Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3158
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: 65275
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Found at i:7548 original size:19 final size:19
Alignment explanation
Indices: 7524--7561 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
7514 GAAATGAATA
*
7524 ATTTCAGGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
7543 ATTTCAAGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
7562 GCAATCTCAA
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:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
ATTTCAAGCAAATAGGTTG
Found at i:8476 original size:19 final size:20
Alignment explanation
Indices: 8443--8482 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
8433 GTATATATAT
8443 ATAAAATAAAGAAAAT-AAA
1 ATAAAATAAAGAAAATGAAA
8462 ATAAAATAACA-AAAATGAAA
1 ATAAAATAA-AGAAAATGAAA
8482 A
1 A
8483 ATGAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAAATAAAGAAAATGAAA
Found at i:8747 original size:18 final size:18
Alignment explanation
Indices: 8724--8770 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
8714 AGAGGTTAGG
*
8724 TTTTTTTCTTTTTCTTCA
1 TTTTTTTATTTTTCTTCA
* *
8742 TTTTTTTATTTTTTTTTA
1 TTTTTTTATTTTTCTTCA
8760 -TTTTTTATTTT
1 TTTTTTTATTTT
8771 GGGTTGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTTTATTTTTCTTCA
Found at i:12342 original size:16 final size:16
Alignment explanation
Indices: 12321--12360 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
12311 TGAATTACTT
12321 ATTACAG-CTCTATTCA
1 ATTACAGTCT-TATTCA
*
12337 ATTACAGTCTTATTCC
1 ATTACAGTCTTATTCA
12353 ATTACAGT
1 ATTACAGT
12361 GAACCAAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (16 bp):
ATTACAGTCTTATTCA
Found at i:13144 original size:25 final size:25
Alignment explanation
Indices: 13100--13177 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 25
13090 GGATTGTAGG
* * *
13100 TTATGTTTAGTTTTTGAAAATATTTT
1 TTATTTTTA-TTTTTAAAAATAATTT
13126 TTATTTTTATTTTTAAAAATTAATTT
1 TTATTTTTATTTTTAAAAA-TAATTT
* *
13152 TCATTTTATATTTCTTTAAAATAATT
1 TTATTTT-TATTT-TTAAAAATAATT
13178 AAAAATGTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
25 9 0.20
26 19 0.43
27 10 0.23
28 6 0.14
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.62
Consensus pattern (25 bp):
TTATTTTTATTTTTAAAAATAATTT
Found at i:13537 original size:11 final size:11
Alignment explanation
Indices: 13523--13548 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13513 CAACGAAGGG
13523 GTCACGATGAA
1 GTCACGATGAA
13534 GTCACGATGAA
1 GTCACGATGAA
13545 GTCA
1 GTCA
13549 TCATTCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (11 bp):
GTCACGATGAA
Found at i:14632 original size:9 final size:9
Alignment explanation
Indices: 14618--14645 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
14608 TTCAAGTGGG
14618 AACATCTAT
1 AACATCTAT
14627 AACATCTAT
1 AACATCTAT
14636 AACATCTAT
1 AACATCTAT
14645 A
1 A
14646 CAATGGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.32
Consensus pattern (9 bp):
AACATCTAT
Found at i:17002 original size:134 final size:132
Alignment explanation
Indices: 16743--16981 Score: 320
Period size: 134 Copynumber: 1.8 Consensus size: 132
16733 TTATATATAC
* * * * *
16743 TTTTTGAATTTCTATATTATTATTATTATTATTATATAGTAGTGTATATTTTTTATTAGCTATGT
1 TTTTTGAATTTCAATATTATTACTATTATTATTATACAGTAGTGTATATTTTATATTAGATATGT
*
16808 ATATGTATATGCATTTATATATAGTATTATTTTAATTACTTTATCATTTTTATTATATTATATTG
66 ATATATATATG-A-TTATATATAGTATTATTTTAATTACTTTATCATTTTTATTATATTATATTG
16873 TTCT
129 TTCT
* * * **
16877 TTTTTGTATTTCAATATTATTACTATTATTATTATACATTAGTGTGTA-TTTATATTCTATATGT
1 TTTTTGAATTTCAATATTATTACTATTATTATTATACAGTAGTGTATATTTTATATTAGATATGT
* *
16941 ATATATATATG-TTATATATAGTGTTATTTTTATTTACTTTA
66 ATATATATATGATTATATATAGTATTA-TTTTAATTACTTTA
16982 CTTTAATATT
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
130 14 0.15
131 13 0.14
133 22 0.24
134 42 0.46
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.59
Consensus pattern (132 bp):
TTTTTGAATTTCAATATTATTACTATTATTATTATACAGTAGTGTATATTTTATATTAGATATGT
ATATATATATGATTATATATAGTATTATTTTAATTACTTTATCATTTTTATTATATTATATTGTT
CT
Found at i:17165 original size:20 final size:19
Alignment explanation
Indices: 17142--17190 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
17132 TGATTAATAC
17142 ATTATTATTTTTACTATATT
1 ATTATTATTTTTAC-ATATT
*
17162 ATTATTCCTTTTTACATATT
1 ATTATT-ATTTTTACATATT
*
17182 ACTATTATT
1 ATTATTATT
17191 GTCATTAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 16 0.64
21 7 0.28
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTATTATTTTTACATATT
Found at i:17308 original size:22 final size:21
Alignment explanation
Indices: 17276--17382 Score: 92
Period size: 22 Copynumber: 5.0 Consensus size: 21
17266 GTTAACTTCG
*
17276 TATTACTATTATTATATATTTT
1 TATTACCATTATTAT-TATTTT
* *
17298 TATTACCATTAATCATTATTAT
1 TATTACCATT-ATTATTATTTT
* **
17320 TATTACCATTATTTTTCATTAACA
1 TATTACCATTATTATT-ATT--TT
*
17344 TATTACTATTATTATTATTTT
1 TATTACCATTATTATTATTTT
17365 T-TTACCA-TATTATTATTT
1 TATTACCATTATTATTATTT
17383 CCTTTTTATA
Statistics
Matches: 69, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
19 11 0.16
20 5 0.07
21 5 0.07
22 27 0.39
23 7 0.10
24 14 0.20
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTACCATTATTATTATTTT
Found at i:17772 original size:16 final size:16
Alignment explanation
Indices: 17753--17783 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17743 TCATTAGAAC
*
17753 ATTATTTTTTTTATTT
1 ATTATTTTCTTTATTT
17769 ATTATTTTCTTTATT
1 ATTATTTTCTTTATT
17784 GTGAATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTATTTTCTTTATTT
Found at i:22669 original size:8 final size:8
Alignment explanation
Indices: 22653--22683 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
22643 ACAAGTGATA
*
22653 TTATATTT
1 TTATTTTT
22661 TTATTTTT
1 TTATTTTT
22669 TTATTTTT
1 TTATTTTT
22677 TTATTTT
1 TTATTTT
22684 AATAAATAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
TTATTTTT
Found at i:24073 original size:74 final size:74
Alignment explanation
Indices: 23910--24054 Score: 215
Period size: 74 Copynumber: 2.0 Consensus size: 74
23900 TCATACATTA
* * *
23910 AAAAT-AGTAATAATTGC-TCTCTTATATTACTTTGTGACATTTTACATCGCTCACCATAATATA
1 AAAATAAGTAATAATTGCAT-TTTTATATTACTTTGTGACATTTTACATCACTCACCATAACATA
23973 CAACTTAACT
65 CAACTTAACT
*
23983 AAAATAAGTAATAATTGCATTTTTATA-TACTTTTGTGACATTTTACATCACTCACCATAACATC
1 AAAATAAGTAATAATTGCATTTTTATATTAC-TTTGTGACATTTTACATCACTCACCATAACATA
24047 CAACTTAA
65 CAACTTAA
24055 TTATTATTTA
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
73 8 0.12
74 56 0.86
75 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.38
Consensus pattern (74 bp):
AAAATAAGTAATAATTGCATTTTTATATTACTTTGTGACATTTTACATCACTCACCATAACATAC
AACTTAACT
Found at i:24358 original size:18 final size:19
Alignment explanation
Indices: 24309--24369 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 19
24299 ATTGTATTTG
24309 TAAAATTGTATTTTATATAAT
1 TAAAATT-TATTTTATAT-AT
*
24330 TAATAA-ATATTTTATAT-T
1 TAA-AATTTATTTTATATAT
*
24348 TAAAATTTATTTAATACTAT
1 TAAAATTTATTTTATA-TAT
24368 TA
1 TA
24370 TTTGATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
17 2 0.06
18 12 0.36
19 1 0.03
20 13 0.39
21 3 0.09
22 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TAAAATTTATTTTATATAT
Found at i:28962 original size:18 final size:18
Alignment explanation
Indices: 28918--28953 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
28908 TTTTCTGCTC
28918 GTATTGTTATTATTATTG
1 GTATTGTTATTATTATTG
*
28936 GTATTGTTATTTTTATTG
1 GTATTGTTATTATTATTG
28954 TTCATGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.17, T:0.64
Consensus pattern (18 bp):
GTATTGTTATTATTATTG
Found at i:29814 original size:40 final size:40
Alignment explanation
Indices: 29756--29832 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
29746 ACACACTATG
*
29756 TGGGGATAAAATCGACCCA-CCTAACCCTACACACCAAGTA
1 TGGGGATAAAATCAACCCATCC-AACCCTACACACCAAGTA
* * *
29796 TGGGGATATAGTCAACCCATCCAGCCCTACACACCAA
1 TGGGGATAAAATCAACCCATCCAACCCTACACACCAA
29833 AAGGTACCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 30 0.94
41 2 0.06
ACGTcount: A:0.35, C:0.34, G:0.16, T:0.16
Consensus pattern (40 bp):
TGGGGATAAAATCAACCCATCCAACCCTACACACCAAGTA
Found at i:34550 original size:15 final size:16
Alignment explanation
Indices: 34521--34556 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
34511 AGTCGGATAA
34521 AATTTTAATTTTTTAT
1 AATTTTAATTTTTTAT
34537 AATTTTAA-TTTTTAT
1 AATTTTAATTTTTTAT
34552 AATTT
1 AATTT
34557 GTAAAGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
AATTTTAATTTTTTAT
Found at i:41552 original size:3 final size:3
Alignment explanation
Indices: 41544--41568 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41534 AAGTCGAAAC
41544 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
41569 GAGGAGGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:41681 original size:6 final size:7
Alignment explanation
Indices: 41666--41690 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41656 TGGGGCAAGC
41666 TTTTCTT
1 TTTTCTT
41673 TTTTCTT
1 TTTTCTT
41680 TTTTCTT
1 TTTTCTT
41687 TTTT
1 TTTT
41691 TATTTAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:48793 original size:13 final size:13
Alignment explanation
Indices: 48775--48799 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48765 CCAAAATTTC
48775 AAAAAAATAAAAT
1 AAAAAAATAAAAT
48788 AAAAAAATAAAA
1 AAAAAAATAAAA
48800 AAATTTCAAA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:49073 original size:15 final size:15
Alignment explanation
Indices: 49055--49105 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 15
49045 AAAAAAGAGC
49055 AAAAAATTCCAGCAAAA
1 AAAAAATTCCAGC--AA
49072 AAAAAATTCCAGCAA
1 AAAAAATTCCAGCAA
*
49087 AAAAAAATCCA--AA
1 AAAAAATTCCAGCAA
49100 AAAAAA
1 AAAAAA
49106 CACTAGCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
13 8 0.24
15 12 0.36
17 13 0.39
ACGTcount: A:0.71, C:0.16, G:0.04, T:0.10
Consensus pattern (15 bp):
AAAAAATTCCAGCAA
Found at i:49077 original size:17 final size:17
Alignment explanation
Indices: 49055--49093 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
49045 AAAAAAGAGC
49055 AAAAAATTCCAGCAAAA
1 AAAAAATTCCAGCAAAA
49072 AAAAAATTCCAGCAAAA
1 AAAAAATTCCAGCAAAA
49089 AAAAA
1 AAAAA
49094 TCCAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.69, C:0.15, G:0.05, T:0.10
Consensus pattern (17 bp):
AAAAAATTCCAGCAAAA
Found at i:49338 original size:21 final size:23
Alignment explanation
Indices: 49311--49360 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
49301 GTTGTTTTCA
*
49311 TATTTTCTTTCCTT-GGTTTTTT
1 TATTTTCTTTCCTTAGATTTTTT
*
49333 T-TTTTCTTTCTTTAGATTTTTT
1 TATTTTCTTTCCTTAGATTTTTT
49355 TATTTT
1 TATTTT
49361 ATTTTCTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 11 0.46
22 9 0.38
23 4 0.17
ACGTcount: A:0.08, C:0.10, G:0.06, T:0.76
Consensus pattern (23 bp):
TATTTTCTTTCCTTAGATTTTTT
Found at i:52141 original size:39 final size:38
Alignment explanation
Indices: 52034--52147 Score: 183
Period size: 38 Copynumber: 3.0 Consensus size: 38
52024 ATTCCACTCC
* * * *
52034 CCCCATGCTACTTTGTTTTATTATTAATTAAAACTACT
1 CCCCATACTATTTTGTTTTATTATTAATTAAAACCATT
52072 CCCCATACTATTTTGTTTTATTATTAATTAAAACCATT
1 CCCCATACTATTTTGTTTTATTATTAATTAAAACCATT
52110 CCCCATACTATTTTGTTTTTATTATTAATTAAAACCAT
1 CCCCATACTATTTTG-TTTTATTATTAATTAAAACCAT
52148 ACTTTATTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
38 49 0.69
39 22 0.31
ACGTcount: A:0.31, C:0.19, G:0.04, T:0.46
Consensus pattern (38 bp):
CCCCATACTATTTTGTTTTATTATTAATTAAAACCATT
Found at i:52793 original size:22 final size:23
Alignment explanation
Indices: 52745--52794 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
52735 AACCCCCTCT
**
52745 AATACAATCTCTTCTCTCCCCAA
1 AATACAATCGATTCTCTCCCCAA
*
52768 AATACAATCGATTCT-TCCTCAA
1 AATACAATCGATTCTCTCCCCAA
52790 AATAC
1 AATAC
52795 CATTGATCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.30
Consensus pattern (23 bp):
AATACAATCGATTCTCTCCCCAA
Found at i:53266 original size:13 final size:13
Alignment explanation
Indices: 53248--53272 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53238 CAGTTTTGAG
53248 TTCTTCGATCTGC
1 TTCTTCGATCTGC
53261 TTCTTCGATCTG
1 TTCTTCGATCTG
53273 TTCCTATAAA
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:0.08, C:0.28, G:0.16, T:0.48
Consensus pattern (13 bp):
TTCTTCGATCTGC
Found at i:53336 original size:37 final size:37
Alignment explanation
Indices: 53286--53360 Score: 116
Period size: 37 Copynumber: 2.0 Consensus size: 37
53276 CTATAAACAC
*
53286 AGGGATGCCAAATCTGCTATCTTCATC-TGTTCCCTAT
1 AGGGATGCCAAATCTGCTAT-TTCAACTTGTTCCCTAT
*
53323 AGGGATGCCAAATCTGCTGTTTCAACTTGTTCCCTAT
1 AGGGATGCCAAATCTGCTATTTCAACTTGTTCCCTAT
53360 A
1 A
53361 AGCATAGGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 5 0.14
37 30 0.86
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (37 bp):
AGGGATGCCAAATCTGCTATTTCAACTTGTTCCCTAT
Found at i:53469 original size:44 final size:44
Alignment explanation
Indices: 53255--53771 Score: 446
Period size: 44 Copynumber: 12.0 Consensus size: 44
53245 GAGTTCTTCG
*
53255 ATCTGCT-TCTTCGATCTGTT-CCTATAAACACAGGGATGCCAA
1 ATCTGCTATCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAA
53297 ATCTGCTATCTTC-ATCTGTTCCCTAT------AGGGATGCCAA
1 ATCTGCTATCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAA
* * *
53334 ATCTGCTGT-TTC-AACTTGTTCCCTATAAGCATAGGGATGCC--
1 ATCTGCTATCTTCGATC-TGTTCCCTATAAGCACAGGGATGCCAA
** * * * * *
53375 ATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAG
1 AT-CTGCTATCTTCGATCTG-TTCCCTATAAGCACAGGGATGCCAA
53421 ATCTGCTATCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAA
1 ATCTGCTATCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAA
* * * *
53465 ATCTGCTGTTTTTC-AACTTGTTCCCTATAAGCACAAGGATGCC--
1 ATCTGCT-ATCTTCGATC-TGTTCCCTATAAGCACAGGGATGCCAA
** * ** * * * *
53508 ATGCTGAAATCGTCGATCTGCTTTACTGTAAGCACAGGAATGTCAG
1 AT-CTGCTATCTTCGATCTG-TTCCCTATAAGCACAGGGATGCCAA
* *
53554 ATATGCTATCTTCGATCTGTTCCCTATAAGCACAAGGATGCCAA
1 ATCTGCTATCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAA
* *
53598 ATCTGCTATTTTC-AACTTGTTCCCTATAAGCACAGGGATGCC--
1 ATCTGCTATCTTCGATC-TGTTCCCTATAAGCACAGGGATGCCAA
** * * * * * *
53640 ATGC-GAAATCTTCGATCTTCTTCGCTCTAAGCACAGGAATGTCAG
1 AT-CTGCTATCTTCGATC-TGTTCCCTATAAGCACAGGGATGCCAA
*
53685 ATCTGCTATCTTCGATCTGTTTCCTATAAGCACAGGGATGCCAA
1 ATCTGCTATCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAA
*
53729 ATCTGCTATCTTC-AACTTGTTCCCTATAAGCACAGGGATGCCA
1 ATCTGCTATCTTCGATC-TGTTCCCTATAAGCACAGGGATGCCA
53772 TGCTGAAATC
Statistics
Matches: 377, Mismatches: 69, Indels: 56
0.75 0.14 0.11
Matches are distributed among these distances:
36 5 0.01
37 29 0.08
41 2 0.01
42 26 0.07
43 59 0.16
44 183 0.49
45 69 0.18
46 4 0.01
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (44 bp):
ATCTGCTATCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAA
Found at i:53701 original size:131 final size:132
Alignment explanation
Indices: 53262--53834 Score: 839
Period size: 131 Copynumber: 4.4 Consensus size: 132
53252 TCGATCTGCT
* * * * *
53262 TCTTCGATCTG-TTC-CTATAAACACAGGGATGCCAAATCTGCTATCTTC-ATCTGTTCCCTAT-
1 TCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATCTGTTCCCTATA
* *
53323 -----AGGGATGCCAAATCTGCT-GTTTCAACTTGTTCCCTATAAGCATAGGGATGCCATGCTGA
66 AGCACAGGGATGCCAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGA
53382 AA
131 AA
53384 TCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATCTGTTCCCTATA
1 TCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATCTGTTCCCTATA
* *
53449 AGCACAGGGATGCCAAATCTGCTGTTTTTCAACTTGTTCCCTATAAGCACAAGGATGCCATGCTG
66 AGCACAGGGATGCCAAATCTGCT-ATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTG
53514 AAA
130 AAA
* * *
53517 TCGTCGATCTGCTTTACTGTAAGCACAGGAATGTCAGATATGCTATCTTCGATCTGTTCCCTATA
1 TCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATCTGTTCCCTATA
*
53582 AGCACAAGGATGCCAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGC-GA
66 AGCACAGGGATGCCAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGA
53646 AA
131 AA
* * * *
53648 TCTTCGATCTTCTTCGCTCTAAGCACAGGAATGTCAGATCTGCTATCTTCGATCTGTTTCCTATA
1 TCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATCTGTTCCCTATA
*
53713 AGCACAGGGATGCCAAATCTGCTATCTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGA
66 AGCACAGGGATGCCAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGA
53778 AA
131 AA
* * * *
53780 TCTTCGATCTGCTTCACTGTAA-CTCAGGAA-GGCGATATCTGCTATCTTTGATCTG
1 TCTTCGATCTGCTTCACTGTAAGCACAGGAATGTC-AGATCTGCTATCTTCGATCTG
53835 CCCCCCGTCT
Statistics
Matches: 408, Mismatches: 30, Indels: 17
0.90 0.07 0.04
Matches are distributed among these distances:
122 11 0.03
123 3 0.01
124 29 0.07
125 13 0.03
130 2 0.00
131 166 0.41
132 60 0.15
133 124 0.30
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (132 bp):
TCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATCTGTTCCCTATA
AGCACAGGGATGCCAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGA
AA
Found at i:53820 original size:87 final size:88
Alignment explanation
Indices: 53428--53827 Score: 291
Period size: 88 Copynumber: 4.6 Consensus size: 88
53418 CAGATCTGCT
* * * * * *
53428 ATCTTCGATCTG-TTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTTCAACTTGTTCCCTA
1 ATCTTCGATCTGCTTCACTATAAGCACAGGAAGGCCATATCTGCT-ATCTTCAACTTGTTCCCTA
53492 TAAGCACAAGGATGCCATGCTGAA
65 TAAGCACAAGGATGCCATGCTGAA
* * * * * * * *
53516 ATCGTCGATCTGCTTTACTGTAAGCACAGGAATGTCAGATATGCTATCTTCGA-TCTGTTCCCTA
1 ATCTTCGATCTGCTTCACTATAAGCACAGGAAGGCCATATCTGCTATCTTCAACT-TGTTCCCTA
**
53580 TAAGCACAAGGATGCCAAAT-CTGCT
65 TAAGCACAAGGATGCC--ATGCTGAA
* * * * * * ** * * *
53605 ATTTTC-AACTTG-TTCCCTATAAGCACAGGGATGCCAT-GC-GAAATCTTCGATCTTCTTCGCT
1 ATCTTCGATC-TGCTTCACTATAAGCACAGGAAGGCCATATCTGCTATCTTC-AACTTGTTCCCT
* * **
53666 CTAAGCAC-AGGAATGTCA-GATCTGCT
64 ATAAGCACAAGG-ATGCCATG--CTGAA
* * * *
53692 ATCTTCGATCTGTTTC-CTATAAGCACAGGGATGCCAAATCTGCTATCTTCAACTTGTTCCCTAT
1 ATCTTCGATCTGCTTCACTATAAGCACAGGAAGGCCATATCTGCTATCTTCAACTTGTTCCCTAT
*
53756 AAGCACAGGGATGCCATGCTGAA
66 AAGCACAAGGATGCCATGCTGAA
* * *
53779 ATCTTCGATCTGCTTCACTGTAA-CTCAGGAAGGCGATATCTGCTATCTT
1 ATCTTCGATCTGCTTCACTATAAGCACAGGAAGGCCATATCTGCTATCTT
53828 TGATCTGCCC
Statistics
Matches: 241, Mismatches: 53, Indels: 37
0.73 0.16 0.11
Matches are distributed among these distances:
85 1 0.00
86 10 0.04
87 89 0.37
88 95 0.39
89 44 0.18
90 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (88 bp):
ATCTTCGATCTGCTTCACTATAAGCACAGGAAGGCCATATCTGCTATCTTCAACTTGTTCCCTAT
AAGCACAAGGATGCCATGCTGAA
Found at i:54315 original size:204 final size:203
Alignment explanation
Indices: 53869--54638 Score: 1197
Period size: 204 Copynumber: 3.8 Consensus size: 203
53859 AAATCTATTT
* * * * * * ** *
53869 CTTCGATTTGTTCCCTGACAATACAGAAATGCCAAATCATCTTAGATTTGCTTTAACGTAAGCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
* * * * *
53934 GTGAAAGCCAAATCAACTATG-ATTCGATTTGCTCCTTGTAAGCATAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
* * * *
53998 GGATCCACTTCAGCATAAACATCCGAAGGTGAGATCTGCTATGTATCTGCTCTCCATCAAAGTGA
131 GGATCTACTTCAG--TAAACATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
54063 AGATGCCAAA
194 AGATGCCAAA
*
54073 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTTTCGTAATCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
* *
54138 GTGAAAGCCAAATCATCTATGTCTTCGATTTGTTTCTTGTAAACACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
* *
54203 GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTACTATGTGTCTGCTCTCCATCAAAGTGA
131 GGATCTACTTCAGT-AAA-CATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
54268 AGATGCCAAA
194 AGATGCCAAA
54278 CTTCGATTCGTTCTCTGAC-ATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
*
54342 GTGAAAGCCAAATCAGCTATGTCTTCAATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
*
54407 GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
131 GGATCTACTTCAGT-AAA-CATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
54472 AGATGCCAAA
194 AGATGCCAAA
54482 CTTCGATTCGTTCTCTGACGAT--AGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
* * *
54545 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCATTGTAAACACAAGGATGCCAAACCATTTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
54610 GGATCTACTTCAGTATAACATCTGAAGGC
131 GGATCTACTTCAGTA-AACATCTGAAGGC
54639 CAGACCTGTT
Statistics
Matches: 530, Mismatches: 31, Indels: 12
0.92 0.05 0.02
Matches are distributed among these distances:
202 12 0.02
203 118 0.22
204 278 0.52
205 122 0.23
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (203 bp):
CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
GGATCTACTTCAGTAAACATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGAAG
ATGCCAAA
Found at i:62690 original size:15 final size:14
Alignment explanation
Indices: 62648--62697 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
62638 ATAACTTTGA
*
62648 ATGCAAATGATGTG
1 ATGCAAATGATGAG
62662 ATG-AAATGTTATGAG
1 ATGCAAATG--ATGAG
62677 ATGCAAATGCATGA-
1 ATGCAAATG-ATGAG
62691 ATGCAAA
1 ATGCAAA
62698 AAGAATATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.32
15 11 0.35
16 5 0.16
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (14 bp):
ATGCAAATGATGAG
Done.