Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014344.1 Corchorus capsularis cultivar CVL-1 contig14365, 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: 42251
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1350 original size:25 final size:24
Alignment explanation
Indices: 1292--1354 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 24
1282 GAAAACTTCG
1292 TTTATGTAAT-ATATTATAGTAAA
1 TTTATGTAATAATATTATAGTAAA
* *
1315 TTT-TTTAAATACATATTGTAGTAAA
1 TTTATGT-AATA-ATATTATAGTAAA
1340 TTTATGTAAT-ATATT
1 TTTATGTAATAATATT
1355 TTTCTTAGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
22 2 0.06
23 11 0.33
25 18 0.55
26 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.51
Consensus pattern (24 bp):
TTTATGTAATAATATTATAGTAAA
Found at i:5787 original size:21 final size:20
Alignment explanation
Indices: 5748--5787 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5738 AGAGATTAAT
*
5748 TAAAAAGAAAACAATTAAAC
1 TAAAAAGAAAACAAGTAAAC
*
5768 TAAAAATAAAACTAAGTAAA
1 TAAAAAGAAAAC-AAGTAAA
5788 TTTAATCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.17
Consensus pattern (20 bp):
TAAAAAGAAAACAAGTAAAC
Found at i:7176 original size:19 final size:18
Alignment explanation
Indices: 7139--7178 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
7129 TTTTTGAAAT
*
7139 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
7157 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
7176 AAT
1 AAT
7179 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:8788 original size:21 final size:21
Alignment explanation
Indices: 8762--8803 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
8752 AGTGTCGACC
8762 CAATCA-AGCAATTCAAAGCAT
1 CAATCATAGC-ATTCAAAGCAT
*
8783 CAATCATAGCATTCATAGCAT
1 CAATCATAGCATTCAAAGCAT
8804 ATGAGTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.24
Consensus pattern (21 bp):
CAATCATAGCATTCAAAGCAT
Found at i:12591 original size:33 final size:33
Alignment explanation
Indices: 12554--12660 Score: 135
Period size: 33 Copynumber: 3.2 Consensus size: 33
12544 AGCACTAGTG
* * *
12554 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* *
12587 ACCGGCCACGTGACTCGGAGATGTCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* *
12620 ACCGGCCACGCGACATGGACATGTCCGGCC-AC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
12652 AACCGGCCA
1 -ACCGGCCA
12661 TCGCTTGGCG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 2 0.03
33 62 0.97
ACGTcount: A:0.23, C:0.38, G:0.29, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
Found at i:18035 original size:33 final size:33
Alignment explanation
Indices: 17995--18079 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 33
17985 AGCACTAGTG
*
17995 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC
* * * *
18028 ACTGGCCACGTGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC
*
18061 ACCGGCCACGCGACATGGA
1 ACCGGCCACGCGACTTGGA
18080 CATGTCTGGC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.24, C:0.36, G:0.31, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC
Found at i:18091 original size:33 final size:33
Alignment explanation
Indices: 17995--18101 Score: 101
Period size: 33 Copynumber: 3.2 Consensus size: 33
17985 AGCACTAGTG
* * * *
17995 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACTCGGACATGCCCGGCCAAC
* * *
18028 ACTGGCCACGTGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACTCGGACATGCCCGGCCAAC
* *
18061 ACCGGCCACGCGACAT-GGACATGTCTGGCC-AC
1 ACCGGCCACGCGAC-TCGGACATGCCCGGCCAAC
18093 AACCGGCCA
1 -ACCGGCCA
18102 TCGCTTGGCA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 2 0.03
33 59 0.95
34 1 0.02
ACGTcount: A:0.23, C:0.37, G:0.29, T:0.10
Consensus pattern (33 bp):
ACCGGCCACGCGACTCGGACATGCCCGGCCAAC
Found at i:19088 original size:49 final size:48
Alignment explanation
Indices: 18992--19570 Score: 683
Period size: 49 Copynumber: 12.1 Consensus size: 48
18982 AAGAAAAGAA
* * * * *
18992 AATAAGAGAAGAAAACTATGACCTTTCGATCGGGAAGAGGCAGTTTTGG
1 AATAAGA-AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGG
* * * * *
19041 AACAAGACAAGAAAAGTGTGATCATCCGACCAGGAAGGGGCATTTTTGG
1 AATAAGA-AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGG
*
19090 AAT-AGAAAG-AAACTGTGACCTTCCAACCGGGAAGGGGCATTTTTGG
1 AATAAGAAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGG
* * * * *
19136 AATAAGAGAAGAACACTGTGACCTTCCGACCAGGAAGGTGTATTTTGGG
1 AATAAGA-AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGG
* * *
19185 AATAAGAAAAGAAAACTGTGACCTTCTGACTGGGAAGGGGCATTTTTGT
1 AATAAG-AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGG
* *
19234 AATAAAACAAGAAAAGTGTGACCTTCCGACCGGGAAGGGGCATTTTTGG
1 AATAAGA-AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGG
*
19283 AAT-AGAAAG-AAACTGTGACCTTCCGACTGGGAAGGGGCATTTTTGG
1 AATAAGAAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGG
* * * *
19329 AATAAGAGAAGAACACTATGACCTTCCGACTGGGAACGGGCATTTTTGG
1 AATAAGA-AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGG
* * *
19378 AAT-A-AAA-AAAACTGTGACCTTCCAACCAGGAAGGGTCATTTTTGG
1 AATAAGAAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGG
* * * *
19423 AATAAAACAAGAAAAGTGTTACCTTCCGACCGGGAAGGGACATTTTTGG
1 AATAAGA-AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGG
*
19472 AAT-AGAAAG-AAACTGTGACTTTCCGACCGGGAAGGGGCATTTTTGG
1 AATAAGAAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGG
* * *
19518 AATAAGAGAAGAACACTGTGACCTTCCAACTGGGAAGGGGCA-TTTTGG
1 AATAAGA-AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGG
19566 AATAA
1 AATAA
19571 AAACAATTAG
Statistics
Matches: 452, Mismatches: 63, Indels: 31
0.83 0.12 0.06
Matches are distributed among these distances:
45 34 0.08
46 112 0.25
47 20 0.04
48 31 0.07
49 254 0.56
50 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (48 bp):
AATAAGAAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGG
Found at i:19167 original size:95 final size:95
Alignment explanation
Indices: 19004--19569 Score: 722
Period size: 95 Copynumber: 5.9 Consensus size: 95
18994 TAAGAGAAGA
* * * * * * * * *
19004 AAACTATGACCTTTCGATCGGGAAGAGGCAGTTTTGGAACAAGACAAGAAAAGTGTGATCATCCG
1 AAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGACAAGAAAACTGTGACCTTCCG
*
19069 ACCAGGAAGGGGCATTTTTGGAATAGAAAG
66 ACCGGGAAGGGGCATTTTTGGAATAGAAAG
* * *
19099 AAACTGTGACCTTCCAACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAACACTGTGACCTTCCG
1 AAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGACAAGAAAACTGTGACCTTCCG
* * * *
19164 ACCAGGAAGGTGTATTTTGGGAATAAGAAAAG
66 ACCGGGAAGGGGCATTTTTGGAAT-AG-AAAG
* * * * *
19196 AAAACTGTGACCTTCTGACTGGGAAGGGGCATTTTTGTAATAAAACAAGAAAAGTGTGACCTTCC
1 -AAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGACAAGAAAACTGTGACCTTCC
19261 GACCGGGAAGGGGCATTTTTGGAATAGAAAG
65 GACCGGGAAGGGGCATTTTTGGAATAGAAAG
* * * *
19292 AAACTGTGACCTTCCGACTGGGAAGGGGCATTTTTGGAATAAGAGAAGAACACTATGACCTTCCG
1 AAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGACAAGAAAACTGTGACCTTCCG
* * *
19357 ACTGGGAACGGGCATTTTTGGAATA-AAAA
66 ACCGGGAAGGGGCATTTTTGGAATAGAAAG
* * * * * *
19386 AAACTGTGACCTTCCAACCAGGAAGGGTCATTTTTGGAATAAAACAAGAAAAGTGTTACCTTCCG
1 AAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGACAAGAAAACTGTGACCTTCCG
*
19451 ACCGGGAAGGGACATTTTTGGAATAGAAAG
66 ACCGGGAAGGGGCATTTTTGGAATAGAAAG
* * * *
19481 AAACTGTGACTTTCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAACACTGTGACCTTCCA
1 AAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGACAAGAAAACTGTGACCTTCCG
*
19546 ACTGGGAAGGGGCA-TTTTGGAATA
66 ACCGGGAAGGGGCATTTTTGGAATA
19570 AAAACAATTA
Statistics
Matches: 404, Mismatches: 63, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
94 90 0.22
95 225 0.56
96 6 0.01
97 6 0.01
98 77 0.19
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (95 bp):
AAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGACAAGAAAACTGTGACCTTCCG
ACCGGGAAGGGGCATTTTTGGAATAGAAAG
Found at i:19489 original size:189 final size:188
Alignment explanation
Indices: 19024--19573 Score: 814
Period size: 189 Copynumber: 2.9 Consensus size: 188
19014 CTTTCGATCG
* * * * * * *
19024 GGAAGAGGCAGTTTTGGAACAAGACAAGAAAAGTGTGATCATCCGACCAGGAAGGGGCATTTTTG
1 GGAAGGGGCATTTTTGGAATAAAACAAGAAAAGTGTGACCTTCCGACCGGGAAGGGGCATTTTTG
*
19089 GAATAGAAAGAAACTGTGACCTTCCAACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAACACTG
66 GAATAGAAAGAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAACACTG
** * * ** **
19154 TGACCTTCCGACCAGGAAGGTGTATTTTGGGAATAAGAAAAGAAAACTGTGACCTTCTGACTG
131 TGACCTTCCGACTGGGAAGG-GCATTTTTGGAAT---AAAA-AAAACTGTGACCTTCCAACCA
*
19217 GGAAGGGGCATTTTTGTAATAAAACAAGAAAAGTGTGACCTTCCGACCGGGAAGGGGCATTTTTG
1 GGAAGGGGCATTTTTGGAATAAAACAAGAAAAGTGTGACCTTCCGACCGGGAAGGGGCATTTTTG
* *
19282 GAATAGAAAGAAACTGTGACCTTCCGACTGGGAAGGGGCATTTTTGGAATAAGAGAAGAACACTA
66 GAATAGAAAGAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAACACTG
19347 TGACCTTCCGACTGGGAACGGGCATTTTTGGAATAAAAAAAACTGTGACCTTCCAACCA
131 TGACCTTCCGACTGGGAA-GGGCATTTTTGGAATAAAAAAAACTGTGACCTTCCAACCA
* * *
19406 GGAAGGGTCATTTTTGGAATAAAACAAGAAAAGTGTTACCTTCCGACCGGGAAGGGACATTTTTG
1 GGAAGGGGCATTTTTGGAATAAAACAAGAAAAGTGTGACCTTCCGACCGGGAAGGGGCATTTTTG
*
19471 GAATAGAAAGAAACTGTGACTTTCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAACACTG
66 GAATAGAAAGAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAACACTG
*
19536 TGACCTTCCAACTGGGAAGGGGCA-TTTTGGAATAAAAA
131 TGACCTTCCGACTGGGAA-GGGCATTTTTGGAATAAAAA
19574 CAATTAGATA
Statistics
Matches: 328, Mismatches: 28, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
188 14 0.04
189 162 0.49
190 4 0.01
193 146 0.45
194 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (188 bp):
GGAAGGGGCATTTTTGGAATAAAACAAGAAAAGTGTGACCTTCCGACCGGGAAGGGGCATTTTTG
GAATAGAAAGAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAACACTG
TGACCTTCCGACTGGGAAGGGCATTTTTGGAATAAAAAAAACTGTGACCTTCCAACCA
Found at i:19807 original size:40 final size:41
Alignment explanation
Indices: 19583--19809 Score: 221
Period size: 41 Copynumber: 5.5 Consensus size: 41
19573 ACAATTAGAT
* * *
19583 AACACCTTCCGAT-TGGAAGGGCAAACTGGG-AATGGAAAC
1 AACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAGTAAAC
* *
19622 AACACCTTCCGATGGGGAAAGGCAAACTGGGAAATGTAAAC
1 AACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAGTAAAC
** *
19663 AACACCTTCCGACCGGGAAGGG-AGAA-TAGGAAAAAGTAAAC
1 AACACCTTCCGATGGGGAAGGGCA-AACT-GGGAAAAGTAAAC
* * * *
19704 GACACCTTCCGGTGGGGAAGGGGAAACTAGGAAAATGACAACTAAAC
1 AACACCTTCCGATGGGGAAGGGCAAACTGGGAAAA-G-----TAAAC
* *
19751 AACACCTTCCGATGGGGAAGGGTAAA-TGGGAAAACTAAAC
1 AACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAGTAAAC
19791 AACACCTTCCGATGGGGAA
1 AACACCTTCCGATGGGGAA
19810 TAAGAGGATT
Statistics
Matches: 157, Mismatches: 19, Indels: 23
0.79 0.10 0.12
Matches are distributed among these distances:
39 13 0.08
40 41 0.26
41 65 0.41
42 3 0.02
46 7 0.04
47 28 0.18
ACGTcount: A:0.39, C:0.20, G:0.28, T:0.14
Consensus pattern (41 bp):
AACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAGTAAAC
Found at i:20556 original size:31 final size:31
Alignment explanation
Indices: 20494--20557 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
20484 ATTTCATTTT
*
20494 TTACTTAAAAATTCAATCCTTATTTACAAAA
1 TTACTTAAAAATTCAATCCTTAATTACAAAA
* * *
20525 TTACTTGAAAGTTCAATCTTTTAATTA-AAAA
1 TTACTTAAAAATTCAATC-CTTAATTACAAAA
20556 TT
1 TT
20558 CAATCTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 22 0.79
32 6 0.21
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (31 bp):
TTACTTAAAAATTCAATCCTTAATTACAAAA
Found at i:20618 original size:51 final size:50
Alignment explanation
Indices: 20492--20641 Score: 160
Period size: 51 Copynumber: 3.0 Consensus size: 50
20482 AGATTTCATT
* * * * *
20492 TTTTACTTAAAAATTCAATCCTTATTTACAAAATTACTTGAAAGTTCAATC
1 TTTTAATTAAAAATCCAATCTTTATATAC-AAATTACTTAAAAGTTCAATC
* *
20543 TTTTAATTAAAAATTCAATCTTTATCAT-CAAATTACTTAAAAGCTTTAATC
1 TTTTAATTAAAAATCCAATCTTTAT-ATACAAATTACTTAAAAG-TTCAATC
* * *
20594 TTTTACTTAAAAATCCAATTTTTATATACAACTTACTTAGAAA-TTCAA
1 TTTTAATTAAAAATCCAATCTTTATATACAAATTACTTA-AAAGTTCAA
20642 CCCTTTCCTT
Statistics
Matches: 85, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
50 19 0.22
51 62 0.73
52 4 0.05
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.42
Consensus pattern (50 bp):
TTTTAATTAAAAATCCAATCTTTATATACAAATTACTTAAAAGTTCAATC
Found at i:25352 original size:10 final size:10
Alignment explanation
Indices: 25337--25364 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
25327 ATGCCCTAAT
25337 TCTCCTCTTA
1 TCTCCTCTTA
25347 TCTCCTCTTA
1 TCTCCTCTTA
25357 TCTCCTCT
1 TCTCCTCT
25365 AACCGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.07, C:0.43, G:0.00, T:0.50
Consensus pattern (10 bp):
TCTCCTCTTA
Found at i:27488 original size:27 final size:27
Alignment explanation
Indices: 27417--27491 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
27407 AAGTGGACTC
* *
27417 AAAATGACCAAAATGCCTAC-AAATGCA
1 AAAATGACCAAAATGCC-CCTGAATGCA
* * *
27444 AGAATGACAAAAATGCCCCTGAATGTA
1 AAAATGACCAAAATGCCCCTGAATGCA
27471 AAAATGACCAAAATGCCCCTG
1 AAAATGACCAAAATGCCCCTG
27492 GGTGACCCTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 1 0.03
27 39 0.98
ACGTcount: A:0.47, C:0.23, G:0.15, T:0.16
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGCA
Found at i:30310 original size:24 final size:24
Alignment explanation
Indices: 30283--30328 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
30273 CAAGGCTTAG
*
30283 ATTGATTCATATGGAAAAGATTAA
1 ATTGACTCATATGGAAAAGATTAA
* *
30307 ATTGACTCGTATGGAAACGATT
1 ATTGACTCATATGGAAAAGATT
30329 TTGGCTTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.33
Consensus pattern (24 bp):
ATTGACTCATATGGAAAAGATTAA
Found at i:30374 original size:93 final size:93
Alignment explanation
Indices: 30215--30392 Score: 248
Period size: 93 Copynumber: 1.9 Consensus size: 93
30205 GAAGTAGGGC
* * * * *
30215 TTGACTCATGTGGAAATGAGTTTGGCTTGTGGAAACGCCTATGTGGCTTGGACGGAACCAAGGCT
1 TTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTGGACAGAACCAAGGCT
* *
30280 TAGATTGATTCATATGGAAAAGATTAAA
66 TAAATTGACTCATATGGAAAAGATTAAA
* * * *
30308 TTGACTCGTATGGAAACGATTTTGGCTTGTGGAAAAGCCTATATGGCTTGGATAGATCCAAGGCT
1 TTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTGGACAGAACCAAGGCT
*
30373 TAAATTGACTCGTATGGAAA
66 TAAATTGACTCATATGGAAA
30393 CGAGTTTGGC
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (93 bp):
TTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTGGACAGAACCAAGGCT
TAAATTGACTCATATGGAAAAGATTAAA
Found at i:30380 original size:69 final size:68
Alignment explanation
Indices: 30303--30689 Score: 629
Period size: 69 Copynumber: 5.7 Consensus size: 68
30293 ATGGAAAAGA
* * *
30303 TTAAATTGACTCGTATGGAAACGATTTTGGCTTGTGGAAAAGCCTATATGGCTTGGATAGATCCA
1 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGAT-GAACCA
30368 AGGC
65 AGGC
30372 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCA
1 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGAT-GAACCA
*
30437 AGCC
65 AGGC
*
30441 TTAAATTGACTCGTATGGAAACGAGTTTGACTTGTGG-AAAGCCTATGTGGCTTGGATGACACCA
1 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGA-ACCA
30505 AGGC
65 AGGC
*
30509 TTAAATTGACTCGTATGGAAACGAGTTTGACTTGTGGAAAAGCCTATGTGGCTTGGATAGAACCA
1 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGAT-GAACCA
30574 AGGC
65 AGGC
30578 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA--TGGCTTGGATGACACCA
1 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGA-ACCA
30641 AGGC
65 AGGC
* *
30645 TT-AATTGACCCGTATGGAAACGAGTTTAGCTTGTGGAAAAGCCTA
1 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
30690 ATTCTTGAAA
Statistics
Matches: 304, Mismatches: 10, Indels: 11
0.94 0.03 0.03
Matches are distributed among these distances:
66 43 0.14
67 22 0.07
68 64 0.21
69 173 0.57
70 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (68 bp):
TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGAACCAA
GGC
Found at i:30550 original size:137 final size:137
Alignment explanation
Indices: 30303--30689 Score: 640
Period size: 137 Copynumber: 2.8 Consensus size: 137
30293 ATGGAAAAGA
* *
30303 TTAAATTGACTCGTATGGAAACGATTTTGGCTTGTGGAAAAGCCTATATGGCTTGGATAGA-TCC
1 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTAT-TGGCTTGGAT-GACACC
* *
30367 AAGGCTTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGG
64 AAGGCTTAAATTGACTCGTATGGAAACGAGTTTGACTTGTGGAAAAGCCTATGTGGCTTGGATAG
30432 AACCAAGCC
129 AACCAAGCC
*
30441 TTAAATTGACTCGTATGGAAACGAGTTTGACTTGTGG-AAAGCCTATGTGGCTTGGATGACACCA
1 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTAT-TGGCTTGGATGACACCA
30505 AGGCTTAAATTGACTCGTATGGAAACGAGTTTGACTTGTGGAAAAGCCTATGTGGCTTGGATAGA
65 AGGCTTAAATTGACTCGTATGGAAACGAGTTTGACTTGTGGAAAAGCCTATGTGGCTTGGATAGA
*
30570 ACCAAGGC
130 ACCAAGCC
30578 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA-TGGCTTGGATGACACCAA
1 TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATTGGCTTGGATGACACCAA
*
30642 GGCTT-AATTGACCCGTATGGAAACGAGTTT-AGCTTGTGGAAAAGCCTA
66 GGCTTAAATTGACTCGTATGGAAACGAGTTTGA-CTTGTGGAAAAGCCTA
30690 ATTCTTGAAA
Statistics
Matches: 237, Mismatches: 9, Indels: 9
0.93 0.04 0.04
Matches are distributed among these distances:
134 1 0.00
135 40 0.17
136 25 0.11
137 128 0.54
138 43 0.18
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (137 bp):
TTAAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATTGGCTTGGATGACACCAA
GGCTTAAATTGACTCGTATGGAAACGAGTTTGACTTGTGGAAAAGCCTATGTGGCTTGGATAGAA
CCAAGCC
Found at i:31568 original size:50 final size:50
Alignment explanation
Indices: 31505--31602 Score: 169
Period size: 50 Copynumber: 2.0 Consensus size: 50
31495 AATGCCCTTG
31505 GAAAAGCGAATTTTGATCTTGGACTCACAAATGAAATGCAATCTTGTTTT
1 GAAAAGCGAATTTTGATCTTGGACTCACAAATGAAATGCAATCTTGTTTT
* * *
31555 GAAAAGCGGATTTTGATTTTGGACTCACAAATGGAATGCAATCTTGTT
1 GAAAAGCGAATTTTGATCTTGGACTCACAAATGAAATGCAATCTTGTT
31603 ATAAAACTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (50 bp):
GAAAAGCGAATTTTGATCTTGGACTCACAAATGAAATGCAATCTTGTTTT
Found at i:31900 original size:17 final size:18
Alignment explanation
Indices: 31870--31909 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
31860 CCCTAAAGCC
31870 TCTTTTTTCATTTTTTTT
1 TCTTTTTTCATTTTTTTT
31888 TCTTTTTTC-TTTTTTTT
1 TCTTTTTTCATTTTTTTT
31905 TCTTT
1 TCTTT
31910 CATTTTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (18 bp):
TCTTTTTTCATTTTTTTT
Found at i:31902 original size:14 final size:15
Alignment explanation
Indices: 31875--31917 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
31865 AAGCCTCTTT
31875 TTTCATTTTTTTTTC
1 TTTCATTTTTTTTTC
31890 TTTTTTC-TTTTTTTTTC
1 ---TTTCATTTTTTTTTC
31907 TTTCATTTTTT
1 TTTCATTTTTT
31918 ACATGCACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.17
15 6 0.25
17 10 0.42
18 4 0.17
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTCATTTTTTTTTC
Found at i:32511 original size:12 final size:12
Alignment explanation
Indices: 32494--32547 Score: 53
Period size: 11 Copynumber: 4.8 Consensus size: 12
32484 TAGGCCAAGG
32494 TTTTTCTTTTCT
1 TTTTTCTTTTCT
*
32506 TTTTTCTCTT-T
1 TTTTTCTTTTCT
32517 TTTTTC--TTCT
1 TTTTTCTTTTCT
*
32527 TTTTT-TTTCCT
1 TTTTTCTTTTCT
32538 TTTTTACTTT
1 TTTTT-CTTT
32548 GAATGCGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
9 2 0.06
10 6 0.17
11 15 0.43
12 9 0.26
13 3 0.09
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:32515 original size:14 final size:13
Alignment explanation
Indices: 32494--32542 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 13
32484 TAGGCCAAGG
*
32494 TTTTTCT-TTTCT
1 TTTTTCTCTTTTT
32506 TTTTTCTCTTTTT
1 TTTTTCTCTTTTT
*
32519 TTTCT-TC-TTTT
1 TTTTTCTCTTTTT
32530 TTTTTC-CTTTTT
1 TTTTTCTCTTTTT
32542 T
1 T
32543 ACTTTGAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 9 0.29
12 14 0.45
13 8 0.26
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTCTCTTTTT
Found at i:32524 original size:23 final size:23
Alignment explanation
Indices: 32494--32542 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
32484 TAGGCCAAGG
32494 TTTTTCTT-TTCTTTTTTCTCTTT
1 TTTTTCTTCTTCTTTTTTC-CTTT
*
32517 TTTTTCTTCTTTTTTTTTCCTTT
1 TTTTTCTTCTTCTTTTTTCCTTT
32540 TTT
1 TTT
32543 ACTTTGAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTCTTCTTCTTTTTTCCTTT
Found at i:33145 original size:33 final size:33
Alignment explanation
Indices: 33079--33145 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
33069 TAACTTTGGA
*
33079 AAACCATTTTATCAAAACCTTTTGAAAATCATG
1 AAACCATTTTATCAAAACCTTTTGAAAACCATG
*
33112 AAACCATTTTATCAAAACCTTTTGAAACCCATG
1 AAACCATTTTATCAAAACCTTTTGAAAACCATG
33145 A
1 A
33146 CTCTTTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (33 bp):
AAACCATTTTATCAAAACCTTTTGAAAACCATG
Found at i:33176 original size:30 final size:31
Alignment explanation
Indices: 33125--33188 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
33115 CCATTTTATC
*
33125 AAAACCTTTTGAAACCCATGACTCTTTTTGA
1 AAAACCTTTTGAAACCCATGACTCTTTTTCA
33156 AAAACCTTTTGAAA-CCATGACTCTTTTTCA
1 AAAACCTTTTGAAACCCATGACTCTTTTTCA
33186 AAA
1 AAA
33189 CCATCGTTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 18 0.56
31 14 0.44
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (31 bp):
AAAACCTTTTGAAACCCATGACTCTTTTTCA
Found at i:33227 original size:15 final size:15
Alignment explanation
Indices: 33207--33253 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
33197 GCTTTTTCTC
33207 TTTTTTTCTTTCTTT
1 TTTTTTTCTTTCTTT
*
33222 TTTTTTTCTTTCTCT
1 TTTTTTTCTTTCTTT
* *
33237 TCTTCTTC-TTCTTT
1 TTTTTTTCTTTCTTT
33251 TTT
1 TTT
33254 ATCATTTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 7 0.26
15 20 0.74
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTTCTTTCTTT
Found at i:33262 original size:29 final size:28
Alignment explanation
Indices: 33200--33262 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 28
33190 CATCGTTGCT
* **
33200 TTTTCTCTTTTTTTCTTTCTTTTTTTTT
1 TTTTCTCTTTTCTTCTTTCTTTTTTTCA
33228 TCTTTCTCTTCTTCTTC-TTCTTTTTTATCA
1 T-TTTCTCTT-TTCTTCTTTCTTTTTT-TCA
33258 TTTTC
1 TTTTC
33263 ATCATCATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.03
29 21 0.72
30 7 0.24
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (28 bp):
TTTTCTCTTTTCTTCTTTCTTTTTTTCA
Found at i:37617 original size:35 final size:35
Alignment explanation
Indices: 37567--37728 Score: 288
Period size: 35 Copynumber: 4.6 Consensus size: 35
37557 AGTAATAAGT
* *
37567 AACTTAATTCGGGGTAATTAAGTAATTCAGGAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* *
37602 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
37637 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
37672 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
37707 AACTTAATTCAGGGTAATTAAG
1 AACTTAATTCAGGGTAATTAAG
37729 AGCTCGTTTG
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 121 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (35 bp):
AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
Found at i:38071 original size:16 final size:16
Alignment explanation
Indices: 38050--38097 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 16
38040 AGCGCAGCAA
38050 AAACAAAACGAAAACG
1 AAACAAAACGAAAACG
*
38066 AAACAAAAACAAAAAC-
1 AAAC-AAAACGAAAACG
*
38082 AGA-AAAACGAAAACG
1 AAACAAAACGAAAACG
38097 A
1 A
38098 TGCCAAACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 10 0.37
15 1 0.04
16 6 0.22
17 10 0.37
ACGTcount: A:0.73, C:0.17, G:0.10, T:0.00
Consensus pattern (16 bp):
AAACAAAACGAAAACG
Found at i:38073 original size:22 final size:25
Alignment explanation
Indices: 38047--38093 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
38037 GACAGCGCAG
38047 CAAAAAC-AAAAC-G-AAAACGAAA
1 CAAAAACAAAAACAGAAAAACGAAA
38069 CAAAAACAAAAACAGAAAAACGAAA
1 CAAAAACAAAAACAGAAAAACGAAA
38094 ACGATGCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.32
23 5 0.23
24 1 0.05
25 9 0.41
ACGTcount: A:0.74, C:0.17, G:0.09, T:0.00
Consensus pattern (25 bp):
CAAAAACAAAAACAGAAAAACGAAA
Found at i:38159 original size:35 final size:35
Alignment explanation
Indices: 38113--38327 Score: 306
Period size: 35 Copynumber: 6.1 Consensus size: 35
38103 AACAACCCCA
*
38113 AAGTGATTCAGTAATCAACTTAATTCAGGGTAATT
1 AAGTGAGTCAGTAATCAACTTAATTCAGGGTAATT
*
38148 AAGTGAGTCAGTAGTCAACTTAATTCAGGGTAATT
1 AAGTGAGTCAGTAATCAACTTAATTCAGGGTAATT
* * *
38183 AAGTAATTCAGTAATTAACTTAATTCAGGGTAATT
1 AAGTGAGTCAGTAATCAACTTAATTCAGGGTAATT
* * *
38218 AAGTGAGTCGGTAATCAACTTAATCCAGGATAATT
1 AAGTGAGTCAGTAATCAACTTAATTCAGGGTAATT
*
38253 AAGTGAGTCAGTAATCAACTGTAATTCAGGATAATT
1 AAGTGAGTCAGTAATCAACT-TAATTCAGGGTAATT
* *
38289 AAGTGAGTTAATAAGT-AACTTAATTCAGGGTAATT
1 AAGTGAGTCAGTAA-TCAACTTAATTCAGGGTAATT
38324 AAGT
1 AAGT
38328 TTAGTAAGAA
Statistics
Matches: 161, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
35 130 0.81
36 30 0.19
37 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (35 bp):
AAGTGAGTCAGTAATCAACTTAATTCAGGGTAATT
Found at i:39269 original size:24 final size:23
Alignment explanation
Indices: 39238--39282 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
39228 TTGTCTGCTT
39238 GCATTTTATTC-TTGTTTATTCAC
1 GCATTTTA-TCATTGTTTATTCAC
39261 GCATGTTTATCATTGTTTATTC
1 GCAT-TTTATCATTGTTTATTC
39283 TTTCCTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.56
Consensus pattern (23 bp):
GCATTTTATCATTGTTTATTCAC
Done.