Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015827.1 Corchorus capsularis cultivar CVL-1 contig15848, whole genome shotgun sequence
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: 18166
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1455 original size:13 final size:14
Alignment explanation
Indices: 1416--1470 Score: 55
Period size: 13 Copynumber: 4.1 Consensus size: 14
1406 TATTCAATCT
1416 TTATATATATTGATA
1 TTATATATATT-ATA
*
1431 --ATA-ATGTTATA
1 TTATATATATTATA
1442 TTATAT-TATTATA
1 TTATATATATTATA
1455 TTATATATATATATA
1 TTATATATAT-TATA
1470 T
1 T
1471 ATCAATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
11 3 0.09
12 4 0.12
13 18 0.55
14 3 0.09
15 5 0.15
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (14 bp):
TTATATATATTATA
Found at i:1623 original size:17 final size:18
Alignment explanation
Indices: 1601--1651 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
1591 GAAATCAAAT
*
1601 CCGAGCCCGAACCCG-AC
1 CCGAGCCCGAACACGAAC
* *
1618 CCGAGCACGAATACGAAC
1 CCGAGCCCGAACACGAAC
*
1636 CCGA-CCCGAACTCGAA
1 CCGAGCCCGAACACGAA
1652 AATACCCGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 21 0.78
18 6 0.22
ACGTcount: A:0.31, C:0.43, G:0.22, T:0.04
Consensus pattern (18 bp):
CCGAGCCCGAACACGAAC
Found at i:1651 original size:23 final size:23
Alignment explanation
Indices: 1608--1651 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1598 AATCCGAGCC
*
1608 CGAACCCGACCCGAGCACGAATA
1 CGAACCCGACCCGAACACGAATA
*
1631 CGAACCCGACCCGAACTCGAA
1 CGAACCCGACCCGAACACGAA
1652 AATACCCGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.41, G:0.20, T:0.05
Consensus pattern (23 bp):
CGAACCCGACCCGAACACGAATA
Found at i:1660 original size:16 final size:17
Alignment explanation
Indices: 1639--1685 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
1629 TACGAACCCG
1639 ACCCGAACTCGAAAAT-
1 ACCCGAACTCGAAAATA
*
1655 ACCCGAACTCG-ACATA
1 ACCCGAACTCGAAAATA
*
1671 ACCCGAACCCGAAAA
1 ACCCGAACTCGAAAA
1686 GCCCGAGCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 3 0.12
16 21 0.81
17 2 0.08
ACGTcount: A:0.43, C:0.36, G:0.13, T:0.09
Consensus pattern (17 bp):
ACCCGAACTCGAAAATA
Found at i:2549 original size:107 final size:104
Alignment explanation
Indices: 2383--2698 Score: 402
Period size: 106 Copynumber: 3.0 Consensus size: 104
2373 AAGATTTTTA
* * *
2383 TTATAGGGTTTTAGAAATAAAATATAAAAAAAATTCACTAAATTTAGTCTCAAATTAAAATTTTA
1 TTATAGGGTTTTAGAAATAAAATAT-AAAATAATTCACTAAGTTTAG-CCCAAATTAAAATTTTA
*
2448 ATTTTATTTTAAGGGTAAATTCAAAAATTAATAACTTATTG
64 ATTTTATTTTAAGGGTAAATTCCAAAATTAATAACTTATTG
*
2489 TTATAGGGTTTTAGAAATAAAATATAAACCTAATTTCACTAAGTTTAGCCCAAAATTAAAATTTT
1 TTATAGGGTTTTAGAAATAAAATATAAA-ATAA-TTCACTAAGTTTAGCCC-AAATTAAAATTTT
** *
2554 AA-TTTATGGTAAGAGTAAATTCCAAAATTAATAACTTATTG
63 AATTTTATTTTAAGGGTAAATTCCAAAATTAATAACTTATTG
* * *
2595 -GATAGGGTTTTAGAAATAAAATATATAAATAATTCATTATAGTTTAACCCCAAATTAAAATTTT
1 TTATAGGGTTTTAGAAATAAAATATA-AAATAATTCACTA-AGTTT-AGCCCAAATTAAAATTTT
* * * *
2659 AATTTTATTTTAAAGATAAAATACCAAAACTAATAACTTA
63 AATTTTATTTTAAGGGT-AAATTCCAAAATTAATAACTTA
2699 GACAAATTAA
Statistics
Matches: 183, Mismatches: 19, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
104 6 0.03
105 50 0.27
106 79 0.43
107 48 0.26
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.38
Consensus pattern (104 bp):
TTATAGGGTTTTAGAAATAAAATATAAAATAATTCACTAAGTTTAGCCCAAATTAAAATTTTAAT
TTTATTTTAAGGGTAAATTCCAAAATTAATAACTTATTG
Found at i:4477 original size:154 final size:154
Alignment explanation
Indices: 4192--4506 Score: 461
Period size: 154 Copynumber: 2.0 Consensus size: 154
4182 TTCTATTTTA
* * * *
4192 ACATTCTGAATACTTGTTATTTTGGGCATTTCGGGACCTGTTAGTTCTGTTTTTAATCAGATTCG
1 ACATTCTGAACACTTGTTATTTTGGGCATTTCGGGACCTATTAGTGCTGTTTTGAATCAGATTCG
*
4257 ATTCGGCAAACCACAAAACTTTTCTTCCCATTGTTTATGGCCTAACTATAATCATTTTGATGAGA
66 ATTCAGCAAACCACAAAACTTTTCTTCCCATTGTTTATGGCCTAACTATAATCATTTTGATGAGA
*
4322 TTAGTCCACTAGGAAGTTGTTAGC
131 TTAGTCCACTAGGAAGTTGTTAAC
** *
4346 ACATTCTGAACACTTGTTATTTTGGGTC-TTTCGGGGTCTATTAGTGCTGTTTTGAATCAGTTTC
1 ACATTCTGAACACTTGTTATTTTGGG-CATTTCGGGACCTATTAGTGCTGTTTTGAATCAGATTC
* ** * *
4410 TATTCAGCAAACCACAAAACTTTTCTTTTCATTGTTTATGGCCTAACTATAATCATTTTGGTTAG
65 GATTCAGCAAACCACAAAACTTTTCTTCCCATTGTTTATGGCCTAACTATAATCATTTTGATGAG
* * *
4475 ATTAGTCTACTATGAAGTTTTTAAC
130 ATTAGTCCACTAGGAAGTTGTTAAC
4500 ACATTCT
1 ACATTCT
4507 AAACTTTTAA
Statistics
Matches: 143, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
154 142 0.99
155 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.41
Consensus pattern (154 bp):
ACATTCTGAACACTTGTTATTTTGGGCATTTCGGGACCTATTAGTGCTGTTTTGAATCAGATTCG
ATTCAGCAAACCACAAAACTTTTCTTCCCATTGTTTATGGCCTAACTATAATCATTTTGATGAGA
TTAGTCCACTAGGAAGTTGTTAAC
Found at i:4905 original size:2 final size:2
Alignment explanation
Indices: 4898--4932 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
4888 TTATGTAGCA
4898 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
4933 GCTAACCAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5827 original size:21 final size:21
Alignment explanation
Indices: 5785--5827 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5775 AATTGCTAAA
* *
5785 TATCGTCCCTTTTTTGCTACT
1 TATCGTCCCCTTTTTACTACT
5806 TATCGTCCCACTTTTTAC-ACT
1 TATCGTCCC-CTTTTTACTACT
5827 T
1 T
5828 TTACTCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.14, C:0.30, G:0.07, T:0.49
Consensus pattern (21 bp):
TATCGTCCCCTTTTTACTACT
Found at i:6243 original size:33 final size:33
Alignment explanation
Indices: 6181--6246 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
6171 GTGCCGCCCC
*
6181 TGCCGCCCCAGGAGGGCAGCAGTGGCCATGGCA
1 TGCCGCCCCAGGAGGGCAGCACTGGCCATGGCA
* *
6214 TGCCGCTCCAGGAGGGC-GACACTGTCCATGGCA
1 TGCCGCCCCAGGAGGGCAG-CACTGGCCATGGCA
6247 GTAGTTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.03
33 28 0.97
ACGTcount: A:0.18, C:0.33, G:0.36, T:0.12
Consensus pattern (33 bp):
TGCCGCCCCAGGAGGGCAGCACTGGCCATGGCA
Found at i:6305 original size:25 final size:25
Alignment explanation
Indices: 6268--6315 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
6258 TAGATTTTTT
* *
6268 TAATTATTGATTATTATTAATTATG
1 TAATAATTAATTATTATTAATTATG
6293 TAATAATTAATTATTATTAATTA
1 TAATAATTAATTATTATTAATTA
6316 GAATGTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (25 bp):
TAATAATTAATTATTATTAATTATG
Found at i:8053 original size:2 final size:2
Alignment explanation
Indices: 8046--8072 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8036 TAGCCTCAAC
8046 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
8073 ACAAAGCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9567 original size:32 final size:32
Alignment explanation
Indices: 9530--9649 Score: 152
Period size: 32 Copynumber: 3.8 Consensus size: 32
9520 TCCGCCCAAC
* * *
9530 CCGAGACCCGAAAGACCCGCATCCCAGATGAT
1 CCGAGACCCGAATGACCCGTAACCCAGATGAT
*
9562 CCGAGACCCGAATGACCCGTAACCCAGATGAC
1 CCGAGACCCGAATGACCCGTAACCCAGATGAT
*
9594 CCGAAACCCGAATGACCCGTAACCC-GAGTGAT
1 CCGAGACCCGAATGACCCGTAACCCAGA-TGAT
* * *
9626 CCGAGAACCGTATGACCCGAAACC
1 CCGAGACCCGAATGACCCGTAACC
9650 TGAATAACCC
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
31 2 0.03
32 75 0.97
ACGTcount: A:0.32, C:0.37, G:0.22, T:0.10
Consensus pattern (32 bp):
CCGAGACCCGAATGACCCGTAACCCAGATGAT
Found at i:9586 original size:16 final size:16
Alignment explanation
Indices: 9528--9661 Score: 103
Period size: 16 Copynumber: 8.4 Consensus size: 16
9518 AATCCGCCCA
* *
9528 ACCCGAGACCCGAAAG
1 ACCCGAAACCCGAATG
* *
9544 ACCCGCATCCC-AGATG
1 ACCCGAAACCCGA-ATG
* *
9560 ATCCGAGACCCGAATG
1 ACCCGAAACCCGAATG
*
9576 ACCCGTAACCC-AGATG
1 ACCCGAAACCCGA-ATG
9592 ACCCGAAACCCGAATG
1 ACCCGAAACCCGAATG
* *
9608 ACCCGTAACCCGAGTG
1 ACCCGAAACCCGAATG
* *
9624 ATCCGAGAA-CCGTATG
1 ACCCGA-AACCCGAATG
* *
9640 ACCCGAAACCTGAATA
1 ACCCGAAACCCGAATG
9656 ACCCGA
1 ACCCGA
9662 GAAGTTAACC
Statistics
Matches: 90, Mismatches: 22, Indels: 12
0.73 0.18 0.10
Matches are distributed among these distances:
15 4 0.04
16 82 0.91
17 4 0.04
ACGTcount: A:0.33, C:0.36, G:0.21, T:0.10
Consensus pattern (16 bp):
ACCCGAAACCCGAATG
Found at i:10530 original size:32 final size:31
Alignment explanation
Indices: 10487--10560 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 31
10477 CCGAAGTCAA
**
10487 AACCCGAACCCGTCCAACCCGAAACCCG-AT
1 AACCCGAACCCGAACAACCCGAAACCCGTAT
**
10517 AGACCCGGAACCCGAATGACCCGAAACCCGTAT
1 A-ACCC-GAACCCGAACAACCCGAAACCCGTAT
10550 AACCCGAACCC
1 AACCCGAACCC
10561 AAATGACCCG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 1 0.03
31 10 0.27
32 23 0.62
33 3 0.08
ACGTcount: A:0.34, C:0.43, G:0.16, T:0.07
Consensus pattern (31 bp):
AACCCGAACCCGAACAACCCGAAACCCGTAT
Found at i:10566 original size:31 final size:32
Alignment explanation
Indices: 10503--10571 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
10493 AACCCGTCCA
*
10503 ACCCGAAACCCGATAGACCCGGAACCCGAATG
1 ACCCGAAACCCGATAGACCCGGAACCCAAATG
10535 ACCCGAAACCCGTATA-ACCC-GAACCCAAATG
1 ACCCGAAACCCG-ATAGACCCGGAACCCAAATG
10566 ACCCGA
1 ACCCGA
10572 TACATGAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
31 16 0.46
32 16 0.46
33 3 0.09
ACGTcount: A:0.36, C:0.39, G:0.17, T:0.07
Consensus pattern (32 bp):
ACCCGAAACCCGATAGACCCGGAACCCAAATG
Found at i:10569 original size:15 final size:15
Alignment explanation
Indices: 10503--10588 Score: 75
Period size: 16 Copynumber: 5.5 Consensus size: 15
10493 AACCCGTCCA
10503 ACCCGAAACCCG-ATAG
1 ACCCG-AACCCGAAT-G
10519 ACCCGGAACCCGAATG
1 ACCC-GAACCCGAATG
* *
10535 ACCCGAAACCCGTATA
1 ACCCG-AACCCGAATG
*
10551 ACCCGAACCCAAATG
1 ACCCGAACCCGAATG
**
10566 ACCCGATACATGAATG
1 ACCCGA-ACCCGAATG
10582 ACCCGAA
1 ACCCGAA
10589 AAAACTGTCT
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
15 15 0.26
16 40 0.69
17 3 0.05
ACGTcount: A:0.37, C:0.36, G:0.17, T:0.09
Consensus pattern (15 bp):
ACCCGAACCCGAATG
Found at i:10569 original size:47 final size:48
Alignment explanation
Indices: 10488--10589 Score: 113
Period size: 47 Copynumber: 2.2 Consensus size: 48
10478 CGAAGTCAAA
* * *
10488 ACCCG-AACCCGTCCAACCCGAAACCCGATAGACCCGGA-ACCCGAATG
1 ACCCGAAACCCGTACAACCCGAAACCCAATAGACCC-GATACACGAATG
* *
10535 ACCCGAAACCCGTATAACCCG-AACCCAA-ATGACCCGATACATGAATG
1 ACCCGAAACCCGTACAACCCGAAACCCAATA-GACCCGATACACGAATG
10582 ACCCGAAA
1 ACCCGAAA
10590 AAACTGTCTG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
46 3 0.06
47 31 0.66
48 13 0.28
ACGTcount: A:0.36, C:0.38, G:0.17, T:0.09
Consensus pattern (48 bp):
ACCCGAAACCCGTACAACCCGAAACCCAATAGACCCGATACACGAATG
Found at i:10586 original size:31 final size:31
Alignment explanation
Indices: 10503--10588 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
10493 AACCCGTCCA
* *
10503 ACCCGAAACCCG-ATAGACCCGGAACCCGAATG
1 ACCCGAAACACGAAT-GACCC-GAACCCAAATG
* * *
10535 ACCCGAAACCCGTATAACCCGAACCCAAATG
1 ACCCGAAACACGAATGACCCGAACCCAAATG
* *
10566 ACCCGATACATGAATGACCCGAA
1 ACCCGAAACACGAATGACCCGAA
10589 AAAACTGTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
31 28 0.61
32 16 0.35
33 2 0.04
ACGTcount: A:0.37, C:0.36, G:0.17, T:0.09
Consensus pattern (31 bp):
ACCCGAAACACGAATGACCCGAACCCAAATG
Found at i:11701 original size:37 final size:37
Alignment explanation
Indices: 11651--11721 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
11641 ATATAGTTAT
* *
11651 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
11688 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
11722 GTTGATCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:14712 original size:24 final size:24
Alignment explanation
Indices: 14654--14946 Score: 406
Period size: 24 Copynumber: 11.8 Consensus size: 24
14644 ATATACCATG
* *
14654 TGGGGACTTAGTTGCCATGAGTCA
1 TGGGGACTTGGTTGCCATGAGCCA
14678 TGTGGGGACTTGGTTGCCATGAGCCA
1 --TGGGGACTTGGTTGCCATGAGCCA
*
14704 TGGGCACTTGGTTGCCATGAGCCA
1 TGGGGACTTGGTTGCCATGAGCCA
*
14728 TGGGCACTTGGTTGCCATGAGCCA
1 TGGGGACTTGGTTGCCATGAGCCA
*
14752 TGAGGGGACTTGGTTGCCATGAACCA
1 T--GGGGACTTGGTTGCCATGAGCCA
14778 TGGGGACTTGGTTGCCATGAGCCA
1 TGGGGACTTGGTTGCCATGAGCCA
*
14802 TGTGGGGACTTGGTTGCCATGAGTCA
1 --TGGGGACTTGGTTGCCATGAGCCA
14828 TGTGGGGACTTGGTTGCCATGAGCCA
1 --TGGGGACTTGGTTGCCATGAGCCA
*
14854 TGGGGACTTGGTTGCCATGAACCA
1 TGGGGACTTGGTTGCCATGAGCCA
*
14878 TGGGGACTTGGTTGCCATGAACCA
1 TGGGGACTTGGTTGCCATGAGCCA
*
14902 TGGGGACTTGGTTGCCATGAGCTA
1 TGGGGACTTGGTTGCCATGAGCCA
*
14926 TGTGGGGACTTAGTTGCCATG
1 --TGGGGACTTGGTTGCCATG
14947 GACTTGGTTG
Statistics
Matches: 249, Mismatches: 12, Indels: 12
0.91 0.04 0.04
Matches are distributed among these distances:
24 139 0.56
26 110 0.44
ACGTcount: A:0.18, C:0.19, G:0.36, T:0.27
Consensus pattern (24 bp):
TGGGGACTTGGTTGCCATGAGCCA
Found at i:14723 original size:50 final size:48
Alignment explanation
Indices: 14654--14986 Score: 423
Period size: 50 Copynumber: 6.9 Consensus size: 48
14644 ATATACCATG
* *
14654 TGGGGACTTAGTTGCCATGAGTCATGTGGGGACTTGGTTGCCATGAGCCA
1 TGGGGACTTGGTTGCCATGAGCCA--TGGGGACTTGGTTGCCATGAGCCA
* *
14704 TGGGCACTTGGTTGCCATGAGCCATGGGCACTTGGTTGCCATGAGCCA
1 TGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGAGCCA
*
14752 TGAGGGGACTTGGTTGCCATGAACCATGGGGACTTGGTTGCCATGAGCCA
1 T--GGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGAGCCA
*
14802 TGTGGGGACTTGGTTGCCATGAGTCATGTGGGGACTTGGTTGCCATGAGCCA
1 --TGGGGACTTGGTTGCCATGAGCCA--TGGGGACTTGGTTGCCATGAGCCA
* *
14854 TGGGGACTTGGTTGCCATGAACCATGGGGACTTGGTTGCCATGAACCA
1 TGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGAGCCA
* *
14902 TGGGGACTTGGTTGCCATGAGCTATGTGGGGACTTAG-T----T--GCCA
1 TGGGGACTTGGTTGCCATGAGCCA--TGGGGACTTGGTTGCCATGAGCCA
14945 T--GGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
1 TGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
14987 TATGGCATAT
Statistics
Matches: 250, Mismatches: 18, Indels: 34
0.83 0.06 0.11
Matches are distributed among these distances:
39 10 0.04
40 1 0.00
41 20 0.08
43 4 0.02
44 1 0.00
45 1 0.00
48 69 0.28
49 1 0.00
50 118 0.47
52 25 0.10
ACGTcount: A:0.18, C:0.20, G:0.36, T:0.27
Consensus pattern (48 bp):
TGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGAGCCA
Found at i:14824 original size:150 final size:149
Alignment explanation
Indices: 14649--14946 Score: 490
Period size: 150 Copynumber: 2.0 Consensus size: 149
14639 GTTCCATATA
14649 CCATGTGGGGACTTAGTTGCCATGAGTCATGTGGGGACTTGGTTGCCATGAGCCATGGGCACTTG
1 CCATGTGGGGACTTAGTTGCCATGAGTCATGTGGGGACTTGGTTGCCATGAGCCATGGGCACTTG
* *
14714 GTTGCCATGAGCCATGGGCACTTGGTTGCCATGAGCCATGAGGGGACTTGGTTGCCATGAACCA-
66 GTTGCCATGAACCATGGGCACTTGGTTGCCATGAACCAT--GGGGACTTGGTTGCCATGAACCAG
*
14778 TGGGGACTTGGTTGCCATGAG
129 TGGGGACTTAGTTGCCATGAG
* *
14799 CCATGTGGGGACTTGGTTGCCATGAGTCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTG
1 CCATGTGGGGACTTAGTTGCCATGAGTCATGTGGGGACTTGGTTGCCATGAGCCATGGGCACTTG
* * *
14864 GTTGCCATGAACCATGGGGACTTGGTTGCCATGAACCATGGGGACTTGGTTGCCATGAGCTATGT
66 GTTGCCATGAACCATGGGCACTTGGTTGCCATGAACCATGGGGACTTGGTTGCCATGAACCA-GT
14929 GGGGACTTAGTTGCCATG
130 GGGGACTTAGTTGCCATG
14947 GACTTGGTTG
Statistics
Matches: 138, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
148 21 0.15
150 117 0.85
ACGTcount: A:0.18, C:0.20, G:0.36, T:0.27
Consensus pattern (149 bp):
CCATGTGGGGACTTAGTTGCCATGAGTCATGTGGGGACTTGGTTGCCATGAGCCATGGGCACTTG
GTTGCCATGAACCATGGGCACTTGGTTGCCATGAACCATGGGGACTTGGTTGCCATGAACCAGTG
GGGACTTAGTTGCCATGAG
Found at i:14951 original size:15 final size:15
Alignment explanation
Indices: 14931--14961 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
14921 AGCTATGTGG
14931 GGACTTAGTTGCCAT
1 GGACTTAGTTGCCAT
*
14946 GGACTTGGTTGCCAT
1 GGACTTAGTTGCCAT
14961 G
1 G
14962 AGCCATGGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.19, G:0.32, T:0.32
Consensus pattern (15 bp):
GGACTTAGTTGCCAT
Found at i:14968 original size:72 final size:72
Alignment explanation
Indices: 14680--14946 Score: 300
Period size: 74 Copynumber: 3.6 Consensus size: 72
14670 ATGAGTCATG
* * * * * *
14680 TGGGGACTTGGTTGCCATGAGCCATGGGCACTTGGTTGCCATGAGCCATGGGCACTTGGTTGCCA
1 TGGGGACTTGGTTGCCATGAGCCATGGGGACTTAGTTGCCATGAACCATGGGGACATGGTAGCCA
*
14745 TGAGCCA
66 TGAACCA
* * * * *
14752 TGAGGGGACTTGGTTGCCATGAACCATGGGGACTTGGTTGCCATGAGCCATGTGGGGACTTGGTT
1 T--GGGGACTTGGTTGCCATGAGCCATGGGGACTTAGTTGCCATGAACCA--TGGGGACATGGTA
**
14817 GCCATGAGTCA
62 GCCATGAACCA
* * *
14828 TGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGAACCATGGGGACTTGGTTGC
1 --TGGGGACTTGGTTGCCATGAGCCATGGGGACTTAGTTGCCATGAACCATGGGGACATGGTAGC
14893 CATGAACCA
64 CATGAACCA
*
14902 TGGGGACTTGGTTGCCATGAGCTATGTGGGGACTTAGTTGCCATG
1 TGGGGACTTGGTTGCCATGAGCCA--TGGGGACTTAGTTGCCATG
14947 GACTTGGTTG
Statistics
Matches: 177, Mismatches: 10, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
72 24 0.14
74 85 0.48
76 67 0.38
78 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.36, T:0.27
Consensus pattern (72 bp):
TGGGGACTTGGTTGCCATGAGCCATGGGGACTTAGTTGCCATGAACCATGGGGACATGGTAGCCA
TGAACCA
Found at i:14969 original size:22 final size:23
Alignment explanation
Indices: 14941--14986 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
14931 GGACTTAGTT
14941 GCCAT-GGACTTGGTTGCCATGA
1 GCCATGGGACTTGGTTGCCATGA
14963 GCCATGGGGACTTGGTTGCCATGA
1 GCCAT-GGGACTTGGTTGCCATGA
14987 TATGGCATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.23
24 17 0.77
ACGTcount: A:0.17, C:0.22, G:0.35, T:0.26
Consensus pattern (23 bp):
GCCATGGGACTTGGTTGCCATGA
Found at i:14982 original size:39 final size:40
Alignment explanation
Indices: 14905--14985 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 40
14895 TGAACCATGG
*
14905 GGACTTGGTTGCCATGAGCTATGTGGGGACTTAGTTGCCAT
1 GGACTTGGTTGCCATGAGCCA-GTGGGGACTTAGTTGCCAT
*
14946 GGACTTGGTTGCCATGAGCCA-TGGGGACTTGGTTGCCAT
1 GGACTTGGTTGCCATGAGCCAGTGGGGACTTAGTTGCCAT
14985 G
1 G
14986 ATATGGCATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 18 0.47
41 20 0.53
ACGTcount: A:0.16, C:0.19, G:0.36, T:0.30
Consensus pattern (40 bp):
GGACTTGGTTGCCATGAGCCAGTGGGGACTTAGTTGCCAT
Found at i:15306 original size:23 final size:22
Alignment explanation
Indices: 15229--15312 Score: 78
Period size: 23 Copynumber: 3.4 Consensus size: 22
15219 CCTTAACAAC
15229 ATAACGTTAAGAATTTAATATAT
1 ATAAC-TTAAGAATTTAATATAT
*
15252 ATAATCTTAAGAATTAAATATAACGTTAT
1 ATAA-CTTAAGAATT-TA-AT-A---TAT
15281 ATAACATTAAGAATTTAATATAT
1 ATAAC-TTAAGAATTTAATATAT
15304 ATAACTTAA
1 ATAACTTAA
15313 TTTACATAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
22 4 0.08
23 21 0.41
24 2 0.04
25 2 0.04
26 2 0.04
27 2 0.04
28 2 0.04
29 16 0.31
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (22 bp):
ATAACTTAAGAATTTAATATAT
Found at i:17362 original size:25 final size:25
Alignment explanation
Indices: 17324--17372 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
17314 CCAAACAATC
*
17324 TTGAGCACTTTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
17349 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
17373 CAAACAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.37
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:17735 original size:23 final size:24
Alignment explanation
Indices: 17700--17748 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
17690 ATTGATTGAC
* *
17700 ATTTTGTGCATAAA-AGTATATAT
1 ATTTTGTACATAAAGAGGATATAT
*
17723 ATTTTGTATATAAAGAGGATATAT
1 ATTTTGTACATAAAGAGGATATAT
17747 AT
1 AT
17749 AAATTTTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (24 bp):
ATTTTGTACATAAAGAGGATATAT
Done.