTGACT
* * * *
30713 TGTGGGCTTTAAAAAGGGTTGTCATTGACT
1 TGTGGGCTTTGAAAA--GATGCCACTGACT
*
30743 TGTAGGCTTTGAAAAGA
1 TGTGGGCTTTGAAAAGA
30760 GGTCGCATTG
Statistics
Matches: 297, Mismatches: 55, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
27 1 0.00
28 198 0.67
29 10 0.03
30 76 0.26
31 2 0.01
32 10 0.03
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (28 bp):
TGTGGGCTTTGAAAAGATGCCACTGACT
Found at i:30786 original size:14 final size:14
Alignment explanation
Indices: 30767--30855 Score: 51
Period size: 14 Copynumber: 6.6 Consensus size: 14
30757 AGAGGTCGCA
30767 TTGACAAAAATTTC
1 TTGACAAAAATTTC
*
30781 TTGAC-AAAGTTTC
1 TTGACAAAAATTTC
* *
30794 -TGACGAACA-TTC
1 TTGACAAAAATTTC
* *
30806 TCGAC-AAAAGTTC
1 TTGACAAAAATTTC
* *
30819 TTGACGATAATTTC
1 TTGACAAAAATTTC
* **
30833 TTAACAACCATTTC
1 TTGACAAAAATTTC
*
30847 TTGATAAAA
1 TTGACAAAA
30856 GGGTCTTGGC
Statistics
Matches: 55, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
12 10 0.18
13 19 0.35
14 26 0.47
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (14 bp):
TTGACAAAAATTTC
Found at i:46749 original size:52 final size:52
Alignment explanation
Indices: 46671--46798 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
46661 CGAAATATGA
*
46671 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
46723 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
46775 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
46799 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 21 0.28
52 48 0.65
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:46825 original size:13 final size:13
Alignment explanation
Indices: 46807--46831 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46797 CAAAGATCAG
46807 TGTATCGATACAA
1 TGTATCGATACAA
46820 TGTATCGATACA
1 TGTATCGATACA
46832 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:46909 original size:33 final size:33
Alignment explanation
Indices: 46872--46938 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
46862 AGTAGCTTAA
46872 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
46905 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
46938 A
1 A
46939 GATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:46912 original size:13 final size:13
Alignment explanation
Indices: 46894--46918 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46884 CAAAAAAATA
46894 TGTATCGATACAT
1 TGTATCGATACAT
46907 TGTATCGATACA
1 TGTATCGATACA
46919 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:47714 original size:2 final size:2
Alignment explanation
Indices: 47707--47739 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
47697 AGGCATTATT
47707 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 T
47740 TCTAGAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50787 original size:70 final size:69
Alignment explanation
Indices: 50691--50825 Score: 225
Period size: 70 Copynumber: 1.9 Consensus size: 69
50681 GAAATTTTCG
* ** *
50691 TCGAAAATGGTTTGTCTGTCTGAAATAGAAAATAAATATTTAATTTTTTATTTAATTATAAAAAA
1 TCGAAAATGGTTTGTCTGACCAAAATAGAAAATAAATATTTAA-TTTTTATTTAATTACAAAAAA
50756 ATTCA
65 ATTCA
50761 TCGAAAATGGTTTGTCTGACCAAAATAGAAAATAAATATTTAATTTTTATTTAATTACAAAAAAA
1 TCGAAAATGGTTTGTCTGACCAAAATAGAAAATAAATATTTAATTTTTATTTAATTACAAAAAAA
50826 ATCAACTAAG
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
69 21 0.34
70 40 0.66
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.39
Consensus pattern (69 bp):
TCGAAAATGGTTTGTCTGACCAAAATAGAAAATAAATATTTAATTTTTATTTAATTACAAAAAAA
TTCA
Found at i:54372 original size:19 final size:18
Alignment explanation
Indices: 54347--54393 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
54337 ATTGAGTAAA
*
54347 TATAAATATAATATAAAT
1 TATAAATATAATAAAAAT
54365 TAATAAATAT-ATAAAAAT
1 T-ATAAATATAATAAAAAT
*
54383 TTTAAATATAA
1 TATAAATATAA
54394 ATATTTATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 7 0.28
18 10 0.40
19 8 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TATAAATATAATAAAAAT
Found at i:54390 original size:17 final size:18
Alignment explanation
Indices: 54348--54392 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
54338 TTGAGTAAAT
*
54348 ATAAATATAATATAAATTA
1 ATAAATAT-ATAAAAATTA
54367 ATAAATATATAAAAATT-
1 ATAAATATATAAAAATTA
*
54384 TTAAATATA
1 ATAAATATA
54393 AATATTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
19 8 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATATATAAAAATTA
Found at i:54397 original size:21 final size:22
Alignment explanation
Indices: 54343--54413 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 22
54333 TTTAATTGAG
54343 TAAATATAAATATAATATAAAT
1 TAAATATAAATATAATATAAAT
*
54365 T-AATA-AATATATAA-A-AATTT
1 TAAATATAA-ATATAATATAA-AT
* *
54385 TAAATATAAATAT-TTATGAAT
1 TAAATATAAATATAATATAAAT
54406 TAAATATA
1 TAAATATA
54414 TTATATTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
19 2 0.05
20 5 0.13
21 28 0.72
22 4 0.10
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (22 bp):
TAAATATAAATATAATATAAAT
Found at i:54636 original size:17 final size:17
Alignment explanation
Indices: 54614--54649 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
54604 TTTATTGGCC
54614 TAAGTGCTCTAAAATCA
1 TAAGTGCTCTAAAATCA
54631 TAAGTGCTCTAAAATCA
1 TAAGTGCTCTAAAATCA
54648 TA
1 TA
54650 GGGATACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.31
Consensus pattern (17 bp):
TAAGTGCTCTAAAATCA
Found at i:54798 original size:11 final size:11
Alignment explanation
Indices: 54756--54819 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
54746 TTAATTTAAA
54756 ATTTTT-TATT
1 ATTTTTATATT
54766 ATTTATTATATT
1 ATTT-TTATATT
***
54778 ATTAAAATATT
1 ATTTTTATATT
54789 ATTTTTATATT
1 ATTTTTATATT
* *
54800 AATATTTAT-CT
1 -ATTTTTATATT
54811 ATTTTTATA
1 ATTTTTATA
54820 ATTAAAATTT
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
10 11 0.27
11 16 0.39
12 14 0.34
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTTTTATATT
Found at i:54813 original size:22 final size:23
Alignment explanation
Indices: 54760--54830 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
54750 TTTAAAATTT
54760 TTTAT-TATTTATTATATTATTAAAA
1 TTTATCTATTT-TTATA--ATTAAAA
*
54785 --TAT-TATTTTTAT-ATTAATA
1 TTTATCTATTTTTATAATTAAAA
54804 TTTATCTATTTTTATAATTAAAA
1 TTTATCTATTTTTATAATTAAAA
54827 TTTA
1 TTTA
54831 AAAAATATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 6 0.15
21 3 0.08
22 13 0.32
23 18 0.45
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTATCTATTTTTATAATTAAAA
Found at i:54869 original size:20 final size:20
Alignment explanation
Indices: 54852--54888 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54842 TTTTATTATT
54852 AAATAA-TAATTTAAATTAG
1 AAATAATTAATTTAAATTAG
*
54871 ACATAATTAATTTAAATT
1 AAATAATTAATTTAAATT
54889 TTTTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
AAATAATTAATTTAAATTAG
Found at i:61423 original size:20 final size:20
Alignment explanation
Indices: 61398--61438 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
61388 TTTCCTATCA
61398 TAATATCCATTTTTAATTGT
1 TAATATCCATTTTTAATTGT
61418 TAATATCCATTTTTAATTGT
1 TAATATCCATTTTTAATTGT
61438 T
1 T
61439 TGGTGCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (20 bp):
TAATATCCATTTTTAATTGT
Found at i:61681 original size:19 final size:19
Alignment explanation
Indices: 61654--61692 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
61644 GCGTCCCTAT
*
61654 TGAAGAGAGAGATTTAGAA
1 TGAAAAGAGAGATTTAGAA
61673 TGAAAAGAGAGATTTAGAA
1 TGAAAAGAGAGATTTAGAA
61692 T
1 T
61693 ACAAGAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.28, T:0.23
Consensus pattern (19 bp):
TGAAAAGAGAGATTTAGAA
Found at i:61870 original size:54 final size:54
Alignment explanation
Indices: 61806--61908 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
61796 ATCTTTGATA
*
61806 GTGATTACAATCAAAGATACGTTAACAATATGCT-AACAATGCAAGATATTCATG
1 GTGATTACAATCAAAGATACGCTAACAATATGCTGAA-AATGCAAGATATTCATG
* * *
61860 GTGATTACAATCAAAGATATGCTGACAATATGTTGAAAATGCAAGATAT
1 GTGATTACAATCAAAGATACGCTAACAATATGCTGAAAATGCAAGATAT
61909 CTTAGTAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 42 0.95
55 2 0.05
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.28
Consensus pattern (54 bp):
GTGATTACAATCAAAGATACGCTAACAATATGCTGAAAATGCAAGATATTCATG
Found at i:67028 original size:20 final size:19
Alignment explanation
Indices: 66995--67056 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
66985 AAAAATTTTG
66995 TTAATTGATAAAAAAATTAAT
1 TTAATT-AT-AAAAAATTAAT
*
67016 TTAATTAATAAAAAA-TCAT
1 TTAATT-ATAAAAAATTAAT
*
67035 ATTAAATATAAAAAATTAAT
1 -TTAATTATAAAAAATTAAT
67055 TT
1 TT
67057 TAAATTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 13 0.37
20 14 0.40
21 8 0.23
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
TTAATTATAAAAAATTAAT
Found at i:67059 original size:20 final size:21
Alignment explanation
Indices: 67005--67061 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
66995 TTAATTGATA
*
67005 AAAAAATTAA-TTTAATTAAT
1 AAAAAATTAATTTTAAATAAT
* *
67025 AAAAAA-TCATATTAAAT-AT
1 AAAAAATTAATTTTAAATAAT
67044 AAAAAATTAATTTTAAAT
1 AAAAAATTAATTTTAAAT
67062 TTATTTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAAATTAATTTTAAATAAT
Found at i:69723 original size:1 final size:1
Alignment explanation
Indices: 69717--69796 Score: 133
Period size: 1 Copynumber: 80.0 Consensus size: 1
69707 AAAGTGTTTG
***
69717 AAAAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
69782 AAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAA
69797 TTTAAATGTA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.96, C:0.00, G:0.01, T:0.03
Consensus pattern (1 bp):
A
Found at i:69825 original size:21 final size:21
Alignment explanation
Indices: 69801--69857 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
69791 AAAAAATTTA
69801 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
69822 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
69843 AATGTATCGATACAT
1 AATGTATCGATACAT
69858 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:69937 original size:19 final size:19
Alignment explanation
Indices: 69913--69980 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
69903 AATTCAACAA
69913 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
69932 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
69947 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
69964 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
69981 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:69952 original size:13 final size:13
Alignment explanation
Indices: 69934--69958 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
69924 ACATAAGTTT
69934 TGTATCGATACAA
1 TGTATCGATACAA
69947 TGTATCGATACA
1 TGTATCGATACA
69959 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:69956 original size:32 final size:32
Alignment explanation
Indices: 69915--69977 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
69905 TTCAACAATT
*
69915 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
69947 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
69978 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:70038 original size:13 final size:13
Alignment explanation
Indices: 70020--70045 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
70010 CATTTTTCTG
70020 TGTATCGATACAT
1 TGTATCGATACAT
70033 TGTATCGATACAT
1 TGTATCGATACAT
70046 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:70042 original size:33 final size:33
Alignment explanation
Indices: 70000--70066 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
69990 GCCAAGGAAA
***
70000 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
70033 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
70066 T
1 T
70067 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:72591 original size:28 final size:27
Alignment explanation
Indices: 72524--72596 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
72514 CTTCACAATC
* *
72524 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
72551 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
72579 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
72597 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:72641 original size:51 final size:51
Alignment explanation
Indices: 72579--72749 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
72569 TTATTTCTGA
* * *
72579 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
72630 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
72683 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
72735 GAGGATACTCCAACC
1 GGGGATACTCCAACC
72750 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:72768 original size:28 final size:28
Alignment explanation
Indices: 72732--72813 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
72722 ATTTTTCACA
*
72732 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
72760 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
72788 --CGAAGGAACACTCCAACCTCGTTATT
1 ATCG--GGGATACTCCAACCTCGTTATT
72814 ATCTCCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
28 43 0.96
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Done.