Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010811.1 Corchorus olitorius cultivar O-4 contig10843, 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: 59681
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1855 original size:29 final size:30
Alignment explanation
Indices: 1794--1855 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
1784 AACTTTCAAA
* * *
1794 TTAATGGGGTCAATGTCTTTAAATTTTCTT
1 TTAATGGGGTCAATGTCTCTAAATTTACCT
1824 TTAATTGGGGTCAAT-T-TCTAAATTTACCT
1 TTAA-TGGGGTCAATGTCTCTAAATTTACCT
1853 TTA
1 TTA
1856 CTTATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 13 0.46
30 5 0.18
31 10 0.36
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (30 bp):
TTAATGGGGTCAATGTCTCTAAATTTACCT
Found at i:2343 original size:72 final size:73
Alignment explanation
Indices: 2222--2382 Score: 249
Period size: 72 Copynumber: 2.2 Consensus size: 73
2212 ATATGTGCAA
2222 ATAT-GATAATTTA-ATGAACATATTTATAAGTAAAATGGAGCAAAGATTATAAAAAA-CAATTA
1 ATATAGATAATTTAGA-GAACATATTTATAAGTAAAATGGAGCAAAGATTATAAAAAACCAATTA
2284 GGAATTAAG
65 GGAATTAAG
* * *
2293 GTATAGATAATTTAGAGAACATATTTATAAGTAAGATGGAGCAAAGATTATAAAAAACCTATTAG
1 ATATAGATAATTTAGAGAACATATTTATAAGTAAAATGGAGCAAAGATTATAAAAAACCAATTAG
2358 GAATTAAG
66 GAATTAAG
2366 ATATAGAGTAA-TTAGAG
1 ATATAGA-TAATTTAGAG
2383 GAGATCTCTT
Statistics
Matches: 82, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
71 3 0.04
72 49 0.60
73 27 0.33
74 3 0.04
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.29
Consensus pattern (73 bp):
ATATAGATAATTTAGAGAACATATTTATAAGTAAAATGGAGCAAAGATTATAAAAAACCAATTAG
GAATTAAG
Found at i:3655 original size:41 final size:41
Alignment explanation
Indices: 3553--3657 Score: 120
Period size: 43 Copynumber: 2.5 Consensus size: 41
3543 TCTCTCTCCC
* * * *
3553 CAAAGTCCCCAAACACATATATAACACAGGGACAACTCTAT
1 CAAAGTCCCTAAAGACATATATAACACAGAGACAACTATAT
* * * *
3594 CTAAAATTCCTCAAGCACATATATAACACAGAGACATCTATAT
1 C-AAAGTCCCTAAAG-ACATATATAACACAGAGACAACTATAT
3637 CAAAGTCCCTAAAGACATATA
1 CAAAGTCCCTAAAGACATATA
3658 ACACAAGGGC
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 8 0.16
42 18 0.35
43 25 0.49
ACGTcount: A:0.45, C:0.26, G:0.09, T:0.21
Consensus pattern (41 bp):
CAAAGTCCCTAAAGACATATATAACACAGAGACAACTATAT
Found at i:7469 original size:15 final size:15
Alignment explanation
Indices: 7446--7494 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
7436 AAGGAAGCAT
* *
7446 TTTCCTTCCTTCTCA
1 TTTCTTTCCTTCCCA
*
7461 TTTCTTTCC-TCCCC
1 TTTCTTTCCTTCCCA
7475 TCTTCTTTCCTTCCCA
1 T-TTCTTTCCTTCCCA
7491 TTTC
1 TTTC
7495 CTCCATACCA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 4 0.14
15 19 0.68
16 5 0.18
ACGTcount: A:0.04, C:0.43, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTCTTTCCTTCCCA
Found at i:7952 original size:118 final size:116
Alignment explanation
Indices: 7744--8192 Score: 592
Period size: 109 Copynumber: 3.9 Consensus size: 116
7734 TTCTTTGGTA
* * * * *
7744 ATTTTCATAATTCATAAAGATTTAAGTGGATCTTTAGTTGAATATGAAA-TCAAGGTTAAGTAAC
1 ATTTTCATAATTCATTAAGATTTAAGTGAATCTTTAATTGAATTTGAAACT-AAGGTTAAGTGAC
* *
7808 CTTAAAACTTTAGGTTTAATTAAGTGATTACAACTTTTAGTTTTGAAATTTGGG
65 CTTAAAACTTTAGGTTTAATTAAGTGATTATAACCTTTAG-TTTGAAA-TTGGG
* *
7862 ATTTTCATAATTCATTATGATTTAAGTGAATCTTTAATTGAATTTGAAGCTAAGGTTAAGTGACC
1 ATTTTCATAATTCATTAAGATTTAAGTGAATCTTTAATTGAATTTGAAACTAAGGTTAAGTGACC
*
7927 TTAAAACTTTAGGTTTAATTAAGTGATTATAACCTTTAG--TG-----GTG
66 TTAAAACTTTAGGTTTAATTAAGTGATTATAACCTTTAGTTTGAAATTGGG
* * *
7971 ATTTTCATGATTCACTATGATTTAAGTGAATCTTTAATTGAATTTGAAACTAAGGTTAAGTGACC
1 ATTTTCATAATTCATTAAGATTTAAGTGAATCTTTAATTGAATTTGAAACTAAGGTTAAGTGACC
* * *
8036 TTAAAAATTTAGGTTTAATTAAGTAATTATAACCTTTAGTTGATAAAAGTTGGG
66 TTAAAACTTTAGGTTTAATTAAGTGATTATAACCTTTAGTT--TGAAA-TTGGG
* * *
8090 AATTTTCATAATTCATTAAGATTTAAGTGAATCTTTAATTGAATTTGAAATTGAGGTTAAATGAC
1 -ATTTTCATAATTCATTAAGATTTAAGTGAATCTTTAATTGAATTTGAAACTAAGGTTAAGTGAC
*
8155 C-TAAAACTTAAGGTTTAATTAAGTGATTATAACCTTTA
65 CTTAAAACTTTAGGTTTAATTAAGTGATTATAACCTTTA
8193 ATAAATAAAC
Statistics
Matches: 293, Mismatches: 26, Indels: 23
0.86 0.08 0.07
Matches are distributed among these distances:
109 101 0.34
113 1 0.00
115 2 0.01
118 93 0.32
119 37 0.13
120 59 0.20
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (116 bp):
ATTTTCATAATTCATTAAGATTTAAGTGAATCTTTAATTGAATTTGAAACTAAGGTTAAGTGACC
TTAAAACTTTAGGTTTAATTAAGTGATTATAACCTTTAGTTTGAAATTGGG
Found at i:8123 original size:120 final size:120
Alignment explanation
Indices: 7971--8260 Score: 366
Period size: 120 Copynumber: 2.4 Consensus size: 120
7961 TTTAGTGGTG
* * * *
7971 ATTTTCATGATTCACTATGATTTAAGTGAATCTTTAATTGAATTTGAAACTAAGGTTAAGTGACC
1 ATTTTCATAATTCATTAAGATTTAAGTGAATCTTTAATTGAATTTGAAACTAAGGTTAAATGACC
* * ** *
8036 TTAAAAATTTAGGTTTAATTAAGTAATTATAACCTTTAGTTGATAAA-AGTTGGGA
66 -TAAAAATTAAGGTTTAATTAAGTAATTATAACCTTTAATAAATAAATAGTTGGAA
* *
8091 ATTTTCATAATTCATTAAGATTTAAGTGAATCTTTAATTGAATTTGAAATTGAGGTTAAATGACC
1 ATTTTCATAATTCATTAAGATTTAAGTGAATCTTTAATTGAATTTGAAACTAAGGTTAAATGACC
* * **
8156 TAAAACTTAAGGTTTAATTAAGTGATTATAACCTTTAATAAATAAACTTTTTTGGAA
66 TAAAAATTAAGGTTTAATTAAGTAATTATAACCTTTAATAAATAAA--TAGTTGGAA
* * * *
8213 ACTTTCATAATTCTTTTAAGATTTAAGTAAATCCTTAATTGAATTTGA
1 ATTTTCATAATTC-ATTAAGATTTAAGTGAATCTTTAATTGAATTTGA
8261 TAAACTTTGA
Statistics
Matches: 147, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
119 40 0.27
120 59 0.40
122 17 0.12
123 31 0.21
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (120 bp):
ATTTTCATAATTCATTAAGATTTAAGTGAATCTTTAATTGAATTTGAAACTAAGGTTAAATGACC
TAAAAATTAAGGTTTAATTAAGTAATTATAACCTTTAATAAATAAATAGTTGGAA
Found at i:10400 original size:15 final size:15
Alignment explanation
Indices: 10380--10412 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
10370 TACCAAATTT
*
10380 ATTTATGTTTGTTTG
1 ATTTATGTTTGATTG
10395 ATTTATGTTTGATTG
1 ATTTATGTTTGATTG
10410 ATT
1 ATT
10413 GATTGATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (15 bp):
ATTTATGTTTGATTG
Found at i:10935 original size:42 final size:43
Alignment explanation
Indices: 10884--10977 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
10874 AAGTGCATAC
* * *
10884 CTAA-ATTCTA-CTCCATCTCTAGGTGATTTATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
10925 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
10970 CTAATATT
1 CTAATATT
10978 AATTGTTATT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:18463 original size:19 final size:18
Alignment explanation
Indices: 18426--18465 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
18416 TTCTTGAGAT
*
18426 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
18444 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
18463 AAT
1 AAT
18466 AAATCCTCAA
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:22916 original size:14 final size:14
Alignment explanation
Indices: 22897--22943 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
22887 TGAAAAATAG
22897 TAAAATGGTAAAAA
1 TAAAATGGTAAAAA
* * *
22911 TAAAAT-TTTAAAT
1 TAAAATGGTAAAAA
*
22924 TAAAATGGTAAAAG
1 TAAAATGGTAAAAA
22938 TAAAAT
1 TAAAAT
22944 AATTATAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.30
Consensus pattern (14 bp):
TAAAATGGTAAAAA
Found at i:23060 original size:151 final size:153
Alignment explanation
Indices: 22758--23065 Score: 433
Period size: 151 Copynumber: 2.0 Consensus size: 153
22748 CACAATAACC
* *
22758 TTTTAAATTAAAATGATAAAAATAAAATATTTATAAAAATATTGAATTTAATTAAATGCAAATGA
1 TTTTAAATTAAAATGATAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAAT-A
* *
22823 AGTTTTTACTTTTTAGTGGAATAAAACTGTATATTAAAATTTTTTAATACATCCAAGATTTTAAT
65 AG----TACTTTTTAGTAGAATAAAACTGTATATTAAAATGTTTTAATACATCCAAGATTTTAAT
* *
22888 GAAAAATAGTAAAATGGTAAAAATAAAA
126 GAAAAATAATAAAATGATAAAAATAAAA
* *
22916 TTTTAAATTAAAATGGTAAAAGTAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAAT-A
1 TTTTAAATTAAAATGATAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAA
* * *
22980 G-AGTTTTTAGTAGAATAAAACTGTATATTAAAATGTTTTAATATAT-CATAGTTTTTAATGAAA
66 GTACTTTTTAGTAGAATAAAACTGTATATTAAAATGTTTTAATACATCCA-AGATTTTAATGAAA
*
23043 AATAATAAAATTATAAAAATAAA
130 AATAATAAAATGATAAAAATAAA
23066 GTAATTATAA
Statistics
Matches: 137, Mismatches: 12, Indels: 9
0.87 0.08 0.06
Matches are distributed among these distances:
150 2 0.01
151 74 0.54
156 2 0.01
158 59 0.43
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (153 bp):
TTTTAAATTAAAATGATAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAA
GTACTTTTTAGTAGAATAAAACTGTATATTAAAATGTTTTAATACATCCAAGATTTTAATGAAAA
ATAATAAAATGATAAAAATAAAA
Found at i:23062 original size:17 final size:18
Alignment explanation
Indices: 23040--23085 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
23030 GTTTTTAATG
23040 AAAAATAATA-AAATTAT
1 AAAAATAATAGAAATTAT
*
23057 AAAAATAA-AGTAATTAT
1 AAAAATAATAGAAATTAT
*
23074 AAAGATAATAGA
1 AAAAATAATAGA
23086 TTTAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 1 0.04
17 21 0.88
18 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (18 bp):
AAAAATAATAGAAATTAT
Found at i:24584 original size:32 final size:32
Alignment explanation
Indices: 24543--24603 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
24533 AAATATATTT
*
24543 GAAAAATAAGGATATAATGGTCGATTCAATTA
1 GAAAAATAAGGATATAATAGTCGATTCAATTA
24575 GAAAAATAAGGATATAATAGTCGATTCAA
1 GAAAAATAAGGATATAATAGTCGATTCAA
24604 AAATTTCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (32 bp):
GAAAAATAAGGATATAATAGTCGATTCAATTA
Found at i:41298 original size:49 final size:49
Alignment explanation
Indices: 41226--41321 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
41216 AGTAGATCGA
41226 GACTTTTAGTAATTTTGGTGGGGTACACAAATAATATATACTCCGGAGC
1 GACTTTTAGTAATTTTGGTGGGGTACACAAATAATATATACTCCGGAGC
*
41275 GACTTTTAGTAATTTTGGTGGGGTATACAAATAATATATACTCCGGA
1 GACTTTTAGTAATTTTGGTGGGGTACACAAATAATATATACTCCGGA
41322 ACATTTGTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (49 bp):
GACTTTTAGTAATTTTGGTGGGGTACACAAATAATATATACTCCGGAGC
Found at i:44350 original size:58 final size:55
Alignment explanation
Indices: 44280--44394 Score: 194
Period size: 58 Copynumber: 2.0 Consensus size: 55
44270 TATCAGTTTC
*
44280 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCCTTATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTATAATAAATCCTAT--CCCC-TATCTCTACTTAATTATT
44338 CTTTCACACAATAAATATTATAATAAATCCTATCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTATAATAAATCCTATCCCCTATCTCTACTTAATTATT
44393 CT
1 CT
44395 ACAAAATAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
55 20 0.36
56 4 0.07
58 32 0.57
ACGTcount: A:0.34, C:0.25, G:0.01, T:0.40
Consensus pattern (55 bp):
CTTTCACACAATAAATATTATAATAAATCCTATCCCCTATCTCTACTTAATTATT
Found at i:44520 original size:42 final size:42
Alignment explanation
Indices: 44457--44539 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
44447 GCTAAGGATC
*
44457 ATGATTTGAGTTGAGTTTTTCTTAATTTACAAAGAATTTTCT
1 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
* *
44499 ATGATTTGAGTTGAGTATTTCTTGATTTACAGAGAATTTTC
1 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
44540 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (42 bp):
ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
Found at i:49364 original size:23 final size:23
Alignment explanation
Indices: 49332--49375 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
49322 AATTAAATTG
*
49332 CATCACAACAGTCACCACTAATC
1 CATCAAAACAGTCACCACTAATC
49355 CATCAAAACAGTCACCACTAA
1 CATCAAAACAGTCACCACTAA
49376 CCTTCTTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.36, G:0.05, T:0.16
Consensus pattern (23 bp):
CATCAAAACAGTCACCACTAATC
Found at i:49601 original size:2 final size:2
Alignment explanation
Indices: 49594--49622 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
49584 AACATTGAAT
49594 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 T
49623 TCAAACCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53309 original size:38 final size:38
Alignment explanation
Indices: 53266--53342 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
53256 CACGTGTAGT
* *
53266 CCGGGACAATACCGAAACAGAACGGGTCTACACGTGGA
1 CCGGGACAACACCGAAACAAAACGGGTCTACACGTGGA
53304 CCGGGACAACACCGAAACAAAACGGGTCTACACGTGGA
1 CCGGGACAACACCGAAACAAAACGGGTCTACACGTGGA
53342 C
1 C
53343 ACAACCGGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.35, C:0.29, G:0.27, T:0.09
Consensus pattern (38 bp):
CCGGGACAACACCGAAACAAAACGGGTCTACACGTGGA
Found at i:54790 original size:71 final size:71
Alignment explanation
Indices: 54670--54813 Score: 261
Period size: 71 Copynumber: 2.0 Consensus size: 71
54660 TTGATGGTGT
*
54670 TTGTCTCCCGTATCTTGAAGCAGCAATTCTTACAGAATTAGAAAGCATTATTTGTGAAACTGATA
1 TTGTCTCCCGTATCTTGAAGCAGCAATTCTTACAGAATTAGAAAACATTATTTGTGAAACTGATA
54735 TGTTCC
66 TGTTCC
* *
54741 TTGTCTCCCGTATCTTGAATCGGCAATTCTTACAGAATTAGAAAACATTATTTGTGAAACTGATA
1 TTGTCTCCCGTATCTTGAAGCAGCAATTCTTACAGAATTAGAAAACATTATTTGTGAAACTGATA
54806 TGTTCC
66 TGTTCC
54812 TT
1 TT
54814 TTGCAGTGGT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (71 bp):
TTGTCTCCCGTATCTTGAAGCAGCAATTCTTACAGAATTAGAAAACATTATTTGTGAAACTGATA
TGTTCC
Found at i:55529 original size:141 final size:136
Alignment explanation
Indices: 55268--55530 Score: 366
Period size: 141 Copynumber: 1.9 Consensus size: 136
55258 TTTTTTATTC
* *
55268 CTTTGCCTTTTGCAGGTCCTTGATGTCACTCTCGCCTTCGCTGTTTGTTGAGGTGAGCCTCTGAA
1 CTTTGCCTTTTGCAGGTCCTTGATGTCACTCTCGCATTCGCTGTTTGTTGAGGTCAGCCTCTGAA
* * *
55333 ATTTTTAATGCTCTTTTGGGTCTTTTGCCTTAAGCGGCTGATAAGCAACTTTTTTGTAGTTATCT
66 ATTTTTAATGCTCTTTTGGGTCTTTTGCCTGAAGCAGCTGATAAGCAACTCTTTTGTAGTTATCT
55398 TGATTT
131 TGATTT
* *
55404 CTTTGCCTTTTGCAGGTCTCCTTGATGTCACTCTCGCATTGGCTGTTTGTTGAGGTCCGCCCATC
1 CTTTGCCTTTTGCAGG--TCCTTGATGTCACTCTCGCATTCGCTGTTTGTTGAGGTCAG-CC-TC
* * * *
55469 TGAAAATTTTT-ATGCTCTTTTTGGTTGTTTTGCCTGAAGCAGCTTATAAGCATCTCTTTTGT
62 TG-AAATTTTTAATGCTC-TTTTGGGTCTTTTGCCTGAAGCAGCTGATAAGCAACTCTTTTGT
55531 TGTTCTCTCT
Statistics
Matches: 110, Mismatches: 11, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
136 16 0.15
138 37 0.34
139 2 0.02
140 10 0.09
141 45 0.41
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.44
Consensus pattern (136 bp):
CTTTGCCTTTTGCAGGTCCTTGATGTCACTCTCGCATTCGCTGTTTGTTGAGGTCAGCCTCTGAA
ATTTTTAATGCTCTTTTGGGTCTTTTGCCTGAAGCAGCTGATAAGCAACTCTTTTGTAGTTATCT
TGATTT
Found at i:58231 original size:41 final size:41
Alignment explanation
Indices: 58131--58259 Score: 141
Period size: 41 Copynumber: 3.1 Consensus size: 41
58121 TCAGGACAGA
* * * * * *
58131 ATTGAGCCAAACAATAATTAGAATCCTAAATCAGGGACTAA
1 ATTGAACCAAATAATAAATAGAATCCTAAATTAGGGACCAT
* * *
58172 ATTGTATCAAATAGTAAATAGAATCCTAAATTAGGGACCAT
1 ATTGAACCAAATAATAAATAGAATCCTAAATTAGGGACCAT
* ** *
58213 ATTGAACCAATTAATAAATATTATCCTATATTAGGGACCAT
1 ATTGAACCAAATAATAAATAGAATCCTAAATTAGGGACCAT
58254 ATTGAA
1 ATTGAA
58260 TACGGAAGCA
Statistics
Matches: 72, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (41 bp):
ATTGAACCAAATAATAAATAGAATCCTAAATTAGGGACCAT
Done.