Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5033.1
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: 35739
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:241 original size:74 final size:74
Alignment explanation
Indices: 126--273 Score: 260
Period size: 74 Copynumber: 2.0 Consensus size: 74
116 TTTTATACAT
* **
126 TCTGTCAATTTGATCGTGATTTTAGAAAATAAAGACAAATGAATGATTTCTTATATAATGTTTTA
1 TCTGCCAATTTGATCACGATTTTAGAAAATAAAGACAAATGAATGATTTCTTATATAATGTTTTA
191 GATTTCTAA
66 GATTTCTAA
*
200 TCTGCCAATTTGATCACGATTTTAGAAAATAAAGACAAATGAATGATTTTTTATATAATGTTTTA
1 TCTGCCAATTTGATCACGATTTTAGAAAATAAAGACAAATGAATGATTTCTTATATAATGTTTTA
265 GATTTCTAA
66 GATTTCTAA
274 AATTTTGTTG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (74 bp):
TCTGCCAATTTGATCACGATTTTAGAAAATAAAGACAAATGAATGATTTCTTATATAATGTTTTA
GATTTCTAA
Found at i:3216 original size:54 final size:54
Alignment explanation
Indices: 3152--3256 Score: 201
Period size: 54 Copynumber: 1.9 Consensus size: 54
3142 CATTATGTTA
3152 ATTTAGTCTTGATTCTAAAAAATTTAACTCTCAAAATCTATATAATGTCTACTG
1 ATTTAGTCTTGATTCTAAAAAATTTAACTCTCAAAATCTATATAATGTCTACTG
*
3206 ATTTAGTCTTGATTCTAAAAAATTTAACTCTTAAAATCTATATAATGTCTA
1 ATTTAGTCTTGATTCTAAAAAATTTAACTCTCAAAATCTATATAATGTCTA
3257 ATTTGATCTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (54 bp):
ATTTAGTCTTGATTCTAAAAAATTTAACTCTCAAAATCTATATAATGTCTACTG
Found at i:7371 original size:68 final size:68
Alignment explanation
Indices: 7225--7359 Score: 261
Period size: 68 Copynumber: 2.0 Consensus size: 68
7215 TCCATCAAAT
*
7225 AAAAAAAAAAAAAAAAGTAAAAACACCTCTTTGGCTCCTCTCAATTTTGATATTGAGCAAATTGG
1 AAAAAAAAAAAAAAAAGAAAAAACACCTCTTTGGCTCCTCTCAATTTTGATATTGAGCAAATTGG
7290 TCA
66 TCA
7293 AAAAAAAAAAAAAAAAGAAAAAACACCTCTTTGGCTCCTCTCAATTTTGATATTGAGCAAATTGG
1 AAAAAAAAAAAAAAAAGAAAAAACACCTCTTTGGCTCCTCTCAATTTTGATATTGAGCAAATTGG
7358 TC
66 TC
7360 CCTTTTAAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (68 bp):
AAAAAAAAAAAAAAAAGAAAAAACACCTCTTTGGCTCCTCTCAATTTTGATATTGAGCAAATTGG
TCA
Found at i:12546 original size:18 final size:17
Alignment explanation
Indices: 12513--12546 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12503 TTTTATTTAA
12513 AAATAAAAAATATAAAT
1 AAATAAAAAATATAAAT
*
12530 AAATAATAAAATTTAAA
1 AAATAA-AAAATATAAA
12547 ATTGAAACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAAAAAATATAAAT
Found at i:13876 original size:53 final size:54
Alignment explanation
Indices: 13794--13902 Score: 202
Period size: 53 Copynumber: 2.0 Consensus size: 54
13784 AAGGTAATAT
13794 ATATATATATATATATAGATAACTCTCTGTTCTCCGCTTTCATATGGTTTTCATG
1 ATATATATATATATATAGATAAC-CTCTGTTCTCCGCTTTCATATGGTTTTCATG
13849 ATATATATATATATATAGATAA-CTCTGTTCTCCGCTTTCATATGGTTTTCATG
1 ATATATATATATATATAGATAACCTCTGTTCTCCGCTTTCATATGGTTTTCATG
13902 A
1 A
13903 AAATGGGTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
53 32 0.59
55 22 0.41
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.45
Consensus pattern (54 bp):
ATATATATATATATATAGATAACCTCTGTTCTCCGCTTTCATATGGTTTTCATG
Found at i:17467 original size:17 final size:17
Alignment explanation
Indices: 17447--17503 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
17437 ATCAAAAAGT
17447 AATTTTTTTAAAAATGA
1 AATTTTTTTAAAAATGA
* * *
17464 AATTTTCATCAAAAA-GT
1 AATTTT-TTTAAAAATGA
*
17481 AATTTTTTTTAAAATGA
1 AATTTTTTTAAAAATGA
17498 AATTTT
1 AATTTT
17504 AGGCGGCCTG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
16 5 0.16
17 20 0.65
18 6 0.19
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (17 bp):
AATTTTTTTAAAAATGA
Found at i:17479 original size:34 final size:34
Alignment explanation
Indices: 17436--17503 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
17426 AATGCGACGA
17436 CATCAAAAAGTAATTTTTTTAAAAATGAAATTTT
1 CATCAAAAAGTAATTTTTTTAAAAATGAAATTTT
*
17470 CATCAAAAAGTAATTTTTTTTAAAATGAAATTTT
1 CATCAAAAAGTAATTTTTTTAAAAATGAAATTTT
17504 AGGCGGCCTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (34 bp):
CATCAAAAAGTAATTTTTTTAAAAATGAAATTTT
Found at i:17596 original size:24 final size:24
Alignment explanation
Indices: 17569--17624 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
17559 ATTTCACTCA
17569 TCTTTATCTATCCCTGT-TTTTCTT
1 TCTTTATCTATCCCT-TCTTTTCTT
* *
17593 TCTTCATCAATCCCTTCTTTTCTT
1 TCTTTATCTATCCCTTCTTTTCTT
17617 TC-TTATCT
1 TCTTTATCT
17625 TGCTTTTCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.11, C:0.29, G:0.02, T:0.59
Consensus pattern (24 bp):
TCTTTATCTATCCCTTCTTTTCTT
Found at i:20688 original size:46 final size:47
Alignment explanation
Indices: 20628--20755 Score: 154
Period size: 46 Copynumber: 2.8 Consensus size: 47
20618 TTTGACATGA
* * * * * *
20628 TGCCATAGTTTCTTTCAACTATAGTCTTACTCATTTTC-CGTCATA-T
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCACATCA-AGT
*
20674 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAAGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCACATCAAGT
*
20720 TGCCATGGTATCTTTTAACCATGGTCTTACACATTT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTT
20756 CATATCAGAG
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
45 5 0.07
46 64 0.90
47 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.41
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCACATCAAGT
Found at i:20756 original size:46 final size:46
Alignment explanation
Indices: 20673--20762 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
20663 TTCCGTCATA
20673 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAG
1 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAG
*
20719 TTGCCATGGTATCTTTTAACCATGGTCTTACACATTTCATATCA
1 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
20763 GAGAGCCCAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (46 bp):
TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAG
Found at i:22348 original size:33 final size:33
Alignment explanation
Indices: 22181--22351 Score: 159
Period size: 32 Copynumber: 5.2 Consensus size: 33
22171 GTGTACATTT
* * * *
22181 CCTTTTCAAATGGTACACACAAAATATACCTTTT
1 CCTTTTCAAGTGGTATACACAAAGTATACC-TTA
*
22215 CC-TTTCTAGTGGTATACACAAAGTATACCTTA
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTA
* * * * * *
22247 CCTTTACAAAT-GTACACACAAAGTGTACATAA
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTA
* * * *
22279 CCTTTTCAAGT-GTATAGACAAAGTGTACATAA
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTA
* *
22311 CCTTTTCATGTGGTATACACAAAGTATACCTTT
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTA
22344 CCTTTTCA
1 CCTTTTCA
22352 CATTCGATAG
Statistics
Matches: 113, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
32 59 0.52
33 52 0.46
34 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.34
Consensus pattern (33 bp):
CCTTTTCAAGTGGTATACACAAAGTATACCTTA
Found at i:22389 original size:29 final size:29
Alignment explanation
Indices: 22344--22410 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
22334 GTATACCTTT
22344 CCTTTTCACATTCGATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
*
22373 CCTTTTCACATTTGATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
22402 CCTTTTCAC
1 CCTTTTCAC
22411 TTGGTACACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.22, C:0.31, G:0.12, T:0.34
Consensus pattern (29 bp):
CCTTTTCACATTCGATAGCCGAAGCTATC
Found at i:23233 original size:21 final size:22
Alignment explanation
Indices: 23187--23229 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
23177 TGTAAAAGTG
*
23187 ATTTCTCTATTAATAACCTTTC
1 ATTTCTCTATTAATAAACTTTC
23209 ATTT-TCTATT-ATAAACTTTC
1 ATTTCTCTATTAATAAACTTTC
23229 A
1 A
23230 ATTTACAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 6 0.30
22 4 0.20
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTCTCTATTAATAAACTTTC
Found at i:24411 original size:19 final size:18
Alignment explanation
Indices: 24385--24435 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
24375 TTTTTTTTAC
24385 TTTTTTTAACTTTTGTCT
1 TTTTTTTAACTTTTGTCT
* *
24403 TTTTCTTTAATTTTTTTCT
1 TTTT-TTTAACTTTTGTCT
*
24422 TTTTTTTAAGTTTT
1 TTTTTTTAACTTTT
24436 ATATTGTAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.12, C:0.08, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTTTTTAACTTTTGTCT
Found at i:24655 original size:44 final size:44
Alignment explanation
Indices: 24606--24920 Score: 427
Period size: 44 Copynumber: 7.2 Consensus size: 44
24596 ACTCATATGG
24606 GAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGGGAGCAGATC
1 GAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGGGAGCAGATC
* *
24650 GAAGATAGCAGATTTGGCGTCTCTGTACTGTCA-GAAGGCAGATC
1 GAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGGGA-GCAGATC
* * *
24694 GAAGATAGTAGATTTGGCGTCTATGTATTGTCAGGGAGCAGATA
1 GAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGGGAGCAGATC
* *
24738 GAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGG-GAAAATC
1 GAAGATAGCAGATTTGGCGTCTCTGTATTGTCAG-GGAGCAGATC
* * *
24782 GAAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATT
1 GAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGGGAGCAGATC
* * * *
24826 GAAGATAGCAGATTTGACATCTCTATATTGTCAGAGAGCAGATC
1 GAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGGGAGCAGATC
* * * * *
24870 GAAGATAGCAGATTTGGCATATCTGTATTGTCAGAGAGCAAATT
1 GAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGGGAGCAGATC
24914 GAAGATA
1 GAAGATA
24921 TAACAGATTT
Statistics
Matches: 242, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
43 3 0.01
44 235 0.97
45 4 0.02
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (44 bp):
GAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGGGAGCAGATC
Found at i:25031 original size:45 final size:45
Alignment explanation
Indices: 24967--25059 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 45
24957 GATCTAAGAT
* *
24967 GATTTAGCGTTTCTGTATTACACGGGGAGCAGATCGAAGATAACA
1 GATTTAGCGTTTCTGTATTACACGGAGAGCAGATCAAAGATAACA
* * *
25012 GATTTGGCGTCTT-TGTATTAGACGGAGAGCAGATCAAAGATAGCA
1 GATTTAGCGT-TTCTGTATTACACGGAGAGCAGATCAAAGATAACA
25057 GAT
1 GAT
25060 ATCGCCTTCT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 40 0.95
46 2 0.05
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (45 bp):
GATTTAGCGTTTCTGTATTACACGGAGAGCAGATCAAAGATAACA
Found at i:25428 original size:19 final size:19
Alignment explanation
Indices: 25403--25493 Score: 152
Period size: 19 Copynumber: 4.9 Consensus size: 19
25393 ATAATCTTCA
25403 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
25422 GTGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
25441 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
25458 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
25476 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
25494 AGATATGATT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 35 0.52
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:25443 original size:14 final size:15
Alignment explanation
Indices: 25424--25479 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
25414 TCTTAGATGT
25424 GATATG-CAATCTTA
1 GATATGACAATCTTA
25438 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
25455 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
25473 GATATGA
1 GATATGA
25480 TATGCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:25473 original size:35 final size:37
Alignment explanation
Indices: 25403--25500 Score: 141
Period size: 35 Copynumber: 2.7 Consensus size: 37
25393 ATAATCTTCA
*
25403 ATGATATGCAATCTTAGATGTGATATGCAATCTTAGAT
1 ATGATA-GCAATCTTAGATATGATATGCAATCTTAGAT
25441 ATGATA-CAATCTTAGATATGAT-TGCAATCTTAGAT
1 ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
25476 ATGATATGCAATCTTAGA-A-GATATG
1 ATGATA-GCAATCTTAGATATGATATG
25501 ATTTTGTACT
Statistics
Matches: 56, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
35 22 0.39
36 18 0.32
37 10 0.18
38 6 0.11
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (37 bp):
ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
Found at i:25919 original size:130 final size:130
Alignment explanation
Indices: 25686--25947 Score: 497
Period size: 130 Copynumber: 2.0 Consensus size: 130
25676 TCACTCAAAT
*
25686 TTCTCTCCCTCTTGCGTTCTTATTTTCTACGGTTTGTTCTTATTTATTCTTTGTTCATTTTCATT
1 TTCTCTCCCTCTTGCGTTCTTATTTTCTACGGTTTGGTCTTATTTATTCTTTGTTCATTTTCATT
*
25751 TTCAACCCTTTTTTATTTTGATTTAATCCCTATTTCCTTGATTTTTAATTCTCTTTTATATTTTA
66 TTCAACCCTTTTTTATTTTGATTTAATCACTATTTCCTTGATTTTTAATTCTCTTTTATATTTTA
*
25816 TTCTCTCCCTCTTGCGTTCTTATTTTCTACGGTTTGGTCTTATTTATTCTTTGTTCATTTTCGTT
1 TTCTCTCCCTCTTGCGTTCTTATTTTCTACGGTTTGGTCTTATTTATTCTTTGTTCATTTTCATT
25881 TTCAACCCTTTTTTATTTTGATTTAATCACTATTTCCTTGATTTTTAATTCTCTTTTATATTTTA
66 TTCAACCCTTTTTTATTTTGATTTAATCACTATTTCCTTGATTTTTAATTCTCTTTTATATTTTA
25946 TT
1 TT
25948 TTTTAATAAT
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 129 1.00
ACGTcount: A:0.15, C:0.19, G:0.07, T:0.60
Consensus pattern (130 bp):
TTCTCTCCCTCTTGCGTTCTTATTTTCTACGGTTTGGTCTTATTTATTCTTTGTTCATTTTCATT
TTCAACCCTTTTTTATTTTGATTTAATCACTATTTCCTTGATTTTTAATTCTCTTTTATATTTTA
Found at i:26127 original size:73 final size:73
Alignment explanation
Indices: 26033--26177 Score: 254
Period size: 73 Copynumber: 2.0 Consensus size: 73
26023 TTCATCTAAT
*
26033 TGAAAAAGTTTTTCTTAAATAAGGCAATGTTTGGCGTTTAGAAATTCGAAAAATAGTGTCCTAAC
1 TGAAAAAGTTTTTCTTAAATAAGGCAATGTTTGGCGTTTAGAAATTCGAAAAATAGTGCCCTAAC
26098 ATGCTGGA
66 ATGCTGGA
* **
26106 TGAAAAAGTTTTTCTTAAATAAGGCAATGTTTGGTGTTTAGAAATTCGGGAAATAGTGCCCTAAC
1 TGAAAAAGTTTTTCTTAAATAAGGCAATGTTTGGCGTTTAGAAATTCGAAAAATAGTGCCCTAAC
26171 ATGCTGG
66 ATGCTGG
26178 GTTGCGATTT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (73 bp):
TGAAAAAGTTTTTCTTAAATAAGGCAATGTTTGGCGTTTAGAAATTCGAAAAATAGTGCCCTAAC
ATGCTGGA
Found at i:26635 original size:13 final size:13
Alignment explanation
Indices: 26619--26661 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
26609 GTTTTCTTAT
*
26619 TTTATTTTGTTTA
1 TTTATTTTATTTA
26632 TTTATTTTATTTA
1 TTTATTTTATTTA
* *
26645 TTTTTTGTTATTAA
1 TTTATT-TTATTTA
26659 TTT
1 TTT
26662 TAAAAAACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 17 0.65
14 9 0.35
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:26643 original size:23 final size:23
Alignment explanation
Indices: 26619--26663 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
26609 GTTTTCTTAT
*
26619 TTTATTTTGT-TTATTTATTTTA
1 TTTATTTTGTGTTATTAATTTTA
*
26641 TTTATTTTTTGTTATTAATTTTA
1 TTTATTTTGTGTTATTAATTTTA
26664 AAAAACTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (23 bp):
TTTATTTTGTGTTATTAATTTTA
Found at i:26656 original size:10 final size:9
Alignment explanation
Indices: 26615--26648 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
26605 ATATGTTTTC
26615 TTATTTTAT
1 TTATTTTAT
26624 TT-TGTTTAT
1 TTAT-TTTAT
26633 TTATTTTAT
1 TTATTTTAT
26642 TTATTTT
1 TTATTTT
26649 TTGTTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.04
9 21 0.91
10 1 0.04
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (9 bp):
TTATTTTAT
Found at i:29812 original size:11 final size:11
Alignment explanation
Indices: 29796--29827 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
29786 TGTATGTTAT
29796 TGATTTGAATA
1 TGATTTGAATA
29807 TGATTTGAATA
1 TGATTTGAATA
29818 TGATTTGAAT
1 TGATTTGAAT
29828 GTTCATTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (11 bp):
TGATTTGAATA
Found at i:34019 original size:8 final size:8
Alignment explanation
Indices: 34005--34050 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
33995 TCTATTTCAA
34005 AAAAAAAGG
1 AAAAAAA-G
34014 AAAAAAAG
1 AAAAAAAG
34022 AAAAAAA-
1 AAAAAAAG
* *
34029 AGAATAAG
1 AAAAAAAG
34037 -AAAAAAG
1 AAAAAAAG
34044 AAAAAAA
1 AAAAAAA
34051 AAAGAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
7 10 0.32
8 14 0.45
9 7 0.23
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:34019 original size:9 final size:9
Alignment explanation
Indices: 34004--34059 Score: 57
Period size: 9 Copynumber: 6.6 Consensus size: 9
33994 TTCTATTTCA
34004 AAAAAAAAG
1 AAAAAAAAG
*
34013 GAAAAAAAG
1 AAAAAAAAG
34022 AAAAAAAAG
1 AAAAAAAAG
*
34031 ---AATAAG
1 AAAAAAAAG
34037 AAAAAAGAA-
1 AAAAAA-AAG
34046 AAAAAAAAG
1 AAAAAAAAG
34055 AAAAA
1 AAAAA
34060 TGGAGAGGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
6 5 0.13
8 2 0.05
9 29 0.76
10 2 0.05
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:34042 original size:13 final size:11
Alignment explanation
Indices: 34014--34059 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
34004 AAAAAAAAGG
34014 AAAAAAAG--A
1 AAAAAAAGAAA
34023 AAAAAAAGAATA
1 AAAAAAAGAA-A
34035 AGAAAAAAGAAA
1 A-AAAAAAGAAA
34047 AAAAAAAGAAA
1 AAAAAAAGAAA
34058 AA
1 AA
34060 TGGAGAGGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
9 8 0.24
11 12 0.36
12 4 0.12
13 9 0.27
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:35146 original size:84 final size:84
Alignment explanation
Indices: 35005--35736 Score: 1206
Period size: 84 Copynumber: 8.7 Consensus size: 84
34995 CAAAATTCAA
35005 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAATA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAATA
35070 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
35089 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAATA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAATA
35154 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
* * * * *
35173 CGCCTTAATCCCCTAAGTAGTAGGGCAACAGGTTAAATTTGTAGAGCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAATA
*
35238 GTGGAGCAGATTGAAGACT
66 GTGGAGCAGATCGAAGACT
* *
35257 CGCCTTAATCCCCTAAGCGGTAGGGTAGCAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAATA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAATA
35322 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
* *
35341 CGCCTTAATCCCCTAAGCGGTAGGGTAGCAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAATA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAATA
35406 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
* *
35425 CGCCTTAATCCCCTAAGCGGTAGGGTAGCAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAATA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAATA
35490 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
* *
35509 CGCCTTAATCCCCTAAGCGGTAGGGTAGCAGGTTAAATTTGCAGATCTTATCTCCCTAAG-AAGT
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAA-T
*
35573 AGTGGAGCAGATCGAAAACT
65 AGTGGAGCAGATCGAAGACT
* ** *
35593 CGCCTTAATCCCCTAATCAGTAGGGTAACAGG-----TTCCCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAATA
*
35653 GCGGAGCAGATCGACGATGACT
66 GTGGAGCAGATCGA--A-GACT
35675 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCA
35737 GTA
Statistics
Matches: 612, Mismatches: 26, Indels: 17
0.93 0.04 0.03
Matches are distributed among these distances:
79 36 0.06
80 1 0.00
81 1 0.00
82 34 0.06
83 2 0.00
84 515 0.84
87 23 0.04
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (84 bp):
CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAATA
GTGGAGCAGATCGAAGACT
Done.