Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007452.1 Corchorus capsularis cultivar CVL-1 contig07473, 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: 31451
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.31
Found at i:855 original size:16 final size:17
Alignment explanation
Indices: 820--851 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
810 CAGTTAAAAT
820 TAAATTAATTATAATCA
1 TAAATTAATTATAATCA
837 TAAA-TAATTA-AATCA
1 TAAATTAATTATAATCA
852 ATAATTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 6 0.40
17 4 0.27
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTAATTATAATCA
Found at i:1243 original size:22 final size:22
Alignment explanation
Indices: 1217--1263 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1207 ATCAGTCAAT
* *
1217 TTAATTAGTAATAATTTAGTAA
1 TTAATTAATAATAAGTTAGTAA
* *
1239 TTAATTAATATTAAGTTATTAA
1 TTAATTAATAATAAGTTAGTAA
1261 TTA
1 TTA
1264 GTGGTAATGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (22 bp):
TTAATTAATAATAAGTTAGTAA
Found at i:4502 original size:25 final size:24
Alignment explanation
Indices: 4467--4528 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
4457 GAATCCGCCC
*
4467 GACCGGAGACCCGACGAACCC-G-T
1 GACCCGAGACCCGAC-AACCCAGAT
4490 GACCCGAATGACCCG-CAACCCAGAT
1 GACCCG-A-GACCCGACAACCCAGAT
4515 GACCCGAGACCCGA
1 GACCCGAGACCCGA
4529 ATGACCCGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
23 16 0.48
24 4 0.12
25 13 0.39
ACGTcount: A:0.29, C:0.40, G:0.26, T:0.05
Consensus pattern (24 bp):
GACCCGAGACCCGACAACCCAGAT
Found at i:4503 original size:16 final size:16
Alignment explanation
Indices: 4491--4601 Score: 127
Period size: 16 Copynumber: 6.9 Consensus size: 16
4481 CGAACCCGTG
*
4491 ACCCGAATGACCCGCA
1 ACCCGAATGACCCGAA
*
4507 ACCC-AGATGACCCGAG
1 ACCCGA-ATGACCCGAA
4523 ACCCGAATGACCCGAA
1 ACCCGAATGACCCGAA
*
4539 ACCC-AGATGACCTGAA
1 ACCCGA-ATGACCCGAA
* *
4555 ACTCGAATGACCCGAG
1 ACCCGAATGACCCGAA
*
4571 ACCCGTATGACCCGAA
1 ACCCGAATGACCCGAA
*
4587 ACCCGAATAACCCGA
1 ACCCGAATGACCCGA
4602 GACATTAACC
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
15 2 0.03
16 75 0.95
17 2 0.03
ACGTcount: A:0.34, C:0.37, G:0.20, T:0.09
Consensus pattern (16 bp):
ACCCGAATGACCCGAA
Found at i:4536 original size:48 final size:47
Alignment explanation
Indices: 4467--4601 Score: 139
Period size: 48 Copynumber: 2.8 Consensus size: 47
4457 GAATCCGCCC
* * ** *
4467 GACCGGAGACCCGACGAACCCGTGACCCGAATGACCCGCAACCC-AGAT
1 GACCCGAGACCCGATG-ACCCGAAACCCGAATGACCCGAAACCCGA-AT
* *
4515 GACCCGAGACCCGAATGACCCGAAACCC-AGATGACCTGAAACTCGAAT
1 GACCCGAGACCCG-ATGACCCGAAACCCGA-ATGACCCGAAACCCGAAT
*
4563 GACCCGAGACCCGTATGACCCGAAACCCGAATAACCCGA
1 GACCCGAGACCCG-ATGACCCGAAACCCGAATGACCCGA
4602 GACATTAACC
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
47 1 0.01
48 68 0.93
49 4 0.05
ACGTcount: A:0.33, C:0.37, G:0.22, T:0.08
Consensus pattern (47 bp):
GACCCGAGACCCGATGACCCGAAACCCGAATGACCCGAAACCCGAAT
Found at i:4602 original size:32 final size:32
Alignment explanation
Indices: 4491--4604 Score: 151
Period size: 32 Copynumber: 3.6 Consensus size: 32
4481 CGAACCCGTG
*
4491 ACCCGAATGACCCGCA-ACCCAGATGACCCGAG
1 ACCCGAATGACCCG-AGACCCAGATGACCCGAA
* *
4523 ACCCGAATGACCCGAAACCCAGATGACCTGAA
1 ACCCGAATGACCCGAGACCCAGATGACCCGAA
*
4555 ACTCGAATGACCCGAGACCC-GTATGACCCGAA
1 ACCCGAATGACCCGAGACCCAG-ATGACCCGAA
*
4587 ACCCGAATAACCCGAGAC
1 ACCCGAATGACCCGAGAC
4605 ATTAACCCGA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
31 2 0.03
32 71 0.97
ACGTcount: A:0.34, C:0.37, G:0.20, T:0.09
Consensus pattern (32 bp):
ACCCGAATGACCCGAGACCCAGATGACCCGAA
Found at i:5218 original size:9 final size:9
Alignment explanation
Indices: 5203--5282 Score: 63
Period size: 9 Copynumber: 9.9 Consensus size: 9
5193 GTAGACCCGA
5203 GACCCGAAT
1 GACCCGAAT
*
5212 GATCCG-A-
1 GACCCGAAT
5219 GACCCGAAT
1 GACCCGAAT
5228 GACCCG-A-
1 GACCCGAAT
5235 GACCCGAAT
1 GACCCGAAT
5244 GACCCG-A-
1 GACCCGAAT
5251 -ACCC-AGAT
1 GACCCGA-AT
5259 GACCCG--T
1 GACCCGAAT
*
5266 AACCCGAAT
1 GACCCGAAT
5275 GACCCGAA
1 GACCCGAA
5283 AAAACTGCAT
Statistics
Matches: 56, Mismatches: 4, Indels: 22
0.68 0.05 0.27
Matches are distributed among these distances:
6 4 0.07
7 18 0.32
8 5 0.09
9 29 0.52
ACGTcount: A:0.33, C:0.36, G:0.23, T:0.09
Consensus pattern (9 bp):
GACCCGAAT
Found at i:5218 original size:16 final size:16
Alignment explanation
Indices: 5196--5281 Score: 124
Period size: 16 Copynumber: 5.4 Consensus size: 16
5186 AGACCTGGTA
5196 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
*
5212 GATCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
5228 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
5244 GACCCGA-ACCC-AGAT
1 GACCCGAGACCCGA-AT
5259 GACCCGTA-ACCCGAAT
1 GACCCG-AGACCCGAAT
5275 GACCCGA
1 GACCCGA
5282 AAAAACTGCA
Statistics
Matches: 65, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
14 1 0.02
15 13 0.20
16 50 0.77
17 1 0.02
ACGTcount: A:0.31, C:0.37, G:0.23, T:0.08
Consensus pattern (16 bp):
GACCCGAGACCCGAAT
Found at i:5264 original size:31 final size:31
Alignment explanation
Indices: 5196--5282 Score: 124
Period size: 31 Copynumber: 2.8 Consensus size: 31
5186 AGACCTGGTA
*
5196 GACCCGAGACCCGAATGATCCGAGACCCGAAT
1 GACCCGAGACCCGAATGACCCGA-ACCCGAAT
5228 GACCCGAGACCCGAATGACCCGAACCC-AGAT
1 GACCCGAGACCCGAATGACCCGAACCCGA-AT
5259 GACCCGTA-ACCCGAATGACCCGAA
1 GACCCG-AGACCCGAATGACCCGAA
5283 AAAACTGCAT
Statistics
Matches: 52, Mismatches: 1, Indels: 5
0.90 0.02 0.09
Matches are distributed among these distances:
30 1 0.02
31 28 0.54
32 23 0.44
ACGTcount: A:0.32, C:0.37, G:0.23, T:0.08
Consensus pattern (31 bp):
GACCCGAGACCCGAATGACCCGAACCCGAAT
Found at i:9224 original size:230 final size:230
Alignment explanation
Indices: 8821--9278 Score: 864
Period size: 230 Copynumber: 2.0 Consensus size: 230
8811 CTAAGACTTA
8821 TCCTTTCAAAACAAGAAAAGTGAATTTTCCCTAATGAAGTTCATTCAAAACAAGGAACCGATCCC
1 TCCTTTCAAAACAAGAAAAGTGAATTTTCCCTAATGAAGTTCATTCAAAACAAGGAACCGATCCC
* *
8886 AATAATAATGCAAATGAGCAAGTAACCAAAAACTATCCCTATAAACAGCCAATACCTCACATTTG
66 AATAATAATGCAAATAAGCAAGTAACCAAAAACTATCCCTATAAACAACCAATACCTCACATTTG
*
8951 CTAAACTCAAGCTGACATCAATAAATTAAATCAAAGCAGGAAAGGACATTAAATTAAGTGATAAT
131 CTAAACTCAAGCTGACATCAATAAATCAAATCAAAGCAGGAAAGGACATTAAATTAAGTGATAAT
9016 TACACATGATTTTGATCTTTGTATCATCTGAATTT
196 TACACATGATTTTGATCTTTGTATCATCTGAATTT
9051 TCCTTTCAAAACAAGAAAAGTGAATTTTCCCTAATGAAGTTCATTCAAAACAAGGAACCGATCCC
1 TCCTTTCAAAACAAGAAAAGTGAATTTTCCCTAATGAAGTTCATTCAAAACAAGGAACCGATCCC
*
9116 AATAA-ATATGCAAATAAGCAAGTAACCAAAAACTATCCCTATAAACAACCAATACCTGACATTT
66 AATAATA-ATGCAAATAAGCAAGTAACCAAAAACTATCCCTATAAACAACCAATACCTCACATTT
9180 GCTAAACTCAAGCTGACATCAATAAATCAAATCAAAGCAGGAAAGGACATTAAATTAAGTGATAA
130 GCTAAACTCAAGCTGACATCAATAAATCAAATCAAAGCAGGAAAGGACATTAAATTAAGTGATAA
9245 TTACACATGATTTTGATCTTTGTATCATCTGAAT
195 TTACACATGATTTTGATCTTTGTATCATCTGAAT
9279 GGTGAACATT
Statistics
Matches: 223, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
229 1 0.00
230 222 1.00
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (230 bp):
TCCTTTCAAAACAAGAAAAGTGAATTTTCCCTAATGAAGTTCATTCAAAACAAGGAACCGATCCC
AATAATAATGCAAATAAGCAAGTAACCAAAAACTATCCCTATAAACAACCAATACCTCACATTTG
CTAAACTCAAGCTGACATCAATAAATCAAATCAAAGCAGGAAAGGACATTAAATTAAGTGATAAT
TACACATGATTTTGATCTTTGTATCATCTGAATTT
Found at i:17982 original size:25 final size:24
Alignment explanation
Indices: 17947--18005 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 24
17937 TTCAAACCCT
* *
17947 AAACTTAATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAA-ATCTTC
*
17972 AAACTTCATTTTTAACAAATCTTC
1 AAACTTCATTTCTAACAAATCTTC
17996 AAA-TTCATTT
1 AAACTTCATTT
18006 TCCTTCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 7 0.23
24 8 0.26
25 16 0.52
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.42
Consensus pattern (24 bp):
AAACTTCATTTCTAACAAATCTTC
Found at i:18044 original size:26 final size:26
Alignment explanation
Indices: 18015--18082 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
18005 TTCCTTCATT
18015 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
18041 TTAATAATAAACTAATTATATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
18067 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
18083 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:18082 original size:15 final size:14
Alignment explanation
Indices: 18021--18113 Score: 58
Period size: 11 Copynumber: 7.1 Consensus size: 14
18011 CATTTTAATC
18021 ATAAACTAATT-AA
1 ATAAACTAATTAAA
18034 AT--ACTAATTAATA
1 ATAAACTAATTAA-A
18047 ATAAACTAATT---
1 ATAAACTAATTAAA
*
18058 ATATACTAATTAAA
1 ATAAACTAATTAAA
18072 CATAAACTAA-TAAA
1 -ATAAACTAATTAAA
* * **
18086 CT-AAGTAATTTTA
1 ATAAACTAATTAAA
*
18099 ATTAACTAATTAAA
1 ATAAACTAATTAAA
18113 A
1 A
18114 CTAATCATAA
Statistics
Matches: 60, Mismatches: 10, Indels: 19
0.67 0.11 0.21
Matches are distributed among these distances:
11 17 0.28
12 6 0.10
13 9 0.15
14 13 0.22
15 15 0.25
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (14 bp):
ATAAACTAATTAAA
Found at i:18106 original size:52 final size:51
Alignment explanation
Indices: 18015--18132 Score: 122
Period size: 52 Copynumber: 2.4 Consensus size: 51
18005 TTCCTTCATT
* *
18015 TTAATCATAAACTAATTAAATACTAATTAATAATAAACTAATTATATACTAA
1 TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTA-AAACTAA
* * *
18067 TTAAACATAAACTAA-TAAACTAAGTAATT-TTAATTAACTAATTAAAACTAA
1 TTAAACATAAACTAATTAAA-T-ACTAATTAATAATAAACTAATTAAAACTAA
18118 -T---CATAAACTAATTAA
1 TTAAACATAAACTAATTAA
18133 TATTAAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
47 10 0.17
48 3 0.05
50 1 0.02
51 10 0.17
52 28 0.48
53 6 0.10
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.35
Consensus pattern (51 bp):
TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTAAAACTAA
Found at i:23920 original size:48 final size:48
Alignment explanation
Indices: 23803--23986 Score: 262
Period size: 48 Copynumber: 3.8 Consensus size: 48
23793 CTCGGTTCTC
* * ** * * *
23803 CCCAAAACGCCCTTCCCGGACGGAAGCCGTTTATCTTTACTTGCTCTTT
1 CCCAAAACGCCATTCCCGGACGGAAGGCACTAATCTTTACCTG-TTTTT
* *
23852 CCCAAAACGCCCTTCCCGGACGGAAGGCACTGAT-TATTACCTGTTTTT
1 CCCAAAACGCCATTCCCGGACGGAAGGCACTAATCT-TTACCTGTTTTT
23900 CCCAAAACGCCATTCCCGGACGGAAGGCACTAATCTTTACCTGTTTTT
1 CCCAAAACGCCATTCCCGGACGGAAGGCACTAATCTTTACCTGTTTTT
23948 CCCAAAACGCCATTCCCGGACGGAAGGCACTAATCTTTA
1 CCCAAAACGCCATTCCCGGACGGAAGGCACTAATCTTTA
23987 AATGCCCTTC
Statistics
Matches: 125, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
48 88 0.70
49 37 0.30
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (48 bp):
CCCAAAACGCCATTCCCGGACGGAAGGCACTAATCTTTACCTGTTTTT
Found at i:23978 original size:96 final size:97
Alignment explanation
Indices: 23803--23978 Score: 273
Period size: 97 Copynumber: 1.8 Consensus size: 97
23793 CTCGGTTCTC
* ** * * *
23803 CCCAAAACGCCCTTCCCGGACGGAAGCCGTTTATCTTTACTTGCTCTTTCCCAAAACGCCCTTCC
1 CCCAAAACGCCATTCCCGGACGGAAGCCACTAATCTTTACCTGCTCTTTCCCAAAACGCCATTCC
23868 CGGACGGAAGGCACTGATTATTACCTGTTTTT
66 CGGACGGAAGGCACTGATTATTACCTGTTTTT
* *
23900 CCCAAAACGCCATTCCCGGACGGAAGGCACTAATCTTTACCTG-TTTTTCCCAAAACGCCATTCC
1 CCCAAAACGCCATTCCCGGACGGAAGCCACTAATCTTTACCTGCTCTTTCCCAAAACGCCATTCC
23964 CGGACGGAAGGCACT
66 CGGACGGAAGGCACT
23979 AATCTTTAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
96 34 0.48
97 37 0.52
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (97 bp):
CCCAAAACGCCATTCCCGGACGGAAGCCACTAATCTTTACCTGCTCTTTCCCAAAACGCCATTCC
CGGACGGAAGGCACTGATTATTACCTGTTTTT
Found at i:24043 original size:49 final size:48
Alignment explanation
Indices: 23986--24204 Score: 183
Period size: 49 Copynumber: 4.5 Consensus size: 48
23976 ACTAATCTTT
*
23986 AAATGCCCTTCCCGGACGGAAGGCACTTA-TTTTACTTGTTATTTTCCAA
1 AAATGCCCTTCCCGGACGGAAGGC-CTTATTTTTACTTGCT-TTTTCCAA
* * *
24035 AAATGCCCTTCCCGGACGGGAGAGG-CTTATTTTTACCTACTTTTTCCCA
1 AAATGCCCTTCCCGGAC-GGA-AGGCCTTATTTTTACTTGCTTTTTCCAA
* * *
24084 AAGTGCCCTTCCCGGAC-GAAGGGCGCTAATTTTTACTTGCTTTTTCCTA
1 AAATGCCCTTCCCGGACGGAA-GGC-CTTATTTTTACTTGCTTTTTCCAA
* * * * ** * ***
24133 AAACGCCCTTCCCGGATGGAAGACGTTGGTTTTACTCGCTTTTTATTA
1 AAATGCCCTTCCCGGACGGAAGGCCTTATTTTTACTTGCTTTTTCCAA
** *
24181 AAATGCCCTTTTCGGACGAAAGGC
1 AAATGCCCTTCCCGGACGGAAGGC
24205 AAGTTCGCTT
Statistics
Matches: 137, Mismatches: 26, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
46 1 0.01
47 4 0.03
48 35 0.26
49 80 0.58
50 14 0.10
51 3 0.02
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.33
Consensus pattern (48 bp):
AAATGCCCTTCCCGGACGGAAGGCCTTATTTTTACTTGCTTTTTCCAA
Found at i:24072 original size:131 final size:129
Alignment explanation
Indices: 23860--24105 Score: 318
Period size: 131 Copynumber: 1.9 Consensus size: 129
23850 TTCCCAAAAC
*
23860 GCCCTTCCCGGACGGAAGGCACTGATTATTACCTGTTTTTCCCAAAACGCCATTCCCGGACGGAA
1 GCCCTTCCCGGACGGAAGGCACTGATTATTACCTGTTTTTCCAAAAACGCCATTCCCGGACGGAA
*
23925 GGCACTAATCTTTACCT-GTTTTTCCCAAAACGCCATTCCCGGACGGAAGGCACTAATCTTTAAA
66 GG-ACTAATCTTTACCTACTTTTTCCCAAAACGCCATTCCCGGAC-GAAGGCACTAATCTTTAAA
23989 T
129 T
* * * *
23990 GCCCTTCCCGGACGGAAGGCACTTATT-TTACTTGTTATTTTCCAAAAATGCCCTTCCCGGACGG
1 GCCCTTCCCGGACGGAAGGCACTGATTATTACCTG-T-TTTTCCAAAAACGCCATTCCCGGAC-G
* * ** *
24054 GAGAGG-CTTATTTTTACCTACTTTTTCCCAAAGTGCCCTTCCCGGACGAAGG
63 GA-AGGACTAATCTTTACCTACTTTTTCCCAAAACGCCATTCCCGGACGAAGG
24106 GCGCTAATTT
Statistics
Matches: 100, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
129 6 0.06
130 27 0.27
131 38 0.38
132 26 0.26
133 3 0.03
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (129 bp):
GCCCTTCCCGGACGGAAGGCACTGATTATTACCTGTTTTTCCAAAAACGCCATTCCCGGACGGAA
GGACTAATCTTTACCTACTTTTTCCCAAAACGCCATTCCCGGACGAAGGCACTAATCTTTAAAT
Found at i:25074 original size:70 final size:70
Alignment explanation
Indices: 24981--25138 Score: 235
Period size: 70 Copynumber: 2.3 Consensus size: 70
24971 CGAATGCTTT
* * *
24981 GGCTTTTCCATAAGTCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAAGCAA
1 GGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGTCAGATCAAGATTTGGTTCCATCCAAGCAA
25046 GCAGA
66 GCAGA
* * * *
25051 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGATTTGGTTCCATCCAAGCAT
1 GGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGTCAGATCAAGATTTGGTTCCATCCAAGCAA
* *
25116 TCAGG
66 GCAGA
25121 GGCTTTTCCATAAGCCAA
1 GGCTTTTCCATAAGCCAA
25139 GTTCAGTGAG
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 79 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (70 bp):
GGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGTCAGATCAAGATTTGGTTCCATCCAAGCAA
GCAGA
Found at i:25369 original size:49 final size:47
Alignment explanation
Indices: 25248--25386 Score: 233
Period size: 47 Copynumber: 2.9 Consensus size: 47
25238 ATCCGGGCAA
*
25248 TCTTCTCTCGCTTCCAGGCGAGTTTTCAATTTAGTGACCAAAGATGG
1 TCTTCTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
* *
25295 TCTTCTCTCGCTTCCACGCGAGTTTTCAATTTGGAGACCAAAGATGG
1 TCTTCTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
25342 TCTTTTCTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAG
1 TC--TTCTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAG
25387 TGTCGCAACG
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
47 46 0.54
49 39 0.46
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (47 bp):
TCTTCTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
Found at i:25803 original size:21 final size:22
Alignment explanation
Indices: 25776--25842 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
25766 AATCGACTAC
25776 TAGGTTAAGCCATTTATTTACT
1 TAGGTTAAGCCATTTATTTACT
* *
25798 TA-GTTACA-CCGAATTGA-CTAC-
1 TAGGTTA-AGCC--ATTTATTTACT
25819 TAGGTTAAGCCATTTATTTACT
1 TAGGTTAAGCCATTTATTTACT
25841 TA
1 TA
25843 ATTGCACCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
20 4 0.12
21 12 0.35
22 14 0.41
23 4 0.12
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40
Consensus pattern (22 bp):
TAGGTTAAGCCATTTATTTACT
Found at i:25818 original size:43 final size:43
Alignment explanation
Indices: 25770--25857 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
25760 ATTCTTAATC
*
25770 GACTACTAGGTTAAGCCATTTATTTACTTAGTTACACCGAATT
1 GACTACTAGGTTAAGCCATTTATTTACTTAATTACACCGAATT
*
25813 GACTACTAGGTTAAGCCATTTATTTACTTAATTGCACCGAATT
1 GACTACTAGGTTAAGCCATTTATTTACTTAATTACACCGAATT
25856 GA
1 GA
25858 GTTAATTACT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (43 bp):
GACTACTAGGTTAAGCCATTTATTTACTTAATTACACCGAATT
Found at i:25887 original size:21 final size:21
Alignment explanation
Indices: 25861--25915 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
25851 GAATTGAGTT
*
25861 AATTACTTAATTTAACTACCA
1 AATTACTTAATTAAACTACCA
*
25882 AATTACTTAACTTAAATTACCA
1 AATTACTTAA-TTAAACTACCA
* *
25904 ATTTTCTTAATT
1 AATTACTTAATT
25916 GCACCGAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTACTTAATTAAACTACCA
Found at i:25954 original size:21 final size:21
Alignment explanation
Indices: 25930--25970 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
25920 CGAATTAAGT
25930 TAATTACCAAATTACTTAATC
1 TAATTACCAAATTACTTAATC
* *
25951 TAATTATCAAATTGCTTAAT
1 TAATTACCAAATTACTTAAT
25971 TACACTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.02, T:0.41
Consensus pattern (21 bp):
TAATTACCAAATTACTTAATC
Found at i:25981 original size:56 final size:57
Alignment explanation
Indices: 25867--26000 Score: 173
Period size: 56 Copynumber: 2.4 Consensus size: 57
25857 AGTTAATTAC
* * * * *
25867 TTAATTTAACTACCAAATTACTTAACTTAAATTACCAATTTTCTTAATTGCACCGAA
1 TTAAGTTAATTACCAAATTACTTAACTTAAATTACCAAATTGCTTAATTACACCGAA
* *
25924 TTAAGTTAATTACCAAATTACTTAA-TCT-AATTATCAAATTGCTTAATTACACTGAA
1 TTAAGTTAATTACCAAATTACTTAACT-TAAATTACCAAATTGCTTAATTACACCGAA
*
25980 TTAAGTTGATTACCAAATTAC
1 TTAAGTTAATTACCAAATTAC
26001 CAATTTACTT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
56 44 0.65
57 24 0.35
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.39
Consensus pattern (57 bp):
TTAAGTTAATTACCAAATTACTTAACTTAAATTACCAAATTGCTTAATTACACCGAA
Found at i:25999 original size:43 final size:43
Alignment explanation
Indices: 25965--26414 Score: 542
Period size: 43 Copynumber: 9.8 Consensus size: 43
25955 TATCAAATTG
* *
25965 CTTAATTACACTGAATTAAGTTGATTACCAAATTACCAATTTA
1 CTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTA
*
26008 CTTAATTACATCGAATTAAGTTGTTTACCAAATTACCAATTTA
1 CTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTA
* *
26051 CTTAATTACACCGAATTAAGTTGTTTACTAGATTACCAATTTA
1 CTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTA
26094 CTTAATTACACCGAATTAAGTTGTTTACCAAATTACTTAATTTAATCACCAATTTA
1 CTTAATTACACCGAATTAAGTTGTTTACC-----A---AA--T--T-ACCAATTTA
26150 CTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTA
1 CTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTA
*
26193 CTTAATTACACCGAATTAAGTTGTTTACCAGATTACCAATTTA
1 CTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTA
26236 CTTAATTACACCGAATTAAAGTTGTTTACCAAATTACTTAATTTAATCACCAATTTA
1 CTTAATTACACCGAATT-AAGTTGTTTACC-----A---AA--T--T-ACCAATTTA
*
26293 CTTAATTACACCGAATTAAGTTGCTTA-CAATATTACCAATTTA
1 CTTAATTACACCGAATTAAGTTGTTTACCAA-ATTACCAATTTA
* **
26336 CTTAATTACACCGAATTAAGTTGTTTATCTGATTACCAATTTA
1 CTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTA
*
26379 CTTAATTACACCGAATTAAGTTATTTACCAAATTAC
1 CTTAATTACACCGAATTAAGTTGTTTACCAAATTAC
26415 TTAATTTAAT
Statistics
Matches: 360, Mismatches: 18, Indels: 58
0.83 0.04 0.13
Matches are distributed among these distances:
43 255 0.71
44 15 0.04
46 2 0.01
47 1 0.00
48 4 0.01
49 1 0.00
50 1 0.00
51 2 0.01
52 1 0.00
53 1 0.00
54 1 0.00
55 2 0.01
56 48 0.13
57 26 0.07
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (43 bp):
CTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTA
Found at i:26145 original size:142 final size:141
Alignment explanation
Indices: 25999--26497 Score: 834
Period size: 142 Copynumber: 3.6 Consensus size: 141
25989 TTACCAAATT
*
25999 ACCAATTTACTTAATTACATCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTACACCG
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTA-CAAATTACCAATTTACTTAATTACACCG
26064 AATTAAGTTGTTTACTAGATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTA
65 AATTAAGTTGTTTACTAGATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTA
26129 CTTAATTTAATC
130 CTTAATTTAATC
26141 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTACACCG
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTA-CAAATTACCAATTTACTTAATTACACCG
*
26206 AATTAAGTTGTTTACCAGATTACCAATTTACTTAATTACACCGAATTAAAGTTGTTTACCAAATT
65 AATTAAGTTGTTTACTAGATTACCAATTTACTTAATTACACCGAATT-AAGTTGTTTACCAAATT
26271 ACTTAATTTAATC
129 ACTTAATTTAATC
*
26284 ACCAATTTACTTAATTACACCGAATTAAGTTGCTTACAATATTACCAATTTACTTAATTACACCG
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACAA-ATTACCAATTTACTTAATTACACCG
*
26349 AATTAAGTTGTTTATCT-GATTACCAATTTACTTAATTACACCGAATTAAGTTATTTACCAAATT
65 AATTAAGTTGTTTA-CTAGATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
26413 ACTTAATTTAATC
129 ACTTAATTTAATC
**
26426 ACCAATTTACTTAATTACATTGAATTAAGTTG-------ATTACCAATTTACTTAATTACACCGA
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACAAATTACCAATTTACTTAATTACACCGA
*
26484 ATTAAGTTGATTAC
66 ATTAAGTTGTTTAC
26498 CAACTGATTT
Statistics
Matches: 346, Mismatches: 8, Indels: 15
0.94 0.02 0.04
Matches are distributed among these distances:
133 1 0.00
134 38 0.11
142 172 0.50
143 134 0.39
144 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (141 bp):
ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACAAATTACCAATTTACTTAATTACACCGA
ATTAAGTTGTTTACTAGATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTAC
TTAATTTAATC
Found at i:26418 original size:21 final size:21
Alignment explanation
Indices: 26394--26439 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
26384 TTACACCGAA
* *
26394 TTAAGTTATTTACCAAATTAC
1 TTAAGTTAATCACCAAATTAC
* *
26415 TTAATTTAATCACCAATTTAC
1 TTAAGTTAATCACCAAATTAC
26436 TTAA
1 TTAA
26440 TTACATTGAA
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:0.39, C:0.15, G:0.02, T:0.43
Consensus pattern (21 bp):
TTAAGTTAATCACCAAATTAC
Found at i:26432 original size:56 final size:56
Alignment explanation
Indices: 26370--26476 Score: 171
Period size: 56 Copynumber: 1.9 Consensus size: 56
26360 TTATCTGATT
26370 ACCAATTTACTTAATTACACCGAATTAAGTT-ATTTACCAAATTACTTAATTTAATC
1 ACCAATTTACTTAATTACACCGAATTAAGTTGA-TTACCAAATTACTTAATTTAATC
** *
26426 ACCAATTTACTTAATTACATTGAATTAAGTTGATTACCAATTTACTTAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATT
26477 ACACCGAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
56 46 0.98
57 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (56 bp):
ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
Found at i:26465 original size:35 final size:35
Alignment explanation
Indices: 26426--26500 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
26416 TAATTTAATC
**
26426 ACCAATTTACTTAATTACATTGAATTAAGTTGATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATT
26461 ACCAATTTACTTAATTACACCGAATTAAGTTGATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATT
26496 ACCAA
1 ACCAA
26501 CTGATTTAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (35 bp):
ACCAATTTACTTAATTACACCGAATTAAGTTGATT
Found at i:26496 original size:19 final size:19
Alignment explanation
Indices: 26447--26497 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
26437 TAATTACATT
26447 GAATTAAGTTGATT--ACC
1 GAATTAAGTTGATTACACC
* * *
26464 -AATTTACTTAATTACACC
1 GAATTAAGTTGATTACACC
26482 GAATTAAGTTGATTAC
1 GAATTAAGTTGATTAC
26498 CAACTGATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
16 10 0.40
18 3 0.12
19 12 0.48
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (19 bp):
GAATTAAGTTGATTACACC
Found at i:27518 original size:50 final size:49
Alignment explanation
Indices: 27452--27584 Score: 158
Period size: 50 Copynumber: 2.7 Consensus size: 49
27442 AAAAAAGATT
* * * * *
27452 CCAATTTTTTATTCAAAGGTTACATCTTTATTTACTAATTACTATAAAAA
1 CCAATCTTTTACTCAAAGGTGACATTTTTATTTACCAATTACTA-AAAAA
* * *
27502 CCAATCTTTTGCTCAAAGGTGACATTTTTACTTACCAATTACTAAAAAT
1 CCAATCTTTTACTCAAAGGTGACATTTTTATTTACCAATTACTAAAAAA
* * *
27551 TCAATCTTTTACCCAAAGATGACATTTTTATTTA
1 CCAATCTTTTACTCAAAGGTGACATTTTTATTTA
27585 AGTTATTTAA
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
49 33 0.47
50 37 0.53
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.41
Consensus pattern (49 bp):
CCAATCTTTTACTCAAAGGTGACATTTTTATTTACCAATTACTAAAAAA
Found at i:27574 original size:49 final size:50
Alignment explanation
Indices: 27473--27580 Score: 137
Period size: 49 Copynumber: 2.2 Consensus size: 50
27463 TTCAAAGGTT
* * * * * *
27473 ACATCTTTATTTACTAATTACTATAAAAACCAATCTTTTGCTCAAAGGTG
1 ACATTTTTACTTACCAATTACTATAAAAACCAATCTTTTACCCAAAGATG
**
27523 ACATTTTTACTTACCAATTACTA-AAAATTCAATCTTTTACCCAAAGATG
1 ACATTTTTACTTACCAATTACTATAAAAACCAATCTTTTACCCAAAGATG
27572 ACATTTTTA
1 ACATTTTTA
27581 TTTAAGTTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
49 30 0.60
50 20 0.40
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.39
Consensus pattern (50 bp):
ACATTTTTACTTACCAATTACTATAAAAACCAATCTTTTACCCAAAGATG
Found at i:28492 original size:23 final size:23
Alignment explanation
Indices: 28466--28510 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
28456 AGGTATCCTC
*
28466 TTTTACTAGCTTTTTGTATTTTT
1 TTTTACAAGCTTTTTGTATTTTT
* **
28489 TTTTCCAATTTTTTTGTATTTT
1 TTTTACAAGCTTTTTGTATTTT
28511 CTTCCAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.13, C:0.09, G:0.07, T:0.71
Consensus pattern (23 bp):
TTTTACAAGCTTTTTGTATTTTT
Found at i:28515 original size:21 final size:22
Alignment explanation
Indices: 28476--28517 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
28466 TTTTACTAGC
*
28476 TTTTTGTATTTTTTTTTCCAATT
1 TTTTTGTA-TTTTTCTTCCAATT
28499 TTTTTGTA-TTTTCTTCCAA
1 TTTTTGTATTTTTCTTCCAA
28518 AAAAAATCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
23 8 0.44
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
TTTTTGTATTTTTCTTCCAATT
Found at i:30606 original size:28 final size:27
Alignment explanation
Indices: 30539--30616 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
30529 CCTAAATGCC
* *
30539 AAAATGACCTAAATGCCCCTGGATGTG
1 AAAATGACCAAAATGCCCCTGGGTGTG
30566 AAAATGACCAAAATGCCCCTGGGTG-G
1 AAAATGACCAAAATGCCCCTGGGTGTG
*
30592 AAAAAATGACCAAAATGCCCTTGGG
1 --AAAATGACCAAAATGCCCCTGGG
30617 CGACCCTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 1 0.02
27 23 0.50
28 22 0.48
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGGGTGTG
Done.