Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009923.1 Corchorus capsularis cultivar CVL-1 contig09944, 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: 52808
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Found at i:3856 original size:48 final size:49
Alignment explanation
Indices: 3797--3895 Score: 191
Period size: 48 Copynumber: 2.0 Consensus size: 49
3787 CTACCAAGGA
3797 TTGGACTTTGTATGAACATTTCTGCTTCTTTCTCTGTCAGAAATAATCC
1 TTGGACTTTGTATGAACATTTCTGCTTCTTTCTCTGTCAGAAATAATCC
3846 TTGGA-TTTGTATGAACATTTCTGCTTCTTTCTCTGTCAGAAATAATCC
1 TTGGACTTTGTATGAACATTTCTGCTTCTTTCTCTGTCAGAAATAATCC
3894 TT
1 TT
3896 TGCCATACAG
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 45 0.90
49 5 0.10
ACGTcount: A:0.22, C:0.19, G:0.14, T:0.44
Consensus pattern (49 bp):
TTGGACTTTGTATGAACATTTCTGCTTCTTTCTCTGTCAGAAATAATCC
Found at i:4994 original size:6 final size:6
Alignment explanation
Indices: 4983--5010 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
4973 GAATAGTTAC
4983 GGGGTT GGGGTT GGGGTT GGGGTT GGGG
1 GGGGTT GGGGTT GGGGTT GGGGTT GGGG
5011 AACAGTGCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.71, T:0.29
Consensus pattern (6 bp):
GGGGTT
Found at i:10968 original size:14 final size:14
Alignment explanation
Indices: 10951--11017 Score: 58
Period size: 12 Copynumber: 5.3 Consensus size: 14
10941 ACATGTATAC
10951 ATATATATATGTAT
1 ATATATATATGTAT
10965 ATATAT-TA-G-AT
1 ATATATATATGTAT
*
10976 ATA-AT-TATCTAT
1 ATATATATATGTAT
10988 ATATA-A-ATGTAT
1 ATATATATATGTAT
* *
11000 ATGTATACATGTAT
1 ATATATATATGTAT
11014 ATAT
1 ATAT
11018 TATGTATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 4 0.09
11 5 0.12
12 15 0.35
13 4 0.09
14 15 0.35
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.46
Consensus pattern (14 bp):
ATATATATATGTAT
Found at i:11157 original size:2 final size:2
Alignment explanation
Indices: 11152--11194 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
11142 TTTGTTCATT
*
11152 TA TA TA TA TA TA TA TA TA TA -A TA TA CA 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
11193 TA
1 TA
11195 CTAGCTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:11360 original size:40 final size:40
Alignment explanation
Indices: 11281--11372 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
11271 TTTTTATGTT
* *
11281 AAATTATGATAATTACACTATTTTTTATAATTTTCTTATG
1 AAATTATGATAATTACACTATTTTTTATAAGTCTCTTATG
*
11321 AAATTATGATAATTACACTATTTTTTATGACGTCT-TTATG
1 AAATTATGATAATTACACTATTTTTTAT-AAGTCTCTTATG
*
11361 AAATTTTGATAA
1 AAATTATGATAA
11373 CCTTCCTATG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
40 44 0.94
41 3 0.06
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (40 bp):
AAATTATGATAATTACACTATTTTTTATAAGTCTCTTATG
Found at i:11617 original size:22 final size:22
Alignment explanation
Indices: 11592--11895 Score: 86
Period size: 22 Copynumber: 14.1 Consensus size: 22
11582 TGAATTGTCA
*
11592 ATAATCACACTCTGAAATTTTG
1 ATAATCACACTATGAAATTTTG
* *
11614 ATAATCATACTATGAAATTGTG
1 ATAATCACACTATGAAATTTTG
* * *
11636 ATAACCTCGCTATGAAATTTTG
1 ATAATCACACTATGAAATTTTG
* * * *
11658 ATAAAC-CTTCCAATAAAATTTTG
1 ATAATCAC--ACTATGAAATTTTG
* *
11681 ATAA-AACTCCT-TGTAAAATTTTG
1 ATAATCAC-ACTATG--AAATTTTG
* *
11704 ATAA-C-CTC-ATGAAATCTTG
1 ATAATCACACTATGAAATTTTG
*
11723 ---AT-A-ACTA-CAAATTTTG
1 ATAATCACACTATGAAATTTTG
* * **
11739 ATAACCTC-CGTATGATTTTTTG
1 ATAATCACAC-TATGAAATTTTG
* *
11761 ATAATCTCATTATGAAATTTTG
1 ATAATCACACTATGAAATTTTG
* * * *
11783 TTAATCTCCCTTTGAAATTTTG
1 ATAATCACACTATGAAATTTTG
* *
11805 AT-CTACATACTATGAAATTTTG
1 ATAAT-CACACTATGAAATTTTG
*
11827 ATAA-C-CTTCTTATGAAATTTTG
1 ATAATCAC-AC-TATGAAATTTTG
* * *
11849 A-AAACTAAACTATGAAATTTTA
1 ATAATC-ACACTATGAAATTTTG
* *
11871 ATAACCTTCA-TATGAAATTTTG
1 ATAATC-ACACTATGAAATTTTG
11893 ATA
1 ATA
11896 TCCTCCCTGA
Statistics
Matches: 207, Mismatches: 50, Indels: 50
0.67 0.16 0.16
Matches are distributed among these distances:
16 9 0.04
17 1 0.00
19 8 0.04
20 1 0.00
21 12 0.06
22 142 0.69
23 34 0.16
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.39
Consensus pattern (22 bp):
ATAATCACACTATGAAATTTTG
Found at i:11676 original size:23 final size:23
Alignment explanation
Indices: 11650--11707 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
11640 CCTCGCTATG
*
11650 AAATTTTGATAAACCTTCC-AATA
1 AAATTTTGATAAAAC-TCCTAATA
**
11673 AAATTTTGATAAAACTCCTTGTA
1 AAATTTTGATAAAACTCCTAATA
11696 AAATTTTGATAA
1 AAATTTTGATAA
11708 CCTCATGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 3 0.10
23 28 0.90
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAAACTCCTAATA
Found at i:11739 original size:16 final size:18
Alignment explanation
Indices: 11696--11743 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
11686 ACTCCTTGTA
*
11696 AAATTTTGATAACCTCATG
1 AAATTTTGATAA-CTCATC
*
11715 AAATCTTGATAACT-A-C
1 AAATTTTGATAACTCATC
11731 AAATTTTGATAAC
1 AAATTTTGATAAC
11744 CTCCGTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 2 0.08
19 11 0.42
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (18 bp):
AAATTTTGATAACTCATC
Found at i:11782 original size:44 final size:44
Alignment explanation
Indices: 11731--11893 Score: 152
Period size: 44 Copynumber: 3.7 Consensus size: 44
11721 TGATAACTAC
* **
11731 AAATTTTGATAACCTCCGTATGATTTTTTGATAATCT-CATTATG
1 AAATTTTGATAACCTCCATATGAAATTTTGA-AATCTACATTATG
* * * *
11775 AAATTTTGTTAATCTCCCTTTGAAATTTTG--ATCTACATACTATG
1 AAATTTTGATAACCTCCATATGAAATTTTGAAATCTACAT--TATG
* * * * *
11819 AAATTTTGATAACCTTCTTATGAAATTTTGAAAACTAAACTATG
1 AAATTTTGATAACCTCCATATGAAATTTTGAAATCTACATTATG
* *
11863 AAATTTTAATAACCTTCATATGAAATTTTGA
1 AAATTTTGATAACCTCCATATGAAATTTTGA
11894 TATCCTCCCT
Statistics
Matches: 98, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
41 4 0.04
42 3 0.03
44 86 0.88
46 5 0.05
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (44 bp):
AAATTTTGATAACCTCCATATGAAATTTTGAAATCTACATTATG
Found at i:17053 original size:15 final size:15
Alignment explanation
Indices: 17033--17061 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17023 TGTAACATTC
17033 GCGACACCCGCAACT
1 GCGACACCCGCAACT
17048 GCGACACCCGCAAC
1 GCGACACCCGCAAC
17062 CGCGTCCGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.48, G:0.21, T:0.03
Consensus pattern (15 bp):
GCGACACCCGCAACT
Found at i:22064 original size:18 final size:18
Alignment explanation
Indices: 22041--22078 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
22031 AGAGCTGCAA
*
22041 GAAGAATAGAGAATTAAG
1 GAAGAATAAAGAATTAAG
*
22059 GAAGAATAAAGATTTAAG
1 GAAGAATAAAGAATTAAG
22077 GA
1 GA
22079 CAATGGGACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.18
Consensus pattern (18 bp):
GAAGAATAAAGAATTAAG
Found at i:22664 original size:19 final size:19
Alignment explanation
Indices: 22637--22674 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
22627 AAGCTGTTGT
22637 TGAAAAAGATGTTGAAGGA
1 TGAAAAAGATGTTGAAGGA
*
22656 TGAAGAAGATGTTGAAGGA
1 TGAAAAAGATGTTGAAGGA
22675 GATTTTTCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.34, T:0.21
Consensus pattern (19 bp):
TGAAAAAGATGTTGAAGGA
Found at i:23009 original size:17 final size:17
Alignment explanation
Indices: 22983--23017 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
22973 CAGCCGCCGC
*
22983 TTCTTGAACCCTAACGT
1 TTCTTAAACCCTAACGT
23000 TTCTTAAACCCTAACGT
1 TTCTTAAACCCTAACGT
23017 T
1 T
23018 CAGGGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.37
Consensus pattern (17 bp):
TTCTTAAACCCTAACGT
Found at i:23150 original size:76 final size:76
Alignment explanation
Indices: 23024--23178 Score: 310
Period size: 76 Copynumber: 2.0 Consensus size: 76
23014 CGTTCAGGGA
23024 AAATAATACAACAAAGTGTAAAAGAGTGTAAAGAGATTAAAAATGATTGATTTGTAAGGTAAATG
1 AAATAATACAACAAAGTGTAAAAGAGTGTAAAGAGATTAAAAATGATTGATTTGTAAGGTAAATG
23089 AAAATTGGTGG
66 AAAATTGGTGG
23100 AAATAATACAACAAAGTGTAAAAGAGTGTAAAGAGATTAAAAATGATTGATTTGTAAGGTAAATG
1 AAATAATACAACAAAGTGTAAAAGAGTGTAAAGAGATTAAAAATGATTGATTTGTAAGGTAAATG
23165 AAAATTGGTGG
66 AAAATTGGTGG
23176 AAA
1 AAA
23179 AAAAAAGGAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 79 1.00
ACGTcount: A:0.50, C:0.03, G:0.22, T:0.26
Consensus pattern (76 bp):
AAATAATACAACAAAGTGTAAAAGAGTGTAAAGAGATTAAAAATGATTGATTTGTAAGGTAAATG
AAAATTGGTGG
Found at i:23649 original size:12 final size:12
Alignment explanation
Indices: 23634--23658 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23624 CTGGAGGTGT
23634 TGTTGAAGGAGA
1 TGTTGAAGGAGA
23646 TGTTGAAGGAGA
1 TGTTGAAGGAGA
23658 T
1 T
23659 CTTTTCCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.40, T:0.28
Consensus pattern (12 bp):
TGTTGAAGGAGA
Found at i:24228 original size:20 final size:18
Alignment explanation
Indices: 24203--24242 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
24193 AGAGCTGCAA
24203 GAAGAATAGAGAAATTTAAG
1 GAAGAATA-A-AAATTTAAG
*
24223 GAAGAATAAAGATTTAAG
1 GAAGAATAAAAATTTAAG
24241 GA
1 GA
24243 CAATGGGACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 1 0.05
20 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.20
Consensus pattern (18 bp):
GAAGAATAAAAATTTAAG
Found at i:24849 original size:12 final size:12
Alignment explanation
Indices: 24828--24853 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
24818 GATGAAGAAC
24828 ATGTTGAAGGAG
1 ATGTTGAAGGAG
24840 ATGTTGAAGGAG
1 ATGTTGAAGGAG
24852 AT
1 AT
24854 CTTTCCCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.38, T:0.27
Consensus pattern (12 bp):
ATGTTGAAGGAG
Found at i:25184 original size:17 final size:17
Alignment explanation
Indices: 25158--25210 Score: 97
Period size: 17 Copynumber: 3.1 Consensus size: 17
25148 CAGCCGCCGC
*
25158 TTCTTGAACCCTAACGT
1 TTCTTAAACCCTAACGT
25175 TTCTTAAACCCTAACGT
1 TTCTTAAACCCTAACGT
25192 TTCTTAAACCCTAACGT
1 TTCTTAAACCCTAACGT
25209 TT
1 TT
25211 AGGGAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.38
Consensus pattern (17 bp):
TTCTTAAACCCTAACGT
Found at i:25308 original size:76 final size:76
Alignment explanation
Indices: 25216--25370 Score: 274
Period size: 76 Copynumber: 2.0 Consensus size: 76
25206 CGTTTAGGGA
*
25216 AAATAATACAACAAAGTATAAAAGAGTGTAAAGAGATTAAAAATGATTAATTTTTAAGGTAAATG
1 AAATAATACAACAAAGTATAAAAGAGTGTAAAGAGATTAAAAATGATTAATTTGTAAGGTAAATG
25281 AAAATTGGTGG
66 AAAATTGGTGG
* * *
25292 AAATAATACAACAAAGTGTAAAAGTGTGTAAAGAGATTAAAAATGATTGATTTGTAAGGTAAATG
1 AAATAATACAACAAAGTATAAAAGAGTGTAAAGAGATTAAAAATGATTAATTTGTAAGGTAAATG
25357 AAAATTGGTGG
66 AAAATTGGTGG
25368 AAA
1 AAA
25371 AAAAATAAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.50, C:0.03, G:0.20, T:0.27
Consensus pattern (76 bp):
AAATAATACAACAAAGTATAAAAGAGTGTAAAGAGATTAAAAATGATTAATTTGTAAGGTAAATG
AAAATTGGTGG
Found at i:25809 original size:12 final size:13
Alignment explanation
Indices: 25792--25825 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
25782 AAGCATTAGA
25792 GACGGTGTTGCT-
1 GACGGTGTTGCTG
25804 GACGGTGTTGCTG
1 GACGGTGTTGCTG
25817 GA-GGTGTTG
1 GACGGTGTTG
25826 TTGAAGGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 19 0.90
13 2 0.10
ACGTcount: A:0.09, C:0.12, G:0.47, T:0.32
Consensus pattern (13 bp):
GACGGTGTTGCTG
Found at i:26647 original size:25 final size:25
Alignment explanation
Indices: 26607--26660 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
26597 GAGCTGCAAG
26607 AAGAATAAAGAATTAAGGAAGAATA
1 AAGAATAAAGAATTAAGGAAGAATA
* *
26632 AAGAATAAATATTTAAGGAAGAATA
1 AAGAATAAAGAATTAAGGAAGAATA
26657 AAGA
1 AAGA
26661 TTTATGGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.63, C:0.00, G:0.19, T:0.19
Consensus pattern (25 bp):
AAGAATAAAGAATTAAGGAAGAATA
Found at i:27259 original size:12 final size:12
Alignment explanation
Indices: 27244--27305 Score: 71
Period size: 12 Copynumber: 5.6 Consensus size: 12
27234 TTGATGCTGT
*
27244 TGTTGAAAAAGA
1 TGTTGAAGAAGA
27256 TGTTGAAG--GA
1 TGTTGAAGAAGA
27266 --T-GAAGAAGA
1 TGTTGAAGAAGA
*
27275 TGTTGAAGGAGA
1 TGTTGAAGAAGA
27287 TGTTGAAGAAGA
1 TGTTGAAGAAGA
27299 TGTTGAA
1 TGTTGAA
27306 TGAGATCTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
7 4 0.10
8 1 0.02
9 2 0.05
10 2 0.05
11 1 0.02
12 32 0.76
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (12 bp):
TGTTGAAGAAGA
Found at i:27274 original size:19 final size:19
Alignment explanation
Indices: 27247--27284 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
27237 ATGCTGTTGT
27247 TGAAAAAGATGTTGAAGGA
1 TGAAAAAGATGTTGAAGGA
*
27266 TGAAGAAGATGTTGAAGGA
1 TGAAAAAGATGTTGAAGGA
27285 GATGTTGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.34, T:0.21
Consensus pattern (19 bp):
TGAAAAAGATGTTGAAGGA
Found at i:27293 original size:24 final size:23
Alignment explanation
Indices: 27244--27311 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 23
27234 TTGATGCTGT
*
27244 TGTTGAAAAAGATGTTGAAG-GA
1 TGTTGAAGAAGATGTTGAAGAGA
27266 ---TGAAGAAGATGTTGAAGGAGA
1 TGTTGAAGAAGATGTTGAA-GAGA
27287 TGTTGAAGAAGATGTTGAATGAGA
1 TGTTGAAGAAGATGTTGAA-GAGA
27311 T
1 T
27312 CTTTTCCTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
19 15 0.38
20 1 0.03
21 2 0.05
24 21 0.54
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (23 bp):
TGTTGAAGAAGATGTTGAAGAGA
Found at i:27311 original size:12 final size:11
Alignment explanation
Indices: 27266--27311 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 11
27256 TGTTGAAGGA
27266 TGAAGAAGATGT
1 TGAAG-AGATGT
27278 TGAAGGAGATGT
1 TGAA-GAGATGT
27290 TGAAGAAGATGT
1 TGAAG-AGATGT
27302 TGAATGAGAT
1 TGAA-GAGAT
27312 CTTTTCCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 1 0.03
12 28 0.90
13 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.35, T:0.26
Consensus pattern (11 bp):
TGAAGAGATGT
Found at i:27785 original size:76 final size:76
Alignment explanation
Indices: 27659--27810 Score: 277
Period size: 76 Copynumber: 2.0 Consensus size: 76
27649 CATTCAGGGA
*
27659 AAATAATACAACAAAGTGTAAAAGAGTGTAAAGAGATTAAAAATGATTGATTTGTATGGTAAATA
1 AAATAATACAACAAAGTGTAAAAGAGTGTAAAAAGATTAAAAATGATTGATTTGTATGGTAAATA
27724 AAAATTGGTGG
66 AAAATTGGTGG
* *
27735 AAATAATACAACAAAGTGTAAAATAGTGTAAAAAGATTAAAAATGATTGATTTGTATGGTAAATG
1 AAATAATACAACAAAGTGTAAAAGAGTGTAAAAAGATTAAAAATGATTGATTTGTATGGTAAATA
27800 AAAATTGGTGG
66 AAAATTGGTGG
27811 GAAAAAAAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.49, C:0.03, G:0.20, T:0.28
Consensus pattern (76 bp):
AAATAATACAACAAAGTGTAAAAGAGTGTAAAAAGATTAAAAATGATTGATTTGTATGGTAAATA
AAAATTGGTGG
Found at i:28256 original size:12 final size:13
Alignment explanation
Indices: 28241--28272 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
28231 GCGTTGTAGG
28241 CGGTGTTGCT-GA
1 CGGTGTTGCTGGA
28253 CGGTGTTGCTGGA
1 CGGTGTTGCTGGA
28266 -GGTGTTG
1 CGGTGTTG
28273 TTGAAGGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 17 0.89
13 2 0.11
ACGTcount: A:0.06, C:0.12, G:0.47, T:0.34
Consensus pattern (13 bp):
CGGTGTTGCTGGA
Found at i:28286 original size:12 final size:12
Alignment explanation
Indices: 28271--28307 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
28261 CTGGAGGTGT
28271 TGTTGAAGGAGA
1 TGTTGAAGGAGA
*
28283 TGTTGAAGAAGA
1 TGTTGAAGGAGA
28295 TGTTGAAGGAGA
1 TGTTGAAGGAGA
28307 T
1 T
28308 CTTCTCCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.38, T:0.27
Consensus pattern (12 bp):
TGTTGAAGGAGA
Found at i:28777 original size:76 final size:76
Alignment explanation
Indices: 28651--28805 Score: 283
Period size: 76 Copynumber: 2.0 Consensus size: 76
28641 CGTTCAGGGA
* *
28651 AAATAATACTACAAAATGTAAAAGAGTGTAAGGAGATTAAAAATGATTGATTTGTAAGGTAAATG
1 AAATAATACAACAAAATGTAAAAGAGTGTAAAGAGATTAAAAATGATTGATTTGTAAGGTAAATG
28716 AAAATTGGTGG
66 AAAATTGGTGG
*
28727 AAATAATACAACAAAGTGTAAAAGAGTGTAAAGAGATTAAAAATGATTGATTTGTAAGGTAAATG
1 AAATAATACAACAAAATGTAAAAGAGTGTAAAGAGATTAAAAATGATTGATTTGTAAGGTAAATG
28792 AAAATTGGTGG
66 AAAATTGGTGG
28803 AAA
1 AAA
28806 AAAAAGGAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.49, C:0.03, G:0.22, T:0.26
Consensus pattern (76 bp):
AAATAATACAACAAAATGTAAAAGAGTGTAAAGAGATTAAAAATGATTGATTTGTAAGGTAAATG
AAAATTGGTGG
Found at i:29844 original size:925 final size:903
Alignment explanation
Indices: 27735--30797 Score: 3898
Period size: 925 Copynumber: 3.4 Consensus size: 903
27725 AAATTGGTGG
* * *
27735 AAATAATACAACAAAGTGTAAAATAGTGTAAAAAGATTAAAAATGATTGATTTGTATGGTAAATG
1 AAATAATACAACAAAGTGTAAAAGAGTGTAAAGAGATTAAAAATGATTGATTTGTAAGGTAAATG
* * *
27800 AAAATTGGTGGGAAAAAAAAAAGGAAATGTAAATGAGAATGAATTGGGCGGTATAAAATAAGCCC
66 AAAATTGGT-GG-AAAAAAAAAGGAAAGGTAAATGAAAATGAATTGGACGGTATAAAATAAGCCC
* * * * *
27865 AATTATATTTGGGGAAAATGAATTGGGCAGTATAAAATAAGCCCAAGGGGAAAATGAATTGGGCG
129 AATAATATTTGGAGAAAAAGAATT-GGCGGTATAAAATAAGCCCAAGGGGAAAATGAATTAGGCG
* **
27930 ATATAAAATAAGTCGGGCATGGGCACTAAGGTGTTAGGAAAGAAAAATTGGTAAAAATAAGGGAA
193 -TATAAAATAAGCCGGGCATGGGCACTAAAATGTTAGGAAAGAAAAATTGGTAAAAATAAGGGAA
*
27995 AGGTAAATGAAAATGAATTGGGCCCTAAAATTTTGGGCAAGAATAAGAGAAGATTAAACTGGCAT
257 AGG---ATG-AAATGAATTGGGCCCTAAAATTTTGGGCAAGAATAAGAGAAGATTAGACTGGCAT
*
28060 CTAACTAAGCCCAATAATATTTAGTAGAGAGTAAGACAAGATGTCTAGGCTTTCAAGGTGGCCGT
318 CTAACTAAGCCCAATAATATTTAGAAGAGAGTAAGACAAGATGTCTAGGCTTTCAAGGTGGCCGT
** * *
28125 TTGTTAACAGCAACTAACCTTCTCAGTTTGTTGATGTTTTTGTCAGCATGAGGACGAGCAGCTAA
383 TTGTTAGTAGCAACTAACATTCTCAGTTTGTTGATGTTTTTGGCAGCATGAGGACGAGCAGCTAA
* * * *
28190 AATTGATTGGAGCCTAGAATTAGATCGTTTGAATCTTTTTAGCGTTGTAGGCGGTGTTG-CTGAC
448 AATTGATTGGAGCCTAGAATTAGATCGTTTGAATCTTCTGAGCGTTGGA-GAGGTGTTGTCTGAC
*
28254 -G--GTGTTGCTGGAGGTGTTGTTGAAGGAGATGTTGAAGAAGATGTTGAAGGAGATCTTCTCCT
512 TGACGTGTTGCTGGAGGTGTTGTTGAA-G-G-TGTTGAAG-AGATGTTGAAGGAGATCTTTTCCT
*
28316 TTTTGCTACTATAAGGAAGAAAATTAGGAGAATAAAAA-AAA-GAAAACAAACT-AGAGAAAAGA
573 TTTTGCTGCTATAAGGAAGAAAATTAGGAGAATAAAAAGAAAGGAAAACAAACTGAGA-AAAAGA
* *
28378 GGAGAGATAAAACATCAAAACTGGAAAAAAGAAGAGAGGACATACCCATGGCAACTGATGGAGCT
637 -GAGAGATAAAGCATCAAAACTGGAAAAAAGGAGAGA-GACATACCCATGGCAACTGATGGAGCT
*
28443 GGAACTGGAGATGTTGAAGGAGATTTTTTCCTTTTTGATGCTATAAGCAAGAAAATTAAGAGAAT
700 GGAACTGGAGATGTTGAAGGAGATTTTTTCCTTTTTGCTGCTATAAGCAAGAAAATTAAGAGAAT
*
28508 AGAAAGAAGGAAAACAAAGTGGAGAAAAGGTGAGAGATAAAGTATCAAAACTAAAAAACGACATA
765 AG-AAGAAGGAAAACAAAGTGGAGAAAAGGAGAGAGATAAAGTATCAAAACTAAAAAACGACATA
* *
28573 CCCATGGCTGATGGAGCTGGAACTGTTTAGGAGCCGCTTCTTGAACCCTAATGTTTCTTGAACCC
829 CCCATGGCTGATGGAGCTGGAACTGTTCA-GA-CCGCTTCTTGAA-CCTAACGTTTCTTGAACCC
* *
28638 TAACGTTCAGGGA
891 TAACATTCAAGGA
* * *
28651 AAATAATACTACAAAATGTAAAAGAGTGTAAGGAGATTAAAAATGATTGATTTGTAAGGTAAATG
1 AAATAATACAACAAAGTGTAAAAGAGTGTAAAGAGATTAAAAATGATTGATTTGTAAGGTAAATG
* * * * * * *
28716 AAAATTGGTGGAAATAATACAA-CAAAGTGTAAA--AGAGTGTAA--AGA-GAT-TAAAA-ATG-
66 AAAATTGGTGGAAA-AA-AAAAGGAAAG-GTAAATGAAAATG-AATTGGACGGTATAAAATAAGC
* * * ** *
28772 ---AT--TGATTTGTAAGGTAAATGAA-AATTGGTGG-A-AAAAAAAG-GAAAGGTAAATGAAAA
127 CCAATAAT-ATTTG-GA-G-AAA--AAGAATTGGCGGTATAAAATAAGCCCAAGG----GGAAAA
*
28828 TGAATTAGGCGTATAAAATAAGCCGGGCATGGACACTAAAATGTTAGGAAAGAAAAATTGGTAAA
182 TGAATTAGGCGTATAAAATAAGCCGGGCATGGGCACTAAAATGTTAGGAAAGAAAAATTGGTAAA
* *
28893 AATAAGGGAAAGGTAAATGAAAATGAATTGGGCCCAAAAATTTTGGGCAAGAATAAGAGAATATT
247 AATAAGGGAAAGG---ATG-AAATGAATTGGGCCCTAAAATTTTGGGCAAGAATAAGAGAAGATT
* * ** *
28958 AGACTGGTATCTAACTAAACATAATAATATTTAGAAGAGAGTAAGACAAGATGTCTAGGCTTTCT
308 AGACTGGCATCTAACTAAGCCCAATAATATTTAGAAGAGAGTAAGACAAGATGTCTAGGCTTTCA
* * *
29023 AGGTGGCCATTTGTTAGTAACAACTAACATTCTCAGTTTGTTGATGTTTTTGGCAGCATGAGAAC
373 AGGTGGCCGTTTGTTAGTAGCAACTAACATTCTCAGTTTGTTGATGTTTTTGGCAGCATGAGGAC
*
29088 GAGCAGCTAAAATTGATTGCAGCCTAGAATTAGATCGTTTGAATCTTCTGAGCGTTGGAGATGGT
438 GAGCAGCTAAAATTGATTGGAGCCTAGAATTAGATCGTTTGAATCTTCTGAGCGTTGGAGA-GGT
29153 GTTGCTAACAGTGATCCTGACTGTGTTGCTGGAGGTGTTGTTGAAGTTGTTGTTGAAGGAGATGT
502 GTTG-T--C--TGA--CTGAC-GTGTTGCTGGAGGTGTTGTTGAAG--G-TGTTGAA-GAGATGT
*
29218 TGAAAGAGATCTTTTCCTTTTTGCTGCTATAAGGAAGAAAATTAGGAGAATAAAAAAAAGAAAGG
555 TGAAGGAGATCTTTTCCTTTTTGCTGCTATAAGGAAGAAAATTAGGAGAAT---AAAAAGAAAGG
* *
29283 AAAACAAACTGAAGAAAAAGAAAGAGATAAAGCATCAAAGCTGGAAAAAAGGAGAGATGACATAC
617 AAAACAAACTG-AGAAAAAGAGAGAGATAAAGCATCAAAACTGGAAAAAAGGAGAGA-GACATAC
*
29348 CCATGGCAACTGATGGAGCTGGAACTGGAGATGTTGAAGGAGATCTTTTCCTTTTTGCTGCTATA
680 CCATGGCAACTGATGGAGCTGGAACTGGAGATGTTGAAGGAGATTTTTTCCTTTTTGCTGCTATA
* * *
29413 AGTAAGAAAATCAAGAGAATAGAAGAATGGAAAACAAAGTGGAGAAAAGGAGAGAGGTAAAGTAT
745 AGCAAGAAAATTAAGAGAATAGAAGAA-GGAAAACAAAGTGGAGAAAAGGAGAGAGATAAAGTAT
*
29478 CAAAACTAAAAAACGACATACCCATGGCTGTTGGAGCTGGAACTGTTCAGCCACCGCTTCTTGAA
809 CAAAACTAAAAAACGACATACCCATGGCTGATGGAGCTGGAACTGTTCAG--ACCGCTTCTTGAA
*
29543 TCCTAACGTTTCTTGACCCCTAACATTCAAGGA
872 -CCTAACGTTTCTTGAACCCTAACATTCAAGGA
* *
29576 AAATAATAGAACAAAGTGTAAAAGATTGTAAAGAGATTAAAAATGATTGATTTGTAAGGTAAATG
1 AAATAATACAACAAAGTGTAAAAGAGTGTAAAGAGATTAAAAATGATTGATTTGTAAGGTAAATG
29641 AAAATTGGTGGAAAAAAAAAGGAAAGGTAAATGAAAATGAATTGGACGGTATAAAATAAGCCCAA
66 AAAATTGGTGGAAAAAAAAAGGAAAGGTAAATGAAAATGAATTGGACGGTATAAAATAAGCCCAA
*
29706 TAATATTTGGAGAAAAAGAATTGGACGGTATAAAATAAGCCCAAGGGGAAAATGAATTGGGCTGT
131 TAATATTTGGAGAAAAAGAATTGG-CGGTATAAAATAAGCCCAAGGGGAAAATGAATTAGGC-GT
*
29771 TTAAAATAAGCCGGGCATGGGCACTAAAATGTTAGGAAAGAAAAATTGGTAAAAATAAGGGAAAG
194 ATAAAATAAGCCGGGCATGGGCACTAAAATGTTAGGAAAGAAAAATTGGTAAAAATAAGGGAAAG
*
29836 GTAAATGAAAATTAATTGGGCCCTAAAATTTTGGGCAAGAATAAGAGAAGATTAGACTGGCATCT
259 G---ATG-AAATGAATTGGGCCCTAAAATTTTGGGCAAGAATAAGAGAAGATTAGACTGGCATCT
* * *
29901 AACTAAGCCTAATAATATTTAGAAGAGAGTCAGACAAGATGTCTAGGCTTTCCAA-ATGGCCGTT
320 AACTAAGCCCAATAATATTTAGAAGAGAGTAAGACAAGATGTCTAGGCTTT-CAAGGTGGCCGTT
*
29965 TGTTAGTAGCAACTAACATTCTCAGTTTGCTT-ATGTTTTTGGCGGCATGAGGACGAGCAGCTAA
384 TGTTAGTAGCAACTAACATTCTCAGTTTG-TTGATGTTTTTGGCAGCATGAGGACGAGCAGCTAA
*
30029 AATTGATTGGAGCCTAGAATTAGATCGTTTGAATCTTCTGAGCGTTGGAGACG-G-TGT-TG-CT
448 AATTGATTGGAGCCTAGAATTAGATCGTTTGAATCTTCTGAGCGTTGGAGAGGTGTTGTCTGACT
*
30090 GACG-G-TG-T-----TGTTG--G-AGGTG-T-------TGTTGAAGGAGATCTTTTCCTTGTTG
513 GACGTGTTGCTGGAGGTGTTGTTGAAGGTGTTGAAGAGATGTTGAAGGAGATCTTTTCCTTTTTG
* * *
30136 CTGCTATAAGGGAGAAAATTAGGAGAATAAAAAGAAAGGAAAACAAACTGGAGAAAAGGGGAGAG
578 CTGCTATAAGGAAGAAAATTAGGAGAATAAAAAGAAAGGAAAACAAACT-GAGAAAAAGAGAGAG
*
30201 ATAAAGCATCAAAACTGGAAAAAAGGAGAGAG---GA--CAT----AC-----GAGCTGGAACTG
642 ATAAAGCATCAAAACTGGAAAAAAGGAGAGAGACATACCCATGGCAACTGATGGAGCTGGAACTG
30252 GAGATGTTGAAGGAGATTTTTTTCCTTTTTGCTGCTATAAGCAAGAAAATTAAGAGAATAGAAGA
707 GAGATGTTGAAGGAGA-TTTTTTCCTTTTTGCTGCTATAAGCAAGAAAATTAAGAGAATAGAAG-
* * *
30317 AAGGAAAACAAAGTGGAGAAAAGGAGAGAGATAAAGGATCAAAACCAAAAAACGAAATACCCATG
770 AAGGAAAACAAAGTGGAGAAAAGGAGAGAGATAAAGTATCAAAACTAAAAAACGACATACCCATG
*
30382 GCTGATGGAGCTGTAACTGTTCAG-CCGC--C--G-------C--TTCTTGAACCCTAACATTC-
835 GCTGATGGAGCTGGAACTGTTCAGACCGCTTCTTGAACCTAACGTTTCTTGAACCCTAACATTCA
30432 AGG-
900 AGGA
*
30435 GAA-AATACAACAAAGTGTAAAAGAGTGTAAAGAGATTAAAAATGATTGATTTGTAAGGTAAATG
1 AAATAATACAACAAAGTGTAAAAGAGTGTAAAGAGATTAAAAATGATTGATTTGTAAGGTAAATG
* * *
30499 AAAATTGGTGG-AAAATAAAGGAAAGGTAAATGAAAATGATTTTGG-CGGTATGAAATAAGCCCA
66 AAAATTGGTGGAAAAAAAAAGGAAAGGTAAATGAAAATGA-ATTGGACGGTATAAAATAAGCCCA
* * * *
30562 ATAATATTTGGGGAAAATGAGTTAGGCGGTATAAAATAAGCCCAATGGGAAAATGAATTAGGCGG
130 ATAATATTTGGAGAAAAAGAATT-GGCGGTATAAAATAAGCCCAAGGGGAAAATGAATTAGGC-G
* * * *
30627 TATAAAATAAGCCGGGAATGGGCACTGAAATGTTTGGAAAGAAAAATTGGTAAAAATAATGGAAA
193 TATAAAATAAGCCGGGCATGGGCACTAAAATGTTAGGAAAGAAAAATTGGTAAAAATAAGGGAAA
* *
30692 GGTAAATGAATATGAATTGGGCCCTAAAATTTTGGGCAAGAATAAGAGAATACTAGACTGGCATC
258 GG---ATGAA-ATGAATTGGGCCCTAAAATTTTGGGCAAGAATAAGAGAAGATTAGACTGGCATC
*
30757 TAACTAAGCCCAATAATATTTAGTAGAGAGTAAGACAAGAT
319 TAACTAAGCCCAATAATATTTAGAAGAGAGTAAGACAAGAT
30798 TGGACGTTAA
Statistics
Matches: 1931, Mismatches: 149, Indels: 193
0.85 0.07 0.08
Matches are distributed among these distances:
856 2 0.00
857 257 0.13
858 76 0.04
859 2 0.00
860 3 0.00
861 18 0.01
863 1 0.00
871 1 0.00
873 1 0.00
875 4 0.00
877 28 0.01
878 125 0.06
879 2 0.00
882 2 0.00
886 3 0.00
888 1 0.00
891 1 0.00
892 62 0.03
893 1 0.00
895 51 0.03
903 1 0.00
904 3 0.00
905 10 0.01
906 9 0.00
907 5 0.00
908 298 0.15
909 19 0.01
910 8 0.00
911 5 0.00
912 3 0.00
913 1 0.00
914 11 0.01
915 10 0.01
916 79 0.04
917 2 0.00
918 1 0.00
919 6 0.00
920 85 0.04
921 1 0.00
922 2 0.00
923 13 0.01
924 17 0.01
925 333 0.17
926 9 0.00
927 6 0.00
928 7 0.00
929 5 0.00
930 21 0.01
931 294 0.15
932 6 0.00
933 10 0.01
934 9 0.00
935 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.24
Consensus pattern (903 bp):
AAATAATACAACAAAGTGTAAAAGAGTGTAAAGAGATTAAAAATGATTGATTTGTAAGGTAAATG
AAAATTGGTGGAAAAAAAAAGGAAAGGTAAATGAAAATGAATTGGACGGTATAAAATAAGCCCAA
TAATATTTGGAGAAAAAGAATTGGCGGTATAAAATAAGCCCAAGGGGAAAATGAATTAGGCGTAT
AAAATAAGCCGGGCATGGGCACTAAAATGTTAGGAAAGAAAAATTGGTAAAAATAAGGGAAAGGA
TGAAATGAATTGGGCCCTAAAATTTTGGGCAAGAATAAGAGAAGATTAGACTGGCATCTAACTAA
GCCCAATAATATTTAGAAGAGAGTAAGACAAGATGTCTAGGCTTTCAAGGTGGCCGTTTGTTAGT
AGCAACTAACATTCTCAGTTTGTTGATGTTTTTGGCAGCATGAGGACGAGCAGCTAAAATTGATT
GGAGCCTAGAATTAGATCGTTTGAATCTTCTGAGCGTTGGAGAGGTGTTGTCTGACTGACGTGTT
GCTGGAGGTGTTGTTGAAGGTGTTGAAGAGATGTTGAAGGAGATCTTTTCCTTTTTGCTGCTATA
AGGAAGAAAATTAGGAGAATAAAAAGAAAGGAAAACAAACTGAGAAAAAGAGAGAGATAAAGCAT
CAAAACTGGAAAAAAGGAGAGAGACATACCCATGGCAACTGATGGAGCTGGAACTGGAGATGTTG
AAGGAGATTTTTTCCTTTTTGCTGCTATAAGCAAGAAAATTAAGAGAATAGAAGAAGGAAAACAA
AGTGGAGAAAAGGAGAGAGATAAAGTATCAAAACTAAAAAACGACATACCCATGGCTGATGGAGC
TGGAACTGTTCAGACCGCTTCTTGAACCTAACGTTTCTTGAACCCTAACATTCAAGGA
Found at i:31003 original size:20 final size:21
Alignment explanation
Indices: 30978--31016 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30968 AAGAACAAAA
*
30978 CATTG-AATTGAAAACAAATC
1 CATTGAAATTCAAAACAAATC
30998 CATTGAAATTCAAAACAAA
1 CATTGAAATTCAAAACAAA
31017 AAATAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (21 bp):
CATTGAAATTCAAAACAAATC
Found at i:31642 original size:17 final size:17
Alignment explanation
Indices: 31620--31652 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31610 CATATCCATA
31620 GTGCACTAATTGTGAAG
1 GTGCACTAATTGTGAAG
31637 GTGCACTAATTGTGAA
1 GTGCACTAATTGTGAA
31653 AGCCAAACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.30
Consensus pattern (17 bp):
GTGCACTAATTGTGAAG
Found at i:33041 original size:21 final size:21
Alignment explanation
Indices: 33017--33061 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
33007 ACCGTGCCAT
33017 CACCGGCCACATTCGAGCCGC
1 CACCGGCCACATTCGAGCCGC
33038 CACCGGCCACATTCGAGCCGC
1 CACCGGCCACATTCGAGCCGC
33059 CAC
1 CAC
33062 TAGTCATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.09
Consensus pattern (21 bp):
CACCGGCCACATTCGAGCCGC
Found at i:38970 original size:3 final size:3
Alignment explanation
Indices: 38962--38988 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
38952 AAGAAAAAAC
38962 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
38989 ACTAGCTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:40880 original size:27 final size:27
Alignment explanation
Indices: 40816--40868 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
40806 TCTTCTTCTT
* * *
40816 CTTCTCGTTCTTCTCCTTTTTTTGCTA
1 CTTCTCGTTCTTCTCCTTCTCTAGCTA
40843 CTTCTCGTTCTTCTCCTTCTCTAGCT
1 CTTCTCGTTCTTCTCCTTCTCTAGCT
40869 GGTTCTGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.04, C:0.34, G:0.08, T:0.55
Consensus pattern (27 bp):
CTTCTCGTTCTTCTCCTTCTCTAGCTA
Found at i:42127 original size:19 final size:19
Alignment explanation
Indices: 42103--42140 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
42093 AAGTCCAATG
*
42103 GATCCGTAAATTCCAAATA
1 GATCCGTAAATCCCAAATA
42122 GATCCGTAAATCCCAAATA
1 GATCCGTAAATCCCAAATA
42141 TGGGTCGACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.24, G:0.11, T:0.24
Consensus pattern (19 bp):
GATCCGTAAATCCCAAATA
Found at i:44809 original size:1 final size:1
Alignment explanation
Indices: 44803--44840 Score: 67
Period size: 1 Copynumber: 38.0 Consensus size: 1
44793 TTGTATCATT
*
44803 AAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
44841 CATACAACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:47036 original size:23 final size:23
Alignment explanation
Indices: 46982--47036 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
46972 GGCTTTATAG
* **
46982 AGACAAAAATCTACAAGTTTGTGT
1 AGAC-AAAATATACAAGTTTGTAC
* *
47006 ATAAAAAATATACAAGTTTGTAC
1 AGACAAAATATACAAGTTTGTAC
47029 AGACAAAA
1 AGACAAAA
47037 ATCTAAAGAC
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.25
Consensus pattern (23 bp):
AGACAAAATATACAAGTTTGTAC
Done.