Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014755.1 Corchorus capsularis cultivar CVL-1 contig14776, 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: 26305
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:941 original size:26 final size:27
Alignment explanation
Indices: 893--962 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 27
883 GTCACCTAGG
* *
893 GGCATTTCGGTCATTTTCGCACT-AAA
1 GGCATTTTGGTCATTTTCACACTCAAA
**
919 GGCATTTTGGTCATTTAT-ACACTCAGG
1 GGCATTTTGGTCATTT-TCACACTCAAA
*
946 GGCATTTTAGTCATTTT
1 GGCATTTTGGTCATTTT
963 TTAAGTCCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 20 0.54
27 17 0.46
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (27 bp):
GGCATTTTGGTCATTTTCACACTCAAA
Found at i:1378 original size:18 final size:18
Alignment explanation
Indices: 1338--1384 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
1328 CTATCCATTT
1338 TCATTTTCTCATTAATCA
1 TCATTTTCTCATTAATCA
1356 T-ATTTT-TACATTAATCA
1 TCATTTTCT-CATTAATCA
1373 TCA-TTTCTCATT
1 TCATTTTCTCATT
1385 GCTCCATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 22 0.85
18 3 0.12
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (18 bp):
TCATTTTCTCATTAATCA
Found at i:3008 original size:16 final size:16
Alignment explanation
Indices: 2987--3023 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2977 GGTTGTAACT
2987 TTTTGGACTTAACCAC
1 TTTTGGACTTAACCAC
**
3003 TTTTGGACTTAGTCAC
1 TTTTGGACTTAACCAC
3019 TTTTG
1 TTTTG
3024 TTGGGCTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.46
Consensus pattern (16 bp):
TTTTGGACTTAACCAC
Found at i:4852 original size:107 final size:107
Alignment explanation
Indices: 4719--4915 Score: 358
Period size: 107 Copynumber: 1.8 Consensus size: 107
4709 TTAATTATGC
*
4719 AATTTACCCTTAAAATAAAGATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATA
1 AATTTACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATA
4784 TTTTATTTCTAAAACCCTACAATAATAAATTATTAAATTTAA
66 TTTTATTTCTAAAACCCTACAATAATAAATTATTAAATTTAA
*
4826 AATTTACCCTTAGAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATA
1 AATTTACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATA
* *
4891 TTTTATTTCTAAAACTCTATAATAA
66 TTTTATTTCTAAAACCCTACAATAA
4916 AAAACCTTTA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 86 1.00
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (107 bp):
AATTTACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATA
TTTTATTTCTAAAACCCTACAATAATAAATTATTAAATTTAA
Found at i:4937 original size:107 final size:107
Alignment explanation
Indices: 4719--4947 Score: 345
Period size: 107 Copynumber: 2.1 Consensus size: 107
4709 TTAATTATGC
*
4719 AATTTACCCTTAAAATAAAGATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATA
1 AATTTACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATA
* * *
4784 TTTTATTTCTAAAACCCTACAATAATAAATTATTAAATTTAA
66 TTTTATTTCTAAAACCCTACAATAAAAAACTATTAAATTCAA
*
4826 AATTTACCCTTAGAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATA
1 AATTTACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATA
* * *
4891 TTTTATTTCTAAAACTCTATAATAAAAAACCT-TT-AATTGCAT
66 TTTTATTTCTAAAACCCTACAATAAAAAA-CTATTAAATT-CAA
*
4933 AATTTACTCTTAAAA
1 AATTTACCCTTAAAA
4948 ATTAAATTTC
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
106 4 0.04
107 105 0.95
108 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.40
Consensus pattern (107 bp):
AATTTACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATA
TTTTATTTCTAAAACCCTACAATAAAAAACTATTAAATTCAA
Found at i:5462 original size:25 final size:25
Alignment explanation
Indices: 5428--5477 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
5418 AATCAGTAAT
*
5428 AATCAATCAATAATTATTTACTTTC
1 AATCAATCAATAATGATTTACTTTC
5453 AATCAATCAATAATGATTTACTTTC
1 AATCAATCAATAATGATTTACTTTC
5478 CATAAAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (25 bp):
AATCAATCAATAATGATTTACTTTC
Found at i:6087 original size:16 final size:15
Alignment explanation
Indices: 6053--6093 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
6043 TCACAACTCA
* *
6053 TAATCATAAAATCAT
1 TAATTATAAAATAAT
6068 TAATTATAACAATAAT
1 TAATTATAA-AATAAT
6084 TAATTATAAA
1 TAATTATAAA
6094 TTATTTCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (15 bp):
TAATTATAAAATAAT
Found at i:8613 original size:27 final size:27
Alignment explanation
Indices: 8582--8690 Score: 73
Period size: 25 Copynumber: 4.0 Consensus size: 27
8572 ACTATATTCC
*
8582 ACCTTTTTTTATTAACTACCATTTTCT
1 ACCTTTTTTTATTAATTACCATTTTCT
* *
8609 ACCTTCGTCTTTTACTAATTACC-TCTTGCTT
1 ACCTT--T-TTTTATTAATTACCAT-TTTC-T
*
8640 A-CTTTTTTTATTGATTACCATTTT-T
1 ACCTTTTTTTATTAATTACCATTTTCT
* * * *
8665 A-CTCTTTTTACTGATTACCCTTTTCT
1 ACCTTTTTTTATTAATTACCATTTTCT
8691 TACTTTGATT
Statistics
Matches: 66, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
25 22 0.33
26 1 0.02
27 19 0.29
28 2 0.03
29 2 0.03
30 18 0.27
31 2 0.03
ACGTcount: A:0.18, C:0.23, G:0.04, T:0.55
Consensus pattern (27 bp):
ACCTTTTTTTATTAATTACCATTTTCT
Found at i:8666 original size:25 final size:26
Alignment explanation
Indices: 8618--8729 Score: 102
Period size: 27 Copynumber: 4.2 Consensus size: 26
8608 TACCTTCGTC
*
8618 TTTTACTAATTACC-TCTTGCTTACTTT
1 TTTTACTGATTACCAT-TT-CTTACTTT
* *
8645 TTTTATTGATTACCATTT-TTACTCT
1 TTTTACTGATTACCATTTCTTACTTT
*
8670 TTTTACTGATTACCCTTTTCTTACTTT
1 TTTTACTGATTA-CCATTTCTTACTTT
* *
8697 GATTTTACTGATTACCCTTTGCTTCCTTT
1 --TTTTACTGATTACCATTT-CTTACTTT
8726 TTTT
1 TTTT
8730 CTTTTACTGA
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
25 17 0.24
26 5 0.07
27 24 0.34
28 6 0.08
29 19 0.27
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.58
Consensus pattern (26 bp):
TTTTACTGATTACCATTTCTTACTTT
Found at i:8695 original size:52 final size:57
Alignment explanation
Indices: 8584--8712 Score: 144
Period size: 52 Copynumber: 2.3 Consensus size: 57
8574 TATATTCCAC
* *
8584 CTTTTTTTATTAACTACCATTTTCTACCTTCGTCTTTTACTAATTACCTCTTGCTTA
1 CTTTTTTTATTGATTACCATTTTCTACCTTCGTCTTTTACTAATTACCTCTTGCTTA
* *
8641 CTTTTTTTATTGATTACCATTTT-TA-C-TC-T-TTTTACTGATTACC-CTTTTCTTA
1 CTTTTTTTATTGATTACCATTTTCTACCTTCGTCTTTTACTAATTACCTC-TTGCTTA
*
8693 CTTTGATTTTACTGATTACC
1 CTTT--TTTTATTGATTACC
8713 CTTTGCTTCC
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
51 1 0.02
52 23 0.36
53 1 0.02
54 15 0.23
55 1 0.02
56 2 0.03
57 21 0.33
ACGTcount: A:0.19, C:0.22, G:0.05, T:0.55
Consensus pattern (57 bp):
CTTTTTTTATTGATTACCATTTTCTACCTTCGTCTTTTACTAATTACCTCTTGCTTA
Found at i:8703 original size:29 final size:26
Alignment explanation
Indices: 8618--8729 Score: 111
Period size: 29 Copynumber: 4.2 Consensus size: 26
8608 TACCTTCGTC
*
8618 TTTTACTAATTACCTCTTGCTTACTTT
1 TTTTACTGATTACCT-TTGCTTACTTT
* *
8645 TTTTATTGATTACCATTT--TTACTCT
1 TTTTACTGATTACC-TTTGCTTACTTT
*
8670 TTTTACTGATTACCCTTTTCTTACTTT
1 TTTTACTGATTA-CCTTTGCTTACTTT
*
8697 GATTTTACTGATTACCCTTTGCTTCCTTT
1 --TTTTACTGATTA-CCTTTGCTTACTTT
8726 TTTT
1 TTTT
8730 CTTTTACTGA
Statistics
Matches: 72, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
25 20 0.28
26 2 0.03
27 24 0.33
28 1 0.01
29 25 0.35
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.58
Consensus pattern (26 bp):
TTTTACTGATTACCTTTGCTTACTTT
Found at i:8776 original size:7 final size:7
Alignment explanation
Indices: 8766--8891 Score: 60
Period size: 7 Copynumber: 17.6 Consensus size: 7
8756 GTTTTACTGA
8766 TTACTCT
1 TTACTCT
*
8773 TTACTTT
1 TTACTCT
8780 TTAC-CAT
1 TTACTC-T
*
8787 ATAACTCT
1 -TTACTCT
**
8795 TTACTAA
1 TTACTCT
8802 TTACTCT
1 TTACTCT
8809 TTACTCT
1 TTACTCT
8816 TTAC-CATT
1 TTACTC--T
*
8824 TTACTAT
1 TTACTCT
**
8831 TTA-TAGA
1 TTACT-CT
*
8838 TTACACT
1 TTACTCT
*
8845 TTACTTT
1 TTACTCT
* *
8852 TTAGTATT
1 TTACT-CT
8860 TTACTCT
1 TTACTCT
**
8867 TTACTGA
1 TTACTCT
8874 TTACTCT
1 TTACTCT
8881 TTACTCT
1 TTACTCT
8888 TTAC
1 TTAC
8892 CATTTTTCTT
Statistics
Matches: 87, Mismatches: 23, Indels: 18
0.68 0.18 0.14
Matches are distributed among these distances:
6 2 0.02
7 69 0.79
8 15 0.17
9 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.02, T:0.53
Consensus pattern (7 bp):
TTACTCT
Found at i:8805 original size:36 final size:36
Alignment explanation
Indices: 8748--8919 Score: 206
Period size: 36 Copynumber: 4.8 Consensus size: 36
8738 GAATACCATT
*
8748 TTTTACTCGTTTTACTGATTACTCTTTACTTTTTACCA
1 TTTTACTC--TTTACTGATTACTCTTTACTCTTTACCA
* * *
8786 TATAACTCTTTACTAATTACTCTTTACTCTTTACCA
1 TTTTACTCTTTACTGATTACTCTTTACTCTTTACCA
* * * **
8822 TTTTACTATTTA-TAGATTACACTTTACTTTTTAGTA
1 TTTTACTCTTTACT-GATTACTCTTTACTCTTTACCA
8858 TTTTACTCTTTACTGATTACTCTTTACTCTTTACCA
1 TTTTACTCTTTACTGATTACTCTTTACTCTTTACCA
*
8894 TTTT--TCTTTGCTGATTACTCTTTACT
1 TTTTACTCTTTACTGATTACTCTTTACT
8920 GATTAGTACT
Statistics
Matches: 114, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
34 21 0.18
35 1 0.01
36 85 0.75
37 1 0.01
38 6 0.05
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.54
Consensus pattern (36 bp):
TTTTACTCTTTACTGATTACTCTTTACTCTTTACCA
Found at i:8997 original size:7 final size:7
Alignment explanation
Indices: 8987--9049 Score: 74
Period size: 7 Copynumber: 9.0 Consensus size: 7
8977 TTCTTTACCA
8987 TTTTACT
1 TTTTACT
8994 TTTTACT
1 TTTTACT
9001 TTTTACT
1 TTTTACT
**
9008 GATT-CT
1 TTTTACT
*
9014 CTTTACT
1 TTTTACT
*
9021 TTTTACCA
1 TTTTA-CT
9029 TTTTACT
1 TTTTACT
9036 TTTTACT
1 TTTTACT
9043 TTTTACT
1 TTTTACT
9050 GATTACTCTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
6 4 0.09
7 37 0.79
8 6 0.13
ACGTcount: A:0.16, C:0.17, G:0.02, T:0.65
Consensus pattern (7 bp):
TTTTACT
Found at i:9018 original size:20 final size:21
Alignment explanation
Indices: 8952--9066 Score: 94
Period size: 22 Copynumber: 5.4 Consensus size: 21
8942 TTTTTACCAA
* *
8952 TTTACTTTCTACAGATTACTC
1 TTTACTTTTTACTGATTACTC
* *
8973 TTTA-TTCTTTACCAT-TTTACTT
1 TTTACTT-TTTA-C-TGATTACTC
8995 TTTACTTTTTACTGATT-CTC
1 TTTACTTTTTACTGATTACTC
* *
9015 TTTACTTTTTACCAT-TTTACTT
1 TTTACTTTTTA-C-TGATTACTC
9037 TTTACTTTTTACTGATTACTC
1 TTTACTTTTTACTGATTACTC
*
9058 TTCACTTTT
1 TTTACTTTT
9067 CACTCTTTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
20 17 0.23
21 27 0.36
22 28 0.38
23 2 0.03
ACGTcount: A:0.18, C:0.20, G:0.03, T:0.59
Consensus pattern (21 bp):
TTTACTTTTTACTGATTACTC
Found at i:9020 original size:49 final size:43
Alignment explanation
Indices: 8858--9066 Score: 183
Period size: 42 Copynumber: 4.7 Consensus size: 43
8848 CTTTTTAGTA
* * *
8858 TTTTACTCTTTACTGATTACTCTTTACTCTTTACCATTTTTCTT
1 TTTTACTTTTTACTGATTACTCTTTACTTTTTACCATTTTAC-T
* * ** * *
8902 TGCTGATTACTCTTTACTGATTAGTACTAATTAC-CATTA-CTTTTTACCA
1 T--T--TTACTTTTTACTGATTACT-CT--TTACTTTTTACCATTTTA-CT
* * *
8951 ATTTACTTTCTACAGATTACTCTTTA-TTCTTTACCATTTTACT
1 TTTTACTTTTTACTGATTACTCTTTACTT-TTTACCATTTTACT
8994 TTTTACTTTTTACTGATT-CTCTTTACTTTTTACCATTTTACT
1 TTTTACTTTTTACTGATTACTCTTTACTTTTTACCATTTTACT
*
9036 TTTTACTTTTTACTGATTACTCTTCACTTTT
1 TTTTACTTTTTACTGATTACTCTTTACTTTT
9067 CACTCTTTTT
Statistics
Matches: 134, Mismatches: 18, Indels: 27
0.75 0.10 0.15
Matches are distributed among these distances:
42 42 0.31
43 32 0.24
44 9 0.07
45 15 0.11
46 1 0.01
47 1 0.01
48 18 0.13
49 7 0.05
50 5 0.04
51 4 0.03
ACGTcount: A:0.20, C:0.21, G:0.04, T:0.56
Consensus pattern (43 bp):
TTTTACTTTTTACTGATTACTCTTTACTTTTTACCATTTTACT
Found at i:9109 original size:27 final size:27
Alignment explanation
Indices: 9070--9124 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
9060 CACTTTTCAC
*
9070 TCTTTTTAACTTAATTACTAAATACCA
1 TCTTTTGAACTTAATTACTAAATACCA
* * *
9097 TCTTTTGACCTTAATTACTGATTACCA
1 TCTTTTGAACTTAATTACTAAATACCA
9124 T
1 T
9125 TTTACTCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (27 bp):
TCTTTTGAACTTAATTACTAAATACCA
Found at i:13989 original size:49 final size:49
Alignment explanation
Indices: 13920--14044 Score: 160
Period size: 49 Copynumber: 2.6 Consensus size: 49
13910 TGACTGAAGA
* *
13920 AAATTAAGAGAAGTAAATCTTAATTCAGCAAAATTAGGGAAAATAAAAG
1 AAATTAAGAGAAGTAAATCTTAATTCAGCAAAATGAAGGAAAATAAAAG
* ** * * * *
13969 AAATTAAGAAAAGTAAATCTTAATTCAGTGAACTGAAGGCACATAAAGG
1 AAATTAAGAGAAGTAAATCTTAATTCAGCAAAATGAAGGAAAATAAAAG
*
14018 AAATTAAGAGAAGTGAATCTTAATTCA
1 AAATTAAGAGAAGTAAATCTTAATTCA
14045 TAGAAATTAA
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.51, C:0.08, G:0.17, T:0.24
Consensus pattern (49 bp):
AAATTAAGAGAAGTAAATCTTAATTCAGCAAAATGAAGGAAAATAAAAG
Found at i:14221 original size:42 final size:40
Alignment explanation
Indices: 14168--14245 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
14158 TAGTTTCAAG
*
14168 GAAACTAGGTAAAGAAAAGAGACTGGTTTAATTTCAAGAAAA
1 GAAACTAGGTAAAG-AAA-AGACTGGCTTAATTTCAAGAAAA
* *
14210 GAAATTAGGTAAAGAAAAGATTGGCTTAATTTCAAG
1 GAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAAG
14246 GAAATTAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 17 0.52
41 3 0.09
42 13 0.39
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.24
Consensus pattern (40 bp):
GAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAAGAAAA
Found at i:14348 original size:36 final size:36
Alignment explanation
Indices: 14301--14529 Score: 336
Period size: 36 Copynumber: 6.4 Consensus size: 36
14291 GGTAAGGATA
* * *
14301 AGCACAGACTTAATTTCAC-AGAAATTAAGTAAAGTC
1 AGCAAAGACTTAATTTCACAAG-AATTAAGTAAAATT
14337 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
* *
14373 GGCAAAGACTTAATTTCACATGAATTAAGT-AAATT
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
* *
14408 AGCGAAGACTTAATTTCACAATAATTAAGTAAAATT
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
*
14444 GGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
* *
14480 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAGTC
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
*
14516 AGCAAAGATTTAAT
1 AGCAAAGACTTAAT
14530 CCAAAGATGA
Statistics
Matches: 175, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
35 31 0.18
36 142 0.81
37 2 0.01
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (36 bp):
AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
Found at i:14438 original size:71 final size:70
Alignment explanation
Indices: 14306--14512 Score: 342
Period size: 71 Copynumber: 2.9 Consensus size: 70
14296 GGATAAGCAC
*
14306 AGACTTAATTTCACAGAAATTAAGTAAAGTCAGCAAAGACTTAATTTCACAAGAATTAAGTAAAA
1 AGACTTAATTTCACAG-AATTAAGTAAA-TTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAA
14371 TTGGCAA
64 TTGGCAA
* *
14378 AGACTTAATTTCACATGAATTAAGTAAATTAGCGAAGACTTAATTTCACAATAATTAAGTAAAAT
1 AGACTTAATTTCACA-GAATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAAT
14443 TGGCAA
65 TGGCAA
14449 AGACTTAATTTCACAAGAATTAAGTAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAA
1 AGACTTAATTTCAC-AGAATTAAGT-AAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAA
14513 GTCAGCAAAG
Statistics
Matches: 127, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
71 63 0.50
72 63 0.50
73 1 0.01
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.29
Consensus pattern (70 bp):
AGACTTAATTTCACAGAATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
GGCAA
Found at i:14449 original size:107 final size:107
Alignment explanation
Indices: 14306--14571 Score: 356
Period size: 107 Copynumber: 2.5 Consensus size: 107
14296 GGATAAGCAC
*
14306 AGACTTAATTTCACAGAAATTAAGTAAAGTCAGCAAAGACTTAATTTCACAAGAATTAAGTAAAA
1 AGACTTAATTTCACAGAAATTAAGTAAAATCAGCAAAGACTTAATTTCACAAGAATTAAGTAAAA
* *
14371 TTGGCAAAGACTTAATTTCACATGAATTAAGTAAATTAGCGA
66 TTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCGA
**
14413 AGACTTAATTTCACA-ATAATTAAGTAAAATTGGCAAAGACTTAATTTCACAAGAATTAAGTAAA
1 AGACTTAATTTCACAGA-AATTAAGTAAAATCAGCAAAGACTTAATTTCACAAGAATTAAGTAAA
* *
14477 ATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAGTCAGCAA
65 ATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAA-TTAGCGA
* * * * * *
14521 AGATTTAA-TCCAAAGATGATTAAGTAAGATCAGACAAAGGGCTTAATTTCA
1 AGACTTAATTTCACAGA-AATTAAGTAAAATCAG-CAAA-GACTTAATTTCA
14572 AGGAAATTAG
Statistics
Matches: 139, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
106 1 0.01
107 97 0.70
108 26 0.19
109 4 0.03
110 11 0.08
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (107 bp):
AGACTTAATTTCACAGAAATTAAGTAAAATCAGCAAAGACTTAATTTCACAAGAATTAAGTAAAA
TTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCGA
Found at i:14543 original size:36 final size:36
Alignment explanation
Indices: 14301--14568 Score: 274
Period size: 36 Copynumber: 7.4 Consensus size: 36
14291 GGTAAGGATA
* * *
14301 AGCACAGACTTAATTTCAC-AGAAATTAAGTAAAGTC
1 AGCAAAGACTTAATTCCACAAG-AATTAAGTAAAATC
* *
14337 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
1 AGCAAAGACTTAATTCCACAAGAATTAAGTAAAATC
* * * *
14373 GGCAAAGACTTAATTTCACATGAATTAAGT-AAATT
1 AGCAAAGACTTAATTCCACAAGAATTAAGTAAAATC
* * * *
14408 AGCGAAGACTTAATTTCACAATAATTAAGTAAAATT
1 AGCAAAGACTTAATTCCACAAGAATTAAGTAAAATC
* * *
14444 GGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
1 AGCAAAGACTTAATTCCACAAGAATTAAGTAAAATC
* *
14480 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAGTC
1 AGCAAAGACTTAATTCCACAAGAATTAAGTAAAATC
* *
14516 AGCAAAGATTTAA-TCCA-AAGATGATTAAGTAAGATC
1 AGCAAAGACTTAATTCCACAAGA--ATTAAGTAAAATC
*
14552 AGACAAAGGGCTTAATT
1 AG-CAAA-GACTTAATT
14569 TCAAGGAAAT
Statistics
Matches: 204, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
34 4 0.02
35 34 0.17
36 154 0.75
37 6 0.03
38 5 0.02
39 1 0.00
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.27
Consensus pattern (36 bp):
AGCAAAGACTTAATTCCACAAGAATTAAGTAAAATC
Found at i:14605 original size:11 final size:11
Alignment explanation
Indices: 14586--14738 Score: 188
Period size: 11 Copynumber: 13.7 Consensus size: 11
14576 AATTAGGCAA
14586 AAGACTGAAAG
1 AAGACTGAAAG
*
14597 AAAACTGAAAG
1 AAGACTGAAAG
*
14608 AAGACTAAAAAG
1 AAGACT-GAAAG
*
14620 AAGACTAAAAG
1 AAGACTGAAAG
14631 AAGACTGAATAG
1 AAGACTGAA-AG
14643 AAGACTGAAAG
1 AAGACTGAAAG
14654 AAGACTGAAAAG
1 AAGACTG-AAAG
14666 AAGACTGAAAG
1 AAGACTGAAAG
*
14677 AAGACTGAAAC
1 AAGACTGAAAG
14688 AAGACTGAAAGAG
1 AAGACTG-AA-AG
14701 AAGACTG--A-
1 AAGACTGAAAG
14709 AA-ACTGAAAG
1 AAGACTGAAAG
14719 AAAGACTGAAAG
1 -AAGACTGAAAG
14731 AAGACTGA
1 AAGACTGA
14739 CTTAATTTCA
Statistics
Matches: 126, Mismatches: 6, Indels: 20
0.83 0.04 0.13
Matches are distributed among these distances:
7 4 0.03
8 2 0.02
9 2 0.02
11 68 0.54
12 42 0.33
13 8 0.06
ACGTcount: A:0.57, C:0.10, G:0.24, T:0.10
Consensus pattern (11 bp):
AAGACTGAAAG
Found at i:14621 original size:23 final size:23
Alignment explanation
Indices: 14586--14738 Score: 178
Period size: 23 Copynumber: 6.9 Consensus size: 23
14576 AATTAGGCAA
*
14586 AAGACTG-AAAGAAAACTGAAAG
1 AAGACTGAAAAGAAGACTGAAAG
* *
14608 AAGACTAAAAAGAAGACTAAAAG
1 AAGACTGAAAAGAAGACTGAAAG
*
14631 AAGACTGAATAGAAGACTGAAAG
1 AAGACTGAAAAGAAGACTGAAAG
14654 AAGACTGAAAAGAAGACTGAAAG
1 AAGACTGAAAAGAAGACTGAAAG
*
14677 AAGACTG-AAACAAGACTGAAAGAG
1 AAGACTGAAAAGAAGACTG-AA-AG
14701 AAGACTG---A-AA-ACTGAAAG
1 AAGACTGAAAAGAAGACTGAAAG
14719 AAAGACTG-AAAGAAGACTGA
1 -AAGACTGAAAAGAAGACTGA
14739 CTTAATTTCA
Statistics
Matches: 115, Mismatches: 8, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
18 2 0.02
19 9 0.08
20 4 0.03
21 3 0.03
22 19 0.17
23 69 0.60
24 9 0.08
ACGTcount: A:0.57, C:0.10, G:0.24, T:0.10
Consensus pattern (23 bp):
AAGACTGAAAAGAAGACTGAAAG
Found at i:14625 original size:34 final size:33
Alignment explanation
Indices: 14586--14738 Score: 170
Period size: 34 Copynumber: 4.6 Consensus size: 33
14576 AATTAGGCAA
*
14586 AAGACTGAAAGAAAACTGAAAGAAGACTAAAAAG
1 AAGACTGAAAGAAAACTGAAAGAAGACT-GAAAG
* *
14620 AAGACTAAAAGAAGACTGAATAGAAGACTGAAAG
1 AAGACTGAAAGAAAACTGAA-AGAAGACTGAAAG
* *
14654 AAGACTGAAAAGAAGACTGAAAGAAGACTGAAAC
1 AAGACTG-AAAGAAAACTGAAAGAAGACTGAAAG
14688 AAGACTGAAAGAGAAGACTG--A-AA-ACTGAAAG
1 AAGACTGAAAGA-AA-ACTGAAAGAAGACTGAAAG
*
14719 AAAGACTGAAAGAAGACTGA
1 -AAGACTGAAAGAAAACTGA
14739 CTTAATTTCA
Statistics
Matches: 105, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
30 4 0.04
31 8 0.08
32 14 0.13
33 6 0.06
34 48 0.46
35 25 0.24
ACGTcount: A:0.57, C:0.10, G:0.24, T:0.10
Consensus pattern (33 bp):
AAGACTGAAAGAAAACTGAAAGAAGACTGAAAG
Found at i:14813 original size:36 final size:35
Alignment explanation
Indices: 14731--14974 Score: 232
Period size: 36 Copynumber: 6.9 Consensus size: 35
14721 AGACTGAAAG
* * * *
14731 AAGACTGACTTAATTTCAAGGAAATTAGGTAAA-AG
1 AAGACTGGCTTAGTTTCAAGGAAA-TAAGTAAAGAA
14766 AAGACTGGCTTAGTTTCAAGGAAATGAAGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAAT-AAGTAAAGAA
* * * *
14802 AAGACTAGCTTAATTTCAAGGAAATTAGGTAAA-AG
1 AAGACTGGCTTAGTTTCAAGGAAA-TAAGTAAAGAA
*
14837 AAGACTGGCTTAGTTTCAAGG--AT-ACTAAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATAAGT-AAAGAA
* *
14870 AAGACTGACTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAA-TAAGTAAAGAA
* *
14906 ATGACTGGCTTAGTTTCAAGGAAACT-AGCTAAAGGA
1 AAGACTGGCTTAGTTTCAAGGAAA-TAAG-TAAAGAA
*
14942 AAGACTGGATT-GATTTCAAGGAAATTAAGTAAA
1 AAGACTGGCTTAG-TTTCAAGGAAA-TAAGTAAA
14975 AAGACACAGG
Statistics
Matches: 174, Mismatches: 23, Indels: 23
0.79 0.10 0.10
Matches are distributed among these distances:
31 1 0.01
32 4 0.02
33 22 0.13
34 1 0.01
35 51 0.29
36 91 0.52
37 4 0.02
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (35 bp):
AAGACTGGCTTAGTTTCAAGGAAATAAGTAAAGAA
Found at i:14815 original size:71 final size:69
Alignment explanation
Indices: 14731--14975 Score: 320
Period size: 71 Copynumber: 3.5 Consensus size: 69
14721 AGACTGAAAG
14731 AAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATGAAGT
1 AAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAAT--AGT
14796 AAAGAA
64 AAAGAA
*
14802 AAGACT-AGCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGG--ATACTA
1 AAGACTGA-CTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATAGT-
14864 AAAGAA
64 AAAGAA
* *
14870 AAGACTGACTTAGTTTCAAGGAAACTAGGT-AAAGAAATGACTGGCTTAGTTTCAAGGAAACTAG
1 AAGACTGACTTAATTTCAAGGAAATTAGGTAAAAG-AA-GACTGGCTTAGTTTCAAGGAAA-TAG
*
14934 CTAAAGGA
63 -TAAAGAA
* *
14942 AAGACTGGA-TTGATTTCAAGGAAATTAAGTAAAA
1 AAGACT-GACTTAATTTCAAGGAAATTAGGTAAAA
14976 AGACACAGGC
Statistics
Matches: 154, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
67 6 0.04
68 34 0.22
69 22 0.14
70 1 0.01
71 55 0.36
72 30 0.19
73 6 0.04
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (69 bp):
AAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATAGTAA
AGAA
Found at i:14902 original size:104 final size:104
Alignment explanation
Indices: 14727--14963 Score: 275
Period size: 104 Copynumber: 2.2 Consensus size: 104
14717 AGAAAGACTG
* * * *
14727 AAAGAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATG
1 AAAGAAGACTGGCTTAGTTTCAAGG--ATTAGCTAAAAGAAGACTGACTTAGTTTCAAGGAAATG
* *
14792 AAGTAAAGAAAAGACTAGCTTAATTTCAAGGAAATTAGGTA
64 AAGTAAAGAAAAGACTAGCTTAATTTCAAGGAAACTAGCTA
14833 AAAGAAGACTGGCTTAGTTTCAAGGA-TA-CTAAAAGAAAAGACTGACTTAGTTTCAAGGAAACT
1 AAAGAAGACTGGCTTAGTTTCAAGGATTAGCTAAAAG--AAGACTGACTTAGTTTCAAGGAAA-T
* * * *
14896 -AGGTAAAGAAATGACTGGCTTAGTTTCAAGGAAACTAGCTA
63 GAAGTAAAGAAAAGACTAGCTTAATTTCAAGGAAACTAGCTA
* *
14937 AAGGAAAGACTGGATT-GATTTCAAGGA
1 AAAG-AAGACTGGCTTAG-TTTCAAGGA
14964 AATTAAGTAA
Statistics
Matches: 114, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
102 6 0.05
103 2 0.02
104 63 0.55
105 20 0.18
106 23 0.20
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.24
Consensus pattern (104 bp):
AAAGAAGACTGGCTTAGTTTCAAGGATTAGCTAAAAGAAGACTGACTTAGTTTCAAGGAAATGAA
GTAAAGAAAAGACTAGCTTAATTTCAAGGAAACTAGCTA
Found at i:14987 original size:140 final size:138
Alignment explanation
Indices: 14731--14994 Score: 363
Period size: 140 Copynumber: 1.9 Consensus size: 138
14721 AGACTGAAAG
*
14731 AAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATGAAGT
1 AAGACTGACTTAATTTCAAGGAAACTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAAT-AAGT
* * * * *
14796 AAAGAAAAGACTAGCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGATA
65 AAAGAAAAGACTAGATTAATTTCAAGGAAATTAAGTAAAAGAACACAGGCTTAATTTCAAGGATA
14861 CTAAAAGAA
130 CTAAAAGAA
*
14870 AAGACTGACTTAGTTTCAAGGAAACTAGGT-AAAGAAATGACTGGCTTAGTTTCAAGGAAACT-A
1 AAGACTGACTTAATTTCAAGGAAACTAGGTAAAAG-AA-GACTGGCTTAGTTTCAAGGAAA-TAA
* * *
14933 GCTAAAGGAAAGACTGGATTGATTTCAAGGAAATTAAGTAAAA-AGACACAGGCTTAATTTCA
63 G-TAAAGAAAAGACTAGATTAATTTCAAGGAAATTAAGTAAAAGA-ACACAGGCTTAATTTCA
14995 CGAAAGGAAA
Statistics
Matches: 110, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
138 4 0.04
139 33 0.30
140 72 0.65
141 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.25
Consensus pattern (138 bp):
AAGACTGACTTAATTTCAAGGAAACTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATAAGTA
AAGAAAAGACTAGATTAATTTCAAGGAAATTAAGTAAAAGAACACAGGCTTAATTTCAAGGATAC
TAAAAGAA
Found at i:15095 original size:32 final size:32
Alignment explanation
Indices: 15003--15115 Score: 120
Period size: 32 Copynumber: 3.4 Consensus size: 32
14993 CACGAAAGGA
* *
15003 AATTAAGTAAAATAAAGAACTTAATTCAGTGT
1 AATTAAGTTAAATAAAGAACTTAATTCAGGGT
* *
15035 AATTAAGTGAGGTCAATAAA-AGAGTTAATTCAGGGT
1 AATTAAGT----TAAATAAAGA-ACTTAATTCAGGGT
*
15071 AATTAAGTTAAATAAAGAACTTAATTCAAGGT
1 AATTAAGTTAAATAAAGAACTTAATTCAGGGT
*
15103 AATTAAGTGAAAT
1 AATTAAGTTAAAT
15116 CAATAAAGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
32 39 0.58
33 1 0.01
35 1 0.01
36 26 0.39
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.30
Consensus pattern (32 bp):
AATTAAGTTAAATAAAGAACTTAATTCAGGGT
Found at i:15128 original size:36 final size:34
Alignment explanation
Indices: 15013--15131 Score: 129
Period size: 36 Copynumber: 3.4 Consensus size: 34
15003 AATTAAGTAA
15013 AATAAAGAACTTAATTC-AGTGTAATTAAGTGAGGTC
1 AATAAAGAACTTAATTCAAG-GTAATTAAGTGA--TC
* * *
15049 AATAAA-AGAGTTAATTCAGGGTAATTAAGT--TA
1 AATAAAGA-ACTTAATTCAAGGTAATTAAGTGATC
15081 AATAAAGAACTTAATTCAAGGTAATTAAGTGAAATC
1 AATAAAGAACTTAATTCAAGGTAATTAAGTG--ATC
15117 AATAAAGAACTTAAT
1 AATAAAGAACTTAAT
15132 CTAAAAAAGA
Statistics
Matches: 70, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
32 27 0.39
33 1 0.01
35 1 0.01
36 40 0.57
37 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (34 bp):
AATAAAGAACTTAATTCAAGGTAATTAAGTGATC
Found at i:15131 original size:68 final size:68
Alignment explanation
Indices: 15003--15131 Score: 190
Period size: 68 Copynumber: 1.9 Consensus size: 68
14993 CACGAAAGGA
** *
15003 AATTAAGTAAAATAAAGAACTTAATTCAGTGTAATTAAGTGAGGTCAATAAAAGAGTTAATTCAG
1 AATTAAGTAAAATAAAGAACTTAATTCAGTGTAATTAAGTGAAATCAATAAAAGACTTAATTCAG
15068 GGT
66 GGT
*
15071 AATTAAGTTAAATAAAGAACTTAATTCAAG-GTAATTAAGTGAAATCAAT-AAAGAACTTAAT
1 AATTAAGTAAAATAAAGAACTTAATTC-AGTGTAATTAAGTGAAATCAATAAAAG-ACTTAAT
15132 CTAAAAAAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
67 4 0.07
68 49 0.89
69 2 0.04
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (68 bp):
AATTAAGTAAAATAAAGAACTTAATTCAGTGTAATTAAGTGAAATCAATAAAAGACTTAATTCAG
GGT
Found at i:18219 original size:44 final size:42
Alignment explanation
Indices: 18169--18287 Score: 179
Period size: 44 Copynumber: 2.8 Consensus size: 42
18159 ACATTTCCAA
18169 TTTAAGTAATTCCAAAAGAAGATTTTGGAAAACAAAGAGTTTCT
1 TTTAAGTAATTCCAAAAGAAGATTTTGGAAAACAAA-AGTTT-T
* *
18213 TTTAAGTTATTCCAAAAGGAGATTTTGGAAAACAAAAGTTTT
1 TTTAAGTAATTCCAAAAGAAGATTTTGGAAAACAAAAGTTTT
*
18255 TTT-AG-AAATCCAAAAGAAGATTTTGGAAAACAA
1 TTTAAGTAATTCCAAAAGAAGATTTTGGAAAACAA
18288 TTGGACAAGT
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
40 25 0.36
41 2 0.03
42 4 0.06
43 5 0.07
44 34 0.49
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (42 bp):
TTTAAGTAATTCCAAAAGAAGATTTTGGAAAACAAAAGTTTT
Found at i:18250 original size:20 final size:20
Alignment explanation
Indices: 18225--18287 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
18215 TAAGTTATTC
18225 CAAAAGGAGATTTTGGAAAA
1 CAAAAGGAGATTTTGGAAAA
*** * *
18245 CAAAA-GTTTTTTTAGAAATC
1 CAAAAGGAGATTTTGGAAA-A
*
18265 CAAAAGAAGATTTTGGAAAA
1 CAAAAGGAGATTTTGGAAAA
18285 CAA
1 CAA
18288 TTGGACAAGT
Statistics
Matches: 30, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
19 9 0.30
20 13 0.43
21 8 0.27
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.25
Consensus pattern (20 bp):
CAAAAGGAGATTTTGGAAAA
Found at i:20307 original size:40 final size:36
Alignment explanation
Indices: 20219--20312 Score: 100
Period size: 37 Copynumber: 2.4 Consensus size: 36
20209 ATAATCAAAG
*
20219 GTGATCCGGAAGACGGTTTCTCAGAAAATCTTTAGAA
1 GTGAT-CGGAAGACGATTTCTCAGAAAATCTTTAGAA
*
20256 GTGCACCGGAAGACGATTTCTCAGAGAGAAT-TTTACAGAA
1 GTG-ATCGGAAGACGATTTCTCAGA-A-AATCTTT--AGAA
20296 GTTGATCGGAAGACGAT
1 G-TGATCGGAAGACGAT
20313 ATTGTCCAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
37 21 0.44
38 5 0.10
39 3 0.06
40 17 0.35
41 2 0.04
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (36 bp):
GTGATCGGAAGACGATTTCTCAGAAAATCTTTAGAA
Found at i:20805 original size:195 final size:196
Alignment explanation
Indices: 20473--21009 Score: 1008
Period size: 195 Copynumber: 2.8 Consensus size: 196
20463 AATTTCACAG
* *
20473 GAAGTACACCAGAAGATGGTTTCTCAAAGAGTTTACAACAGTTGATCAGAAGATGATCTTGTTAA
1 GAAGTACACTAGAAGATGGTTTCTCAAAGAGTTTACAGCAGTTGATCAGAAGATGATCTTGTTAA
20538 GAGATACACAGAAGGAGTTTTTAGAAGTTGATC-GGAAGATGATCTTGTTACGAGATATATCAAA
66 GAGATACACAGAAGGAGTTTTTAGAAGTTGATCAGGAAGATGATCTTGTTACGAGATATATCAAA
20602 ATACGGTTTCTTAGAAAATTTCACAGGAGAAGTTTTCAGAAGTTGATCGGAAGACGATCTTGTCA
131 ATACGGTTTCTTAGAAAATTTCACAGGAGAAGTTTTCAGAAGTTGATCGGAAGACGATCTTGTCA
20667 A
196 A
20668 GAAGTACACTAGAAGATGGTTTCTCAAAGAGTTTACAGCAGTTGATCAGAAGATGATCTTGTTAA
1 GAAGTACACTAGAAGATGGTTTCTCAAAGAGTTTACAGCAGTTGATCAGAAGATGATCTTGTTAA
20733 GAGATACACAGAAGGAGTTTTTAGAAGTTGATCAGGAAGATGATCTTGTTACGAGATATATC-AA
66 GAGATACACAGAAGGAGTTTTTAGAAGTTGATCAGGAAGATGATCTTGTTACGAGATATATCAAA
20797 ATACGGTTTCTTAGAAAATTTCACAGGAGAAGTTTTCAGAAGTTGATCGGAAGACGATCTTGTCA
131 ATACGGTTTCTTAGAAAATTTCACAGGAGAAGTTTTCAGAAGTTGATCGGAAGACGATCTTGTCA
20862 A
196 A
*
20863 GAAGTACACTAGAAGATGGTTTCTCAAAGAGTTTACAGCAGTTGATCAGAAGATGATCTTCTTAA
1 GAAGTACACTAGAAGATGGTTTCTCAAAGAGTTTACAGCAGTTGATCAGAAGATGATCTTGTTAA
*
20928 GAGATACACAGAAGGAGTTTTTAGAAGTTGATCA-GAAGATGATCTTGTTAAGAGATATATCAAA
66 GAGATACACAGAAGGAGTTTTTAGAAGTTGATCAGGAAGATGATCTTGTTACGAGATATATCAAA
*
20992 ATACGGCTTCTTAGAAAA
131 ATACGGTTTCTTAGAAAA
21010 GTTCTAGAAG
Statistics
Matches: 335, Mismatches: 5, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
194 26 0.08
195 281 0.84
196 28 0.08
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (196 bp):
GAAGTACACTAGAAGATGGTTTCTCAAAGAGTTTACAGCAGTTGATCAGAAGATGATCTTGTTAA
GAGATACACAGAAGGAGTTTTTAGAAGTTGATCAGGAAGATGATCTTGTTACGAGATATATCAAA
ATACGGTTTCTTAGAAAATTTCACAGGAGAAGTTTTCAGAAGTTGATCGGAAGACGATCTTGTCA
A
Found at i:21381 original size:50 final size:50
Alignment explanation
Indices: 21321--21537 Score: 317
Period size: 50 Copynumber: 4.3 Consensus size: 50
21311 AGATTTTCTC
* *
21321 AAGATTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGATGGAATTGGAAGACAATTCCAAGGATAAGCGGAAGACGGTCCTTTT
* *
21371 AAGATGGAATTGGAAGACAGTTCCGAGGATAAGCGGAAGACGGTCCTTTT
1 AAGATGGAATTGGAAGACAATTCCAAGGATAAGCGGAAGACGGTCCTTTT
* * **
21421 AAGATGGAATTGGAAGACAGTTCCAAGGATAAGCGGATGACAATCCTTTT
1 AAGATGGAATTGGAAGACAATTCCAAGGATAAGCGGAAGACGGTCCTTTT
* * * *
21471 AAGATGGAATTGGAGGACAATTCTAAGGATAAACAGAAGACGGTCCTTTT
1 AAGATGGAATTGGAAGACAATTCCAAGGATAAGCGGAAGACGGTCCTTTT
*
21521 AAGATTGAATTGGAAGA
1 AAGATGGAATTGGAAGA
21538 TGATTCGAAG
Statistics
Matches: 149, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 149 1.00
ACGTcount: A:0.37, C:0.12, G:0.28, T:0.24
Consensus pattern (50 bp):
AAGATGGAATTGGAAGACAATTCCAAGGATAAGCGGAAGACGGTCCTTTT
Found at i:21435 original size:27 final size:27
Alignment explanation
Indices: 21355--21438 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 27
21345 AAGGATAAGC
21355 GGAAGACGGTCCTTTTAAGATGGAATT
1 GGAAGACGGTCCTTTTAAGATGGAATT
* * * **
21382 GGAAGACAGTTCC---GAGGAT--AAGC
1 GGAAGAC-GGTCCTTTTAAGATGGAATT
21405 GGAAGACGGTCCTTTTAAGATGGAATT
1 GGAAGACGGTCCTTTTAAGATGGAATT
21432 GGAAGAC
1 GGAAGAC
21439 AGTTCCAAGG
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
22 4 0.10
23 9 0.22
25 8 0.20
27 16 0.39
28 4 0.10
ACGTcount: A:0.32, C:0.13, G:0.32, T:0.23
Consensus pattern (27 bp):
GGAAGACGGTCCTTTTAAGATGGAATT
Found at i:21588 original size:52 final size:52
Alignment explanation
Indices: 21506--21620 Score: 142
Period size: 52 Copynumber: 2.2 Consensus size: 52
21496 AGGATAAACA
* * * *
21506 GAAGACGGTCCTTTTAAGATTGAATTGGAAGATGATTCGAAGAAGTTGATTCG
1 GAAGACGATCCTTTTAAGATTGAATCGGAAGACGATTCGAAGAAGCTGA-TCG
* * * *
21559 GAAGACGATCC-TTTATGATTGAATCGGAAGGCGGTTTGAAGAAGCTGATCG
1 GAAGACGATCCTTTTAAGATTGAATCGGAAGACGATTCGAAGAAGCTGATCG
21610 GAAGACGATCC
1 GAAGACGATCC
21621 ACTTAGAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
51 14 0.26
52 30 0.56
53 10 0.19
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (52 bp):
GAAGACGATCCTTTTAAGATTGAATCGGAAGACGATTCGAAGAAGCTGATCG
Found at i:21888 original size:26 final size:27
Alignment explanation
Indices: 21839--21909 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 27
21829 AGTCACCTAG
* *
21839 GGGCATTTCGGTCATTTTCGCACT-AA
1 GGGCATTTTGGTCATTTTCACACTCAA
*
21865 GGGCATTTTGGTCATTTAT-ACACTCAG
1 GGGCATTTTGGTCATTT-TCACACTCAA
* *
21892 GGGCATTTTAGTGATTTT
1 GGGCATTTTGGTCATTTT
21910 TAAAGTCCAC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
26 21 0.55
27 17 0.45
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTTCACACTCAA
Found at i:22954 original size:16 final size:16
Alignment explanation
Indices: 22936--23010 Score: 80
Period size: 16 Copynumber: 4.8 Consensus size: 16
22926 TTTTTTGGGT
*
22936 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAATG
* *
22952 ACCCGAATCC-AAACG
1 ACCCGAACCCGAAATG
*
22967 ACCCGAATCCGAAATG
1 ACCCGAACCCGAAATG
* **
22983 ACCCAAACCTAAAATG
1 ACCCGAACCCGAAATG
22999 ACCCGAACCCGA
1 ACCCGAACCCGA
23011 TCAACCCGAC
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
15 13 0.28
16 34 0.72
ACGTcount: A:0.40, C:0.37, G:0.13, T:0.09
Consensus pattern (16 bp):
ACCCGAACCCGAAATG
Found at i:22972 original size:31 final size:31
Alignment explanation
Indices: 22936--23010 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
22926 TTTTTTGGGT
* *
22936 ACCCGAACCCGAAATTACCCGAATCC-AAACG
1 ACCCGAACCCGAAATGACCC-AAACCAAAACG
* *
22967 ACCCGAATCCGAAATGACCCAAACCTAAAATG
1 ACCCGAACCCGAAATGACCCAAACC-AAAACG
22999 ACCCGAACCCGA
1 ACCCGAACCCGA
23011 TCAACCCGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 4 0.11
31 18 0.49
32 15 0.41
ACGTcount: A:0.40, C:0.37, G:0.13, T:0.09
Consensus pattern (31 bp):
ACCCGAACCCGAAATGACCCAAACCAAAACG
Found at i:23817 original size:2 final size:2
Alignment explanation
Indices: 23806--23840 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
23796 TTTTGATTCT
23806 TA TA TA -A TA TA TA TA TA TA TA TA TA CTA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA T
23841 TTGTTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:24036 original size:2 final size:2
Alignment explanation
Indices: 24019--24063 Score: 67
Period size: 2 Copynumber: 23.0 Consensus size: 2
24009 GATTTGAAAG
24019 TA TA T- TA TA T- 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 TA TA
24059 GTA TA
1 -TA TA
24064 AATCAGAGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.05
2 36 0.90
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24568 original size:20 final size:18
Alignment explanation
Indices: 24531--24569 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
24521 TTTCTTAACC
*
24531 AAAAACTGACCCAACCCA
1 AAAAACTGACCAAACCCA
24549 AAAAACTGAACACAAACCCA
1 AAAAACTG-AC-CAAACCCA
24569 A
1 A
24570 CCCGACCCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 2 0.11
20 8 0.44
ACGTcount: A:0.56, C:0.33, G:0.05, T:0.05
Consensus pattern (18 bp):
AAAAACTGACCAAACCCA
Done.