Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010118.1 Corchorus capsularis cultivar CVL-1 contig10139, 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: 107395
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:2027 original size:14 final size:14
Alignment explanation
Indices: 2008--2045 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
1998 CTTTCAATTT
2008 TTTTTTTTTGCTT-C
1 TTTTTTTTT-CTTGC
2022 TTTTTTTTTCTTGC
1 TTTTTTTTTCTTGC
2036 TTTTCTTTTT
1 TTTT-TTTTT
2046 TCTTTTGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 14 0.64
15 5 0.23
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (14 bp):
TTTTTTTTTCTTGC
Found at i:2041 original size:19 final size:17
Alignment explanation
Indices: 2005--2049 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
1995 TTTCTTTCAA
*
2005 TTTTTTTTTTTTGCTTC
1 TTTTTTTTTCTTGCTTC
2022 TTTTTTTTTCTTGCTT-
1 TTTTTTTTTCTTGCTTC
*
2038 TTCTTTTTTCTT
1 TTTTTTTTTCTT
2050 TTGCTGATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTCTTGCTTC
Found at i:5820 original size:87 final size:86
Alignment explanation
Indices: 5606--5909 Score: 441
Period size: 87 Copynumber: 3.5 Consensus size: 86
5596 TTCCTTTTTT
* *
5606 ATATCTTCTAAAGCTCCCACAATTTGGCAAGATTTAGAAAATATTTTCATTATTATTAAATCTTT
1 ATATCTTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTT
*
5671 ATAATTT-TTTTGTTTCTTAAA
66 ATAATTTATTAT-TTTCTTAAA
* * * * * *
5692 ATA-CTCCTAAACCTTCCACAACTTGACAAGATTTAGAAAATATTATCATCATTATTATATCTTT
1 ATATCTTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTT
5756 ATAATTTACTTATTTTCTTAAA
66 ATAATTTA-TTATTTTCTTAAA
* *
5778 ATATATTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTC
1 ATATCTTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTT
5843 ATAATTTATTTATTTTCTTAAA
66 ATAATTTA-TTATTTTCTTAAA
* * *
5865 ATATCTTCTAAATCTCCCACAATTTGGTAAGATTTAGAAAATATT
1 ATATCTTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATT
5910 CTCTTTACAA
Statistics
Matches: 193, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
85 60 0.31
86 15 0.08
87 118 0.61
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.43
Consensus pattern (86 bp):
ATATCTTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTT
ATAATTTATTATTTTCTTAAA
Found at i:7858 original size:29 final size:28
Alignment explanation
Indices: 7795--7860 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
7785 ATTGCCAATT
*
7795 TTTTTACCAAAGTATAACATTTGGAAAAC
1 TTTTTCCCAAAGTATAACATTT-GAAAAC
*
7824 TTTTTCCCAAAGTATAACACTTT-TAAAC
1 TTTTTCCCAAAGTATAACA-TTTGAAAAC
7852 TTATTTCCC
1 TT-TTTCCC
7861 TAATTATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 6 0.18
29 24 0.73
30 3 0.09
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (28 bp):
TTTTTCCCAAAGTATAACATTTGAAAAC
Found at i:8955 original size:7 final size:7
Alignment explanation
Indices: 8943--8975 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
8933 CACTTTGTGT
8943 GAAGAGG
1 GAAGAGG
8950 GAAGAGG
1 GAAGAGG
8957 GAAGAGG
1 GAAGAGG
8964 GAAGAGG
1 GAAGAGG
8971 GAAGA
1 GAAGA
8976 AAATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (7 bp):
GAAGAGG
Found at i:17750 original size:33 final size:33
Alignment explanation
Indices: 17706--17835 Score: 242
Period size: 33 Copynumber: 3.9 Consensus size: 33
17696 GAAGATTGTA
*
17706 CAAAGATAATACAAAAGCTCTCACAAGGAGTCC
1 CAAAGACAATACAAAAGCTCTCACAAGGAGTCC
*
17739 TAAAGACAATACAAAAGCTCTCACAAGGAGTCC
1 CAAAGACAATACAAAAGCTCTCACAAGGAGTCC
17772 CAAAGACAATACAAAAGCTCTCACAAGGAGTCC
1 CAAAGACAATACAAAAGCTCTCACAAGGAGTCC
17805 CAAAGACAATACAAAAGCTCTCACAAGGAGT
1 CAAAGACAATACAAAAGCTCTCACAAGGAGT
17836 ACCGTATGCA
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 94 1.00
ACGTcount: A:0.46, C:0.25, G:0.15, T:0.14
Consensus pattern (33 bp):
CAAAGACAATACAAAAGCTCTCACAAGGAGTCC
Found at i:20086 original size:12 final size:13
Alignment explanation
Indices: 20053--20096 Score: 54
Period size: 12 Copynumber: 3.3 Consensus size: 13
20043 TACCTTTATC
*
20053 TTTTTCTTTTTCA
1 TTTTTATTTTTCA
20066 TTATTTTATTTTT-A
1 -T-TTTTATTTTTCA
20080 TTTTTATTTTTCA
1 TTTTTATTTTTCA
20093 TTTT
1 TTTT
20097 AGTGCTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 10 0.37
13 6 0.22
14 2 0.07
15 9 0.33
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTTCA
Found at i:26114 original size:669 final size:671
Alignment explanation
Indices: 24834--26175 Score: 2526
Period size: 669 Copynumber: 2.0 Consensus size: 671
24824 CAAGATCTAC
*
24834 AACTTTCGTGTTTTGGTCGAAGCCCAGTTCGGACGTTTCCATGGACGAAAATGCCCCTGAAGTCA
1 AACTTTCGTGTTTTGGTCGAACCCCAGTTCGGACGTTTCCATGGACGAAAATGCCCCTGAAGTCA
*
24899 GCGGAAAGAAACTGTCTTGGGTCTTTCTTGCGGGATTGACCAATTTGAGCCCAAATTCTTATTTG
66 GCGGAAAGAAACTGTCTTGGGCCTTTCTTGCGGGATTGACCAATTTGAGCCCAAATTCTTATTTG
24964 GATTAGCTTGAAGACTTGGAGAGCAGTCCAGCACGTCCTTAGGGTTTGTTTTAGCCATCTTAAAC
131 GATTAGCTTGAAGACTTGGAGAGCAGTCCAGCACGTCCTTAGGGTTTGTTTTAGCCATCTTAAAC
25029 TCTAAAATCTACCCTAGGCCGTCCCCTATATATACCCTCTTATCCTAGAACTCTAGCGACACGAT
196 TCTAAAATCTACCCTAGGCCGTCCCCTATATATACCCTCTTATCCTAGAACTCTAGCGA-ACGAT
25094 CTTTTAACAACTTACAAAACAACTTTTATCTCTTTTTCTCTCTAGGTTTTGCGCTTTGGGAGAGG
260 CTTTTAACAACTTACAAAACAACTTTTATCTCTTTTTCTCTCTAGGTTTTGCGCTTTGGGAGAGG
25159 AGGCAGCCACCTCCTCCTCTTTTCCTCTTGGGTTTGTAAGTTTTCAATCTCTCATGGATTGGAAA
325 AGGCAGCCACCTCCTCCTCTTTTCCTCTTGGGTTTGTAAGTTTTCAATCTCTCATGGATTGGAAA
25224 CTCCAATCCATGAGAGGTTAAACCTTTATACGTCTTTTCCTTAGATATTTTTGATCAATAAATTT
390 CTCCAATCCATGAGAGGTTAAACCTTTATACGTCTTTTCCTTAGATATTTTTGATCAATAAATTT
25289 ATGGTGAGACTTTTGTTCTTAATAATTTGATTTTTCTGTTTGAATATGTTTCTTATCCCTGTGCT
455 ATGGTGAGACTTTTGTTCTTAATAATTTGATTTTTCTGTTTGAATATGTTTCTTATCCCTGTGCT
25354 TCATCTTATGTGTTCATATTTTGATAGATTTGGAGTACTACTTGTCTTGATAATATGAATGCTAT
520 TCATCTTATGTGTTCATATTTTGATAGATTTGGAGTACTACTTGTCTTGATAATATGAATGCTAT
*
25419 TGTTAGATTCAAGTAGATTGAGTCAAGCTAATGTTGGTCGAAGTGACAATTGTTAATCTAGAAGT
585 TGTTAGATTCAAGTAGATTGAGTCAAGCTAAAGTTGGTCGAAGTGACAATTGTTAATCTAGAAGT
25484 TCTAGGTTCAATGGGATACCAA
650 TCTAGGTTCAATGGGATACCAA
25506 AACTTTCGTGTTTTGGTCGAACCCCAGTTCGGACGTTTCCATGGACGAAAATGCCCCTGAAGTCA
1 AACTTTCGTGTTTTGGTCGAACCCCAGTTCGGACGTTTCCATGGACGAAAATGCCCCTGAAGTCA
*
25571 GCGGACAGAAACTGTCTTGGGCCTTTCTTGCGGGATTGACCAATTTGAGCCCAAATTCTTATTTG
66 GCGGAAAGAAACTGTCTTGGGCCTTTCTTGCGGGATTGACCAATTTGAGCCCAAATTCTTATTTG
25636 GATTAGCTTGAAGACTTGGAGAGCAGTCCAGCACGTCCTTAGGGTTTGTTTTAGCCATCTTAAAC
131 GATTAGCTTGAAGACTTGGAGAGCAGTCCAGCACGTCCTTAGGGTTTGTTTTAGCCATCTTAAAC
25701 TCTAAAATCTACCCTAGGCCGTCCCCTATATATACCCTCTTATCCTAGAACTCTAGCG-AC-ATC
196 TCTAAAATCTACCCTAGGCCGTCCCCTATATATACCCTCTTATCCTAGAACTCTAGCGAACGATC
*
25764 TTTTAACAACTTACAACACAACTTTTATCTCTTTTTCTCTCTAGGTTTTGCGCTTTGGGAGAGGA
261 TTTTAACAACTTACAAAACAACTTTTATCTCTTTTTCTCTCTAGGTTTTGCGCTTTGGGAGAGGA
** *
25829 GGCAGCTGCCTCCTCCTCTTTTCCTCTTGGGTTTGTAAGTTTTCAATCTCTCATTGATTGGAAAC
326 GGCAGCCACCTCCTCCTCTTTTCCTCTTGGGTTTGTAAGTTTTCAATCTCTCATGGATTGGAAAC
* *
25894 TCCAATCCATGAGAGGTTAAACCTTTATACTTCTTTTCCTTAGGTATTTTTGATCAATAAATTTA
391 TCCAATCCATGAGAGGTTAAACCTTTATACGTCTTTTCCTTAGATATTTTTGATCAATAAATTTA
25959 TGGTGAGACTTTTGTTCTTAATAATTTGATTTTTCTGTTTGAATATGTTTCTTATCCCTGTGCTT
456 TGGTGAGACTTTTGTTCTTAATAATTTGATTTTTCTGTTTGAATATGTTTCTTATCCCTGTGCTT
* *
26024 CATCTTATGTGTTCATATTTTGATGGATTTGGAGTAGTACTTGTCTTGATAATATGAATGCTATT
521 CATCTTATGTGTTCATATTTTGATAGATTTGGAGTACTACTTGTCTTGATAATATGAATGCTATT
* *
26089 GTTAGATTCAAGTAGCTTGAGTCAAGTTAAAGTTGGTCGAAGTGACAATTGTTAATCTAGAAGTT
586 GTTAGATTCAAGTAGATTGAGTCAAGCTAAAGTTGGTCGAAGTGACAATTGTTAATCTAGAAGTT
*
26154 CTAGGTTCAATGGGATATCAA
651 CTAGGTTCAATGGGATACCAA
26175 A
1 A
26176 CCTTGTTGAA
Statistics
Matches: 655, Mismatches: 15, Indels: 3
0.97 0.02 0.00
Matches are distributed among these distances:
669 403 0.62
670 2 0.00
672 250 0.38
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (671 bp):
AACTTTCGTGTTTTGGTCGAACCCCAGTTCGGACGTTTCCATGGACGAAAATGCCCCTGAAGTCA
GCGGAAAGAAACTGTCTTGGGCCTTTCTTGCGGGATTGACCAATTTGAGCCCAAATTCTTATTTG
GATTAGCTTGAAGACTTGGAGAGCAGTCCAGCACGTCCTTAGGGTTTGTTTTAGCCATCTTAAAC
TCTAAAATCTACCCTAGGCCGTCCCCTATATATACCCTCTTATCCTAGAACTCTAGCGAACGATC
TTTTAACAACTTACAAAACAACTTTTATCTCTTTTTCTCTCTAGGTTTTGCGCTTTGGGAGAGGA
GGCAGCCACCTCCTCCTCTTTTCCTCTTGGGTTTGTAAGTTTTCAATCTCTCATGGATTGGAAAC
TCCAATCCATGAGAGGTTAAACCTTTATACGTCTTTTCCTTAGATATTTTTGATCAATAAATTTA
TGGTGAGACTTTTGTTCTTAATAATTTGATTTTTCTGTTTGAATATGTTTCTTATCCCTGTGCTT
CATCTTATGTGTTCATATTTTGATAGATTTGGAGTACTACTTGTCTTGATAATATGAATGCTATT
GTTAGATTCAAGTAGATTGAGTCAAGCTAAAGTTGGTCGAAGTGACAATTGTTAATCTAGAAGTT
CTAGGTTCAATGGGATACCAA
Found at i:27914 original size:14 final size:14
Alignment explanation
Indices: 27882--27915 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
27872 AAGTATAATA
*
27882 AAAAATGTTTAGAT
1 AAAAATGTTTAAAT
27896 AAAAATGTTTAAATT
1 AAAAATGTTTAAA-T
27911 AAAAA
1 AAAAA
27916 GAATTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (14 bp):
AAAAATGTTTAAAT
Found at i:32661 original size:42 final size:42
Alignment explanation
Indices: 32598--32682 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
32588 CTCAAAGCTA
*
32598 CACCTAAGGCTCGGGCTGGAGCTTATAGCACATTTAGAAGGC
1 CACCTAAGGCTCCGGCTGGAGCTTATAGCACATTTAGAAGGC
* * *
32640 CACCTAAGGCTCCGG-TGGGAGCTTTTAGCACGTTTAGGAGGC
1 CACCTAAGGCTCCGGCT-GGAGCTTATAGCACATTTAGAAGGC
32682 C
1 C
32683 TAAACGTGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 1 0.03
42 37 0.97
ACGTcount: A:0.22, C:0.25, G:0.31, T:0.22
Consensus pattern (42 bp):
CACCTAAGGCTCCGGCTGGAGCTTATAGCACATTTAGAAGGC
Found at i:33458 original size:17 final size:17
Alignment explanation
Indices: 33436--33470 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
33426 GCTACGCACT
*
33436 GCCTAAAGATTTAAAAG
1 GCCTAAAGATTCAAAAG
*
33453 GCCTAAAGGTTCAAAAG
1 GCCTAAAGATTCAAAAG
33470 G
1 G
33471 GAATAAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (17 bp):
GCCTAAAGATTCAAAAG
Found at i:39041 original size:45 final size:45
Alignment explanation
Indices: 38956--39052 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 45
38946 TCTGATCACC
*
38956 ATATAAATTATTTTAGGGATTGTGTGATGTATCAAAGGGAGAATT
1 ATATAAATTATTTTAGGGATTGTGTGATGTATCAAAGGGAGAAAT
* *
39001 ATATAAATTATTTTAGGGATTGTGTGATGTA-CTGACGGGAGAAAT
1 ATATAAATTATTTTAGGGATTGTGTGATGTATC-AAAGGGAGAAAT
39046 ATA-AAAT
1 ATATAAAT
39053 GTGCACTAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
44 5 0.10
45 43 0.90
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (45 bp):
ATATAAATTATTTTAGGGATTGTGTGATGTATCAAAGGGAGAAAT
Found at i:45549 original size:121 final size:117
Alignment explanation
Indices: 45348--45600 Score: 274
Period size: 121 Copynumber: 2.1 Consensus size: 117
45338 AGCCAATTGG
* * * * * *
45348 TACAATTTGTAACGCCTAATAATGTTAGAATTAGTTAACTAGTACAATTAGTAACACCTGAAATT
1 TACAA-TTGTAACGCCCAAAAAAGTTAGAATCAGTCAACAAGTACAATTAGTAACACCTGAAATT
* * *
45413 ATTAGAATCAGCCAATCAACAGTACAATCTGTAAGGCATGAAAATTAGCCAACCAA
65 ATTACAATCAACCAATC--CA-TACAATCTGTAAGGCATGAAAATTAACCAACCAA
* ** *
45469 TACAACTTGTAACGCCCAAAAAAGTTGGAATCAGTCAACAAGTACAATTTTTAACGCCTAGAAA-
1 TACAA-TTGTAACGCCCAAAAAAGTTAGAATCAGTCAACAAGTACAATTAGTAACACCT-GAAAT
* * * * *
45533 TGTTACAATCAACCAATCTATACAATCTGTAATGCATGAAAATTAACCAACTAG
64 TATTACAATCAACCAATCCATACAATCTGTAAGGCATGAAAATTAACCAACCAA
45587 TACAATCTGTAACG
1 TACAAT-TGTAACG
45601 TCTGAAAATG
Statistics
Matches: 111, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
117 1 0.01
118 42 0.38
119 1 0.01
121 63 0.57
122 4 0.04
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (117 bp):
TACAATTGTAACGCCCAAAAAAGTTAGAATCAGTCAACAAGTACAATTAGTAACACCTGAAATTA
TTACAATCAACCAATCCATACAATCTGTAAGGCATGAAAATTAACCAACCAA
Found at i:45607 original size:34 final size:34
Alignment explanation
Indices: 45543--45609 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
45533 TGTTACAATC
*
45543 AACCAATCTATACAATCTGTAATGCATGAAAATT
1 AACCAATCTATACAATCTGTAACGCATGAAAATT
45577 AACCAA-CTAGTACAATCTGTAACGTC-TGAAAAT
1 AACCAATCTA-TACAATCTGTAACG-CATGAAAAT
45610 GTTAGAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 3 0.10
34 26 0.87
35 1 0.03
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.27
Consensus pattern (34 bp):
AACCAATCTATACAATCTGTAACGCATGAAAATT
Found at i:45639 original size:24 final size:25
Alignment explanation
Indices: 45594--45641 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
45584 TAGTACAATC
*
45594 TGTAACGTCTGAAAATGTTAGAATT
1 TGTAACGCCTGAAAATGTTAGAATT
*
45619 TGTAACGCCT-AAATTGTTAGAAT
1 TGTAACGCCTGAAAATGTTAGAAT
45642 CGACCAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (25 bp):
TGTAACGCCTGAAAATGTTAGAATT
Found at i:45689 original size:66 final size:66
Alignment explanation
Indices: 45578--45745 Score: 221
Period size: 66 Copynumber: 2.5 Consensus size: 66
45568 ATGAAAATTA
* * * * *
45578 ACCAACTAGTACAATCTGTAACG-TCTGAAAATGTTAGAATTTGTAACGCCTAAATTGTTAGAAT
1 ACCAACCAGTATAATCTGTAACGCT-TGAAAATGTTAGAATCTGTAACGCCCAAAATGTTAGAAT
45642 CG
65 CG
* * *
45644 ACCAACCAGTATAATTTGTAACGCTTGAAAAGGTTAGAATCTGTAACGCCCAAAATGTTAGTATC
1 ACCAACCAGTATAATCTGTAACGCTTGAAAATGTTAGAATCTGTAACGCCCAAAATGTTAGAATC
45709 G
66 G
* * *
45710 ACAAACCTGTATAATCTGTAACGCCTGAAAATGTTA
1 ACCAACCAGTATAATCTGTAACGCTTGAAAATGTTA
45746 AAATATTAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
66 87 0.99
67 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (66 bp):
ACCAACCAGTATAATCTGTAACGCTTGAAAATGTTAGAATCTGTAACGCCCAAAATGTTAGAATC
G
Found at i:46003 original size:84 final size:83
Alignment explanation
Indices: 45863--46031 Score: 248
Period size: 84 Copynumber: 2.0 Consensus size: 83
45853 ATCTGTAACG
* * * * * *
45863 TCTGAAGTTGTTAGAATTAGCAATCAAAACAATTTATAACTCATGAAGATCAACCAACTAGTACC
1 TCTGAAATTGATAGAATTAGCAACCAAAACAATTTATAACACATGAAAATCAACCAACTAGTACA
*
45928 ATCCATAATGCATGAAAA
66 ATCCATAATGCACGAAAA
*
45946 TCTGAAATTGATAGAATTAGCTAACCAAAACAATTTATAACACATGAAAATGAACCAACTAGTAC
1 TCTGAAATTGATAGAATTAGC-AACCAAAACAATTTATAACACATGAAAATCAACCAACTAGTAC
*
46011 AATCTATAATGCACGAAAA
65 AATCCATAATGCACGAAAA
46030 TC
1 TC
46032 AACTAACCAT
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
83 19 0.25
84 57 0.75
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (83 bp):
TCTGAAATTGATAGAATTAGCAACCAAAACAATTTATAACACATGAAAATCAACCAACTAGTACA
ATCCATAATGCACGAAAA
Found at i:47020 original size:128 final size:128
Alignment explanation
Indices: 46780--47032 Score: 309
Period size: 128 Copynumber: 2.0 Consensus size: 128
46770 GTGAATAAAT
* * * *
46780 AATAGTACATGATTTTATGGTCAACAAATGTGTTTACATTGAAGTGGTTAAAAACCCTTGTAATT
1 AATAATACATGATTTTATGGTCAACAAATGTGTTCAAATTGAAGTGGTTAAAAACCCTTGCAATT
* * *
46845 ACAAAAAAAGGCGGAGGAAAAAGGAGTGTTGAGAAAATAATTAGAGGG-CATTCTTAGTAAGTA
66 ACAAAAAAAGGCGGAGGAAAAAGGAATGGTAAGAAAATAATTAGAGGGTC-TTCTTAGTAAGTA
* * *
46908 AATAATACATGATTTTATGGTCAATAAATGCT-TTCAAATT-CAGTTGGTTAAAAACTCTTGCAA
1 AATAATACATGATTTTATGGTCAACAAATG-TGTTCAAATTGAAG-TGGTTAAAAACCCTTGCAA
* * *
46971 TTAC-AAAAAAGGCCTGGAGGAGAAGGGAATGGTAAGAAACTAATT-GAGGGTCTTCTTAGTAA
64 TTACAAAAAAAGG-C-GGAGGAAAAAGGAATGGTAAGAAAATAATTAGAGGGTCTTCTTAGTAA
47033 TTAACCAAGT
Statistics
Matches: 107, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
127 10 0.09
128 71 0.66
129 26 0.24
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.29
Consensus pattern (128 bp):
AATAATACATGATTTTATGGTCAACAAATGTGTTCAAATTGAAGTGGTTAAAAACCCTTGCAATT
ACAAAAAAAGGCGGAGGAAAAAGGAATGGTAAGAAAATAATTAGAGGGTCTTCTTAGTAAGTA
Found at i:49238 original size:66 final size:66
Alignment explanation
Indices: 49128--49288 Score: 200
Period size: 66 Copynumber: 2.4 Consensus size: 66
49118 TCAACCAACT
* * * * *
49128 AGTACAATTTGTAACG-TCTGAAAATGTTAGAATCTGTAATGCCTAAAATGTTAGAATCGGCCAA
1 AGTATAATCTGTAACGCT-TGAAAATGTTAGAATCAGTAATGCCTAAAATGTTAGAATCGACAAA
49192 CC
65 CC
* * *
49194 AGTATCATCTGTAACGCTTGAAAATGTTAGAATCAGT-ATCGCCTAATATGTTAGTATCGACAAA
1 AGTATAATCTGTAACGCTTGAAAATGTTAGAATCAGTAAT-GCCTAAAATGTTAGAATCGACAAA
49258 CC
65 CC
* *
49260 TGTATAATCTGTAACGCCTGAAAATGTTA
1 AGTATAATCTGTAACGCTTGAAAATGTTA
49289 AAATATTAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 2 0.02
66 79 0.96
67 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (66 bp):
AGTATAATCTGTAACGCTTGAAAATGTTAGAATCAGTAATGCCTAAAATGTTAGAATCGACAAAC
C
Found at i:49538 original size:84 final size:84
Alignment explanation
Indices: 49408--49574 Score: 219
Period size: 84 Copynumber: 2.0 Consensus size: 84
49398 CTGTAACGTC
* * * * *
49408 TGAAGTTGTTAGAATTAGCCAATCAAAACAATTTATAACTCATGAAAATCAACCAACTAGTA-AC
1 TGAAATTGATAGAATTAGCCAACCAAAACAATTTATAACGCATGAAAATAAACCAACTAGTACA-
* *
49472 ATCCATTATGCATGAAAATA
65 ATCAATAATGCATGAAAATA
* ** *
49492 TGAAATTGATAGAATTAGCTAACCAAAGTAATTTGTAACGCATGAAAATAAACCAACTAGTACAA
1 TGAAATTGATAGAATTAGCCAACCAAAACAATTTATAACGCATGAAAATAAACCAACTAGTACAA
49557 TCAATAATGCATGAAAAT
66 TCAATAATGCATGAAAAT
49575 CAATTAACCA
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
84 70 0.99
85 1 0.01
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (84 bp):
TGAAATTGATAGAATTAGCCAACCAAAACAATTTATAACGCATGAAAATAAACCAACTAGTACAA
TCAATAATGCATGAAAATA
Found at i:53310 original size:15 final size:15
Alignment explanation
Indices: 53290--53320 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
53280 CCATTATGCA
53290 TTTCTCAGGAAGTCG
1 TTTCTCAGGAAGTCG
53305 TTTCTCAGGAAGTCG
1 TTTCTCAGGAAGTCG
53320 T
1 T
53321 AAAAATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (15 bp):
TTTCTCAGGAAGTCG
Found at i:54267 original size:11 final size:11
Alignment explanation
Indices: 54251--54275 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54241 CTAAAAAGGG
54251 TAATTATTTGA
1 TAATTATTTGA
54262 TAATTATTTGA
1 TAATTATTTGA
54273 TAA
1 TAA
54276 ACCGGTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (11 bp):
TAATTATTTGA
Found at i:54391 original size:19 final size:19
Alignment explanation
Indices: 54369--54411 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
54359 TAGTCCCTAA
54369 AGGACACATGTCACCCTTC
1 AGGACACATGTCACCCTTC
54388 AGGACACATGTCACCCTTC
1 AGGACACATGTCACCCTTC
54407 AGGAC
1 AGGAC
54412 CCGCTTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.35, G:0.19, T:0.19
Consensus pattern (19 bp):
AGGACACATGTCACCCTTC
Found at i:65309 original size:32 final size:32
Alignment explanation
Indices: 65273--65334 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
65263 GGTTTTGATA
65273 TCATTTGTGAACTTGATACCCCTAGTCAAAAT
1 TCATTTGTGAACTTGATACCCCTAGTCAAAAT
* *
65305 TCATTTTTGAACTTGATACCTCTAGTCAAA
1 TCATTTGTGAACTTGATACCCCTAGTCAAA
65335 GATGCACATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (32 bp):
TCATTTGTGAACTTGATACCCCTAGTCAAAAT
Found at i:70088 original size:6 final size:6
Alignment explanation
Indices: 70077--70103 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
70067 AAAGCAAAGC
70077 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
70104 GCAGATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:73208 original size:21 final size:21
Alignment explanation
Indices: 73184--73246 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
73174 AGTCTCGTGG
73184 TGGCGTGGCATGGTGCGCGGA
1 TGGCGTGGCATGGTGCGCGGA
* *
73205 TGGCATGGCATTG-GC-CGGACA
1 TGGCGTGGCATGGTGCGCGG--A
73226 TGGCCG-GGCATGGTGCGCGGA
1 TGG-CGTGGCATGGTGCGCGGA
73247 CAAGACCGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
19 3 0.09
20 2 0.06
21 22 0.67
22 3 0.09
23 3 0.09
ACGTcount: A:0.13, C:0.22, G:0.48, T:0.17
Consensus pattern (21 bp):
TGGCGTGGCATGGTGCGCGGA
Found at i:76930 original size:6 final size:6
Alignment explanation
Indices: 76919--76951 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
76909 AAAGCAAAGC
76919 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
76952 GCAGATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:77903 original size:10 final size:10
Alignment explanation
Indices: 77888--77912 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
77878 GAGGACTCTA
77888 GAATTTTCTG
1 GAATTTTCTG
77898 GAATTTTCTG
1 GAATTTTCTG
77908 GAATT
1 GAATT
77913 GAGCAGGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:84493 original size:6 final size:6
Alignment explanation
Indices: 84484--84510 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
84474 TATATATTTA
84484 TATCTT TATCTT TATCTT TATCTT TAT
1 TATCTT TATCTT TATCTT TATCTT TAT
84511 ATAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.67
Consensus pattern (6 bp):
TATCTT
Found at i:84960 original size:44 final size:40
Alignment explanation
Indices: 84876--84952 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
84866 TAAACATGTA
* *
84876 TTTTTATTTCATTTAGATTAATTAGTTGTGTAATTATTAT
1 TTTTTATTTCATTTAAATTAATTAATTGTGTAATTATTAT
84916 TTTTTATTTCATTTAAATTAATTAATTAG-GTAATTAT
1 TTTTTATTTCATTTAAATTAATTAATT-GTGTAATTAT
84953 GTTTTATTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (40 bp):
TTTTTATTTCATTTAAATTAATTAATTGTGTAATTATTAT
Found at i:87252 original size:17 final size:17
Alignment explanation
Indices: 87230--87263 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
87220 TTGGAACTAG
87230 GGAAAATACTAGGGAAA
1 GGAAAATACTAGGGAAA
**
87247 GGAAAATTTTAGGGAAA
1 GGAAAATACTAGGGAAA
87264 ATTGAAATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.29, T:0.18
Consensus pattern (17 bp):
GGAAAATACTAGGGAAA
Found at i:87781 original size:21 final size:21
Alignment explanation
Indices: 87756--87799 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
87746 TATAAGGATA
*
87756 AATGTATAAAGTGAGGGTGAT
1 AATGTATAAAGTGAGAGTGAT
* *
87777 AATGTATAAGGTTAGAGTGAT
1 AATGTATAAAGTGAGAGTGAT
87798 AA
1 AA
87800 GTCTCATAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (21 bp):
AATGTATAAAGTGAGAGTGAT
Found at i:94361 original size:42 final size:41
Alignment explanation
Indices: 94231--94362 Score: 131
Period size: 42 Copynumber: 3.1 Consensus size: 41
94221 AACGCATAAA
* * **
94231 AATTAGCTAACCAGTACAAGTTGTAACGCCTAAAAATGTTGG
1 AATTAGCCAACCAGTACAA-TTGTAACGCCTAGAAATGTTAC
* * * *
94273 GATCAGTCAACAAGTACAATTTGTAACGCCT-GAAAATGTTAC
1 AATTAGCCAACCAGTACAA-TTGTAACGCCTAG-AAATGTTAC
* *
94315 AATTAGCCAACCAGTACAATCTGTAACACCTAGAAATGTTAT
1 AATTAGCCAACCAGTACAAT-TGTAACGCCTAGAAATGTTAC
94357 AATTAG
1 AATTAG
94363 GCAATTAGCC
Statistics
Matches: 72, Mismatches: 15, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
41 1 0.01
42 70 0.97
43 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (41 bp):
AATTAGCCAACCAGTACAATTGTAACGCCTAGAAATGTTAC
Found at i:94535 original size:42 final size:42
Alignment explanation
Indices: 94466--94546 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
94456 GAACCATTTC
* *
94466 GTACAATCTGTAACGCCTGACAATGTTAAAATTGGCCAACTA
1 GTACAATCTGTAACGCATGACAATGTTAAAATTAGCCAACTA
* *
94508 GTACAATCTGTAACGTATGA-AATTGTTAGAATTAGCCAA
1 GTACAATCTGTAACGCATGACAA-TGTTAAAATTAGCCAA
94547 TCAAAACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.06
42 32 0.94
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (42 bp):
GTACAATCTGTAACGCATGACAATGTTAAAATTAGCCAACTA
Found at i:95337 original size:19 final size:19
Alignment explanation
Indices: 95313--95356 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
95303 TATTGACTAT
95313 GAGAGAG-C-AAGTGGGAG
1 GAGAGAGACTAAGTGGGAG
* *
95330 GAGAGAGACTTAGTGGGGG
1 GAGAGAGACTAAGTGGGAG
95349 GAGAGAGA
1 GAGAGAGA
95357 AGAGGGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.30
18 1 0.04
19 15 0.65
ACGTcount: A:0.34, C:0.05, G:0.52, T:0.09
Consensus pattern (19 bp):
GAGAGAGACTAAGTGGGAG
Found at i:103726 original size:2 final size:2
Alignment explanation
Indices: 103714--103743 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
103704 GTTAGATGTT
*
103714 TA TA AA 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
103744 GAATTGGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:104291 original size:32 final size:32
Alignment explanation
Indices: 104255--104319 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
104245 TCCGGTTTTG
104255 AATTCATTTGTGAACTTGATACCTCTAGTCAA
1 AATTCATTTGTGAACTTGATACCTCTAGTCAA
*
104287 AATTCATTTTTGAACTTGATACCTCTAGTCAA
1 AATTCATTTGTGAACTTGATACCTCTAGTCAA
104319 A
1 A
104320 GATGCACATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.38
Consensus pattern (32 bp):
AATTCATTTGTGAACTTGATACCTCTAGTCAA
Found at i:106000 original size:44 final size:40
Alignment explanation
Indices: 105916--105992 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
105906 TAAACATGTA
* **
105916 TTTTTATTTCATTTAGATTAATTAGTTGTGTAATTATTAT
1 TTTTTATTTCATTTAGATTAATTAATTACGTAATTATTAT
105956 TTTTTATTTCATTTAGATTAATTAATTACGTAATTAT
1 TTTTTATTTCATTTAGATTAATTAATTACGTAATTAT
105993 GTTTTATTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.30, C:0.04, G:0.08, T:0.58
Consensus pattern (40 bp):
TTTTTATTTCATTTAGATTAATTAATTACGTAATTATTAT
Done.