Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013876.1 Corchorus olitorius cultivar O-4 contig13909, 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: 76497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:557 original size:24 final size:25
Alignment explanation
Indices: 522--572 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
512 GATCGTGAAG
522 AAGAAAAGAGAAAAAGGA-AGGA-AA
1 AAGAAAAGAG-AAAAGGACAGGAGAA
546 AAGAAGAA-AGAAAAGGACAGGAGAA
1 AAGAA-AAGAGAAAAGGACAGGAGAA
571 AA
1 AA
573 ACAGCGTCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 7 0.29
24 11 0.46
25 6 0.25
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (25 bp):
AAGAAAAGAGAAAAGGACAGGAGAA
Found at i:873 original size:14 final size:14
Alignment explanation
Indices: 850--882 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
840 AGAATCCAAA
850 ATTA-AAATTAGAT
1 ATTAGAAATTAGAT
*
863 TTTAGAAATTAGAT
1 ATTAGAAATTAGAT
877 ATTAGA
1 ATTAGA
883 TTAATTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (14 bp):
ATTAGAAATTAGAT
Found at i:7166 original size:9 final size:9
Alignment explanation
Indices: 7152--7197 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
7142 AATTCCCATT
7152 GAAAAAAAA
1 GAAAAAAAA
*
7161 GAAAAAAAT
1 GAAAAAAAA
*
7170 GAAAAAAAT
1 GAAAAAAAA
*
7179 GAAAAAGAA
1 GAAAAAAAA
7188 GAAGAAAAAA
1 GAA-AAAAAA
7198 AAAGACACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
9 27 0.84
10 5 0.16
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.04
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:7174 original size:18 final size:19
Alignment explanation
Indices: 7151--7197 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
7141 AAATTCCCAT
7151 TGAAAAAAAAGAAAAA-AA
1 TGAAAAAAAAGAAAAAGAA
*
7169 TGAAAAAAATGAAAAAGAA
1 TGAAAAAAAAGAAAAAGAA
7188 -GAAGAAAAAA
1 TGAA-AAAAAA
7198 AAAGACACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (19 bp):
TGAAAAAAAAGAAAAAGAA
Found at i:9190 original size:151 final size:144
Alignment explanation
Indices: 8952--9643 Score: 866
Period size: 145 Copynumber: 4.6 Consensus size: 144
8942 CAAAGTTGCA
8952 TTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAA
1 TTTAAGTTTCAAAA-CAAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAA
* * *
9017 TTCCAGAAACCTCCGAGTATTAATTCTGATAAATCCTTCGGGTATCA-CTTCATTTCATCAAGTT
65 TTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATC-TCATTTCATCAAGTT
* *
9081 GCTAATCAAAATTATG
129 GTTAATCAAAATTGTG
* *
9097 TTTAAGTTTCAAAA-AAAACCTTGCTTAAGGTCTCTACTCAGAGTTTGCACTTGTAAGACCTCCG
1 TTTAAGTTTCAAAACAAAACCTTGCTCAAGG-------TC-GAGTTTGCATTTGTAAGACCTCCG
* * * *
9161 GGCACCATTTTAGAAACCTCTGGGTATTAATTCTTATAAATCCTCCGGGTATCATCTCATTTCAT
58 GGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATCTCATTTCAT
* *
9226 CAAGTTTTTAATCAAAGTTGTG
123 CAAGTTGTTAATCAAAATTGTG
9248 TTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAA
1 TTTAAGTTTCAAAA-CAAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAA
* *
9313 TTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATCTCATTTCAGCAAGTTT
65 TTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATCTCATTTCATCAAGTTG
* *
9378 TTAATCAAAGTTGCG
130 TTAATCAAAATTGTG
9393 TTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAA
1 TTTAAGTTTCAAAA-CAAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAA
* * * * *
9458 TTCCAGAAACCTCCGGATATTAATTCTGATAAATTCTCCAGGTATCACCTCATTTCATCAAGTTG
65 TTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATCTCATTTCATCAAGTTG
*
9523 TTAATCGAAATTGTG
130 TTAATCAAAATTGTG
* * * * *
9538 TTTAAGTTTTTTTTTAAAAAAAAACCTTGCTCAAAGTCCCTATTCAAAGTTGACATTTGTAAGAC
1 TTTAAG-----TTTCAAAACAAAACCTTGCTCAAGGT--CGAGT-----TTG-CATTTGTAAGAC
* **
9603 CTTCGGGCACAATTTCAGAAACCTCTAGGTATTAATTCTGA
53 CTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGA
9644 CAAGACCTTC
Statistics
Matches: 482, Mismatches: 41, Indels: 36
0.86 0.07 0.06
Matches are distributed among these distances:
143 15 0.03
145 259 0.54
146 2 0.00
149 16 0.03
150 9 0.02
151 114 0.24
152 1 0.00
153 15 0.03
156 3 0.01
157 48 0.10
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (144 bp):
TTTAAGTTTCAAAACAAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAAT
TTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATCTCATTTCATCAAGTTGT
TAATCAAAATTGTG
Found at i:9347 original size:145 final size:145
Alignment explanation
Indices: 8931--9546 Score: 898
Period size: 145 Copynumber: 4.2 Consensus size: 145
8921 CCATTTTGGT
* **
8931 AAGTTTTTAAGCAAAGTTGCATTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTCGAGTTTGCAT
1 AAGTTTTTAATCAAAGTTGTGTTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTCGAGTTTGCAT
* *
8996 TTGTAAGACCTCCGGGCACAATTCCAGAAACCTCCGAGTATTAATTCTGATAAATCCTTCGGGTA
66 TTGTAAGACCTCCGGGCACAATTCCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTA
9061 TCA-CTTCATTTCATC
131 TCATC-TCATTTCATC
** * * *
9076 AAGTTGCTAATCAAAATTATGTTTAAGTTTCAAAA--AAAACCTTGCTTAAGGTCTCTACTCAGA
1 AAGTTTTTAATCAAAGTTGTGTTTAAGTTTCAAAATCAAAACCTTGCTCAAGG-------TC-GA
* * ** * *
9139 GTTTGCACTTGTAAGACCTCCGGGCACCATTTTAGAAACCTCTGGGTATTAATTCTTATAAATCC
58 GTTTGCATTTGTAAGACCTCCGGGCACAATTCCAGAAACCTCCGGGTATTAATTCTGATAAATCC
9204 TCCGGGTATCATCTCATTTCATC
123 TCCGGGTATCATCTCATTTCATC
9227 AAGTTTTTAATCAAAGTTGTGTTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTCGAGTTTGCAT
1 AAGTTTTTAATCAAAGTTGTGTTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTCGAGTTTGCAT
*
9292 TTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTA
66 TTGTAAGACCTCCGGGCACAATTCCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTA
*
9357 TCATCTCATTTCAGC
131 TCATCTCATTTCATC
*
9372 AAGTTTTTAATCAAAGTTGCGTTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTCGAGTTTGCAT
1 AAGTTTTTAATCAAAGTTGTGTTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTCGAGTTTGCAT
* * *
9437 TTGTAAGACCTCCGGGCACAATTCCAGAAACCTCCGGATATTAATTCTGATAAATTCTCCAGGTA
66 TTGTAAGACCTCCGGGCACAATTCCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTA
*
9502 TCACCTCATTTCATC
131 TCATCTCATTTCATC
*
9517 AAGTTGTTAATCGAAA-TTGTGTTTAAGTTT
1 AAGTTTTTAATC-AAAGTTGTGTTTAAGTTT
9547 TTTTTTAAAA
Statistics
Matches: 423, Mismatches: 36, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
143 15 0.04
145 274 0.65
146 5 0.01
150 2 0.00
151 111 0.26
152 1 0.00
153 15 0.04
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (145 bp):
AAGTTTTTAATCAAAGTTGTGTTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTCGAGTTTGCAT
TTGTAAGACCTCCGGGCACAATTCCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTA
TCATCTCATTTCATC
Found at i:10779 original size:2 final size:2
Alignment explanation
Indices: 10772--10806 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
10762 TTTGGTCATC
10772 AT AT AT AT 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 AT AT AT AT A
10807 AATTTAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18210 original size:31 final size:31
Alignment explanation
Indices: 18163--18335 Score: 99
Period size: 31 Copynumber: 5.7 Consensus size: 31
18153 AGAATTTTTG
*
18163 ACATCAGGCTCTTATTTGAGCATTTTGGCAA
1 ACATCAGGCCCTTATTTGAGCATTTTGGCAA
* ** *
18194 ACATTAGGCCCTTATTTG-GCCA---AAGTAA
1 ACATCAGGCCCTTATTTGAG-CATTTTGGCAA
* * *
18222 ATGACCGGGCCCTTATTTGAGCATTTTGGCAA
1 A-CATCAGGCCCTTATTTGAGCATTTTGGCAA
* * *** *
18254 ACGTTAGGCCCTTATTTG-GTCAAACT--AAA
1 ACATCAGGCCCTTATTTGAG-CATTTTGGCAA
* * *
18283 AGATCAAGCCCTTATTTGAGCATTTTTGCAA
1 ACATCAGGCCCTTATTTGAGCATTTTGGCAA
* *
18314 ACGTTAGGCCCTTATTTGAGCA
1 ACATCAGGCCCTTATTTGAGCA
18336 ATTAGCCAAG
Statistics
Matches: 99, Mismatches: 33, Indels: 20
0.65 0.22 0.13
Matches are distributed among these distances:
28 4 0.04
29 34 0.34
30 4 0.04
31 53 0.54
32 4 0.04
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (31 bp):
ACATCAGGCCCTTATTTGAGCATTTTGGCAA
Found at i:18266 original size:60 final size:60
Alignment explanation
Indices: 18173--18331 Score: 246
Period size: 60 Copynumber: 2.6 Consensus size: 60
18163 ACATCAGGCT
* * * **
18173 CTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAAGTAAATGACCGGGCC
1 CTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAACTAAAAGACCAAGCC
* *
18233 CTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGTCAAACTAAAAGATCAAGCC
1 CTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAACTAAAAGACCAAGCC
*
18293 CTTATTTGAGCATTTTTGCAAACGTTAGGCCCTTATTTG
1 CTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
18332 AGCAATTAGC
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 91 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Consensus pattern (60 bp):
CTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAACTAAAAGACCAAGCC
Found at i:18670 original size:23 final size:23
Alignment explanation
Indices: 18644--18692 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
18634 AGAAATTTAG
* *
18644 CTTTATAGAGACGATTGTTTAAA
1 CTTTATAGAGACGACTATTTAAA
*
18667 CTTTATAGAGATGACTATTTAAA
1 CTTTATAGAGACGACTATTTAAA
18690 CTT
1 CTT
18693 AGAAATTTAG
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:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (23 bp):
CTTTATAGAGACGACTATTTAAA
Found at i:19635 original size:21 final size:19
Alignment explanation
Indices: 19609--19667 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 19
19599 CGCTGCTCTA
19609 ATAATCTCATTTGTACAGT
1 ATAATCTCATTTGTACAGT
* *
19628 ACCTAATCTAAATTGTAC-GAT
1 A--TAATCTCATTTGTACAG-T
*
19649 ATAATCTCATCTGTACAGT
1 ATAATCTCATTTGTACAGT
19668 TGCTAAACAG
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
19 14 0.45
20 2 0.06
21 15 0.48
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (19 bp):
ATAATCTCATTTGTACAGT
Found at i:26938 original size:19 final size:23
Alignment explanation
Indices: 26892--26940 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
26882 ATCGACCTTT
*
26892 TTAATATATATTATATTTTATTA
1 TTAATATATATTATATTATATTA
26915 TTAATA-ATA-TATATTATA-TA
1 TTAATATATATTATATTATATTA
26935 -TAATAT
1 TTAATAT
26941 TTTCCATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 2 0.08
21 8 0.33
22 3 0.12
23 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAATATATATTATATTATATTA
Found at i:29693 original size:17 final size:18
Alignment explanation
Indices: 29668--29702 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
29658 GTAATTGTTA
29668 TTACATAAAA-TAAAATT
1 TTACATAAAATTAAAATT
*
29685 TTACTTAAAATTAAAATT
1 TTACATAAAATTAAAATT
29703 ATTCAGTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
TTACATAAAATTAAAATT
Found at i:32609 original size:25 final size:24
Alignment explanation
Indices: 32554--32610 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
32544 GTCAGCCTTG
*
32554 AATCT-TTTAATGTTTAATTCTTA
1 AATCTATTTAATGTTTAATTATTA
* *
32577 AATTTATTTAATGTCTTAATTATTC
1 AATCTATTTAATGT-TTAATTATTA
32602 AATCTATTT
1 AATCTATTT
32611 TACAATCCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 4 0.14
24 8 0.29
25 16 0.57
ACGTcount: A:0.32, C:0.09, G:0.04, T:0.56
Consensus pattern (24 bp):
AATCTATTTAATGTTTAATTATTA
Found at i:33992 original size:2 final size:2
Alignment explanation
Indices: 33985--34019 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
33975 TAAATCTATC
33985 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34020 TAAGTTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36492 original size:42 final size:38
Alignment explanation
Indices: 36408--36492 Score: 100
Period size: 42 Copynumber: 2.1 Consensus size: 38
36398 TCATTTTCAA
* *
36408 AAAAAGAAAAGAAGAAAATGTTTTTTTTTTAAAAATCG
1 AAAAAGAAAAGAAGAAAATGTTTTTTTTTTAAAAACCC
36446 AAAAA-AAAAGAAGAAAAGTGAATTTTTTTTTATTAAAAACCC
1 AAAAAGAAAAGAAGAAAA-TG---TTTTTTTT-TTAAAAACCC
36488 AAAAA
1 AAAAA
36493 TTAGGGGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
37 12 0.30
38 7 0.17
41 8 0.20
42 13 0.32
ACGTcount: A:0.56, C:0.05, G:0.11, T:0.28
Consensus pattern (38 bp):
AAAAAGAAAAGAAGAAAATGTTTTTTTTTTAAAAACCC
Found at i:36622 original size:21 final size:19
Alignment explanation
Indices: 36589--36627 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
36579 CCTGGCCCAA
36589 TTTTTTTAAAAAAAATATT
1 TTTTTTTAAAAAAAATATT
36608 TTTTTTTAATCAAAAAATAT
1 TTTTTTTAA--AAAAAATAT
36628 GACTTGGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTTTTAAAAAAAATATT
Found at i:39551 original size:11 final size:11
Alignment explanation
Indices: 39527--39561 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
39517 TTGACAGCGC
39527 AACAAAAACAA
1 AACAAAAACAA
* *
39538 AACGAAAACGA
1 AACAAAAACAA
39549 AACAAAAACAA
1 AACAAAAACAA
39560 AA
1 AA
39562 AACTGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:40698 original size:2 final size:2
Alignment explanation
Indices: 40693--40722 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
40683 CTTTCAAAAA
40693 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A
40723 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:41053 original size:17 final size:18
Alignment explanation
Indices: 41033--41067 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
41023 TTTTTCTAAT
41033 AATTATATTAAG-AATTA
1 AATTATATTAAGTAATTA
41050 AATTATATTAAGTAATTA
1 AATTATATTAAGTAATTA
41068 TATAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (18 bp):
AATTATATTAAGTAATTA
Found at i:42078 original size:11 final size:11
Alignment explanation
Indices: 42062--42086 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42052 TGATGATTAT
42062 AAAAAAAAACA
1 AAAAAAAAACA
42073 AAAAAAAAACA
1 AAAAAAAAACA
42084 AAA
1 AAA
42087 GAAGAAGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:43926 original size:58 final size:58
Alignment explanation
Indices: 43830--43942 Score: 174
Period size: 58 Copynumber: 1.9 Consensus size: 58
43820 ATTAATCAAA
*
43830 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCGAGCCT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCGAGCCT
* * *
43888 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACGTTTTAGGACCGAG
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCGAG
43943 GCATGATGCT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 35 0.70
59 15 0.30
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCGAGCCT
Found at i:46158 original size:39 final size:40
Alignment explanation
Indices: 46104--46184 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
46094 ATACCTAAGA
*
46104 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
46143 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
46183 AT
1 AT
46185 AGGAATTAAA
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:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:62234 original size:29 final size:28
Alignment explanation
Indices: 62199--62258 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
62189 GATGATGTCA
* *
62199 TTTTTTTATTAACAATAGTCAAAGGCTTT
1 TTTTTTTATGAA-AATAGTCAAAGGCATT
*
62228 TTTTTTTGTGAAAATAGTCAAAGGCATT
1 TTTTTTTATGAAAATAGTCAAAGGCATT
62256 TTT
1 TTT
62259 ACAACTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.48
Consensus pattern (28 bp):
TTTTTTTATGAAAATAGTCAAAGGCATT
Done.