Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014035.1 Corchorus capsularis cultivar CVL-1 contig14056, 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: 48931
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:1415 original size:22 final size:22
Alignment explanation
Indices: 1389--1437 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
1379 GAATTTCAAG
*
1389 AACCTTTTTAT-AAATTTTTTTT
1 AACCTTTTTATGAAA-TTTTGTT
1411 AACCTTTTTATGAAATTTTGTT
1 AACCTTTTTATGAAATTTTGTT
1433 AACCT
1 AACCT
1438 CTCTAAGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.55
Consensus pattern (22 bp):
AACCTTTTTATGAAATTTTGTT
Found at i:1611 original size:22 final size:22
Alignment explanation
Indices: 1463--1739 Score: 101
Period size: 22 Copynumber: 12.5 Consensus size: 22
1453 AAGACCTCAA
1463 TATGAAATTTTGATAACTTC-C-C
1 TATGAAATTTTGATAA--TCACAC
* *
1485 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAATC-ACAC
* * * *
1508 TATGAGATGTTGATAACCTTCA-
1 TATGAAATTTTGATAATC-ACAC
* *
1530 TATGATATATTGATAA-C-CAC
1 TATGAAATTTTGATAATCACAC
* * *
1550 GTATGAAAATTTAAAAAGCTC-CA-
1 -TATGAAATTTTGATAA--TCACAC
1573 TATG-AATTGTT-AGTAATCACAC
1 TATGAAATT-TTGA-TAATCACAC
*
1595 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAATCACAC
* * * * *
1617 TAAGAAATTATGATAACCTCGC
1 TATGAAATTTTGATAATCACAC
*
1639 TATTGAAATTTTGATAAATCTTC-C
1 TA-TGAAATTTTGAT-AATC-ACAC
* * * *
1663 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AATCACAC
* *
1686 TATGAAATTTTGAT-CTACATAC
1 TATGAAATTTTGATAAT-CACAC
* *
1708 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAATC-ACAC
1730 TATGAAATTT
1 TATGAAATTT
1740 CTATATCCTC
Statistics
Matches: 197, Mismatches: 37, Indels: 42
0.71 0.13 0.15
Matches are distributed among these distances:
19 2 0.01
20 3 0.02
21 19 0.10
22 100 0.51
23 62 0.31
24 9 0.05
25 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAC
Found at i:1670 original size:23 final size:23
Alignment explanation
Indices: 1621--1699 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
1611 TCACACTAAG
* * *
1621 AAATTATGAT-AACCTCGCTATTG
1 AAATTTTGATAAACCTCCCTA-TA
* *
1644 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
*
1667 AAATTTTGATAAACCTCCCTATG
1 AAATTTTGATAAACCTCCCTATA
1690 AAATTTTGAT
1 AAATTTTGAT
1700 CTACATACTA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 40 0.85
24 7 0.15
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:1692 original size:46 final size:45
Alignment explanation
Indices: 1597--1699 Score: 122
Period size: 46 Copynumber: 2.3 Consensus size: 45
1587 AATCACACTC
*
1597 TGAAATTTTGATAATCACACTAAGAAATTATGATAACCTCGCTAT
1 TGAAATTTTGATAATCACACTAAGAAATTATGATAACCTCCCTAT
* *
1642 TGAAATTTTGATAAATCTTC-CTATA-AAATTTTGATAAACCTCCCTA-
1 TGAAATTTTGAT-AATC-ACACTA-AGAAATTATGAT-AACCTCCCTAT
1688 TGAAATTTTGAT
1 TGAAATTTTGAT
1700 CTACATACTA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
45 12 0.24
46 28 0.55
47 11 0.22
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (45 bp):
TGAAATTTTGATAATCACACTAAGAAATTATGATAACCTCCCTAT
Found at i:1894 original size:22 final size:22
Alignment explanation
Indices: 1869--1993 Score: 94
Period size: 22 Copynumber: 5.7 Consensus size: 22
1859 AATCGAATTT
1869 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
*
1891 TGAAATTTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* * * *
1913 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTTTA
* * *
1935 TG-AAATTCTGATAATCACATTA
1 TGAAAATT-TGATAACCTCTTTA
* * *
1957 TGTAATTTTGATAACCTCGCTT-
1 TGAAAATTTGATAACCTC-TTTA
*
1979 TGAAATTTTGATAAC
1 TGAAAATTTGATAAC
1994 AACACTATGA
Statistics
Matches: 81, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
21 5 0.06
22 70 0.86
23 6 0.07
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:1937 original size:44 final size:44
Alignment explanation
Indices: 1871--2035 Score: 129
Period size: 44 Copynumber: 3.8 Consensus size: 44
1861 TCGAATTTTG
* ** * *
1871 AAAA-TTTGATAACCTCTTTATGAAATTTTGATAACCTCTTTAT
1 AAAATTTTGATAACCCCGCTATGAAATTTTGATAACCACATTAT
* * * * *
1914 AAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCACATTAT
1 AAAATTTTGATAACCCCGCTATGAAATTTTGATAACCACATTAT
** * * * *
1958 GTAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACACTAT
1 AAAATTTTGATAACCCCGCTATGAAATTTTGATAACCACATTAT
* **
2002 GAAATTTTGATAATCTTC-CTAT-AAATTTTGATAA
1 AAAATTTTGATAA-CCCCGCTATGAAATTTTGATAA
2036 TCTGATCTCT
Statistics
Matches: 98, Mismatches: 22, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
43 16 0.16
44 79 0.81
45 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (44 bp):
AAAATTTTGATAACCCCGCTATGAAATTTTGATAACCACATTAT
Found at i:1985 original size:66 final size:66
Alignment explanation
Indices: 1888--2016 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 66
1878 GATAACCTCT
* * * ** *
1888 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCAC
1 TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
1953 A
66 A
* * *
1954 TTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACACTATGAAATTTTGATAATC
1 TTATGAAATTTTGATAACCTC-CTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATC
2017 TTCCTATAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 51 0.96
67 2 0.04
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
A
Found at i:2004 original size:22 final size:22
Alignment explanation
Indices: 1932--2080 Score: 117
Period size: 22 Copynumber: 6.7 Consensus size: 22
1922 GTTGACCCCT
*
1932 CTATGAAATTCTGATAATCACA
1 CTATGAAATTTTGATAATCACA
* * * * *
1954 TTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACA
*
1976 CTTTGAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATC-ACA
*
1998 CTATGAAATTTTGATAATCTTC-
1 CTATGAAATTTTGATAATC-ACA
*
2020 CTAT-AAATTTTGATAATCTGATCT
1 CTATGAAATTTTGATAATC--A-CA
* *
2044 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACA
*
2066 CTATGAGA-TTTGATA
1 CTATGAAATTTTGATA
2081 TCCTTCTATC
Statistics
Matches: 102, Mismatches: 19, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
21 21 0.21
22 60 0.59
23 4 0.04
24 4 0.04
25 13 0.13
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACA
Found at i:2150 original size:22 final size:21
Alignment explanation
Indices: 2121--2258 Score: 77
Period size: 22 Copynumber: 6.4 Consensus size: 21
2111 AAACTGAGAC
2121 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* *
2142 TTTTGATAACCACACTATAAAA
1 TTTTGATAACCTCA-TATGAAA
**
2164 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CATATGAAA
* *
2186 -TTAG-TAACCTCCTAATGAAA
1 TTTTGATAACCTCAT-ATGAAA
* * * *
2206 TTTCGTTAACCACGCTATGAAA
1 TTTTGATAACCTC-ATATGAAA
* *
2228 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTC-ATATGAAA
2250 TTTTGATAA
1 TTTTGATAA
2259 TCTCTTTGAT
Statistics
Matches: 94, Mismatches: 14, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
19 2 0.02
20 12 0.13
21 14 0.15
22 62 0.66
23 4 0.04
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.36
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:2184 original size:44 final size:44
Alignment explanation
Indices: 2136--2258 Score: 101
Period size: 42 Copynumber: 2.8 Consensus size: 44
2126 TAACCTTCAT
*
2136 ATGAAATTTTGATAACCACACTATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCC
* * * * * * *
2180 ATGAAA-TTAG-TAACCTC-CTAATGAAATTTCGTTAACCACGCT
1 ATGAAATTTTGATAACCACACT-ATGAAATTTTGATAACCTCCCC
* * *
2222 ATGAAATTCTT-ATAACCTCGCTATGACATTTTGATAA
1 ATGAAATT-TTGATAACCACACTATGAAATTTTGATAA
2259 TCTCTTTGAT
Statistics
Matches: 62, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
41 2 0.03
42 28 0.45
43 4 0.06
44 26 0.42
45 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (44 bp):
ATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCC
Found at i:2195 original size:20 final size:20
Alignment explanation
Indices: 2170--2207 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2160 AAAATTTTGA
*
2170 TAACCTCCCCATGAAATTAG
1 TAACCTCCCAATGAAATTAG
*
2190 TAACCTCCTAATGAAATT
1 TAACCTCCCAATGAAATT
2208 TCGTTAACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.26, G:0.08, T:0.29
Consensus pattern (20 bp):
TAACCTCCCAATGAAATTAG
Found at i:2367 original size:46 final size:45
Alignment explanation
Indices: 2317--2417 Score: 111
Period size: 44 Copynumber: 2.3 Consensus size: 45
2307 GAAATTTCAA
2317 TAACCAAC-CTAAAAAATTTTAATAACATGATCC-TATGAAATTTTGG
1 TAACCAACACTAAAAAATTTTAATAAC-T--TCCATATGAAATTTTGG
** **
2363 TAACC-ACACTATGAAATTTTGGTAACTTCCATATGAAATTTTGG
1 TAACCAACACTAAAAAATTTTAATAACTTCCATATGAAATTTTGG
2407 TAACC-ACACTA
1 TAACCAACACTA
2418 TGGAATTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
43 3 0.06
44 24 0.49
45 3 0.06
46 19 0.39
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.33
Consensus pattern (45 bp):
TAACCAACACTAAAAAATTTTAATAACTTCCATATGAAATTTTGG
Found at i:2377 original size:22 final size:22
Alignment explanation
Indices: 2349--2518 Score: 150
Period size: 22 Copynumber: 7.7 Consensus size: 22
2339 TAACATGATC
*
2349 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
2371 CTATGAAATTTTGGTAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
*
2394 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* * *
2415 CTATGGAATTTTGATACCCTC-
1 CTATGAAATTTTGATAACCACA
* *
2436 CTCATGAAATTATAATAACCACA
1 CT-ATGAAATTTTGATAACCACA
* * *
2459 CTATGGAATTTTGATACCCTC-
1 CTATGAAATTTTGATAACCACA
* *
2480 CTCATGAAATTATAATAACCACA
1 CT-ATGAAATTTTGATAACCACA
*
2503 CTATGGAATTTTGATA
1 CTATGAAATTTTGATA
2519 CCCTCCTCAT
Statistics
Matches: 118, Mismatches: 22, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.01
21 6 0.05
22 104 0.88
23 6 0.05
24 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:2406 original size:44 final size:44
Alignment explanation
Indices: 2363--2530 Score: 257
Period size: 44 Copynumber: 3.8 Consensus size: 44
2353 GAAATTTTGG
* * * * * **
2363 TAACCACACTATGAAATTTTGGTAACTTCCAT-ATGAAATTTTGG
1 TAACCACACTATGGAATTTTGATACCCTCC-TCATGAAATTATAA
2407 TAACCACACTATGGAATTTTGATACCCTCCTCATGAAATTATAA
1 TAACCACACTATGGAATTTTGATACCCTCCTCATGAAATTATAA
2451 TAACCACACTATGGAATTTTGATACCCTCCTCATGAAATTATAA
1 TAACCACACTATGGAATTTTGATACCCTCCTCATGAAATTATAA
2495 TAACCACACTATGGAATTTTGATACCCTCCTCATGA
1 TAACCACACTATGGAATTTTGATACCCTCCTCATGA
2531 CATCTTATGA
Statistics
Matches: 116, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
43 1 0.01
44 115 0.99
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (44 bp):
TAACCACACTATGGAATTTTGATACCCTCCTCATGAAATTATAA
Found at i:2751 original size:19 final size:19
Alignment explanation
Indices: 2720--2756 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2710 TATTAACATT
2720 TAAAAATTGAAATTAAAAG
1 TAAAAATTGAAATTAAAAG
2739 TAAAATATT-AAATTAAAA
1 TAAAA-ATTGAAATTAAAA
2757 AAATAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
TAAAAATTGAAATTAAAAG
Found at i:3877 original size:114 final size:113
Alignment explanation
Indices: 3749--3975 Score: 330
Period size: 114 Copynumber: 2.0 Consensus size: 113
3739 CGCACTTTAT
*
3749 ATATAGTATAGATAGTTATAAAGTCATGACCTAATAAGATATAGAATCTGAATATTCAAACTAAT
1 ATATAGTATAGATAGTTATAAAGTCATGACCTAATAAGATATAGAATCTGAATAAT-AAACTAAT
* * * * *
3814 TGCCCACCAAAACGGATCAAAAAAAAA-CCTATATGAATGAGAAATTGAA
65 TGACAACCAAAACGAAT-AAAAAAAAAGCATATAGGAATGAGAAATTGAA
* *
3863 ATATAGTATAGATAGTTATAAAGTCATGGCCTAATAAGATATATAATCTGAATAATAAACTAATT
1 ATATAGTATAGATAGTTATAAAGTCATGACCTAATAAGATATAGAATCTGAATAATAAACTAATT
*
3928 GACAACCAAAATGAATAAAAAAAAAGGTCATATAGGAATGAGAAATTG
66 GACAACCAAAACGAATAAAAAAAAA-G-CATATAGGAATGAGAAATTG
3976 GACCATCTAA
Statistics
Matches: 101, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
112 9 0.09
113 21 0.21
114 53 0.52
115 18 0.18
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (113 bp):
ATATAGTATAGATAGTTATAAAGTCATGACCTAATAAGATATAGAATCTGAATAATAAACTAATT
GACAACCAAAACGAATAAAAAAAAAGCATATAGGAATGAGAAATTGAA
Found at i:4273 original size:29 final size:29
Alignment explanation
Indices: 4241--4299 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
4231 ATTATTTAGT
4241 AATGG-CAATTTAGAAATATATTTTAAAAA
1 AATGGACAA-TTAGAAATATATTTTAAAAA
*
4270 AATGGTACAATTGGAAATATATTTTAAAAA
1 AATGG-ACAATTAGAAATATATTTTAAAAA
4300 TAAGAGTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 5 0.19
30 19 0.70
31 3 0.11
ACGTcount: A:0.51, C:0.03, G:0.12, T:0.34
Consensus pattern (29 bp):
AATGGACAATTAGAAATATATTTTAAAAA
Found at i:4289 original size:30 final size:31
Alignment explanation
Indices: 4253--4317 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 31
4243 TGGCAATTTA
*
4253 GAAATATATTTTAAAAA-AATG-GTACAATTG
1 GAAATATATTTTAAAAATAA-GAGTACAATCG
4283 GAAATATATTTTAAAAATAAGAGTACAATCG
1 GAAATATATTTTAAAAATAAGAGTACAATCG
4314 GAAA
1 GAAA
4318 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 18 0.56
31 14 0.44
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.29
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGAGTACAATCG
Found at i:9448 original size:76 final size:77
Alignment explanation
Indices: 9294--9457 Score: 258
Period size: 76 Copynumber: 2.1 Consensus size: 77
9284 GGCCCTCAAA
** * * * *
9294 TATTTGATGTATACAATTTAGGACTAAATTGGGTTTTAATTAATTATAACAATCTAGTTGTGTTA
1 TATTTGATGGGTACAATGTAGGACTAAATTGGATTTTAATTAATAATAACAATCTAGTTGGGTTA
9359 AATTGGAGAAAT
66 AATTGGAGAAAT
*
9371 TATTTGATGGGTACAATGTAGGGCTAAATTGGATTTTAATT-ATAATAACAATCTAGTTGGGTTA
1 TATTTGATGGGTACAATGTAGGACTAAATTGGATTTTAATTAATAATAACAATCTAGTTGGGTTA
9435 AATTGGAGAAAT
66 AATTGGAGAAAT
9447 TATTTGATGGG
1 TATTTGATGGG
9458 CCGTCCATTA
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
76 44 0.55
77 36 0.45
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (77 bp):
TATTTGATGGGTACAATGTAGGACTAAATTGGATTTTAATTAATAATAACAATCTAGTTGGGTTA
AATTGGAGAAAT
Found at i:11750 original size:132 final size:132
Alignment explanation
Indices: 11597--11861 Score: 496
Period size: 132 Copynumber: 2.0 Consensus size: 132
11587 GGAAATCTTT
11597 TTTTTTTCTTTAATTTGTTTGTGGTAGGTCTACCAACTGCAATTTTTAATAATTACTAACTATTT
1 TTTTTTTCTTTAATTTGTTTGTGGTAGGTCTACCAACTGCAATTTTTAATAATTACTAACTATTT
* *
11662 TCAACATTAATAAGGAATATAATTATAAACAAATATATATATATATATATATATTTTTGGTCCCA
66 TCAACATTAATAAGGAATATAATAATAAAC-AATATATATATATATATATATATATTTGGTCCCA
11727 TTA
130 TTA
11730 TTTTTTTC-TTAATTTGTTTGTGGTAGGTCTACCAACTGCAATTTTTAATAATTACTAACTATTT
1 TTTTTTTCTTTAATTTGTTTGTGGTAGGTCTACCAACTGCAATTTTTAATAATTACTAACTATTT
11794 TCAACATTAATAAGGAATATAATAATAAACAATATATATATATATATATATATATTTGGTCCCAT
66 TCAACATTAATAAGGAATATAATAATAAACAATATATATATATATATATATATATTTGGTCCCAT
11859 TA
131 TA
11861 T
1 T
11862 GATATGTGAT
Statistics
Matches: 130, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
131 37 0.28
132 85 0.65
133 8 0.06
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (132 bp):
TTTTTTTCTTTAATTTGTTTGTGGTAGGTCTACCAACTGCAATTTTTAATAATTACTAACTATTT
TCAACATTAATAAGGAATATAATAATAAACAATATATATATATATATATATATATTTGGTCCCAT
TA
Found at i:13771 original size:41 final size:41
Alignment explanation
Indices: 13726--13805 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
13716 TTAGTTCAGA
*
13726 GTTTAACTCATACCAAAATAAACAATATGTAAATGGTAATT
1 GTTTAACCCATACCAAAATAAACAATATGTAAATGGTAATT
* * *
13767 GTTTAGCCCATTCCAAAATAAACCATATGTAAATGGTAA
1 GTTTAACCCATACCAAAATAAACAATATGTAAATGGTAA
13806 ATTCTCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (41 bp):
GTTTAACCCATACCAAAATAAACAATATGTAAATGGTAATT
Found at i:26758 original size:2 final size:2
Alignment explanation
Indices: 26751--26782 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
26741 ACAGCCTTAC
26751 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
26783 CATAGTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28330 original size:171 final size:171
Alignment explanation
Indices: 28045--28380 Score: 663
Period size: 171 Copynumber: 2.0 Consensus size: 171
28035 TTATCAGCAA
28045 ATTTAACATTCTCATTTTATAAATAATTGTGATATATTTGTATAAAATACATTAATGATTAATAT
1 ATTTAACATTCTCATTTTATAAATAATTGTGATATATTTGTATAAAATACATTAATGATTAATAT
*
28110 TTATTTGTTATTGTATTTGACGCCTTGACTCAACTGGTAGATACATGCTTCCGATTGTTGTATCC
66 TTATTTGTTATTGCATTTGACGCCTTGACTCAACTGGTAGATACATGCTTCCGATTGTTGTATCC
28175 TAAAAGAAAAATCATTCCTAGGTTCGTCAGGTGTAAAATAC
131 TAAAAGAAAAATCATTCCTAGGTTCGTCAGGTGTAAAATAC
28216 ATTTAACATTCTCATTTTATAAATAATTGTGATATATTTGTATAAAATACATTAATGATTAATAT
1 ATTTAACATTCTCATTTTATAAATAATTGTGATATATTTGTATAAAATACATTAATGATTAATAT
28281 TTATTTGTTATTGCATTTGACGCCTTGACTCAACTGGTAGATACATGCTTCCGATTGTTGTATCC
66 TTATTTGTTATTGCATTTGACGCCTTGACTCAACTGGTAGATACATGCTTCCGATTGTTGTATCC
28346 TAAAAGAAAAATCATTCCTAGGTTCGTCAGGTGTA
131 TAAAAGAAAAATCATTCCTAGGTTCGTCAGGTGTA
28381 GGCCCATCGG
Statistics
Matches: 164, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 164 1.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (171 bp):
ATTTAACATTCTCATTTTATAAATAATTGTGATATATTTGTATAAAATACATTAATGATTAATAT
TTATTTGTTATTGCATTTGACGCCTTGACTCAACTGGTAGATACATGCTTCCGATTGTTGTATCC
TAAAAGAAAAATCATTCCTAGGTTCGTCAGGTGTAAAATAC
Found at i:37886 original size:13 final size:13
Alignment explanation
Indices: 37868--37894 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
37858 TTAGTCACTA
37868 TCAAACTAATTAC
1 TCAAACTAATTAC
37881 TCAAACTAATTAC
1 TCAAACTAATTAC
37894 T
1 T
37895 AGGAGAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (13 bp):
TCAAACTAATTAC
Found at i:38210 original size:29 final size:29
Alignment explanation
Indices: 38168--38253 Score: 145
Period size: 29 Copynumber: 3.0 Consensus size: 29
38158 TGGTCAGAAC
38168 CATGGATGACATGGTGAAACCGATCCATA
1 CATGGATGACATGGTGAAACCGATCCATA
38197 CATGGATGACATGGTGAAACCGATCCATA
1 CATGGATGACATGGTGAAACCGATCCATA
* * *
38226 CATGAATGGCATAGTGAAACCGATCCAT
1 CATGGATGACATGGTGAAACCGATCCAT
38254 CTAAAATTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (29 bp):
CATGGATGACATGGTGAAACCGATCCATA
Found at i:38683 original size:6 final size:5
Alignment explanation
Indices: 38653--38682 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
38643 TTGACATGGT
38653 TTTTA TTTTA TTTTA TTTTA TTTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTT
38683 TTTGGCTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:39513 original size:4 final size:4
Alignment explanation
Indices: 39506--39542 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
39496 ATGTGAAAAA
**
39506 AAAG AAAG AAAG AAAG AAAG AAAG ATTG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
39543 TAATTCTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.05
Consensus pattern (4 bp):
AAAG
Done.