Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017107.1 Corchorus olitorius cultivar O-4 contig17140, 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: 61171
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:17959 original size:14 final size:14
Alignment explanation
Indices: 17942--17969 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17932 TACACCAGGA
17942 AAATGACGATCGAC
1 AAATGACGATCGAC
17956 AAATGACGATCGAC
1 AAATGACGATCGAC
17970 GATAACAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
AAATGACGATCGAC
Found at i:21479 original size:399 final size:394
Alignment explanation
Indices: 20738--21533 Score: 1441
Period size: 399 Copynumber: 2.0 Consensus size: 394
20728 AGCATGTGAG
20738 TTACTGTTCATCAATATGCTTTTGTGTTTTGGAAAAACATGAAAACACAAAATTTTTGCTTCTAC
1 TTACTGTTCATCAATATGCTTTTGTGTTTTGGAAAAACATGAAAACACAAAATTTTTGCTTCTAC
*
20803 TTTTTTCCAAAACACTGCTTTATTTTCAAAATGGAAACGAAAACAGCCTGTCAAACATGTTTTCA
66 TTTTTTCCAAAACACTGCTTTATTTTCAAAATGGAAACGAAAACAGCCTGCCAAACATGTTTTCA
* *
20868 CTGTTTTGTTTTCAAAGACAAAATTAGCAACAGAAAACAGGATACGGAAATGATGCCAAACAAAC
131 CTGTTTTGTTTCCAAAGACAAAATTAGCAACAGAAAACAGGATACGGAAACGATGCCAAACAAAC
*
20933 TCAATTATTTTTTTAGTTATCGAAATAATACTTTCATTTTTTTTTTCAACTTAAGAGCCATAAAA
196 TCAATTATTTTTTTAGTTATCGAAATAAAACTTTCATTTTTTTTTTCAACTTAAGAGCCATAAAA
20998 AAAATGTCAAAGCCATAGCATTTGATAGTATTTTGTTTATATATAGCTTATCAAAGCCCGGCCCG
261 AAAATGTCAAAGCCATAGCATTTGATAGTATTTTGTTTATATATAGCTTATCAAAGCCCGGCCCG
* **
21063 ACTAAGTGGGCTTCTATTTATGCCCAAGCCTGTCCAATGATTGTCCAAGATTTGTCCAAACTCAT
326 ACTAAGCGGGCTTCTATTTATGCCCAAGCCTGTCCAATGATTGTCCAAGATCCGTCCAAACTCAT
21128 CTGT
391 CTGT
21132 TTACTGTTCATCAATATGCTTTTGTGTTTTGGAAAAACATGAAAACACAAAATTTTTGCTTCTAC
1 TTACTGTTCATCAATATGCTTTTGTGTTTTGGAAAAACATGAAAACACAAAATTTTTGCTTCTAC
*
21197 TTTTTTCCAAAACACTGCTTTTGTTTTCAAAATTTTTGGAAACGAAAACAGCCTGCCAAACATGT
66 TTTTTTCCAAAACACTGC-TTTATTTTCAAAA----TGGAAACGAAAACAGCCTGCCAAACATGT
21262 TTTCACTGTTTTGTTTCCAAAGACAAAATTAGCAACAGAAAACAGGATACGGAAACGATGCCAAA
126 TTTCACTGTTTTGTTTCCAAAGACAAAATTAGCAACAGAAAACAGGATACGGAAACGATGCCAAA
*
21327 CAAACTCAATTATTCTTTTTAGTTATCGGAATAAAACTTTCA-TTTTTTTTTCAACTTAAGAGCC
191 CAAACTCAATTATT-TTTTTAGTTATCGAAATAAAACTTTCATTTTTTTTTTCAACTTAAGAGCC
21391 ATAAAAAAAATGTCAAAGCCATAGCATTTGATAGTATTTTGTTTATATATAGCTTATCAAAGCCC
255 ATAAAAAAAATGTCAAAGCCATAGCATTTGATAGTATTTTGTTTATATATAGCTTATCAAAGCCC
*
21456 GGCCCGACTAAGCGGGTTTCTATTTATGCCCAAGCCTGTCCAATGATTGTCCAAGATCCGTCCAA
320 GGCCCGACTAAGCGGGCTTCTATTTATGCCCAAGCCTGTCCAATGATTGTCCAAGATCCGTCCAA
21521 ACTCATCTGT
385 ACTCATCTGT
21531 TTA
1 TTA
21534 GTAAAAGTAA
Statistics
Matches: 386, Mismatches: 10, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
394 83 0.22
395 12 0.03
399 266 0.69
400 25 0.06
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (394 bp):
TTACTGTTCATCAATATGCTTTTGTGTTTTGGAAAAACATGAAAACACAAAATTTTTGCTTCTAC
TTTTTTCCAAAACACTGCTTTATTTTCAAAATGGAAACGAAAACAGCCTGCCAAACATGTTTTCA
CTGTTTTGTTTCCAAAGACAAAATTAGCAACAGAAAACAGGATACGGAAACGATGCCAAACAAAC
TCAATTATTTTTTTAGTTATCGAAATAAAACTTTCATTTTTTTTTTCAACTTAAGAGCCATAAAA
AAAATGTCAAAGCCATAGCATTTGATAGTATTTTGTTTATATATAGCTTATCAAAGCCCGGCCCG
ACTAAGCGGGCTTCTATTTATGCCCAAGCCTGTCCAATGATTGTCCAAGATCCGTCCAAACTCAT
CTGT
Found at i:23103 original size:129 final size:128
Alignment explanation
Indices: 22905--23143 Score: 304
Period size: 129 Copynumber: 1.9 Consensus size: 128
22895 AACTGAATAA
* * *
22905 AATACATGATTTTATGATCAACAAATGTGTTTACATTAAATTGATTAAAAACCCTTGTAATTACA
1 AATACATGATTTTATGATCAACAAATGTGTTCACATTAAACTGATTAAAAACCCTTGCAATTAC-
*
22970 AAAAAAAGGCCGGAAGAAAAAGTG-ATGGTGAAAAACTAATTGAGGGTCTTCTTCGTAAATAAAT
65 AAAAAAAGGCCGG-AGAAAAAGGGAATGGTGAAAAACTAATTGAGGGTCTTCTTCGTAAATAAAT
* * * *
23034 AATACATGATTTTATGGTCAATAAATGCT-TTCACATTCAACTGATTAAAAACCTTTGCAATTAT
1 AATACATGATTTTATGATCAACAAATG-TGTTCACATTAAACTGATTAAAAACCCTTGCAATTA-
* * * * *
23098 C-AAAAAGGGCTGGAGGAGAAGGGAATGGTGAGAAACTAATTGAGGG
64 CAAAAAAAGGCCGGAGAAAAAGGGAATGGTGAAAAACTAATTGAGGG
23144 CTTTCTTAGT
Statistics
Matches: 94, Mismatches: 13, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
127 7 0.07
128 31 0.33
129 54 0.57
130 2 0.02
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.28
Consensus pattern (128 bp):
AATACATGATTTTATGATCAACAAATGTGTTCACATTAAACTGATTAAAAACCCTTGCAATTACA
AAAAAAGGCCGGAGAAAAAGGGAATGGTGAAAAACTAATTGAGGGTCTTCTTCGTAAATAAAT
Found at i:26559 original size:19 final size:18
Alignment explanation
Indices: 26519--26560 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
26509 TATTAATTAT
* *
26519 TTTAATATTATATTTTTA
1 TTTAATATTACACTTTTA
26537 TTTATATATTACACTTTTA
1 TTTA-ATATTACACTTTTA
26556 TTTAA
1 TTTAA
26561 AAACTACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATATTACACTTTTA
Found at i:27124 original size:26 final size:25
Alignment explanation
Indices: 27072--27124 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
27062 TGCATGTTCC
27072 AAAGTAGTACTTAAAAGATTGAAAAA
1 AAAGTAGTACTTAAAAGA-TGAAAAA
*
27098 AAAGTAGTACTTAAAAGA-GAAATA
1 AAAGTAGTACTTAAAAGATGAAAAA
27122 AAA
1 AAA
27125 CAAGTCAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 8 0.31
26 18 0.69
ACGTcount: A:0.60, C:0.04, G:0.15, T:0.21
Consensus pattern (25 bp):
AAAGTAGTACTTAAAAGATGAAAAA
Found at i:34597 original size:39 final size:40
Alignment explanation
Indices: 34541--34621 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
34531 TTTAATTCCT
34541 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
34581 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
34620 AT
1 AT
34622 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:34648 original size:25 final size:24
Alignment explanation
Indices: 34612--34658 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
34602 AATACTTACA
34612 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
34636 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
34659 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Found at i:35683 original size:36 final size:36
Alignment explanation
Indices: 35636--35705 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
35626 AAGATTTTGG
* *
35636 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
35672 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
35706 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:38266 original size:11 final size:11
Alignment explanation
Indices: 38233--38284 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
38223 GTTTGACATC
*
38233 GTTTTCGTTTT
1 GTTTTTGTTTT
38244 -TTTGTT-TTTT
1 GTTT-TTGTTTT
38254 GTTTTTGTTTT
1 GTTTTTGTTTT
*
38265 GTTTTCGTTTT
1 GTTTTTGTTTT
38276 GTTTTTGTT
1 GTTTTTGTT
38285 GCGCTGTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
10 9 0.26
11 26 0.74
ACGTcount: A:0.00, C:0.04, G:0.17, T:0.79
Consensus pattern (11 bp):
GTTTTTGTTTT
Found at i:38281 original size:6 final size:6
Alignment explanation
Indices: 38242--38284 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
38232 CGTTTTCGTT
*
38242 TTTTTG TTTTTTG TTTTTG -TTTTG TTTTCG -TTTTG TTTTTG TT
1 TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TT
38285 GCGCTGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 9 0.28
6 17 0.53
7 6 0.19
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.81
Consensus pattern (6 bp):
TTTTTG
Found at i:39400 original size:19 final size:20
Alignment explanation
Indices: 39370--39433 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
39360 TTGACACTGT
39370 TTAGCAACTGTACATATGAGA
1 TTAGC-ACTGTACATATGAGA
*
39391 TTA-CACTGTACATATTAGA
1 TTAGCACTGTACATATGAGA
* *
39410 TTAGGTACTGTACAGATGAGA
1 TTA-GCACTGTACATATGAGA
39431 TTA
1 TTA
39434 TTAGAGCAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.46
20 1 0.03
21 19 0.51
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
TTAGCACTGTACATATGAGA
Found at i:39421 original size:21 final size:19
Alignment explanation
Indices: 39376--39433 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
39366 CTGTTTAGCA
39376 ACTGTACATATGAGATTAC
1 ACTGTACATATGAGATTAC
* *
39395 ACTGTACATATTAGATTAGGT
1 ACTGTACATATGAGATTA--C
*
39416 ACTGTACAGATGAGATTA
1 ACTGTACATATGAGATTA
39434 TTAGAGCAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (19 bp):
ACTGTACATATGAGATTAC
Found at i:45771 original size:15 final size:15
Alignment explanation
Indices: 45752--45798 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
45742 GACCTTTTTC
*
45752 AAAAATGATTTTCAA
1 AAAAATGACTTTCAA
* *
45767 GAAAA-GGCTTTCAA
1 AAAAATGACTTTCAA
45781 AAAAATGACTTTCCAA
1 AAAAATGACTTT-CAA
45797 AA
1 AA
45799 TGAGTTTTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 11 0.44
15 9 0.36
16 5 0.20
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.26
Consensus pattern (15 bp):
AAAAATGACTTTCAA
Found at i:46492 original size:10 final size:10
Alignment explanation
Indices: 46449--46508 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
46439 GAAGCAATCT
*
46449 AAAGAAAAAG
1 AAAGAAAAAA
* *
46459 AAA-AAAGAG
1 AAAGAAAAAA
46468 AAAGCAAAGAAA
1 AAAG-AAA-AAA
46480 AAAGTGAAAAAA
1 AAA--GAAAAAA
46492 AAAGAAAAAA
1 AAAGAAAAAA
46502 AAAGAAA
1 AAAGAAA
46509 GAAAGAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
9 8 0.19
10 17 0.40
11 3 0.07
12 10 0.24
13 3 0.07
14 1 0.02
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:46503 original size:14 final size:15
Alignment explanation
Indices: 46449--46519 Score: 53
Period size: 14 Copynumber: 4.9 Consensus size: 15
46439 GAAGCAATCT
46449 AAAGAAA-AAGAAAAA
1 AAAGAAAGAA-AAAAA
* *
46464 AGAGAAAGCAAAGAAA
1 AAAGAAAG-AAAAAAA
*
46480 AAAG--TG-AAAAAA
1 AAAGAAAGAAAAAAA
*
46492 AAAGAAA-AAAAAAG
1 AAAGAAAGAAAAAAA
46506 AAAGAAAGAAAAAA
1 AAAGAAAGAAAAAA
46520 TCAAAAGGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
12 9 0.21
14 13 0.30
15 12 0.28
16 7 0.16
17 2 0.05
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.01
Consensus pattern (15 bp):
AAAGAAAGAAAAAAA
Found at i:46530 original size:18 final size:17
Alignment explanation
Indices: 46455--46519 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 17
46445 ATCTAAAGAA
*
46455 AAAGAAAAAAGAGAAAG
1 AAAGAAAAAAGAAAAAG
*
46472 CAAAGAAAAAAGTGAAAAAA
1 -AAAGAAAAAA--GAAAAAG
*
46492 AAAGAAAAAAAAAGAAAG
1 AAAGAAAAAAGAA-AAAG
46510 AAAGAAAAAA
1 AAAGAAAAAA
46520 TCAAAAGGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.05
18 23 0.57
19 10 0.25
20 5 0.12
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (17 bp):
AAAGAAAAAAGAAAAAG
Found at i:46532 original size:37 final size:37
Alignment explanation
Indices: 46444--46532 Score: 110
Period size: 37 Copynumber: 2.4 Consensus size: 37
46434 ATGGTGAAGC
* *
46444 AATCTAAAGAAAAAGAAAAAAGAGAAAGCAAAGAAAA
1 AATCAAAAGAAAAAGAAAAAAAAGAAAGCAAAGAAAA
*
46481 AAGTGAAAA-AAAAAGAAAAAAAAAGAAAG-AAAGAAAA
1 AA-TCAAAAGAAAAAG-AAAAAAAAGAAAGCAAAGAAAA
*
46518 AATCAAAAGGAAAAG
1 AATCAAAAGAAAAAG
46533 GTTCAAATTG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
36 5 0.11
37 23 0.52
38 16 0.36
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.04
Consensus pattern (37 bp):
AATCAAAAGAAAAAGAAAAAAAAGAAAGCAAAGAAAA
Found at i:47565 original size:74 final size:73
Alignment explanation
Indices: 47470--47928 Score: 571
Period size: 74 Copynumber: 6.2 Consensus size: 73
47460 ACGAAATTCA
* * *
47470 GTCTCATCAAAACCTTGTTCAAGATTTCTGTTTAGGTGTCTTATTAAATCCTTATTTAAGGTCCA
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC-
47535 TGTTTAGGT
65 TGTTTAGGT
* *
47544 GTTTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGT-CC
*
47609 TATTTAGGT
65 TGTTTAGGT
* * * * * * *
47618 GTCTTAT-TAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTTATCAAATCCTTATTTAAAGTCC
1 GTCTCATCAAAAT-CTTGTTCAAGATTCCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
*
47682 TTATTTAGGT
65 -TGTTTAGGT
* * *
47692 GTCTCATCAAAATCTTGTTTAAGA-TCCTTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTGT
1 GTCTCATCAAAATCTTGTTCAAGATTCC-TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGT-C
47756 CTGTTTAGGT
64 CTGTTTAGGT
* ** * * * *
47766 TTCTTGTCAAAATTTTTGTTTAAGATCCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCC
1 GTCTCATCAAAA-TCTTGTTCAAGATTCCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGT-C
47831 CTGTTTAGGT
64 CTGTTTAGGT
* * *
47841 GTCTCATCAAAATCTTGTTCAAAATTCCTGTTTAGGTTTCTTATTAAATCCTTATTTAAGGTACC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGT-CC
47906 TGTTTAGGT
65 TGTTTAGGT
*
47915 GTCTCTTCAAAATC
1 GTCTCATCAAAATC
47929 CCAGTTTAGG
Statistics
Matches: 336, Mismatches: 41, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
73 8 0.02
74 255 0.76
75 71 0.21
76 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.45
Consensus pattern (73 bp):
GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCT
GTTTAGGT
Found at i:47576 original size:37 final size:37
Alignment explanation
Indices: 47475--47929 Score: 312
Period size: 37 Copynumber: 12.3 Consensus size: 37
47465 ATTCAGTCTC
* *
47475 ATCAAAA-CCTTGTTCAAGATTTCTGTTTAGGTGTCTT
1 ATCAAAATCCTTGTTTAAGATTCCTGTTTAGGTGT-TT
* * *
47512 AT-TAAATCCTTATTTAAG-GTCCATGTTTAGGTGTTT
1 ATCAAAATCCTTGTTTAAGATTCC-TGTTTAGGTGTTT
*
47548 CATCAAAAT-CTTGTTCAAGATTCCTGTTTAGGTGTCTT
1 -ATCAAAATCCTTGTTTAAGATTCCTGTTTAGGTGT-TT
* * *
47586 ATC-AAATCCTTGTTTAAGGTCCCTATTTAGGTGTCTT
1 ATCAAAATCCTTGTTTAAGATTCCTGTTTAGGTGT-TT
* * * *
47623 AT-TAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTT
1 ATCAAAATCCTTGTTTAAGATTCCTGTTTAGGTGT-TT
* * * *
47660 ATC-AAATCCTTATTTAA-AGTCCTTATTTAGGTGTCTC
1 ATCAAAATCCTTGTTTAAGATTCC-TGTTTAGGTGT-TT
*
47697 ATCAAAAT-CTTGTTTAAGA-TCCTTGTTTAGGTTTCTT
1 ATCAAAATCCTTGTTTAAGATTCC-TGTTTAGGTGT-TT
* * *
47734 ATC-AAATCCTTATTTAAGGTGT-CTGTTTAGGTTTCTT
1 ATCAAAATCCTTGTTTAAGAT-TCCTGTTTAGGTGT-TT
* ** * *
47771 GTCAAAATTTTTGTTTAAGATCCCTGTTTAGGTTTCTT
1 ATCAAAATCCTTGTTTAAGATTCCTGTTTAGGTGT-TT
* * * *
47809 ATC-AAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTC
1 ATCAAAATCCTTGTTTAAGATTCCTGTTTAGGTGT-TT
* * *
47846 ATCAAAAT-CTTGTTCAAAATTCCTGTTTAGGTTTCTT
1 ATCAAAATCCTTGTTTAAGATTCCTGTTTAGGTGT-TT
* * * *
47883 AT-TAAATCCTTATTTAAGGTACCTGTTTAGGTGTCTCT
1 ATCAAAATCCTTGTTTAAGATTCCTGTTTAGGTGT-T-T
47921 -TCAAAATCC
1 ATCAAAATCC
47930 CAGTTTAGGT
Statistics
Matches: 343, Mismatches: 54, Indels: 41
0.78 0.12 0.09
Matches are distributed among these distances:
36 21 0.06
37 265 0.77
38 56 0.16
39 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (37 bp):
ATCAAAATCCTTGTTTAAGATTCCTGTTTAGGTGTTT
Found at i:47689 original size:111 final size:111
Alignment explanation
Indices: 47470--47918 Score: 453
Period size: 111 Copynumber: 4.0 Consensus size: 111
47460 ACGAAATTCA
* * * * ** *
47470 GTCTCATCAAAACCTTGTTCAAGATTTCTGTTTAGGTGTCTTATTAAATCCTTATTTAAGGTCCA
1 GTCTTATCAAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTATTAAATCCTTATTTAAGGTCCC
* * *
47535 TGTTTAGGTGT-TTCATCAAAAT-CTTGTTCAAGATTCCTGTTTAGGT
66 TGTTTAGGTGTCTT-ATCAAAATCCTTATTTAA-AGTCCTGTTTAGGT
*
47581 GTCTTATCAAATCCTTGTTTAAGGTCCCTATTTAGGTGTCTTATTAAATCCTTATTTAAGGTCCC
1 GTCTTATCAAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTATTAAATCCTTATTTAAGGTCCC
*
47646 TGTTTAGGTGTCTTATC-AAATCCTTATTTAAAGTCCTTATTTAGGT
66 TGTTTAGGTGTCTTATCAAAATCCTTATTTAAAGTCC-TGTTTAGGT
* * * * * **
47692 GTCTCATCAAAAT-CTTGTTTAAGATCCTTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTGT
1 GTCTTATC-AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTATTAAATCCTTATTTAAGGTCC
* * ** *
47756 CTGTTTAGGTTTCTTGTCAAAATTTTTGTTT-AAGATCCCTGTTTAGGT
65 CTGTTTAGGTGTCTTATCAAAATCCTTATTTAAAG-T-CCTGTTTAGGT
* * * * * * ** *
47804 TTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCAAAAT-CTTGTTCAAAATTC
1 GTCTTATCAAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTAT-TAAATCCTTATTTAAGGTCC
* * *
47868 CTGTTTAGGTTTCTTAT-TAAATCCTTATTTAAGGTACCTGTTTAGGT
65 CTGTTTAGGTGTCTTATCAAAATCCTTATTTAAAGT-CCTGTTTAGGT
47915 GTCT
1 GTCT
47919 CTTCAAAATC
Statistics
Matches: 280, Mismatches: 48, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
110 8 0.03
111 184 0.66
112 82 0.29
113 6 0.02
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.45
Consensus pattern (111 bp):
GTCTTATCAAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTATTAAATCCTTATTTAAGGTCCC
TGTTTAGGTGTCTTATCAAAATCCTTATTTAAAGTCCTGTTTAGGT
Found at i:49568 original size:136 final size:137
Alignment explanation
Indices: 49317--49570 Score: 395
Period size: 136 Copynumber: 1.9 Consensus size: 137
49307 TTATAGTTTT
*
49317 ACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTTTTAC
1 ACTCAACTAAAAACTCTATTTTGATTTAATTAAATCTAATATCCTTATAACTATTTTATTTTTAC
* * * * **
49382 CATTTTATTATTTTAATTAAAAAACTTATATATGATAAAATTTTTTAAATATACTTTTATAGTTT
66 CATTTTACTAATTTAATTAAAAAACTTAGATATGATAAAACTTTAAAAATATACTTTTATAGTTT
49447 TACTTTA
131 TACTTTA
* *
49454 ACTCAACTAACAACTCTATTTTGATTTAA-TAAATCTAATATCCTTATACCTATTTTATTTTTAC
1 ACTCAACTAAAAACTCTATTTTGATTTAATTAAATCTAATATCCTTATAACTATTTTATTTTTAC
*
49518 CATTTTACTAATTTAATTAAAAAACTTAGATAT-ATTAGAACTTTAAAAATATA
66 CATTTTACTAATTTAATTAAAAAACTTAGATATGA-TAAAACTTTAAAAATATA
49571 TTTCTTAAAT
Statistics
Matches: 106, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
135 1 0.01
136 78 0.74
137 27 0.25
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (137 bp):
ACTCAACTAAAAACTCTATTTTGATTTAATTAAATCTAATATCCTTATAACTATTTTATTTTTAC
CATTTTACTAATTTAATTAAAAAACTTAGATATGATAAAACTTTAAAAATATACTTTTATAGTTT
TACTTTA
Found at i:50404 original size:14 final size:14
Alignment explanation
Indices: 50382--50416 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
50372 TTTTTTTACT
*
50382 TTTAT-TTTATTTA
1 TTTATATTTATATA
50395 TTTATATTTATATA
1 TTTATATTTATATA
50409 TTTATATT
1 TTTATATT
50417 ATTAATGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATATTTATATA
Found at i:51679 original size:50 final size:49
Alignment explanation
Indices: 51605--51706 Score: 150
Period size: 50 Copynumber: 2.1 Consensus size: 49
51595 GTAAAACCTA
* *
51605 ATAGAAAAAATCATCAAGTAATTACTAATTAATTATGGATAATTATTTG
1 ATAGAAAAAATCACCAAGAAATTACTAATTAATTATGGATAATTATTTG
* **
51654 ATAGAAAAAAATCGCCAAGAAATTACTAATTGGTTATGGATAATTATTTG
1 ATAG-AAAAAATCACCAAGAAATTACTAATTAATTATGGATAATTATTTG
51704 ATA
1 ATA
51707 CACTGACAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 4 0.09
50 43 0.91
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (49 bp):
ATAGAAAAAATCACCAAGAAATTACTAATTAATTATGGATAATTATTTG
Found at i:52133 original size:20 final size:20
Alignment explanation
Indices: 52092--52154 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 20
52082 TATCAAGTGG
* *
52092 TTTTAGATAT-TTTAGTTCAA
1 TTTTA-ATATATTTAATTTAA
52112 TTTTAATATATTTAATTTAA
1 TTTTAATATATTTAATTTAA
* * *
52132 TTATAAAAATATTAAATTTAA
1 TT-TTAATATATTTAATTTAA
52153 TT
1 TT
52155 AAAAATAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
19 4 0.11
20 15 0.42
21 17 0.47
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (20 bp):
TTTTAATATATTTAATTTAA
Found at i:52143 original size:21 final size:20
Alignment explanation
Indices: 52119--52159 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
52109 CAATTTTAAT
*
52119 ATATTTAATTTAATTATAAAA
1 ATATTAAATTTAATTA-AAAA
52140 ATATTAAATTTAATTAAAAA
1 ATATTAAATTTAATTAAAAA
52160 TAAAAAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATTAAATTTAATTAAAAA
Found at i:52688 original size:41 final size:41
Alignment explanation
Indices: 52631--52710 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
52621 TCGTGCCTTG
* * *
52631 CCATATGGTGAGGCGCCTCCTGGGGATGCCTCCCCATATCC
1 CCATATGGTCAGGCGCCCCCTGGGGACGCCTCCCCATATCC
*
52672 CCATATGGTCAGGCGCCCCCTGGGGACGCCTCGCCATAT
1 CCATATGGTCAGGCGCCCCCTGGGGACGCCTCCCCATAT
52711 GGTTAGGCGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.15, C:0.38, G:0.28, T:0.20
Consensus pattern (41 bp):
CCATATGGTCAGGCGCCCCCTGGGGACGCCTCCCCATATCC
Found at i:53296 original size:13 final size:13
Alignment explanation
Indices: 53278--53302 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53268 TTCAATGTTC
53278 TAAATATTATTTA
1 TAAATATTATTTA
53291 TAAATATTATTT
1 TAAATATTATTT
53303 GTAATTCCAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:58135 original size:6 final size:6
Alignment explanation
Indices: 58124--58150 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
58114 TAAGTCTCTT
58124 TGCTCA TGCTCA TGCTCA TGCTCA TGC
1 TGCTCA TGCTCA TGCTCA TGCTCA TGC
58151 GTTTACATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.19, T:0.33
Consensus pattern (6 bp):
TGCTCA
Found at i:60445 original size:20 final size:20
Alignment explanation
Indices: 60422--60468 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
60412 CCCTTAATCA
*
60422 ATAATTAATTCTAATAATTC
1 ATAATTAATTCCAATAATTC
*
60442 ATAATTAATTCCAATAATTT
1 ATAATTAATTCCAATAATTC
60462 ATAATTA
1 ATAATTA
60469 GAATACATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAATTAATTCCAATAATTC
Done.