Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015278.1 Corchorus olitorius cultivar O-4 contig15311, 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: 26942
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Found at i:1117 original size:32 final size:32
Alignment explanation
Indices: 1071--1198 Score: 175
Period size: 32 Copynumber: 3.9 Consensus size: 32
1061 GTCAGTCAGT
* * *
1071 AAAGAGTAAAATGGTAACTAGTAATCAAATTCA
1 AAAG-GTAAAATAGTAATTAGCAATCAAATTCA
* * * *
1104 AATGGTAAAATGGTAATTAGTAATCAAGTTCA
1 AAAGGTAAAATAGTAATTAGCAATCAAATTCA
1136 AAAGGGTAAAATAGTAATTAGCAATCAAATTCA
1 AAA-GGTAAAATAGTAATTAGCAATCAAATTCA
1169 AAAGGTAAAATAGTAATTAGCAATCAAATT
1 AAAGGTAAAATAGTAATTAGCAATCAAATT
1199 TAAAGAGTAA
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
32 55 0.63
33 32 0.37
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.27
Consensus pattern (32 bp):
AAAGGTAAAATAGTAATTAGCAATCAAATTCA
Found at i:1185 original size:65 final size:65
Alignment explanation
Indices: 1071--1209 Score: 190
Period size: 65 Copynumber: 2.2 Consensus size: 65
1061 GTCAGTCAGT
* * * * *
1071 AAAGAGTAAAATGGTAACTAGTAATCAAATTCAAATGGTAAAATGGTAATTAGTAATCAAGTTCA
1 AAAGAGTAAAATAGTAACTAGCAATCAAATTCAAAAGGTAAAATAGTAATTAGCAATCAAGTTCA
* * * *
1136 AAAGGGTAAAATAGTAATTAGCAATCAAATTCAAAAGGTAAAATAGTAATTAGCAATCAAATT-T
1 AAAGAGTAAAATAGTAACTAGCAATCAAATTCAAAAGGTAAAATAGTAATTAGCAATCAAGTTCA
1200 AAAGAGTAAA
1 AAAGAGTAAA
1210 CTGGTGGTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
64 9 0.14
65 55 0.86
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (65 bp):
AAAGAGTAAAATAGTAACTAGCAATCAAATTCAAAAGGTAAAATAGTAATTAGCAATCAAGTTCA
Found at i:1359 original size:21 final size:21
Alignment explanation
Indices: 1325--1445 Score: 122
Period size: 21 Copynumber: 5.8 Consensus size: 21
1315 TGGCAATGGC
*
1325 AAAGAGTAAAGAGTAATCAGT
1 AAAGGGTAAAGAGTAATCAGT
* *
1346 GAAAGGGT-AAGAGTAGTTAGT
1 -AAAGGGTAAAGAGTAATCAGT
* *
1367 AAAGAGTCAAGAGTAATCAAG-
1 AAAGGGTAAAGAGTAATC-AGT
*
1388 AAACGGTAAAGAGTAATCAGT
1 AAAGGGTAAAGAGTAATCAGT
*
1409 AAAGGAGT-AATAGTAATCAGT
1 AAAGG-GTAAAGAGTAATCAGT
*
1430 AAAGAGTAAAGAGTAA
1 AAAGGGTAAAGAGTAA
1446 AGGAGTAATA
Statistics
Matches: 81, Mismatches: 13, Indels: 11
0.77 0.12 0.10
Matches are distributed among these distances:
20 10 0.12
21 61 0.75
22 10 0.12
ACGTcount: A:0.50, C:0.05, G:0.26, T:0.19
Consensus pattern (21 bp):
AAAGGGTAAAGAGTAATCAGT
Found at i:1372 original size:42 final size:42
Alignment explanation
Indices: 1325--1445 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 42
1315 TGGCAATGGC
* *
1325 AAAGAGTAAAGAGTAATCAGTGAAAGGGT-AAGAGTAGTTAGT
1 AAAGAGT-AAGAGTAATCAGTGAAAGGGTAAAGAGTAATCAGT
* *
1367 AAAGAGTCAAGAGTAATCA-AGAAACGGTAAAGAGTAATCAGT
1 AAAGAGT-AAGAGTAATCAGTGAAAGGGTAAAGAGTAATCAGT
* *
1409 AAAGGAGTAATAGTAATCAGT-AAAGAGTAAAGAGTAA
1 AAA-GAGTAAGAGTAATCAGTGAAAGGGTAAAGAGTAA
1446 AGGAGTAATA
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
41 7 0.10
42 56 0.84
43 4 0.06
ACGTcount: A:0.50, C:0.05, G:0.26, T:0.19
Consensus pattern (42 bp):
AAAGAGTAAGAGTAATCAGTGAAAGGGTAAAGAGTAATCAGT
Found at i:1403 original size:35 final size:35
Alignment explanation
Indices: 1364--1553 Score: 174
Period size: 35 Copynumber: 5.4 Consensus size: 35
1354 AAGAGTAGTT
* * *
1364 AGTAAAGAGTCAA-GAGTAATCAAGAAACGGTAAAG
1 AGTAAAGAGTAAAGGAGTAAT-AAGAATCAGTAAAG
**
1399 AGTAATCAGTAAAGGAGTAAT-AGTAATCAGTAAAG
1 AGTAAAGAGTAAAGGAGTAATAAG-AATCAGTAAAG
* *
1434 AGTAAAGAGTAAAGGAGTAATAATAGTCAGTAAAG
1 AGTAAAGAGTAAAGGAGTAATAAGAATCAGTAAAG
*
1469 AGTAAAGAGTAAAAAGAGTAAT-AGTAATCAGTAAAGG
1 AGTAAAGAGT-AAAGGAGTAATAAG-AATCAGTAAA-G
* * * *
1506 AGTAAACAGTACAATG-GTAAT-AGCAATGAGCAAAG
1 AGTAAAGAGTA-AAGGAGTAATAAG-AATCAGTAAAG
1541 AGTAAAGAGTAAA
1 AGTAAAGAGTAAA
1554 AATGGTAATA
Statistics
Matches: 130, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
34 4 0.03
35 70 0.54
36 43 0.33
37 13 0.10
ACGTcount: A:0.52, C:0.06, G:0.24, T:0.18
Consensus pattern (35 bp):
AGTAAAGAGTAAAGGAGTAATAAGAATCAGTAAAG
Found at i:1453 original size:8 final size:7
Alignment explanation
Indices: 1325--1553 Score: 73
Period size: 7 Copynumber: 32.4 Consensus size: 7
1315 TGGCAATGGC
1325 AAAGAGT
1 AAAGAGT
1332 AAAGAGT
1 AAAGAGT
**
1339 AATCAGT
1 AAAGAGT
*
1346 GAAAGGGT
1 -AAAGAGT
1354 -AAGAGT
1 AAAGAGT
***
1360 AGTTAGT
1 AAAGAGT
1367 AAAGAGT
1 AAAGAGT
*
1374 CAAGAGT
1 AAAGAGT
1381 AATCA-AG-
1 AA--AGAGT
1388 AAACG-GT
1 AAA-GAGT
1395 AAAGAGT
1 AAAGAGT
**
1402 AATCAGT
1 AAAGAGT
1409 AAAGGAGT
1 AAA-GAGT
*
1417 -AATAGT
1 AAAGAGT
**
1423 AATCAGT
1 AAAGAGT
1430 AAAGAGT
1 AAAGAGT
1437 AAAGAGT
1 AAAGAGT
1444 AAAGGAGT
1 AAA-GAGT
1452 AATA-A-T
1 AA-AGAGT
***
1458 AGTCAGT
1 AAAGAGT
1465 AAAGAGT
1 AAAGAGT
1472 AAAGAGT
1 AAAGAGT
1479 AAAAAGAGT
1 --AAAGAGT
*
1488 -AATAGT
1 AAAGAGT
**
1494 AATCAGT
1 AAAGAGT
1501 AAAGGAGT
1 AAA-GAGT
*
1509 AAACAGT
1 AAAGAGT
1516 ACAATG-GT
1 A-AA-GAGT
* *
1524 -AATAGC
1 AAAGAGT
* *
1530 AATGAGC
1 AAAGAGT
1537 AAAGAGT
1 AAAGAGT
1544 AAAGAGT
1 AAAGAGT
1551 AAA
1 AAA
1554 AATGGTAATA
Statistics
Matches: 159, Mismatches: 41, Indels: 44
0.65 0.17 0.18
Matches are distributed among these distances:
5 1 0.01
6 21 0.13
7 103 0.65
8 25 0.16
9 9 0.06
ACGTcount: A:0.51, C:0.05, G:0.25, T:0.19
Consensus pattern (7 bp):
AAAGAGT
Found at i:1544 original size:72 final size:71
Alignment explanation
Indices: 1395--1571 Score: 216
Period size: 72 Copynumber: 2.5 Consensus size: 71
1385 AAGAAACGGT
** * * *
1395 AAAGAGTAATCAGT-AAAGGAGTAATAGTAATCAGTAAAGAGTAAAGAGTAAAGGAGTAATAATA
1 AAAGAGTAAAGAGTAAAAAGAGTAATAGTAATCAGTAAAGAGTAAACAGTAAAGGAGTAATAACA
* *
1459 GTCAGT
66 ATCAGC
* *
1465 AAAGAGTAAAGAGTAAAAAGAGTAATAGTAATCAGTAAAGGAGTAAACAGTACAATG-GTAATAG
1 AAAGAGTAAAGAGTAAAAAGAGTAATAGTAATCAGTAAA-GAGTAAACAGTA-AAGGAGTAATAA
*
1529 CAATGAGC
64 CAATCAGC
1537 AAAGAGTAAAGAGTAAAAATG-GTAATAGTAATCAG
1 AAAGAGTAAAGAGTAAAAA-GAGTAATAGTAATCAG
1572 CAAAATAGTA
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
70 12 0.13
71 23 0.25
72 54 0.58
73 4 0.04
ACGTcount: A:0.51, C:0.05, G:0.24, T:0.20
Consensus pattern (71 bp):
AAAGAGTAAAGAGTAAAAAGAGTAATAGTAATCAGTAAAGAGTAAACAGTAAAGGAGTAATAACA
ATCAGC
Found at i:1575 original size:36 final size:36
Alignment explanation
Indices: 1393--1571 Score: 204
Period size: 35 Copynumber: 5.0 Consensus size: 36
1383 TCAAGAAACG
** *
1393 GTAAAGAGTAATCAGT-AAAGGAGTAATAGTAATCA
1 GTAAAGAGTAAAGAGTAAAATGAGTAATAGTAATCA
* * *
1428 GTAAAGAGTAAAGAGT-AAAGGAGTAATAATAGTCA
1 GTAAAGAGTAAAGAGTAAAATGAGTAATAGTAATCA
*
1463 GTAAAGAGTAAAGAGTAAAAAGAGTAATAGTAATCA
1 GTAAAGAGTAAAGAGTAAAATGAGTAATAGTAATCA
* * * *
1499 GTAAAGGAGTAAACAGTACAATG-GTAATAGCAATGA
1 GTAAA-GAGTAAAGAGTAAAATGAGTAATAGTAATCA
*
1535 GCAAAGAGTAAAGAGTAAAAATG-GTAATAGTAATCA
1 GTAAAGAGTAAAGAGT-AAAATGAGTAATAGTAATCA
1571 G
1 G
1572 CAAAATAGTA
Statistics
Matches: 124, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
35 57 0.46
36 53 0.43
37 14 0.11
ACGTcount: A:0.51, C:0.05, G:0.24, T:0.20
Consensus pattern (36 bp):
GTAAAGAGTAAAGAGTAAAATGAGTAATAGTAATCA
Found at i:1582 original size:21 final size:21
Alignment explanation
Indices: 1552--1597 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1542 GTAAAGAGTA
* * *
1552 AAAATGGTAATAGTAATCAGC
1 AAAATAGTAAGAGTAATCAAC
*
1573 AAAATAGTAAGAGTAGTCAAC
1 AAAATAGTAAGAGTAATCAAC
1594 AAAA
1 AAAA
1598 GAGAAACAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (21 bp):
AAAATAGTAAGAGTAATCAAC
Found at i:1585 original size:36 final size:37
Alignment explanation
Indices: 1415--1587 Score: 164
Period size: 36 Copynumber: 4.8 Consensus size: 37
1405 CAGTAAAGGA
* *
1415 GTAATAGTAATCAG-TAAAGAGTAAAGAGT--AAAGG
1 GTAATAGTAATCAGCAAAAGAGTAAAGAGTAAAAATG
* * *
1449 AGTAATAATAGTCAG-TAAAGAGTAAAGAGTAAAAA-G
1 -GTAATAGTAATCAGCAAAAGAGTAAAGAGTAAAAATG
* * * *
1485 AGTAATAGTAATCAGTAAAGGAGTAAACAGT-ACAATG
1 -GTAATAGTAATCAGCAAAAGAGTAAAGAGTAAAAATG
* *
1522 GTAATAGCAATGAGC-AAAGAGTAAAGAGTAAAAATG
1 GTAATAGTAATCAGCAAAAGAGTAAAGAGTAAAAATG
*
1558 GTAATAGTAATCAGCAAAATAGT-AAGAGTA
1 GTAATAGTAATCAGCAAAAGAGTAAAGAGTA
1588 GTCAACAAAA
Statistics
Matches: 115, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
35 39 0.34
36 54 0.47
37 22 0.19
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.20
Consensus pattern (37 bp):
GTAATAGTAATCAGCAAAAGAGTAAAGAGTAAAAATG
Found at i:1660 original size:26 final size:25
Alignment explanation
Indices: 1601--1689 Score: 92
Period size: 25 Copynumber: 3.5 Consensus size: 25
1591 AACAAAAGAG
*
1601 AAACAATAATCAGTAAAAAGAGTAA
1 AAACAGTAATCAGTAAAAAGAGTAA
*
1626 AAACAGTAATCAGTAAAAGGAGTAA
1 AAACAGTAATCAGTAAAAAGAGTAA
*
1651 AAA-ATGGTAATCAGTAATCAAGAAGT-A
1 AAACA--GTAATCAGTAA-AAAG-AGTAA
*
1678 AAAGAGTAATCA
1 AAACAGTAATCA
1690 AGTGTAAGAT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
24 1 0.02
25 26 0.47
26 18 0.33
27 6 0.11
28 4 0.07
ACGTcount: A:0.57, C:0.08, G:0.17, T:0.18
Consensus pattern (25 bp):
AAACAGTAATCAGTAAAAAGAGTAA
Found at i:13238 original size:2 final size:2
Alignment explanation
Indices: 13231--13256 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13221 TTGTTAGTGC
13231 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
13257 GTATGTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16411 original size:29 final size:29
Alignment explanation
Indices: 16368--16425 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
16358 GGGTTTTATT
*
16368 TTTCTGTTTACTGTTATTAGCATGTGGGC
1 TTTCTGTTTACTGTTATTAGCATATGGGC
* * *
16397 TTTCTTTTTATTGTTATTGGCATATGGGC
1 TTTCTGTTTACTGTTATTAGCATATGGGC
16426 CTGATTCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.12, G:0.22, T:0.52
Consensus pattern (29 bp):
TTTCTGTTTACTGTTATTAGCATATGGGC
Found at i:17623 original size:32 final size:32
Alignment explanation
Indices: 17577--17720 Score: 173
Period size: 32 Copynumber: 4.4 Consensus size: 32
17567 GTCAGTCAGT
* *
17577 AAAGAGTAAAATGGTAACTAGTAATCAAATTCA
1 AAAG-GTAAAATGGTAATTAGCAATCAAATTCA
** * *
17610 AATTGTAAAATGGTAATTAGTAATCAAGTTCA
1 AAAGGTAAAATGGTAATTAGCAATCAAATTCA
*
17642 AAAGGATAAAATAGTAATTAGCAATCAAATTCA
1 AAAGG-TAAAATGGTAATTAGCAATCAAATTCA
* *
17675 AAAGGTAAAATAGTAATTAGCAATCAAATT-T
1 AAAGGTAAAATGGTAATTAGCAATCAAATTCA
17706 AAAGAGTAAAATGGT
1 AAAG-GTAAAATGGT
17721 GGTTAGTAAC
Statistics
Matches: 98, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
31 4 0.04
32 63 0.64
33 31 0.32
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.27
Consensus pattern (32 bp):
AAAGGTAAAATGGTAATTAGCAATCAAATTCA
Found at i:17887 original size:21 final size:21
Alignment explanation
Indices: 17831--17953 Score: 76
Period size: 21 Copynumber: 5.8 Consensus size: 21
17821 TGGCAATGGC
*
17831 AAAGAGTAAAGACTAATCAGTG
1 AAAGAGT-AAGAGTAATCAGTG
* * *
17853 AAAGGGTAATAGTAGTCAGT-
1 AAAGAGTAAGAGTAATCAGTG
*
17873 AAAGAGTCAAGAGTAATCA-AG
1 AAAGAGT-AAGAGTAATCAGTG
*
17894 AAATG-GTAAAGAGTAATAAGT-
1 AAA-GAGT-AAGAGTAATCAGTG
* *
17915 AAATGACTAATAGTAATCAGT-
1 AAA-GAGTAAGAGTAATCAGTG
17936 AAAGAGTAAAGGAGTAAT
1 AAAGAGT-AA-GAGTAAT
17954 AATAGTCAGT
Statistics
Matches: 78, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
20 9 0.12
21 55 0.71
22 14 0.18
ACGTcount: A:0.50, C:0.06, G:0.24, T:0.21
Consensus pattern (21 bp):
AAAGAGTAAGAGTAATCAGTG
Found at i:17890 original size:42 final size:42
Alignment explanation
Indices: 17831--17979 Score: 113
Period size: 42 Copynumber: 3.4 Consensus size: 42
17821 TGGCAATGGC
*
17831 AAAGAGTAAAGACTAATCAGTGAAAGGGTAATAGTAGTCAGT
1 AAAGAGTAAAGAGTAATCAGTGAAAGGGTAATAGTAGTCAGT
* * * * * *
17873 AAAGAGTCAAGAGTAATCA-AGAAATGGTAAAGAGTAATAAGT
1 AAAGAGTAAAGAGTAATCAGTGAAAGGGT-AATAGTAGTCAGT
* * *
17915 AAATGACT-AATAGTAATCAGTAAAGAGTAAAGGAGTAATAATAGTCAGT
1 AAA-GAGTAAAGAGTAATCAGT-----G-AAAGG-GTAATAGTAGTCAGT
17964 AAAGAGTAAAGAGTAA
1 AAAGAGTAAAGAGTAA
17980 AAAGAGAAAT
Statistics
Matches: 79, Mismatches: 17, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
41 7 0.09
42 40 0.51
43 3 0.04
48 4 0.05
49 23 0.29
50 2 0.03
ACGTcount: A:0.50, C:0.05, G:0.23, T:0.21
Consensus pattern (42 bp):
AAAGAGTAAAGAGTAATCAGTGAAAGGGTAATAGTAGTCAGT
Found at i:17936 original size:28 final size:28
Alignment explanation
Indices: 17912--17974 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
17902 AAGAGTAATA
* *
17912 AGTAAATGACTAATAGTAATCAGTAAAG
1 AGTAAAGGACTAATAATAATCAGTAAAG
* *
17940 AGTAAAGGAGTAATAATAGTCAGTAAAG
1 AGTAAAGGACTAATAATAATCAGTAAAG
17968 AGTAAAG
1 AGTAAAG
17975 AGTAAAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (28 bp):
AGTAAAGGACTAATAATAATCAGTAAAG
Found at i:18027 original size:36 final size:35
Alignment explanation
Indices: 17933--18067 Score: 146
Period size: 36 Copynumber: 3.8 Consensus size: 35
17923 AATAGTAATC
* * *
17933 AGTAAAGAGT-AAAGGAGTAATAATAGTCAGTAAAG
1 AGTAAAGAGTAAAATG-GTAATAGTAATCAGTAAAG
* *
17968 AGTAAAGAGTAAAAAGAGAAATAGTAATCAGTAAAGG
1 AGTAAAGAGTAAAATG-GTAATAGTAATCAGTAAA-G
* * * *
18005 AGTAAACAGTAAAATGGTAATAGCAATGAGCAAAG
1 AGTAAAGAGTAAAATGGTAATAGTAATCAGTAAAG
18040 AGTAAAGAGTAAAAATGGTAATAGTAAT
1 AGTAAAGAGT-AAAATGGTAATAGTAAT
18068 AAGCAAAATA
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
35 20 0.24
36 50 0.59
37 15 0.18
ACGTcount: A:0.53, C:0.04, G:0.24, T:0.19
Consensus pattern (35 bp):
AGTAAAGAGTAAAATGGTAATAGTAATCAGTAAAG
Found at i:18081 original size:21 final size:21
Alignment explanation
Indices: 18051--18117 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
18041 GTAAAGAGTA
*
18051 AAAATGGTAATAGTAATAAGC
1 AAAATAGTAATAGTAATAAGC
* * *
18072 AAAATAGTAAGAGTAGTCAGC
1 AAAATAGTAATAGTAATAAGC
* * * *
18093 AAGAGAGAAATAGTAATAAGT
1 AAAATAGTAATAGTAATAAGC
18114 AAAA
1 AAAA
18118 AGAGTAAAAA
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.19
Consensus pattern (21 bp):
AAAATAGTAATAGTAATAAGC
Found at i:18084 original size:36 final size:37
Alignment explanation
Indices: 17964--18086 Score: 137
Period size: 36 Copynumber: 3.4 Consensus size: 37
17954 AATAGTCAGT
* * *
17964 AAAGAGTAAAGAGTAAAAA-GAGAAATAGTAATCAGTA
1 AAAGAGTAAAGAGTAAAAATG-GTAATAGTAATAAGCA
* * * *
18001 AAGGAGTAAACAGT-AAAATGGTAATAGCAATGAGC-
1 AAAGAGTAAAGAGTAAAAATGGTAATAGTAATAAGCA
18036 AAAGAGTAAAGAGTAAAAATGGTAATAGTAATAAGCA
1 AAAGAGTAAAGAGTAAAAATGGTAATAGTAATAAGCA
*
18073 AAATAGT-AAGAGTA
1 AAAGAGTAAAGAGTA
18087 GTCAGCAAGA
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
35 12 0.17
36 41 0.57
37 19 0.26
ACGTcount: A:0.55, C:0.04, G:0.23, T:0.18
Consensus pattern (37 bp):
AAAGAGTAAAGAGTAAAAATGGTAATAGTAATAAGCA
Found at i:18160 original size:26 final size:25
Alignment explanation
Indices: 18100--18188 Score: 83
Period size: 25 Copynumber: 3.4 Consensus size: 25
18090 AGCAAGAGAG
*
18100 AAATAGTAATAAGTAAAAAGAGTAAA
1 AAAT-GTAATCAGTAAAAAGAGTAAA
*
18126 AACA-ATAATCAGTAAAAAGAGTAAA
1 AA-ATGTAATCAGTAAAAAGAGTAAA
*
18151 AAATGGTAATCAGTAATCAAGAAGTAAA
1 AAAT-GTAATCAGTAA-AAAG-AGTAAA
*
18179 AGA-GTAATCA
1 AAATGTAATCA
18189 AGTGTAAGAT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
24 1 0.02
25 21 0.40
26 19 0.36
27 4 0.08
28 8 0.15
ACGTcount: A:0.60, C:0.06, G:0.16, T:0.19
Consensus pattern (25 bp):
AAATGTAATCAGTAAAAAGAGTAAA
Found at i:19369 original size:13 final size:13
Alignment explanation
Indices: 19347--19386 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
19337 CAGAGAATAT
19347 TATCAACAGAAGA
1 TATCAACAGAAGA
*
19360 TATCATCAGAAGA
1 TATCAACAGAAGA
* *
19373 TTTCAACTGAAGA
1 TATCAACAGAAGA
19386 T
1 T
19387 TATCTGGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:19399 original size:11 final size:11
Alignment explanation
Indices: 19379--19409 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
19369 AAGATTTCAA
19379 CTGAAGATTAT
1 CTGAAGATTAT
*
19390 CTGGAGATTAT
1 CTGAAGATTAT
19401 CTGAAGATT
1 CTGAAGATT
19410 TAAGTAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (11 bp):
CTGAAGATTAT
Found at i:19866 original size:15 final size:16
Alignment explanation
Indices: 19846--19875 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19836 GATCTTCCAA
19846 TCTTAAGTT-TTTATT
1 TCTTAAGTTGTTTATT
19861 TCTTAAGTTGTTTAT
1 TCTTAAGTTGTTTAT
19876 ATTGTTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (16 bp):
TCTTAAGTTGTTTATT
Found at i:19970 original size:41 final size:41
Alignment explanation
Indices: 19924--20002 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
19914 AAATTACCTT
19924 TGACACCAGAAGTTGTCACCTTAGTAAATTAAAATTACTGC
1 TGACACCAGAAGTTGTCACCTTAGTAAATTAAAATTACTGC
* * *
19965 TGACACTAGAAGTTGTCACCTTGGTAAATTGAAATTAC
1 TGACACCAGAAGTTGTCACCTTAGTAAATTAAAATTAC
20003 CTTTTGACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (41 bp):
TGACACCAGAAGTTGTCACCTTAGTAAATTAAAATTACTGC
Found at i:22532 original size:33 final size:33
Alignment explanation
Indices: 22469--22532 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
22459 ATACTGAATA
**
22469 ATATTGCCCCTGAAGAGGCATAAATTCATGAGC
1 ATATTGCCCCTGAAGAGGCATAAACCCATGAGC
* * *
22502 ATATTGCCCTTGTAGTGGCATAAACCCATGA
1 ATATTGCCCCTGAAGAGGCATAAACCCATGA
22533 AAAGATCACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (33 bp):
ATATTGCCCCTGAAGAGGCATAAACCCATGAGC
Found at i:24568 original size:12 final size:12
Alignment explanation
Indices: 24551--24584 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
24541 AGAGATACAG
24551 AGAGAATATTCC
1 AGAGAATATTCC
24563 AGAGAATATTCC
1 AGAGAATATTCC
24575 AGAGAATATT
1 AGAGAATATT
24585 ATCAACAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (12 bp):
AGAGAATATTCC
Found at i:24606 original size:13 final size:13
Alignment explanation
Indices: 24584--24623 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
24574 CAGAGAATAT
24584 TATCAACAGAAGA
1 TATCAACAGAAGA
*
24597 TATCATCAGAAGA
1 TATCAACAGAAGA
* *
24610 TTTCAACTGAAGA
1 TATCAACAGAAGA
24623 T
1 T
24624 TATCTGGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:24636 original size:11 final size:11
Alignment explanation
Indices: 24616--24646 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
24606 AAGATTTCAA
24616 CTGAAGATTAT
1 CTGAAGATTAT
*
24627 CTGGAGATTAT
1 CTGAAGATTAT
24638 CTGAAGATT
1 CTGAAGATT
24647 TAAGTAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (11 bp):
CTGAAGATTAT
Found at i:25964 original size:6 final size:6
Alignment explanation
Indices: 25953--25988 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
25943 CTTGGGTAAT
25953 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
25989 ATGTTGACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
TTCGGG
Done.