Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015033.1 Corchorus olitorius cultivar O-4 contig15066, 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: 76473
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:1090 original size:58 final size:58
Alignment explanation
Indices: 980--1090 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 58
970 ATTAATCAAA
*
980 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAAGACGTTTTCGGACCAAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCAT-AAAAAAAGACGTTTTAGGACCAAGACT
* * *
1039 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACGTTTTAGGACC
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACC
1091 GAGGCATGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
58 19 0.40
59 13 0.28
60 15 0.32
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT
Found at i:3266 original size:203 final size:203
Alignment explanation
Indices: 2911--3295 Score: 666
Period size: 203 Copynumber: 1.9 Consensus size: 203
2901 GCTTAATAAC
* *
2911 TTTATGAATGGTGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTAAATAA
1 TTTATCAATGGTGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAATAAATAA
* *
2976 GATACAACACATTATTATTAATTATATATAACTATAACAAAAAAAGTAGTTGAACATTAGTGGTT
66 GATACAACACATTACTATTAATTATATAGAACTATAACAAAAAAAGTAGTTGAACATTAGTGGTT
3041 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
131 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
3106 CCGATTTT
196 CCGATTTT
*
3114 TTTATCAATGGTGAATGTTATTAATTT-TTAAGTCTAAGATTACTAACAAAGTTGTAATGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAATAAATAA
* * *
3178 GATACAACACATTACTGTT-ATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGG
66 GATACAACACATTACTATTAAT-TATATAGAACTATAAC-AAAAAAAGTAGTTGAACATTAGTGG
3242 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAA
129 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAA
3296 TTAAAAATAT
Statistics
Matches: 172, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
201 2 0.01
202 66 0.38
203 104 0.60
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (203 bp):
TTTATCAATGGTGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAATAAATAA
GATACAACACATTACTATTAATTATATAGAACTATAACAAAAAAAGTAGTTGAACATTAGTGGTT
GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
CCGATTTT
Found at i:3793 original size:6 final size:6
Alignment explanation
Indices: 3744--3785 Score: 75
Period size: 6 Copynumber: 6.8 Consensus size: 6
3734 GTTTAGACTT
3744 ATATAG TATATAG ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
3786 TAGATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (6 bp):
ATATAG
Found at i:14969 original size:75 final size:75
Alignment explanation
Indices: 14875--15024 Score: 264
Period size: 75 Copynumber: 2.0 Consensus size: 75
14865 AAATCATCAA
* *
14875 CCAAATGTTTTTGGGAGAATTTAAAAAAAGGGCAAAACACCAATAATATTTTGAGCTTACTACCA
1 CCAAATGTTTTTGGGAGAATTTAAAAAAAGGACAAAACACCAATAATATTTTGAGCTTACAACCA
14940 TAGGAAATTT
66 TAGGAAATTT
* *
14950 CCAAATGTTTTTGGGAGAATTTCAAAAAAGGACAAAGCACCAATAATATTTTGAGCTTACAACCA
1 CCAAATGTTTTTGGGAGAATTTAAAAAAAGGACAAAACACCAATAATATTTTGAGCTTACAACCA
15015 TAGGAAATTT
66 TAGGAAATTT
15025 TAATTACTAG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (75 bp):
CCAAATGTTTTTGGGAGAATTTAAAAAAAGGACAAAACACCAATAATATTTTGAGCTTACAACCA
TAGGAAATTT
Found at i:16733 original size:15 final size:16
Alignment explanation
Indices: 16713--16751 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
16703 TAAAATGGCA
16713 GATGAA-AATAAACAT
1 GATGAACAATAAACAT
16728 GATGAAGCCAATAAACAT
1 GATGAA--CAATAAACAT
16746 GATGAA
1 GATGAA
16752 GTCCAAGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
18 15 0.71
ACGTcount: A:0.54, C:0.10, G:0.18, T:0.18
Consensus pattern (16 bp):
GATGAACAATAAACAT
Found at i:16740 original size:18 final size:19
Alignment explanation
Indices: 16719--16757 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
16709 GGCAGATGAA
16719 AATAAACATGATGAAG-CC
1 AATAAACATGATGAAGTCC
16737 AATAAACATGATGAAGTCC
1 AATAAACATGATGAAGTCC
16756 AA
1 AA
16758 GTCCATGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.18
Consensus pattern (19 bp):
AATAAACATGATGAAGTCC
Found at i:22040 original size:32 final size:32
Alignment explanation
Indices: 22001--22066 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
21991 AATACTATCA
22001 TTTTTCTAATCACCTTGCTTTAATATTCAAAT
1 TTTTTCTAATCACCTTGCTTTAATATTCAAAT
22033 TTTTTCTAATCACCTTGCTTTAATATTCAAAT
1 TTTTTCTAATCACCTTGCTTTAATATTCAAAT
22065 TT
1 TT
22067 CAAAAGCTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.27, C:0.18, G:0.03, T:0.52
Consensus pattern (32 bp):
TTTTTCTAATCACCTTGCTTTAATATTCAAAT
Found at i:22464 original size:23 final size:24
Alignment explanation
Indices: 22420--22466 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
22410 GCTGTTAATA
*
22420 ATATTCTAATCCAACTTCATTTTG
1 ATATTCTAATCCAACTTAATTTTG
*
22444 ATATTTTAAT-CAACTTAATTTTG
1 ATATTCTAATCCAACTTAATTTTG
22467 TCTAAAACCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.32, C:0.15, G:0.04, T:0.49
Consensus pattern (24 bp):
ATATTCTAATCCAACTTAATTTTG
Found at i:28843 original size:2 final size:2
Alignment explanation
Indices: 28836--28877 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
28826 TTATTTAAAA
*
28836 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28878 GATTTTGCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33818 original size:18 final size:19
Alignment explanation
Indices: 33792--33829 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
33782 ATAGTCTTCA
33792 AAGAACAATAGG-AATGGC
1 AAGAACAATAGGAAATGGC
*
33810 AAGAGCAATAGGAAATGGC
1 AAGAACAATAGGAAATGGC
33829 A
1 A
33830 CAAGCATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.50, C:0.11, G:0.29, T:0.11
Consensus pattern (19 bp):
AAGAACAATAGGAAATGGC
Found at i:51613 original size:72 final size:72
Alignment explanation
Indices: 51496--51911 Score: 591
Period size: 72 Copynumber: 5.8 Consensus size: 72
51486 TCCTCTTCTT
* * * *
51496 CATTGCGATTGTTGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAA
1 CATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTA
*
51561 TCTTTCA
66 TCTTCCA
51568 CATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTA
1 CATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTA
*
51633 TCTTCCG
66 TCTTCCA
* *
51640 TATTGCGGTTGTAGCCGAGGCAGTTCCAACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTA
1 CATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTA
* *
51705 TTTTCCG
66 TCTTCCA
* * * ** * ** *
51712 TATTGGGGATGTAGCCGAGGTGGTTCCAACATTTGGCAGTCCTTCGCACAATCCTTACATGATAA
1 CATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTA
51777 TCTTCCA
66 TCTTCCA
* * *
51784 TATTGCGGTTGTAGCCGAGGCAGTTCCCACGTTTGGCAGTCTTTCGCACAATCCTTATGTGATTA
1 CATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTA
* *
51849 TCTCCCT
66 TCTTCCA
* *
51856 CATTGCGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCGCAATCCTTA
1 CATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
51912 ATCCCCGGGG
Statistics
Matches: 309, Mismatches: 35, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
71 23 0.07
72 286 0.93
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (72 bp):
CATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTA
TCTTCCA
Found at i:52565 original size:16 final size:16
Alignment explanation
Indices: 52540--52572 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
52530 CTGCAAAATC
52540 TTGCCACAACAGAATG
1 TTGCCACAACAGAATG
*
52556 TTGCCGCAACAGAATG
1 TTGCCACAACAGAATG
52572 T
1 T
52573 CCCTTGTAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.21
Consensus pattern (16 bp):
TTGCCACAACAGAATG
Found at i:53431 original size:43 final size:42
Alignment explanation
Indices: 53109--53437 Score: 423
Period size: 43 Copynumber: 7.8 Consensus size: 42
53099 CCAATAACCA
*
53109 AAAGTCCCCAAACACATATATAACACA-AGGGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGA-GGCATCTATATT-C
* *
53152 AAAGTCCTCAAACACATATATAACACAGAGGCACCTATATTC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTC
* * * * *
53194 -AAGTCCCCAAACACATATATAATATAGGGGCACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATT-C
*
53236 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATA-TC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTC
* * * *
53277 AAAGTCCCCCAACACATATATAACACAGGGGCACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATT-C
* *
53320 AAAGTCCTCAAACACATATATAACACAGATGCATCTATA-TC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTC
* *
53361 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATT-C
*
53404 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
53438 TTCTCCTTAT
Statistics
Matches: 248, Mismatches: 31, Indels: 14
0.85 0.11 0.05
Matches are distributed among these distances:
41 106 0.43
42 6 0.02
43 135 0.54
44 1 0.00
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.22
Consensus pattern (42 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTC
Found at i:53466 original size:84 final size:84
Alignment explanation
Indices: 53109--53437 Score: 543
Period size: 84 Copynumber: 3.9 Consensus size: 84
53099 CCAATAACCA
* * *
53109 AAAGTCCCCAAACACATATATAACACAAGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
*
53174 ACACAGAGGCACCTATATTC
66 ACACAGAGGCATCTATA-TC
* * *
53194 -AAGTCCCCAAACACATATATAATATAGGGGCACCTTTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
53258 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
* *
53277 AAAGTCCCCCAACACATATATAACACAGGGGCACCTTTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
*
53342 ACACAGATGCATCTATATC
66 ACACAGAGGCATCTATATC
*
53361 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
53426 ACACAGAGGCAT
66 ACACAGAGGCAT
53438 TTCTCCTTAT
Statistics
Matches: 228, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
83 2 0.01
84 226 0.99
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.22
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:55776 original size:10 final size:11
Alignment explanation
Indices: 55762--55790 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
55752 CATCTTCCTC
55762 CAAAACAAAAG
1 CAAAACAAAAG
55773 -AAAACAAAAG
1 CAAAACAAAAG
55783 CAAAACAA
1 CAAAACAA
55791 GATCAAGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.76, C:0.17, G:0.07, T:0.00
Consensus pattern (11 bp):
CAAAACAAAAG
Found at i:61407 original size:56 final size:57
Alignment explanation
Indices: 61323--61432 Score: 152
Period size: 56 Copynumber: 1.9 Consensus size: 57
61313 TTTAATCTGA
* * *
61323 CACCTTTATTTCTTTTTATCTTTCTTAATAT-TTTCTTAAGTTTTGCTGATTAATCCT
1 CACCTTAATTTCTTTTTATCTTTATTAATATATTT-TGAAGTTTTGCTGATTAATCCT
* *
61380 CACCTTAATTTC-TTTTATCTTTATTAATATATTTTGGAGTTTTGTTGATTAAT
1 CACCTTAATTTCTTTTTATCTTTATTAATATATTTTGAAGTTTTGCTGATTAAT
61433 ATATTCTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
56 33 0.70
57 14 0.30
ACGTcount: A:0.22, C:0.14, G:0.07, T:0.57
Consensus pattern (57 bp):
CACCTTAATTTCTTTTTATCTTTATTAATATATTTTGAAGTTTTGCTGATTAATCCT
Found at i:65972 original size:20 final size:20
Alignment explanation
Indices: 65947--65986 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
65937 CTCAACTTAT
65947 TTTACAAGAAATTGGCCATA
1 TTTACAAGAAATTGGCCATA
65967 TTTACAAGAAATTGGCCATA
1 TTTACAAGAAATTGGCCATA
65987 AAACGTTACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (20 bp):
TTTACAAGAAATTGGCCATA
Found at i:66233 original size:10 final size:10
Alignment explanation
Indices: 66218--66263 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
66208 TATTCTCGAT
66218 ATATCCGTAA
1 ATATCCGTAA
66228 ATATCCGTAA
1 ATATCCGTAA
* **
66238 GTATTTGTAA
1 ATATCCGTAA
*
66248 ATATCTGTAA
1 ATATCCGTAA
66258 ATATCC
1 ATATCC
66264 ATATTAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:66700 original size:40 final size:40
Alignment explanation
Indices: 66656--66735 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
66646 TAACATTCCC
66656 ATTTTGGTATTCGACACAACACTTCTATGGCTTGAATATT
1 ATTTTGGTATTCGACACAACACTTCTATGGCTTGAATATT
*
66696 ATTTTGGTATTCGACACAACACTTTTATGGCTTGAATATT
1 ATTTTGGTATTCGACACAACACTTCTATGGCTTGAATATT
66736 TTAACTAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (40 bp):
ATTTTGGTATTCGACACAACACTTCTATGGCTTGAATATT
Found at i:67304 original size:13 final size:12
Alignment explanation
Indices: 67265--67316 Score: 68
Period size: 12 Copynumber: 4.2 Consensus size: 12
67255 CGATATTTCA
*
67265 ATATATTCATCG
1 ATATATCCATCG
67277 ATATATCCATCG
1 ATATATCCATCG
*
67289 ATATATCCGTTCG
1 ATATATCC-ATCG
*
67302 ATATATCCATAG
1 ATATATCCATCG
67314 ATA
1 ATA
67317 CCTGTATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 24 0.69
13 11 0.31
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.37
Consensus pattern (12 bp):
ATATATCCATCG
Found at i:74499 original size:25 final size:25
Alignment explanation
Indices: 74471--74525 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
74461 ATAACTGAAA
74471 TATTTACATTAATT-AAATTCTTAGG
1 TATTT-CATTAATTCAAATTCTTAGG
**
74496 TATTTTTTTAATTCAAATTCTTAGG
1 TATTTCATTAATTCAAATTCTTAGG
74521 TATTT
1 TATTT
74526 GTGCAAACGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 6 0.22
25 21 0.78
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (25 bp):
TATTTCATTAATTCAAATTCTTAGG
Found at i:74507 original size:24 final size:25
Alignment explanation
Indices: 74479--74525 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
74469 AATATTTACA
74479 TTAATT-AAATTCTTAGGTATTTTT
1 TTAATTCAAATTCTTAGGTATTTTT
74503 TTAATTCAAATTCTTAGGTATTT
1 TTAATTCAAATTCTTAGGTATTT
74526 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 (25 bp):
TTAATTCAAATTCTTAGGTATTTTT
Found at i:75042 original size:203 final size:204
Alignment explanation
Indices: 74597--75199 Score: 1053
Period size: 203 Copynumber: 3.0 Consensus size: 204
74587 TTCCTTAATA
*
74597 ATAAATAAATCGGATC-TTAATATCTTTTA-AAGTTTTGAAATTTTGTTTGACATTGATC---CT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAA-TTTTGAAATTTTGTTTGACATTGATCTAATT
74657 TAATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTTCTATATATATAAT
65 TAATTTAATAAATCAACCACTAATGTTCAACTAA-TTTTTTTTGGTATAGTTCTATATATATAAT
74722 AGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAAC
129 AGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAAC
74787 ATTCACCATTG
194 ATTCACCATTG
74798 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
74863 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAG
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAG
*
74928 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGAATT-AAAAATTAATAACAT
131 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
*
74992 TTACCATTG
196 TCACCATTG
*
75001 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATTTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* * *
75066 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTTGTATAGTT-T-TATATATAATAA
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAG
75129 TAATGTGTTGTATCTTATTCA-TCACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACA
131 TAATGTGTTGTATCTTATTCACT-ACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACA
75193 TTCACCA
195 TTCACCA
75200 AAGTTATTAA
Statistics
Matches: 386, Mismatches: 9, Indels: 13
0.95 0.02 0.03
Matches are distributed among these distances:
200 1 0.00
201 73 0.19
202 60 0.16
203 137 0.35
204 80 0.21
205 35 0.09
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (204 bp):
ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAG
TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
TCACCATTG
Done.