Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011458.1 Corchorus olitorius cultivar O-4 contig11491, 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: 63800
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5346 original size:25 final size:25
Alignment explanation
Indices: 5316--5363 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
5306 ATGCAATGTC
5316 AAATTAGATTTGAGCTACATGAATG
1 AAATTAGATTTGAGCTACATGAATG
*
5341 AAATTAGCTTTGAGCTACATGAA
1 AAATTAGATTTGAGCTACATGAA
5364 CGCAAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (25 bp):
AAATTAGATTTGAGCTACATGAATG
Found at i:5619 original size:29 final size:27
Alignment explanation
Indices: 5501--5630 Score: 104
Period size: 29 Copynumber: 4.7 Consensus size: 27
5491 AAGTGGACTC
* *
5501 AAAATGACCAACATGCCCCTGAATATGC-
1 AAAATGACCAAAATGCCCCTG-AT-TTCA
* *
5529 -AAATGACCAAAATG-CCCTTATTGCA
1 AAAATGACCAAAATGCCCCTGATTTCA
* * * *
5554 AAAATGACCATAATGCCACTGAATGTGA
1 AAAATGACCAAAATGCCCCTG-ATTTCA
* *
5582 AAACTGACCAAAATGCCCCTGGATTTTTA
1 AAAATGACCAAAATGCCCCT-GA-TTTCA
5611 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
5631 AGGTGATCCT
Statistics
Matches: 82, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
24 3 0.04
25 2 0.02
26 17 0.21
27 16 0.20
28 21 0.26
29 23 0.28
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.22
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGATTTCA
Found at i:5963 original size:50 final size:50
Alignment explanation
Indices: 5900--6270 Score: 598
Period size: 50 Copynumber: 7.4 Consensus size: 50
5890 GGCAGAGAGA
* *
5900 TTTGGCTTATGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAA
1 TTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG
* *
5950 CTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAG
1 TTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG
* *
6000 TTTGGCTTGTGGAAAAGGCTATGTTGATCATTGACTCGTATGGAAACGAG
1 TTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG
6050 TTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG
1 TTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG
* * *
6100 TTTGGCTTGTGGAAAAGCCCATGTTGATCATTGACTCATATGGAAACGAG
1 TTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG
* * *
6150 TTTGACTTGTGGAAAAGCCCATGTTGATAATTGACTCTTATGGAAACGAG
1 TTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG
* * *
6200 TTTGGCTTGTGGAAAAGCCTGTGTTGATAATTGATTTGTATGGAAACGAG
1 TTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG
*
6250 TTCGGCTTGTGGAAAAGCCTA
1 TTTGGCTTGTGGAAAAGCCTA
6271 AAGCATTCGG
Statistics
Matches: 297, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 297 1.00
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (50 bp):
TTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG
Found at i:6995 original size:50 final size:50
Alignment explanation
Indices: 6929--7375 Score: 689
Period size: 50 Copynumber: 8.9 Consensus size: 50
6919 CTTCACTGTC
* * *
6929 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAACGGAAAGCAATTTTA
1 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
*
6979 CTTTGAAAGGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
* * * *
7029 CTTTG-AAAGGAGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTA
1 CTTTGAAAAGCA-AATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
* * *
7079 CTTTGAAAAGCAAATTTTGGTCTTGAACTCACAAATGGAATGCAATCTTA
1 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
*
7129 GTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
*
7179 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
* *
7229 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCTATTTTA
1 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
* *
7279 CTTTGAAAAGCGAATTTTGATCTTGAACTAACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
* * *
7329 CTTTGAAAAGCGAATTTTTGATCTTGAACTCATAAATGGAAATCAAT
1 CTTTGAAAAGC-AAATTTTGATCTTGAACTCACAAATGGAAAGCAAT
7376 CTTATTGTAA
Statistics
Matches: 368, Mismatches: 26, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
49 4 0.01
50 329 0.89
51 35 0.10
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (50 bp):
CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
Found at i:8035 original size:15 final size:15
Alignment explanation
Indices: 8013--8053 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
8003 CTTGATTTGA
8013 TTTGATTTTTT-TTGT
1 TTTGATTTTTTATT-T
*
8028 TTTTATTTTTTATTT
1 TTTGATTTTTTATTT
8043 TTTGATTTTTT
1 TTTGATTTTTT
8054 GATTGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 21 0.91
16 2 0.09
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (15 bp):
TTTGATTTTTTATTT
Found at i:8054 original size:8 final size:8
Alignment explanation
Indices: 8013--8057 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
8003 CTTGATTTGA
8013 TTTGATTT
1 TTTGATTT
8021 TTT--TTGT
1 TTTGATT-T
*
8028 TTTTATTT
1 TTTGATTT
8036 TTT-ATTT
1 TTTGATTT
8043 TTTGATTT
1 TTTGATTT
8051 TTTGATT
1 TTTGATT
8058 GATTATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
6 2 0.06
7 11 0.33
8 18 0.55
9 2 0.06
ACGTcount: A:0.11, C:0.00, G:0.09, T:0.80
Consensus pattern (8 bp):
TTTGATTT
Found at i:8780 original size:15 final size:15
Alignment explanation
Indices: 8744--8802 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
8734 CAAACAGAAC
*
8744 ACAGAAAACAGAGTTTG
1 ACAGAAAACA-A-TTAG
8761 ACAGAAAACAATTAG
1 ACAGAAAACAATTAG
* *
8776 ACAGAAAATAATTAA
1 ACAGAAAACAATTAG
8791 ACTAGAAAACAA
1 AC-AGAAAACAA
8803 AGCAAAGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 18 0.49
16 9 0.24
17 10 0.27
ACGTcount: A:0.59, C:0.12, G:0.14, T:0.15
Consensus pattern (15 bp):
ACAGAAAACAATTAG
Found at i:11545 original size:28 final size:29
Alignment explanation
Indices: 11477--11551 Score: 102
Period size: 27 Copynumber: 2.7 Consensus size: 29
11467 ATGTGAACTT
* *
11477 AAAATGACCAGAATGCCCCTGGACGTGCG
1 AAAATGACCAAAATGCCCCTGGAAGTGCG
*
11506 --AATGACCAAAATGCCCCTGGAATTG-G
1 AAAATGACCAAAATGCCCCTGGAAGTGCG
11532 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
11552 AGTTGATTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 1 0.02
27 22 0.54
28 18 0.44
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.16
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTGGAAGTGCG
Found at i:11707 original size:23 final size:23
Alignment explanation
Indices: 11681--11729 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
11671 CTAAATTTCT
* *
11681 AAGTTTAAATATTCATCTCTATA
1 AAGTTTAAACAATCATCTCTATA
*
11704 AAGTTTAAACAATCGTCTCTATA
1 AAGTTTAAACAATCATCTCTATA
11727 AAG
1 AAG
11730 CTAAATTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (23 bp):
AAGTTTAAACAATCATCTCTATA
Found at i:18542 original size:16 final size:16
Alignment explanation
Indices: 18502--18628 Score: 96
Period size: 16 Copynumber: 7.9 Consensus size: 16
18492 CGAACCTGAG
*
18502 ACCCGAATGACTCGTA
1 ACCCGAATGACTCGAA
* * *
18518 ACTCAAATGACTCGAG
1 ACCCGAATGACTCGAA
*
18534 ACCCGAATGACGC-ATA
1 ACCCGAATGACTCGA-A
*
18550 ACCC-AGATGACCCGAA
1 ACCCGA-ATGACTCGAA
* *
18566 ACCCGAATGACCCGTA
1 ACCCGAATGACTCGAA
*
18582 ACCCGAGTGACTCGAA
1 ACCCGAATGACTCGAA
* * *
18598 ACCCGATTAACCCGAA
1 ACCCGAATGACTCGAA
* *
18614 AGCTGAATGACTCGA
1 ACCCGAATGACTCGA
18629 GAATTTAACC
Statistics
Matches: 86, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
15 2 0.02
16 82 0.95
17 2 0.02
ACGTcount: A:0.35, C:0.31, G:0.20, T:0.14
Consensus pattern (16 bp):
ACCCGAATGACTCGAA
Found at i:18575 original size:48 final size:48
Alignment explanation
Indices: 18523--18630 Score: 114
Period size: 48 Copynumber: 2.2 Consensus size: 48
18513 TCGTAACTCA
*
18523 AATGACTCGAGACCCGAATGACGC-ATAACCCAGA-TGACCCGAAACCCG
1 AATGACTCGAGACCCGAATGACGCGA-AACCC-GATTAACCCGAAACCCG
* * * * *
18571 AATGACCCGTA-ACCCGAGTGACTCGAAACCCGATTAACCCGAAAGCTG
1 AATGACTCG-AGACCCGAATGACGCGAAACCCGATTAACCCGAAACCCG
18619 AATGACTCGAGA
1 AATGACTCGAGA
18631 ATTTAACCCG
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
47 3 0.06
48 44 0.90
49 2 0.04
ACGTcount: A:0.35, C:0.31, G:0.21, T:0.13
Consensus pattern (48 bp):
AATGACTCGAGACCCGAATGACGCGAAACCCGATTAACCCGAAACCCG
Found at i:18611 original size:32 final size:32
Alignment explanation
Indices: 18502--18603 Score: 125
Period size: 32 Copynumber: 3.2 Consensus size: 32
18492 CGAACCTGAG
* * * *
18502 ACCCGAATGACTCGTAACTCAAATGACTCGAG
1 ACCCGAATGACCCGTAACCCAGATGACTCGAA
* * *
18534 ACCCGAATGACGCATAACCCAGATGACCCGAA
1 ACCCGAATGACCCGTAACCCAGATGACTCGAA
18566 ACCCGAATGACCCGTAACCC-GAGTGACTCGAA
1 ACCCGAATGACCCGTAACCCAGA-TGACTCGAA
18598 ACCCGA
1 ACCCGA
18604 TTAACCCGAA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
31 2 0.03
32 58 0.97
ACGTcount: A:0.34, C:0.33, G:0.20, T:0.13
Consensus pattern (32 bp):
ACCCGAATGACCCGTAACCCAGATGACTCGAA
Found at i:18777 original size:54 final size:51
Alignment explanation
Indices: 18662--18777 Score: 135
Period size: 54 Copynumber: 2.2 Consensus size: 51
18652 AATATTATAA
* * *
18662 ATTA-AAATTATCTTTTATTTAATAAAATCTACATTGTTATAATTTTACCT
1 ATTATAAATTATCATTTATTTAATAAAATATACATTGTTATAATTTCACCT
* * * *
18712 ATTCTATATTATCATTTATTTAATAAAATTTATATTATTGTTTTAATTTCACCT
1 ATTATAAATTATCATTTATTTAATAAAA--TATA-CATTGTTATAATTTCACCT
18766 ATTATAAATTAT
1 ATTATAAATTAT
18778 TATTAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
50 3 0.06
51 21 0.40
53 3 0.06
54 26 0.49
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.53
Consensus pattern (51 bp):
ATTATAAATTATCATTTATTTAATAAAATATACATTGTTATAATTTCACCT
Found at i:27973 original size:15 final size:16
Alignment explanation
Indices: 27948--27977 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
27938 CATATATAGA
27948 AAAATAATAATTATTC
1 AAAATAATAATTATTC
27964 AAAA-AATAATTATT
1 AAAATAATAATTATT
27978 AATTATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATAATAATTATTC
Found at i:32232 original size:15 final size:16
Alignment explanation
Indices: 32190--32236 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
32180 AATTTGCTAA
*
32190 AATTCATTATACGAAC
1 AATTCATTATATGAAC
32206 AATTTCATTATATGAAC
1 AA-TTCATTATATGAAC
32223 AATT-ATTATATGAA
1 AATTCATTATATGAA
32237 TAAATACTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 10 0.34
16 4 0.14
17 15 0.52
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (16 bp):
AATTCATTATATGAAC
Found at i:33368 original size:130 final size:133
Alignment explanation
Indices: 33190--33452 Score: 331
Period size: 130 Copynumber: 2.0 Consensus size: 133
33180 AATAATGTTA
* * *
33190 ATATTTTAAAAATTCTAATATATCTAAATTTTTTAATTAAATTAGTAAAATGAT-AAAA-TAAAG
1 ATATTTAAAAAATACTAATATATCTAAATTTTTTAATTAAAATAGTAAAATGATAAAAATTAAA-
* * *
33253 TTG-TATAAGGATATTAGATTTAATTTAA-AAAACTAG-A-GTTTTTAGTTAAGTAAAACTATAA
65 TAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAATGTTTTTAGTTAAGTAAAACTATAA
33314 AAGT
130 AAGT
* * * *
33318 ATATTTAAAAAATACTAATATGTATTTAAGTTTTTTATTTAAAATAGTAAAATGGTAAAAATTAA
1 ATATTTAAAAAATACTAATA--TATCTAAATTTTTTAATTAAAATAGTAAAATGATAAAAATTAA
* * * *
33383 ATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAATTTTTTTAGTTGAGTGAAATTATA
64 ATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAATGTTTTTAGTTAAGTAAAACTATA
33448 AAAGT
129 AAAGT
33453 TTAAACAATG
Statistics
Matches: 113, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
128 18 0.16
130 29 0.26
131 6 0.05
132 28 0.25
133 7 0.06
134 1 0.01
135 24 0.21
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (133 bp):
ATATTTAAAAAATACTAATATATCTAAATTTTTTAATTAAAATAGTAAAATGATAAAAATTAAAT
AGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAATGTTTTTAGTTAAGTAAAACTATAAA
AGT
Found at i:39576 original size:29 final size:30
Alignment explanation
Indices: 39526--39584 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
39516 TAAATAAAAA
*
39526 ATGCAAAAACTGACCATAATGCCCCTGGAT
1 ATGCAAAAACTGACCAAAATGCCCCTGGAT
*
39556 ATGCAAAAA-TGATCAAAATGCCCCTGGAT
1 ATGCAAAAACTGACCAAAATGCCCCTGGAT
39585 GACCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (30 bp):
ATGCAAAAACTGACCAAAATGCCCCTGGAT
Found at i:39591 original size:29 final size:30
Alignment explanation
Indices: 39529--39592 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
39519 ATAAAAAATG
* *
39529 CAAAAACTGACCATAATGCCCCTGGATATG
1 CAAAAACTGACCAAAATGCCCCTGGATATC
*
39559 CAAAAA-TGATCAAAATGCCCCTGGATGA-C
1 CAAAAACTGACCAAAATGCCCCTGGAT-ATC
39588 CAAAA
1 CAAAA
39593 TACCTCTAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.42, C:0.25, G:0.16, T:0.17
Consensus pattern (30 bp):
CAAAAACTGACCAAAATGCCCCTGGATATC
Found at i:39639 original size:30 final size:28
Alignment explanation
Indices: 39583--39715 Score: 115
Period size: 28 Copynumber: 4.6 Consensus size: 28
39573 ATGCCCCTGG
* * *
39583 ATGACCAAAATACCTCTAGATGTGCAAA
1 ATGACCAAAATGCCCCTAAATGTGCAAA
*
39611 CACGACCAAAATGCCCCTAAATTGTGCAAAAA
1 -ATGACCAAAATGCCCCTAAA-TGTGC--AAA
*
39643 ATGACCAAAATG-CCCTCGAATGTGCAAA
1 ATGACCAAAATGCCCCT-AAATGTGCAAA
*** ** *
39671 ATGACCAAAATGCAAATGGATATGCAAA
1 ATGACCAAAATGCCCCTAAATGTGCAAA
39699 ATGACCAAAATGCCCCT
1 ATGACCAAAATGCCCCT
39716 GAGTGTGCGA
Statistics
Matches: 85, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
28 38 0.45
29 17 0.20
30 14 0.16
31 13 0.15
32 3 0.04
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.18
Consensus pattern (28 bp):
ATGACCAAAATGCCCCTAAATGTGCAAA
Found at i:46244 original size:178 final size:177
Alignment explanation
Indices: 45930--46287 Score: 479
Period size: 178 Copynumber: 2.0 Consensus size: 177
45920 CCTCTAGAAA
* * *
45930 TTACTAAAGGCTCCCATCAACTTTTAATGTGGGAGAACCTTTTCACCCCATTTTGGTCTTTTCTC
1 TTACTAAAGGCCCCCATCAACTTTTAATGTGGAAGAACCTTATCACCCCATTTTGGTCTTTTCTC
* * *
45995 ATGTCTAACATGTTTACTGAAATATCCCCTAAGCCTAACATGTTTTCTTTAGATCCATTGCCTTT
66 ACGTCT---ATGATTACTGAAATATCCCCTAAGCCTAACATGTTTTCTTCAGATCCATTGCCTTT
*
46060 GTGTGTAATTTGGCCATTGAGTTCTAATAAATGTTGTTCCCA-CATAAAT
128 GTGTGTAATTTGGCCATTGAGTTCTAATAAATGATGTTCCCACCATAAAT
* * *
46109 TTACTAAAGGATCCCCCATCAACTTTTGATGTGGAATG-ACCTTATCGCCCCGTTTTGGTCTTTT
1 TTACTAAAGG--CCCCCATCAACTTTTAATGTGGAA-GAACCTTATCACCCCATTTTGGTCTTTT
* * **
46173 CTCACGTGGT-TGATTACTGAAATATCCCTTAAGCCTAACATGTTTTCTTCAGATCCATTGTTTT
63 CTCACGT-CTATGATTACTGAAATATCCCCTAAGCCTAACATGTTTTCTTCAGATCCATTGCCTT
* * *
46237 TGTGTGTAATTTGGCCATTGAGTTCTGATAAGTGATGTTCTCACCATAAAT
127 TGTGTGTAATTTGGCCATTGAGTTCTAATAAATGATGTTCCCACCATAAAT
46288 CCTTTGGTTT
Statistics
Matches: 157, Mismatches: 17, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
178 88 0.56
179 17 0.11
181 50 0.32
182 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (177 bp):
TTACTAAAGGCCCCCATCAACTTTTAATGTGGAAGAACCTTATCACCCCATTTTGGTCTTTTCTC
ACGTCTATGATTACTGAAATATCCCCTAAGCCTAACATGTTTTCTTCAGATCCATTGCCTTTGTG
TGTAATTTGGCCATTGAGTTCTAATAAATGATGTTCCCACCATAAAT
Found at i:46869 original size:19 final size:19
Alignment explanation
Indices: 46828--46869 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
46818 TATATCAATT
*
46828 CTTTTTACATGAACTGATT
1 CTTTTTACATGAACTGATG
* *
46847 CTTTTTACATGGATTGATG
1 CTTTTTACATGAACTGATG
46866 CTTT
1 CTTT
46870 AGATTCCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (19 bp):
CTTTTTACATGAACTGATG
Found at i:47746 original size:23 final size:23
Alignment explanation
Indices: 47699--47753 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
47689 TCCGCGCAAA
*
47699 TCAAA-TCTCAAGCTCCGTGCTT
1 TCAAACTCTCAAGCTCCGTGCCT
*
47721 TCAAACTCTCAAGC-CCTTGGCCT
1 TCAAACTCTCAAGCTCCGT-GCCT
47744 TCAAATCTCT
1 TCAAA-CTCT
47754 TTTATGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 8 0.29
23 16 0.57
24 4 0.14
ACGTcount: A:0.24, C:0.35, G:0.11, T:0.31
Consensus pattern (23 bp):
TCAAACTCTCAAGCTCCGTGCCT
Found at i:52250 original size:29 final size:29
Alignment explanation
Indices: 52186--52256 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
52176 ACACAAAACG
***
52186 GCCAAATAAGCCCCTGAACTTTAATTGCA
1 GCCAAATAAGCCCCTGAACTTTAATAAAA
*
52215 GCAAAATAAGCCCCTGAACTCTTAA-AAAA
1 GCCAAATAAGCCCCTGAACT-TTAATAAAA
52244 GCCAAATAAGCCC
1 GCCAAATAAGCCC
52257 TTTTTTAACG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 32 0.89
30 4 0.11
ACGTcount: A:0.41, C:0.28, G:0.13, T:0.18
Consensus pattern (29 bp):
GCCAAATAAGCCCCTGAACTTTAATAAAA
Found at i:58266 original size:80 final size:80
Alignment explanation
Indices: 58130--58286 Score: 278
Period size: 80 Copynumber: 2.0 Consensus size: 80
58120 ATATACTAGC
* * * *
58130 TAAAATATACTACCCTTCTTGATAATAGGATTTTCTACATTTATTACTCATCTTTTTCTTATTTA
1 TAAAATATACTACCCTACTTGATAATAAGATTTTCTACATTTATCACTCATATTTTTCTTATTTA
58195 AGATAAGGTGTACGT
66 AGATAAGGTGTACGT
58210 TAAAATATACTACCCTACTTGATAATAAGATTTTCTACATTTATCACTCATATTTTTCTTATTTA
1 TAAAATATACTACCCTACTTGATAATAAGATTTTCTACATTTATCACTCATATTTTTCTTATTTA
58275 AGATAAGGTGTA
66 AGATAAGGTGTA
58287 TGTATAAATT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 73 1.00
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (80 bp):
TAAAATATACTACCCTACTTGATAATAAGATTTTCTACATTTATCACTCATATTTTTCTTATTTA
AGATAAGGTGTACGT
Found at i:59010 original size:42 final size:40
Alignment explanation
Indices: 58951--59034 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 40
58941 TTTAATTCCT
58951 ATGTAATATATATAATAACTAAAATACTTATAACATTAATTAA
1 ATGTAATATATATAATAACTAAAATAC-T-T-ACATTAATTAA
* *
58994 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
59033 AT
1 AT
59035 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
39 13 0.33
40 1 0.03
41 1 0.03
42 16 0.41
43 8 0.21
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Done.