Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004449.1 Kokia drynarioides strain JFW-HI SEQ_117851, 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: 81391
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:5785 original size:16 final size:16
Alignment explanation
Indices: 5766--5800 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5756 TCAGTCTAAG
5766 AACTTCAATAAGTAAT
1 AACTTCAATAAGTAAT
5782 AACTTCAATAAGTAAT
1 AACTTCAATAAGTAAT
5798 AAC
1 AAC
5801 AACCATGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (16 bp):
AACTTCAATAAGTAAT
Found at i:12172 original size:76 final size:76
Alignment explanation
Indices: 12086--12328 Score: 280
Period size: 76 Copynumber: 3.2 Consensus size: 76
12076 ATTGTTCATT
* * * * * *
12086 TTTTTTATTTTTTTAGGGTAAATTCTAAATAAGTATATTGTTTATGTAAAATACT-ATA-GA-AT
1 TTTTTCATTTTTTT--GGTAAATTGTAAATAAGTATACTATTAATGTAAAA-ACTAATACAATAT
12148 ACAATACAAACAAA
63 ACAATACAAACAAA
*
12162 TTTTTCATTTTTTTGGTAAATTGTAAATAAGTATACTATTAATGTAAAAATTAATACAATATACA
1 TTTTTCATTTTTTTGGTAAATTGTAAATAAGTATACTATTAATGTAAAAACTAATACAATATACA
* *
12227 ATATAAGCAAA
66 ATACAAACAAA
* * *
12238 TTTTTCATTTTTTTGGTAAATTGTAAATAAGTATTCTATTGATG-CAAAACTTCAATACAATATA
1 TTTTTCATTTTTTTGGTAAATTGTAAATAAGTATACTATTAATGTAAAAAC-T-AATACAATATA
12302 CAATACAAAC-AA
64 CAATACAAACAAA
*
12314 TTTGTTCCTTTTTTT
1 TTT-TTCATTTTTTT
12329 TTATAAACGT
Statistics
Matches: 145, Mismatches: 16, Indels: 11
0.84 0.09 0.06
Matches are distributed among these distances:
73 2 0.01
74 34 0.23
75 5 0.03
76 75 0.52
77 29 0.20
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (76 bp):
TTTTTCATTTTTTTGGTAAATTGTAAATAAGTATACTATTAATGTAAAAACTAATACAATATACA
ATACAAACAAA
Found at i:12616 original size:12 final size:12
Alignment explanation
Indices: 12601--12632 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
12591 TCTTTATCTC
12601 CACCTCCACCTT
1 CACCTCCACCTT
12613 CACCTCCACCTT
1 CACCTCCACCTT
12625 CACCTCCA
1 CACCTCCA
12633 TCTCCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.19, C:0.59, G:0.00, T:0.22
Consensus pattern (12 bp):
CACCTCCACCTT
Found at i:12649 original size:24 final size:24
Alignment explanation
Indices: 12622--12673 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
12612 TCACCTCCAC
*
12622 CTTCACCTCCATCTCCATTTTGGT
1 CTTCACCTCCATCTCCATCTTGGT
* * * *
12646 CTTCATCTTCATCTTCATCTTGTT
1 CTTCACCTCCATCTCCATCTTGGT
12670 CTTC
1 CTTC
12674 CGTGTTATAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.35, G:0.06, T:0.48
Consensus pattern (24 bp):
CTTCACCTCCATCTCCATCTTGGT
Found at i:12666 original size:18 final size:18
Alignment explanation
Indices: 12583--12666 Score: 60
Period size: 18 Copynumber: 4.7 Consensus size: 18
12573 TATTCTTTTT
*
12583 CATCTTCATCTTTATCTC
1 CATCTTCATCTTCATCTC
* * * *
12601 CACCTCCACCTTCACCTC
1 CATCTTCATCTTCATCTC
* * *
12619 CACCTTCACCTCCATCTC
1 CATCTTCATCTTCATCTC
* ** *
12637 CATTTTGGTCTTCATCTT
1 CATCTTCATCTTCATCTC
12655 CATCTTCATCTT
1 CATCTTCATCTT
12667 GTTCTTCCGT
Statistics
Matches: 48, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.15, C:0.42, G:0.02, T:0.40
Consensus pattern (18 bp):
CATCTTCATCTTCATCTC
Found at i:16930 original size:9 final size:9
Alignment explanation
Indices: 16916--16944 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
16906 AATCATCGAT
16916 ATTTTTAAA
1 ATTTTTAAA
16925 ATTTTTAAA
1 ATTTTTAAA
16934 A-TTTTAAA
1 ATTTTTAAA
16942 ATT
1 ATT
16945 ATGAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:16951 original size:17 final size:17
Alignment explanation
Indices: 16918--16952 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
16908 TCATCGATAT
* *
16918 TTTTAAAATTTTTAAAA
1 TTTTAAAATTATGAAAA
16935 TTTTAAAATTATGAAAA
1 TTTTAAAATTATGAAAA
16952 T
1 T
16953 AAAATAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TTTTAAAATTATGAAAA
Found at i:17021 original size:23 final size:23
Alignment explanation
Indices: 16995--17050 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
16985 AGAGAAGAAT
*
16995 TTGAGAGAAATTAAATGAAAAAA
1 TTGAGAGAAAATAAATGAAAAAA
* * **
17018 TTGAGAATAAAATAATTGAGGAAA
1 TTGAG-AGAAAATAAATGAAAAAA
17042 TTGAGAGAA
1 TTGAGAGAA
17051 TAGGATGGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.23
Consensus pattern (23 bp):
TTGAGAGAAAATAAATGAAAAAA
Found at i:31597 original size:24 final size:24
Alignment explanation
Indices: 31565--31633 Score: 102
Period size: 24 Copynumber: 2.8 Consensus size: 24
31555 TAATCTAGAC
31565 TAAACAGAGTTTAACTGAAACAAA
1 TAAACAGAGTTTAACTGAAACAAA
* *
31589 TAAACAGAGTTTAATTAAAACAAA
1 TAAACAGAGTTTAACTGAAACAAA
*
31613 TAAATAGAGTTTAACTCGAAA
1 TAAACAGAGTTTAACT-GAAA
31634 ATTATTTCTC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 36 0.92
25 3 0.08
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.25
Consensus pattern (24 bp):
TAAACAGAGTTTAACTGAAACAAA
Found at i:33618 original size:30 final size:30
Alignment explanation
Indices: 33582--33638 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
33572 AAATAATATT
*
33582 AAAAATTACTTAAATATCAAAATAAAATAA
1 AAAAATTAATTAAATATCAAAATAAAATAA
* *
33612 AAAAATTAATTAATTATGAAAATAAAA
1 AAAAATTAATTAAATATCAAAATAAAA
33639 CATTTGCGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (30 bp):
AAAAATTAATTAAATATCAAAATAAAATAA
Found at i:34666 original size:94 final size:94
Alignment explanation
Indices: 34501--34695 Score: 255
Period size: 94 Copynumber: 2.1 Consensus size: 94
34491 TTAACAATAA
** * * * * * *
34501 AAATTTAGCTGTGCTAATAATTGAATATGAATTTCGAAATCTTAAAAATAGAGAGGCTAAATTCT
1 AAATTTAGCAATGTTAATAATCGAATATGAATTTCAAAATCTAAAAAATAAAGAGGCTAAATTCC
* *
34566 TAAAAATAAAAGTCAAGAGACTAAATTCT
66 TAAAAATAAAAATCAAAAGACTAAATTCT
* * *
34595 CAATTTAGCAATGTTAATAATCGAATCTGAATTTTAAAATCTAAAAAATAAAGAGGCTAAATTCC
1 AAATTTAGCAATGTTAATAATCGAATATGAATTTCAAAATCTAAAAAATAAAGAGGCTAAATTCC
* *
34660 TGAAAATAAAAATCAAAAGACTGAATTCT
66 TAAAAATAAAAATCAAAAGACTAAATTCT
34689 AAATTTA
1 AAATTTA
34696 TGAAGAATAC
Statistics
Matches: 85, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
94 85 1.00
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (94 bp):
AAATTTAGCAATGTTAATAATCGAATATGAATTTCAAAATCTAAAAAATAAAGAGGCTAAATTCC
TAAAAATAAAAATCAAAAGACTAAATTCT
Found at i:44142 original size:19 final size:21
Alignment explanation
Indices: 44118--44174 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
44108 TTCTCATCAT
44118 ATTATTTATGAT-TTTT-TTA
1 ATTATTTATGATATTTTATTA
*
44137 ATTATTTAATTATATTTTATTA
1 ATTATTT-ATGATATTTTATTA
* *
44159 ATTTTTTATGCTATTT
1 ATTATTTATGATATTT
44175 ATACATAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 7 0.23
20 4 0.13
21 11 0.35
22 9 0.29
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (21 bp):
ATTATTTATGATATTTTATTA
Found at i:44153 original size:22 final size:23
Alignment explanation
Indices: 44123--44166 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
44113 ATCATATTAT
*
44123 TTATGATTTTTTTAATTATTTAA
1 TTATGATTTTATTAATTATTTAA
*
44146 TTAT-ATTTTATTAATTTTTTA
1 TTATGATTTTATTAATTATTTA
44167 TGCTATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TTATGATTTTATTAATTATTTAA
Found at i:44165 original size:32 final size:33
Alignment explanation
Indices: 44129--44200 Score: 78
Period size: 32 Copynumber: 2.2 Consensus size: 33
44119 TTATTTATGA
* *
44129 TTTTTTTAATTATTTA-A-TTATATTTTATTAAT
1 TTTTTTTAACTATTTATACATA-ATTTTATTAAT
* *
44161 TTTTTAT-GCTATTTATACATAATTTTATTAAT
1 TTTTTTTAACTATTTATACATAATTTTATTAAT
44193 TTTTTTTA
1 TTTTTTTA
44201 CTTTGAACCT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
31 6 0.19
32 24 0.75
33 2 0.06
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (33 bp):
TTTTTTTAACTATTTATACATAATTTTATTAAT
Found at i:44767 original size:1 final size:1
Alignment explanation
Indices: 44761--44801 Score: 55
Period size: 1 Copynumber: 41.0 Consensus size: 1
44751 CTCCTGGCAT
* * *
44761 AAAAAAAAAAAAAAGAAAAAAAGAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
44802 GGAAAATCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:44789 original size:20 final size:20
Alignment explanation
Indices: 44762--44807 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 20
44752 TCCTGGCATA
44762 AAAAAAAAAAAAAGAAAAAAAG
1 AAAAAAAAAAAAAG--AAAAAG
*
44784 AAAAAAAAAAAAAGAAAAGG
1 AAAAAAAAAAAAAGAAAAAG
44804 AAAA
1 AAAA
44808 TCAATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.39
22 14 0.61
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAAGAAAAAG
Found at i:44807 original size:14 final size:14
Alignment explanation
Indices: 44762--44807 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
44752 TCCTGGCATA
*
44762 AAAAAAAAAAAAAG
1 AAAAAAAGAAAAAG
*
44776 AAAAAAAGAAAAAA
1 AAAAAAAGAAAAAG
*
44790 AAAAAAAGAAAAGG
1 AAAAAAAGAAAAAG
44804 AAAA
1 AAAA
44808 TCAATAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:47004 original size:24 final size:25
Alignment explanation
Indices: 46976--47041 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 25
46966 AATAAAAATC
*
46976 TATTTTTATCA-TTTAAATAATTTA
1 TATTTTTATAATTTTAAATAATTTA
47000 TATTTTTATAATTTTTAAATAA-TTA
1 TATTTTTATAA-TTTTAAATAATTTA
*
47025 -AATTTTA-AATTTTAAAT
1 TATTTTTATAATTTTAAAT
47042 TTTAAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.21
23 2 0.05
24 16 0.42
25 3 0.08
26 9 0.24
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTTTTATAATTTTAAATAATTTA
Found at i:47034 original size:7 final size:7
Alignment explanation
Indices: 47012--47053 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
47002 TTTTTATAAT
47012 TTTTAAA
1 TTTTAAA
*
47019 TAATTAAA
1 T-TTTAAA
47027 TTTTAAA
1 TTTTAAA
47034 TTTTAAA
1 TTTTAAA
47041 TTTTAAA
1 TTTTAAA
47048 TTTTAA
1 TTTTAA
47054 GGAAAGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
7 26 0.81
8 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
TTTTAAA
Found at i:55410 original size:12 final size:12
Alignment explanation
Indices: 55393--55418 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55383 AGAAAACAGT
55393 TTGTTCACTCTA
1 TTGTTCACTCTA
55405 TTGTTCACTCTA
1 TTGTTCACTCTA
55417 TT
1 TT
55419 ATACCAATAA
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:0.15, C:0.23, G:0.08, T:0.54
Consensus pattern (12 bp):
TTGTTCACTCTA
Found at i:61024 original size:483 final size:483
Alignment explanation
Indices: 60103--61072 Score: 1561
Period size: 483 Copynumber: 2.0 Consensus size: 483
60093 CACAACTTCA
*
60103 TGCAGTTGGGTTCTCTCCTCTTGAGTTGCACTGAGCAGCTGCTCTGCTTCCAGAAACTCATTCTC
1 TGCAGTAGGGTTCTCTCCTCTTGAGTTGCACTGAGCAGCTGCTCTGCTTCCAGAAACTCATTCTC
* * *
60168 CTTCTGGCATAGTAGATCCTTTCCCTTCACGACTTCAGCATTTAACTGATCGCAAACAGATCTAA
66 CTTCAGGCATAATAGATCCTTTCCCTTCACAACTTCAGCATTTAACTGATCGCAAACAGATCTAA
* *
60233 CTGAAACTAGTTCATTCTCCAAATTCTGCACCGTATCCTTGAGATGTGAGTTTACCATTTGTGTT
131 CTGAAACTAGCTCATTCTCCAAATTCTGCACCGTATCCTTGAGATGTGAGTTTACCATTTGCGTT
*
60298 TCTTCAAACTTGATCCCCATTATCCTCAGTTTTCCCTCAAGATTATCATTGAAACATTTGAGTTT
196 TCTTCAAACTTGATCCCCATTATCCTCAGTTTTCCCTCAAGATCATCATTGAAACATTTGAGTTT
*
60363 ATCCAGATTGGCACTGAGATGCTTTATTTCAACAAAATTATCAGTAATAATGTCCTTAAGAATAT
261 ATCCAGATTGGCACTGAGATGCTTTATTTCAACAAAATTATCAGTAATAATGTCCTTAAGAATAA
* * *
60428 GTGAAATGTTACTTTGAGATATTGCTTCAGCAAAGACAGCGCAGTTTTCCTCTTCTAGATTGTGT
326 GAGAAATGTTACTTTGAGATATTGCTTCAGCAAAGACAGCACAATTTTCCTCTTCTAGATTGTGT
* *
60493 TTCTCCATGCCCAAGTCTGAAACAAATTTCATCAAAGTCCTTTTCTCATCTAGCACCTTGTGGTT
391 TTCTCCATGCCCAAATCTGAAACAAACTTCATCAAAGTCCTTTTCTCATCTAGCACCTTGTGGTT
60558 CTCTTCAACTAAACTTTGATATGCCCTT
456 CTCTTCAACTAAACTTTGATATGCCCTT
* * * * *
60586 TGCAGTAGGTTTCTTTCCTCTTGAGTTGCACTGAGCATCTTCTCTGCTTCCA-AAAGCTCCTTCT
1 TGCAGTAGGGTTCTCTCCTCTTGAGTTGCACTGAGCAGCTGCTCTGCTTCCAGAAA-CTCATTCT
*
60650 CCTTCAGGCATAATAGATCCTTTCCCTTCACAACTTC-GTCATTTAACTGATCGCATACAGATCT
65 CCTTCAGGCATAATAGATCCTTTCCCTTCACAACTTCAG-CATTTAACTGATCGCAAACAGATCT
* * *
60714 AACTGAAATTAGCTCATTCTCCAAGTTCTGCACTGTATCCTTGAGATGTGAGTTTACCATTTGCG
129 AACTGAAACTAGCTCATTCTCCAAATTCTGCACCGTATCCTTGAGATGTGAGTTTACCATTTGCG
* * * *
60779 TTTCTTCAAGCTTGATCTCCATTATCCTCAGTTTTCCCTCAAGATCGTCATTGGAACATTTGAGT
194 TTTCTTCAAACTTGATCCCCATTATCCTCAGTTTTCCCTCAAGATCATCATTGAAACATTTGAGT
* * * *
60844 TTGTCCAGATTGGCACTGAGATGCTTTATTTCCACAAAATTATCAGTAATAATGTTCTTGAGAAT
259 TTATCCAGATTGGCACTGAGATGCTTTATTTCAACAAAATTATCAGTAATAATGTCCTTAAGAAT
*
60909 AAGAGCAATGTTACTTTGAGATATTGCTTC-GCCAAAGACAGCACAATTTTCCTCTTCTAGATTG
324 AAGAGAAATGTTACTTTGAGATATTGCTTCAG-CAAAGACAGCACAATTTTCCTCTTCTAGATTG
***
60973 TGTTTCT-CATTGCCCAAATCTGAAACTTCCTTCATCAAAGTCCTTTTCTCATCTAGCACCTTGT
388 TGTTTCTCCA-TGCCCAAATCTGAAACAAACTTCATCAAAGTCCTTTTCTCATCTAGCACCTTGT
*
61037 GGTTCTCTTCAACTGAACTTTGATATGCCCTT
452 GGTTCTCTTCAACTAAACTTTGATATGCCCTT
61069 TGCA
1 TGCA
61073 ACTCTGATAG
Statistics
Matches: 448, Mismatches: 35, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
482 7 0.02
483 441 0.98
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (483 bp):
TGCAGTAGGGTTCTCTCCTCTTGAGTTGCACTGAGCAGCTGCTCTGCTTCCAGAAACTCATTCTC
CTTCAGGCATAATAGATCCTTTCCCTTCACAACTTCAGCATTTAACTGATCGCAAACAGATCTAA
CTGAAACTAGCTCATTCTCCAAATTCTGCACCGTATCCTTGAGATGTGAGTTTACCATTTGCGTT
TCTTCAAACTTGATCCCCATTATCCTCAGTTTTCCCTCAAGATCATCATTGAAACATTTGAGTTT
ATCCAGATTGGCACTGAGATGCTTTATTTCAACAAAATTATCAGTAATAATGTCCTTAAGAATAA
GAGAAATGTTACTTTGAGATATTGCTTCAGCAAAGACAGCACAATTTTCCTCTTCTAGATTGTGT
TTCTCCATGCCCAAATCTGAAACAAACTTCATCAAAGTCCTTTTCTCATCTAGCACCTTGTGGTT
CTCTTCAACTAAACTTTGATATGCCCTT
Found at i:63373 original size:855 final size:861
Alignment explanation
Indices: 61256--64694 Score: 3717
Period size: 888 Copynumber: 3.9 Consensus size: 861
61246 TTATTCTCAG
* *
61256 TTTCAGCCTCTAGTTTCTGTTGCCTAAG-AATTCCAATAAGAACTGAATTCTCAATTATGAATTG
1 TTTCAGCCTCTAGTTTCAGTTGCCCAAGCAA-TCCAATAAGAACTGAATTCTCAATTATGAATTG
* *
61320 TTGATTTTCATCCAGAGACATTAGAAGTGAATTTTGCATCTTTTGGAGCCTGCCAAATATACAGT
65 CTGATTTTCATCCAGAGACTTTA-AAGTGAATTTTGCATCTTTTGGAGCCTGCCAAATATACAGT
* * *
61385 CAAGAACTGATTGGTCTTGTTTGAT-TGCATCATCAAAACCACGGATAGCATCAACT-TCAAGAG
129 CAAGAACTGATTGGTCTTGTTTGATCTGTATCATCATAACCATGGATAGCATCAA-TATCAAGAG
* * * * *
61448 TCCTCAACATCTGATAAATCCCCATCCTCAGTACAG-AATTTTGATCAAATAAGGCTTTTATCTC
193 TCCTCAACATCTGAT-AAGCCCCATCCTCAGTATAGTAA-TTAGATC-AGTAAGGATTTTATCTC
** * * * ** * *
61512 TGTCT-TTTTTATGGAATTTCCAAGCTCCAATTCTGAGATAAGTTCTTCTGATAATTTAGAGGCT
255 CATCTGTTTTT-TGGAATTTCCGAGCTCCAATTCAGAGATAAGTTTTTAGGA-AAATTGGAGGCT
* ** * *
61576 TCCAAGAGGTTCCTACACTCAAGCACCAAGGATAAATTCTTCTCTTCCAGATCTTGTGCACATTT
318 TCCAAGAGTTTCCTACACTCAAGCAATAGGGATAAATTCTTCTCTTCCAGATCTTGTGCACATCT
* * *
61641 TTGCAAGATGAAGGTTTCTACATGAGCATTCATGGCCTTAT-CTAGCTCCTCTTCATATTCTTTT
383 CTGCAAAATGAAGGTTTCTACATGAG----CAT-GCC--ATGC--G-T-C-C-TC----TC--GT
* * * *
61705 TTCATACGCAGGCTTTCTCCTTGTAGAAAATGGATCTGAGATTCCATAGAAGTAGC-CTTGGATT
429 TGCATA-G-A----TTCCCCTTGTAGAAAATGGATCTGAGATTCCATAGAAGTAACTC-GGGATT
* * * * *
61769 CATTCAACTTCACAACACTATCATGTTGC-TGCGTTTCAGCATCTAATGACCTTTGTAGTTCTTC
487 CATTCAACTTCACAAAACTAGCATGTT-CTTGCATTTCAGCATCTAATGACTTTTGTAGCTCTTC
** *
61833 TACTTCATGAAGCATTGATTCTCTCTCTTTCTCCAGGA-CCACATACTTTTCTTCTAATCCCTGA
551 TACTTCATGAAGTGTTGATTCTCTCTCTTTCTCCA-GACCCACATATTTTTCTTCTAATCCCTGA
* *
61897 TATCTTTTTTCCAAATCTTCCATCCTTTTCTGACTGATATTCAACTCAGAAATCAAACCTTCTCT
615 TATCTTTTTTCCAAATCTTCCAGCCTTTTCTGACTGACATTCAACTCAGAAATCAAACCTTCTCT
*
61962 CTGTGTTAGCAGACCAGACTTCTCATCACCAAGTAGCTGGTATGAAATTTCTAAGCTCTTTAATT
680 CTGTGTTAGCAGACCAGACTTCTCATCACCAAGCAGCTGGTATGAAATTTCTAAGCTCTTTAATT
* *
62027 TTGTCC-TCAATCCTTCAACTTCAGCATTTGCATCACAAAGATAATTCTT-CACTTCCGAAAACT
745 TTG-CCTTCAATCCTTCAACTTCAGCATTTGCATCACAAAGATGATT-TTCCACTTCAGAAAACT
62090 GCTCAGACTGAACCTTCAACTCCTGATGCAGTGAGTTATTTTCTGTTGCAAGAT
808 GCTCAGACTGAACCTTCAACTCCTGATGCAGTGAGTTATTTTCTGTTGCAAGAT
*
62144 TTTCAGCCTCTAGCTTCAGTTGCCCAAGCAATCCAATAAGAACTGAATTCTCAATTATGAATTGC
1 TTTCAGCCTCTAGTTTCAGTTGCCCAAGCAATCCAATAAGAACTGAATTCTCAATTATGAATTGC
* * *
62209 TGATTTTCATCCTGAGACTTCAAAAGTGAATTTTGCATCTTTTGGAGTCTGCCAAATATACAGTC
66 TGATTTTCATCCAGAGACTT-TAAAGTGAATTTTGCATCTTTTGGAGCCTGCCAAATATACAGTC
* ** * **
62274 AAGAACTGATCGGTCTTGTTTGATCATG-A-CATCATAACTGTGGATAGCATCGATCCCAAGAGT
130 AAGAACTGATTGGTCTTGTTTGATC-TGTATCATCATAACCATGGATAGCATCAATATCAAGAGT
* * * *
62337 CCTCAACATCTGATTAAGTCCCATCCTCAATATGGTAATTAGATCAAATAAGGATTTTATCTCCA
194 CCTCAACATCTGA-TAAGCCCCATCCTCAGTATAGTAATTAGATC-AGTAAGGATTTTATCTCCA
* * * * ** * *
62402 TCTGTTTTCTGGAATTTCCTAGCTCCAATTCAGAGATAAGTATTTCA-GACAATTTCAACGTTTC
257 TCTGTTTTTTGGAATTTCCGAGCTCCAATTCAGAGATAAGT-TTTTAGGA-AAATTGGAGGCTTC
* *
62466 CAAGAGCTTCCTACACTCAAGCAATAGGGATAAATTCTTATCTTCCAGATCTTGTGCACATCTCT
320 CAAGAGTTTCCTACACTCAAGCAATAGGGATAAATTCTTCTCTTCCAGATCTTGTGCACATCTCT
*
62531 GCAAAACGAAGGTTTCTACATGAGCAT-CCATG-G-CCT-T-G-T-CA-AG-TTCCCCTTGTAGA
385 GCAAAATGAAGGTTTCTACATGAGCATGCCATGCGTCCTCTCGTTGCATAGATTCCCCTTGTAGA
* *
62587 AAATGGATCTGAGATACCATAGAAGTAACTCGGGTTTCATTCAACTTCACAAAACTAGCATGTTC
450 AAATGGATCTGAGATTCCATAGAAGTAACTCGGGATTCATTCAACTTCACAAAACTAGCATGTTC
** * * * *
62652 TTGCATTTCAATATCCAATGACTTTTGTAGCTCTTGTACTCCATGAAGTGCTGATTCTCTCTCTT
515 TTGCATTTCAGCATCTAATGACTTTTGTAGCTCTTCTACTTCATGAAGTGTTGATTCTCTCTCTT
* * *
62717 TCTCCAAACCCACATATTTTTCTTCTAATTCCTGATAT-TGTTTTTCCAAATCTTTCAGCCTTTT
580 TCTCCAGACCCACATATTTTTCTTCTAATCCCTGATATCT-TTTTTCCAAATCTTCCAGCCTTTT
* *
62781 CTGGCTGACATTCAACTCA-AAAGTCAAACCTTCTCTCTGTGTTAGCAGACCAGACTTTTCATCA
644 CTGACTGACATTCAACTCAGAAA-TCAAACCTTCTCTCTGTGTTAGCAGACCAGACTTCTCATCA
62845 CCAAGCAGCTGGTATGAAATTTCTAAGCTCTTTAATTTTGCCTTCAATCCTTCAACTTCAGCATT
708 CCAAGCAGCTGGTATGAAATTTCTAAGCTCTTTAATTTTGCCTTCAATCCTTCAACTTCAGCATT
* *
62910 TGCATCACAAAGATGATTTTCCACTTCAGAAAATTGCTCAGACTGAACCTTCAGCTCCTGATGCA
773 TGCATCACAAAGATGATTTTCCACTTCAGAAAACTGCTCAGACTGAACCTTCAACTCCTGATGCA
*
62975 GTGAATTATTTTCTGTTGCAAGAT
838 GTGAGTTATTTTCTGTTGCAAGAT
*
62999 TTTCAGCCTCTAGTTTCAGTTGCCCAAGCAATCCAATAAGAACTGAATTCTCAATTATGAACTGC
1 TTTCAGCCTCTAGTTTCAGTTGCCCAAGCAATCCAATAAGAACTGAATTCTCAATTATGAATTGC
* *
63064 TCATTTTCATCCAGAGACTTTAGAAGTGAATTTTGCATCTTTTGGAGCCTGCCAGATATACAGTC
66 TGATTTTCATCCAGAGACTTTA-AAGTGAATTTTGCATCTTTTGGAGCCTGCCAAATATACAGTC
* * *
63129 AAGAATTGATTGATCTTGTTTGAT-TGTATCATCATAACCATGGATAGCATCAAAATCAAGAGTC
130 AAGAACTGATTGGTCTTGTTTGATCTGTATCATCATAACCATGGATAGCATCAATATCAAGAGTC
* * * * *
63193 CTCAACATCTGATAGAGCCCCATCTTCAGTATAGTGATTTGATCAGTTAAGGATTCTATCTCCAC
195 CTCAACATCTGATA-AGCCCCATCCTCAGTATAGTAATTAGATCAG-TAAGGATTTTATCTCCAT
* * * * *
63258 CTGTTTTTTGGAATTTCCGAGCTCCAACTCGGAGATAAGTTTTTTGGATAATCTGGTGGCTTCCA
258 CTGTTTTTTGGAATTTCCGAGCTCCAATTCAGAGATAAGTTTTTAGGAAAAT-TGGAGGCTTCCA
* *
63323 AGAGTTTGCTACACTCACA-CAATAGGGATAAATTCTTCTCTTCGAGATCTTGTGCACATCTCTG
322 AGAGTTTCCTACACTCA-AGCAATAGGGATAAATTCTTCTCTTCCAGATCTTGTGCACATCTCTG
*
63387 CAAAATGAAGGTTTCTACATGAGCATTCATGGCCCTGTCCAGTTCCTCCTCGTATTCTTTCTTCC
386 CAAAATGAAGGTTTCTACATGAG----CAT-GCCATG--C-G-TCCT-CTCG----------T--
* * * *
63452 TGCATAGACTTTCTCCTTGTAGAAAATGGATTTGAGATTCCATAGAAGTGACTCGGGCTTCATTC
429 TGCATAGA--TTCCCCTTGTAGAAAATGGATCTGAGATTCCATAGAAGTAACTCGGGATTCATTC
* * * * *
63517 GACTTCACAAATCTAGCATGTTCTTGCTTTTCCGCATCTAGTGACTTTTGTAGCTCTTCTACTTC
492 AACTTCACAAAACTAGCATGTTCTTGCATTTCAGCATCTAATGACTTTTGTAGCTCTTCTACTTC
** * * *
63582 ACAAAGTGTTGTTTCTCTCTCTTTCTCCAGACCCACGTATTTTTCCTCTAATCCCTGATATCTTT
557 ATGAAGTGTTGATTCTCTCTCTTTCTCCAGACCCACATATTTTTCTTCTAATCCCTGATATCTTT
** * *
63647 CCTCCAAATCTTCCAGCCTTTTCTGACTGACATTCAACTCAGATATCAAATCTTCTCTCTGTGTT
622 TTTCCAAATCTTCCAGCCTTTTCTGACTGACATTCAACTCAGAAATCAAACCTTCTCTCTGTGTT
* * * * * *
63712 AGCA-AGCCAGACTTCTCTTCACCAAGCTGCAGGCATGAACTTTCTAAGCTC-CTAAGTTTTGCT
687 AGCAGA-CCAGACTTCTCATCACCAAGCAGCTGGTATGAAATTTCTAAGCTCTTTAA-TTTTGC-
* * * * * * * * * * *
63775 CTTGATAT--TTCAAGTTCAGCATTTGCATTAAAAAG-GGAAGTCTCCAATTCTGAGAACTGTTC
749 CTTCA-ATCCTTCAACTTCAGCATTTGCATCACAAAGATG-ATTTTCCACTTCAGAAAACTGCTC
* * * *
63837 -GAACTGAACCTTCAACTCCTGGTGCAGTGAGTTCTTCTCTGTAGCAAGAT
812 AG-ACTGAACCTTCAACTCCTGATGCAGTGAGTTATTTTCTGTTGCAAGAT
* * *
63887 TTTCTGCCTCAAGTTTCAGTTGCCCAAGCAATCCAATAAGAACTGAATTCTCGATTATGAATTGC
1 TTTCAGCCTCTAGTTTCAGTTGCCCAAGCAATCCAATAAGAACTGAATTCTCAATTATGAATTGC
* * * *
63952 TGATTATCATCCAGAGACTTTAAATGTGAGTTCTGCATCTTTTGGATCCCT-CCAAATATACAGT
66 TGATTTTCATCCAGAGACTTTAAA-GTGAATTTTGCATCTTTTGGA-GCCTGCCAAATATACAGT
* *
64016 CAAGAACTAATTGGTCTTGTTTGATCT-TATCATCATAACCATGG--A-CATCAATTTCAAGAG-
129 CAAGAACTGATTGGTCTTGTTTGATCTGTATCATCATAACCATGGATAGCATCAATATCAAGAGT
* * * *
64076 CATTCAGCATTTGATAAAGCCCCATCCTCAGTATAGTAATTCGATCAAGTAAGGATTTTATCTCC
194 C-CTCAACATCTGAT-AAGCCCCATCCTCAGTATAGTAATTAGATC-AGTAAGGATTTTATCTCC
* * * *
64141 ATCTCTTTTTCGGAATTTCTGAGCTCCAATTCAGAGATAAGTTTTTCAGAAAAATTGGAGGCTTC
256 ATCTGTTTTTTGGAATTTCCGAGCTCCAATTCAGAGATAAGTTTTT-AGGAAAATTGGAGGCTTC
* * * *
64206 CAGGAGTTTCCTACACTCAAGCAGTAGGGATAAATTCTTCTCTTCCATATCTTGTGCACATTTCT
320 CAAGAGTTTCCTACACTCAAGCAATAGGGATAAATTCTTCTCTTCCAGATCTTGTGCACATCTCT
* *
64271 GCAAGATGAAGGTTTCTACATGAGCATTCATAGACC-TGTCCAGTTCCTCTTCATATTCTTTCTT
385 GCAAAATGAAGGTTTCTACATGAG----CAT-G-CCATG--C-G----TC--C----TC--TC-G
* * * *
64335 TCTGCACAGACTTTCCCCTTGTAGAAAACGGATCTGAGATTCCATAGCAGTAACTCGGGTTTCAT
428 T-TGCATAGA--TTCCCCTTGTAGAAAATGGATCTGAGATTCCATAGAAGTAACTCGGGATTCAT
* ** * * * * *
64400 TCAACTGCATGAAACTGGCATATTCTTGCTTTTCCGCATCTAGTGACTTTTGTAGCTCTTCTACT
490 TCAACTTCACAAAACTAGCATGTTCTTGCATTTCAGCATCTAATGACTTTTGTAGCTCTTCTACT
* * ** *
64465 TCACT-AAGTGTTAATTCTCTCTCTTTCTCCAGGCCCATGTATTTTTCTTCTAAACCCTGATATC
555 TCA-TGAAGTGTTGATTCTCTCTCTTTCTCCAGACCCACATATTTTTCTTCTAATCCCTGATATC
* * * * *
64529 TTTTTTCCAAATCTTCCAACCTTTTCTGACTGATACTCAACTCAGAAATCAAGCCTTCTCTTTGT
619 TTTTTTCCAAATCTTCCAGCCTTTTCTGACTGACATTCAACTCAGAAATCAAACCTTCTCTCTGT
* * * * * * * *
64594 CTTATCAGGCCA-ATCTTCTCATCACCAAGCAGCAGGCATGAATTTTCTAAGCTCATTACCTTTA
684 GTTAGCAGACCAGA-CTTCTCATCACCAAGCAGCTGGTATGAAATTTCTAAGCTCTTTA-ATTT-
* * *
64658 T-CC-TCAATCCTCCAAGTTCAGCATTTGCATCAAAAAG
746 TGCCTTCAATCCTTCAACTTCAGCATTTGCATCACAAAG
64695 GGAATTCTCC
Statistics
Matches: 2198, Mismatches: 258, Indels: 193
0.83 0.10 0.07
Matches are distributed among these distances:
853 2 0.00
854 20 0.01
855 722 0.33
856 2 0.00
859 3 0.00
861 5 0.00
862 1 0.00
863 2 0.00
864 1 0.00
865 1 0.00
867 3 0.00
868 1 0.00
869 1 0.00
870 1 0.00
873 1 0.00
874 1 0.00
875 1 0.00
878 1 0.00
880 2 0.00
882 2 0.00
883 3 0.00
884 10 0.00
885 508 0.23
886 18 0.01
887 10 0.00
888 843 0.38
889 24 0.01
890 5 0.00
893 1 0.00
894 1 0.00
895 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (861 bp):
TTTCAGCCTCTAGTTTCAGTTGCCCAAGCAATCCAATAAGAACTGAATTCTCAATTATGAATTGC
TGATTTTCATCCAGAGACTTTAAAGTGAATTTTGCATCTTTTGGAGCCTGCCAAATATACAGTCA
AGAACTGATTGGTCTTGTTTGATCTGTATCATCATAACCATGGATAGCATCAATATCAAGAGTCC
TCAACATCTGATAAGCCCCATCCTCAGTATAGTAATTAGATCAGTAAGGATTTTATCTCCATCTG
TTTTTTGGAATTTCCGAGCTCCAATTCAGAGATAAGTTTTTAGGAAAATTGGAGGCTTCCAAGAG
TTTCCTACACTCAAGCAATAGGGATAAATTCTTCTCTTCCAGATCTTGTGCACATCTCTGCAAAA
TGAAGGTTTCTACATGAGCATGCCATGCGTCCTCTCGTTGCATAGATTCCCCTTGTAGAAAATGG
ATCTGAGATTCCATAGAAGTAACTCGGGATTCATTCAACTTCACAAAACTAGCATGTTCTTGCAT
TTCAGCATCTAATGACTTTTGTAGCTCTTCTACTTCATGAAGTGTTGATTCTCTCTCTTTCTCCA
GACCCACATATTTTTCTTCTAATCCCTGATATCTTTTTTCCAAATCTTCCAGCCTTTTCTGACTG
ACATTCAACTCAGAAATCAAACCTTCTCTCTGTGTTAGCAGACCAGACTTCTCATCACCAAGCAG
CTGGTATGAAATTTCTAAGCTCTTTAATTTTGCCTTCAATCCTTCAACTTCAGCATTTGCATCAC
AAAGATGATTTTCCACTTCAGAAAACTGCTCAGACTGAACCTTCAACTCCTGATGCAGTGAGTTA
TTTTCTGTTGCAAGAT
Found at i:64695 original size:885 final size:884
Alignment explanation
Indices: 62574--64705 Score: 2820
Period size: 885 Copynumber: 2.4 Consensus size: 884
62564 CCTTGTCAAG
*
62574 TTCCCCTTGTAGAAAATGGATCTGAGATACCATAGAAGTAACTCGGGTTTCATTCAACTTCACAA
1 TTCCCCTTGTAGAAAATGGATCTGAGATTCCATAGAAGTAACTCGGGTTTCATTCAACTTCA-AA
* *** * * * * *
62639 AACTAGCATGTTCTTGCATTTCAATATCCAATGACTTTTGTAGCTCTTGTACTCCA-TGAAGTGC
65 AACTAGCATGTTCTTGCTTTTCCGCATCTAGTGACTTTTGTAGCTCTTCTACTTCACT-AAGTGT
* * *
62703 TGATTCTCTCTCTTTCTCCAAACCCACATATTTTTCTTCTAATTCCTGATAT-TGTTTTTCCAAA
129 TGATTCTCTCTCTTTCTCCAGACCCACGTATTTTTCTTCTAATCCCTGATATCT-TTTTTCCAAA
* * *
62767 TCTTTCAGCCTTTTCTGGCTGACATTCAACTCA-AAAGTCAAACCTTCTCTCTGTGTTAGCAGAC
193 TCTTCCAGCCTTTTCTGACTGACATTCAACTCAGAAA-TCAAACCTTCTCTCTGTGTTAGCAGGC
* * *
62831 CAGACTTTTCATCACCAAGCAGCTGGTATGAAATTTCTAAGCTCTTTAATTTTGCCTTCAATCCT
257 CAGACTTCTCATCACCAAGCAGCAGGCATGAAATTTCTAAGCTC-TTAATTTTGCC-TCAATCCT
* * * * * *
62896 TCAACTTCAGCATTTGCATCACAAAGATG-ATTTTCCACTTCAGAAAATTGCTCAGACTGAACCT
320 TCAAGTTCAGCATTTGCATCAAAAAG-GGAATTCTCCAATTCAGAAAACTGCTCAGACTGAACCT
* * * *
62960 TCAGCTCCTGATGCAGTGAATTATTTTCTGTTGCAAGATTTTCAGCCTCTAGTTTCAGTTGCCCA
384 TCAACTCCTGATGCAGTGAATTATTCTCTGTAGCAAGATTTTCAGCCTCAAGTTTCAGTTGCCCA
*
63025 AGCAATCCAATAAGAACTGAATTCTCAATTATGAACTGCTCATTTTCATCCAGAGACTTTAGAAG
449 AGCAATCCAATAAGAACTGAATTCTCAATTATGAACTGCTCATTATCATCCAGAGACTTTAGAAG
* * * * *
63090 TGAATTTTGCATCTTTTGGAGCCTGCCAGATATACAGTCAAGAATTGATTGATCTTGTTTGATTG
514 TGAATTCTGCATCTTTTGGACCCTGCCAAATATACAGTCAAGAACTAATTGATCTTGTTTGATTG
* *
63155 TATCATCATAACCATGGATAGCATCAAAATCAAGAGTCCTCAACATCTGATAGAGCCCCATCTTC
579 TATCATCATAACCATGGA-AGCATCAAAATCAAGAGTCCTCAACATCTGATAAAGCCCCATCCTC
* * * *
63220 AGTATAGTGATTTGATCAGTTAAGGATTCTATCTCCACCTGTTTTTTGGAATTTCCGAGCTCCAA
643 AGTATAGTAATTCGATCAGTTAAGGATTCTATCTCCACCTCTTTTTCGGAATTTCCGAGCTCCAA
* * * * * *
63285 CTCGGAGATAAGTTTTTTGGATAATCTGGTGGCTTCCAAGAGTTTGCTACACTCACACAATAGGG
708 CTCAGAGATAAGTTTTTAGAAAAATCTGGAGGCTTCCAAGAGTTTCCTACACTCACACAATAGGG
*
63350 ATAAATTCTTCTCTTCGAGATCTTGTGCACATCTCTGCAAAATGAAGGTTTCTACATGAGCATTC
773 ATAAATTCTTCTCTTCCAGATCTTGTGCACATCTCTGCAAAATGAAGGTTTCTACATGAGCATTC
* * * *
63415 ATGGCCCTGTCCAGTTCCTCCTCGTATTCTTTCTTCCTGCATAGACT
838 ATAGACCTGTCCAGTTCCTCCTCATATTCTTTCTTCCTGCACAGACT
* * * * *
63462 TTCTCCTTGTAGAAAATGGATTTGAGATTCCATAGAAGTGACTCGGGCTTCATTCGACTTCACAA
1 TTCCCCTTGTAGAAAATGGATCTGAGATTCCATAGAAGTAACTCGGGTTTCATTCAACTTCA-AA
* *
63527 ATCTAGCATGTTCTTGCTTTTCCGCATCTAGTGACTTTTGTAGCTCTTCTACTTCACAAAGTGTT
65 AACTAGCATGTTCTTGCTTTTCCGCATCTAGTGACTTTTGTAGCTCTTCTACTTCACTAAGTGTT
* * **
63592 GTTTCTCTCTCTTTCTCCAGACCCACGTATTTTTCCTCTAATCCCTGATATCTTTCCTCCAAATC
130 GATTCTCTCTCTTTCTCCAGACCCACGTATTTTTCTTCTAATCCCTGATATCTTTTTTCCAAATC
* * *
63657 TTCCAGCCTTTTCTGACTGACATTCAACTCAGATATCAAATCTTCTCTCTGTGTTAGCAAGCCAG
195 TTCCAGCCTTTTCTGACTGACATTCAACTCAGAAATCAAACCTTCTCTCTGTGTTAGCAGGCCAG
* * * * ** **
63722 ACTTCTCTTCACCAAGCTGCAGGCATGAACTTTCTAAGCTCCTAAGTTTTGCTCTTGATATTTCA
260 ACTTCTCATCACCAAGCAGCAGGCATGAAATTTCTAAGCTCTTAA-TTTTGC-CTCAATCCTTCA
* * * * *
63787 AGTTCAGCATTTGCATTAAAAAGGGAAGTCTCCAATTCTGAGAACTGTTC-GAACTGAACCTTCA
323 AGTTCAGCATTTGCATCAAAAAGGGAATTCTCCAATTCAGAAAACTGCTCAG-ACTGAACCTTCA
* * * *
63851 ACTCCTGGTGCAGTGAGTTCTTCTCTGTAGCAAGATTTTCTGCCTCAAGTTTCAGTTGCCCAAGC
387 ACTCCTGATGCAGTGAATTATTCTCTGTAGCAAGATTTTCAGCCTCAAGTTTCAGTTGCCCAAGC
* * *
63916 AATCCAATAAGAACTGAATTCTCGATTATGAATTGCTGATTATCATCCAGAGACTTTA-AATGTG
452 AATCCAATAAGAACTGAATTCTCAATTATGAACTGCTCATTATCATCCAGAGACTTTAGAA-GTG
* *
63980 AGTTCTGCATCTTTTGGATCCCT-CCAAATATACAGTCAAGAACTAATTGGTCTTGTTTGATCT-
516 AATTCTGCATCTTTTGGA-CCCTGCCAAATATACAGTCAAGAACTAATTGATCTTGTTTGAT-TG
** * * *
64043 TATCATCATAACCATGG-A-CATCAATTTCAAGAG-CATTCAGCATTTGATAAAGCCCCATCCTC
579 TATCATCATAACCATGGAAGCATCAAAATCAAGAGTC-CTCAACATCTGATAAAGCCCCATCCTC
* * *
64105 AGTATAGTAATTCGATCAAG-TAAGGATTTTATCTCCATCTCTTTTTCGGAATTTCTGAGCTCCA
643 AGTATAGTAATTCGATC-AGTTAAGGATTCTATCTCCACCTCTTTTTCGGAATTTCCGAGCTCCA
* * *
64169 ATTCAGAGATAAGTTTTTCAGAAAAAT-TGGAGGCTTCCAGGAGTTTCCTACACTCA-AGCAGTA
707 ACTCAGAGATAAGTTTTT-AGAAAAATCTGGAGGCTTCCAAGAGTTTCCTACACTCACA-CAATA
* * *
64232 GGGATAAATTCTTCTCTTCCATATCTTGTGCACATTTCTGCAAGATGAAGGTTTCTACATGAGCA
770 GGGATAAATTCTTCTCTTCCAGATCTTGTGCACATCTCTGCAAAATGAAGGTTTCTACATGAGCA
* *
64297 TTCATAGACCTGTCCAGTTCCTCTTCATATTCTTTCTTTCTGCACAGACT
835 TTCATAGACCTGTCCAGTTCCTCCTCATATTCTTTCTTCCTGCACAGACT
* * * *
64347 TTCCCCTTGTAGAAAACGGATCTGAGATTCCATAGCAGTAACTCGGGTTTCATTCAACTGCATGA
1 TTCCCCTTGTAGAAAATGGATCTGAGATTCCATAGAAGTAACTCGGGTTTCATTCAACTTCA-AA
* *
64412 AACTGGCATATTCTTGCTTTTCCGCATCTAGTGACTTTTGTAGCTCTTCTACTTCACTAAGTGTT
65 AACTAGCATGTTCTTGCTTTTCCGCATCTAGTGACTTTTGTAGCTCTTCTACTTCACTAAGTGTT
* * * *
64477 AATTCTCTCTCTTTCTCCAGGCCCATGTATTTTTCTTCTAAACCCTGATATCTTTTTTCCAAATC
130 GATTCTCTCTCTTTCTCCAGACCCACGTATTTTTCTTCTAATCCCTGATATCTTTTTTCCAAATC
* * * * * * *
64542 TTCCAACCTTTTCTGACTGATACTCAACTCAGAAATCAAGCCTTCTCTTTGTCTTATCAGGCCA-
195 TTCCAGCCTTTTCTGACTGACATTCAACTCAGAAATCAAACCTTCTCTCTGTGTTAGCAGGCCAG
* * *
64606 ATCTTCTCATCACCAAGCAGCAGGCATGAATTTTCTAAGCTCATTACCTTTAT-CCTCAATCCTC
260 A-CTTCTCATCACCAAGCAGCAGGCATGAAATTTCTAAGCTC-TTA-ATTT-TGCCTCAATCCTT
64670 CAAGTTCAGCATTTGCATCAAAAAGGGAATTCTCCA
321 CAAGTTCAGCATTTGCATCAAAAAGGGAATTCTCCA
64706 GCACGTTATT
Statistics
Matches: 1078, Mismatches: 148, Indels: 39
0.85 0.12 0.03
Matches are distributed among these distances:
884 3 0.00
885 543 0.50
886 14 0.01
887 8 0.01
888 502 0.47
889 8 0.01
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (884 bp):
TTCCCCTTGTAGAAAATGGATCTGAGATTCCATAGAAGTAACTCGGGTTTCATTCAACTTCAAAA
ACTAGCATGTTCTTGCTTTTCCGCATCTAGTGACTTTTGTAGCTCTTCTACTTCACTAAGTGTTG
ATTCTCTCTCTTTCTCCAGACCCACGTATTTTTCTTCTAATCCCTGATATCTTTTTTCCAAATCT
TCCAGCCTTTTCTGACTGACATTCAACTCAGAAATCAAACCTTCTCTCTGTGTTAGCAGGCCAGA
CTTCTCATCACCAAGCAGCAGGCATGAAATTTCTAAGCTCTTAATTTTGCCTCAATCCTTCAAGT
TCAGCATTTGCATCAAAAAGGGAATTCTCCAATTCAGAAAACTGCTCAGACTGAACCTTCAACTC
CTGATGCAGTGAATTATTCTCTGTAGCAAGATTTTCAGCCTCAAGTTTCAGTTGCCCAAGCAATC
CAATAAGAACTGAATTCTCAATTATGAACTGCTCATTATCATCCAGAGACTTTAGAAGTGAATTC
TGCATCTTTTGGACCCTGCCAAATATACAGTCAAGAACTAATTGATCTTGTTTGATTGTATCATC
ATAACCATGGAAGCATCAAAATCAAGAGTCCTCAACATCTGATAAAGCCCCATCCTCAGTATAGT
AATTCGATCAGTTAAGGATTCTATCTCCACCTCTTTTTCGGAATTTCCGAGCTCCAACTCAGAGA
TAAGTTTTTAGAAAAATCTGGAGGCTTCCAAGAGTTTCCTACACTCACACAATAGGGATAAATTC
TTCTCTTCCAGATCTTGTGCACATCTCTGCAAAATGAAGGTTTCTACATGAGCATTCATAGACCT
GTCCAGTTCCTCCTCATATTCTTTCTTCCTGCACAGACT
Found at i:68775 original size:16 final size:16
Alignment explanation
Indices: 68752--68786 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
68742 CTTAAAATGG
*
68752 AATTTTTTT-TATTTA
1 AATTTTTTTAAATTTA
68767 AATTTTTTTAAATTTA
1 AATTTTTTTAAATTTA
68783 AATT
1 AATT
68787 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
AATTTTTTTAAATTTA
Found at i:71879 original size:22 final size:22
Alignment explanation
Indices: 71849--71899 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
71839 GTTTTTTTTC
* **
71849 TGTTGTTGTTTCGTTGCCATTT
1 TGTTATTGTTTCACTGCCATTT
* *
71871 TGTTATTGTTTTACTGTCATTT
1 TGTTATTGTTTCACTGCCATTT
71893 TGTTATT
1 TGTTATT
71900 ATATTGTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.10, C:0.10, G:0.18, T:0.63
Consensus pattern (22 bp):
TGTTATTGTTTCACTGCCATTT
Found at i:74221 original size:23 final size:23
Alignment explanation
Indices: 74173--74228 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
74163 CATGTGTACC
* *
74173 TTTTAATGATAACAATAATTAGT
1 TTTTAATAATAACAATAATAAGT
*
74196 TTTTAATAATAA-AATAGATAATT
1 TTTTAATAATAACAATA-ATAAGT
74219 TTTTCAATAA
1 TTTT-AATAA
74229 AATGACCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.14
23 19 0.68
24 5 0.18
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (23 bp):
TTTTAATAATAACAATAATAAGT
Done.