Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1530
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: 46195
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2544 original size:39 final size:39
Alignment explanation
Indices: 2427--2604 Score: 281
Period size: 39 Copynumber: 4.6 Consensus size: 39
2417 TATACATATA
2427 TGCTTCAGTTAGCC-TCGGGCTTCCGTTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATG
*
2465 TGCTTCAGTTAGCCTTCGGGCTT-TGTTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATG
*
2503 TGCTTCAGTTAGCC-TCTGGGCTTCCATTTAGCACTTATG
1 TGCTTCAGTTAGCCTTC-GGGCTTCCGTTTAGCACTTATG
2542 TGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATG
* **
2581 TGCTTCAGCTAGATTTCGGGCTTC
1 TGCTTCAGTTAGCCTTCGGGCTTC
2605 AGATCACGAT
Statistics
Matches: 129, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
37 2 0.02
38 48 0.37
39 77 0.60
40 2 0.02
ACGTcount: A:0.13, C:0.25, G:0.23, T:0.39
Consensus pattern (39 bp):
TGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATG
Found at i:2553 original size:77 final size:77
Alignment explanation
Indices: 2427--2588 Score: 290
Period size: 77 Copynumber: 2.1 Consensus size: 77
2417 TATACATATA
* *
2427 TGCTTCAGTTAGCCTCGGGCTTCCGTTTAGCACTTATGTGCTTCAGTTAGCCTTCGGGCTT-TGT
1 TGCTTCAGTTAGCCTCGGGCTTCCATTTAGCACTTATGTGCTTCAGTTAGCCTTCGGGCTTCCGT
2491 TTAGCACTTATG
66 TTAGCACTTATG
2503 TGCTTCAGTTAGCCTCTGGGCTTCCATTTAGCACTTATGTGCTTCAGTTAGCCTTCGGGCTTCCG
1 TGCTTCAGTTAGCCTC-GGGCTTCCATTTAGCACTTATGTGCTTCAGTTAGCCTTCGGGCTTCCG
2568 TTTAGCACTTATG
65 TTTAGCACTTATG
2581 TGCTTCAG
1 TGCTTCAG
2589 CTAGATTTCG
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
76 16 0.20
77 44 0.54
78 22 0.27
ACGTcount: A:0.14, C:0.25, G:0.23, T:0.39
Consensus pattern (77 bp):
TGCTTCAGTTAGCCTCGGGCTTCCATTTAGCACTTATGTGCTTCAGTTAGCCTTCGGGCTTCCGT
TTAGCACTTATG
Found at i:3949 original size:31 final size:31
Alignment explanation
Indices: 3911--4029 Score: 125
Period size: 31 Copynumber: 3.8 Consensus size: 31
3901 GAAAATGACA
*
3911 AGTGAAAAGCAGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTAGTAGCTTCGGCTACCTGATC
* *
3942 AGTGAAAAGTGGTAGCTCCGGCTACCTGAT-
1 AGTGAAAAGTAGTAGCTTCGGCTACCTGATC
* * *
3972 AGATAAAAAAATGGTAGC-TCTGGCTACCTGATC
1 AG-T-GAAAAGTAGTAGCTTC-GGCTACCTGATC
* *
4005 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTAGTAGCTTCGGCTAC
4030 AAGTGACAAG
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
30 2 0.03
31 45 0.61
32 25 0.34
33 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.24
Consensus pattern (31 bp):
AGTGAAAAGTAGTAGCTTCGGCTACCTGATC
Found at i:4108 original size:44 final size:45
Alignment explanation
Indices: 4058--4143 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 45
4048 GATTTCCGTA
*
4058 TAAGACCATATCTGGGATATGGCATC-AGTGTGATATGTGATGTG
1 TAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGATGTG
* * * *
4102 TAAGACCATGGCTGGGCTATGGCTTCGGTGTGTGATATGTGA
1 TAAGACCATAGCTGGGATATGGCATC-GAGTGTGATATGTGA
4144 CTATGCGCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 22 0.63
46 13 0.37
ACGTcount: A:0.23, C:0.13, G:0.33, T:0.31
Consensus pattern (45 bp):
TAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGATGTG
Found at i:5993 original size:39 final size:39
Alignment explanation
Indices: 5934--6113 Score: 281
Period size: 39 Copynumber: 4.6 Consensus size: 39
5924 TATACATATA
*
5934 TGCTTCAGTTAGCCTCCGGGCTTCCATTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATG
*
5973 TGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATG
6012 TGCTTCAGTTAGCC-TCTGGGCTTCCATTTAGCACTTATG
1 TGCTTCAGTTAGCCTTC-GGGCTTCCATTTAGCACTTATG
*
6051 TGCTTCAGTTAGCCTTCAGGCTTCCATTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATG
* * **
6090 TGCTTTAGCTAGATTTCGGGCTTC
1 TGCTTCAGTTAGCCTTCGGGCTTC
6114 AGATCACGAT
Statistics
Matches: 130, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
38 2 0.02
39 126 0.97
40 2 0.02
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (39 bp):
TGCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATG
Found at i:7401 original size:31 final size:31
Alignment explanation
Indices: 7363--7481 Score: 123
Period size: 31 Copynumber: 3.8 Consensus size: 31
7353 ACAAATGACA
* *
7363 AGTGAAAAGCAGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTAGTAGCTCCGGCTACCTGATC
* *
7394 AGTGAAAAGTGGTAGCTCCGGCTACCTAAT-
1 AGTGAAAAGTAGTAGCTCCGGCTACCTGATC
* * *
7424 AGATAAAAAAATGGTAGCTCCGGCTACCTGATC
1 AG-T-GAAAAGTAGTAGCTCCGGCTACCTGATC
* * *
7457 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTAGTAGCTCCGGCTAC
7482 AAGTGACAAG
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
30 2 0.03
31 45 0.61
32 25 0.34
33 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (31 bp):
AGTGAAAAGTAGTAGCTCCGGCTACCTGATC
Found at i:9452 original size:39 final size:39
Alignment explanation
Indices: 9393--9572 Score: 263
Period size: 39 Copynumber: 4.6 Consensus size: 39
9383 TATACATATA
*
9393 TGCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATG
9432 TGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATG
* * *
9471 TGCTTCTGTTAGCC-TCTGGGCGTCCATTTAGCACTTATG
1 TGCTTCAGTTAGCCTTC-GGGCTTCCGTTTAGCACTTATG
**
9510 CACTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATG
* **
9549 TGCTTCAGCTAGATTTCGGGCTTC
1 TGCTTCAGTTAGCCTTCGGGCTTC
9573 AGATCACGAT
Statistics
Matches: 125, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
38 2 0.02
39 121 0.97
40 2 0.02
ACGTcount: A:0.13, C:0.27, G:0.23, T:0.37
Consensus pattern (39 bp):
TGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATG
Found at i:10992 original size:46 final size:46
Alignment explanation
Indices: 10936--11111 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
10926 TATTTGGGCA
* *
10936 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAGGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
10982 TCTGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
11029 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
11075 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
11112 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 5 0.05
45 3 0.03
46 63 0.58
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:11091 original size:93 final size:93
Alignment explanation
Indices: 10932--11104 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
10922 GGGATATTTG
* * * *
10932 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAGGCAAATGTCTGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGAGGCAAACGCCCGAACTCGTTGAG
10997 TTGAGTCCGAGTTCATGAGATGTAACTA
66 TTGAGTCCGAGTTCATGAGATGTAACTA
* * *
11025 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGAGGCAAACGCCCGAACTCGTTGAG
*
11090 TTGAGTCTGAGTTCA
66 TTGAGTCCGAGTTCA
11105 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGAGGCAAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCATGAGATGTAACTA
Found at i:12974 original size:15 final size:15
Alignment explanation
Indices: 12954--12985 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12944 CAAATCCTGC
*
12954 AATGCCGAAAGTCGA
1 AATGCCGAAAGCCGA
12969 AATGCCGAAAGCCGA
1 AATGCCGAAAGCCGA
12984 AA
1 AA
12986 AGTAATTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.22, G:0.25, T:0.09
Consensus pattern (15 bp):
AATGCCGAAAGCCGA
Found at i:13156 original size:29 final size:28
Alignment explanation
Indices: 13123--13184 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
13113 GAAAGCATGA
* *
13123 ATATGAAAGTGATTTGGGCCTAATGGGCC
1 ATATGAAAGAGA-ATGGGCCTAATGGGCC
* *
13152 ATATGAATGAGAATGGGCCTAGTGGGCC
1 ATATGAAAGAGAATGGGCCTAATGGGCC
13180 ATATG
1 ATATG
13185 CATGTATGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 19 0.66
29 10 0.34
ACGTcount: A:0.29, C:0.13, G:0.32, T:0.26
Consensus pattern (28 bp):
ATATGAAAGAGAATGGGCCTAATGGGCC
Found at i:16891 original size:19 final size:19
Alignment explanation
Indices: 16867--16904 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
16857 TCAAATACTA
16867 GTTTTAGATGTCCCTTTTT
1 GTTTTAGATGTCCCTTTTT
16886 GTTTTAGATGTCCCTTTTT
1 GTTTTAGATGTCCCTTTTT
16905 CTGTCTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.58
Consensus pattern (19 bp):
GTTTTAGATGTCCCTTTTT
Found at i:17486 original size:20 final size:21
Alignment explanation
Indices: 17449--17499 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
17439 CAAAGACACA
**
17449 AATGTGCAGTCAGAGGCACC-
1 AATGTGCAAACAGAGGCACCG
*
17469 AATGTGCAAACAGGGGCACCG
1 AATGTGCAAACAGAGGCACCG
17490 AA-GTGCAAAC
1 AATGTGCAAAC
17500 TCGTACAAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.35, C:0.24, G:0.29, T:0.12
Consensus pattern (21 bp):
AATGTGCAAACAGAGGCACCG
Found at i:18538 original size:15 final size:15
Alignment explanation
Indices: 18518--18554 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
18508 AGATGATACC
*
18518 TTATTTTTATTTTAT
1 TTATTTATATTTTAT
*
18533 TTATTTATGTTTTAT
1 TTATTTATATTTTAT
18548 TTATTTA
1 TTATTTA
18555 ATTACAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTATTTATATTTTAT
Found at i:18550 original size:19 final size:19
Alignment explanation
Indices: 18518--18554 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
18508 AGATGATACC
18518 TTATTTTTATTTTATTTAT
1 TTATTTTTATTTTATTTAT
18537 TTATGTTTTA-TTTATTTA
1 TTAT-TTTTATTTTATTTA
18555 ATTACAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (19 bp):
TTATTTTTATTTTATTTAT
Found at i:22679 original size:492 final size:499
Alignment explanation
Indices: 21749--23051 Score: 1834
Period size: 492 Copynumber: 2.6 Consensus size: 499
21739 GGCTACTATG
* * * * *
21749 TTGCAACATAGGGGACGTTTCATGCCATAAAAGTCATTTTGTGGGCTTGGAAGTTCTTATCGTGC
1 TTGCAACATAGGGGGCGTGTCACGCCATAGAAGTCATTTTGTGGGCTTGGAAGTTCTTATCATGC
* * *
21814 TTTTATGGCGTGTGAAGCTTGTGCAACACTCATCCCACATTCCTACATCAATTGGGCCTAGAATT
66 TTTTATGGCATGAGAAGCTTGTACAACACTCATCCCACATTCCTACATCAATTGGGCCTAGAATT
* ** *
21879 AAGCATCTTGTACACTAAAATACACAAATTAAACCTAATTATGGTCCGTGTCTGCCTAATAGGTC
131 AAGCATCTTGTACACTTAAATACACAAATTAAACCTACCTATGGTCTGTGTCTGCCTAATAGGTC
* * * * *
21944 ACTAATACTAAAAAATGTGTCATATCATGACCCTTCCATGTCGCAACATCAGATTCTAATGTTGC
196 ACTAACACTAAAAAATGTGTCATATCATGACCCTTCGATGTCGCAACATCGGACTCTGATGTTGC
* * * *
22009 AACACTGTAGGCTTGTGTTGCAACCAACCCCCTGCATAGCCCAAAAATCCCTTGTGTACAGAGAC
261 AACACTGCAGGCCTATGTTGCAACCAACCCCCTGCATAGCCCAAAAACCCCTTGTGTACAGAGAC
*
22074 CTCTTATTTATAGGCTAAAATATGTGCACTTTATGCCTGATATGCCCCCGATACTAATAAATGTG
326 CTCTTATTTATAGGCTAAAATATGTGCACTTTATCCCTGATATGCCCCCGATACTAATAAATGTG
* *
22139 AAATATCAAATGATATCATAAAATCTTTTCAAACACGACCATTGACGTCATTATTACTTGTGACT
391 AAATATCAAATGATATCATAAAATCTTTTCAAACACGACCACTGACGTCATTATTACTTATGACT
* *
22204 CATGTTCAGGCTACGTTTCAACATAGGAGATG-CT-AC-A-T-C
456 CATGTTCAGGCTACGTCTCAACATAAGAGATGACTAACAAGTGC
* * *
22243 -T-CAACATAGGGGGCGTGTCACGCCGTAGAAGTCATTTTGTGGGCTTGGAAGTTCCTGTCATGC
1 TTGCAACATAGGGGGCGTGTCACGCCATAGAAGTCATTTTGTGGGCTTGGAAGTTCTTATCATGC
* *
22306 TTTTATGGCATGGGAAGCTTGTACAACACTCATCCCATATTCCTACATCAATTGGGCCTAGAATT
66 TTTTATGGCATGAGAAGCTTGTACAACACTCATCCCACATTCCTACATCAATTGGGCCTAGAATT
*
22371 AAGCATCTTGTACACTTAAATACACAAATTAAGCCTACCTATGGTCTGTGTCTGCCTAATAGGTC
131 AAGCATCTTGTACACTTAAATACACAAATTAAACCTACCTATGGTCTGTGTCTGCCTAATAGGTC
* * * * * *
22436 ACTGACACTAAAAAATGTGTCATATCATGACCTTTTGATGTTGCGACATCGGACTCGGATGTTGC
196 ACTAACACTAAAAAATGTGTCATATCATGACCCTTCGATGTCGCAACATCGGACTCTGATGTTGC
* *
22501 AACACTGCAAGCCTATGTTGCAACCAACCCCCTGCATAGCCCAAAAGCCCCTTGTGTACAGAGAC
261 AACACTGCAGGCCTATGTTGCAACCAACCCCCTGCATAGCCCAAAAACCCCTTGTGTACAGAGAC
* * * *
22566 CTTTTATTTATAGTG-TAGAATATGTGCACTTTATCCCTTATATGCCCCCGATACTAGTAAATGT
326 CTCTTATTTATAG-GCTAAAATATGTGCACTTTATCCCTGATATGCCCCCGATACTAATAAATGT
22630 GAAATATCAAATGATATCATAAAATCTTTTCAAACACGACCACTGACGTCATTATTACTTATGAC
390 GAAATATCAAATGATATCATAAAATCTTTTCAAACACGACCACTGACGTCATTATTACTTATGAC
22695 TCATGTTCAGGCTACGTCTCAACATAAGAGATGCTACACTCAACATAGGGCTGC
455 TCATGTTCAGGCTACGTCTCAACATAAGAGATG----ACT-AACA-A--G-TGC
* * **
22749 TATGTTGCAACATAGGGAGCGTGTCACGCCATAGAAGTCATTTTGTGGACTTCAAAGTTCTTATC
1 ----TTGCAACATAGGGGGCGTGTCACGCCATAGAAGTCATTTTGTGGGCTTGGAAGTTCTTATC
* * * * *
22814 ATGCTTGTATGGCATGAGAAGCTTGTACAACACTCGTCCCACATTCCTACATTAGTTGGGCCTAA
62 ATGCTTTTATGGCATGAGAAGCTTGTACAACACTCATCCCACATTCCTACATCAATTGGGCCTAG
* * * **
22879 AATTAAGTATCTTGCACACTTAAATACACAAATTAAATCTACCTAAAGTCCT-TGTCTGCCTAAT
127 AATTAAGCATCTTGTACACTTAAATACACAAATTAAACCTACCTATGGT-CTGTGTCTGCCTAAT
* * *
22943 AGGTCACTAACACCAAAAAATGTGCCATATCATGACCCTTCGATGTCGCAACATTGGACTCTGAT
191 AGGTCACTAACACTAAAAAATGTGTCATATCATGACCCTTCGATGTCGCAACATCGGACTCTGAT
* *
23008 GTTGCAACACTACAGGCCTATGTTGCAACCAA-CCCCTGCGTAGC
256 GTTGCAACACTGCAGGCCTATGTTGCAACCAACCCCCTGCATAGC
23052 TTAAAAGCTC
Statistics
Matches: 712, Mismatches: 75, Indels: 27
0.87 0.09 0.03
Matches are distributed among these distances:
492 439 0.62
493 2 0.00
497 2 0.00
499 2 0.00
501 1 0.00
505 1 0.00
506 1 0.00
511 12 0.02
512 250 0.35
513 2 0.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (499 bp):
TTGCAACATAGGGGGCGTGTCACGCCATAGAAGTCATTTTGTGGGCTTGGAAGTTCTTATCATGC
TTTTATGGCATGAGAAGCTTGTACAACACTCATCCCACATTCCTACATCAATTGGGCCTAGAATT
AAGCATCTTGTACACTTAAATACACAAATTAAACCTACCTATGGTCTGTGTCTGCCTAATAGGTC
ACTAACACTAAAAAATGTGTCATATCATGACCCTTCGATGTCGCAACATCGGACTCTGATGTTGC
AACACTGCAGGCCTATGTTGCAACCAACCCCCTGCATAGCCCAAAAACCCCTTGTGTACAGAGAC
CTCTTATTTATAGGCTAAAATATGTGCACTTTATCCCTGATATGCCCCCGATACTAATAAATGTG
AAATATCAAATGATATCATAAAATCTTTTCAAACACGACCACTGACGTCATTATTACTTATGACT
CATGTTCAGGCTACGTCTCAACATAAGAGATGACTAACAAGTGC
Found at i:27283 original size:47 final size:47
Alignment explanation
Indices: 27169--27299 Score: 201
Period size: 47 Copynumber: 2.8 Consensus size: 47
27159 GTACGAGTGA
* *
27169 TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTTCAGTGAAGAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTA-CTCAGGGAAGAGT
*
27217 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCGGGATA-AGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCAGGGA-AGAGT
*
27264 TACCTTGATTTGGCTACGGGCCATGGTATAAGTACT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
27300 TATCGATTGA
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
47 43 0.55
48 35 0.45
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCAGGGAAGAGT
Found at i:32124 original size:42 final size:43
Alignment explanation
Indices: 32010--32162 Score: 143
Period size: 44 Copynumber: 3.6 Consensus size: 43
32000 ATAGGATTCT
* * * *
32010 GATATGTGATTTCATGTAAGACCACGTTTGGGAC-GTTGGCATC
1 GATATTTGATTACATGTAAGACCATGTTTGGGACAG-TGACATC
* *
32053 GGT-TTGAGATTTACATGTAAGACCATGTTTGGGACA-TCGACATC
1 GATATT-TGA-TTACATGTAAGACCATGTTTGGGACAGT-GACATC
* * * * *
32097 G-TATTTGTTTTCGTGTAAGACCCTGTTTGGGACAGTGGCATC
1 GATATTTGATTACATGTAAGACCATGTTTGGGACAGTGACATC
32139 GATATTTGATTACATGTAAGACCA
1 GATATTTGATTACATGTAAGACCA
32163 AGTCTGGGCG
Statistics
Matches: 87, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
42 30 0.34
43 26 0.30
44 31 0.36
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (43 bp):
GATATTTGATTACATGTAAGACCATGTTTGGGACAGTGACATC
Found at i:32179 original size:42 final size:43
Alignment explanation
Indices: 32010--32179 Score: 159
Period size: 42 Copynumber: 4.0 Consensus size: 43
32000 ATAGGATTCT
* * *
32010 GATATGTGATTTCATGTAAGACCACGTTTGGGACGTTGGCATC
1 GATATTTGATTACATGTAAGACCATGTTTGGGACGTTGGCATC
* * * * *
32053 GGT-TTGAGATTTACATGTAAGACCATGTTTGGGACATCGACATC
1 GATATT-TGA-TTACATGTAAGACCATGTTTGGGACGTTGGCATC
* * * *
32097 G-TATTTGTTTTCGTGTAAGACCCTGTTTGGGACAG-TGGCATC
1 GATATTTGATTACATGTAAGACCATGTTTGGGAC-GTTGGCATC
* *
32139 GATATTTGATTACATGTAAGACCAAGTCTGGG-CGTTGGCAT
1 GATATTTGATTACATGTAAGACCATGTTTGGGACGTTGGCAT
32180 TGTACGAGCT
Statistics
Matches: 99, Mismatches: 22, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
41 1 0.01
42 36 0.36
43 30 0.30
44 32 0.32
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.34
Consensus pattern (43 bp):
GATATTTGATTACATGTAAGACCATGTTTGGGACGTTGGCATC
Found at i:35634 original size:27 final size:27
Alignment explanation
Indices: 35604--35781 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
35594 ATATTGAGTC
* * * *
35604 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
35631 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
35658 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
35686 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
35713 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
35740 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
35767 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
35782 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:35743 original size:82 final size:81
Alignment explanation
Indices: 35625--35780 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
35615 TGCTATATAA
* *
35625 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
35690 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
35707 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
35771 CACTTAGTGC
65 CACTTAGTGC
35781 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:43685 original size:27 final size:27
Alignment explanation
Indices: 43655--43832 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
43645 ATATTGAGTC
* * * *
43655 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
43682 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43709 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
43737 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
43764 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
43791 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43818 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43833 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:43794 original size:82 final size:81
Alignment explanation
Indices: 43676--43831 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
43666 TGCTATATAA
* *
43676 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
43741 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
43758 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
43822 CACTTAGTGC
65 CACTTAGTGC
43832 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Done.