Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013161.1 Corchorus olitorius cultivar O-4 contig13194, 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: 35758
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:5645 original size:2 final size:2
Alignment explanation
Indices: 5633--5668 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5623 CGACATCAAG
5633 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5669 CTAATACTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5675 original size:6 final size:6
Alignment explanation
Indices: 5666--5718 Score: 76
Period size: 6 Copynumber: 9.2 Consensus size: 6
5656 ATATATATAT
5666 ATACTA ATACTA ATACTA ATACTA ATTACTA ATACTA ATA-T- ATACT-
1 ATACTA ATACTA ATACTA ATACTA A-TACTA ATACTA ATACTA ATACTA
5712 ATACTA A
1 ATACTA A
5719 ATAGTATTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
4 3 0.07
5 7 0.16
6 28 0.64
7 6 0.14
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (6 bp):
ATACTA
Found at i:5697 original size:19 final size:18
Alignment explanation
Indices: 5666--5718 Score: 76
Period size: 19 Copynumber: 3.1 Consensus size: 18
5656 ATATATATAT
5666 ATACTAATACTAATACTA
1 ATACTAATACTAATACTA
5684 ATACTAATTACTAATACTA
1 ATACTAA-TACTAATACTA
5703 ATA-T-ATACT-ATACTA
1 ATACTAATACTAATACTA
5718 A
1 A
5719 ATAGTATTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.21
16 4 0.12
17 1 0.03
18 8 0.24
19 14 0.41
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (18 bp):
ATACTAATACTAATACTA
Found at i:5701 original size:25 final size:23
Alignment explanation
Indices: 5654--5712 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 23
5644 ATATATATAT
5654 ATATATA-TATATATACTAATACTA
1 ATATATACTA-AT-TACTAATACTA
5678 ATACTAATACTAATTACTAATACTA
1 ATA-T-ATACTAATTACTAATACTA
5703 ATATATACTA
1 ATATATACTA
5713 TACTAAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
23 6 0.19
24 4 0.12
25 15 0.47
26 5 0.16
27 2 0.06
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (23 bp):
ATATATACTAATTACTAATACTA
Found at i:5712 original size:10 final size:10
Alignment explanation
Indices: 5636--5712 Score: 53
Period size: 8 Copynumber: 8.2 Consensus size: 10
5626 CATCAAGATA
5636 TAATATATA-
1 TAATATATAC
5645 T-ATATATA-
1 TAATATATAC
5653 T-ATATATA-
1 TAATATATAC
5661 T-ATATATAC
1 TAATATATAC
5670 TAATACTAATAC
1 TAATA-T-ATAC
*
5682 TAATACTA-AT
1 TAATA-TATAC
*
5692 TACTA-ATAC
1 TAATATATAC
5701 TAATATATAC
1 TAATATATAC
5711 TA
1 TA
5713 TACTAAATAG
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
8 24 0.41
9 7 0.12
10 14 0.24
11 2 0.03
12 11 0.19
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (10 bp):
TAATATATAC
Found at i:5721 original size:16 final size:15
Alignment explanation
Indices: 5644--5718 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 15
5634 TATAATATAT
5644 ATATATA-TATA-TA
1 ATATATACTATACTA
5657 TATATATA-TATACTA
1 -ATATATACTATACTA
5672 ATACTAATACTAATACT-
1 ATA-T-ATACT-ATACTA
5689 A-AT-TACTAATACTA
1 ATATATACT-ATACTA
5703 ATATATACTATACTA
1 ATATATACTATACTA
5718 A
1 A
5719 ATAGTATTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 15
0.78 0.00 0.22
Matches are distributed among these distances:
13 10 0.19
14 15 0.28
15 13 0.25
16 8 0.15
17 2 0.04
18 5 0.09
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATATACTATACTA
Found at i:9535 original size:19 final size:20
Alignment explanation
Indices: 9507--9547 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
9497 TTGAAGAGTG
*
9507 TTTGTCATTTT-TATTTAAT
1 TTTGTAATTTTATATTTAAT
*
9526 TTTGTAATTTTATTTTTAAT
1 TTTGTAATTTTATATTTAAT
9546 TT
1 TT
9548 CAGAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTGTAATTTTATATTTAAT
Found at i:13210 original size:32 final size:32
Alignment explanation
Indices: 13173--13260 Score: 140
Period size: 32 Copynumber: 2.8 Consensus size: 32
13163 GTCTTCAGAC
*
13173 AGATATCACTCATCTCACAAACTATCTATCAG
1 AGATATCACTCATCTCACAAACCATCTATCAG
* *
13205 AGATATCACTCATCTCACAAACCATTTCTCAG
1 AGATATCACTCATCTCACAAACCATCTATCAG
*
13237 AGATATCACTCATCTCAAAAACCA
1 AGATATCACTCATCTCACAAACCA
13261 GCTCCTGAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.39, C:0.30, G:0.06, T:0.26
Consensus pattern (32 bp):
AGATATCACTCATCTCACAAACCATCTATCAG
Found at i:19994 original size:15 final size:16
Alignment explanation
Indices: 19961--20000 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
19951 TTACTTTGCT
19961 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
19977 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
19992 TTGCTTTCT
1 TTGTTTTCT
20001 TTCAATCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:23790 original size:22 final size:22
Alignment explanation
Indices: 23765--23819 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
23755 CATAATGATA
*
23765 CTATGCAATTTCGAA-AACATTC
1 CTATGCAATTTC-AAGAACATCC
23787 CTAT-CAAATTTCAAGAACATCC
1 CTATGC-AATTTCAAGAACATCC
*
23809 CTATGAAATTT
1 CTATGCAATTT
23820 TTTAATGTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33
Consensus pattern (22 bp):
CTATGCAATTTCAAGAACATCC
Found at i:23971 original size:22 final size:22
Alignment explanation
Indices: 23836--23971 Score: 71
Period size: 22 Copynumber: 6.1 Consensus size: 22
23826 GTCCCTATAG
* *
23836 AATTTTGA-AATCATTACTATAA
1 AATTTTGATAATCA-CACTATGA
* * *
23858 AATTTTAATAATCTC-CATGTGA
1 AATTTTGATAATCACAC-TATGA
* * *
23880 AATGTTGGTAAGCACACTATGA
1 AATTTTGATAATCACACTATGA
* * * * *
23902 TATTTTTTATAACCTCCCTATGA
1 -AATTTTGATAATCACACTATGA
* * *
23925 AATTTT-AGTGATCACACTGTAA
1 AATTTTGA-TAATCACACTATGA
23947 AATTTTGATAATCACACTATGA
1 AATTTTGATAATCACACTATGA
23969 AAT
1 AAT
23972 CGTAATGACC
Statistics
Matches: 80, Mismatches: 28, Indels: 12
0.67 0.23 0.10
Matches are distributed among these distances:
21 2 0.03
22 57 0.71
23 21 0.26
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (22 bp):
AATTTTGATAATCACACTATGA
Found at i:24052 original size:22 final size:23
Alignment explanation
Indices: 23986--24069 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
23976 ATGACCTCGG
* *
23986 TATAAAAGTTTGATAAACATTCA
1 TATAAAAGTTTGATAAACCTCCA
* *
24009 TATAAAATTTTGATAAACCTCCC
1 TATAAAAGTTTGATAAACCTCCA
*
24032 TATAAAAGTTTGAT-AACCTCCT
1 TATAAAAGTTTGATAAACCTCCA
* *
24054 TATGAAATTTTGATAA
1 TATAAAAGTTTGATAA
24070 TCACAAATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
22 19 0.37
23 33 0.63
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (23 bp):
TATAAAAGTTTGATAAACCTCCA
Found at i:24250 original size:22 final size:22
Alignment explanation
Indices: 23994--24577 Score: 174
Period size: 22 Copynumber: 27.1 Consensus size: 22
23984 GGTATAAAAG
* *
23994 TTTGATAAACATTCATATAAAAT
1 TTTGAT-AACCTTCATATGAAAT
* * * *
24017 TTTGATAAACCTCCCTATAAAAG
1 TTTGAT-AACCTTCATATGAAAT
* *
24040 TTTGATAACCTCCTTATGAAAT
1 TTTGATAACCTTCATATGAAAT
*
24062 TTTGATAA---TC--A-CAAAT
1 TTTGATAACCTTCATATGAAAT
* *
24078 TTTGATAACCTCCCTATG--AT
1 TTTGATAACCTTCATATGAAAT
*
24098 TTCCCGATAA-CTTCATTATGAAAT
1 TT--TGATAACCTTCA-TATGAAAT
* *
24122 TTTGTTAACCTTCCTATGAAAT
1 TTTGATAACCTTCATATGAAAT
*
24144 TTTGATAACC-TC-TATAAAAT
1 TTTGATAACCTTCATATGAAAT
* **
24164 TTTGA-AAACTAAACTATGAAAT
1 TTTGATAACCTTCA-TATGAAAT
* * *
24186 TTTGATATCCTCCCTATGAAAT
1 TTTGATAACCTTCATATGAAAT
* * *
24208 TTTGATAATCC-CCCTTTGAAAT
1 TTTGATAA-CCTTCATATGAAAT
* *
24230 TTTGATAACCTTAATACGAAAT
1 TTTGATAACCTTCATATGAAAT
* * * * *
24252 GTTGGTAA-CTGCACAAATGTAATT
1 TTTGATAACCT--TCATATG-AAAT
*
24276 TTTGATAACC-TCACTTTGAAAT
1 TTTGATAACCTTCA-TATGAAAT
*** *
24298 ACCG-CAA---TC-TA--AAAT
1 TTTGATAACCTTCATATGAAAT
* * *
24313 TTGGATAA--TAACATTATAAAAT
1 TTTGATAACCT-TCA-TATGAAAT
* *
24335 TTCGATAACCTTCTTATGAAAT
1 TTTGATAACCTTCATATGAAAT
* * *
24357 TTCGATAACCTCCTTATGAAAT
1 TTTGATAACCTTCATATGAAAT
* *
24379 TTTGCTAACCTCTC-TACGAAAT
1 TTTGATAACCT-TCATATGAAAT
* *
24401 TTTGATAATCATACA-ATGAAA-
1 TTTGATAA-CCTTCATATGAAAT
* *
24422 TTTGA-AACCTACATATAAAAT
1 TTTGATAACCTTCATATGAAAT
* *
24443 TTTAATAACC-ACAATATGATAATT
1 TTTGATAACCTTC-ATATGA-AA-T
* *
24467 TTTCATAACC-TCACT-GGAAATT
1 TTTGATAACCTTCA-TATGAAA-T
* * *
24489 TTTGATAACC-TCGCTTTAAAAT
1 TTTGATAACCTTC-ATATGAAAT
*
24511 TTTGATAACCTTCATATAAAAT
1 TTTGATAACCTTCATATGAAAT
* *
24533 TTTGATAATC-ACATTATG-AAT
1 TTTGATAACCTTCA-TATGAAAT
* *
24554 TTTGATAACATTCGTATGAAAT
1 TTTGATAACCTTCATATGAAAT
24576 TT
1 TT
24578 AGAATTTTAT
Statistics
Matches: 422, Mismatches: 91, Indels: 97
0.69 0.15 0.16
Matches are distributed among these distances:
15 5 0.01
16 14 0.03
17 2 0.00
18 1 0.00
19 12 0.03
20 25 0.06
21 40 0.09
22 243 0.58
23 53 0.13
24 26 0.06
25 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTGATAACCTTCATATGAAAT
Found at i:24571 original size:21 final size:21
Alignment explanation
Indices: 24508--24573 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
24498 CTCGCTTTAA
* *
24508 AATTTTGATAACCTTCATATAA
1 AATTTTGATAACATTCATAT-G
24530 AATTTTGATAATCA--CATTATG
1 AATTTTGATAA-CATTCA-TATG
*
24551 AATTTTGATAACATTCGTATG
1 AATTTTGATAACATTCATATG
24572 AA
1 AA
24574 ATTTAGAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 2 0.05
21 19 0.51
22 15 0.41
23 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (21 bp):
AATTTTGATAACATTCATATG
Found at i:24592 original size:28 final size:29
Alignment explanation
Indices: 24550--24604 Score: 87
Period size: 28 Copynumber: 1.9 Consensus size: 29
24540 ATCACATTAT
24550 GAATTTTGATAACATT-CGTATGAAATTTA
1 GAATTTTGATAACATTAC-TATGAAATTTA
24579 GAATTTT-ATAACATTACTATGAAATT
1 GAATTTTGATAACATTACTATGAAATT
24605 CTAGTAACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (29 bp):
GAATTTTGATAACATTACTATGAAATTTA
Found at i:24703 original size:22 final size:22
Alignment explanation
Indices: 24580--24704 Score: 94
Period size: 22 Copynumber: 5.7 Consensus size: 22
24570 TGAAATTTAG
* *
24580 AATTTT-ATAACATTACTATGA
1 AATTTTAATAACCTCACTATGA
* * * *
24601 AATTCTAGTAACCACACTATAA
1 AATTTTAATAACCTCACTATGA
*
24623 AATCATTAATAACCTC-CTTAT-A
1 AAT-TTTAATAACCTCAC-TATGA
* *
24645 TAATTTTGATAACCACACTATGA
1 -AATTTTAATAACCTCACTATGA
* * *
24668 AATTCTGATAACCTCGCTATGA
1 AATTTTAATAACCTCACTATGA
24690 AATTTTAATAACCTC
1 AATTTTAATAACCTC
24705 TTTGATAGCC
Statistics
Matches: 80, Mismatches: 18, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
21 5 0.06
22 59 0.74
23 16 0.20
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (22 bp):
AATTTTAATAACCTCACTATGA
Found at i:24733 original size:22 final size:22
Alignment explanation
Indices: 24705--24803 Score: 110
Period size: 22 Copynumber: 4.4 Consensus size: 22
24695 TAATAACCTC
*
24705 TTTGATAGCCTTCCTATGAAAT
1 TTTGATAACCTTCCTATGAAAT
*
24727 TTTGATAACTTTCCTATGAAAT
1 TTTGATAACCTTCCTATGAAAT
*
24749 TTTAATAACCTAATCCATATGAAAT
1 TTTGATAACCT--TCC-TATGAAAT
*
24774 TTTGATAACC-ACTCTATGAAAT
1 TTTGATAACCTTC-CTATGAAAT
*
24796 TTTAATAA
1 TTTGATAA
24804 TCTTTTAATA
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
22 45 0.68
23 1 0.02
24 3 0.05
25 17 0.26
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.40
Consensus pattern (22 bp):
TTTGATAACCTTCCTATGAAAT
Found at i:24863 original size:99 final size:102
Alignment explanation
Indices: 24663--24904 Score: 305
Period size: 98 Copynumber: 2.4 Consensus size: 102
24653 ATAACCACAC
* * * * * **
24663 TATGAAATTCTGATAACCTCGCTATGAAATTTTAATAACCTCTTTGATAGCCTTCCTATGAAATT
1 TATGAAATTTTGATAACCACTCTATGAAATTTTAATAACCTCTTTAATAGCC-TACTAAAAAATT
*
24728 TTGATAACTTTCCTATGAAATTTTAATAACCTAATCCA
65 TTGATAACCTTCCTATGAAATTTTAATAACCTAATCCA
*
24766 TATGAAATTTTGATAACCACTCTATGAAATTTTAATAATCT-TTTAATA-CC-AC-AAAAAATAT
1 TATGAAATTTTGATAACCACTCTATGAAATTTTAATAACCTCTTTAATAGCCTACTAAAAAAT-T
* * *
24827 TTGATACCCTTCCTTTGAAATTTTAATAACCTAATCCC
65 TTGATAACCTTCCTATGAAATTTTAATAACCTAATCCA
* *
24865 TAT-AAATTTTGATAACCACTCGATGAAATTTTGATAACCT
1 TATGAAATTTTGATAACCACTCTATGAAATTTTAATAACCT
24905 TCATATGAAA
Statistics
Matches: 123, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
98 39 0.32
99 39 0.32
101 2 0.02
102 6 0.05
103 37 0.30
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.38
Consensus pattern (102 bp):
TATGAAATTTTGATAACCACTCTATGAAATTTTAATAACCTCTTTAATAGCCTACTAAAAAATTT
TGATAACCTTCCTATGAAATTTTAATAACCTAATCCA
Found at i:24896 original size:22 final size:22
Alignment explanation
Indices: 24864--25060 Score: 172
Period size: 22 Copynumber: 9.0 Consensus size: 22
24854 AACCTAATCC
*
24864 CTAT-AAATTTTGATAACCACT
1 CTATGAAATTTTGATAACCACA
* *
24885 CGATGAAATTTTGATAACCTTCA
1 CTATGAAATTTTGATAACC-ACA
*
24908 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
24929 CTATGAAA-TTTAAGTAACCACA
1 CTATGAAATTTTGA-TAACCACA
* * *
24951 ATATGAATTTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* *
24972 CTGATAAAATTTTG-TAACCAGA
1 CT-ATGAAATTTTGATAACCACA
*
24994 CTATGAAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
***
25015 CTAATGAAATTTTGATAATGTCA
1 CT-ATGAAATTTTGATAACCACA
* *
25038 TTATGAAATTTTGATCACCACA
1 CTATGAAATTTTGATAACCACA
25060 C
1 C
25061 AAAGACAACA
Statistics
Matches: 138, Mismatches: 28, Indels: 19
0.75 0.15 0.10
Matches are distributed among these distances:
21 26 0.19
22 106 0.77
23 6 0.04
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:24935 original size:44 final size:44
Alignment explanation
Indices: 24842--25058 Score: 155
Period size: 44 Copynumber: 4.9 Consensus size: 44
24832 ACCCTTCCTT
* * *
24842 TGAAATTTTAATAACCTAATCCCTAT-AAATTTTGATAACCA-CTCGA
1 TGAAATTTTGATAACCT--T-CATATGAAATTTTGATAACCACCT-AA
*
24888 TGAAATTTTGATAACCTTCATATGAAATTTTGGTAACCACACT-A
1 TGAAATTTTGATAACCTTCATATGAAATTTTGATAACCAC-CTAA
* * * * *
24932 TGAAA-TTTAAGTAACC-ACAATATGAATTTTTGATAACCTCCTGA
1 TGAAATTTTGA-TAACCTTC-ATATGAAATTTTGATAACCACCTAA
* ** *
24976 TAAAATTTTG-TAACC-AGACTATGAAATTTTGATAACCTCCTAA
1 TGAAATTTTGATAACCTTCA-TATGAAATTTTGATAACCACCTAA
*
25019 TGAAATTTTGATAA--TGTCATTATGAAATTTTGATCACCAC
1 TGAAATTTTGATAACCT-TCA-TATGAAATTTTGATAACCAC
25059 ACAAAGACAA
Statistics
Matches: 141, Mismatches: 19, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
42 1 0.01
43 48 0.34
44 71 0.50
45 3 0.02
46 18 0.13
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (44 bp):
TGAAATTTTGATAACCTTCATATGAAATTTTGATAACCACCTAA
Found at i:25047 original size:65 final size:63
Alignment explanation
Indices: 24864--25060 Score: 184
Period size: 65 Copynumber: 3.0 Consensus size: 63
24854 AACCTAATCC
*
24864 CTAT-AAATTTTGATAACCACTCGATGAAATTTTGATAACCTTCA-TATGAAATTTTGGTAACCA
1 CTATGAAATTTTGATAACCACT-AATGAAATTTTGATAA--TTCATTATGAAATTTT-GTAACCA
24927 CA
62 CA
* * * * * * * *
24929 CTATGAAA-TTTAAGTAACCACAATATGAATTTTTGATAACCTCCTGATAAAATTTTGTAACCAG
1 CTATGAAATTTTGA-TAACCACTA-ATGAAATTTTGATAA-TTCATTATGAAATTTTGTAACCAC
24993 A
63 A
* *
24994 CTATGAAATTTTGATAACCTCCTAATGAAATTTTGATAATGTCATTATGAAATTTTGATCACCAC
1 CTATGAAATTTTGATAACC-ACTAATGAAATTTTGATAAT-TCATTATGAAATTTTG-TAACCAC
25059 A
63 A
25060 C
1 C
25061 AAAGACAACA
Statistics
Matches: 105, Mismatches: 19, Indels: 15
0.76 0.14 0.11
Matches are distributed among these distances:
65 59 0.56
66 46 0.44
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (63 bp):
CTATGAAATTTTGATAACCACTAATGAAATTTTGATAATTCATTATGAAATTTTGTAACCACA
Found at i:34227 original size:21 final size:21
Alignment explanation
Indices: 34203--34269 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
34193 GTAATATAAA
34203 TAATAACTAAAATACTTACAT
1 TAATAACTAAAATACTTACAT
* ** *
34224 TAATTAAATGTAATA-ATAC-T
1 TAA-TAACTAAAATACTTACAT
*
34244 ATAATAACTAAAACACTTACAT
1 -TAATAACTAAAATACTTACAT
34266 TAAT
1 TAAT
34270 TAAATTCTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 8 0.24
21 16 0.48
22 9 0.27
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.34
Consensus pattern (21 bp):
TAATAACTAAAATACTTACAT
Found at i:34632 original size:203 final size:202
Alignment explanation
Indices: 34383--34795 Score: 633
Period size: 203 Copynumber: 2.0 Consensus size: 202
34373 GTTTCCTTAA
34383 TGATAAATAAAATCGGATCTTAATATTTTTAATTTATAATTTTGAAATTTTGTTTGACATTGATC
1 TGATAAATAAAATCGGATCTTAATATTTTTAA-TTATAATTTTGAAATTTTGTTTGACATTGATC
34448 TAATTTAATTTAATAAATCAACCACTAATGTTCAACTAAT-TTTTTTTGGTATAGTTCTATATAT
65 TAATTTAATTTAATAAATCAACCACTAATGTTCAACTAATCTTTTTTTGGTATAG-T-TATATAT
**
34512 ATAATTGTAATGTGTTGTATC-TATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTA
128 ATAATAATAATGTGTTGTATCTTATTCACTACAA----GTTAGTAATCTTAGACTTAAAAAATTA
34576 ATAACATTCACCAT
189 ATAACATTCACCAT
*
34590 TGATAAAT-AAATCGGATCTTTAATATCTTTT-A-TA-AA-TTTGAAATTTTGTTTGGCATTGAT
1 TGATAAATAAAATCGGATC-TTAATAT-TTTTAATTATAATTTTGAAATTTTGTTTGACATTGAT
* * *
34650 CTAATTTAGTTTAATAAATCAACCACTAATGTTCAACTACTCTTTTTTTGTTATAGTTATATATA
64 CTAATTTAATTTAATAAATCAACCACTAATGTTCAACTAATCTTTTTTTGGTATAGTTATATATA
34715 TAATAATAATGTGTTGTATCTTATTCACTACAAGTTAGTAATCTTAGACTTAAAAAATTAATAAC
129 TAATAATAATGTGTTGTATCTTATTCACTACAAGTTAGTAATCTTAGACTTAAAAAATTAATAAC
34780 ATTCACCAT
194 ATTCACCAT
*
34789 TCATAAA
1 TGATAAA
34796 GTTATTAAGC
Statistics
Matches: 195, Mismatches: 7, Indels: 16
0.89 0.03 0.07
Matches are distributed among these distances:
199 47 0.24
202 26 0.13
203 75 0.38
204 15 0.08
205 2 0.01
206 10 0.05
207 16 0.08
208 4 0.02
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (202 bp):
TGATAAATAAAATCGGATCTTAATATTTTTAATTATAATTTTGAAATTTTGTTTGACATTGATCT
AATTTAATTTAATAAATCAACCACTAATGTTCAACTAATCTTTTTTTGGTATAGTTATATATATA
ATAATAATGTGTTGTATCTTATTCACTACAAGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
TCACCAT
Done.