Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018917.1 Corchorus olitorius cultivar O-4 contig18950, 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: 95291
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:3101 original size:24 final size:24
Alignment explanation
Indices: 3065--3115 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
3055 TCATTTTCAC
*
3065 CATTTTCAACATTCTCACCTTCTG
1 CATTTTCAACATTCTCACCATCTG
*
3089 CATTTTCACCATTCTCACCATCTG
1 CATTTTCAACATTCTCACCATCTG
3113 CAT
1 CAT
3116 GCTCACCAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.35, G:0.04, T:0.39
Consensus pattern (24 bp):
CATTTTCAACATTCTCACCATCTG
Found at i:3121 original size:24 final size:24
Alignment explanation
Indices: 3074--3123 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
3064 CCATTTTCAA
* **
3074 CATTCTCACCTTCTGCATTTTCAC
1 CATTCTCACCATCTGCATGCTCAC
3098 CATTCTCACCATCTGCATGCTCAC
1 CATTCTCACCATCTGCATGCTCAC
3122 CA
1 CA
3124 GCATTCTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.20, C:0.40, G:0.06, T:0.34
Consensus pattern (24 bp):
CATTCTCACCATCTGCATGCTCAC
Found at i:5325 original size:61 final size:60
Alignment explanation
Indices: 5227--5375 Score: 190
Period size: 61 Copynumber: 2.5 Consensus size: 60
5217 CACCAAGTCA
* * * *
5227 AAAACCCAACACATTAAAGAAAGAAAATTGACCAACTTCCCATATATTATATTCGAATAC
1 AAAACCCAACACATAAAAAAAACAAAATTGACCAACTTCCCATATATTATATTCAAATAC
* * * *
5287 AAAACCCAACACATAAAACAAAACAAAATTTACTAACTTTCCATATATTCTATTCAAATAC
1 AAAACCCAACACATAAAA-AAAACAAAATTGACCAACTTCCCATATATTATATTCAAATAC
* *
5348 AATACCCAACACATAAAAGAAAATAAAA
1 AAAACCCAACACATAAAA-AAAACAAAA
5376 AATTTCCAAC
Statistics
Matches: 77, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
60 17 0.22
61 60 0.78
ACGTcount: A:0.53, C:0.21, G:0.03, T:0.22
Consensus pattern (60 bp):
AAAACCCAACACATAAAAAAAACAAAATTGACCAACTTCCCATATATTATATTCAAATAC
Found at i:5414 original size:61 final size:61
Alignment explanation
Indices: 5230--5407 Score: 189
Period size: 61 Copynumber: 2.9 Consensus size: 61
5220 CAAGTCAAAA
* * * * * *
5230 ACCCAACACAT-TAAAGAAAGAAAATTGACCAACTTCCCATATATTATATTCGAATACAAA
1 ACCCAACACATAAAAAAAAAAAAAATTTACCAACTTACCATATATTATATTCGAATACAAT
* * * * * *
5290 ACCCAACACATAAAACAAAACAAAATTTACTAACTTTCCATATATTCTATTCAAATACAAT
1 ACCCAACACATAAAAAAAAAAAAAATTTACCAACTTACCATATATTATATTCGAATACAAT
* * *
5351 ACCCAACACATAAAAGAAAATAAAAAATTT-CCAACTTACTATATATTTTATTTGAAT
1 ACCCAACACATAAAA-AAAA-AAAAAATTTACCAACTTACCATATATTATATTCGAAT
5408 GCATACCACC
Statistics
Matches: 97, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
60 11 0.11
61 54 0.56
62 24 0.25
63 8 0.08
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.28
Consensus pattern (61 bp):
ACCCAACACATAAAAAAAAAAAAAATTTACCAACTTACCATATATTATATTCGAATACAAT
Found at i:11165 original size:7 final size:7
Alignment explanation
Indices: 11153--11178 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
11143 TTTTGTTATT
11153 ATTTCCA
1 ATTTCCA
11160 ATTTCCA
1 ATTTCCA
11167 ATTTCCA
1 ATTTCCA
11174 ATTTC
1 ATTTC
11179 TATTTTCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (7 bp):
ATTTCCA
Found at i:18718 original size:25 final size:25
Alignment explanation
Indices: 18685--18735 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
18675 TGCATCAAGG
*
18685 AACATGCAAACACTGGA-AATTAATC
1 AACACGCAAACA-TGGAGAATTAATC
*
18710 AACACGCAAACATGGAGCATTAATC
1 AACACGCAAACATGGAGAATTAATC
18735 A
1 A
18736 CAACCAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.47, C:0.22, G:0.14, T:0.18
Consensus pattern (25 bp):
AACACGCAAACATGGAGAATTAATC
Found at i:21305 original size:58 final size:58
Alignment explanation
Indices: 21185--21306 Score: 145
Period size: 58 Copynumber: 2.1 Consensus size: 58
21175 TTGTTACGTG
* * * * *
21185 TGATAACTCTTGCATAATCGAGTTTGTATGATCATTCCTCAATGCGAATAAAGGATGG
1 TGATGACTCTTGCATAATCGAGTTTGTAGGATCATTCCTCAATACGAATAAAGGACGA
* * * * **
21243 TGATGACTCTTGCATAATCGAGTTTGTAGGATTATTCCTGAATATGGATATGGGACGA
1 TGATGACTCTTGCATAATCGAGTTTGTAGGATCATTCCTCAATACGAATAAAGGACGA
21301 TGATGA
1 TGATGA
21307 TGTGCTACAA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.34
Consensus pattern (58 bp):
TGATGACTCTTGCATAATCGAGTTTGTAGGATCATTCCTCAATACGAATAAAGGACGA
Found at i:38959 original size:36 final size:36
Alignment explanation
Indices: 38918--38991 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
38908 TATTAAACCG
38918 GAAACACTATTTCCTGTTCTCGATGACCAATAAGCA
1 GAAACACTATTTCCTGTTCTCGATGACCAATAAGCA
38954 GAAACACTATTTCCTGTTCTCGATGACCAATAAGCA
1 GAAACACTATTTCCTGTTCTCGATGACCAATAAGCA
38990 GA
1 GA
38992 TAAATTTACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (36 bp):
GAAACACTATTTCCTGTTCTCGATGACCAATAAGCA
Found at i:43133 original size:6 final size:6
Alignment explanation
Indices: 43122--43150 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
43112 CATATTAGGC
43122 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
43151 TCAGTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:43646 original size:22 final size:21
Alignment explanation
Indices: 43617--43697 Score: 90
Period size: 22 Copynumber: 3.8 Consensus size: 21
43607 TGAATATTTG
*
43617 TATGAAATTTTGATAATTACCC
1 TATGAAATTTTGATAATTA-CA
*
43639 TATTAAATTTTGATAATTACA
1 TATGAAATTTTGATAATTACA
* * *
43660 TATGAAATTGTGATAAACTCCA
1 TATGAAATTTTGAT-AATTACA
*
43682 TATGAAACTTTGATAA
1 TATGAAATTTTGATAA
43698 CCTAACTATA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
21 15 0.30
22 35 0.70
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.40
Consensus pattern (21 bp):
TATGAAATTTTGATAATTACA
Found at i:43974 original size:2 final size:2
Alignment explanation
Indices: 43969--44004 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
43959 AGTGTGTGTG
43969 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44005 CACACACATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44773 original size:35 final size:35
Alignment explanation
Indices: 44727--44793 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
44717 TAAGCTTTGT
* *
44727 AAACATCTTAAGACCCCACTAACTTCAGTATCTCC
1 AAACACCTTAAGACCCCACTAACTTCAATATCTCC
* *
44762 AAACACCTTAAGATCCTACTAACTTCAATATC
1 AAACACCTTAAGACCCCACTAACTTCAATATC
44794 AAAGAGGATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.37, C:0.31, G:0.04, T:0.27
Consensus pattern (35 bp):
AAACACCTTAAGACCCCACTAACTTCAATATCTCC
Found at i:45617 original size:16 final size:16
Alignment explanation
Indices: 45598--45629 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
45588 CATGGTCATT
45598 GTACCTTATGGACTTA
1 GTACCTTATGGACTTA
45614 GTACCTTATGGACTTA
1 GTACCTTATGGACTTA
45630 CGTTTAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (16 bp):
GTACCTTATGGACTTA
Found at i:46728 original size:21 final size:21
Alignment explanation
Indices: 46702--46747 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
46692 TAGGTGAAAG
46702 ATTATATTAGGTTGGATGAGA
1 ATTATATTAGGTTGGATGAGA
46723 ATTATATTAGGTTGGATGAGA
1 ATTATATTAGGTTGGATGAGA
46744 ATTA
1 ATTA
46748 AAAAATCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (21 bp):
ATTATATTAGGTTGGATGAGA
Found at i:47294 original size:2 final size:2
Alignment explanation
Indices: 47287--47316 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
47277 AAGAGGGAGG
47287 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
47317 AGGGCTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:49082 original size:26 final size:26
Alignment explanation
Indices: 49053--49106 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
49043 AAATTCATTA
49053 TTCATAATGTTCAAGTCTCTTGAATG
1 TTCATAATGTTCAAGTCTCTTGAATG
49079 TTCATAATGTTCAAGTCTCTTGAATG
1 TTCATAATGTTCAAGTCTCTTGAATG
49105 TT
1 TT
49107 AATCACAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (26 bp):
TTCATAATGTTCAAGTCTCTTGAATG
Found at i:49857 original size:27 final size:29
Alignment explanation
Indices: 49827--49896 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
49817 GCTGTGAAAC
* * *
49827 TTTAAAATGGTT-A-ACAAGGTTGACAGT
1 TTTAAAATGGTTGACAAAAAGTTGAAAGT
49854 TTTAAAATGGTTGACAAAAAGTTGAAAGT
1 TTTAAAATGGTTGACAAAAAGTTGAAAGT
49883 TTTAAAATGGTTGA
1 TTTAAAATGGTTGA
49897 TAAGGGTTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 12 0.32
28 1 0.03
29 25 0.66
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.34
Consensus pattern (29 bp):
TTTAAAATGGTTGACAAAAAGTTGAAAGT
Found at i:51624 original size:41 final size:41
Alignment explanation
Indices: 51559--51841 Score: 270
Period size: 41 Copynumber: 6.7 Consensus size: 41
51549 AAATTGCCCT
*
51559 TGTGTTATAATTGTGTTT-AGGGACTTTAGTATGGATGCCTC
1 TGTGTTATAAATGTGTTTGA-GGACTTTAGTATGGATGCCTC
* *
51600 TATGTTATAAATGTGTTTGAGGACTTTTAG-ATAGAATTGCC-C
1 TGTGTTATAAATGTGTTTGAGGAC-TTTAGTAT-GGA-TGCCTC
* * *
51642 TTGTGTTATAATTGTGTTTGGGGACTTT-GATATAGATGCCTC
1 -TGTGTTATAAATGTGTTTGAGGACTTTAG-TATGGATGCCTC
* * * *
51684 TGTGTTATAAATGTGTTTGAGGACTTTGGAATAGAGGTGCCCC
1 TGTGTTATAAATGTGTTTGAGGACTTTAGTAT-G-GATGCCTC
* * *
51727 TGTGTTATAAATGTGTTTGGGGACTTTTGTATTGATGCCTC
1 TGTGTTATAAATGTGTTTGAGGACTTTAGTATGGATGCCTC
* *
51768 TGTGTTATAAATGTGTTTGAGGACTTTAGAAAGAGAATTGTCCT-
1 TGTGTTATAAATGTGTTTGAGGACTTTAGTATG-G-A-TG-CCTC
* *
51812 TGTGTTATAATTGTGTTTGGGGACTTTAGT
1 TGTGTTATAAATGTGTTTGAGGACTTTAGT
51842 TATTGGGTAA
Statistics
Matches: 199, Mismatches: 28, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
41 88 0.44
42 16 0.08
43 63 0.32
44 29 0.15
45 3 0.02
ACGTcount: A:0.22, C:0.09, G:0.27, T:0.42
Consensus pattern (41 bp):
TGTGTTATAAATGTGTTTGAGGACTTTAGTATGGATGCCTC
Found at i:51648 original size:84 final size:84
Alignment explanation
Indices: 51545--51841 Score: 436
Period size: 84 Copynumber: 3.5 Consensus size: 84
51535 CATTTGCCAT
* * *
51545 ATAGAAATTGCCCTTGTGTTATAATTGTGTTTAGGGACTTTAGTATGGATGCCTCTATGTTATAA
1 ATAG-AATTGCCCTTGTGTTATAATTGTGTTTGGGGACTTTAGTATAGATGCCTCTGTGTTATAA
51610 ATGTGTTTGAGGACTTTTAG-
65 ATGTGTTTGAGGAC-TTTAGA
51630 ATAGAATTGCCCTTGTGTTATAATTGTGTTTGGGGACTTT-GATATAGATGCCTCTGTGTTATAA
1 ATAGAATTGCCCTTGTGTTATAATTGTGTTTGGGGACTTTAG-TATAGATGCCTCTGTGTTATAA
*
51694 ATGTGTTTGAGGACTTTGGA
65 ATGTGTTTGAGGACTTTAGA
** * * * *
51714 ATAGAGGTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTTGTATTGATGCCTCTGTGTTATAAA
1 ATAGAATTGCCCTTGTGTTATAATTGTGTTTGGGGACTTTAGTATAGATGCCTCTGTGTTATAAA
51779 TGTGTTTGAGGACTTTAGAA
66 TGTGTTTGAGGACTTTAG-A
* *
51799 AGAGAATTGTCCTTGTGTTATAATTGTGTTTGGGGACTTTAGT
1 ATAGAATTGCCCTTGTGTTATAATTGTGTTTGGGGACTTTAGT
51842 TATTGGGTAA
Statistics
Matches: 191, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
83 5 0.03
84 144 0.75
85 42 0.22
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.42
Consensus pattern (84 bp):
ATAGAATTGCCCTTGTGTTATAATTGTGTTTGGGGACTTTAGTATAGATGCCTCTGTGTTATAAA
TGTGTTTGAGGACTTTAGA
Found at i:56234 original size:56 final size:56
Alignment explanation
Indices: 56158--56268 Score: 195
Period size: 56 Copynumber: 2.0 Consensus size: 56
56148 TCCTATCGTT
* *
56158 TTCATGTCTTGTGAAGGTGTTTTTATGACTTTTTGAGGTGATTTGCTGCTTAGTTC
1 TTCATGTCTTGCGAAGGTGTTTTTATGACTTTTTGAGGTGATTTGCTACTTAGTTC
*
56214 TTCATGTCTTGCGAATGTGTTTTTATGACTTTTTGAGGTGATTTGCTACTTAGTT
1 TTCATGTCTTGCGAAGGTGTTTTTATGACTTTTTGAGGTGATTTGCTACTTAGTT
56269 TGTTCATTTG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.15, C:0.11, G:0.23, T:0.50
Consensus pattern (56 bp):
TTCATGTCTTGCGAAGGTGTTTTTATGACTTTTTGAGGTGATTTGCTACTTAGTTC
Found at i:56466 original size:22 final size:22
Alignment explanation
Indices: 56428--56470 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
56418 TTCTCTTGTT
*
56428 TCGACCTTCTGACGGGTCGAAC
1 TCGACCTTCTCACGGGTCGAAC
56450 TCGACCTTCATCA-GGGTCGAA
1 TCGACCTTC-TCACGGGTCGAA
56471 ACAGGCTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (22 bp):
TCGACCTTCTCACGGGTCGAAC
Found at i:61755 original size:30 final size:31
Alignment explanation
Indices: 61696--61758 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
61686 TATCTCTTCC
*
61696 ACACAATATCCAAGATATGTCAGAAAATCTA
1 ACACAATAGCCAAGATATGTCAGAAAATCTA
* * *
61727 ACACAATAGCCAATA-ATTTCAGAGAATCTA
1 ACACAATAGCCAAGATATGTCAGAAAATCTA
61757 AC
1 AC
61759 CTTATCTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.22
Consensus pattern (31 bp):
ACACAATAGCCAAGATATGTCAGAAAATCTA
Found at i:61857 original size:134 final size:136
Alignment explanation
Indices: 61608--61945 Score: 439
Period size: 135 Copynumber: 2.5 Consensus size: 136
61598 TAATTTTATC
* * * *
61608 TTCACAGAATCTAACCCTATCTCAATCTAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCAT
1 TTCAGAGAATCTAACCTTATCTCAATCCAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCGT
* *** * * * *
61673 TAATTTGAATCGTTATCTCTTCCACACAATATCCAAGATATGTCAGAAAATCTAACACAATAGCC
66 TGATGAAAAACGTTATCTCTTCCACACAATATCCAAGATATGTCAAAAAATATAACACAACAGCC
*
61738 AATAAT
131 AATAAA
* *
61744 TTCAGAGAATCTAACCTTATCTTAATCCAACCGTTGGA-TAAAATTTG-GATTCAAATGTGACCG
1 TTCAGAGAATCTAACCTTATCTCAATCCAACCGTTGGATTAAAA-GTGAGATTCAAATGTGACCG
*
61807 TTGATGAAAAAC-TTATCTCTTCCACACAATATCCAAGATATGTCAAAAAATATAACACAACAGT
65 TTGATGAAAAACGTTATCTCTTCCACACAATATCCAAGATATGTCAAAAAATATAACACAACAGC
61871 CAATAAA
130 CAATAAA
* * * * * *
61878 TTGATGATAATTTAACATTATCTCAATCCAACCGTTGGATTCAAAGTGAGATTGAAATGTGACCG
1 TTCA-GAGAATCTAACCTTATCTCAATCCAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCG
61943 TTG
65 TTG
61946 TTTGAATCCT
Statistics
Matches: 174, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
134 57 0.33
135 59 0.34
136 58 0.33
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (136 bp):
TTCAGAGAATCTAACCTTATCTCAATCCAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCGT
TGATGAAAAACGTTATCTCTTCCACACAATATCCAAGATATGTCAAAAAATATAACACAACAGCC
AATAAA
Found at i:61969 original size:134 final size:135
Alignment explanation
Indices: 61608--61968 Score: 449
Period size: 136 Copynumber: 2.7 Consensus size: 135
61598 TAATTTTATC
* ** * *
61608 TTCACAGAATCTAACCCTATCTCAATCTAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCAT
1 TTCAGAGAATCTAACATTATCTCAATCCAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCGT
* * * * *
61673 TAATTTGAATCGTTATCTCTTCCACACAATATCCAAGATATGTCAGAAAATCTAACACAATAGCC
66 T-GTTTGAATCCTTATCTCTTCCACACAATATCCAAGATATGTCAAAAAATATAACACAACAGCC
*
61738 AATAAT
130 AATAAA
* * *
61744 TTCAGAGAATCTAACCTTATCTTAATCCAACCGTTGGA-TAAAATTTG-GATTCAAATGTGACCG
1 TTCAGAGAATCTAACATTATCTCAATCCAACCGTTGGATTAAAA-GTGAGATTCAAATGTGACCG
* ** *
61807 TTG-ATGAAAAACTTATCTCTTCCACACAATATCCAAGATATGTCAAAAAATATAACACAACAGT
65 TTGTTTG-AATCCTTATCTCTTCCACACAATATCCAAGATATGTCAAAAAATATAACACAACAGC
61871 CAATAAA
129 CAATAAA
* * * * *
61878 TTGATGATAATTTAACATTATCTCAATCCAACCGTTGGATTCAAAGTGAGATTGAAATGTGACCG
1 TTCA-GAGAATCTAACATTATCTCAATCCAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCG
*
61943 TTGTTTGAATCCTTATCTGTTCCACA
65 TTGTTTGAATCCTTATCTCTTCCACA
61969 AATTGTGTCT
Statistics
Matches: 191, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
133 2 0.01
134 59 0.31
135 54 0.28
136 74 0.39
137 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (135 bp):
TTCAGAGAATCTAACATTATCTCAATCCAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCGT
TGTTTGAATCCTTATCTCTTCCACACAATATCCAAGATATGTCAAAAAATATAACACAACAGCCA
ATAAA
Found at i:63345 original size:23 final size:23
Alignment explanation
Indices: 63312--63384 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
63302 TTATTTTGTT
*
63312 TTTTAAATTTATTTAAGTTGTAA
1 TTTTAACTTTATTTAAGTTGTAA
63335 TTTTAACTTTATTTAAGTTGT--
1 TTTTAACTTTATTTAAGTTGTAA
*
63356 TTTTAACTTAATTTAAGTTGTAA
1 TTTTAACTTTATTTAAGTTGTAA
63379 TTTTAA
1 TTTTAA
63385 GTTAAGTATA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.43
23 26 0.57
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.58
Consensus pattern (23 bp):
TTTTAACTTTATTTAAGTTGTAA
Found at i:63361 original size:21 final size:21
Alignment explanation
Indices: 63311--63376 Score: 96
Period size: 21 Copynumber: 3.0 Consensus size: 21
63301 TTTATTTTGT
*
63311 TTTTTAAATTTATTTAAGTTG
1 TTTTTAACTTTATTTAAGTTG
63332 TAATTTTAACTTTATTTAAGTTG
1 T--TTTTAACTTTATTTAAGTTG
*
63355 TTTTTAACTTAATTTAAGTTG
1 TTTTTAACTTTATTTAAGTTG
63376 T
1 T
63377 AATTTTAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
21 21 0.51
23 20 0.49
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (21 bp):
TTTTTAACTTTATTTAAGTTG
Found at i:63606 original size:12 final size:12
Alignment explanation
Indices: 63589--63633 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
63579 ATTATTCAAT
63589 ATATAAATGTAA
1 ATATAAATGTAA
**
63601 ATATAAATCAAA
1 ATATAAATGTAA
63613 ATATAAATTGTGAA
1 ATATAAA-TGT-AA
63627 ATATAAA
1 ATATAAA
63634 AAAGATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 17 0.63
13 1 0.04
14 9 0.33
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (12 bp):
ATATAAATGTAA
Found at i:63616 original size:24 final size:24
Alignment explanation
Indices: 63584--63649 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 24
63574 TTGTAATTAT
*
63584 TCAATATATAAATGTAAATATAAA
1 TCAAAATATAAATGTAAATATAAA
63608 TCAAAATATAAATTGTGAAATATAAA
1 TCAAAATATAAA-TGT-AAATATAAA
63634 --AAAGATATAAATGTAA
1 TCAAA-ATATAAATGTAA
63650 CTAAAGGAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 2 0.05
24 17 0.45
25 10 0.26
26 9 0.24
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.30
Consensus pattern (24 bp):
TCAAAATATAAATGTAAATATAAA
Found at i:85651 original size:76 final size:76
Alignment explanation
Indices: 85525--85678 Score: 308
Period size: 76 Copynumber: 2.0 Consensus size: 76
85515 TCTTAAGCGG
85525 CTTTGTTGTATCCCAAATACAATTTGTTTGAGATAGTCAGATAATATTATATTTGAGAAAGCTTG
1 CTTTGTTGTATCCCAAATACAATTTGTTTGAGATAGTCAGATAATATTATATTTGAGAAAGCTTG
85590 CTCCTCAAAGT
66 CTCCTCAAAGT
85601 CTTTGTTGTATCCCAAATACAATTTGTTTGAGATAGTCAGATAATATTATATTTGAGAAAGCTTG
1 CTTTGTTGTATCCCAAATACAATTTGTTTGAGATAGTCAGATAATATTATATTTGAGAAAGCTTG
85666 CTCCTCAAAGT
66 CTCCTCAAAGT
85677 CT
1 CT
85679 CGTTCACAAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (76 bp):
CTTTGTTGTATCCCAAATACAATTTGTTTGAGATAGTCAGATAATATTATATTTGAGAAAGCTTG
CTCCTCAAAGT
Found at i:89258 original size:1 final size:1
Alignment explanation
Indices: 89252--89282 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
89242 GAATTCTAGC
89252 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
89283 GCATCTAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.