Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009614.1 Corchorus capsularis cultivar CVL-1 contig09635, 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: 86696
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5003 original size:37 final size:37
Alignment explanation
Indices: 4959--5029 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
4949 CTTGATCAAC
* **
4959 ATACATGTCTTTTCATGTAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
4996 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGA
5030 ATAATCATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Found at i:14549 original size:30 final size:30
Alignment explanation
Indices: 14513--14574 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
14503 TTCAATATCT
* *
14513 TTTTATAATTTATAAATAAAAGTTTAATGA
1 TTTTATAATTAATAAACAAAAGTTTAATGA
14543 TTTTATAATTAATAAACAAAAGTTTAATGA
1 TTTTATAATTAATAAACAAAAGTTTAATGA
14573 TT
1 TT
14575 AAAAATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (30 bp):
TTTTATAATTAATAAACAAAAGTTTAATGA
Found at i:14762 original size:35 final size:35
Alignment explanation
Indices: 14723--14793 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
14713 TACTATAATA
14723 TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
1 TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
14758 TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
1 TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
14793 T
1 T
14794 CGAGTTCGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (35 bp):
TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
Found at i:14889 original size:8 final size:8
Alignment explanation
Indices: 14862--14898 Score: 56
Period size: 8 Copynumber: 4.4 Consensus size: 8
14852 AGTATAGTAT
14862 ATAGTAAG
1 ATAGTAAG
14870 ATAAGATAAG
1 AT-AG-TAAG
14880 ATAGTAAG
1 ATAGTAAG
14888 ATAGTAAG
1 ATAGTAAG
14896 ATA
1 ATA
14899 TATCTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 17 0.63
9 4 0.15
10 6 0.22
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (8 bp):
ATAGTAAG
Found at i:15030 original size:2 final size:2
Alignment explanation
Indices: 15025--15054 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
15015 TGTGTGTGTC
15025 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15055 CTGAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15265 original size:13 final size:13
Alignment explanation
Indices: 15247--15276 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
15237 CAAGGAGCAA
15247 GGATGTCTGCTTT
1 GGATGTCTGCTTT
15260 GGATGTCTGCTTT
1 GGATGTCTGCTTT
15273 GGAT
1 GGAT
15277 AGTTCAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.10, C:0.13, G:0.33, T:0.43
Consensus pattern (13 bp):
GGATGTCTGCTTT
Found at i:17960 original size:14 final size:14
Alignment explanation
Indices: 17941--17967 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17931 AACAGAAACC
17941 GCATATGCTTATTT
1 GCATATGCTTATTT
17955 GCATATGCTTATT
1 GCATATGCTTATT
17968 AAAGGATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (14 bp):
GCATATGCTTATTT
Found at i:44431 original size:22 final size:22
Alignment explanation
Indices: 44378--44424 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
44368 ATGATCCCAT
* *
44378 TATGAAATTTTGATAATCTTAC
1 TATGAAATTTTAATAATCATAC
*
44400 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTAATAATCATAC
44422 TAT
1 TAT
44425 AGAATTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (22 bp):
TATGAAATTTTAATAATCATAC
Found at i:44660 original size:22 final size:22
Alignment explanation
Indices: 44635--44679 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
44625 ATTGTCAGTG
* * *
44635 ATCATACTTTAAAATTTTGATA
1 ATCACACTATAAAATTGTGATA
*
44657 ATCACACTATGAAATTGTGATA
1 ATCACACTATAAAATTGTGATA
44679 A
1 A
44680 CCTCGTTATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (22 bp):
ATCACACTATAAAATTGTGATA
Found at i:44718 original size:23 final size:23
Alignment explanation
Indices: 44644--44745 Score: 84
Period size: 22 Copynumber: 4.5 Consensus size: 23
44634 GATCATACTT
* * *
44644 TAAAATTTTGAT-AATCACACTA
1 TAAAATTTTGATAAACCTCCCTA
* * **
44666 TGAAATTGTGAT-AACCTCGTTA
1 TAAAATTTTGATAAACCTCCCTA
* * *
44688 TGAAATTTTGATAAATCTTCCC-G
1 TAAAATTTTGATAAA-CCTCCCTA
44711 TAAAATTTTGATAAACCTCCCTA
1 TAAAATTTTGATAAACCTCCCTA
44734 TAAAATTTTGAT
1 TAAAATTTTGAT
44746 GACTTTCTTA
Statistics
Matches: 63, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
22 32 0.51
23 28 0.44
24 3 0.05
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (23 bp):
TAAAATTTTGATAAACCTCCCTA
Found at i:44803 original size:22 final size:22
Alignment explanation
Indices: 44775--44947 Score: 100
Period size: 22 Copynumber: 7.9 Consensus size: 22
44765 GATAATTACA
*
44775 AATTTTGATAAGCTCCCTATGG
1 AATTTTGATAACCTCCCTATGG
** **
44797 TTTTTTGATAACCTCATTATGG
1 AATTTTGATAACCTCCCTATGG
* *
44819 AATTTTGTTAACCTCCCTATGA
1 AATTTTGATAACCTCCCTATGG
* * * *
44841 AATTTTGATCTACAT-ACTATGA
1 AATTTTGAT-AACCTCCCTATGG
* *
44863 AATTTTGATAACC-CTCTTATGA
1 AATTTTGATAACCTC-CCTATGG
* ** *
44885 AATTTTGA-AAACTAAACTATGA
1 AATTTTGATAACCT-CCCTATGG
*** *
44907 AATTTTGATAACCTTTATATGA
1 AATTTTGATAACCTCCCTATGG
*
44929 AATTTTGATATCCTCCCTA
1 AATTTTGATAACCTCCCTA
44948 AATTTTGATT
Statistics
Matches: 114, Mismatches: 31, Indels: 12
0.73 0.20 0.08
Matches are distributed among these distances:
21 5 0.04
22 102 0.89
23 7 0.06
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.41
Consensus pattern (22 bp):
AATTTTGATAACCTCCCTATGG
Found at i:44847 original size:44 final size:44
Alignment explanation
Indices: 44465--45714 Score: 252
Period size: 44 Copynumber: 28.9 Consensus size: 44
44455 TTAACTTTCT
* * * * * * *
44465 TATGAAATTTCGTTAACATCCTTAAGGAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATA-ACCTCAC
* * * *
44509 TATGAAATTTTGATAACTTCCCAATTAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACC-TCAC
* * * * * *
44554 TATGAGATGTTGATAACCTCCATAT-AATATATCGATAACCAT-GC
1 TATGAAATTTTGATAACCTCCCTATGAA-ATTTTGATAACC-TCAC
* * * * * * * *
44598 TATGAAAATTTAAAAACCTCCATATG-AATTGTCAGTGATCAT-AC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGA-T-AACCTCAC
* * * * * * **
44642 TTTAAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* *
44686 TATGAAATTTTGATAAATCTTCCCGTA--AAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AA-CCTCCC-TATGAAATTTTGAT-AACCTCAC
* * * * * *
44732 TATAAAATTTTGATGACTTTCTTATGAAATCTTGATAA--T---
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * *** *
44771 TA-CAAATTTTGATAAGCTCCCTATGGTTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * *
44814 TATGGAATTTTGTTAACCTCCCTATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGAT-AACCTCAC
* * *
44858 TATGAAATTTTGATAACC-CTCTTATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCTC-CCTATGAAATTTTGATAACCT-CAC
*** *
44902 TATGAAATTTTGATAACCTTTATATGAAATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* ** * * * * *
44945 -CT-AAATTTTGAT-TTCTCCATAATAAAAGTTTAATAACCT-TC
1 TATGAAATTTTGATAACCTCCCT-ATGAAATTTTGATAACCTCAC
* * * *
44986 -AT--AA-TTTGGTAACCAT-ACTATGAAATTTTGATAATCTCCC
1 TATGAAATTTTGATAACC-TCCCTATGAAATTTTGATAACCTCAC
* * * * *
45026 CA-G-AA-----AT-A-C-CACTATGAAATTTTTG-TAATCACAT
1 TATGAAATTTTGATAACCTCCCTATGAAA-TTTTGATAACCTCAC
* * ** ***
45060 TTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTTTT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * * * * *
45104 TATAAAATTTTGTTGA-CTCCTCTATGAAATTCTGATAATCACAT
1 TATGAAATTTTGATAACCTCC-CTATGAAATTTTGATAACCTCAC
* * * * **
45148 TGTGTAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * ** ***
45192 TATGAAATTTTGATGA-TTTTC-ATGTAAATTTTGATAATCCGATTTT
1 TATGAAATTTTGATAACCTCCCTATG-AAATTTTGATAA-CC--TCAC
* * * * * *
45238 TATGAAATTTCGATAATCACTCTATGAGA-TTTGATAACCT-TC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * * *
45280 TATCAAATTTTGGT-A-CTCCTTGTGAAATTGAGACTTTTATAACCTTCA-
1 TATGAAATTTTGATAACCTCCCTATGAAA-T-----TTTGATAACC-TCAC
* * * *
45328 TATGAAATTTTAATAACCAT-ACTATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACC-TCCCTATGAAATTTTGATAACCTCAC
* * * * *
45372 AATCAAATATT-AGTAACCT-CCTAAT-AAGATTTTGCTAACCACAC
1 TATGAAATTTTGA-TAACCTCCCT-ATGAA-ATTTTGATAACCTCAC
* * * * *
45416 TTTCAAA-TTCGTATAACCTCGCTATGACATTTTGA-AA--T--C
1 TATGAAATTTTG-ATAACCTCCCTATGAAATTTTGATAACCTCAC
* ** * * * *
45455 --T----TTTCGATAACCTTTCTATAAAATTGTGATAATTAACCACCC
1 TATGAAATTTTGATAACCTCCCTATGAAATT-T--TGA-TAACCTCAC
** ** ** * *
45497 TATGAAATTTCAATAACCAACCTAAAAAATTTTAATAACCTGATCC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCA--C
* * * *
45543 TATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACCTCAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * *
45587 TATGAAATTTTGGTAACCTCACTATAAAATTTT-AGTAACCACAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGA-TAACCTCAC
* * * *
45631 TATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * *
45674 TCATGGAATTATAATAACCAT-CTTATGAAATTTTGATAACC
1 T-ATGAAATTTTGATAACC-TCCCTATGAAATTTTGATAACC
45715 ACATAGAGAC
Statistics
Matches: 871, Mismatches: 239, Indels: 192
0.67 0.18 0.15
Matches are distributed among these distances:
33 15 0.02
34 20 0.02
35 7 0.01
36 5 0.01
37 2 0.00
38 27 0.03
39 22 0.03
40 17 0.02
41 33 0.04
42 20 0.02
43 49 0.06
44 435 0.50
45 83 0.10
46 77 0.09
47 16 0.02
48 34 0.04
49 2 0.00
50 6 0.01
51 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
Found at i:45178 original size:22 final size:22
Alignment explanation
Indices: 45062--45205 Score: 105
Period size: 22 Copynumber: 6.5 Consensus size: 22
45052 AATCACATTT
* *
45062 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCCTTA
**
45084 TGAAATTTTGATAACCTTTTTA
1 TGAAATTTTGATAACCTCCTTA
* * *
45106 TAAAATTTTGTTGA-CTCCTCTA
1 TGAAATTTTGATAACCTCCT-TA
* * * * *
45128 TGAAATTCTGATAATCACATTG
1 TGAAATTTTGATAACCTCCTTA
*
45150 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-CTTA
**
45172 TGAAATTTTGATAACAACAC-TA
1 TGAAATTTTGATAACCTC-CTTA
45194 TGAAATTTTGAT
1 TGAAATTTTGAT
45206 GATTTTCATG
Statistics
Matches: 95, Mismatches: 23, Indels: 8
0.75 0.18 0.06
Matches are distributed among these distances:
21 4 0.04
22 86 0.91
23 5 0.05
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCCTTA
Found at i:45247 original size:25 final size:26
Alignment explanation
Indices: 45206--45255 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
45196 AAATTTTGAT
*
45206 GATTTTCATGTAAATTTTGATAATCC
1 GATTTTCATGTAAATTTCGATAATCC
*
45232 GATTTTTATG-AAATTTCGATAATC
1 GATTTTCATGTAAATTTCGATAATC
45256 ACTCTATGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (26 bp):
GATTTTCATGTAAATTTCGATAATCC
Found at i:45344 original size:22 final size:21
Alignment explanation
Indices: 45314--45368 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
45304 AAATTGAGAC
*
45314 TTTTATAACCTT-CATATGAAA
1 TTTTATAACCTTAC-TATAAAA
*
45335 TTTTAATAACCATACTATAAAA
1 TTTT-ATAACCTTACTATAAAA
45357 TTTTGATAACCT
1 TTTT-ATAACCT
45369 CCCAATCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 4 0.14
22 23 0.82
23 1 0.04
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.42
Consensus pattern (21 bp):
TTTTATAACCTTACTATAAAA
Found at i:45379 original size:22 final size:21
Alignment explanation
Indices: 45354--45411 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
45344 CCATACTATA
45354 AAATTTTGATAACCTCCCAAT
1 AAATTTTGATAACCTCCCAAT
* *
45375 CAAATATT-AGTAACCTCCTAAT
1 -AAATTTTGA-TAACCTCCCAAT
*
45397 AAGATTTTGCTAACC
1 AA-ATTTTGATAACC
45412 ACACTTTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 3 0.10
22 26 0.90
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33
Consensus pattern (21 bp):
AAATTTTGATAACCTCCCAAT
Found at i:45550 original size:24 final size:22
Alignment explanation
Indices: 45488--45715 Score: 117
Period size: 22 Copynumber: 10.3 Consensus size: 22
45478 TTGTGATAAT
* *
45488 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
**
45510 TAACCAACCTAAAAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
45532 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
**
45556 TAACC-ACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* **
45578 TAACC-TCACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* * *
45600 TAACC-TCACTATAAAATTTTAG
1 TAACCAAC-CTATGAAATTTTAA
**
45622 TAACC-ACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* *
45644 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* * *
45666 TAACC-TCCTCATGGAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * *
45688 TAACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
45710 TAACCA
1 TAACCA
45716 CATAGAGACA
Statistics
Matches: 176, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
21 3 0.02
22 153 0.87
23 3 0.02
24 17 0.10
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:45642 original size:66 final size:66
Alignment explanation
Indices: 45488--45717 Score: 223
Period size: 66 Copynumber: 3.5 Consensus size: 66
45478 TTGTGATAAT
* *** ** * * *
45488 TAACCACCCTATGAAATTTCAATAACCA-ACCTAAAAAATTTTAATAACCTGATCCTATGAAATT
1 TAACCACACTATGAAATTTTGGTAACCACA-CTATGAAATTTTGATAACCTCA--CTATAAAATT
*
45552 TTGG
63 TTAG
* *
45556 TAACCACACTATGAAATTTTGGTAACCTCACTATGAAATTTTGGTAACCTCACTATAAAATTTTA
1 TAACCACACTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCACTATAAAATTTTA
45621 G
66 G
* ** *
45622 TAACCACACTATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCTC-CTCATGGAATTAT
1 TAACCACACTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCACT-ATAAAATTTT
*
45686 AA
65 AG
* *
45688 TAACCATC-TTATGAAATTTTGATAACCACA
1 TAACCA-CACTATGAAATTTTGGTAACCACA
45718 TAGAGACAAG
Statistics
Matches: 138, Mismatches: 21, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
65 2 0.01
66 94 0.68
67 1 0.01
68 40 0.29
69 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (66 bp):
TAACCACACTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCACTATAAAATTTTA
G
Found at i:45911 original size:19 final size:20
Alignment explanation
Indices: 45880--45917 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
45870 TATTAACATT
45880 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
45899 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
45918 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:46223 original size:166 final size:165
Alignment explanation
Indices: 45931--46258 Score: 441
Period size: 166 Copynumber: 2.0 Consensus size: 165
45921 AATAGTAAAG
* * * *
45931 GAAATTTGCATGTTCATCGACTAAAATCAATTTGACAAACTTATAATTTGGTCTAAATTGAATTT
1 GAAATTTGCATGTTCATCCAATAAAATCAATTTGACAAAATTATAATTCGGTCTAAATTGAATTT
* *
45996 TTTAAATGATAAAATTATACTAAATTTTAATAATGGAAATTTAGAAATATATTTAGAAAAAAGGG
66 TATAAAT-ATAAAATTATAATAAATTTTAATAATGGAAATTTAGAAATATATTTAGAAAAAAGGG
* *
46061 TGCAATCGGAAAATATAAAGTTTCCCATTATTTGTA
130 TACAATCAGAAAATATAAAGTTTCCCATTATTTGTA
46097 GAAATTTGCATGTTCA-CCAATGAAAATCAAATTT-ACAAAATTATAATTCGGTCTAAATTGAAA
1 GAAATTTGCATGTTCATCCAAT-AAAATC-AATTTGACAAAATTATAATTCGGTCTAAATTG-AA
** **
46160 TTTTAT-AAT-TAATTTTTAAATAATAAATTTTAATAATGTCAATTTAGAAATATATTT-GAAAA
63 TTTTATAAATATAA-AATT--ATAATAAATTTTAATAATGGAAATTTAGAAATATATTTAGAAAA
*
46222 AAGGGTACAATCAGAAAATATAAAGTTTTCCATTATT
125 AAGGGTACAATCAGAAAATATAAAGTTTCCCATTATT
46259 CGTACTATTA
Statistics
Matches: 143, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
164 3 0.02
165 5 0.03
166 88 0.62
167 47 0.33
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (165 bp):
GAAATTTGCATGTTCATCCAATAAAATCAATTTGACAAAATTATAATTCGGTCTAAATTGAATTT
TATAAATATAAAATTATAATAAATTTTAATAATGGAAATTTAGAAATATATTTAGAAAAAAGGGT
ACAATCAGAAAATATAAAGTTTCCCATTATTTGTA
Found at i:48207 original size:2 final size:2
Alignment explanation
Indices: 48194--48226 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
48184 TTTAAAAATA
48194 AT AT AT AGT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A
48227 ATCTAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49439 original size:437 final size:434
Alignment explanation
Indices: 48553--50004 Score: 1627
Period size: 438 Copynumber: 3.3 Consensus size: 434
48543 CTCAAAAGTA
** * * * *
48553 TTTTTAGAATTGAAACATGAAAATTAGCTTTTGAGTCTTTCATGAAAGTTGTAGATCATAAAATT
1 TTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGT-TTTCATGAAAATTGTAGATCATGAAATT
* * ** * * *
48618 ACTTTTTAATACATACCCGAATTACCTTAATTGGATAAATAGAACAAAGAAAATTAAAAAAGATG
65 ACTTTTTAATAGACACTTGAATCACCTTAATCGGACAAATAG-A-AAA-AAAA-TAAAAAA-AT-
* * * * *
48683 AAGTGCTAAATCG-AG--TGAGATAGAATTTGTAAAGAACTAAGTAACATAAAATATAAAATAGA
124 AAATGCTAAAT-GTAGATTAAGATAGAATTTGTAAAGGACTAAG-----T--AGTATAAAGTAGA
* ** * * *
48745 AAAGTATGAGGGTCATTTGATAACTAATTTAAATAAGAAAATATTTCTTAATGGATATCTTGAA-
181 AAAGTATGAGGGTCATTTGATAAATAATCCAAATAAAAAAATATTTGTTAATGGAAATCTTGAAC
* *
48809 ATATAAAATTTCCCTTTTGAACCCTTCACGAAACTCGTAGATCAAA-TTAACTTTCGGGTTCTTC
246 ATA-AAAA-TTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAACTTTCGGGTCCTTC
* ** * * * * * *
48873 ATGAAAGTCATGGATCTTACAGTAACCTTTTAACCGATACTTGAATAACTTTAATCGGACATATA
309 ATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGACATATG
* * ** ** * * *
48938 GATC-GAAAATTATATGG-TATTAAATAGACCAACAATTGAAACGACCAAATTTAGGAAGCAT
374 GA-CAAAAAATTATA-GGATATTAAATTGACCGGCAATCAAAACCACAAAATTTCGGAAGCAT
* * * * * *
48999 TTTTTTGAATTAAAACATAAAAATTTGCTTTTGAGTCTTTCATGAAAGTTGTAAATCATGAAATT
1 TTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGT-TTTCATGAAAATTGTAGATCATGAAATT
* * *
49064 AAC-TTTTAATAGACACATGAATCAACTTAATTGGACAAATAGAACAAAAAATAAAAAAATAAAT
65 -ACTTTTTAATAGACACTTGAATCACCTTAATCGGACAAATAGAA-AAAAAATAAAAAAATAAAT
** *
49128 TTTAAATGTTAGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGG
128 GCTAAATG-TAGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAGTATGAGG
* *
49193 GTCGTTTGATAAATAATCCAAATAAAAAAATATTTGTTAATGGAAATTTTGAACATAAAAATTCC
192 GTCATTTGATAAATAATCCAAATAAAAAAATATTTGTTAATGGAAATCTTGAACATAAAAATTCC
**
49258 CTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAACTTTAAGGTCCTTCATGAAAGTCGTAA
257 CTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAACTTTCGGGTCCTTCATGAAAGTCGTAA
* * * * *
49323 ATCATGCATTAACCTTTTGACCGACACTTCAATAACTTCAATTGGACATGTGGACAAAAAATTAT
322 ATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGACATATGGACAAAAAATTAT
*
49388 AGGATATTAAATTGACCGGCAATCAAAACCACAAAATTTCGGAAACAT
387 AGGATATTAAATTGACCGGCAATCAAAACCACAAAATTTCGGAAGCAT
*
49436 TTTTTAGAATCAAAACATTAAAATTGGCTTTTGAG---T-ATAAAAATTGTAGATCATGAAATTA
1 TTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTTTTCATGAAAATTGTAGATCATGAAATTA
49497 CTTTTTAATAGACACTTGAATCACCTTAATCGGACAAATAGGAAAAAAAATATACAAAAATAAAT
66 CTTTTTAATAGACACTTGAATCACCTTAATCGGACAAATA-GAAAAAAAATA-A-AAAAATAAAT
* * * ** * * * * *
49562 GCGAACACGTCAAATCGTCTAACCTATAA-TCGTAAAGGACTAAATAGCATAAAGTATAAAAGTA
128 GCTAA-ATGT-AGA---T-TAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAGTA
* * * ** * *
49626 TGAAGATCATTAGATAAATAATCCAACGAAAAAAATGTTTGTTAATGGAGATCTTGAACATAAAA
187 TGAGGGTCATTTGATAAATAATCCAAATAAAAAAATATTTGTTAATGGAAATCTTGAACATAAAA
* *
49691 ACTCCCTTTTGAGCCCTTCATGAAACTCGTAGATCAAATTTAACTTTCGGGTCCTTCATGAAAGT
252 ATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAACTTTCGGGTCCTTCATGAAAGT
* * *
49756 CGTAAATCATTCAATAACCTTTTAACCGACATTTTAATAACTTCAATCGGACATATGGACAAAAA
317 CGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGACATATGGAC-AAAA
*
49821 AATTATACGATATTAAATTGACCGGCAATCAAAACCACAAAATTTCGGAAGCA-
381 AATTATAGGATATTAAATTGACCGGCAATCAAAACCACAAAATTTCGGAAGCAT
* *
49874 TTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTTCTGCATGAAAAATGTAGATCATGAAATT
1 TTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTT-TTCATGAAAATTGTAGATCATGAAATT
* * * *
49939 ACCTTTTAATAGACACTTGAATTACCTTAATCGGACAAATAAGAAAAAAAATACAATAATAAATG
65 ACTTTTTAATAGACACTTGAATCACCTTAATCGGACAAAT-AGAAAAAAAATAAAAAAATAAATG
50004 C
129 C
50005 GAACGCGTTA
Statistics
Matches: 871, Mismatches: 108, Indels: 59
0.84 0.10 0.06
Matches are distributed among these distances:
431 2 0.00
432 64 0.07
433 5 0.01
434 13 0.01
435 4 0.00
436 39 0.04
437 214 0.25
438 239 0.27
439 63 0.07
440 1 0.00
441 19 0.02
442 4 0.00
443 78 0.09
444 30 0.03
445 3 0.00
446 91 0.10
447 2 0.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (434 bp):
TTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTTTTCATGAAAATTGTAGATCATGAAATTA
CTTTTTAATAGACACTTGAATCACCTTAATCGGACAAATAGAAAAAAAATAAAAAAATAAATGCT
AAATGTAGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAGTATGAGGGTCA
TTTGATAAATAATCCAAATAAAAAAATATTTGTTAATGGAAATCTTGAACATAAAAATTCCCTTT
TGAACCCTTCATGAAACTCGTAGATCAAATTTAACTTTCGGGTCCTTCATGAAAGTCGTAAATCA
TACAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGACATATGGACAAAAAATTATAGGA
TATTAAATTGACCGGCAATCAAAACCACAAAATTTCGGAAGCAT
Found at i:49710 original size:438 final size:437
Alignment explanation
Indices: 48735--50116 Score: 1648
Period size: 438 Copynumber: 3.2 Consensus size: 437
48725 AACATAAAAT
* * * * * ** *
48735 ATAAAATAGAAAAGTATGAGGGTCATTTGATAACTAATTTAA-ATAAGAAAATATTTCTTAATGG
1 ATAAAGTATAAAAGTATGAGGATCATTAGATAAATAATCCAACA-AA-AAAATATTTGTTAATGG
* *
48799 ATATCTTGAA-ATATAAAATTTCCCTTTTGAACCCTTCACGAAACTCGTAGATCAAA-TTAACTT
64 AGATCTTGAACATA-AAAA-TTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAACTT
* * ** * * * * *
48862 TCGGGTTCTTCATGAAAGTCATGGATCTTACAGTAACCTTTTAACCGATACTTGAATAACTTTAA
127 TCGGGTCCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAA
* * * ** ** * *
48927 TCGGACATATAGATC-GAAAATTATATGG-TATTAAATAGACCAACAATTGAAACGACCAAATTT
192 TCGGACATATGGA-CAAAAAATTATA-GGATATTAAATTGACCGGCAATCAAAACCACAAAATTT
* * * * * * * *
48990 AGGAAGCATTTTTTTGAATTAAAACATAAAAATTTGCTTTTGAGTCTTTCATGAAAGTTGTAAAT
255 CGGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAG---TTCATAAAAATTGTAGAT
* * *
49055 CATGAAATTAACTTTTAATAGACACATGAATCAACTTAATTGGACAAATAGAACAAAAAATA-A-
317 CATGAAATT-ACTTTTAATAGACACTTGAATCACCTTAATCGGACAAATAGAA-AAAAAATATAC
*** * * ** * * *
49118 AAAAATAAATTTTAA-ATGTTAGA---T-TAAGATAGAATTTGTAAAGGACTAAGTAGT
380 AAAAATAAATGCGAACACGTTAAATCGTCTAACCTATAA-TTGTAAAGGACTAAATAGC
* * * * * *
49172 ATAAAGTAGAAAAATATGAGGGTCGTTTGATAAATAATCCAAATAAAAAAATATTTGTTAATGGA
1 ATAAAGTATAAAAGTATGAGGATCATTAGATAAATAATCC-AACAAAAAAATATTTGTTAATGGA
* * **
49237 AATTTTGAACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAACTTTAA
65 GATCTTGAACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAACTTTCG
* * * *
49302 GGTCCTTCATGAAAGTCGTAAATCATGCATTAACCTTTTGACCGACACTTCAATAACTTCAATTG
130 GGTCCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCG
*
49367 GACATGTGGACAAAAAATTATAGGATATTAAATTGACCGGCAATCAAAACCACAAAATTTCGGAA
195 GACATATGGACAAAAAATTATAGGATATTAAATTGACCGGCAATCAAAACCACAAAATTTCGGAA
*
49432 ACATTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAG-T-ATAAAAATTGTAGATCATGAAAT
260 GCATTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTTCATAAAAATTGTAGATCATGAAAT
49495 TACTTTTTAATAGACACTTGAATCACCTTAATCGGACAAATAGGAAAAAAAATATACAAAAATAA
325 TAC-TTTTAATAGACACTTGAATCACCTTAATCGGACAAATA-GAAAAAAAATATACAAAAATAA
* *
49560 ATGCGAACACGTCAAATCGTCTAACCTATAATCGTAAAGGACTAAATAGC
388 ATGCGAACACGTTAAATCGTCTAACCTATAATTGTAAAGGACTAAATAGC
* *
49610 ATAAAGTATAAAAGTATGAAGATCATTAGATAAATAATCCAACGAAAAAAATGTTTGTTAATGGA
1 ATAAAGTATAAAAGTATGAGGATCATTAGATAAATAATCCAAC-AAAAAAATATTTGTTAATGGA
* *
49675 GATCTTGAACATAAAAACTCCCTTTTGAGCCCTTCATGAAACTCGTAGATCAAATTTAACTTTCG
65 GATCTTGAACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAACTTTCG
* * *
49740 GGTCCTTCATGAAAGTCGTAAATCATTCAATAACCTTTTAACCGACATTTTAATAACTTCAATCG
130 GGTCCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCG
*
49805 GACATATGGACAAAAAAATTATACGATATTAAATTGACCGGCAATCAAAACCACAAAATTTCGGA
195 GACATATGGAC-AAAAAATTATAGGATATTAAATTGACCGGCAATCAAAACCACAAAATTTCGGA
49870 AGCA-TTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTTCTGCATGAAAAA-TGTAGATCAT
259 AGCATTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAG-T-T-CAT-AAAAATTGTAGATCAT
* *
49933 GAAATTACCTTTTAATAGACACTTGAATTACCTTAATCGGACAAATA-AGAAAAAAA-ATACAAT
320 GAAATTA-CTTTTAATAGACACTTGAATCACCTTAATCGGACAAATAGA-AAAAAAATATACAAA
* * * *
49996 AATAAATGCGAACGCGTTAAATCGTCCAACCTATAATTGTAAAGGATTAAATAAC
383 AATAAATGCGAACACGTTAAATCGTCTAACCTATAATTGTAAAGGACTAAATAGC
** * * * *
50051 ATAAAACATAAAAGTACGAGGATCATTAGATAAATAATCAAACAAAAAAATATTAGTTTATGGAG
1 ATAAAGTATAAAAGTATGAGGATCATTAGATAAATAATCCAACAAAAAAATATTTGTTAATGGAG
50116 A
66 A
50117 ATGGGACCCA
Statistics
Matches: 823, Mismatches: 97, Indels: 47
0.85 0.10 0.05
Matches are distributed among these distances:
431 2 0.00
432 64 0.08
433 5 0.01
434 12 0.01
435 5 0.01
436 39 0.05
437 208 0.25
438 241 0.29
439 63 0.08
440 20 0.02
441 95 0.12
442 7 0.01
443 56 0.07
444 6 0.01
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (437 bp):
ATAAAGTATAAAAGTATGAGGATCATTAGATAAATAATCCAACAAAAAAATATTTGTTAATGGAG
ATCTTGAACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAACTTTCGG
GTCCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCGG
ACATATGGACAAAAAATTATAGGATATTAAATTGACCGGCAATCAAAACCACAAAATTTCGGAAG
CATTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTTCATAAAAATTGTAGATCATGAAATT
ACTTTTAATAGACACTTGAATCACCTTAATCGGACAAATAGAAAAAAAATATACAAAAATAAATG
CGAACACGTTAAATCGTCTAACCTATAATTGTAAAGGACTAAATAGC
Found at i:55953 original size:19 final size:16
Alignment explanation
Indices: 55925--55967 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 16
55915 TATTTTTCAT
55925 TAATATATATATAGTAATAA
1 TAATA-ATATAT-G-AAT-A
55945 TAATAATATATGAATA
1 TAATAATATATGAATA
55961 TAATAAT
1 TAATAAT
55968 GCAGTGATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.35
17 3 0.13
18 1 0.04
19 6 0.26
20 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (16 bp):
TAATAATATATGAATA
Found at i:56454 original size:18 final size:18
Alignment explanation
Indices: 56412--56452 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
56402 CAATTTCTGT
* *
56412 TTGGGATTTGGTGGCGGG
1 TTGGGATCTGGTGGCGGC
56430 TTGGGATCTGGTGGCAGGC
1 TTGGGATCTGGTGGC-GGC
56449 TTGG
1 TTGG
56453 ATTCGGTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.07, C:0.10, G:0.51, T:0.32
Consensus pattern (18 bp):
TTGGGATCTGGTGGCGGC
Found at i:59079 original size:19 final size:21
Alignment explanation
Indices: 59050--59091 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
59040 ATAAACTATG
59050 AACTAAAATTG-AAATAATTA
1 AACTAAAATTGCAAATAATTA
*
59070 AACT-AAATTGCAAGTAATTA
1 AACTAAAATTGCAAATAATTA
59090 AA
1 AA
59092 ATAGAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (21 bp):
AACTAAAATTGCAAATAATTA
Found at i:80397 original size:31 final size:28
Alignment explanation
Indices: 80349--80418 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 28
80339 TTCTCTTTTT
*
80349 ATATATAAAAAGTTAGATTAGATTAGATATGA
1 ATATAT-AATAGTTAGATTAGA-T--ATATGA
80381 ATATATAATAGTTAGATTAGATATATGA
1 ATATATAATAGTTAGATTAGATATATGA
80409 ATATAATAAT
1 ATAT-ATAAT
80419 GCAGTCATTG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
28 10 0.28
29 5 0.14
30 1 0.03
31 14 0.39
32 6 0.17
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (28 bp):
ATATATAATAGTTAGATTAGATATATGA
Found at i:80403 original size:26 final size:28
Alignment explanation
Indices: 80366--80418 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
80356 AAAAGTTAGA
80366 TTAGATTAG-ATATGAATAT-ATAATAG
1 TTAGATTAGAATATGAATATAATAATAG
80392 TTAGATTAGATATATGAATATAATAAT
1 TTAGATTAGA-ATATGAATATAATAAT
80419 GCAGTCATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 9 0.38
28 10 0.42
29 5 0.21
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (28 bp):
TTAGATTAGAATATGAATATAATAATAG
Found at i:84494 original size:23 final size:23
Alignment explanation
Indices: 84466--84528 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
84456 TGTGGCCGGT
* *
84466 TGTGGCCAGGCATGGCCGAATCA
1 TGTGGCCGGGCATGGCCAAATCA
84489 TGTGGCCGGGCATGGCCAAATCA
1 TGTGGCCGGGCATGGCCAAATCA
84512 TGTGGCCGGGCATGGCC
1 TGTGGCCGGGCATGGCC
84529 TTGTCGCGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.17, C:0.27, G:0.38, T:0.17
Consensus pattern (23 bp):
TGTGGCCGGGCATGGCCAAATCA
Found at i:84551 original size:33 final size:33
Alignment explanation
Indices: 84514--84578 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
84504 CCAAATCATG
**
84514 TGGCCGGGCATGGCCTTGTCGCGTGGCCGGTGA
1 TGGCCGGGCATGGCCAAGTCGCGTGGCCGGTGA
**
84547 TGGCCGGGCATTTCCAAGTCGCGTGGCCGGTG
1 TGGCCGGGCATGGCCAAGTCGCGTGGCCGGTG
84579 TTGCGCGGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.08, C:0.28, G:0.43, T:0.22
Consensus pattern (33 bp):
TGGCCGGGCATGGCCAAGTCGCGTGGCCGGTGA
Found at i:86218 original size:61 final size:62
Alignment explanation
Indices: 86141--86265 Score: 155
Period size: 61 Copynumber: 2.0 Consensus size: 62
86131 TTTTACGGGC
* * * *
86141 AGATAATCCATTTGCCTTTGTATCTAACGTTATTTGCCTCTGA-TTCTTGATATTTAGAGGCAA
1 AGATAAT-CATTTGCCTTTGTATCTAACATTATTTGCCTCTAATTTC-TAACATTTAGAGGCAA
* * *
86204 AGATAAT-ATTTGCCTTTGTATGTAATATTATTTGTCTCTAATTTCTAACATTTAGAGGCAA
1 AGATAATCATTTGCCTTTGTATCTAACATTATTTGCCTCTAATTTCTAACATTTAGAGGCAA
86265 A
1 A
86266 AAAGTATATG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
61 44 0.81
62 3 0.06
63 7 0.13
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.42
Consensus pattern (62 bp):
AGATAATCATTTGCCTTTGTATCTAACATTATTTGCCTCTAATTTCTAACATTTAGAGGCAA
Done.