Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016378.1 Corchorus olitorius cultivar O-4 contig16411, 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: 151586
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:9613 original size:2 final size:2
Alignment explanation
Indices: 9606--9648 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
9596 TAAATAAGTG
9606 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9647 TA
1 TA
9649 AGATAAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9872 original size:11 final size:11
Alignment explanation
Indices: 9829--9866 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
9819 TTCCTATGTA
*
9829 AAATAAATTAT
1 AAATTAATTAT
9840 CAAA-TAATTAT
1 -AAATTAATTAT
9851 AAATTAATTAT
1 AAATTAATTAT
9862 AAATT
1 AAATT
9867 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:19882 original size:60 final size:60
Alignment explanation
Indices: 19768--19882 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
19758 TGAATAAGAC
* * * * *
19768 AACTCAAGCTTATCCCAGATTAGTAAATCAAAACTGATGAACTACATATTTACAGTAGAT
1 AACTCAAGCTTATACCAGATTAGTAAATCAAAACCGATCAACAACATATGTACAGTAGAT
* *
19828 AACTCAAGCTTATACCAGATTAGTAAATCAGAACCGA-CCACAACATCATGTACAG
1 AACTCAAGCTTATACCAGATTAGTAAATCAAAACCGATCAACAACAT-ATGTACAG
19883 ATTGGTAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
59 6 0.13
60 41 0.87
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24
Consensus pattern (60 bp):
AACTCAAGCTTATACCAGATTAGTAAATCAAAACCGATCAACAACATATGTACAGTAGAT
Found at i:21789 original size:25 final size:25
Alignment explanation
Indices: 21755--21808 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
21745 ATAATTATAC
21755 ATGTTCCAGATTTACAAGACTTACT
1 ATGTTCCAGATTTACAAGACTTACT
21780 ATGTTCCAGATTTACAAGACTTACT
1 ATGTTCCAGATTTACAAGACTTACT
21805 ATGT
1 ATGT
21809 AAATTTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (25 bp):
ATGTTCCAGATTTACAAGACTTACT
Found at i:23204 original size:16 final size:17
Alignment explanation
Indices: 23110--23229 Score: 60
Period size: 16 Copynumber: 7.1 Consensus size: 17
23100 TATATAATTT
23110 TATATATTA-TATATAA
1 TATATATTATTATATAA
*
23126 TA-AT-TAAATT-T-TAA
1 TATATAT-TATTATATAA
*
23140 TATATATATATTAGATAA
1 TATATAT-TATTATATAA
* *
23158 TAGAATATTATTATTTTAA
1 TA-TATATTATTA-TATAA
23177 TACT-T-TTCATTA-ATAA
1 TA-TATATT-ATTATATAA
23193 TATATATTATTAT-TAA
1 TATATATTATTATATAA
*
23209 TATATAAATAATTATATAA
1 TATAT--ATTATTATATAA
23228 TA
1 TA
23230 AATGAACGTT
Statistics
Matches: 79, Mismatches: 10, Indels: 27
0.68 0.09 0.23
Matches are distributed among these distances:
14 6 0.08
15 7 0.09
16 26 0.33
17 4 0.05
18 22 0.28
19 14 0.18
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
TATATATTATTATATAA
Found at i:23295 original size:35 final size:35
Alignment explanation
Indices: 23256--23330 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
23246 TTATATAAAC
23256 GAACACTTAAATGAACAATAAACGAGCCTATTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTATTCGT
* *
23291 GAACACTTAAATGAACAATAAACGAGTCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTATTCGT
23326 GAACA
1 GAACA
23331 TAAACGAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.23
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGCCTATTCGT
Found at i:33216 original size:17 final size:17
Alignment explanation
Indices: 33196--33238 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
33186 TTGGTTGGGA
**
33196 GTGATCTTTGATCACCG
1 GTGATCTTACATCACCG
*
33213 GTGATCTTACATCACTG
1 GTGATCTTACATCACCG
33230 GTGATCTTA
1 GTGATCTTA
33239 GATTACTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (17 bp):
GTGATCTTACATCACCG
Found at i:33250 original size:17 final size:17
Alignment explanation
Indices: 33213--33253 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
33203 TTGATCACCG
*
33213 GTGATCTTACATCACTG
1 GTGATCTTACATCACTA
* *
33230 GTGATCTTAGATTACTA
1 GTGATCTTACATCACTA
33247 GTGATCT
1 GTGATCT
33254 GGGGGTGATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (17 bp):
GTGATCTTACATCACTA
Found at i:56529 original size:22 final size:22
Alignment explanation
Indices: 56501--56542 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
56491 CTTACCCACT
56501 AAAAGTTTATAAACAAATTATC
1 AAAAGTTTATAAACAAATTATC
*
56523 AAAAGTTTATAATCAAATTA
1 AAAAGTTTATAAACAAATTA
56543 ACTTCGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (22 bp):
AAAAGTTTATAAACAAATTATC
Found at i:56973 original size:122 final size:128
Alignment explanation
Indices: 56835--57088 Score: 385
Period size: 122 Copynumber: 2.0 Consensus size: 128
56825 CATTGTTTAA
*
56835 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C-T-T-TA
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
*
56896 -TGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAA-TTTTTAAATAT
66 TTGATTTTTACCATTTTACTATGTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
*
56957 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATATC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCC-T-TATC
* * *
57022 TATTTTATTTTTATCATTTTACTATGTTATTTAAAAAACTTATATATATTAGAATTTTTTAAATA
64 TA-TTGATTTTTACCATTTTACTATGTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
57087 T
128 T
57088 A
1 A
57089 TTTCTTAAAT
Statistics
Matches: 117, Mismatches: 6, Indels: 9
0.89 0.05 0.07
Matches are distributed among these distances:
122 54 0.46
123 1 0.01
126 1 0.01
127 1 0.01
128 2 0.02
130 46 0.39
131 12 0.10
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.50
Consensus pattern (128 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
TTGATTTTTACCATTTTACTATGTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:57036 original size:23 final size:22
Alignment explanation
Indices: 57010--57053 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
57000 TTAAATCTAA
* *
57010 TATCCTTATATCTATTTTATTTT
1 TATCATTATA-CTATGTTATTTT
*
57033 TATCATTTTACTATGTTATTT
1 TATCATTATACTATGTTATTT
57054 AAAAAACTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.23, C:0.11, G:0.02, T:0.64
Consensus pattern (22 bp):
TATCATTATACTATGTTATTTT
Found at i:61526 original size:40 final size:40
Alignment explanation
Indices: 61482--61558 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
61472 AATCTATCTG
61482 CTTTCAGCTCCTGCTAGTAATCTCATTACTTTTCATGAGT
1 CTTTCAGCTCCTGCTAGTAATCTCATTACTTTTCATGAGT
61522 CTTTCAGCTCCTGCTAGTAATCTCATTACTTTTCATG
1 CTTTCAGCTCCTGCTAGTAATCTCATTACTTTTCATG
61559 TTGCACTCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.19, C:0.26, G:0.12, T:0.43
Consensus pattern (40 bp):
CTTTCAGCTCCTGCTAGTAATCTCATTACTTTTCATGAGT
Found at i:65315 original size:26 final size:27
Alignment explanation
Indices: 65272--65323 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
65262 CATAGGTAGT
*
65272 TGGGAAAATGTGTAATTATTATAAGTG
1 TGGGAAAATGTATAATTATTATAAGTG
*
65299 TGGG-AAATGTATTATTATTATAAGT
1 TGGGAAAATGTATAATTATTATAAGT
65324 TAAATGAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (27 bp):
TGGGAAAATGTATAATTATTATAAGTG
Found at i:67927 original size:29 final size:29
Alignment explanation
Indices: 67891--67949 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
67881 ATAGCGGTGG
67891 TTGGCTATGTGGTTTTATGTTTAGTGGCA
1 TTGGCTATGTGGTTTTATGTTTAGTGGCA
67920 TTGGCTATGTGGTTTTATGTTTAGTGGCA
1 TTGGCTATGTGGTTTTATGTTTAGTGGCA
67949 T
1 T
67950 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.14, C:0.07, G:0.31, T:0.49
Consensus pattern (29 bp):
TTGGCTATGTGGTTTTATGTTTAGTGGCA
Found at i:67955 original size:2 final size:2
Alignment explanation
Indices: 67948--67987 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
67938 GTTTAGTGGC
67948 AT AT AT AT AT AT AT 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
67988 GGAAAATCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:91470 original size:2 final size:2
Alignment explanation
Indices: 91459--91495 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
91449 ACTAAAATAG
91459 TA TA -A 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 TA
91496 ACTCAACCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:92882 original size:12 final size:13
Alignment explanation
Indices: 92865--92893 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
92855 ATTAATAATT
92865 TAAATAAA-TAAA
1 TAAATAAATTAAA
92877 TAAATAAATTAAA
1 TAAATAAATTAAA
92890 TAAA
1 TAAA
92894 AATAAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAATAAATTAAA
Found at i:92902 original size:21 final size:21
Alignment explanation
Indices: 92858--92902 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
92848 TATTAATATT
* *
92858 AATAATTTAAATAAATAAATA
1 AATAAATTAAATAAATAAAAA
92879 AATAAATTAAATAAA-AATAAA
1 AATAAATTAAATAAATAA-AAA
92900 AAT
1 AAT
92903 GAGTTTAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AATAAATTAAATAAATAAAAA
Found at i:97801 original size:18 final size:20
Alignment explanation
Indices: 97778--97814 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
97768 TCCCTTGATT
97778 TGCAGAAA-CAAG-TCTGGG
1 TGCAGAAATCAAGTTCTGGG
97796 TGCAGAAATCAAGTTCTGG
1 TGCAGAAATCAAGTTCTGG
97815 TTCGTAGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 4 0.24
20 5 0.29
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.22
Consensus pattern (20 bp):
TGCAGAAATCAAGTTCTGGG
Found at i:104354 original size:18 final size:17
Alignment explanation
Indices: 104328--104362 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
104318 ATTCATTGAA
*
104328 AAAAGAAAAAGGAAATT
1 AAAAGAAAAAGAAAATT
104345 AAAAGAAAAAAGAAAATT
1 AAAAG-AAAAAGAAAATT
104363 GCTAGCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.11
Consensus pattern (17 bp):
AAAAGAAAAAGAAAATT
Found at i:104543 original size:19 final size:19
Alignment explanation
Indices: 104519--104570 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
104509 TTAGCAACTT
104519 TACAGATGAGATTACACTA
1 TACAGATGAGATTACACTA
104538 TACAGATGAGATTACACTA
1 TACAGATGAGATTACACTA
*
104557 TACAGATTAGATTA
1 TACAGATGAGATTA
104571 GGTATTGTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (19 bp):
TACAGATGAGATTACACTA
Found at i:105636 original size:3 final size:3
Alignment explanation
Indices: 105623--105656 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
105613 TTCAAAAGAA
* *
105623 AAT ACT AAT AAT AAT AAT AAT AAT AAT AGT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
105657 TATTTTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:108468 original size:25 final size:25
Alignment explanation
Indices: 108440--108495 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
108430 AAACGACTAT
108440 TCAATACCAAAATTTTTATAGGGAA
1 TCAATACCAAAATTTTTATAGGGAA
** * *
108465 TCAATTTTCAATATTTTTTTAGGGAA
1 TCAA-TACCAAAATTTTTATAGGGAA
108491 TCAAT
1 TCAAT
108496 TTCAATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (25 bp):
TCAATACCAAAATTTTTATAGGGAA
Found at i:108498 original size:25 final size:26
Alignment explanation
Indices: 108451--108506 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
108441 CAATACCAAA
108451 ATTTTTATAGGGAATCAATTTTCAAT
1 ATTTTTATAGGGAATCAATTTTCAAT
*
108477 ATTTTTTTAGGGAATCAA-TTTCAAT
1 ATTTTTATAGGGAATCAATTTTCAAT
108502 ATTTT
1 ATTTT
108507 AAAATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (26 bp):
ATTTTTATAGGGAATCAATTTTCAAT
Found at i:117515 original size:44 final size:44
Alignment explanation
Indices: 117452--117539 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
117442 TGTGCTCAGT
117452 GCTCTTTCGATGAAGTCTTGCCTAGTTCAAAACAATCAGGATGA
1 GCTCTTTCGATGAAGTCTTGCCTAGTTCAAAACAATCAGGATGA
*
117496 GCTCTTTCGATGCAGTCTTGCCTAGTTCAAAACAATCAGGATGA
1 GCTCTTTCGATGAAGTCTTGCCTAGTTCAAAACAATCAGGATGA
117540 AAAATGAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
GCTCTTTCGATGAAGTCTTGCCTAGTTCAAAACAATCAGGATGA
Found at i:118176 original size:6 final size:6
Alignment explanation
Indices: 118165--118191 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
118155 TTGTTGGACA
118165 ATGACC ATGACC ATGACC ATGACC ATG
1 ATGACC ATGACC ATGACC ATGACC ATG
118192 CCCCATGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.30, G:0.19, T:0.19
Consensus pattern (6 bp):
ATGACC
Found at i:122353 original size:14 final size:15
Alignment explanation
Indices: 122324--122358 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
122314 GCCTTCTATT
122324 TTATTTTAAGGGTAA
1 TTATTTTAAGGGTAA
122339 TTATTTTAA-GGTAA
1 TTATTTTAAGGGTAA
122353 TTATTT
1 TTATTT
122359 AATATACTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.54
Consensus pattern (15 bp):
TTATTTTAAGGGTAA
Found at i:123102 original size:31 final size:31
Alignment explanation
Indices: 123036--123204 Score: 232
Period size: 31 Copynumber: 5.4 Consensus size: 31
123026 TATGATGTTG
* * *
123036 ACGTGACATGTCACATCAGTCGAAAAATTGCC
1 ACGTGGCATGCCACATCAGTCG-AAAACTGCC
*
123068 ACGTGGCATGCCATATCAGTCGAAAACTGCC
1 ACGTGGCATGCCACATCAGTCGAAAACTGCC
*
123099 ACGTGGCATGTCACATCAGTCGAAAACTGCC
1 ACGTGGCATGCCACATCAGTCGAAAACTGCC
123130 ACGTGGCATGCCACATCAGTCGAAAACTGCC
1 ACGTGGCATGCCACATCAGTCGAAAACTGCC
* * *
123161 ACGTGGCATGCCACATCA-TCCAAAAATTGTC
1 ACGTGGCATGCCACATCAGT-CGAAAACTGCC
*
123192 ACATGGCATGCCA
1 ACGTGGCATGCCA
123205 TGTCAGCACA
Statistics
Matches: 125, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
30 1 0.01
31 105 0.84
32 19 0.15
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.20
Consensus pattern (31 bp):
ACGTGGCATGCCACATCAGTCGAAAACTGCC
Found at i:130924 original size:92 final size:91
Alignment explanation
Indices: 130757--130943 Score: 290
Period size: 92 Copynumber: 2.0 Consensus size: 91
130747 TTCATTACTT
130757 CTTCTCTCCATGACTTTGTCCTTCTATTCTTGATACTTATCAAGAAATATTAGTATTTCCTATTA
1 CTTCTCTCCATGACTTTGTCCTTCTATTCTTGATACTTATCAAGAAATATTA-TATTTCCTATTA
130822 GTACTAAATATCTT-ATGCCAAACTTGC
65 GTACTAAATAT-TTCATGCCAAACTTGC
*
130849 CTTCTCTCCATGACTTTGTCCTTCTATTCTTGATGCTTATCAAGAAATA-T-TATTTCCTATTAG
1 CTTCTCTCCATGACTTTGTCCTTCTATTCTTGATACTTATCAAGAAATATTATATTTCCTATTAG
*
130912 TACTACTTAATATTTCATTCCAAACTTGC
66 TACTA---AATATTTCATGCCAAACTTGC
130941 CTT
1 CTT
130944 TTGCAATCCA
Statistics
Matches: 89, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
89 18 0.20
91 3 0.03
92 68 0.76
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.44
Consensus pattern (91 bp):
CTTCTCTCCATGACTTTGTCCTTCTATTCTTGATACTTATCAAGAAATATTATATTTCCTATTAG
TACTAAATATTTCATGCCAAACTTGC
Found at i:131145 original size:29 final size:30
Alignment explanation
Indices: 131113--131180 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 30
131103 ATGCAATTTG
*
131113 GGATATAACGTTAC-AAAACAAATAATTAA
1 GGATATAACGTTACAAAAACAAACAATTAA
* * *
131142 GGATATAATGTTACGAAAAACGAGCAATTAA
1 GGATATAACGTTAC-AAAAACAAACAATTAA
131173 GGATATAA
1 GGATATAA
131181 TCCATTAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 13 0.39
31 20 0.61
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.24
Consensus pattern (30 bp):
GGATATAACGTTACAAAAACAAACAATTAA
Found at i:131358 original size:30 final size:31
Alignment explanation
Indices: 131300--131376 Score: 120
Period size: 30 Copynumber: 2.5 Consensus size: 31
131290 CTTACTGATT
* *
131300 ATATCCTTAGTTGCTTGAAATCAAAAACGTC
1 ATATCCTTAATTGCTTAAAATCAAAAACGTC
*
131331 ATATCCTTAATTGCTTAAAAT-AAAAACGTT
1 ATATCCTTAATTGCTTAAAATCAAAAACGTC
131361 ATATCCTTAATTGCTT
1 ATATCCTTAATTGCTT
131377 GTTTTGTAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 24 0.56
31 19 0.44
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (31 bp):
ATATCCTTAATTGCTTAAAATCAAAAACGTC
Found at i:131402 original size:59 final size:60
Alignment explanation
Indices: 131325--131437 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
131315 TGAAATCAAA
* *
131325 AACGTCATATCCTTAATTGCTTAAAATA-AAAACGTTATATCCTTAATTGCTTGTTTTGT
1 AACGTCATATCCTTAATTGCTTAAAACAGAAAACGTTATATCCTAAATTGCTTGTTTTGT
* ***
131384 AACGTTATATCCTTAATTGCTTACGGCAGAAAACGTTATATCCTAAATTGCTTG
1 AACGTCATATCCTTAATTGCTTAAAACAGAAAACGTTATATCCTAAATTGCTTG
131438 CTTATCATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 23 0.49
60 24 0.51
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (60 bp):
AACGTCATATCCTTAATTGCTTAAAACAGAAAACGTTATATCCTAAATTGCTTGTTTTGT
Found at i:132505 original size:31 final size:31
Alignment explanation
Indices: 132433--132542 Score: 125
Period size: 31 Copynumber: 3.6 Consensus size: 31
132423 TTAGCTGCCA
* ***
132433 CAAGCAATTAAGGATATAACG-TTAC-AAAA
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
* *
132462 CAAGCAATTAAGGATGTAACGTTTTCTATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
* * *
132493 CAAGTAATTAAGGATATGATGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
132524 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
132543 TCAGTTAGGT
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
29 20 0.30
30 3 0.04
31 44 0.66
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCGATTT
Found at i:132745 original size:29 final size:31
Alignment explanation
Indices: 132671--132737 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
132661 CCTAACGGAC
132671 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
*
132702 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
132731 TATATCC
1 TATATCC
132738 CAAATTGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGCTTTTCGTAACGT
Found at i:143617 original size:1 final size:1
Alignment explanation
Indices: 143611--143635 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
143601 TACGTGTCAG
143611 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
143636 AAGATATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:151355 original size:339 final size:341
Alignment explanation
Indices: 150735--151586 Score: 1464
Period size: 339 Copynumber: 2.5 Consensus size: 341
150725 GGAGCTTAGT
* * * *
150735 TAAAATTTTGCAAAAACTGACTCGAAAATTTATTTCCTCAATACTTTTCCAAAATACTCCTAAAA
1 TAAAATTTTGCAAAAACTGACCCGAAAATTTTTTTCCTCAATTCTTTGCCAAAATACTCCTAAAA
*
150800 AATATATAAATCAGCGTCAAAAAGATTGACATGCTTTTCACACTTCAAATATTGTTTTT--TTTT
66 AATATATAAATCAGCGCCAAAAAGATTGACATGCTTTTCACACTTCAAATATTGTTTTTCCTTTT
* * *
150863 TTTCCGAAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATCAAACCAAATCCTTAAA
131 TTTCCGAATTAATTTCCAATTAAATCGAAACAAGATTCAGATGCTCATAAAACCAAATCCTT-AA
*
150928 TAATCTAAGGAGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTCCTGCCAAAA
195 TAATCTAAGGAGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTCCTGCCAAAA
150993 ATCAAGCAAAACTGAGCCGGGGCCCCGGAACACATTTTTACTTTTAAGCCAAAAACCGTGAT-GT
260 ATCAAGCAAAACTGAGCCGGGGCCCCGGAACACATTTTTACTTTTAAGCCAAAAACCGTGATGGT
151057 TAGTACACGATTTCGGC
325 TAGTACACGATTTCGGC
151074 TAAAATTTTGCAAAAAGCTGACCCGAAAATTTTTTTCCTCAATTCTTTGCCAAAATACTCCTAAA
1 TAAAATTTTGCAAAAA-CTGACCCGAAAATTTTTTTCCTCAATTCTTTGCCAAAATACTCCTAAA
151139 AAATATATAAATCAGCGCCAAAAAGATTGACATGCTTTTCACACTTCAAATATTGTTTTTCCTTT
65 AAATATATAAATCAGCGCCAAAAAGATTGACATGCTTTTCACACTTCAAATATTGTTTTTCCTTT
* *
151204 TTTTCCGAATTAATTTCGAATTAAATCGAAACAAGATTAAGATGCTCATAAAACCAAATCCTT-A
130 TTTTCCGAATTAATTTCCAATTAAATCGAAACAAGATTCAGATGCTCATAAAACCAAATCCTTAA
*
151268 -AATCTAAGGAGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAA
195 TAATCTAAGGAGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTCCTGCCAAAA
*
151332 ATCAAGCAAAACTGAGCCGGGGCCCCGGAACACATTTTTACTTTTAAGCCAAATACCGTGATGGT
260 ATCAAGCAAAACTGAGCCGGGGCCCCGGAACACATTTTTACTTTTAAGCCAAAAACCGTGATGGT
*
151397 TAGTTCACGATTTCGGC
325 TAGTACACGATTTCGGC
*
151414 TAAAATTTTGCAAAAACTGATCCGAAAA-TTTTTTCCTCAATTCTTTGCCAAAATACTCCTAAAA
1 TAAAATTTTGCAAAAACTGACCCGAAAATTTTTTTCCTCAATTCTTTGCCAAAATACTCCTAAAA
* ** *
151478 AATATATAAATCAGCGCCAAACAGATTGACATGCTTTTCACACTTCAAATAACGTTTTTCCGTTT
66 AATATATAAATCAGCGCCAAAAAGATTGACATGCTTTTCACACTTCAAATATTGTTTTTCCTTTT
*
151543 TTACCGAATTAATTTCCAATTAAATCGAAACAAGATTCAGATGC
131 TTTCCGAATTAATTTCCAATTAAATCGAAACAAGATTCAGATGC
Statistics
Matches: 488, Mismatches: 21, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
338 138 0.28
339 150 0.31
340 138 0.28
342 62 0.13
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (341 bp):
TAAAATTTTGCAAAAACTGACCCGAAAATTTTTTTCCTCAATTCTTTGCCAAAATACTCCTAAAA
AATATATAAATCAGCGCCAAAAAGATTGACATGCTTTTCACACTTCAAATATTGTTTTTCCTTTT
TTTCCGAATTAATTTCCAATTAAATCGAAACAAGATTCAGATGCTCATAAAACCAAATCCTTAAT
AATCTAAGGAGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTCCTGCCAAAAA
TCAAGCAAAACTGAGCCGGGGCCCCGGAACACATTTTTACTTTTAAGCCAAAAACCGTGATGGTT
AGTACACGATTTCGGC
Done.