Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024434.1 Corchorus olitorius cultivar O-4 contig24467, 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: 44623
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1252 original size:21 final size:21
Alignment explanation
Indices: 1226--1267 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1216 GCATCTTAGA
1226 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
*
1247 CAACTCTGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
1268 TTCTTCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:6962 original size:10 final size:10
Alignment explanation
Indices: 6929--6989 Score: 58
Period size: 10 Copynumber: 6.1 Consensus size: 10
6919 TAATATCTAG
6929 TATATT-TAT
1 TATATTATAT
6938 TATTATTATA-
1 TA-TATTATAT
6948 T-TATTATAT
1 TATATTATAT
6957 TATATTATAT
1 TATATTATAT
6967 T-TATATATAT
1 TATAT-TATAT
6977 ATATATTTATAT
1 -TATA-TTATAT
6989 T
1 T
6990 CTACATATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
8 7 0.16
9 6 0.14
10 19 0.43
11 4 0.09
12 7 0.16
13 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATATTATAT
Found at i:6970 original size:16 final size:16
Alignment explanation
Indices: 6935--6989 Score: 67
Period size: 16 Copynumber: 3.2 Consensus size: 16
6925 CTAGTATATT
6935 TATTATTATTATATTATTA
1 TATTA-TATTATA-T-TTA
6954 TATTATATTATATTTA
1 TATTATATTATATTTA
6970 TA-TATATATATATTTA
1 TATTATAT-TATATTTA
6986 TATT
1 TATT
6990 CTACATATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.15
16 15 0.44
17 2 0.06
18 7 0.21
19 5 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTATATTTA
Found at i:6973 original size:8 final size:8
Alignment explanation
Indices: 6929--6988 Score: 54
Period size: 8 Copynumber: 7.4 Consensus size: 8
6919 TAATATCTAG
6929 TATATTTA
1 TATATTTA
6937 T-TA-TTA
1 TATATTTA
6943 T-TATATTA
1 TATAT-TTA
6951 TTATATTATA
1 -TATATT-TA
6961 TTATATTTA
1 -TATATTTA
*
6970 TATATATA
1 TATATTTA
6978 TATATTTA
1 TATATTTA
6986 TAT
1 TAT
6989 TCTACATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
6 6 0.13
7 2 0.04
8 21 0.47
9 4 0.09
10 12 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTTA
Found at i:7447 original size:223 final size:220
Alignment explanation
Indices: 6989--7432 Score: 626
Period size: 223 Copynumber: 2.0 Consensus size: 220
6979 ATATTTATAT
* * * *
6989 TCTACATATTATTTTTGTAACCATGTGAAATTACTAAATGCTCCTTCTAACTTTTAACCTGGTAC
1 TCTAAATATT-TTTTTGTAACCAGGTGAAATAACTAAATGCTCCTTCTAACTTTTAACCTGGGAC
*
7054 GACATTATCGCCCCGTTTTAGTCATTCCTCACATGCGGTTCAACTGAATCGATTCGTATTCCATC
65 GACATTATCGCCCCGTTTTAGTCATTCCTCACATGCGGTTCAACTGAACCGATTCGTATTCCATC
7119 ACCCTATAACGTCATAAATCATATTTATTATATTGAAACTCACAGAAAACGCGTTCACATTTACA
130 ACCCTATAACGTCATAAATCATATTTATTATATTGAAACTCAC---AAACGCGTTCACATTTACA
*
7184 GAGCAAAAAAGCAATCTATAAAAATTGAC
192 GAGCAAAAAAACAATCTATAAAAATTGAC
* *
7213 TCTACATATTTTTTTGTAACCAGGTGAAATAACTAAATGCTCCTTCTAACTTTTAACCTGGGGCG
1 TCTAAATATTTTTTTGTAACCAGGTGAAATAACTAAATGCTCCTTCTAACTTTTAACCTGGGACG
* * * * * *
7278 ACCTTATTGCTCCGTTTTAGTCATTTCTCACGTGTGGTT-ACACTGAACCGATTCGTATTCCATC
66 ACATTATCGCCCCGTTTTAGTCATTCCTCACATGCGGTTCA-ACTGAACCGATTCGTATTCCATC
* * * * * *
7342 ACTCTATAACTTCAATAAATCATATTTATTATATTTAAAC-C-C-ACCGCGTTGATATTTACAGA
130 ACCCTATAACGTC-ATAAATCATATTTATTATATTGAAACTCACAAACGCGTTCACATTTACAGA
7404 GCAAAAAAACAATCTATAAAAATTGAC
194 GCAAAAAAACAATCTATAAAAATTGAC
7431 TC
1 TC
7433 ATATGATAAT
Statistics
Matches: 200, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
218 45 0.22
222 2 0.01
223 118 0.59
224 35 0.17
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.34
Consensus pattern (220 bp):
TCTAAATATTTTTTTGTAACCAGGTGAAATAACTAAATGCTCCTTCTAACTTTTAACCTGGGACG
ACATTATCGCCCCGTTTTAGTCATTCCTCACATGCGGTTCAACTGAACCGATTCGTATTCCATCA
CCCTATAACGTCATAAATCATATTTATTATATTGAAACTCACAAACGCGTTCACATTTACAGAGC
AAAAAAACAATCTATAAAAATTGAC
Found at i:8199 original size:19 final size:20
Alignment explanation
Indices: 8177--8224 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 20
8167 TTAGATGTGG
8177 AAACAAGTATACACATGCA-
1 AAACAAGTATACACATGCAT
*
8196 AAACAA--ATA-ACATGTAT
1 AAACAAGTATACACATGCAT
8213 AAACAAGTATAC
1 AAACAAGTATAC
8225 CCATATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
16 6 0.25
17 9 0.38
19 9 0.38
ACGTcount: A:0.56, C:0.17, G:0.08, T:0.19
Consensus pattern (20 bp):
AAACAAGTATACACATGCAT
Found at i:10104 original size:56 final size:56
Alignment explanation
Indices: 10018--10132 Score: 203
Period size: 56 Copynumber: 2.1 Consensus size: 56
10008 TGCTCCTTAA
* *
10018 CTACAAAAAATTAGGCCTTCCTTATGCAGAAGCCAAATTCTTCCACTTACCCGAGT
1 CTACAAAAAATTAGGCCTTCCTTACGCAGAAGCCAAATTCTTCCACCTACCCGAGT
*
10074 CTACAAAAAATTAGGCCTTCCTTACGCAGAAGCCAAATTCTTCCACCTATCCGAGT
1 CTACAAAAAATTAGGCCTTCCTTACGCAGAAGCCAAATTCTTCCACCTACCCGAGT
10130 CTA
1 CTA
10133 TTAATTTAAC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.32, C:0.30, G:0.12, T:0.26
Consensus pattern (56 bp):
CTACAAAAAATTAGGCCTTCCTTACGCAGAAGCCAAATTCTTCCACCTACCCGAGT
Found at i:10287 original size:46 final size:45
Alignment explanation
Indices: 10221--10309 Score: 142
Period size: 46 Copynumber: 2.0 Consensus size: 45
10211 AACAACAATT
*
10221 AATATTAGCTTTATTTTGATGAATTATATAGAGATGGAAGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACATAGAGATGGAAGAGTAG
* *
10266 AATATTTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGT
1 AATA-TTAGCTTTATTTTGATGAATTACATAGAGATGGAAGAGT
10310 TAAATTTAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 4 0.10
46 36 0.90
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.38
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACATAGAGATGGAAGAGTAG
Found at i:10776 original size:11 final size:11
Alignment explanation
Indices: 10760--10789 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
10750 GCCGCTGGCC
*
10760 AAAGAAAATAA
1 AAAGAAAAGAA
10771 AAAGAAAAGAA
1 AAAGAAAAGAA
10782 AAAGAAAA
1 AAAGAAAA
10790 AAGCGAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:15054 original size:160 final size:161
Alignment explanation
Indices: 14740--15063 Score: 607
Period size: 160 Copynumber: 2.0 Consensus size: 161
14730 GAAGTAGAAC
14740 GAGGAGCTGGTGCCAGATTTTTTATTGTGTCAACAGTTTAGATCCATTTTTATATTGGAATTGGT
1 GAGGAGCTGGTGCCAGATTTTTTATTGTGTCAACAGTTTAGATCCATTTTTATATTGGAATTGGT
14805 GATATGATATCATTAGTACTGGTGCACTAGGAAATTAGGATGCATGGGTTTCATCCTTTACAATC
66 GATATGATATCATTA-TACTGGTGCACTAGGAAATTAGGATGCATGGGTTTCATCCTTTACAATC
14870 ATCCTTTTTCCCCTTTTTGCAGCCTCCTGCTT
130 ATCCTTTTTCCCCTTTTTGCAGCCTCCTGCTT
*
14902 GAGGAGCTGGTGCCAGATTTTTTATTGTGTTAACAGTTTAGATCCATTTTTATATTGGAATTGGT
1 GAGGAGCTGGTGCCAGATTTTTTATTGTGTCAACAGTTTAGATCCATTTTTATATTGGAATTGGT
14967 GATATGATATTCA-T-TACTGGTGCACTAGGAAATTAGGATGCATGGGTTTCATCCTTTACAATC
66 GATATGATA-TCATTATACTGGTGCACTAGGAAATTAGGATGCATGGGTTTCATCCTTTACAATC
15030 ATCCTTTTTCCCCTTTTTGCAGCCTCCTGCTT
130 ATCCTTTTTCCCCTTTTTGCAGCCTCCTGCTT
15062 GA
1 GA
15064 TATTGGGTTT
Statistics
Matches: 160, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
160 83 0.52
162 74 0.46
163 3 0.02
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (161 bp):
GAGGAGCTGGTGCCAGATTTTTTATTGTGTCAACAGTTTAGATCCATTTTTATATTGGAATTGGT
GATATGATATCATTATACTGGTGCACTAGGAAATTAGGATGCATGGGTTTCATCCTTTACAATCA
TCCTTTTTCCCCTTTTTGCAGCCTCCTGCTT
Found at i:30873 original size:21 final size:21
Alignment explanation
Indices: 30849--30961 Score: 176
Period size: 21 Copynumber: 5.4 Consensus size: 21
30839 CTTAGGCAAT
*
30849 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
30870 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
30891 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
30912 TCAAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
30933 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
30954 TCCAATGA
1 TCCAATGA
30962 ACTCCTAGCA
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
20 3 0.03
21 85 0.97
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:33224 original size:29 final size:29
Alignment explanation
Indices: 33187--33325 Score: 251
Period size: 29 Copynumber: 4.8 Consensus size: 29
33177 TTAAAATGAC
* *
33187 GGGAACTTTCCCTAAATTGAAAACTTGAT
1 GGGATCTTTCCCTAAATTGAAAACTTAAT
33216 GGGATCTTTCCCTAAATTGAAAACTTAAT
1 GGGATCTTTCCCTAAATTGAAAACTTAAT
*
33245 AGGATCTTTCCCTAAATTGAAAACTTAAT
1 GGGATCTTTCCCTAAATTGAAAACTTAAT
33274 GGGATCTTTCCCTAAATTGAAAACTTAAT
1 GGGATCTTTCCCTAAATTGAAAACTTAAT
33303 GGGATCTTTCCCTAAATTGAAAA
1 GGGATCTTTCCCTAAATTGAAAA
33326 TCTTGAAGAG
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 106 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (29 bp):
GGGATCTTTCCCTAAATTGAAAACTTAAT
Found at i:33259 original size:58 final size:58
Alignment explanation
Indices: 33187--33397 Score: 287
Period size: 58 Copynumber: 3.4 Consensus size: 58
33177 TTAAAATGAC
*
33187 GGGAACTTTCCCTAAATTGAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTAAT
1 GGGATCTTTCCCTAAATTGAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTAAT
* *
33245 AGGATCTTTCCCTAAATTGAAAACTTAATGGGATCTTTCCCTAAATTGAAAACTTAAT
1 GGGATCTTTCCCTAAATTGAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTAAT
33303 GGGATCTTTCCCTAAATTGAAAATCTTGAAGAGACTGATGGGATCTTTCCCTAAATTTGAAAACT
1 GGGATCTTTCCCTAAATTGAAAA-C-T--------TGATGGGATCTTTCCCTAAA-TTGAAAACT
*
33368 TGAT
55 TAAT
33372 GGGATCTTTCCCTAAATTGAAAACTT
1 GGGATCTTTCCCTAAATTGAAAACTT
33398 CAAAACTACT
Statistics
Matches: 136, Mismatches: 6, Indels: 21
0.83 0.04 0.13
Matches are distributed among these distances:
58 77 0.57
59 2 0.01
60 1 0.01
67 1 0.01
68 20 0.15
69 35 0.26
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (58 bp):
GGGATCTTTCCCTAAATTGAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTAAT
Found at i:33288 original size:87 final size:94
Alignment explanation
Indices: 33187--33397 Score: 310
Period size: 87 Copynumber: 2.3 Consensus size: 94
33177 TTAAAATGAC
* *
33187 GGGAACTTTCCCTAAATTGAAAACTTGATGGGATCTTTCCCTAAATTGAAAA-CTT-A-A-T-A-
1 GGGATCTTTCCCTAAATTGAAAACTTAATGGGATCTTTCCCTAAATTGAAAATCTTAAGACTGAG
33246 GGATCTTTCCCTAAA-TTGAAAACTTAAT
66 GGATCTTTCCCTAAATTTGAAAACTTAAT
33274 GGGATCTTTCCCTAAATTGAAAACTTAATGGGATCTTTCCCTAAATTGAAAATCTTGAAGAGACT
1 GGGATCTTTCCCTAAATTGAAAACTTAATGGGATCTTTCCCTAAATTGAAAATCTT--A-AGACT
*
33339 GATGGGATCTTTCCCTAAATTTGAAAACTTGAT
63 GA-GGGATCTTTCCCTAAATTTGAAAACTTAAT
33372 GGGATCTTTCCCTAAATTGAAAACTT
1 GGGATCTTTCCCTAAATTGAAAACTT
33398 CAAAACTACT
Statistics
Matches: 110, Mismatches: 3, Indels: 11
0.89 0.02 0.09
Matches are distributed among these distances:
87 50 0.45
88 3 0.03
92 1 0.01
93 1 0.01
94 1 0.01
95 1 0.01
97 15 0.14
98 38 0.35
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (94 bp):
GGGATCTTTCCCTAAATTGAAAACTTAATGGGATCTTTCCCTAAATTGAAAATCTTAAGACTGAG
GGATCTTTCCCTAAATTTGAAAACTTAAT
Found at i:33344 original size:39 final size:37
Alignment explanation
Indices: 33290--33443 Score: 139
Period size: 40 Copynumber: 4.2 Consensus size: 37
33280 TTTCCCTAAA
*
33290 TTGAAAACTTAATGGGATCTTTCCCTAAATTGAAAATC
1 TTGAAAAC-TGATGGGATCTTTCCCTAAATTGAAAATC
33328 TTGAAGAGACTGATGGGATCTTTCCC-----T--AAAT-
1 TTGAA-A-ACTGATGGGATCTTTCCCTAAATTGAAAATC
33359 TTGAAAACTTGATGGGATCTTTCCCTAAATTGAAAA-C
1 TTGAAAAC-TGATGGGATCTTTCCCTAAATTGAAAATC
*
33396 TTCAAAACTACTGGATGGGATCTTTCCCTAAATTGAAAA-C
1 TT-GAAA--ACT-GATGGGATCTTTCCCTAAATTGAAAATC
33436 TTTGAAAA
1 -TTGAAAA
33444 AACTTCTTTT
Statistics
Matches: 97, Mismatches: 3, Indels: 32
0.73 0.02 0.24
Matches are distributed among these distances:
29 2 0.02
30 17 0.18
31 5 0.05
32 4 0.04
34 1 0.01
35 1 0.01
37 5 0.05
38 9 0.09
39 17 0.18
40 34 0.35
41 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (37 bp):
TTGAAAACTGATGGGATCTTTCCCTAAATTGAAAATC
Found at i:33372 original size:30 final size:29
Alignment explanation
Indices: 33338--33397 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 29
33328 TTGAAGAGAC
33338 TGATGGGATCTTTCCCTAAATTTGAAAACT
1 TGATGGGATCTTTCCCTAAA-TTGAAAACT
33368 TGATGGGATCTTTCCCTAAATTGAAAACT
1 TGATGGGATCTTTCCCTAAATTGAAAACT
33397 T
1 T
33398 CAAAACTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (29 bp):
TGATGGGATCTTTCCCTAAATTGAAAACT
Found at i:33382 original size:69 final size:69
Alignment explanation
Indices: 33272--33437 Score: 264
Period size: 69 Copynumber: 2.4 Consensus size: 69
33262 TGAAAACTTA
* *
33272 ATGGGATCTTTCCCTAAATTGAAAACTTAATGGGATCTTTCCCTAAATTGAAAATCTTGAAGA-G
1 ATGGGATCTTTCCCTAAATTGAAAACTTAATGGGATCTTTCCCTAAATTGAAAA-CTTCAAAACG
33336 ACT-G
65 ACTGG
* *
33340 ATGGGATCTTTCCCTAAATTTGAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTCAAAACT
1 ATGGGATCTTTCCCTAAA-TTGAAAACTTAATGGGATCTTTCCCTAAATTGAAAACTTCAAAACG
33405 ACTGG
65 ACTGG
33410 ATGGGATCTTTCCCTAAATTGAAAACTT
1 ATGGGATCTTTCCCTAAATTGAAAACTT
33438 TGAAAAAACT
Statistics
Matches: 91, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
68 24 0.26
69 48 0.53
70 19 0.21
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (69 bp):
ATGGGATCTTTCCCTAAATTGAAAACTTAATGGGATCTTTCCCTAAATTGAAAACTTCAAAACGA
CTGG
Found at i:33470 original size:8 final size:8
Alignment explanation
Indices: 33457--33482 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
33447 TTCTTTTTGA
33457 TTTTGAAT
1 TTTTGAAT
33465 TTTTGAAT
1 TTTTGAAT
33473 TTTTGAAT
1 TTTTGAAT
33481 TT
1 TT
33483 CTCTTAGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (8 bp):
TTTTGAAT
Found at i:36106 original size:30 final size:30
Alignment explanation
Indices: 36072--36141 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
36062 ACCTGTTAAC
*
36072 GCTTATGTGGCT-TTCTAATTACCTGTATTT
1 GCTTATGTGGCTCTT-TAATTACATGTATTT
*
36102 GCTTATGTGGCTCTTTGATTACATGTATTT
1 GCTTATGTGGCTCTTTAATTACATGTATTT
*
36132 GTTTATGTGG
1 GCTTATGTGG
36142 AGTCATAGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 34 0.94
31 2 0.06
ACGTcount: A:0.16, C:0.13, G:0.21, T:0.50
Consensus pattern (30 bp):
GCTTATGTGGCTCTTTAATTACATGTATTT
Found at i:37555 original size:13 final size:13
Alignment explanation
Indices: 37539--37582 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
37529 TAAAACTCTT
37539 TTCAGGAACTGTC
1 TTCAGGAACTGTC
37552 TTCA-GAACCTGTC
1 TTCAGGAA-CTGTC
37565 TTC-GTGAACTGTC
1 TTCAG-GAACTGTC
37578 TTCAG
1 TTCAG
37583 ATTCACTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.11
13 20 0.74
14 4 0.15
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.34
Consensus pattern (13 bp):
TTCAGGAACTGTC
Found at i:37598 original size:41 final size:41
Alignment explanation
Indices: 37553--37634 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
37543 GGAACTGTCT
**
37553 TCAGAACCTGTCTTCGTGAACTGTCTTCAGATTCACTCTTA
1 TCAGAACCCATCTTCGTGAACTGTCTTCAGATTCACTCTTA
* * * *
37594 TCAGAACCCATCTTTGTGAGCTGTCTTTAGATTCAGTCTTA
1 TCAGAACCCATCTTCGTGAACTGTCTTCAGATTCACTCTTA
37635 AATATCATTC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (41 bp):
TCAGAACCCATCTTCGTGAACTGTCTTCAGATTCACTCTTA
Found at i:37752 original size:58 final size:59
Alignment explanation
Indices: 37645--38021 Score: 521
Period size: 60 Copynumber: 6.4 Consensus size: 59
37635 AATATCATTC
* * * * * * *
37645 AGGAACTGTCTTCAGAACCCGTCTATGAGCCGTCTTCA-TACTCACTCTTAAAAT-ATTTT
1 AGGAACTGTCTTCAG-ATCCATCTGTGAGCTGTCTTCAGT-CTTAATCTTAAAATCTTTTT
*
37704 AGGAATTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGTCTTAATCTTAAAATC-TTTT
1 AGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGTCTTAATCTTAAAATCTTTTT
37762 AGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAG-CTTTAAATCTTAAAATCTTTTT
1 AGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGTC-TT-AATCTTAAAATCTTTTT
*
37822 AGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTTAAATCTTAAAATCTTTTT
1 AGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGTC-TT-AATCTTAAAATCTTTTT
* * *
37883 AGGAAATGTCTTCAGATCCATCTGTGAGCTGTCTTCAATCTCAAATCTTAAAATCTTTTT
1 AGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGTCT-TAATCTTAAAATCTTTTT
* *
37943 AGGAACTGTCTTCAGATCCATCTATGAGCTGTCTTCAGTCTCAATCTTAAAATC-TTTT
1 AGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGTCTTAATCTTAAAATCTTTTT
*
38001 AGGAACTGTCTTTAGATCCAT
1 AGGAACTGTCTTCAGATCCAT
38022 TTCTGATGAA
Statistics
Matches: 294, Mismatches: 17, Indels: 15
0.90 0.05 0.05
Matches are distributed among these distances:
57 1 0.00
58 97 0.33
59 39 0.13
60 98 0.33
61 59 0.20
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (59 bp):
AGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGTCTTAATCTTAAAATCTTTTT
Found at i:37929 original size:121 final size:117
Alignment explanation
Indices: 37608--38021 Score: 539
Period size: 121 Copynumber: 3.5 Consensus size: 117
37598 AACCCATCTT
* * * * * * * * *
37608 TGTGAGCTGTCTTTAGATTCAGTCTTAAATATCATTCAGGAACTGTCTTCAGAACCCGTCTATGA
1 TGTGAGCTGTCTTCAGCTTTAATCTTAAA-ATCTTTTAGGAACTGTCTTCAG-ATCCATCTGTGA
* * * *
37673 GCCGTCTTCATACTC-ACTCTTAAAAT-ATTTTAGGAATTGTCTTCAGATCCATC
64 GCTGTCTTCAT-CTCAAATCTTAAAATCTTTTTAGGAACTGTCTTCAGATCCATC
37726 TGTGAGCTGTCTTCAG-TCTTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAG
1 TGTGAGCTGTCTTCAGCT-TTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAG
* *
37790 CTGTCTTCAGCTTTAAATCTTAAAATCTTTTTAGGAACTGTCTTCAGATCCATC
65 CTGTCTTCATC-TCAAATCTTAAAATCTTTTTAGGAACTGTCTTCAGATCCATC
*
37844 TGTGAGCTGTCTTCAGCCTTTAAATCTTAAAATCTTTTTAGGAAATGTCTTCAGATCCATCTGTG
1 TGTGAGCTGTCTTCAG-CTTT-AATCTTAAAATC-TTTTAGGAACTGTCTTCAGATCCATCTGTG
37909 AGCTGTCTTCAATCTCAAATCTTAAAATCTTTTTAGGAACTGTCTTCAGATCCATC
63 AGCTGTCTTC-ATCTCAAATCTTAAAATCTTTTTAGGAACTGTCTTCAGATCCATC
* * *
37965 TATGAGCTGTCTTCAG-TCTCAATCTTAAAATCTTTTAGGAACTGTCTTTAGATCCAT
1 TGTGAGCTGTCTTCAGCT-TTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATCCAT
38022 TTCTGATGAA
Statistics
Matches: 265, Mismatches: 21, Indels: 20
0.87 0.07 0.07
Matches are distributed among these distances:
115 1 0.00
116 19 0.07
117 31 0.12
118 88 0.33
119 15 0.06
120 14 0.05
121 95 0.36
122 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.39
Consensus pattern (117 bp):
TGTGAGCTGTCTTCAGCTTTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAGC
TGTCTTCATCTCAAATCTTAAAATCTTTTTAGGAACTGTCTTCAGATCCATC
Found at i:39434 original size:3 final size:3
Alignment explanation
Indices: 39419--39474 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
39409 TTGTTTTTTC
*
39419 GTT GTT TTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
39467 GTT -TT GTT
1 GTT GTT GTT
39475 TTTTGTTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.00, C:0.00, G:0.30, T:0.70
Consensus pattern (3 bp):
GTT
Found at i:39434 original size:12 final size:12
Alignment explanation
Indices: 39409--39491 Score: 82
Period size: 12 Copynumber: 7.1 Consensus size: 12
39399 GTCGTAATTT
*
39409 TTGTTTTT-TCG
1 TTGTTTTTGTTG
39420 TTGTTTTTGTTG
1 TTGTTTTTGTTG
*
39432 TTGTTGTTGTTG
1 TTGTTTTTGTTG
*
39444 TTGTTGTTGTTG
1 TTGTTTTTGTTG
*
39456 TTGTTGTTGTTG
1 TTGTTTTTGTTG
*
39468 TT-TTGTTTTTTG
1 TTGTT-TTTGTTG
*
39480 TT-TTTTTTTTG
1 TTGTTTTTGTTG
39491 T
1 T
39492 GACCTGGCTC
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
11 18 0.27
12 48 0.73
ACGTcount: A:0.00, C:0.01, G:0.24, T:0.75
Consensus pattern (12 bp):
TTGTTTTTGTTG
Found at i:39487 original size:11 final size:12
Alignment explanation
Indices: 39406--39491 Score: 59
Period size: 15 Copynumber: 6.6 Consensus size: 12
39396 CTCGTCGTAA
39406 TTTTTGTTTT-T
1 TTTTTGTTTTGT
**
39417 TCGTTGTTTTTGT
1 TTTTTG-TTTTGT
39430 TGTTGTTGTTGTTGT
1 T-TT-TTGTT-TTGT
39445 TGTTGTTGTTGTTGT
1 T-TT-TTGTT-TTGT
39460 TGTTGTTGTTTTGT
1 T-TT-TTGTTTTGT
39474 TTTTTGTTTT-T
1 TTTTTGTTTTGT
39485 TTTTTGT
1 TTTTTGT
39492 GACCTGGCTC
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
11 12 0.18
12 11 0.17
13 4 0.06
14 7 0.11
15 32 0.48
ACGTcount: A:0.00, C:0.01, G:0.23, T:0.76
Consensus pattern (12 bp):
TTTTTGTTTTGT
Found at i:43347 original size:15 final size:16
Alignment explanation
Indices: 43323--43362 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
43313 AGAGGTTGAA
*
43323 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
43338 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
43354 AGAAAACAA
1 AGAAAACAA
43363 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Done.