Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022537.1 Corchorus olitorius cultivar O-4 contig22570, 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: 43396
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:2600 original size:43 final size:44
Alignment explanation
Indices: 2540--2642 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 44
2530 CATAGTTATG
* * * *
2540 TTATCAAAGTTTCATATGGAGTTTATCACAATTTTATA-GGTAA
1 TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGGGTAA
* *
2583 TTATCAAAATTTTATATGGTGGTTATCAAAATTTAATAGGGTAA
1 TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGGGTAA
2627 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
2643 AAAATATTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
43 32 0.62
44 20 0.38
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.42
Consensus pattern (44 bp):
TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGGGTAA
Found at i:2611 original size:22 final size:22
Alignment explanation
Indices: 2540--2638 Score: 103
Period size: 22 Copynumber: 4.5 Consensus size: 22
2530 CATAGTTATG
* * *
2540 TTATCAAAGTTTCATATGG-AGT
1 TTATCAAAATTTTATATGGTA-A
*
2562 TTATCACAATTTTATA-GGTAA
1 TTATCAAAATTTTATATGGTAA
**
2583 TTATCAAAATTTTATATGGTGG
1 TTATCAAAATTTTATATGGTAA
* *
2605 TTATCAAAATTTAATAGGGTAA
1 TTATCAAAATTTTATATGGTAA
2627 TTATCAAAATTT
1 TTATCAAAATTT
2639 CATAAAAATA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
21 17 0.27
22 47 0.73
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTTATATGGTAA
Found at i:2727 original size:3 final size:3
Alignment explanation
Indices: 2711--2800 Score: 54
Period size: 3 Copynumber: 31.3 Consensus size: 3
2701 TATATATATA
*
2711 TAT TAT T-T TTT TAT TAT TA- TAT TA- TAT TAT TAT TAT TAT CTA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
*
2753 TACCT TAT T-T TAT T-T T-T TAT T-T TAT TTT TAT TA- TAT CTAT TAT
1 TA--T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
2796 ATAT T
1 -TAT T
2801 CTTTTTACTA
Statistics
Matches: 71, Mismatches: 3, Indels: 26
0.71 0.03 0.26
Matches are distributed among these distances:
2 18 0.25
3 43 0.61
4 8 0.11
5 2 0.03
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2733 original size:19 final size:19
Alignment explanation
Indices: 2709--2813 Score: 70
Period size: 19 Copynumber: 5.1 Consensus size: 19
2699 AGTATATATA
2709 TATATTATTTTTTTATTAT
1 TATATTATTTTTTTATTAT
2728 TATATTATATTATTATTATTAT
1 TATATTAT-TT-TT-TTATTAT
*
2750 CTATACCTTATTTTATTTTTTAT
1 -TATA--TTATTTT-TTTATTAT
* *
2773 TTTATT-TTTATTATATCTAT
1 TATATTATTT-TTTTAT-TAT
*
2793 TATA-TATTCTTTTTACTAT
1 TATATTATT-TTTTTATTAT
2812 TA
1 TA
2814 AAATTATCCC
Statistics
Matches: 68, Mismatches: 7, Indels: 22
0.70 0.07 0.23
Matches are distributed among these distances:
19 20 0.29
20 17 0.25
21 3 0.04
22 10 0.15
23 11 0.16
24 3 0.04
25 4 0.06
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (19 bp):
TATATTATTTTTTTATTAT
Found at i:2735 original size:11 final size:11
Alignment explanation
Indices: 2705--2800 Score: 65
Period size: 11 Copynumber: 8.5 Consensus size: 11
2695 AACTAGTATA
2705 TATATATATTAT
1 TATAT-TATTAT
* *
2717 TTTTTTATTAT
1 TATATTATTAT
2728 TATATTA-TAT
1 TATATTATTAT
2738 TATTATTATTAT
1 TA-TATTATTAT
2750 CTATACCTTATT-T
1 -TATA--TTATTAT
*
2763 TAT-TTTTTAT
1 TATATTATTAT
* *
2773 TTTATTTTTAT
1 TATATTATTAT
2784 TATATCTATTA-
1 TATAT-TATTAT
2795 TATATT
1 TATATT
2801 CTTTTTACTA
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
9 4 0.06
10 9 0.13
11 32 0.47
12 15 0.22
13 3 0.04
14 5 0.07
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (11 bp):
TATATTATTAT
Found at i:3169 original size:3 final size:3
Alignment explanation
Indices: 3161--3209 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
3151 TAATATCTAG
*
3161 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
3207 TTA
1 TTA
3210 AAAGTTATCT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:4005 original size:13 final size:13
Alignment explanation
Indices: 3987--4011 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3977 TTTTTTCATT
3987 AAAATAATAATTA
1 AAAATAATAATTA
4000 AAAATAATAATT
1 AAAATAATAATT
4012 TAATTAGGAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATAATAATTA
Found at i:8178 original size:28 final size:28
Alignment explanation
Indices: 8146--8225 Score: 115
Period size: 28 Copynumber: 2.9 Consensus size: 28
8136 CGAAAATGAC
8146 GGGAACTTTCCCAATTTGAAAACTGGAT
1 GGGAACTTTCCCAATTTGAAAACTGGAT
* *
8174 GGGAACCTTCCCAATTTGAAAATTGGAT
1 GGGAACTTTCCCAATTTGAAAACTGGAT
* * *
8202 GGAAACTTCCCCAATTTGAGAACT
1 GGGAACTTTCCCAATTTGAAAACT
8226 TGGAAAAAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (28 bp):
GGGAACTTTCCCAATTTGAAAACTGGAT
Found at i:8322 original size:23 final size:22
Alignment explanation
Indices: 8279--8323 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
8269 AGGAAATATC
***
8279 TTTTGATTTTTGAATTTTTTTT
1 TTTTGATTTTTGAAACCTTTTT
8301 TTTTGGATTTTTGAAACCTTTTT
1 TTTT-GATTTTTGAAACCTTTTT
8324 ATTAGTTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.16, C:0.04, G:0.11, T:0.69
Consensus pattern (22 bp):
TTTTGATTTTTGAAACCTTTTT
Found at i:12217 original size:60 final size:60
Alignment explanation
Indices: 12108--12282 Score: 230
Period size: 60 Copynumber: 3.0 Consensus size: 60
12098 AACTGAAAGT
* * * * *
12108 GACCAGTC-AGTGGTCGACA-T-AACTGAGAAAGACCTGTCTGAGATTTGAAACTGAAGAA
1 GACCAGTCTA-TGGTCGATACTAAACTGAGAATGACCTGTCTGAGGTCTGAAATTGAAGAA
* * *
12166 GACCAGTTTGTGGTTGATACTAAACTGAGAATGACCTGTCTGAGGTCTGAAATTGAAGAA
1 GACCAGTCTATGGTCGATACTAAACTGAGAATGACCTGTCTGAGGTCTGAAATTGAAGAA
* *
12226 GACCTGTCTATGGTCGATACTAAACTGAGAATGACATGTCTGAGGTCTGAAATTGAA
1 GACCAGTCTATGGTCGATACTAAACTGAGAATGACCTGTCTGAGGTCTGAAATTGAA
12283 AAACTAAGAA
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
58 14 0.14
59 1 0.01
60 86 0.85
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (60 bp):
GACCAGTCTATGGTCGATACTAAACTGAGAATGACCTGTCTGAGGTCTGAAATTGAAGAA
Found at i:12234 original size:28 final size:29
Alignment explanation
Indices: 12193--12282 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 29
12183 TACTAAACTG
12193 AGAATGACCTGTCTGAGGTCTGAAATTGA
1 AGAATGACCTGTCTGAGGTCTGAAATTGA
* *
12222 AGAA-GACCTGTCT-ATGGTCGATACTAAACTG-
1 AGAATGACCTGTCTGA-GGTC--T--GAAATTGA
*
12253 AGAATGACATGTCTGAGGTCTGAAATTGA
1 AGAATGACCTGTCTGAGGTCTGAAATTGA
12282 A
1 A
12283 AAACTAAGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
27 1 0.02
28 18 0.38
29 5 0.10
30 2 0.04
31 4 0.08
32 17 0.35
33 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (29 bp):
AGAATGACCTGTCTGAGGTCTGAAATTGA
Found at i:12266 original size:32 final size:33
Alignment explanation
Indices: 12155--12272 Score: 94
Period size: 32 Copynumber: 3.8 Consensus size: 33
12145 CTGAGATTTG
* * *
12155 AAACTGAAGAA-GACCAGTTTG-TGGTTGATACT
1 AAACTG-AGAATGACCTGTCTGATGGTCGATACT
*
12187 AAACTGAGAATGACCTGTCTGA-GGTC--T--G
1 AAACTGAGAATGACCTGTCTGATGGTCGATACT
*
12215 AAATTGAAGAA-GACCTGTCT-ATGGTCGATACT
1 AAACTG-AGAATGACCTGTCTGATGGTCGATACT
*
12247 AAACTGAGAATGACATGTCTGA-GGTC
1 AAACTGAGAATGACCTGTCTGATGGTC
12273 TGAAATTGAA
Statistics
Matches: 68, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
27 1 0.01
28 18 0.26
29 4 0.06
30 2 0.03
31 8 0.12
32 34 0.50
33 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.26
Consensus pattern (33 bp):
AAACTGAGAATGACCTGTCTGATGGTCGATACT
Found at i:12522 original size:39 final size:38
Alignment explanation
Indices: 12339--12610 Score: 436
Period size: 38 Copynumber: 7.1 Consensus size: 38
12329 TGTGGTCGAT
* * *
12339 TTTGATAACTACTGGAAGATGACATGTTTCCAGCCAAC
1 TTTGATAACTACTGAAAGATGACCTGTTTCCAGTCAAC
*
12377 TTTGATAACTACTGAAAGATGACCTGTTTACAGTCAAC
1 TTTGATAACTACTGAAAGATGACCTGTTTCCAGTCAAC
12415 TTTGATAACTACTGAAAGATGACCTGTTTCCAGTCAAC
1 TTTGATAACTACTGAAAGATGACCTGTTTCCAGTCAAC
*
12453 TTTGATAACTACTGAAAGATGACCTATTTCCAGTCAAC
1 TTTGATAACTACTGAAAGATGACCTGTTTCCAGTCAAC
12491 TTTGATAACTACTTGAAAGATGACCTGTTTCCAGTCAAC
1 TTTGATAACTAC-TGAAAGATGACCTGTTTCCAGTCAAC
* *
12530 TTTGATAACTGCTTAAAAGATGACCTGTTTCCAGTCAAC
1 TTTGATAACTAC-TGAAAGATGACCTGTTTCCAGTCAAC
**
12569 TTTGATAACCGCTGAAAAGATGACCTGTTTCCAGTCAAC
1 TTTGATAACTACTG-AAAGATGACCTGTTTCCAGTCAAC
12608 TTT
1 TTT
12611 TGATCGGTCG
Statistics
Matches: 221, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
38 121 0.55
39 100 0.45
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (38 bp):
TTTGATAACTACTGAAAGATGACCTGTTTCCAGTCAAC
Found at i:14913 original size:40 final size:41
Alignment explanation
Indices: 14858--14957 Score: 193
Period size: 40 Copynumber: 2.5 Consensus size: 41
14848 TAATGGTGCT
14858 ATGAAAATATCTAAAACTTTTTTCTTTTTC-TTTTTTCATC
1 ATGAAAATATCTAAAACTTTTTTCTTTTTCTTTTTTTCATC
14898 ATGAAAATATCTAAAACTTTTTTCTTTTTCTTTTTTTCATC
1 ATGAAAATATCTAAAACTTTTTTCTTTTTCTTTTTTTCATC
14939 ATGAAAATATCTAAAACTT
1 ATGAAAATATCTAAAACTT
14958 AATACTAACA
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 30 0.51
41 29 0.49
ACGTcount: A:0.32, C:0.14, G:0.03, T:0.51
Consensus pattern (41 bp):
ATGAAAATATCTAAAACTTTTTTCTTTTTCTTTTTTTCATC
Found at i:23843 original size:26 final size:27
Alignment explanation
Indices: 23778--23848 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
23768 ATTAAAGTCA
* *
23778 TCCATGGGCATTTTAGTCATTTGCACG
1 TCCAGGGGCATTTTGGTCATTTGCACG
*
23805 TCCAGGGGCATTTTGGTCATTTGTAC-
1 TCCAGGGGCATTTTGGTCATTTGCACG
*
23831 TTCAGGGGCATTTTGGTC
1 TCCAGGGGCATTTTGGTC
23849 TTTTTTAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 17 0.43
27 23 0.57
ACGTcount: A:0.15, C:0.20, G:0.27, T:0.38
Consensus pattern (27 bp):
TCCAGGGGCATTTTGGTCATTTGCACG
Found at i:23860 original size:26 final size:26
Alignment explanation
Indices: 23783--23860 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 26
23773 AGTCATCCAT
* * * *
23783 GGGCATTTTAGTCATTTGCACGTCCAG
1 GGGCATTTTGGTCATTTGTA-ATTCAG
*
23810 GGGCATTTTGGTCATTTGTACTTCAG
1 GGGCATTTTGGTCATTTGTAATTCAG
* *
23836 GGGCATTTTGGTCTTTTTTAATTCA
1 GGGCATTTTGGTCATTTGTAATTCA
23861 TTACTAGCTT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
26 26 0.59
27 18 0.41
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.42
Consensus pattern (26 bp):
GGGCATTTTGGTCATTTGTAATTCAG
Found at i:24203 original size:19 final size:19
Alignment explanation
Indices: 24179--24221 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
24169 CTTGTTTTTA
*
24179 GCATTGGGCTTGCACTTGG
1 GCATTGGGCTTGCACTTAG
*
24198 GCATTGGGCTTGCATTTAG
1 GCATTGGGCTTGCACTTAG
24217 GCATT
1 GCATT
24222 TTAGCTTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.33, T:0.35
Consensus pattern (19 bp):
GCATTGGGCTTGCACTTAG
Found at i:27999 original size:28 final size:28
Alignment explanation
Indices: 27961--28026 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
27951 TTTCCAACGT
27961 CGTTTCGACAGGGTTCCCCAGACCCGAA
1 CGTTTCGACAGGGTTCCCCAGACCCGAA
**
27989 CGTTTCGACAGGGTTCCCTGGACCCGAA
1 CGTTTCGACAGGGTTCCCCAGACCCGAA
28017 CGTTTCGACA
1 CGTTTCGACA
28027 CAATCCATGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.20, C:0.33, G:0.26, T:0.21
Consensus pattern (28 bp):
CGTTTCGACAGGGTTCCCCAGACCCGAA
Found at i:28878 original size:20 final size:20
Alignment explanation
Indices: 28853--28891 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28843 CATATAAAAT
*
28853 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
28873 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
28892 TTTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:29918 original size:11 final size:11
Alignment explanation
Indices: 29881--29924 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
29871 TTTCTATACA
*
29881 AAATAAATTAT
1 AAATTAATTAT
29892 CAAA-TAATTAT
1 -AAATTAATTAT
29903 AAATTAATTAT
1 AAATTAATTAT
*
29914 AAATTTATTAT
1 AAATTAATTAT
29925 GAATATACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 3 0.10
11 23 0.79
12 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:30855 original size:30 final size:30
Alignment explanation
Indices: 30815--30887 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
30805 ATTTGATTTT
*
30815 AAGCTTTTTAACTGTGTTGCGGTTGGCATC
1 AAGCTTTTTAACTGTGTTGCAGTTGGCATC
*
30845 AAGCTCTTTAACTGTGTTGCAGTTGGCATC
1 AAGCTTTTTAACTGTGTTGCAGTTGGCATC
30875 AAGCTTTTTAACT
1 AAGCTTTTTAACT
30888 CTTCAATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (30 bp):
AAGCTTTTTAACTGTGTTGCAGTTGGCATC
Found at i:31175 original size:41 final size:42
Alignment explanation
Indices: 31101--31180 Score: 117
Period size: 41 Copynumber: 1.9 Consensus size: 42
31091 CCACAATAGA
* * *
31101 AAGAATATTAGGGGAATAACTCTTAGAAGGAGAACTCTTAGG
1 AAGAATATTAGGGGAAGAACCCTTAGAAAGAGAACTCTTAGG
*
31143 AAGAATATTA-GGGAAGAACCCTTCGAAAGAGAACTCTT
1 AAGAATATTAGGGGAAGAACCCTTAGAAAGAGAACTCTT
31181 TTTTTTTGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
41 24 0.71
42 10 0.29
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.23
Consensus pattern (42 bp):
AAGAATATTAGGGGAAGAACCCTTAGAAAGAGAACTCTTAGG
Found at i:39989 original size:132 final size:132
Alignment explanation
Indices: 39840--40102 Score: 379
Period size: 132 Copynumber: 2.0 Consensus size: 132
39830 ATTTAAGAAA
* *
39840 TATATTTTAAAAATTCTAATATATCTAAGTTTTATTAATTAA-ATTAGTAAAATGGTAAAAATAT
1 TATATTTTAAAAATTCTAATATATATAAGTTTTATTAATTAAGA-TAGTAAAATGGTAAAAATAA
* * * * *
39904 AATGAG-TATAAGGATATTAGATTTCATGAAATGAAAATAGATTTTTTAGTTGAGTAAAACTATA
65 AAT-AGTTATAAGAATATTAGATTTAATGAAATAAAAATAGAGTTTTTAGCTGAGTAAAACTATA
39968 AAAG
129 AAAG
* *
39972 TATA-TTTAAAAATTTCTAGTATATATAAGTTTTTTTAATTAAGATAGTAAAATGGTAAAAATAA
1 TATATTTTAAAAA-TTCTAATATATATAAGTTTTATTAATTAAGATAGTAAAATGGTAAAAATAA
* *
40036 AATAGTTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGCTGAGTAAAATTATAA
65 AATAGTTATAAGAATATTAGATTTAATGAAATAAAAATAGAGTTTTTAGCTGAGTAAAACTATAA
40101 AA
130 AA
40103 ATTTAAAAAA
Statistics
Matches: 117, Mismatches: 11, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
131 10 0.09
132 106 0.91
133 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (132 bp):
TATATTTTAAAAATTCTAATATATATAAGTTTTATTAATTAAGATAGTAAAATGGTAAAAATAAA
ATAGTTATAAGAATATTAGATTTAATGAAATAAAAATAGAGTTTTTAGCTGAGTAAAACTATAAA
AG
Found at i:42472 original size:31 final size:31
Alignment explanation
Indices: 42434--42501 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
42424 TTGAAAATAG
*
42434 CGGCGTCTCAAAATGAAACGCCGTTATTTAA
1 CGGCGTCTCAAAATGAAACGCCGCTATTTAA
42465 CGGCGTCTCAAAATGAAACGCCGCTATTTAA
1 CGGCGTCTCAAAATGAAACGCCGCTATTTAA
42496 CGGCGT
1 CGGCGT
42502 TTATACATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (31 bp):
CGGCGTCTCAAAATGAAACGCCGCTATTTAA
Done.