Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1464
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: 59853
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:632 original size:15 final size:16
Alignment explanation
Indices: 607--639 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
597 ATCGATTTCG
*
607 TTTGAAGCTTCTTCAT
1 TTTGAAGCTTCCTCAT
623 TTTG-AGCTTCCTCAT
1 TTTGAAGCTTCCTCAT
638 TT
1 TT
640 GAACACTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.15, C:0.21, G:0.12, T:0.52
Consensus pattern (16 bp):
TTTGAAGCTTCCTCAT
Found at i:4747 original size:24 final size:25
Alignment explanation
Indices: 4699--4747 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
4689 TACAAGCCAA
**
4699 TGTATCGATACAATTTTTTGTGTAT
1 TGTATCGATACAATACTTTGTGTAT
4724 TGTATCGATAC-ATACTTTGTGTAT
1 TGTATCGATACAATACTTTGTGTAT
4748 CGATACAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.49
Consensus pattern (25 bp):
TGTATCGATACAATACTTTGTGTAT
Found at i:6618 original size:34 final size:32
Alignment explanation
Indices: 6575--6639 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
6565 TACAAGCCAA
6575 TGTATCGATACAAT-TTGGTCATGTATCGATACAT
1 TGTATCGATAC-ATCTT-GT-ATGTATCGATACAT
6609 TGTATCGATACATCTTGTATGTATCGATACA
1 TGTATCGATACATCTTGTATGTATCGATACA
6640 AACAGTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 13 0.43
33 4 0.13
34 13 0.43
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATCTTGTATGTATCGATACAT
Found at i:6628 original size:15 final size:13
Alignment explanation
Indices: 6596--6621 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6586 AATTTGGTCA
6596 TGTATCGATACAT
1 TGTATCGATACAT
6609 TGTATCGATACAT
1 TGTATCGATACAT
6622 CTTGTATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6758 original size:33 final size:33
Alignment explanation
Indices: 6703--6766 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
6693 TTCTTTGCAA
*
6703 GTATCGATACATTTGCTCATGTAACGATACAAT
1 GTATCGATACATGTGCTCATGTAACGATACAAT
* *
6736 GTATCGATAC-TGTGCATTATGTATCGATACA
1 GTATCGATACATGTGC-TCATGTAACGATACA
6767 TCTGAAGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (33 bp):
GTATCGATACATGTGCTCATGTAACGATACAAT
Found at i:7510 original size:20 final size:20
Alignment explanation
Indices: 7485--7535 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
7475 GTTACAAGCA
7485 ATGTATCGATACAATT-CATC
1 ATGTATCGATAC-ATTGCATC
*
7505 ATGTATCGATACATTGTATC
1 ATGTATCGATACATTGCATC
7525 ATGTATCGATA
1 ATGTATCGATA
7536 GAAACAGTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCATC
Found at i:7591 original size:19 final size:19
Alignment explanation
Indices: 7567--7619 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
7557 CTACCAATTT
*
7567 CATGTATCGATACAATGAA
1 CATGTATCGATACAATAAA
7586 CATGTATCGATACAATAAA
1 CATGTATCGATACAATAAA
**
7605 TGTGTATCGATACAA
1 CATGTATCGATACAA
7620 AGCATAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (19 bp):
CATGTATCGATACAATAAA
Found at i:8237 original size:22 final size:22
Alignment explanation
Indices: 8212--8253 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
8202 AGATAAACAT
*
8212 ATTTCTCCCCTTTTATCAAAGC
1 ATTTCTCCCCCTTTATCAAAGC
*
8234 ATTTCTCCCCCTTTGTCAAA
1 ATTTCTCCCCCTTTATCAAA
8254 TCTTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.33, G:0.05, T:0.40
Consensus pattern (22 bp):
ATTTCTCCCCCTTTATCAAAGC
Found at i:16330 original size:33 final size:33
Alignment explanation
Indices: 16287--16352 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
16277 GCCATTACAA
* *
16287 GCAATGTATTGATACAATT-CATCATGTATCGAT
1 GCAATATATTGATAC-ATTGCACCATGTATCGAT
*
16320 GCAATATATTGATACATTGTACCATGTATCGAT
1 GCAATATATTGATACATTGCACCATGTATCGAT
16353 ACAAATAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (33 bp):
GCAATATATTGATACATTGCACCATGTATCGAT
Found at i:16410 original size:20 final size:20
Alignment explanation
Indices: 16385--16444 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
16375 CTGCCAATTT
16385 CATGTATCGATACAATTATC
1 CATGTATCGATACAATTATC
* *
16405 CATGTATCGATACAATGA-A
1 CATGTATCGATACAATTATC
16424 CATGTATCGATACAATATATC
1 CATGTATCGATACAAT-TATC
16445 GATACAAAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTATC
Found at i:27425 original size:20 final size:20
Alignment explanation
Indices: 27395--27443 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
27385 TAATAAGTAG
27395 AAATCAAAAGT-AAAAAATTAA
1 AAAT-AAAAGTGAAAAAA-TAA
27416 AAATAAAAGTGAAAAAATAA
1 AAATAAAAGTGAAAAAATAA
*
27436 AAGTAAAA
1 AAATAAAA
27444 AAAAATTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.16
Consensus pattern (20 bp):
AAATAAAAGTGAAAAAATAA
Found at i:27446 original size:14 final size:14
Alignment explanation
Indices: 27414--27446 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
27404 GTAAAAAATT
*
27414 AAAAATAAAAGTGA
1 AAAAATAAAAGTAA
27428 AAAAATAAAAGTAA
1 AAAAATAAAAGTAA
27442 AAAAA
1 AAAAA
27447 AATTATCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (14 bp):
AAAAATAAAAGTAA
Found at i:27883 original size:16 final size:17
Alignment explanation
Indices: 27843--27887 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
27833 GGAAATGACG
*
27843 GCAACGTGAAGGAGCAC
1 GCAACGTGAAAGAGCAC
27860 GACAACGTGAAAGAGCA-
1 G-CAACGTGAAAGAGCAC
27877 GCAACGTGAAA
1 GCAACGTGAAA
27888 AAATAGCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 10 0.38
17 2 0.08
18 14 0.54
ACGTcount: A:0.42, C:0.20, G:0.31, T:0.07
Consensus pattern (17 bp):
GCAACGTGAAAGAGCAC
Found at i:28225 original size:43 final size:43
Alignment explanation
Indices: 28140--28227 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
28130 CTCCAACCTT
*
28140 CACGAGCACAGTAACAACTTCCACGAGCAACCGACAGCAACTC
1 CACGAGCACAGTAACAACTTCCACGAGCAACCGACAACAACTC
* * * * * * *
28183 CACGAGTACAGTAGCAGCTTTCATGAGCAACCGATAATAACTC
1 CACGAGCACAGTAACAACTTCCACGAGCAACCGACAACAACTC
28226 CA
1 CA
28228 GCTTCCACGA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.36, C:0.32, G:0.17, T:0.15
Consensus pattern (43 bp):
CACGAGCACAGTAACAACTTCCACGAGCAACCGACAACAACTC
Found at i:28633 original size:19 final size:19
Alignment explanation
Indices: 28609--28676 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
28599 AATTCAACAA
28609 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
28628 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
28643 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
28660 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
28677 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:28648 original size:13 final size:13
Alignment explanation
Indices: 28630--28654 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28620 ACATAAGTTT
28630 TGTATCGATACAA
1 TGTATCGATACAA
28643 TGTATCGATACA
1 TGTATCGATACA
28655 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:28652 original size:32 final size:32
Alignment explanation
Indices: 28611--28673 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
28601 TTCAACAATT
*
28611 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
28643 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
28674 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:28734 original size:13 final size:13
Alignment explanation
Indices: 28716--28741 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28706 CATTTTTCTG
28716 TGTATCGATACAT
1 TGTATCGATACAT
28729 TGTATCGATACAT
1 TGTATCGATACAT
28742 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:28738 original size:33 final size:33
Alignment explanation
Indices: 28696--28762 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
28686 GCCAAGGAAA
***
28696 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
28729 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
28762 T
1 T
28763 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:31188 original size:51 final size:52
Alignment explanation
Indices: 31112--31498 Score: 195
Period size: 52 Copynumber: 7.4 Consensus size: 52
31102 AATTCTCCGC
* ***
31112 AATCGGGGATATTCCATTTCCGATTTTATTTTC-AAAACACTAATTTTCTAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACTAATTTTCTAT
* * *
31163 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAAACACATATTTTTC-AG
1 AATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAAACAC-TAATTTTCTAT
* ** ** * * * ** *
31216 AATCGGGGATACTCCAACCCC-A-TTAATCATCGGGGATACTCCAA--CCCCATT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTC--AAAAACACTAATTTTCTA-T
* * * * *
31267 ATTTCCGAGAGGATACTCCAACCCCTG-CTTTATTCTT--AAAATATTGA-TTTCTCAT
1 A-AT-CG-G-GGATACTCCAACCCC-GATTTTATT-TTCAAAAACACTAATTTTCT-AT
* * * * *
31322 AATCGGGGATACTCCAACCCCGATTTTA-TTGCTAAAATACTAATTTTTCCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACTAA-TTTTCTAT
** * *
31374 AATCGGGGATACTCCAACCCCGATTTTATTTT-TGAAACACCAATTTTCCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACTAATTTT-CTAT
* * * * * *
31426 AATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAACACCAATTTTTTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACTAA-TTTTCT-AT
*
31480 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
31499 TCGTTATTTC
Statistics
Matches: 253, Mismatches: 57, Indels: 49
0.70 0.16 0.14
Matches are distributed among these distances:
49 2 0.01
50 3 0.01
51 69 0.27
52 74 0.29
53 48 0.19
54 33 0.13
55 18 0.07
56 1 0.00
57 4 0.02
58 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.34
Consensus pattern (52 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACTAATTTTCTAT
Found at i:31224 original size:53 final size:51
Alignment explanation
Indices: 31112--31233 Score: 165
Period size: 51 Copynumber: 2.4 Consensus size: 51
31102 AATTCTCCGC
* ** *
31112 AATCGGGGATATTCCATTTCCGATTTTATTTTCAAAACACTAATTTTCTAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTAG
*
31163 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAAACACATATTTTTC-AG
1 AATCGGGGATACTCCAACTCCGATTTTATTTTC--AAAACAC-TAATTTTCTAG
31216 AATCGGGGATACTCCAAC
1 AATCGGGGATACTCCAAC
31234 CCCATTAATC
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
51 30 0.48
53 26 0.41
54 7 0.11
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.35
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTAG
Found at i:31289 original size:28 final size:26
Alignment explanation
Indices: 31219--31291 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 26
31209 TTTTCAGAAT
31219 CGGGGATACTCCAACCCCATTAATCA
1 CGGGGATACTCCAACCCCATTAATCA
*
31245 TCGGGGATACTCCAACCCCATTATTTC-
1 -CGGGGATACTCCAACCCCATTA-ATCA
31272 CGAGAGGATACTCCAACCCC
1 CG-G-GGATACTCCAACCCC
31292 TGCTTTATTC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 2 0.05
27 23 0.55
28 17 0.40
ACGTcount: A:0.27, C:0.36, G:0.16, T:0.21
Consensus pattern (26 bp):
CGGGGATACTCCAACCCCATTAATCA
Found at i:31509 original size:31 final size:28
Alignment explanation
Indices: 31481--31557 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
31471 TTTTTTCACA
*
31481 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
**
31509 ATCGAGGATACTCCAACCCCGTTACCTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
31537 --CGAGGGGATACTCCAACCCCG
1 ATCGA--GGATACTCCAACCCCG
31558 GCTTTATTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 3 0.07
28 41 0.93
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.22
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTATTTC
Found at i:31581 original size:265 final size:262
Alignment explanation
Indices: 31111--31606 Score: 724
Period size: 265 Copynumber: 1.9 Consensus size: 262
31101 CAATTCTCCG
* *** *
31111 CAATCGGGGATATTCCATTTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACT
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACT
* * *
31176 CCAACTCCGATTTTATTTTCAAAAAACACATATTTTTCAGAATCGGGGATACTCCAACCCCATTA
66 CCAACTCCGATTTTATTTCCAAAAAACACATATTTTTCACAATCGAGGATACTCCAACCCCATTA
* ** * **
31241 ATCATCGGGGATACTCCAACCCCATTATTTCCGAGAGGATACTCCAACCCCTGCTTTATTCTTAA
131 ATCATCGAGGATACTCCAACCCCATTACCTCCGAGAGGATACTCCAACCCCGGCTTTATTCCCAA
31306 AATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAATACTAATTTTTC
196 AATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAATACTAATTTTTC
31371 CA
261 CA
** *
31373 CAATCGGGGATACTCCAACCCCGATTTTATTTTTGAAACACCAATTTTCCTTTAATCGGGGATAC
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATAC
* * * *
31438 TCCAACTCTGATTTTATTTCC-AAAAACACCAATTTTTTTCACAATCGAGGATACTCCAACCTCG
65 TCCAACTCCGATTTTATTTCCAAAAAACA-C-ATATTTTTCACAATCGAGGATACTCCAACCCCA
* * *
31502 TTATTTCATCGAGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTC
128 TTA-ATCATCGAGGATACTCCAACCCCATTACCTCCGAGAGGATACTCCAACCCCGGCTTTATTC
*
31567 CCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCC
192 CCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCC
31607 TGTTATTTTC
Statistics
Matches: 205, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
262 48 0.23
263 35 0.17
264 31 0.15
265 91 0.44
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (262 bp):
CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACT
CCAACTCCGATTTTATTTCCAAAAAACACATATTTTTCACAATCGAGGATACTCCAACCCCATTA
ATCATCGAGGATACTCCAACCCCATTACCTCCGAGAGGATACTCCAACCCCGGCTTTATTCCCAA
AATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAATACTAATTTTTC
CA
Found at i:33819 original size:149 final size:149
Alignment explanation
Indices: 33540--33819 Score: 361
Period size: 149 Copynumber: 1.9 Consensus size: 149
33530 TTTTATGCCC
* * *
33540 ACTCAAGTCATGTTTTCATATTCCCATGGTTTTCTGTAGGAGTATGAAAATTTTTAACACCTTTT
1 ACTCAAGTCATGTTTTCATATTCCCATGGTTTTCTGAAGGAGTATGAAAAATTTTAACACCTTTC
* * * * * *
33605 GCATCTCCTAGTTTTTCTATTGGGTGCGAAACGTAACTTTTGAAATTAGAAGTTAAATTTTAAAA
66 GCATCTCCTAGTTTTTCTATCGGATACGAAACATAACTTTTAAAATTAGAAGTTAAATTTAAAAA
33670 AAAGTGGTCGGTTGTGCTG
131 AAAGTGGTCGGTTGTGCTG
* ** *
33689 ACTCCAGTCATGTTTTCATATTCGTATGGTTTTCTTGAAGG-GTATGAAAAATTTTAATACCTTT
1 ACTCAAGTCATGTTTTCATATTCCCATGGTTTTC-TGAAGGAGTATGAAAAATTTTAACACCTTT
* * *
33753 CGTATCTCCTAGTTTTTC-GTCGGATACGAAACATAA-TTTTCAAAACTTTGAAGTT-AATTTAA
65 CGCATCTCCTAGTTTTTCTATCGGATACGAAACATAACTTTT-AAAA-TTAGAAGTTAAATTTAA
33815 AAAAA
128 AAAAA
33820 TCAAATTTTG
Statistics
Matches: 112, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
147 4 0.04
148 27 0.24
149 76 0.68
150 5 0.04
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (149 bp):
ACTCAAGTCATGTTTTCATATTCCCATGGTTTTCTGAAGGAGTATGAAAAATTTTAACACCTTTC
GCATCTCCTAGTTTTTCTATCGGATACGAAACATAACTTTTAAAATTAGAAGTTAAATTTAAAAA
AAAGTGGTCGGTTGTGCTG
Found at i:43696 original size:20 final size:20
Alignment explanation
Indices: 43671--43721 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
43661 GTTATAAGCA
43671 ATGTATCGATACAATT-CATC
1 ATGTATCGATAC-ATTGCATC
*
43691 ATGTATCGATACATTGTATC
1 ATGTATCGATACATTGCATC
43711 ATGTATCGATA
1 ATGTATCGATA
43722 TAAACAGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCATC
Found at i:43817 original size:33 final size:32
Alignment explanation
Indices: 43756--43817 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
43746 CAAGTTCATG
*
43756 TATCGATACAATGAACATGTATCAATACAATA
1 TATCGATACAAAGAACATGTATCAATACAATA
*
43788 TATCGATACAAAGCATA-ATGTATCGATACA
1 TATCGATACAAAG-A-ACATGTATCAATACA
43818 TCTTGGTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 12 0.46
33 13 0.50
34 1 0.04
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.27
Consensus pattern (32 bp):
TATCGATACAAAGAACATGTATCAATACAATA
Found at i:44404 original size:22 final size:22
Alignment explanation
Indices: 44342--44397 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
44332 AGTTTTCGTT
*
44342 TTTCTCCCCCTTAATTAAAGAA
1 TTTCTCCCCCTTAATCAAAGAA
*
44364 TTTCTCCCCCTTAATCAAAGCA
1 TTTCTCCCCCTTAATCAAAGAA
44386 TTTCTCCCCCTT
1 TTTCTCCCCCTT
44398 TGTCAAATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.23, C:0.36, G:0.04, T:0.38
Consensus pattern (22 bp):
TTTCTCCCCCTTAATCAAAGAA
Found at i:52391 original size:20 final size:20
Alignment explanation
Indices: 52366--52425 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
52356 CTGCCAAGTT
52366 CATGTATCGATACAATTATC
1 CATGTATCGATACAATTATC
* * *
52386 CATGTAGCGATACAATGA-A
1 CATGTATCGATACAATTATC
52405 CATGTATCGATACAATGTATC
1 CATGTATCGATACAAT-TATC
52426 GATACAAAGC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTATC
Found at i:52410 original size:19 final size:20
Alignment explanation
Indices: 52366--52421 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
52356 CTGCCAAGTT
* *
52366 CATGTATCGATACAATTATC
1 CATGTATCGATACAATGATA
*
52386 CATGTAGCGATACAATGA-A
1 CATGTATCGATACAATGATA
52405 CATGTATCGATACAATG
1 CATGTATCGATACAATG
52422 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAATGATA
Found at i:52424 original size:13 final size:13
Alignment explanation
Indices: 52406--52432 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52396 TACAATGAAC
52406 ATGTATCGATACA
1 ATGTATCGATACA
52419 ATGTATCGATACA
1 ATGTATCGATACA
52432 A
1 A
52433 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:55672 original size:41 final size:43
Alignment explanation
Indices: 55614--55849 Score: 127
Period size: 41 Copynumber: 5.6 Consensus size: 43
55604 TAAACGTTGG
* *
55614 GAGACTTTTTCTACCTTATTCTGCCTTG-TCGAC-TTGACCCTA
1 GAGAC-TTTCCTACCTTAGTCTGCCTTGTTCGACTTTGACCCTA
* * * *
55656 GAGACTTTCCTACCTTAGTCTCCCTTGTTTGGCTTTGACCCTG
1 GAGACTTTCCTACCTTAGTCTGCCTTGTTCGACTTTGACCCTA
* * * *
55699 GAGAC-TTCCTATACCTTAGTCTGCCTAG-T-GGCTTTGACCTTG
1 GAGACTTTCC--TACCTTAGTCTGCCTTGTTCGACTTTGACCCTA
* * * *
55741 GAGAC-TTCCTTCCCTTAGTTTGCC-TGTTAG-CTTTGACCATAA
1 GAGACTTTCC-TACCTTAGTCTGCCTTGTTCGACTTTGACCCT-A
** * * * *
55783 GAGAACTTTTTTCCCTTAGTCCTGCC-T-ATCGAC-TGGACCTTA
1 GAG-ACTTTCCTACCTTAGT-CTGCCTTGTTCGACTTTGACCCTA
55825 -AGACTGTTCCTACCTTAGTCCTGCC
1 GAGACT-TTCCTACCTTAGT-CTGCC
55850 AGCGGCTTTG
Statistics
Matches: 157, Mismatches: 25, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
40 4 0.03
41 59 0.38
42 38 0.24
43 33 0.21
44 23 0.15
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.37
Consensus pattern (43 bp):
GAGACTTTCCTACCTTAGTCTGCCTTGTTCGACTTTGACCCTA
Found at i:55731 original size:42 final size:42
Alignment explanation
Indices: 55625--55778 Score: 163
Period size: 41 Copynumber: 3.7 Consensus size: 42
55615 AGACTTTTTC
* * * *
55625 TACCTTATTCTGCCTTGTCGAC-TTGACCCTAGAGACTTTCC-
1 TACCTTAGTCTGCCTTGTTGGCTTTGACCCTGGAGAC-TTCCT
*
55666 TACCTTAGTCTCCCTTGTTTGGCTTTGACCCTGGAGACTTCCT
1 TACCTTAGTCTGCCTTG-TTGGCTTTGACCCTGGAGACTTCCT
* *
55709 ATACCTTAGTCTGCCTAG-TGGCTTTGACCTTGGAGACTTCCT
1 -TACCTTAGTCTGCCTTGTTGGCTTTGACCCTGGAGACTTCCT
* * *
55751 TCCCTTAGTTTGCC-TGTTAGCTTTGACC
1 TACCTTAGTCTGCCTTGTTGGCTTTGACC
55779 ATAAGAGAAC
Statistics
Matches: 96, Mismatches: 12, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
40 1 0.01
41 37 0.39
42 30 0.31
43 13 0.14
44 15 0.16
ACGTcount: A:0.14, C:0.29, G:0.18, T:0.38
Consensus pattern (42 bp):
TACCTTAGTCTGCCTTGTTGGCTTTGACCCTGGAGACTTCCT
Found at i:57801 original size:21 final size:22
Alignment explanation
Indices: 57777--57824 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
57767 GGCAGCAGTT
57777 TCCATAAGCAACC-ACAAGCAA-
1 TCCATAAGCAACCAAC-AGCAAC
*
57798 TCCACAAGCAACCAACAGCAAC
1 TCCATAAGCAACCAACAGCAAC
57820 TCCAT
1 TCCAT
57825 GGGCACGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.44, C:0.38, G:0.08, T:0.10
Consensus pattern (22 bp):
TCCATAAGCAACCAACAGCAAC
Found at i:57819 original size:10 final size:10
Alignment explanation
Indices: 57782--57811 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
57772 CAGTTTCCAT
57782 AAGCAACCAC
1 AAGCAACCAC
57792 AAGCAATCCAC
1 AAGCAA-CCAC
57803 AAGCAACCA
1 AAGCAACCA
57812 ACAGCAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.50, C:0.37, G:0.10, T:0.03
Consensus pattern (10 bp):
AAGCAACCAC
Done.