Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018641.1 Corchorus olitorius cultivar O-4 contig18674, 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: 8803
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:1203 original size:37 final size:38
Alignment explanation
Indices: 1153--1226 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
1143 TGTAATTTTT
1153 CTTGATTGACCGCAC-TGGATCAC-CTTTAGGAAACTTC
1 CTTGATTGACCGCACGTGGATCACAC-TTAGGAAACTTC
1190 CTTGATTGACCGCACGTGGATCACACTTAGGAAACTT
1 CTTGATTGACCGCACGTGGATCACACTTAGGAAACTT
1227 AAACCACTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
37 15 0.43
38 19 0.54
39 1 0.03
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (38 bp):
CTTGATTGACCGCACGTGGATCACACTTAGGAAACTTC
Found at i:1330 original size:101 final size:99
Alignment explanation
Indices: 1221--1423 Score: 334
Period size: 101 Copynumber: 2.0 Consensus size: 99
1211 CACACTTAGG
* *
1221 AAACTTAAACCACTGTAAACTTGATTGATCGCACTGGATTACTTGAAGAAAAACCTAAACCACTG
1 AAACTTAAACCACTGTAAACCTGATTGATCGCACTGGATCACTTGAAGAAAAACCTAAACCACTG
1286 TAAACTTGATTGATCGCACTGGATCACTTTGAAGAA
66 TAAACTTGATTGATCGCACT-GATCAC-TTGAAGAA
* * * *
1322 AAACTTAAACGACTGTAAACCTGATTGATTGCACTGGATCATTTGAAGAAAAACTTAAACCACTG
1 AAACTTAAACCACTGTAAACCTGATTGATCGCACTGGATCACTTGAAGAAAAACCTAAACCACTG
1387 TAAACTTGATTGATCGCACTGATCACTTGAAGAA
66 TAAACTTGATTGATCGCACTGATCACTTGAAGAA
1421 AAA
1 AAA
1424 TTGAAGAATG
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
99 11 0.11
100 6 0.06
101 79 0.82
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (99 bp):
AAACTTAAACCACTGTAAACCTGATTGATCGCACTGGATCACTTGAAGAAAAACCTAAACCACTG
TAAACTTGATTGATCGCACTGATCACTTGAAGAA
Found at i:1339 original size:51 final size:50
Alignment explanation
Indices: 1221--1423 Score: 336
Period size: 50 Copynumber: 4.1 Consensus size: 50
1211 CACACTTAGG
*
1221 AAACTTAAACCACTGTAAACTTGATTGATCGCACTGGATTACTTGAAGAA
1 AAACTTAAACCACTGTAAACTTGATTGATCGCACTGGATCACTTGAAGAA
*
1271 AAACCTAAACCACTGTAAACTTGATTGATCGCACTGGATCACTTTGAAGAA
1 AAACTTAAACCACTGTAAACTTGATTGATCGCACTGGATCAC-TTGAAGAA
* * * *
1322 AAACTTAAACGACTGTAAACCTGATTGATTGCACTGGATCATTTGAAGAA
1 AAACTTAAACCACTGTAAACTTGATTGATCGCACTGGATCACTTGAAGAA
1372 AAACTTAAACCACTGTAAACTTGATTGATCGCACT-GATCACTTGAAGAA
1 AAACTTAAACCACTGTAAACTTGATTGATCGCACTGGATCACTTGAAGAA
1421 AAA
1 AAA
1424 TTGAAGAATG
Statistics
Matches: 141, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
49 16 0.11
50 80 0.57
51 45 0.32
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (50 bp):
AAACTTAAACCACTGTAAACTTGATTGATCGCACTGGATCACTTGAAGAA
Found at i:1492 original size:26 final size:25
Alignment explanation
Indices: 1460--1514 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
1450 TGAAATTAAC
* *
1460 TGAAGAATGATTGCCCTTGG-TCAACT
1 TGAAGAAAGATCGCCC-TGGATCAA-T
1486 TGAAGAAAGATCGCCCTGGATCAAT
1 TGAAGAAAGATCGCCCTGGATCAAT
1511 TGAA
1 TGAA
1515 ACTAACTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (25 bp):
TGAAGAAAGATCGCCCTGGATCAAT
Found at i:1525 original size:96 final size:96
Alignment explanation
Indices: 1425--1661 Score: 339
Period size: 96 Copynumber: 2.5 Consensus size: 96
1415 GAAGAAAAAT
* * * * *
1425 TGAAGAATGATCGCCCTAGTTTGATTGAAATTAACTGAAGAATGATTGCCCTTGGTCAACTTGAA
1 TGAAGAAAGATCGCCCTAGATTGATTGAAATCAACTGAAGAAAGATTGCCCTGGGTCAACTTGAA
*
1490 GAAAGATCGCCCTGGATCAATTGAAACTAAC
66 GAAAGATCGCCCTGGATCAATTAAAACTAAC
*
1521 TGAAGAAAGATCGCCCTGGATTGATTGAAATCAACTGAAGAAAGATTGCCCTGGGTCAACTTGAA
1 TGAAGAAAGATCGCCCTAGATTGATTGAAATCAACTGAAGAAAGATTGCCCTGGGTCAACTTGAA
* *
1586 GAGAGATCGCCTTGGATCAATTAAAACTAAC
66 GAAAGATCGCCCTGGATCAATTAAAACTAAC
* * ** * *
1617 TGAAGAAAGATCCCCCTGGATCAATTGAAGTAAACTGAAGAAAGA
1 TGAAGAAAGATCGCCCTAGATTGATTGAAATCAACTGAAGAAAGA
1662 CCGCCCCAGT
Statistics
Matches: 127, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 127 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (96 bp):
TGAAGAAAGATCGCCCTAGATTGATTGAAATCAACTGAAGAAAGATTGCCCTGGGTCAACTTGAA
GAAAGATCGCCCTGGATCAATTAAAACTAAC
Found at i:1532 original size:35 final size:36
Alignment explanation
Indices: 1486--2209 Score: 243
Period size: 35 Copynumber: 20.9 Consensus size: 36
1476 TTGGTCAACT
1486 TGAAGAAAGATCGCCCTGGATCAATTGAAACT-AAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACTAAAC
** *
1521 TGAAGAAAGATCGCCCTGGATTGATTGAAA-TCAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACTAAAC
* *
1556 TGAAGAAAGATTGCCCTGGGTC------AACT----
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACTAAAC
* * *
1582 TGAAGAGAGATCGCCTTGGATCAATTAAAACT-AAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACTAAAC
* *
1617 TGAAGAAAGATCCCCCTGGATCAATTG-AAGTAAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACTAAAC
* ** * *
1652 TGAAGAAAGACCGCCCCAGTTCAACTGAAA-TAAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACTAAAC
* * * * *
1687 TGAAGAACGACCACCC-----C---CGACA-TAAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACTAAAC
* * * **
1714 TGAAGAAAGACCACCCTGGGTCAACGGAAA-TAAAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACT-AAAC
* * * * * *
1750 TGAATAACGACCACCCTCGATCATTTTG--ACGTAAAC
1 TGAAGAAAGATCGCCCTGGATCA-ATTGAAAC-TAAAC
* * * * *
1786 TGAAGAAAAAACAACCCTGGGTCGATTGAAA-TAAAC
1 TGAAGAAAGATC-GCCCTGGATCAATTGAAACTAAAC
* * * *
1822 TGAAGAAAGACCGCCCTGGGTCAACTG-AAGTAAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACTAAAC
* * *
1857 TGAAGAATGATCGCCTTGGATCAATTG-AAGTAAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACTAAAC
* * * * * *
1892 TGAAGAACGACCGCCCTGGGTTAACT-AAAATAAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACTAAAC
** * * * * *
1927 TGAAGAACTACCACCCTCGATCATTCTGAGA-TAAAC
1 TGAAGAAAGATCGCCCTGGATCAAT-TGAAACTAAAC
* * * ** * * * *
1963 TGAAGAAACACCACTTTGGGTCAACT-AAAATAAAT
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACTAAAC
* * *
1998 TGAAGAAAGACCGCCCTGGGTCAACTGAAA-TAAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACTAAAC
* * * * **
2033 TGAA-AAATGACCACCCTCGATCATTCTGGCA-TAAAC
1 TGAAGAAA-GATCGCCCTGGATCAAT-TGAAACTAAAC
* * * *
2069 TGAAGAAAAGACCACCCT-TAGTCAACTGAAA-TAAAC
1 TGAAG-AAAGATCGCCCTGGA-TCAATTGAAACTAAAC
* * * *
2105 TGAAGAAAGACCGCCCTGGGTCAACTGAAA-TGAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACTAAAC
* * * * * *
2140 TAAAGAACGACCACCCTCGATCATTCTG--ACGTAAAC
1 TGAAGAAAGATCGCCCTGGATCAAT-TGAAAC-TAAAC
* *
2176 TGAAGAAAGACCGCCCTGGGTCAATATGAAACTA
1 TGAAGAAAGATCGCCCTGGATCAAT-TGAAACTA
2210 TCTAAGAGAC
Statistics
Matches: 531, Mismatches: 113, Indels: 88
0.73 0.15 0.12
Matches are distributed among these distances:
26 18 0.03
27 23 0.04
29 2 0.00
30 2 0.00
32 5 0.01
34 12 0.02
35 303 0.57
36 134 0.25
37 26 0.05
38 6 0.01
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (36 bp):
TGAAGAAAGATCGCCCTGGATCAATTGAAACTAAAC
Found at i:1586 original size:61 final size:60
Alignment explanation
Indices: 1521--1646 Score: 155
Period size: 61 Copynumber: 2.1 Consensus size: 60
1511 TGAAACTAAC
** * ** *
1521 TGAAGAAAGATCGCCCTGGATTGATTGAAA-TCAACTGAAGAAAGATTGCCCTGGGTCAACT
1 TGAAGAAAGATCGCCCTGGATCAATTAAAACT-AACTGAAGAAAGATCCCCCTGGATCAA-T
* *
1582 TGAAGAGAGATCGCCTTGGATCAATTAAAACTAACTGAAGAAAGATCCCCCTGGATCAAT
1 TGAAGAAAGATCGCCCTGGATCAATTAAAACTAACTGAAGAAAGATCCCCCTGGATCAAT
1642 TGAAG
1 TGAAG
1647 TAAACTGAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
60 6 0.11
61 49 0.88
62 1 0.02
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (60 bp):
TGAAGAAAGATCGCCCTGGATCAATTAAAACTAACTGAAGAAAGATCCCCCTGGATCAAT
Found at i:1605 original size:26 final size:25
Alignment explanation
Indices: 1550--1605 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
1540 ATTGATTGAA
*
1550 ATCAACTGAAGAAAGATTGCCCTGG
1 ATCAACTGAAGAAAGATCGCCCTGG
* * *
1575 GTCAACTTGAAGAGAGATCGCCTTGG
1 ATCAAC-TGAAGAAAGATCGCCCTGG
1601 ATCAA
1 ATCAA
1606 TTAAAACTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (25 bp):
ATCAACTGAAGAAAGATCGCCCTGG
Found at i:1721 original size:62 final size:63
Alignment explanation
Indices: 1647--1765 Score: 177
Period size: 62 Copynumber: 1.9 Consensus size: 63
1637 TCAATTGAAG
* * *
1647 TAAACTGAAGAAAGACCGCCCCAGTTCAACTGAAAT-AAACTGAAGAACGACCACCCCCGACA
1 TAAACTGAAGAAAGACCACCCCAGGTCAACGGAAATAAAACTGAAGAACGACCACCCCCGACA
** *
1709 TAAACTGAAGAAAGACCACCCTGGGTCAACGGAAATAAAACTGAATAACGACCACCC
1 TAAACTGAAGAAAGACCACCCCAGGTCAACGGAAATAAAACTGAAGAACGACCACCC
1766 TCGATCATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
62 31 0.62
63 19 0.38
ACGTcount: A:0.43, C:0.29, G:0.17, T:0.12
Consensus pattern (63 bp):
TAAACTGAAGAAAGACCACCCCAGGTCAACGGAAATAAAACTGAAGAACGACCACCCCCGACA
Found at i:1967 original size:106 final size:106
Alignment explanation
Indices: 1781--2199 Score: 454
Period size: 106 Copynumber: 3.9 Consensus size: 106
1771 CATTTTGACG
* ** * * ** * * *
1781 TAAACTGAAGAAAAAACAACCCTGGGTCGATTGAAATAAACTGAAGAAAGACCGCCCTGGGTCA-
1 TAAACTGAAG-AAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAACTACCACCCTCGATCAT
* * * * * *
1845 ACTGA-AGTAAACTGAAGAATGATCGCCTTGGATCAATTGAAG
65 TCTGAGA-TAAACTGAAGAAAGACCGCCTTGGGTCAACTGAAA
* * *
1887 TAAACTGAAGAACGACCGCCCTGGGTTAACTAAAATAAACTGAAGAACTACCACCCTCGATCATT
1 TAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAACTACCACCCTCGATCATT
* * * *
1952 CTGAGATAAACTGAAGAAACACCACTTTGGGTCAACTAAAA
66 CTGAGATAAACTGAAGAAAGACCGCCTTGGGTCAACTGAAA
* *
1993 TAAATTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAA-AAATGACCACCCTCGATCAT
1 TAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAACT-ACCACCCTCGATCAT
* *
2057 TCTG-GCATAAACTGAAGAAAAGACCACCCTT-AGTCAACTGAAA
65 TCTGAG-ATAAACTGAAG-AAAGACC-GCCTTGGGTCAACTGAAA
* * *
2100 TAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATGAACTAAAGAACGACCACCCTCGATCATT
1 TAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAACTACCACCCTCGATCATT
*
2165 CTGACG-TAAACTGAAGAAAGACCGCCCTGGGTCAA
66 CTGA-GATAAACTGAAGAAAGACCGCCTTGGGTCAA
2200 TATGAAACTA
Statistics
Matches: 262, Mismatches: 41, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
105 47 0.18
106 122 0.47
107 87 0.33
108 5 0.02
109 1 0.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.18
Consensus pattern (106 bp):
TAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAACTACCACCCTCGATCATT
CTGAGATAAACTGAAGAAAGACCGCCTTGGGTCAACTGAAA
Found at i:2187 original size:71 final size:70
Alignment explanation
Indices: 1708--2199 Score: 355
Period size: 71 Copynumber: 6.9 Consensus size: 70
1698 CACCCCCGAC
* * * * * * * * * *
1708 ATAAACTGAAGAAAGACCACCCTGGGTCAACGGAAATAAAACTGAATAACGACCACCCTCGATCA
1 ATAAACTGAAGAAAGACCACCCTCGATCATCTGAAGT-AAACTGAAGAAAGACCGCCCTGGGTCA
** *
1773 TTTTGAC
65 -ACTGAA
* * * * * *
1780 GTAAACTGAAGAAAAAACAACCCTGGGTCGAT-TGAAATAAACTGAAGAAAGACCGCCCTGGGTC
1 ATAAACTGAAG-AAAGACCACCCTCGATC-ATCTGAAGTAAACTGAAGAAAGACCGCCCTGGGTC
1844 AACTGAA
64 AACTGAA
* * * * * * * *
1851 GTAAACTGAAGAATGATCGCCTTGGATCAAT-TGAAGTAAACTGAAGAACGACCGCCCTGGGTTA
1 ATAAACTGAAGAAAGACCACCCTCGATC-ATCTGAAGTAAACTGAAGAAAGACCGCCCTGGGTCA
*
1915 ACTAAA
65 ACTGAA
** * * **
1921 ATAAACTGAAGAACTACCACCCTCGATCATTCTG-AGATAAACTGAAGAAACACCACTTTGGGTC
1 ATAAACTGAAGAAAGACCACCCTCGATCA-TCTGAAG-TAAACTGAAGAAAGACCGCCCTGGGTC
*
1985 AACTAAA
64 AACTGAA
* * * * * * * * *
1992 ATAAATTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAA-AAATGACCACCCTCGATCA
1 ATAAACTGAAGAAAGACCACCCTCGATCATCTGAAGTAAACTGAAGAAA-GACCGCCCTGGGTCA
* **
2056 TTCTGGC
65 -ACTGAA
* * *
2063 ATAAACTGAAGAAAAGACCACCCT-TAGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTC
1 ATAAACTGAAG-AAAGACCACCCTCGA-TCATCTGAAGTAAACTGAAGAAAGACCGCCCTGGGTC
2127 AACTGAA
64 AACTGAA
* * * *
2134 ATGAACTAAAGAACGACCACCCTCGATCATTCTGACGTAAACTGAAGAAAGACCGCCCTGGGTCA
1 ATAAACTGAAGAAAGACCACCCTCGATCA-TCTGAAGTAAACTGAAGAAAGACCGCCCTGGGTCA
2199 A
65 A
2200 TATGAAACTA
Statistics
Matches: 335, Mismatches: 72, Indels: 27
0.77 0.17 0.06
Matches are distributed among these distances:
69 4 0.01
70 107 0.32
71 126 0.38
72 74 0.22
73 23 0.07
74 1 0.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.18
Consensus pattern (70 bp):
ATAAACTGAAGAAAGACCACCCTCGATCATCTGAAGTAAACTGAAGAAAGACCGCCCTGGGTCAA
CTGAA
Found at i:3386 original size:7 final size:7
Alignment explanation
Indices: 3374--3446 Score: 55
Period size: 7 Copynumber: 10.3 Consensus size: 7
3364 GAGCTTCATC
3374 TTTTCTT
1 TTTTCTT
3381 TTTTCTT
1 TTTTCTT
*
3388 TTCTCTT
1 TTTTCTT
3395 TTTT-TT
1 TTTTCTT
3401 TTCTT-TT
1 TT-TTCTT
3408 GATTTCTCTT
1 --TTT-TCTT
3418 TTTTC-T
1 TTTTCTT
3424 TTTTCTT
1 TTTTCTT
3431 CTTTT-TT
1 -TTTTCTT
*
3438 TTTTATT
1 TTTTCTT
3445 TT
1 TT
3447 ACTTCACTAT
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
6 14 0.25
7 29 0.52
8 8 0.14
9 3 0.05
10 2 0.04
ACGTcount: A:0.03, C:0.14, G:0.01, T:0.82
Consensus pattern (7 bp):
TTTTCTT
Found at i:3396 original size:19 final size:18
Alignment explanation
Indices: 3372--3446 Score: 71
Period size: 19 Copynumber: 3.9 Consensus size: 18
3362 TAGAGCTTCA
3372 TCTTTTCTTTTTTCTTTTC
1 TCTTTT-TTTTTTCTTTTC
*
3391 TCTTTTTTTTTTCTTTTGA
1 TCTTTTTTTTTTCTTTT-C
*
3410 T-TTCTCTTTTTTCTTTTTC
1 TCTT-TTTTTTTTC-TTTTC
*
3429 TTCTTTTTTTTTTATTTT
1 -TCTTTTTTTTTTCTTTT
3447 ACTTCACTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
18 13 0.28
19 19 0.41
20 12 0.26
21 2 0.04
ACGTcount: A:0.03, C:0.15, G:0.01, T:0.81
Consensus pattern (18 bp):
TCTTTTTTTTTTCTTTTC
Found at i:3400 original size:23 final size:22
Alignment explanation
Indices: 3374--3435 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
3364 GAGCTTCATC
*
3374 TTTTCTTTTTTCTTTTCTCTTT
1 TTTTTTTTTTTCTTTTCTCTTT
**
3396 TTTTTTTCTTTTGATTTCTCTTT
1 TTTTTTT-TTTTCTTTTCTCTTT
*
3419 TTTCTTTTTCTTCTTTT
1 TTT-TTTTTTTTCTTTT
3436 TTTTTTATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
22 6 0.19
23 22 0.69
24 4 0.12
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (22 bp):
TTTTTTTTTTTCTTTTCTCTTT
Found at i:4287 original size:19 final size:19
Alignment explanation
Indices: 4251--4286 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4241 CTTTTCTTTG
*
4251 ATTTTTTTTTTCATTTTTC
1 ATTTTTTTCTTCATTTTTC
4270 ATTTTTTTCTTC-TTTTT
1 ATTTTTTTCTTCATTTTT
4287 TTTATGGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (19 bp):
ATTTTTTTCTTCATTTTTC
Found at i:5961 original size:13 final size:13
Alignment explanation
Indices: 5943--5967 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5933 AAAAATATCA
5943 AAAAAATAAAAAT
1 AAAAAATAAAAAT
5956 AAAAAATAAAAA
1 AAAAAATAAAAA
5968 ATTTTCGACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Done.