Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold210
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: 317021
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
File 1 of 3
Found at i:2888 original size:22 final size:21
Alignment explanation
Indices: 2839--2891 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
2829 TGATTTAAAC
*
2839 TCAAATT--ATTATTAATTGT
1 TCAAATTCAATTATTAATTAT
2858 TCAAATTCAATTATTAACTTAT
1 TCAAATTCAATTATTAA-TTAT
*
2880 TTAAATTCAATT
1 TCAAATTCAATT
2892 TGGTTTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 7 0.24
21 8 0.28
22 14 0.48
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (21 bp):
TCAAATTCAATTATTAATTAT
Found at i:3071 original size:18 final size:19
Alignment explanation
Indices: 3037--3073 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3027 AATTAAATAT
3037 AATAAAAATATATATTAAA
1 AATAAAAATATATATTAAA
*
3056 AATAAAAATTTA-ATTAAA
1 AATAAAAATATATATTAAA
3074 TTTATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAAAAATATATATTAAA
Found at i:3087 original size:16 final size:14
Alignment explanation
Indices: 3068--3110 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 14
3058 TAAAAATTTA
3068 ATTAAATTTATAAATT
1 ATTAAATTTA-AAA-T
3084 ATTAAATATTAAAAT
1 ATTAAAT-TTAAAAT
3099 ATATAAATTTAA
1 AT-TAAATTTAA
3111 CTCGATTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 7 0.28
16 15 0.60
17 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTAAATTTAAAAT
Found at i:6610 original size:29 final size:25
Alignment explanation
Indices: 6576--6632 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 25
6566 ATTTTTATTT
6576 AATTTAAAAAATTAATAATTTTATAATTA
1 AATTTAAAAAATT--T--TTTTATAATTA
*
6605 AATTTAAATAATTTTTTTATAATTA
1 AATTTAAAAAATTTTTTTATAATTA
6630 AAT
1 AAT
6633 AAATTTCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 14 0.52
27 1 0.04
29 12 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AATTTAAAAAATTTTTTTATAATTA
Found at i:7130 original size:92 final size:91
Alignment explanation
Indices: 6964--7270 Score: 426
Period size: 92 Copynumber: 3.4 Consensus size: 91
6954 TTGACTCGTA
* * * * * *
6964 TAGGTAATTT-TCTTGTTTTATTTTGAAACATCCTTA-ATACTACCCCGAAAGTGGCACTAGGAC
1 TAGGTAATTTCTCTTGTTTTATTTTGAACCATCCTTACACA-TTCCACGAAAGTGGCACCAAGAC
7027 CATAGCAGCTGACTCGTATATTATTAT
65 CATAGCAGCTGACTCGTATATTATTAT
* * *
7054 TAGTTAATTTCTCTTGTTTTATTTTGAAGCATCCTTAGCACATTCCACAAAAGTGGCACCAAGAC
1 TAGGTAATTTCTCTTGTTTTATTTTGAACCATCCTTA-CACATTCCACGAAAGTGGCACCAAGAC
7119 CATAGCAGCTGACTCGTATATTATTAT
65 CATAGCAGCTGACTCGTATATTATTAT
* * * *
7146 TAGGTAATTTCTCTTGTTCTATTTTGAACCGTCCTTACA-ACTTCCACGAAGGTGGCACGAAGAC
1 TAGGTAATTTCTCTTGTTTTATTTTGAACCATCCTTACACA-TTCCACGAAAGTGGCACCAAGAC
*
7210 CATAGCAGTTGACTCGTATA-T-TTAT
65 CATAGCAGCTGACTCGTATATTATTAT
7235 TAGGTAATTTCTCTTGTTTTATTTTGAACCATCCTT
1 TAGGTAATTTCTCTTGTTTTATTTTGAACCATCCTT
7271 TATGACCAAA
Statistics
Matches: 195, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
89 38 0.19
90 11 0.06
91 66 0.34
92 78 0.40
93 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (91 bp):
TAGGTAATTTCTCTTGTTTTATTTTGAACCATCCTTACACATTCCACGAAAGTGGCACCAAGACC
ATAGCAGCTGACTCGTATATTATTAT
Found at i:11085 original size:27 final size:26
Alignment explanation
Indices: 11044--11094 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
11034 GTCTATCCCT
*
11044 TATTTTTATTGAATTTAAAAAATTAA
1 TATTTTTATTAAATTTAAAAAATTAA
*
11070 TATTTTTAATTAAATTTAAATAATT
1 TATTTTT-ATTAAATTTAAAAAATT
11095 TTTTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
TATTTTTATTAAATTTAAAAAATTAA
Found at i:31344 original size:1 final size:1
Alignment explanation
Indices: 31334--31422 Score: 70
Period size: 1 Copynumber: 89.0 Consensus size: 1
31324 TGGCAATTGG
* * * ** * * * **
31334 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAAACAAAACAAAAAAAAGGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
31399 AAGAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAA
31423 GGTGAAGATT
Statistics
Matches: 68, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.87, C:0.06, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:31367 original size:16 final size:16
Alignment explanation
Indices: 31348--31409 Score: 79
Period size: 16 Copynumber: 3.8 Consensus size: 16
31338 AGAAAAAAAC
31348 AAAACAAAAAAAAGGA
1 AAAACAAAAAAAAGGA
* **
31364 AAAAGAAAAAAAAAAA
1 AAAACAAAAAAAAGGA
31380 CAAAACAAAAAAAAGGA
1 -AAAACAAAAAAAAGGA
*
31397 AAAAGAAAAAAAA
1 AAAACAAAAAAAA
31410 AACAAAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
16 25 0.66
17 13 0.34
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAACAAAAAAAAGGA
Found at i:31390 original size:32 final size:33
Alignment explanation
Indices: 31335--31422 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
31325 GGCAATTGGA
31335 AAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAG
1 AAAA-AAAAAAACAAAACAAAAAAAAGGAAAAAG
31369 AAAAAAAAAAACAAAACAAAAAAAAGGAAAAAG
1 AAAAAAAAAAACAAAACAAAAAAAAGGAAAAAG
31402 -AAAAAAAAAACAAAA-AAAAAA
1 AAAAAAAAAAACAAAACAAAAAA
31423 GGTGAAGATT
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
31 6 0.11
32 15 0.28
33 29 0.54
34 4 0.07
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (33 bp):
AAAAAAAAAAACAAAACAAAAAAAAGGAAAAAG
Found at i:31420 original size:27 final size:26
Alignment explanation
Indices: 31334--31420 Score: 113
Period size: 27 Copynumber: 3.2 Consensus size: 26
31324 TGGCAATTGG
*
31334 AAAAAGAAAAAAACAAAACAAAAAAAA
1 AAAAAGAAAAAAA-AAAACAAAACAAA
31361 GGAAAAAGAAAAAAAAAAACAAAACAAA
1 --AAAAAGAAAAAAAAAAACAAAACAAA
31389 AAAAAGGAAAAAGAAAAAA-AAAACAAA
1 AAAAA-GAAAAA-AAAAAACAAAACAAA
31416 AAAAA
1 AAAAA
31421 AAGGTGAAGA
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
26 5 0.09
27 19 0.35
28 18 0.33
29 13 0.24
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (26 bp):
AAAAAGAAAAAAAAAAACAAAACAAA
Found at i:52352 original size:15 final size:17
Alignment explanation
Indices: 52322--52353 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
52312 TTATATGAAT
52322 TTTTATGTTGAAATTTA
1 TTTTATGTTGAAATTTA
52339 TTTTAT-TT-AAATTTA
1 TTTTATGTTGAAATTTA
52354 AGATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTTATGTTGAAATTTA
Found at i:52416 original size:18 final size:18
Alignment explanation
Indices: 52392--52428 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
52382 CAATACGAAT
*
52392 ATTTTTAATTT-TTTAAA
1 ATTTTTTATTTATTTAAA
52409 ATTTTTTATTTATTTAAA
1 ATTTTTTATTTATTTAAA
52427 AT
1 AT
52429 ATTATATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTTTATTTATTTAAA
Found at i:54906 original size:16 final size:15
Alignment explanation
Indices: 54887--54940 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 15
54877 TGTTAATCTT
54887 TTTTATATAAATATAA
1 TTTTATAT-AATATAA
*
54903 TTTTA-AT--TATTA
1 TTTTATATAATATAA
*
54915 TTTAATATAATATAA
1 TTTTATATAATATAA
54930 TTTTGATATAA
1 TTTT-ATATAA
54941 ATTTTTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
12 8 0.27
13 2 0.07
15 9 0.30
16 11 0.37
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TTTTATATAATATAA
Found at i:55264 original size:23 final size:24
Alignment explanation
Indices: 55225--55285 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
55215 AAGTAAGATA
* *
55225 TTTTTTTAATA-ATAGGTGAGTAC
1 TTTTTTTAATATAAAGGTGAATAC
55248 -TTTTTTAATATAAAGGTGAATAC
1 TTTTTTTAATATAAAGGTGAATAC
55271 TTTTTTTAATATAAA
1 TTTTTTTAATATAAA
55286 ATTATTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 10 0.29
23 10 0.29
24 14 0.41
ACGTcount: A:0.36, C:0.03, G:0.11, T:0.49
Consensus pattern (24 bp):
TTTTTTTAATATAAAGGTGAATAC
Found at i:55496 original size:23 final size:25
Alignment explanation
Indices: 55465--55518 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
55455 TGAACATAAA
*
55465 TATAATGTAAATATTAAAT-ATA-T
1 TATATTGTAAATATTAAATAATATT
**
55488 TATATTGTATTTATTAAATAATATT
1 TATATTGTAAATATTAAATAATATT
55513 TATATT
1 TATATT
55519 ATTAATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 16 0.62
24 3 0.12
25 7 0.27
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (25 bp):
TATATTGTAAATATTAAATAATATT
Found at i:55526 original size:23 final size:24
Alignment explanation
Indices: 55477--55535 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
55467 TAATGTAAAT
*
55477 ATTAAATATA-TTATATTGTATTT
1 ATTAAATATATTTATATTGTATTA
55500 ATTAAATAATATTTATA-T-TATTA
1 ATTAAAT-ATATTTATATTGTATTA
*
55523 ATTATATTATATT
1 ATTA-AATATATT
55536 ATGACATGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 20 0.65
24 6 0.19
25 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTAAATATATTTATATTGTATTA
Found at i:56252 original size:24 final size:25
Alignment explanation
Indices: 56224--56276 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
56214 ATTCAAATGA
56224 ATTTTGATAT-AATAATAATAA-TTT
1 ATTTT-ATATAAATAATAATAAGTTT
**
56248 ATTTTATATAAATTTTAATAAGTTT
1 ATTTTATATAAATAATAATAAGTTT
56273 ATTT
1 ATTT
56277 ATTCGTGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.16
24 14 0.56
25 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (25 bp):
ATTTTATATAAATAATAATAAGTTT
Found at i:57905 original size:23 final size:23
Alignment explanation
Indices: 57878--57921 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
57868 TTTAAGAAAT
*
57878 TGCTACAATTACTGATTGAAGAC
1 TGCTACAATTACAGATTGAAGAC
57901 TGCTACAATTACAGATTGAAG
1 TGCTACAATTACAGATTGAAG
57922 TGTTTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (23 bp):
TGCTACAATTACAGATTGAAGAC
Found at i:58471 original size:18 final size:17
Alignment explanation
Indices: 58444--58477 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
58434 TTGATATGTA
58444 GAAAAAAATAATAATAG
1 GAAAAAAATAATAATAG
58461 GAAAGAAAATAATAATA
1 GAAA-AAAATAATAATA
58478 AAAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (17 bp):
GAAAAAAATAATAATAG
Found at i:59228 original size:6 final size:6
Alignment explanation
Indices: 59211--59260 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
59201 TTAATTTATG
* *
59211 TATTTA TA-TTA TATTTA TATGTA TA--TA TATTTA TA-TTA TAATTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
59255 TATTTA
1 TATTTA
59261 AGCATTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
4 4 0.11
5 10 0.26
6 24 0.63
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (6 bp):
TATTTA
Found at i:59233 original size:21 final size:22
Alignment explanation
Indices: 59207--59247 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
59197 TCTATTAATT
*
59207 TATGTATTTATA-TTATATTTA
1 TATGTATATATATTTATATTTA
59228 TATGTATATATATTTATATT
1 TATGTATATATATTTATATT
59248 ATAATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (22 bp):
TATGTATATATATTTATATTTA
Found at i:63669 original size:5 final size:5
Alignment explanation
Indices: 63659--63720 Score: 51
Period size: 5 Copynumber: 13.0 Consensus size: 5
63649 ATGTTTTGAC
* * *
63659 ATATT ATATT ATATT -TATT ATATT ATTTTT TTATT -TATT -TAAT ATATT
1 ATATT ATATT ATATT ATATT ATATT A-TATT ATATT ATATT ATATT ATATT
*
63707 AT-TG ATATT ATATT
1 ATATT ATATT ATATT
63721 TTCGTATCAT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
4 14 0.30
5 29 0.63
6 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (5 bp):
ATATT
Found at i:63679 original size:9 final size:9
Alignment explanation
Indices: 63659--63720 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 9
63649 ATGTTTTGAC
63659 ATATTATATT
1 ATATT-TATT
63669 ATATTTATT
1 ATATTTATT
63678 ATA-TTATT
1 ATATTTATT
*
63686 -TTTTTATT
1 ATATTTATT
*
63694 -TATTTAAT
1 ATATTTATT
63702 ATA-TTATT
1 ATATTTATT
63710 GATATTATATT
1 -ATATT-TATT
63721 TTCGTATCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
7 1 0.02
8 20 0.47
9 12 0.28
10 6 0.14
11 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
ATATTTATT
Found at i:63696 original size:12 final size:13
Alignment explanation
Indices: 63660--63720 Score: 63
Period size: 14 Copynumber: 4.7 Consensus size: 13
63650 TGTTTTGACA
63660 TATTATATTATATT
1 TATTATATTAT-TT
63674 TATTATATTATTT
1 TATTATATTATTT
*
63687 TTTTAT-TTA-TT
1 TATTATATTATTT
* *
63698 TAATATATTATTGA
1 TATTATATTATT-T
63712 TATTATATT
1 TATTATATT
63721 TTCGTATCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 6 0.15
12 6 0.15
13 8 0.21
14 19 0.49
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (13 bp):
TATTATATTATTT
Found at i:66608 original size:16 final size:16
Alignment explanation
Indices: 66587--66633 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 16
66577 CAAGTGAGTA
66587 ATTTTTAAAATTAAAT
1 ATTTTTAAAATTAAAT
66603 ATTTTTAAATATATAAAT
1 ATTTTTAAA-AT-TAAAT
66621 -TTTCTTAAAATTA
1 ATTT-TTAAAATTA
66634 TTAATTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 11 0.39
17 7 0.25
18 10 0.36
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTTTAAAATTAAAT
Found at i:66756 original size:15 final size:16
Alignment explanation
Indices: 66736--66769 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
66726 ATAATATAAA
66736 ATAAATT-TTAGTTTT
1 ATAAATTATTAGTTTT
66751 ATAAATTATTAGTTTT
1 ATAAATTATTAGTTTT
66767 ATA
1 ATA
66770 GTATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
ATAAATTATTAGTTTT
Found at i:68942 original size:13 final size:15
Alignment explanation
Indices: 68924--68981 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 15
68914 TGAGTAATAT
68924 TAAATATAAT-T-AA
1 TAAATATAATATAAA
68937 TAAATATAATATAAA
1 TAAATATAATATAAA
68952 TAAA-ATAAT-TAAA
1 TAAATATAATATAAA
68965 TAATAATATAATATAAA
1 T-A-AATATAATATAAA
68982 AATATTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
13 15 0.38
14 7 0.18
15 8 0.21
16 5 0.13
17 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAATATAATATAAA
Found at i:68949 original size:5 final size:5
Alignment explanation
Indices: 68926--69087 Score: 57
Period size: 5 Copynumber: 34.4 Consensus size: 5
68916 AGTAATATTA
*
68926 AATAT AAT-T AATA- AATAT AATAT AA-AT AAAAT AAT-T AAATAAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT -AAT-AT AATAT
* * * * *
68974 AATAT AA-A- AATAT -TTAA AATTT TATAT AATAT AA-AT TA-AT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
* * ** * *
69019 ATTAA AAT-T TTTAT ATATAT AATAT --TTT AAAAT AATTAT AATAT AATA-
1 AATAT AATAT AATAT A-ATAT AATAT AATAT AATAT AA-TAT AATAT AATAT
*
69067 AA-AT ACATA- AAAAT AATAT AA
1 AATAT A-ATAT AATAT AATAT AA
69088 ATATTCGAAT
Statistics
Matches: 113, Mismatches: 25, Indels: 38
0.64 0.14 0.22
Matches are distributed among these distances:
3 5 0.04
4 29 0.26
5 66 0.58
6 12 0.11
7 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:68983 original size:27 final size:27
Alignment explanation
Indices: 68918--69008 Score: 89
Period size: 27 Copynumber: 3.3 Consensus size: 27
68908 ACATATTGAG
*
68918 TAATATTAAATATAATTAATAAATATAATA
1 TAATA-TAAAAATAATT-A-AAATATAATA
68948 TAA-AT-AAAATAATT-AAATAATAATA
1 TAATATAAAAATAATTAAAAT-ATAATA
* * *
68973 TAATATAAAAATATTTAAAATTTTATA
1 TAATATAAAAATAATTAAAATATAATA
69000 TAATATAAA
1 TAATATAAA
69009 TTAATAATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
24 4 0.08
25 9 0.17
26 2 0.04
27 29 0.55
28 5 0.09
29 1 0.02
30 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
TAATATAAAAATAATTAAAATATAATA
Found at i:69001 original size:57 final size:57
Alignment explanation
Indices: 68935--69087 Score: 158
Period size: 57 Copynumber: 2.7 Consensus size: 57
68925 AAATATAATT
68935 AATAA-ATATAATATAAATAAAATA-ATTAAATAATAATATAATATAAAA-ATATTTAA
1 AATAATATATAATATAAATAAAATACATTAAA-AATAATATAATATAAAATAT-TTTAA
** * * ** *
68991 AATTTTATATAATATAAATTAATAATATATTAAAATTTTTAT-ATATATAATATTTTAA
1 AATAATATATAATATAAA-TAA-AATACATTAAAAATAATATAATATAAAATATTTTAA
69049 AATAAT-TATAATAT-AATAAAATACA-TAAAAATAATATAA
1 AATAATATATAATATAAATAAAATACATTAAAAATAATATAA
69088 ATATTCGAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
53 9 0.11
54 6 0.08
55 3 0.04
56 5 0.06
57 20 0.25
58 19 0.24
59 11 0.14
60 6 0.08
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (57 bp):
AATAATATATAATATAAATAAAATACATTAAAAATAATATAATATAAAATATTTTAA
Found at i:69003 original size:32 final size:32
Alignment explanation
Indices: 68967--69043 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
68957 TAATTAAATA
68967 ATAATATAATATAAAAATAT-TTAAAATTTTAT
1 ATAATATAATATAAAAATATATTAAAATTTT-T
*
68999 ATAATATAA-ATTAATAATATATTAAAATTTTT
1 ATAATATAATA-TAAAAATATATTAAAATTTTT
69031 ATATATATAATAT
1 ATA-ATATAATAT
69044 TTTAAAATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
31 1 0.03
32 21 0.52
33 17 0.43
34 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
ATAATATAATATAAAAATATATTAAAATTTTT
Found at i:69034 original size:16 final size:16
Alignment explanation
Indices: 68983--69046 Score: 51
Period size: 17 Copynumber: 3.9 Consensus size: 16
68973 TAATATAAAA
68983 ATAT-TTAAAA-TTTT
1 ATATATTAAAATTTTT
* * *
68997 ATATAATATAAATTAATA
1 ATATATTA-AAATT-TTT
69015 ATATATTAAAATTTTT
1 ATATATTAAAATTTTT
*
69031 ATATATATAATATTTT
1 ATATAT-TAAAATTTT
69047 AAAATAATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
14 4 0.11
15 2 0.05
16 10 0.26
17 14 0.37
18 8 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATATTAAAATTTTT
Found at i:69040 original size:25 final size:24
Alignment explanation
Indices: 69012--69066 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
69002 ATATAAATTA
**
69012 ATAATATATTAAAATTTTTATATAT
1 ATAATATATTAAAATAATTATA-AT
*
69037 ATAATATTTTAAAATAATTATAAT
1 ATAATATATTAAAATAATTATAAT
69061 ATAATA
1 ATAATA
69067 AAATACATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 8 0.30
25 19 0.70
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATAATATATTAAAATAATTATAAT
Found at i:70434 original size:16 final size:16
Alignment explanation
Indices: 70398--70439 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
70388 TATTTATATA
**
70398 AATATATTTAAAATTT
1 AATATATTTAAAAGAT
*
70414 TATATATTTAAAAGAT
1 AATATATTTAAAAGAT
70430 AATAT-TTTAA
1 AATATATTTAA
70440 TATTTATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
AATATATTTAAAAGAT
Found at i:70502 original size:25 final size:29
Alignment explanation
Indices: 70447--70504 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
70437 TAATATTTAT
* *
70447 ATATAAATATATATTTATATAAATATTAA
1 ATATAAATATATATTTATAAAAATATAAA
70476 ATATAAATAT-T-TTTA-AAAAATA-AAA
1 ATATAAATATATATTTATAAAAATATAAA
70501 ATAT
1 ATAT
70505 TTAAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 6 0.22
26 6 0.22
27 4 0.15
28 1 0.04
29 10 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
ATATAAATATATATTTATAAAAATATAAA
Found at i:70813 original size:25 final size:24
Alignment explanation
Indices: 70749--70816 Score: 64
Period size: 25 Copynumber: 2.8 Consensus size: 24
70739 TTCAATTTTA
**
70749 ATTAATAAAGTTAATAATATGATAT
1 ATTAATAAAAATAA-AATATGATAT
** * *
70774 AAAAATATAACTAAAATATGATAT
1 ATTAATAAAAATAAAATATGATAT
70798 ATTTAATAAAAATAAAATA
1 A-TTAATAAAAATAAAATA
70817 ATTTAATAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
24 11 0.33
25 22 0.67
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (24 bp):
ATTAATAAAAATAAAATATGATAT
Found at i:74845 original size:210 final size:210
Alignment explanation
Indices: 74034--74841 Score: 1251
Period size: 210 Copynumber: 3.8 Consensus size: 210
74024 AGAAGGCTGC
* * * *
74034 AAAAGTCTTAGGAGTCTTCCAACCAAAATTGGAATGAAATCTCTTGAAAAATTAATTCTTTCAGG
1 AAAAGTCTTAGGAGTCTTCCAGCCAAAATCGGAATGGAATCTCTTGAAGAATTAATTCTTTCAGG
* * * *
74099 CTGCTCAAATCTTGAAAGGTTTCCAGAGATTGAGGGCAAAATCGAATGTTTTCTGGAGCTTTCCT
66 CTGCTCAAATCTTAAAAGCTTTCCAGAGATCGAGGGCAAAATCGAATGTTTGCTGGAGCTTTCCT
74164 TAGATGGGAAAGGCATTGAAGGACTTCCCTCTTCCATCGGAAGTCTCAACAGACTCAAAGTTTTG
131 TAGATGGGAAAGGCATTGAAGGACTTCCCTCTTCCATCGGAAGTCTCAACAGACTCAAAGTTTTG
74229 AATTTAAGAGACTGT
196 AATTTAAGAGACTGT
74244 AAAAGTCTTAGGAGTCTTCCAGCCAAAATCGGAATGGAATCTCTTGAAGAATTAATTCTTTCAGG
1 AAAAGTCTTAGGAGTCTTCCAGCCAAAATCGGAATGGAATCTCTTGAAGAATTAATTCTTTCAGG
* * * *
74309 CTGCTCAAATCTTGAAAGGTTTCCAGAGATTGAGGGCAAAATCGAATGTTTTCTGGAGCTTTCCT
66 CTGCTCAAATCTTAAAAGCTTTCCAGAGATCGAGGGCAAAATCGAATGTTTGCTGGAGCTTTCCT
74374 TAGATGGGAAAGGCATTGAAGGACTTCCCTCTTCCATCGGAAGTCTCAACAGACTCAAAGTTTTG
131 TAGATGGGAAAGGCATTGAAGGACTTCCCTCTTCCATCGGAAGTCTCAACAGACTCAAAGTTTTG
74439 AATTTAAGAGACTGT
196 AATTTAAGAGACTGT
74454 AAAAGTCTTAGGAGTCTTCCAGCCAAAATCGGAATGGAATCTCTTGAAGAATTAATTCTTTCAGG
1 AAAAGTCTTAGGAGTCTTCCAGCCAAAATCGGAATGGAATCTCTTGAAGAATTAATTCTTTCAGG
* * * * * * **
74519 CTGCTCAAATCTTAAAAGCTTTCCAGAGATCGATGGCGAAATGGAATGTTTGCAGAATCTTTGTT
66 CTGCTCAAATCTTAAAAGCTTTCCAGAGATCGAGGGCAAAATCGAATGTTTGCTGGAGCTTTCCT
* * *
74584 TAGATGGGACAGGCATTGAAGGACTTCCCTCTTCCATCGGAAGTCTCAGCAGACTTAAAGTTTTG
131 TAGATGGGAAAGGCATTGAAGGACTTCCCTCTTCCATCGGAAGTCTCAACAGACTCAAAGTTTTG
* * *
74649 GATTTAACAAACTGT
196 AATTTAAGAGACTGT
74664 AAAAGTCTTAGGAGTCTTCCAGCCAAAATCGGAATGGAATCTCTTGAAG-ATCTAATTCTTTCAG
1 AAAAGTCTTAGGAGTCTTCCAGCCAAAATCGGAATGGAATCTCTTGAAGAAT-TAATTCTTTCAG
* * ** * *
74728 GCTGCTCAAATCTTAAAAGCTTTCCAGAGATCGATGGCGAAAT-GAAATGTTTGGGGGCGCTTTA
65 GCTGCTCAAATCTTAAAAGCTTTCCAGAGATCGAGGGCAAAATCG-AATGTTTGCTGGAGCTTTC
* ** * *
74792 TTTAGATGGGACGGGCATTGAAGGGCTTCCCTCTTCCATCGGAAATCTCA
129 CTTAGATGGGAAAGGCATTGAAGGACTTCCCTCTTCCATCGGAAGTCTCA
74842 GCAGTCTTTA
Statistics
Matches: 565, Mismatches: 31, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
209 3 0.01
210 562 0.99
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (210 bp):
AAAAGTCTTAGGAGTCTTCCAGCCAAAATCGGAATGGAATCTCTTGAAGAATTAATTCTTTCAGG
CTGCTCAAATCTTAAAAGCTTTCCAGAGATCGAGGGCAAAATCGAATGTTTGCTGGAGCTTTCCT
TAGATGGGAAAGGCATTGAAGGACTTCCCTCTTCCATCGGAAGTCTCAACAGACTCAAAGTTTTG
AATTTAAGAGACTGT
Found at i:76896 original size:11 final size:11
Alignment explanation
Indices: 76882--76906 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
76872 TTAAAAAAAA
76882 ATTAAATATAT
1 ATTAAATATAT
76893 ATTAAATATAT
1 ATTAAATATAT
76904 ATT
1 ATT
76907 CATATTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTAAATATAT
Found at i:77081 original size:2 final size:2
Alignment explanation
Indices: 77072--77112 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
77062 GAGAGAAGTA
77072 AT AT -T 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 AT AT AT
77113 TCTAGAGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:78217 original size:7 final size:8
Alignment explanation
Indices: 78188--78215 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
78178 ATAATTTTTT
78188 AAAAATAA
1 AAAAATAA
78196 AAAAATAA
1 AAAAATAA
78204 AAAAATAA
1 AAAAATAA
78212 AAAA
1 AAAA
78216 TATATTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAATAA
Found at i:78792 original size:27 final size:27
Alignment explanation
Indices: 78733--78796 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
78723 AGCCATAATT
78733 TATTTGTCAAATATAGTGGTTACTTTA
1 TATTTGTCAAATATAGTGGTTACTTTA
* *
78760 TGTTTGTCAAATATAGTGGTTACTTTG
1 TATTTGTCAAATATAGTGGTTACTTTA
78787 TATTTG-CAAA
1 TATTTGTCAAA
78797 AAATGATGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 4 0.12
27 30 0.88
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (27 bp):
TATTTGTCAAATATAGTGGTTACTTTA
Found at i:83217 original size:27 final size:27
Alignment explanation
Indices: 83183--83243 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
83173 AGCTATCATT
83183 TGTTTGTCAAATATGGTGGTTACTTTG
1 TGTTTGTCAAATATGGTGGTTACTTTG
83210 TGTTTGTCAAATATGGTGGTTACTTTG
1 TGTTTGTCAAATATGGTGGTTACTTTG
*
83237 TATTTGT
1 TGTTTGT
83244 AAAAAATAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.18, C:0.07, G:0.25, T:0.51
Consensus pattern (27 bp):
TGTTTGTCAAATATGGTGGTTACTTTG
Found at i:83255 original size:27 final size:27
Alignment explanation
Indices: 83198--83255 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
83188 GTCAAATATG
* * * *
83198 GTGGTTACTTTGTGTTTGTCAAATATG
1 GTGGTTACTTTGTATTTGTAAAAAATA
83225 GTGGTTACTTTGTATTTGTAAAAAATA
1 GTGGTTACTTTGTATTTGTAAAAAATA
83252 GTGG
1 GTGG
83256 CATGTTGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.05, G:0.26, T:0.45
Consensus pattern (27 bp):
GTGGTTACTTTGTATTTGTAAAAAATA
Found at i:85939 original size:16 final size:16
Alignment explanation
Indices: 85918--85948 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
85908 ATATTATCAT
85918 AATATTAATTATAAAA
1 AATATTAATTATAAAA
85934 AATATTAATTATAAA
1 AATATTAATTATAAA
85949 TATCAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATATTAATTATAAAA
Found at i:85985 original size:25 final size:26
Alignment explanation
Indices: 85940--86006 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 26
85930 AAAAAATATT
*
85940 AATTATAAA-TATCAAATTATTAA-AAA
1 AATTA-AAATTAT-AAAATATTAATAAA
*
85966 AATTAAAATTATAAAATATTAATAAT
1 AATTAAAATTATAAAATATTAATAAA
85992 AATTAAATATTATAA
1 AATTAAA-ATTATAA
86007 TCGTTATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 12 0.33
26 17 0.47
27 7 0.19
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (26 bp):
AATTAAAATTATAAAATATTAATAAA
Found at i:90948 original size:32 final size:32
Alignment explanation
Indices: 90840--90949 Score: 98
Period size: 32 Copynumber: 3.4 Consensus size: 32
90830 TTTTATCTCA
* * *
90840 TAATATATATATATAAAAATTTTGATATTTTAT
1 TAATTTATAT-TATATAAATTTTGACATTTTAT
* * * *
90873 TAATTTTTATTATGTAGATTTT-ATCATATTAT
1 TAATTTATATTATATAAATTTTGA-CATTTTAT
**
90905 TAATTCGTATTATATAAATTTTGACATTTTA-
1 TAATTTATATTATATAAATTTTGACATTTTAT
90936 TATATTTATATTAT
1 TA-ATTTATATTAT
90950 GTTATAATTA
Statistics
Matches: 60, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
31 3 0.05
32 48 0.80
33 9 0.15
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (32 bp):
TAATTTATATTATATAAATTTTGACATTTTAT
Found at i:91228 original size:23 final size:24
Alignment explanation
Indices: 91195--91239 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
91185 AATATATTCA
*
91195 ATATAATTATAATA-AAATAAAAT
1 ATATAAATATAATATAAATAAAAT
91218 ATATAAATATAATATAAATAAA
1 ATATAAATATAATATAAATAAA
91240 TTCACAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
ATATAAATATAATATAAATAAAAT
Found at i:91240 original size:15 final size:15
Alignment explanation
Indices: 91172--91240 Score: 61
Period size: 15 Copynumber: 4.6 Consensus size: 15
91162 TATCAAAATT
91172 TAAATAAATATAAAA
1 TAAATAAATATAAAA
* * *
91187 TATATTCAATAT-AAT
1 TA-AATAAATATAAAA
91202 TATAATAAA-ATAAAA
1 TA-AATAAATATAAAA
* *
91217 TATATAAATATAATA
1 TAAATAAATATAAAA
91232 TAAATAAAT
1 TAAATAAAT
91241 TCACAAATTT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
14 7 0.17
15 28 0.67
16 7 0.17
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAATAAATATAAAA
Found at i:103379 original size:34 final size:34
Alignment explanation
Indices: 103315--103497 Score: 260
Period size: 34 Copynumber: 5.4 Consensus size: 34
103305 TCAGGCAGCA
* *
103315 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
103348 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
103382 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
103416 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
103450 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
103484 TGTTGATTAAATGG
1 TGTTGATTAAATGG
103498 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 11 0.08
34 121 0.92
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:103856 original size:19 final size:19
Alignment explanation
Indices: 103800--103862 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
103790 TGGTTGTCGA
**
103800 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
103819 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
103838 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
103857 GTTACT
1 GGTACT
103863 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:107994 original size:34 final size:34
Alignment explanation
Indices: 107928--108112 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
107918 AAGTGGGAGA
* *
107928 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
107961 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
107995 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
108029 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
108063 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
108097 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
108113 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:109449 original size:32 final size:32
Alignment explanation
Indices: 109412--109511 Score: 130
Period size: 32 Copynumber: 3.1 Consensus size: 32
109402 GTTTATGATA
*
109412 TATATAAATTTTGATATTTTATTAATTCATAT
1 TATATAGATTTTGATATTTTATTAATTCATAT
* * *
109444 TATATAGATTTTGTTATATTATTAATTCGTAT
1 TATATAGATTTTGATATTTTATTAATTCATAT
*
109476 TATATAGATTTTGATATGTTTA-TATATTTATAT
1 TATATAGATTTTGATAT-TTTATTA-ATTCATAT
109509 TAT
1 TAT
109512 GTTTGTATTG
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
32 46 0.79
33 12 0.21
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (32 bp):
TATATAGATTTTGATATTTTATTAATTCATAT
Found at i:111434 original size:27 final size:27
Alignment explanation
Indices: 111337--111435 Score: 144
Period size: 27 Copynumber: 3.7 Consensus size: 27
111327 AATAACATGG
* * *
111337 CACCATTTTTGACAAATAAAAAGAAAC
1 CACCATTTTTGACAAACACAAAGTAAC
* * *
111364 TACCATTTTTGACAAATACAAAATAAC
1 CACCATTTTTGACAAACACAAAGTAAC
111391 CACCATTTTTGACAAACACAAAGTAAC
1 CACCATTTTTGACAAACACAAAGTAAC
111418 CACCATTTTTGACAAACA
1 CACCATTTTTGACAAACA
111436 AATGGTGGCT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 65 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.25
Consensus pattern (27 bp):
CACCATTTTTGACAAACACAAAGTAAC
Found at i:115990 original size:27 final size:27
Alignment explanation
Indices: 115960--116028 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
115950 AAGAAACAAT
115960 CATTTTTGACAAACACAAAATAACCAC
1 CATTTTTGACAAACACAAAATAACCAC
* * *
115987 CATTTTTAACAAACACAAAGTAGCCAC
1 CATTTTTGACAAACACAAAATAACCAC
*
116014 AATTTTTGACAAACA
1 CATTTTTGACAAACA
116029 AATGGTGACT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.25
Consensus pattern (27 bp):
CATTTTTGACAAACACAAAATAACCAC
Found at i:118443 original size:23 final size:23
Alignment explanation
Indices: 118417--118467 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
118407 GGGTCTGTAT
*
118417 CAAGAC-TTTAAATGTTAAAAGAC
1 CAAGACTTTTAAACGTT-AAAGAC
118440 CAAGACTTTTAAACGTTAAAGAC
1 CAAGACTTTTAAACGTTAAAGAC
*
118463 TAAGA
1 CAAGA
118468 AAAAACAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (23 bp):
CAAGACTTTTAAACGTTAAAGAC
Found at i:118458 original size:69 final size:68
Alignment explanation
Indices: 118346--118482 Score: 229
Period size: 69 Copynumber: 2.0 Consensus size: 68
118336 TTATGTATAG
* * *
118346 ATCAAGACGTTAGATGTTAAAAGACCAAGACTTTTAAATGTTAAAGGCTAAGAAAAAAACAGGGT
1 ATCAAGACGTTAAATGTTAAAAGACCAAGACTTTTAAACGTTAAAGACTAAG-AAAAAACAGGGT
118411 CTGT
65 CTGT
*
118415 ATCAAGACTTTAAATGTTAAAAGACCAAGACTTTTAAACGTTAAAGACTAAGAAAAAACAGGGTC
1 ATCAAGACGTTAAATGTTAAAAGACCAAGACTTTTAAACGTTAAAGACTAAGAAAAAACAGGGTC
118480 TGT
66 TGT
118483 GCAAGTAATA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
68 16 0.25
69 48 0.75
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (68 bp):
ATCAAGACGTTAAATGTTAAAAGACCAAGACTTTTAAACGTTAAAGACTAAGAAAAAACAGGGTC
TGT
Found at i:119961 original size:32 final size:32
Alignment explanation
Indices: 119918--119996 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 32
119908 TTAAGATATA
* *
119918 TATATTAATTTTGACATGTTATTAAATT-GTAT
1 TATATAAATTTTGACATATTATT-AATTCGTAT
* *
119950 TATATAGATTTTGATATATTATTAATTCGTAT
1 TATATAAATTTTGACATATTATTAATTCGTAT
119982 TATATAAATTTTGAC
1 TATATAAATTTTGAC
119997 TCATTCATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
31 4 0.10
32 36 0.90
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (32 bp):
TATATAAATTTTGACATATTATTAATTCGTAT
Found at i:120226 original size:26 final size:24
Alignment explanation
Indices: 120179--120226 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
120169 AAATTACACA
* *
120179 AATATGATAAAAAAAATTAAATAC
1 AATATGACAAAAAAAATCAAATAC
120203 AATATGACATAAAAAAATACAAAT
1 AATATGACA-AAAAAAAT-CAAAT
120227 CTATCTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 8 0.40
26 4 0.20
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.23
Consensus pattern (24 bp):
AATATGACAAAAAAAATCAAATAC
Found at i:120286 original size:16 final size:17
Alignment explanation
Indices: 120265--120320 Score: 62
Period size: 16 Copynumber: 3.3 Consensus size: 17
120255 AAATTTATAT
*
120265 AAATATAAAATAT-TTA
1 AAATATAAAATATAATA
*
120281 AAATAT-AATTATAATA
1 AAATATAAAATATAATA
120297 AAATATATAAATATAATA
1 AAATATA-AAATATAATA
120315 CAAATA
1 -AAATA
120321 AATACTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 5 0.15
16 14 0.42
18 9 0.27
19 5 0.15
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATATAAAATATAATA
Found at i:120306 original size:18 final size:19
Alignment explanation
Indices: 120283--120320 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
120273 AATATTTAAA
*
120283 ATATAATTATAATA-AAAT
1 ATATAAATATAATACAAAT
120301 ATATAAATATAATACAAAT
1 ATATAAATATAATACAAAT
120320 A
1 A
120321 AATACTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
ATATAAATATAATACAAAT
Found at i:121116 original size:28 final size:28
Alignment explanation
Indices: 121084--121146 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
121074 ACAAAAATCA
121084 CCTTTTGTATTTGTCAAAAATGGTAGTT
1 CCTTTTGTATTTGTCAAAAATGGTAGTT
* * *
121112 CC-TTTATATTTGTCAAATATGGTGGTT
1 CCTTTTGTATTTGTCAAAAATGGTAGTT
*
121139 CATTTTGT
1 CCTTTTGT
121147 TTATAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 23 0.79
28 6 0.21
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.49
Consensus pattern (28 bp):
CCTTTTGTATTTGTCAAAAATGGTAGTT
Found at i:121259 original size:13 final size:13
Alignment explanation
Indices: 121241--121273 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
121231 GGCTCTCTCT
121241 TCCCTCTCAAGCA
1 TCCCTCTCAAGCA
*
121254 TCCCTCTCAAGTA
1 TCCCTCTCAAGCA
121267 TCCCTCT
1 TCCCTCT
121274 TCAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.45, G:0.06, T:0.30
Consensus pattern (13 bp):
TCCCTCTCAAGCA
Found at i:123754 original size:21 final size:22
Alignment explanation
Indices: 123725--123770 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
123715 TGTTCAGACA
** *
123725 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
123747 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
123768 AGT
1 AGT
123771 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:130138 original size:12 final size:12
Alignment explanation
Indices: 130121--130148 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
130111 TAAATCATTA
130121 TCACCCATGACC
1 TCACCCATGACC
130133 TCACCCATGACC
1 TCACCCATGACC
130145 TCAC
1 TCAC
130149 GAGCAGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.50, G:0.07, T:0.18
Consensus pattern (12 bp):
TCACCCATGACC
Found at i:132247 original size:13 final size:13
Alignment explanation
Indices: 132231--132255 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
132221 GATGGATACA
132231 AATATGTTATCTG
1 AATATGTTATCTG
132244 AATATGTTATCT
1 AATATGTTATCT
132256 ACACAAGTAC
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:0.08, G:0.12, T:0.48
Consensus pattern (13 bp):
AATATGTTATCTG
Found at i:136136 original size:24 final size:24
Alignment explanation
Indices: 136101--136149 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
136091 TTGTAAATGG
*
136101 TTACTTTTAATACTTGATTGAGTA
1 TTACTTTAAATACTTGATTGAGTA
136125 TTACTTTAAATACTTGATTGAGTA
1 TTACTTTAAATACTTGATTGAGTA
136149 T
1 T
136150 GACAAACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.49
Consensus pattern (24 bp):
TTACTTTAAATACTTGATTGAGTA
Found at i:136887 original size:48 final size:48
Alignment explanation
Indices: 136816--136910 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
136806 CAATAATAAG
*
136816 AAAATTTCAAAAATCTTGGATGCATAACATTTTAATATTATATTTATC
1 AAAATTCCAAAAATCTTGGATGCATAACATTTTAATATTATATTTATC
136864 AAAATTCCAAAAATCTTGGATGCATAACATTTTAATATTATATTTAT
1 AAAATTCCAAAAATCTTGGATGCATAACATTTTAATATTATATTTAT
136911 TTAATTTATC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.41
Consensus pattern (48 bp):
AAAATTCCAAAAATCTTGGATGCATAACATTTTAATATTATATTTATC
Found at i:138126 original size:210 final size:209
Alignment explanation
Indices: 137764--139429 Score: 2505
Period size: 210 Copynumber: 7.9 Consensus size: 209
137754 GGCTTAAACG
* * * * *
137764 TTTGAATTTAGAAGGCTGCGAAAGTCTTAGGAGTCTTCCAACCAAAATTGGAATGGAATCTCTTG
1 TTTGGATTTAGGAGACTGCAAAAGTCTTAGGAGTCTTCCAGCCAAAATTGGAATGGAATCTCTTG
* * * *
137829 AAACATTAGTTCTTTCAGGCTGCACAAATCTTGGAAGCTTTCCAGAGATTAATGGCAAAATGGAA
66 AAAAATTAATTCTTTCAGGCTGCACAAATCTTGAAAGCTTTCCAGAGATTGATGGCAAAATGGAA
*
137894 TGTTTGCTGGAGCTTGATTTAGATGGGACAGGCATTGAAGAACTTCCCTCTTCCATTGGAAATCT
131 TGTTTGCTGGAGCTTTATTTAGATGGGACAGGCATTGAAGAACTTCCCTCTTCCATTGGAAATCT
*
137959 CAGCAGACTTAGACG
196 CAGCAGACTT-GACT
* * * * *
137974 TTTGGATTTAGGAGGCTGCAAAAGTTTTAGGAGTCCTCCGGTCAAAATTGGAATGGAATCTCTTG
1 TTTGGATTTAGGAGACTGCAAAAGTCTTAGGAGTCTTCCAGCCAAAATTGGAATGGAATCTCTTG
* *
138039 AAATATTAATTCTTTCATGCTGCACAAATCTTGAAAGCTTTCCAGAGATTGATGGCAAAATGGAA
66 AAAAATTAATTCTTTCAGGCTGCACAAATCTTGAAAGCTTTCCAGAGATTGATGGCAAAATGGAA
138104 TGTTTGCTGGAGCTTTATTTAGATGGGACAGGCATTGAAGAACTTCCCTCTTCCATTGGAAATCT
131 TGTTTGCTGGAGCTTTATTTAGATGGGACAGGCATTGAAGAACTTCCCTCTTCCATTGGAAATCT
* * *
138169 TAGCAGACTTAAAT
196 CAGCAGACTTGACT
* * * *
138183 TTCT-GAGTTTAAGAAACTGTAAAAGTCTTAGGAGTCTTCCAGCAAAAATTGGAATGGAATCTCT
1 TT-TGGA-TTTAGGAGACTGCAAAAGTCTTAGGAGTCTTCCAGCCAAAATTGGAATGGAATCTCT
* *
138247 TGAAAAATTATTTCTTTCAGGCTGCACAAATCTTGAAAGGTTTCCAGAGATTGATGGCAAAATGG
64 TGAAAAATTAATTCTTTCAGGCTGCACAAATCTTGAAAGCTTTCCAGAGATTGATGGCAAAATGG
* *
138312 AATGTTTGCTGGAGCTTTATTTAAATGGGACAGGCATTGAAGGACTTCCCTCTTCCATTGGAAAT
129 AATGTTTGCTGGAGCTTTATTTAGATGGGACAGGCATTGAAGAACTTCCCTCTTCCATTGGAAAT
138377 CTCAGCAGACTTGAACT
194 CTCAGCAGACTTG-ACT
*
138394 TTTGGATTTAGGAGACTGCAAAAGTCTTAGGAGTCTTCCAGCCCAAATTGGAATGGAATCTCTTG
1 TTTGGATTTAGGAGACTGCAAAAGTCTTAGGAGTCTTCCAGCCAAAATTGGAATGGAATCTCTTG
* *
138459 AAAAATTAATTCTTTCAGACTGCTCAAATCTTGAAAGCTTTCCAGAGATTGATGGCAAAATGGAA
66 AAAAATTAATTCTTTCAGGCTGCACAAATCTTGAAAGCTTTCCAGAGATTGATGGCAAAATGGAA
* * * * ** * *
138524 TGTTTGCTGCA--TTCACTTAAATGGGACAGATATTGAAGAACTTTCCTATTCCATTGGAAATCT
131 TGTTTGCTGGAGCTTTATTTAGATGGGACAGGCATTGAAGAACTTCCCTCTTCCATTGGAAATCT
*
138587 CAGCAGACTTGAAT
196 CAGCAGACTTGACT
* * * *
138601 TCTTGAATTTAGGAGGCTGCAAAAGTCTTAGGAGTCTGCCAGCCAAAATTGGAATGGGATCTCTT
1 T-TTGGATTTAGGAGACTGCAAAAGTCTTAGGAGTCTTCCAGCCAAAATTGGAATGGAATCTCTT
* * * * **
138666 AAAAAATTAATTCTTTCAGGCTGCTCAAATCTTGAAAGGTTTTCAGAGATTGGGGGCAAAATGGA
65 GAAAAATTAATTCTTTCAGGCTGCACAAATCTTGAAAGCTTTCCAGAGATTGATGGCAAAATGGA
* *
138731 ATGTTTGCTGGAGCTTTATTTAGATGGGACAGGCATTGAAGGACTTCCCTCTTCCATCGGAAATC
130 ATGTTTGCTGGAGCTTTATTTAGATGGGACAGGCATTGAAGAACTTCCCTCTTCCATTGGAAATC
*
138796 TCAGCAGACTTGCATT
195 TCAGCAGACTTG-ACT
*
138812 TTTGAATTTAGGAGACTGCAAAAGTCTTAGGAGTCTTCCAGCCAAAATTGGAATGGAATCTCTTG
1 TTTGGATTTAGGAGACTGCAAAAGTCTTAGGAGTCTTCCAGCCAAAATTGGAATGGAATCTCTTG
*
138877 AAAAATTAATTCTTTCAGGCTGCACAAATCTTGAAAGCTTTCCGGAGATTGATGGCAAAATGGAA
66 AAAAATTAATTCTTTCAGGCTGCACAAATCTTGAAAGCTTTCCAGAGATTGATGGCAAAATGGAA
* *
138942 TGTTTGCTGGAGCTTTATTTAGATGGGACAGGCATTGAAGAACTTTCCTCTTCCATTAGAAATCT
131 TGTTTGCTGGAGCTTTATTTAGATGGGACAGGCATTGAAGAACTTCCCTCTTCCATTGGAAATCT
* *
139007 CAGCAGACTTAAAT
196 CAGCAGACTTGACT
* * * *
139021 TTCT-GAGTTTAAGAAACTGTAAAAGTCTTAGGAGTCTTCCAGCAAAAATTGGAATGGAATCTCT
1 TT-TGGA-TTTAGGAGACTGCAAAAGTCTTAGGAGTCTTCCAGCCAAAATTGGAATGGAATCTCT
* *
139085 TGAAAAATTATTTCTTTCAGGCTGCACAAATCTTGAAAGGTTTCCAGAGATTGATGGCAAAATGG
64 TGAAAAATTAATTCTTTCAGGCTGCACAAATCTTGAAAGCTTTCCAGAGATTGATGGCAAAATGG
* *
139150 AATGTTTGCTGGAGCTTTATTTAAATGGGACAGGCATTGAAGGACTTCCCTCTTCCATTGGAAAT
129 AATGTTTGCTGGAGCTTTATTTAGATGGGACAGGCATTGAAGAACTTCCCTCTTCCATTGGAAAT
139215 CTCAGCAGACTTGAACT
194 CTCAGCAGACTTG-ACT
* *
139232 TTTGGATTTAGGAGACTGTAAAAGTCTTAAGAGTCTTCCAGCCAAAATTGGAATGGAATCTCTTG
1 TTTGGATTTAGGAGACTGCAAAAGTCTTAGGAGTCTTCCAGCCAAAATTGGAATGGAATCTCTTG
* * **
139297 AACAATTAAATCTTTCAGGCTGTTCAAATCTTGAAAGCTTTCCAGAGATTGATGGCAAAATGGAA
66 AAAAATTAATTCTTTCAGGCTGCACAAATCTTGAAAGCTTTCCAGAGATTGATGGCAAAATGGAA
* * * *
139362 TGTTTGCTGCAGCTTCACTT-GAATGGGACAGGCATTGAAAAACTTCCCTCTTCCATTGGAAATC
131 TGTTTGCTGGAGCTTTATTTAG-ATGGGACAGGCATTGAAGAACTTCCCTCTTCCATTGGAAATC
139426 TCAG
195 TCAG
139430 TGGTCTTGTT
Statistics
Matches: 1321, Mismatches: 122, Indels: 26
0.90 0.08 0.02
Matches are distributed among these distances:
207 3 0.00
208 184 0.14
209 10 0.01
210 1109 0.84
211 15 0.01
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (209 bp):
TTTGGATTTAGGAGACTGCAAAAGTCTTAGGAGTCTTCCAGCCAAAATTGGAATGGAATCTCTTG
AAAAATTAATTCTTTCAGGCTGCACAAATCTTGAAAGCTTTCCAGAGATTGATGGCAAAATGGAA
TGTTTGCTGGAGCTTTATTTAGATGGGACAGGCATTGAAGAACTTCCCTCTTCCATTGGAAATCT
CAGCAGACTTGACT
Found at i:141054 original size:13 final size:13
Alignment explanation
Indices: 141036--141065 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
141026 GTTTTTTTTA
141036 AATATTTATATAT
1 AATATTTATATAT
*
141049 AATATTTATATCT
1 AATATTTATATAT
141062 AATA
1 AATA
141066 CATTTTGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
AATATTTATATAT
Found at i:141123 original size:28 final size:27
Alignment explanation
Indices: 141073--141131 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
141063 ATACATTTTG
* **
141073 ATATAAATATAAATATAACTTTTTAAAT
1 ATATAAAAATAAATA-AAAATTTTAAAT
* *
141101 ATATAAAAATAATTAAAAATTTTATAT
1 ATATAAAAATAAATAAAAATTTTAAAT
141128 ATAT
1 ATAT
141132 TCGTATTGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATAAAAATAAATAAAAATTTTAAAT
Found at i:141580 original size:12 final size:12
Alignment explanation
Indices: 141563--141601 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
141553 GAAACCAAGT
*
141563 TATGTATACATG
1 TATGTATACATA
*
141575 TATGTATATATA
1 TATGTATACATA
*
141587 TATGTATATATA
1 TATGTATACATA
141599 TAT
1 TAT
141602 ATATCTGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (12 bp):
TATGTATACATA
Found at i:141591 original size:16 final size:16
Alignment explanation
Indices: 141567--141605 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
141557 CCAAGTTATG
* *
141567 TATACATGTATGTATA
1 TATATATGTATATATA
141583 TATATATGTATATATA
1 TATATATGTATATATA
141599 TATATAT
1 TATATAT
141606 CTGGTTACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (16 bp):
TATATATGTATATATA
Found at i:142106 original size:17 final size:17
Alignment explanation
Indices: 142086--142138 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
142076 AGATAATATA
142086 AATTTTAAAATATTATT
1 AATTTTAAAATATTATT
* * *
142103 AA-TTTATATTA-TATA
1 AATTTTAAAATATTATT
*
142118 AATTTTAATATATTATT
1 AATTTTAAAATATTATT
142135 AATT
1 AATT
142139 CACATTATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
15 5 0.19
16 13 0.48
17 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTTTAAAATATTATT
Found at i:142118 original size:32 final size:32
Alignment explanation
Indices: 142081--142315 Score: 211
Period size: 32 Copynumber: 7.3 Consensus size: 32
142071 GATTAAGATA
* *
142081 ATATAAATTTTAAAATATTATTAATTTATATT
1 ATATAAATTTTAATATATTATTAATTCATATT
*
142113 ATATAAATTTTAATATATTATTAATTCACATT
1 ATATAAATTTTAATATATTATTAATTCATATT
* * *
142145 ATATAGATTTTGATATA-TAGTTAATTTATATT
1 ATATAAATTTTAATATATTA-TTAATTCATATT
* * * ** ** *
142177 ATATAGATTTTGACACGTTATTAATGAATGTT
1 ATATAAATTTTAATATATTATTAATTCATATT
* * * *
142209 ATATAAATTTTAATACATAATTAATTCGTATC
1 ATATAAATTTTAATATATTATTAATTCATATT
* ** * *
142241 ATATAAATTTTAACATGCTATTAATTAATGTT
1 ATATAAATTTTAATATATTATTAATTCATATT
** *
142273 ATATAAATTTTAATACGTTATTAATTCGTATT
1 ATATAAATTTTAATATATTATTAATTCATATT
*
142305 ATATAGATTTT
1 ATATAAATTTT
142316 GAGATGTTAT
Statistics
Matches: 162, Mismatches: 39, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
31 2 0.01
32 158 0.98
33 2 0.01
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (32 bp):
ATATAAATTTTAATATATTATTAATTCATATT
Found at i:142149 original size:64 final size:64
Alignment explanation
Indices: 142081--142325 Score: 249
Period size: 64 Copynumber: 3.8 Consensus size: 64
142071 GATTAAGATA
* * * * * * **
142081 ATATAAATTTTAAAATATTATTAATTTATATTATATAAATTTTAATATATTATTAATTCACATT
1 ATATAAATTTTAATACATTATTAATTCATATTATATAAATTTTAACATGTTATTAATTAATGTT
* * * * * * * *
142145 ATATAGATTTTGATATA-TAGTTAATTTATATTATATAGATTTTGACACGTTATTAATGAATGTT
1 ATATAAATTTTAATACATTA-TTAATTCATATTATATAAATTTTAACATGTTATTAATTAATGTT
* * * *
142209 ATATAAATTTTAATACATAATTAATTCGTATCATATAAATTTTAACATGCTATTAATTAATGTT
1 ATATAAATTTTAATACATTATTAATTCATATTATATAAATTTTAACATGTTATTAATTAATGTT
* * * * *
142273 ATATAAATTTTAATACGTTATTAATTCGTATTATATAGATTTTGAGATGTTAT
1 ATATAAATTTTAATACATTATTAATTCATATTATATAAATTTTAACATGTTAT
142326 ATAAATTTTG
Statistics
Matches: 148, Mismatches: 31, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
63 2 0.01
64 145 0.98
65 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (64 bp):
ATATAAATTTTAATACATTATTAATTCATATTATATAAATTTTAACATGTTATTAATTAATGTT
Found at i:142187 original size:96 final size:96
Alignment explanation
Indices: 142072--142315 Score: 247
Period size: 96 Copynumber: 2.5 Consensus size: 96
142062 CATAATAGTG
* * ** * * *
142072 ATTAAGATAATATAAATTTTAAAATATTATTAATTTATATTATATAAATTTTAATATATTATTAA
1 ATTAATATTATATAAATTTTAAAACGTTATTAATTAATATTATATAAATTTTAATACATAATTAA
* * * *
142137 TTCACATTATATAGATTTTGATAT-ATAGTTA
66 TTCACATCATATAAATTTTAACATGATA-TTA
* * * * * *
142168 ATTTATATTATATAGATTTTGACACGTTATTAATGAATGTTATATAAATTTTAATACATAATTAA
1 ATTAATATTATATAAATTTTAAAACGTTATTAATTAATATTATATAAATTTTAATACATAATTAA
** *
142233 TTCGTATCATATAAATTTTAACATGCTATTA
66 TTCACATCATATAAATTTTAACATGATATTA
* * ** *
142264 ATTAATGTTATATAAATTTTAATACGTTATTAATTCGTATTATATAGATTTT
1 ATTAATATTATATAAATTTTAAAACGTTATTAATTAATATTATATAAATTTT
142316 GAGATGTTAT
Statistics
Matches: 117, Mismatches: 30, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
96 115 0.98
97 2 0.02
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (96 bp):
ATTAATATTATATAAATTTTAAAACGTTATTAATTAATATTATATAAATTTTAATACATAATTAA
TTCACATCATATAAATTTTAACATGATATTA
Found at i:142327 original size:19 final size:19
Alignment explanation
Indices: 142303--142340 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
142293 TTAATTCGTA
*
142303 TTATATAGATTTTGAGATG
1 TTATATAAATTTTGAGATG
142322 TTATATAAATTTTGAGATG
1 TTATATAAATTTTGAGATG
142341 ATATTAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (19 bp):
TTATATAAATTTTGAGATG
Found at i:142328 original size:51 final size:51
Alignment explanation
Indices: 142268--142375 Score: 162
Period size: 51 Copynumber: 2.1 Consensus size: 51
142258 CTATTAATTA
* * *
142268 ATGTTATATAAATTTTAATACGTTATTAATTCGTATTATATAGATTTTGAG
1 ATGTTATATAAATTTTAAGACGATATTAATTCGTATTATATAAATTTTGAG
* * *
142319 ATGTTATATAAATTTTGAGATGATATTAATTCGTATTATATAAATTTTGAT
1 ATGTTATATAAATTTTAAGACGATATTAATTCGTATTATATAAATTTTGAG
142370 ATGTTA
1 ATGTTA
142376 CTAATTTGTG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.49
Consensus pattern (51 bp):
ATGTTATATAAATTTTAAGACGATATTAATTCGTATTATATAAATTTTGAG
Found at i:142344 original size:17 final size:18
Alignment explanation
Indices: 142304--142400 Score: 59
Period size: 19 Copynumber: 5.8 Consensus size: 18
142294 TAATTCGTAT
*
142304 TATATAGATTTTGAGATG
1 TATATAAATTTTGAGATG
142322 TTATATAAATTTTGAGATG
1 -TATATAAATTTTGAGATG
* * *
142341 -ATATTAA-TTCG-TAT-
1 TATATAAATTTTGAGATG
*
142355 TATATAAATTTTGATATG
1 TATATAAATTTTGAGATG
*
142373 T-TACT-AA-TTTGTG-T-
1 TATA-TAAATTTTGAGATG
142387 TATATAAATTTTGA
1 TATATAAATTTTGA
142401 CACGTTCATA
Statistics
Matches: 61, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
14 2 0.03
15 13 0.21
16 14 0.23
17 13 0.21
18 2 0.03
19 17 0.28
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.49
Consensus pattern (18 bp):
TATATAAATTTTGAGATG
Found at i:142346 original size:83 final size:83
Alignment explanation
Indices: 142241--142400 Score: 212
Period size: 83 Copynumber: 1.9 Consensus size: 83
142231 AATTCGTATC
* * *
142241 ATATAAATTTTAACATGCTATTAATTAATGTTATATAAATTTTAATACGTTATTAATTCGTATTA
1 ATATAAATTTTAACATGATATTAATTAATATTATATAAATTTTAATACGTTACTAATTCGTATTA
*
142306 TATAGATTTTGAGATGTT
66 TATAAATTTTGAGATGTT
* * ** * * * *
142324 ATATAAATTTTGAGATGATATTAATTCGTATTATATAAATTTTGATATGTTACTAATTTGTGTTA
1 ATATAAATTTTAACATGATATTAATTAATATTATATAAATTTTAATACGTTACTAATTCGTATTA
142389 TATAAATTTTGA
66 TATAAATTTTGA
142401 CACGTTCATA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
83 65 1.00
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.49
Consensus pattern (83 bp):
ATATAAATTTTAACATGATATTAATTAATATTATATAAATTTTAATACGTTACTAATTCGTATTA
TATAAATTTTGAGATGTT
Found at i:142363 original size:32 final size:32
Alignment explanation
Indices: 142322--142400 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 32
142312 TTTTGAGATG
*
142322 TTATATAAATTTTGAGATGATATTAATTCGTA
1 TTATATAAATTTTGAGATGATACTAATTCGTA
* * * *
142354 TTATATAAATTTTGATATGTTACTAATTTGTG
1 TTATATAAATTTTGAGATGATACTAATTCGTA
142386 TTATATAAATTTTGA
1 TTATATAAATTTTGA
142401 CACGTTCATA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (32 bp):
TTATATAAATTTTGAGATGATACTAATTCGTA
Found at i:142447 original size:17 final size:19
Alignment explanation
Indices: 142419--142455 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
142409 TATATTTATA
142419 TCATGTTAATATTAT-TTT
1 TCATGTTAATATTATATTT
142437 TCATGTT-ATATTATATTT
1 TCATGTTAATATTATATTT
142455 T
1 T
142456 ATCTTGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (19 bp):
TCATGTTAATATTATATTT
Found at i:145440 original size:5 final size:5
Alignment explanation
Indices: 145430--145492 Score: 62
Period size: 5 Copynumber: 13.2 Consensus size: 5
145420 TATGTTTCAA
* *
145430 TATAT TATAT TATAT T-TAT TATAT TATTT TCATA- TATAT T-TAA TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT T-ATAT TATAT TATAT TATAT
*
145478 TAT-T AATAT TATAT T
1 TATAT TATAT TATAT T
145493 TTCACATTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
4 13 0.28
5 32 0.68
6 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:145492 original size:11 final size:10
Alignment explanation
Indices: 145430--145492 Score: 62
Period size: 9 Copynumber: 6.6 Consensus size: 10
145420 TATGTTTCAA
145430 TATATTATAT
1 TATATTATAT
145440 TATATT-TAT
1 TATATTATAT
*
145449 TATATTATTT
1 TATATTATAT
145459 TCATA-TATAT
1 T-ATATTATAT
*
145469 T-TAATATAT
1 TATATTATAT
*
145478 TAT-TAATAT
1 TATATTATAT
145487 TATATT
1 TATATT
145493 TTCACATTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
8 2 0.05
9 22 0.51
10 16 0.37
11 3 0.07
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
TATATTATAT
Found at i:149286 original size:7 final size:7
Alignment explanation
Indices: 149276--149301 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
149266 ATAAAAATAA
149276 ATTATTT
1 ATTATTT
149283 ATTATTT
1 ATTATTT
149290 ATTATTT
1 ATTATTT
149297 ATTAT
1 ATTAT
149302 ATTTAATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
ATTATTT
Found at i:149728 original size:171 final size:172
Alignment explanation
Indices: 149433--149770 Score: 507
Period size: 171 Copynumber: 2.0 Consensus size: 172
149423 ATGCAGGTCC
* *
149433 ATTTCTGGTTTATGTTTCTCTAATGCATATAATTTGTCAAATAGCCATTAAATTTCTTACTCTTG
1 ATTTCTGGTGTATGTTTCTCTAATGCATATAATTTGTCAAAGAGCCATTAAATTTCTTACTCTTG
* * * *
149498 TGTACTGTATAATTATGAATAGATATGCTATGGATAATGATATTTGAATTTTGATTCATTTTTG-
66 TATACTGTATAATTATGAATAGATATGCTATGGATAATGATAGTTGAACTCTGATTCATTTTTGT
* *
149562 TTCCATCAGCGGCATCTGCAGCAACTTCTGCTAGATCATTAA
131 TTCCATCAGCGGCATCTGCAGCAACTACTGCAAGATCATTAA
* ** * *
149604 ATTTTTGGTGTATGTTTCTCTAATGTGTATAATTTGTCAAAGAGTCATTAAATTTCTTAGTCTTG
1 ATTTCTGGTGTATGTTTCTCTAATGCATATAATTTGTCAAAGAGCCATTAAATTTCTTACTCTTG
* *
149669 TATACTGTGTAATTATGAATAGATATGCTATGGATTATGATAGTTGAACTCTGATTCATTTTTGT
66 TATACTGTATAATTATGAATAGATATGCTATGGATAATGATAGTTGAACTCTGATTCATTTTTGT
* * *
149734 TTCTATCTGCGGCATCTGCAGCAGCTACTGCAAGATC
131 TTCCATCAGCGGCATCTGCAGCAACTACTGCAAGATC
149771 GTCATCGATC
Statistics
Matches: 148, Mismatches: 18, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
171 116 0.78
172 32 0.22
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.43
Consensus pattern (172 bp):
ATTTCTGGTGTATGTTTCTCTAATGCATATAATTTGTCAAAGAGCCATTAAATTTCTTACTCTTG
TATACTGTATAATTATGAATAGATATGCTATGGATAATGATAGTTGAACTCTGATTCATTTTTGT
TTCCATCAGCGGCATCTGCAGCAACTACTGCAAGATCATTAA
Found at i:150545 original size:27 final size:27
Alignment explanation
Indices: 150515--150585 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
150505 AAAAATCACC
* *
150515 CTTTGTGTTTGTAAAAAATGGTGGTTA
1 CTTTGTGTTTGTCAAAAATAGTGGTTA
* *
150542 CTTTGTATTTGTCAAAAATAGTGGTTC
1 CTTTGTGTTTGTCAAAAATAGTGGTTA
*
150569 CTTTTTGTTTGTCAAAA
1 CTTTGTGTTTGTCAAAA
150586 TTTATGACTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.46
Consensus pattern (27 bp):
CTTTGTGTTTGTCAAAAATAGTGGTTA
Found at i:150717 original size:13 final size:13
Alignment explanation
Indices: 150672--150718 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
150662 GGCTCCCTCC
150672 TCCCTCTCAAGCA
1 TCCCTCTCAAGCA
* *
150685 TCCCGCTTAAGCA
1 TCCCTCTCAAGCA
*
150698 TCTCTCTCAAGCA
1 TCCCTCTCAAGCA
150711 TCCCTCTC
1 TCCCTCTC
150719 TTGTATCCCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.19, C:0.45, G:0.09, T:0.28
Consensus pattern (13 bp):
TCCCTCTCAAGCA
Found at i:155135 original size:27 final size:27
Alignment explanation
Indices: 155104--155176 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
155094 AAAAACCAGC
155104 CTTTGTGTTTGTCAAAAATGGTGGTTA
1 CTTTGTGTTTGTCAAAAATGGTGGTTA
* *
155131 CTTTGTATTTGTCAAAAATGGTGGTTC
1 CTTTGTGTTTGTCAAAAATGGTGGTTA
* *
155158 CTTTTTGTTTGTAAAAAAT
1 CTTTGTGTTTGTCAAAAAT
155177 TATGGCTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.25, C:0.08, G:0.21, T:0.47
Consensus pattern (27 bp):
CTTTGTGTTTGTCAAAAATGGTGGTTA
Found at i:155206 original size:24 final size:24
Alignment explanation
Indices: 155109--155207 Score: 83
Period size: 27 Copynumber: 3.9 Consensus size: 24
155099 CCAGCCTTTG
155109 TGTTTGTCAAAAATGGTGG-TTACTT
1 TGTTTGTCAAAAATGGTGGCTTA--T
*
155134 TGTATTTGTCAAAAATGGTGGTTCCTTTT
1 TG--TTTGTCAAAAATGGTGG---CTTAT
* **
155163 TGTTTGTAAAAAATTATGGCTTAT
1 TGTTTGTCAAAAATGGTGGCTTAT
*
155187 TGTTTGTCAAAATTGGTGGCT
1 TGTTTGTCAAAAATGGTGGCT
155208 AATTTTTATT
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
24 21 0.36
25 2 0.03
27 31 0.53
29 3 0.05
31 2 0.03
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.45
Consensus pattern (24 bp):
TGTTTGTCAAAAATGGTGGCTTAT
Found at i:155319 original size:26 final size:25
Alignment explanation
Indices: 155264--155319 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
155254 TCCCTCCTCT
*
155264 CTCTCAAGTATCCCTCTTAAGCATCT
1 CTCTCAAGTATCCCTCTT-AGCATCC
*
155290 CTCTCAAGTATTCCTCTCTT-GTATCC
1 CTCTCAAGTA-TCC-CTCTTAGCATCC
155316 CTCT
1 CTCT
155320 TCAATTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 18 0.69
27 3 0.12
28 5 0.19
ACGTcount: A:0.18, C:0.36, G:0.07, T:0.39
Consensus pattern (25 bp):
CTCTCAAGTATCCCTCTTAGCATCC
Found at i:156183 original size:117 final size:119
Alignment explanation
Indices: 155973--156288 Score: 442
Period size: 120 Copynumber: 2.7 Consensus size: 119
155963 TTATATATTT
* * * *
155973 AAATTTAATAGCTCAAATAAGTTGA-CAAAACATTAATCATTTACTTGTACATTTTTTTAATTTT
1 AAATTTAATAGCTCAAACAAGTT-ATCAAAACATTAATTATTTACTTATAGATTTTTTTAA-TTT
* *
156037 TTTCTCTCGTTTTTTTCTCCTCTCTAGTTTGTCA-TTT-TTTTTAGTCGCACGCTC
64 TTTCTCTAGTTTTTTTCTCCTCTCTAGTTTGTCATTTTATTTTTAATCGCACGCTC
156091 AAATTTAATAGCTCAAACAAGTTATCAAAACATTAATTATTTACTTATAGATTTTTTTAATTTTT
1 AAATTTAATAGCTCAAACAAGTTATCAAAACATTAATTATTTACTTATAGATTTTTTTAATTTTT
* *
156156 TCTCTAGTTTTTTTCTCCTCTCTAGTTTGTCATCTTTTATTTTTAATTGCACGCTT
66 TCTCTAGTTTTTTTCTCCTCTCTAGTTTGTCA--TTTTATTTTTAATCGCACGCTC
* * * * * *
156212 AAATTTAATAG-TTAAACAAATTATCAAAAAATTAACTATTTAATTATTGATTTTTTTAATTTTT
1 AAATTTAATAGCTCAAACAAGTTATCAAAACATTAATTATTTACTTATAGATTTTTTTAATTTTT
156276 TCTCTAGTTTTTT
66 TCTCTAGTTTTTT
156289 CTTTTTCCCC
Statistics
Matches: 179, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
117 37 0.21
118 54 0.30
120 63 0.35
121 25 0.14
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.51
Consensus pattern (119 bp):
AAATTTAATAGCTCAAACAAGTTATCAAAACATTAATTATTTACTTATAGATTTTTTTAATTTTT
TCTCTAGTTTTTTTCTCCTCTCTAGTTTGTCATTTTATTTTTAATCGCACGCTC
Found at i:156521 original size:115 final size:111
Alignment explanation
Indices: 156359--156645 Score: 283
Period size: 115 Copynumber: 2.5 Consensus size: 111
156349 TTATCTTTTC
* * ** *
156359 TTTTTTATTACACATTCAAATTTAATAGCTCAAATAAACCGTTAAAATATTAATTATTTACTTAT
1 TTTTTTATTACACCTT-AAATTTAATAGCTCAAATAAGCTATCAAAATATTAATTATTTACTTAT
*
156424 AAATTTTTTTAATTTTTTTTCTCTA-ATTTTTTTCCTCACTAGTTTGTC-TT
65 -AA-TTTTTTAA--TATTTT-TCTAGATTTTTTTCCTCACTAGTTTGTCATT
* ** *
156474 TTTTTTATTACACCCTTAAATTTAATAGCTCAAATAAGTTATCAAAATATTAACCATTTACTTGT
1 TTTTTTATTACA-CCTTAAATTTAATAGCTCAAATAAGCTATCAAAATATTAATTATTTACTTAT
* * ***
156539 AATTTTTTAATATTTTTCTAGTTTTTTTTCTTTTTTAGTTTGTCATT
65 AATTTTTTAATATTTTTCTAGATTTTTTTCCTCACTAGTTTGTCATT
* ** * * *
156586 TTTTTTATTGCGTGCTCAAATTTAATAGCTCAAACAAGCTA-CTAAAACATTAATTATTTA
1 TTTTTTATTAC-ACCTTAAATTTAATAGCTCAAATAAGCTATC-AAAATATTAATTATTTA
156646 TTTGTCATTT
Statistics
Matches: 143, Mismatches: 24, Indels: 13
0.79 0.13 0.07
Matches are distributed among these distances:
110 4 0.03
111 24 0.17
112 50 0.35
113 8 0.06
114 2 0.01
115 52 0.36
116 3 0.02
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (111 bp):
TTTTTTATTACACCTTAAATTTAATAGCTCAAATAAGCTATCAAAATATTAATTATTTACTTATA
ATTTTTTAATATTTTTCTAGATTTTTTTCCTCACTAGTTTGTCATT
Found at i:156671 original size:93 final size:94
Alignment explanation
Indices: 156560--156744 Score: 275
Period size: 94 Copynumber: 2.0 Consensus size: 94
156550 ATTTTTCTAG
* * **
156560 TTTTTTTTCTTTTTTAGTTTGTCATTTTTTTT-ATTGCGTGCTCAAATTTAATAGCTCAAACAAG
1 TTTTTTTTCTTCTTTAGTTTGTCATTTTTTTTAATCGCACGCTCAAATTTAATAGCTCAAACAAG
*
156624 -CTACTAAAACATTAATTATTTATTTGTCA
66 TC-ACTAAAACATTAACTATTTATTTGTCA
*
156653 TTTTTTTTCTTCTTTAGTTTGTCATTTTTTTTAATCGCACGCTCAAATTTAATAGCTTAAACAAG
1 TTTTTTTTCTTCTTTAGTTTGTCATTTTTTTTAATCGCACGCTCAAATTTAATAGCTCAAACAAG
* *
156718 TCATTAAAATATTAACTATTTATTTGT
66 TCACTAAAACATTAACTATTTATTTGT
156745 AGATTTCTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
93 31 0.38
94 50 0.61
95 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (94 bp):
TTTTTTTTCTTCTTTAGTTTGTCATTTTTTTTAATCGCACGCTCAAATTTAATAGCTCAAACAAG
TCACTAAAACATTAACTATTTATTTGTCA
Found at i:156900 original size:13 final size:13
Alignment explanation
Indices: 156882--156931 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
156872 TATATTCTTT
156882 TAATTTTTTTCTC
1 TAATTTTTTTCTC
* *
156895 TAATTTTTCTTTTG
1 TAATTTTT-TTCTC
*
156909 TATCTTTTTTTCTC
1 TA-ATTTTTTTCTC
156923 TAATTTTTT
1 TAATTTTTT
156932 ATTTTTCCTC
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
13 14 0.48
14 10 0.34
15 5 0.17
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72
Consensus pattern (13 bp):
TAATTTTTTTCTC
Found at i:156937 original size:156 final size:156
Alignment explanation
Indices: 156757--157058 Score: 363
Period size: 156 Copynumber: 1.9 Consensus size: 156
156747 ATTTCTTTAA
** * *
156757 TTTTTTTCTCTTGTTTGTTCTTTTTTCT-TCTCTCTAGTGTATTATCATTTATTGTTAATTACAC
1 TTTTTTTCTCTAATTTGTTATTTTTCCTCT-TCTCTAGTGTATTATCATTTATTGTTAATTACAC
* * * * * *
156821 GCTCAAATTTAATAGTTTAAATAAGATATCAAAACATTAACCATTTGCTTATATATTCTTTTAAT
65 ACTCAAATTTAATAGCTCAAATAAGATATCAAAACATTAACCATTTACTTATAGATTATTTTAAT
156886 TTTTTTCTCTAATTTTTCTTTTGTATC
130 TTTTTTCTCTAATTTTTCTTTTGTATC
* * * * * * ***
156913 TTTTTTTCTCTAATTTTTTATTTTTCCTCTTCTCTAGTTTATTATCTTTTTTTTTTTATTATTTA
1 TTTTTTTCTCTAATTTGTTATTTTTCCTCTTCTCTAGTGTATTATCATTTATTGTTAATTACACA
* * * * *
156978 TTCAAATTTAATAGCTCAAATAAGTTGTCAAAACATTAATCATTTACTTGTAGATTATTTTAATT
66 CTCAAATTTAATAGCTCAAATAAGATATCAAAACATTAACCATTTACTTATAGATTATTTTAATT
*
157043 TTTTTCTCTCATTTTT
131 TTTTTCTCTAATTTTT
157059 TTCTACTCTC
Statistics
Matches: 120, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
156 119 0.99
157 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.05, T:0.57
Consensus pattern (156 bp):
TTTTTTTCTCTAATTTGTTATTTTTCCTCTTCTCTAGTGTATTATCATTTATTGTTAATTACACA
CTCAAATTTAATAGCTCAAATAAGATATCAAAACATTAACCATTTACTTATAGATTATTTTAATT
TTTTTCTCTAATTTTTCTTTTGTATC
Found at i:157102 original size:404 final size:400
Alignment explanation
Indices: 156654--157578 Score: 964
Period size: 397 Copynumber: 2.3 Consensus size: 400
156644 TATTTGTCAT
* *
156654 TTTTTTTCTTCTTTAGTTTGTCA-TTTTTTTTAATCGCACGCTCAAATTTAATAGCTTAAACAAG
1 TTTTTTTCTTCTTTAGTTTGTAATTTTTTTTTAATCGCACGCTCAAATTTAATAGCTTAAACAAA
* * * *
156718 TCATTAAAATATTAACTATTTATTTGTAGATTTCTTTAATTTTTTTCTCTTGTTTGTTCTTTTTT
66 TCATCAAAACATTAACTATTTACTTGTAGATTT-TTTAATTTTTTTCTC----TAG-T-TTTTTT
* * *
156783 CTTCTCTCTAGTGT-ATTATCATTTATTGTTAATTACACGCTCAAATTTAATAGTTTAAATAAGA
124 CTTCTCTCTAGT-TCATCATCATTTATTGTTAATTACACGCTCAAATTTAATAGTTCAAACAAGA
* ** *
156847 TATCAAAACATTAACCATTTGCTTA-T-ATATTCTTTTAATTTTTTTCTCTAA-TTTTTCTTTTG
188 TATCAAAAAATTAACCATTTAATTATTGAT-TTC-TTTAA-TTTTTT-TCTAATTTTTTCTCTT-
* * *
156909 TA-T-CT-TTT-TTTCTC-TAATTTT-T-TA-TTTTTCCTCTT-C-TCTAGTTTATTATCTTTTT
248 TACTCCTATTTATTTCTCATAATTTTCTCTAGTTTTTCCTCTTCCATCTAATTTATTATATTTTC
* *** ** *
156964 TTTTTTATTATTTATTCAAATTTAATAGCTCAAATAAGTTGTCAAAACATTAATCATTTACTTGT
313 TTTTTGATTACGCATTCAAATTTAATAGCTCAAATAAACTGTCAAAACATTAATCATTTACTTAT
*
157029 AGATTATTTT-AATTTTTTTCTCTCA
378 A-ATT-TTTTAAAATTTTTTCTCT-A
* *
157054 TTTTTTTCTACTCTCTAGTTTGTAATCTTTTTTTTAGTCGCACGCTCAAATTTAATAGCTTAAAC
1 TTTTTTTCT--TCTTTAGTTTGTAAT-TTTTTTTTAATCGCACGCTCAAATTTAATAGCTTAAAC
* * * *
157119 AAATTATCAAAACATTAATTATTTACTTGTATATTTTTTAATTTTTTTCTCTAGTTTTTTTCTTT
63 AAATCATCAAAACATTAACTATTTACTTGTAGATTTTTTAATTTTTTTCTCTAGTTTTTTTCTTC
* * ** * * *
157184 TCTCTAGTTCATCATCTTTTATTTTTAATTGTACTCTTAAATTTAATAGTTCAAACAAGTTATCA
128 TCTCTAGTTCATCATCATTTATTGTTAATTACACGCTCAAATTTAATAGTTCAAACAAGATATCA
157249 AAAAATTAACCATTTAATTATTGATTTCTTTAATTTTTTTCTAATTTTTTCTCTTTACTCCTATT
193 AAAAATTAACCATTTAATTATTGATTTCTTTAATTTTTTTCTAATTTTTTCTCTTTACTCCTATT
* ** ** *
157314 TAGTTTGTCATTTTTTTCTCTAGTTTTTTTTCTTCCTATCTAATTTGTTATATTTTCTTTTTGAT
258 TA-TTTCTCATAATTTTCTCTAGTTTTTCCTCTTCC-ATCTAATTTATTATATTTTCTTTTTGAT
* *
157379 TACGCATTCAAATTTAATAGCTCAAATAAACTGTCAAAATATTAATTATTTACTTATAATTTTTT
321 TACGCATTCAAATTTAATAGCTCAAATAAACTGTCAAAACATTAATCATTTACTTATAATTTTTT
157444 AAAATTTTTTCTCTA
386 AAAATTTTTTCTCTA
* * * ** * * *
157459 TTTTTTTCTTCTTTAGTTTGTTATTTTTTTATT-A---CACACTTAAATTTAATAATTTTAATAT
1 TTTTTTTCTTCTTTAGTTTGTAATTTTTTT-TTAATCGCACGCTCAAATTTAATAGCTTAAACAA
* * * *
157520 GTTATCAAAACATTAACCATTTAC-TGTA-ATTATTTAA--TTTTT-TCTAGTTTTTTTCTTCT
65 ATCATCAAAACATTAACTATTTACTTGTAGATTTTTTAATTTTTTTCTCTAGTTTTTTTCTTCT
157579 TTAGTTTGTT
Statistics
Matches: 443, Mismatches: 60, Indels: 50
0.80 0.11 0.09
Matches are distributed among these distances:
394 16 0.04
395 12 0.03
396 17 0.04
397 94 0.21
398 12 0.03
399 45 0.10
400 14 0.03
401 5 0.01
402 19 0.04
403 32 0.07
404 75 0.17
405 15 0.03
406 15 0.03
407 72 0.16
ACGTcount: A:0.27, C:0.13, G:0.05, T:0.55
Consensus pattern (400 bp):
TTTTTTTCTTCTTTAGTTTGTAATTTTTTTTTAATCGCACGCTCAAATTTAATAGCTTAAACAAA
TCATCAAAACATTAACTATTTACTTGTAGATTTTTTAATTTTTTTCTCTAGTTTTTTTCTTCTCT
CTAGTTCATCATCATTTATTGTTAATTACACGCTCAAATTTAATAGTTCAAACAAGATATCAAAA
AATTAACCATTTAATTATTGATTTCTTTAATTTTTTTCTAATTTTTTCTCTTTACTCCTATTTAT
TTCTCATAATTTTCTCTAGTTTTTCCTCTTCCATCTAATTTATTATATTTTCTTTTTGATTACGC
ATTCAAATTTAATAGCTCAAATAAACTGTCAAAACATTAATCATTTACTTATAATTTTTTAAAAT
TTTTTCTCTA
Found at i:157129 original size:120 final size:121
Alignment explanation
Indices: 156979--157290 Score: 371
Period size: 121 Copynumber: 2.6 Consensus size: 121
156969 TATTATTTAT
* * *
156979 TCAAATTTAATAGCTCAAATAAGTTGTCAAAACATTAATCATTTACTTGTAGATTATTTTAATTT
1 TCAAATTTAATAGCTTAAACAAGTTATCAAAACATTAATCATTTACTTGTAGATT-TTTTAATTT
** *
157044 TTTTCTCTCA-TTTTTTTCTACTCTCTAGTTTGTAATC-TTT-TTTTTAGTCGCACGC
65 TTTTCTCT-AGTTTTTTTCTACTCTCTAGTTCATAATCTTTTATTTTTAATCGCACGC
* * *
157099 TCAAATTTAATAGCTTAAACAAATTATCAAAACATTAATTATTTACTTGTATATTTTTTAATTTT
1 TCAAATTTAATAGCTTAAACAAGTTATCAAAACATTAATCATTTACTTGTAGATTTTTTAATTTT
** * * * *
157164 TTTCTCTAGTTTTTTTCTTTTCTCTAGTTCATCATCTTTTATTTTTAATTGTACTC
66 TTTCTCTAGTTTTTTTCTACTCTCTAGTTCATAATCTTTTATTTTTAATCGCACGC
* * * * * *
157220 TTAAATTTAATAG-TTCAAACAAGTTATCAAAAAATTAACCATTTAATTATTGATTTCTTTAATT
1 TCAAATTTAATAGCTT-AAACAAGTTATCAAAACATTAATCATTTACTTGTAGATTT-TTTAATT
157284 TTTTTCT
64 TTTTTCT
157291 AATTTTTTCT
Statistics
Matches: 163, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
118 1 0.01
119 39 0.24
120 54 0.33
121 55 0.34
122 14 0.09
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.51
Consensus pattern (121 bp):
TCAAATTTAATAGCTTAAACAAGTTATCAAAACATTAATCATTTACTTGTAGATTTTTTAATTTT
TTTCTCTAGTTTTTTTCTACTCTCTAGTTCATAATCTTTTATTTTTAATCGCACGC
Found at i:157487 original size:112 final size:108
Alignment explanation
Indices: 157371--157595 Score: 247
Period size: 112 Copynumber: 2.0 Consensus size: 108
157361 TTATATTTTC
* * * * **
157371 TTTTTGATTACGCA-TTCAAATTTAATAGCTCAAATAAACTGTCAAAATATTAATTATTTACTTA
1 TTTTTGATTACACACTT-AAATTTAATAACTCAAATAAACTATCAAAACATTAACCATTTAC-TA
*
157435 TAATTTTTTAAAATTTTTTCTCTA-TTTTTTTCTTCTTTAGTTTGTTAT
64 TAATTATTT--AA-TTTTT-TCTAGTTTTTTTCTTCTTTAGTTTGTTAT
* * ** *** *
157483 TTTTTTATTACACACTTAAATTTAATAATTTTAATATGTTATCAAAACATTAACCATTTACTGTA
1 TTTTTGATTACACACTTAAATTTAATAACTCAAATAAACTATCAAAACATTAACCATTTACTATA
157548 ATTATTTAATTTTTTCTAGTTTTTTTCTTCTTTAGTTTGTTAT
66 ATTATTTAATTTTTTCTAGTTTTTTTCTTCTTTAGTTTGTTAT
157591 TTTTT
1 TTTTT
157596 ATTTTTGATT
Statistics
Matches: 96, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
107 4 0.04
108 34 0.35
109 2 0.02
111 9 0.09
112 45 0.47
113 2 0.02
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (108 bp):
TTTTTGATTACACACTTAAATTTAATAACTCAAATAAACTATCAAAACATTAACCATTTACTATA
ATTATTTAATTTTTTCTAGTTTTTTTCTTCTTTAGTTTGTTAT
Found at i:157640 original size:17 final size:17
Alignment explanation
Indices: 157618--157653 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
157608 GCGCTCAAAT
157618 TTAATAACTTAAACAAG
1 TTAATAACTTAAACAAG
157635 TTAATAACTTAAACAAG
1 TTAATAACTTAAACAAG
157652 TT
1 TT
157654 GTTAAAACAT
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:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (17 bp):
TTAATAACTTAAACAAG
Found at i:157875 original size:113 final size:116
Alignment explanation
Indices: 157635--157920 Score: 319
Period size: 113 Copynumber: 2.5 Consensus size: 116
157625 CTTAAACAAG
* * * ** * *
157635 TTAATAACTTAAACAAGTTGTTAAAACATTAATCGTTTATTTATAGATTTTTTTATTTTTTATTT
1 TTAATAACTCAAACAAATTGTTAAAATATTAATAATTTACTTATAAATTTTTTTA-TTTTTATTT
** * * * * * *
157700 TTTTCTTTTTCTTTCTATTTAATTTGTTATTTTTTTGATTACGCACTCAAAT
65 AATTATTTTTCTTTCTATCTAATTTATAATTTTTTTAATTACACACTCAAAT
* *
157752 TTAATAACTCAAATAAATTGTTAAAATATTAATAATTTACTTGTAAATTTTTTTA-TTTT-TTTA
1 TTAATAACTCAAACAAATTGTTAAAATATTAATAATTTACTTATAAATTTTTTTATTTTTATTTA
* * *
157815 ATTATTTTTCTTT-TCTCTAATTTATAATTTTTTTAATTACACATTTAAAT
66 ATTATTTTTCTTTCTATCTAATTTATAATTTTTTTAATTACACACTCAAAT
* *
157865 TTAATAACTCAAACAAATT-TATAAAATATTAATTACTTACTTATAAATTTCTTTTA
1 TTAATAACTCAAACAAATTGT-TAAAATATTAATAATTTACTTATAAATTT-TTTTA
157921 GCACCTGTTA
Statistics
Matches: 143, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
112 1 0.01
113 73 0.51
114 19 0.13
115 4 0.03
117 46 0.32
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.54
Consensus pattern (116 bp):
TTAATAACTCAAACAAATTGTTAAAATATTAATAATTTACTTATAAATTTTTTTATTTTTATTTA
ATTATTTTTCTTTCTATCTAATTTATAATTTTTTTAATTACACACTCAAAT
Found at i:158709 original size:16 final size:17
Alignment explanation
Indices: 158643--158710 Score: 68
Period size: 17 Copynumber: 3.9 Consensus size: 17
158633 AATTCTTAAA
158643 ATTTATATTAAAAATTATAT
1 ATTTATATT--AAA-TATAT
158663 CATTTA-ATTAAATATAT
1 -ATTTATATTAAATATAT
*
158680 ATTTTTATTAAATATAT
1 ATTTATATTAAATATAT
*
158697 A-TTATATTTAATAT
1 ATTTATATTAAATAT
158711 TGATTTTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
16 15 0.35
17 17 0.40
18 3 0.07
20 3 0.07
21 5 0.12
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATATTAAATATAT
Found at i:159917 original size:21 final size:20
Alignment explanation
Indices: 159902--159949 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
159892 AATTACAAAC
*
159902 TTAATAAATAT-TATTATAA
1 TTAATAAATATATATTAAAA
*
159921 TTAATAATTATATATTAAAAA
1 TTAATAAATATATATT-AAAA
159942 TTAA-AAAT
1 TTAATAAAT
159950 TAAAATCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 10 0.42
20 7 0.29
21 7 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATAAATATATATTAAAA
Found at i:160396 original size:35 final size:35
Alignment explanation
Indices: 160350--160421 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
160340 TTCTTTATTC
160350 GTGTCATAATTCTGTTAATTTCACTGATCAAAATG
1 GTGTCATAATTCTGTTAATTTCACTGATCAAAATG
*
160385 GTGTCATAATTCTGTTAATTTCACTGATCGAAATG
1 GTGTCATAATTCTGTTAATTTCACTGATCAAAATG
160420 GT
1 GT
160422 TATCGGAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (35 bp):
GTGTCATAATTCTGTTAATTTCACTGATCAAAATG
Found at i:161727 original size:17 final size:16
Alignment explanation
Indices: 161707--161748 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
161697 TAAAAAGTTA
161707 AAAAATAAATAATTTTT
1 AAAAATAAAT-ATTTTT
*
161724 AAAATTAAATATTTTT
1 AAAAATAAATATTTTT
*
161740 AAATATAAA
1 AAAAATAAA
161749 ATATATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAAATAAATATTTTT
Found at i:161732 original size:40 final size:41
Alignment explanation
Indices: 161688--161771 Score: 93
Period size: 40 Copynumber: 2.1 Consensus size: 41
161678 AAGTGCATTT
161688 TTAAAAATTTAAAAAGT-TAAAAAATA-AATAATTT-TTAAAA
1 TTAAAAATTTAAAAA-TATAAAAAATATAA-AATTTCTTAAAA
* ** *
161728 TTAAATATTTTTAAATATAAAATATATAAAATTTCTTAAAA
1 TTAAAAATTTAAAAATATAAAAAATATAAAATTTCTTAAAA
161769 TTA
1 TTA
161772 TTATTTTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
39 1 0.03
40 25 0.68
41 11 0.30
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (41 bp):
TTAAAAATTTAAAAATATAAAAAATATAAAATTTCTTAAAA
Found at i:164499 original size:14 final size:13
Alignment explanation
Indices: 164465--164539 Score: 71
Period size: 13 Copynumber: 5.7 Consensus size: 13
164455 TTTAAAATTT
*
164465 TATATATTTAAAA
1 TATATATTTAATA
*
164478 AATAATATTTTAATA
1 TAT-ATA-TTTAATA
*
164493 TTTATATTTAA-A
1 TATATATTTAATA
164505 TATATATTTAATA
1 TATATATTTAATA
* *
164518 TAAATATTAAATA
1 TATATATTTAATA
*
164531 TAAATATTT
1 TATATATTT
164540 TAAAAGAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
12 11 0.22
13 27 0.53
14 6 0.12
15 7 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TATATATTTAATA
Found at i:164514 original size:25 final size:26
Alignment explanation
Indices: 164465--164542 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 26
164455 TTTAAAATTT
*
164465 TATATATTTAAAAAATAATATTTTAATA
1 TATATATTT-AAATAT-ATATTTTAATA
*
164493 TTTATATTTAAATATATA-TTTAATA
1 TATATATTTAAATATATATTTTAATA
*
164518 TAAATA-TTAAATATAAATATTTTAA
1 TATATATTTAAATAT--ATATTTTAA
164543 AAGAATAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
24 8 0.19
25 11 0.26
26 6 0.14
27 10 0.23
28 8 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TATATATTTAAATATATATTTTAATA
Found at i:164523 original size:17 final size:18
Alignment explanation
Indices: 164490--164524 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
164480 TAATATTTTA
*
164490 ATATTTATATTTAAATAT
1 ATATTTATATATAAATAT
164508 ATATTTA-ATATAAATAT
1 ATATTTATATATAAATAT
164525 TAAATATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTTATATATAAATAT
Found at i:164563 original size:19 final size:19
Alignment explanation
Indices: 164527--164563 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
164517 ATAAATATTA
* *
164527 AATATAAATATTTTAAAAG
1 AATAAAAATATTTAAAAAG
164546 AATAAAAATATTTAAAAA
1 AATAAAAATATTTAAAAA
164564 TTACTAAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
AATAAAAATATTTAAAAAG
Found at i:164866 original size:25 final size:24
Alignment explanation
Indices: 164802--164869 Score: 64
Period size: 25 Copynumber: 2.8 Consensus size: 24
164792 CTCAATTTTA
**
164802 ATTAATAAAGTTAATAATATGATAT
1 ATTAATAAAAATAA-AATATGATAT
** * *
164827 AAAAATATAACTAAAATATGATAT
1 ATTAATAAAAATAAAATATGATAT
164851 ATTTAATAAAAATAAAATA
1 A-TTAATAAAAATAAAATA
164870 ATTTAATAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
24 11 0.33
25 22 0.67
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (24 bp):
ATTAATAAAAATAAAATATGATAT
Found at i:168313 original size:24 final size:25
Alignment explanation
Indices: 168285--168354 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 25
168275 AATAAAAATT
*
168285 GGCCACCAATTTTGACAAACAACAA
1 GGCCACCAATTTTGACAAACAAAAA
168310 -GCCA-CAATTTTTGACAAACAAAAA
1 GGCCACCAA-TTTTGACAAACAAAAA
*
168334 GGAACCACCATTTTTGACAAA
1 GG--CCACCAATTTTGACAAA
168355 TACAAAGTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
23 3 0.08
24 19 0.50
25 1 0.03
27 13 0.34
28 2 0.05
ACGTcount: A:0.44, C:0.24, G:0.11, T:0.20
Consensus pattern (25 bp):
GGCCACCAATTTTGACAAACAAAAA
Found at i:168349 original size:27 final size:27
Alignment explanation
Indices: 168287--168383 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 27
168277 TAAAAATTGG
* *
168287 CCACCAATTTTGACAAACAACAA-G--
1 CCACCATTTTTGACAAACAAAAAGGAA
*
168311 CCACAATTTTTGACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* * *
168338 CCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* *
168365 CCATCATTGTTGACAAACA
1 CCACCATTTTTGACAAACA
168384 CATGGTGGCT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
24 20 0.33
25 1 0.02
27 39 0.65
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.22
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:168402 original size:24 final size:25
Alignment explanation
Indices: 168371--168428 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
168361 GTAACCATCA
*
168371 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
*
168395 TTGTTGACAAACACAAAGGGTGGTTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
168421 TTGTTGAC
1 TTGTTGAC
168429 TAGCCACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 14 0.47
26 16 0.53
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:172945 original size:27 final size:26
Alignment explanation
Indices: 172883--172958 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 26
172873 AATAAAAATT
* * *
172883 AACCACCAATTTTGACAAACAACAAG
1 AACCACCATTTTTGAAAAACAAAAAG
*
172909 --CCACAATTTTTGAAAAACAAAAAGG
1 AACCACCATTTTTGAAAAACAAAAA-G
172934 AACCACCATTTTTGACAAATACAAA
1 AACCACCATTTTTGA-AAA-ACAAA
172959 GTAACCATCA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
24 19 0.47
25 1 0.03
27 12 0.30
28 3 0.08
29 5 0.12
ACGTcount: A:0.50, C:0.22, G:0.08, T:0.20
Consensus pattern (26 bp):
AACCACCATTTTTGAAAAACAAAAAG
Found at i:172959 original size:27 final size:27
Alignment explanation
Indices: 172909--172983 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
172899 AAACAACAAG
* * * *
172909 CCACAATTTTTGAAAAACAAAAAGGAA
1 CCACCATTTTTGACAAATACAAAGGAA
*
172936 CCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAATACAAAGGAA
* *
172963 CCATCATTGTTGACAAATACA
1 CCACCATTTTTGACAAATACA
172984 TGGTGGCTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (27 bp):
CCACCATTTTTGACAAATACAAAGGAA
Found at i:173487 original size:210 final size:210
Alignment explanation
Indices: 173118--173516 Score: 604
Period size: 210 Copynumber: 1.9 Consensus size: 210
173108 TGGATTTACA
*
173118 AGACTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGAAATGATATCTCTTGAAAAATTAATTC
1 AGACTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGAAATGATAGCTCTTGAAAAATTAATTC
* * * *
173183 TTTCAGGCTGCTCAAATCTTGAAAGGTTTCCAGAGATTGAGGGCAAAATCGAATGTTTGCTGGAG
66 TTTCAGGCTGCTCAAATCTTAAAAGCTTTCCAGAGATTGAGGACAAAATCGAATGTTTGCGGGAG
* *
173248 CTTTCATTAGATGGGAAAGGCATTGAAGGACTTTCCTCTTCCATCGGAAGTCTCAGCAGACACAA
131 CTTTCATTAGATGGGAAAGGCATTGAAGGACTTCCCTCTTCCATCGGAAATCTCAGCAGACACAA
173313 AGTTTTAAATTTAAG
196 AGTTTTAAATTTAAG
* * * *
173328 AGACTGTAAAAGTCTTAGGAGTCTTTCAGCCAAAATT-AGAATGGA-AGCTCTTGAAGAATTAAT
1 AGACTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGA-AAT-GATAGCTCTTGAAAAATTAAT
* * * *
173391 TCTTTCAGGCTGCTCAAATCTTAAAAGCTTTTCAGAGATTGATGACGAAATGGAATGTTTGCGGG
64 TCTTTCAGGCTGCTCAAATCTTAAAAGCTTTCCAGAGATTGAGGACAAAATCGAATGTTTGCGGG
* * *
173456 AGCTTTCTTTAGATGGGACAGGCATTGAAGGACTTCCCTCTTCCATTGGAAATCTCAGCAG
129 AGCTTTCATTAGATGGGAAAGGCATTGAAGGACTTCCCTCTTCCATCGGAAATCTCAGCAG
173517 TCTTCATCGG
Statistics
Matches: 169, Mismatches: 18, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
209 1 0.01
210 166 0.98
211 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.30
Consensus pattern (210 bp):
AGACTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGAAATGATAGCTCTTGAAAAATTAATTC
TTTCAGGCTGCTCAAATCTTAAAAGCTTTCCAGAGATTGAGGACAAAATCGAATGTTTGCGGGAG
CTTTCATTAGATGGGAAAGGCATTGAAGGACTTCCCTCTTCCATCGGAAATCTCAGCAGACACAA
AGTTTTAAATTTAAG
Found at i:174487 original size:20 final size:20
Alignment explanation
Indices: 174437--174498 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
174427 ATTGAAGAGA
*
174437 GATACAAGAGAGAGATGAGG
1 GATACAAGAGAGGGATGAGG
174457 GATACAAGAGAGGGATGAGG
1 GATACAAGAGAGGGATGAGG
** *
174477 GATACTTGAGAGGGAGGAGG
1 GATACAAGAGAGGGATGAGG
174497 GA
1 GA
174499 GCTTCCTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.39, C:0.05, G:0.45, T:0.11
Consensus pattern (20 bp):
GATACAAGAGAGGGATGAGG
Found at i:179050 original size:20 final size:20
Alignment explanation
Indices: 179000--179061 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
178990 ATTGAAGAGA
*
179000 GATACAAGAGAGAGATGAGG
1 GATACAAGAGAGGGATGAGG
179020 GATACAAGAGAGGGATGAGG
1 GATACAAGAGAGGGATGAGG
** *
179040 GATACTTGAGAGGGAGGAGG
1 GATACAAGAGAGGGATGAGG
179060 GA
1 GA
179062 GCTTCCTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.39, C:0.05, G:0.45, T:0.11
Consensus pattern (20 bp):
GATACAAGAGAGGGATGAGG
Found at i:182339 original size:13 final size:13
Alignment explanation
Indices: 182320--182376 Score: 69
Period size: 13 Copynumber: 4.4 Consensus size: 13
182310 GATACAAGAA
*
182320 AGGGATGCTTGAG
1 AGGGATGCTTAAG
* *
182333 AGAGATGATTAAG
1 AGGGATGCTTAAG
*
182346 AGGGATACTTAAG
1 AGGGATGCTTAAG
*
182359 AGGGATGCTTGAG
1 AGGGATGCTTAAG
182372 AGGGA
1 AGGGA
182377 GGAGGGAGCC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.33, C:0.05, G:0.40, T:0.21
Consensus pattern (13 bp):
AGGGATGCTTAAG
Done.