Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006274.1 Kokia drynarioides strain JFW-HI SEQ_120845, 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: 164310
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1040 original size:46 final size:44
Alignment explanation
Indices: 990--1083 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
980 TGTTCGCTGT
990 AATGGAATAAAACTGTAATTAGTATTTCAGT-TGTTTGGTTGAATGA
1 AATGGAATAAAACTGTAA-TAGTA-TTC-GTGTGTTTGGTTGAATGA
* * * *
1036 AATGGAATAGAGCTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAAAACTGTAATAGTATTCGTGTGTTTGGTTGAATGA
1080 AATG
1 AATG
1084 ATGTTGTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.49
45 5 0.12
46 16 0.37
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (44 bp):
AATGGAATAAAACTGTAATAGTATTCGTGTGTTTGGTTGAATGA
Found at i:1332 original size:25 final size:24
Alignment explanation
Indices: 1304--1354 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1294 TAATATAATT
*
1304 ATTATTAAAATATGA-ATTAATAAAA
1 ATTA-TAAAATATAATATTAA-AAAA
*
1329 ATTATAATATATAATATTAAAAAA
1 ATTATAAAATATAATATTAAAAAA
1353 AT
1 AT
1355 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAAAAAA
Found at i:3228 original size:2 final size:2
Alignment explanation
Indices: 3221--3249 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3211 ATTCTAAATC
3221 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 A
3250 ATTACTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15328 original size:32 final size:32
Alignment explanation
Indices: 15287--15350 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
15277 CTATACTTCT
15287 ACCGATACATGCATGGGTTCTACTAGAACAAG
1 ACCGATACATGCATGGGTTCTACTAGAACAAG
*
15319 ACCGATACATGCATGGGTTCTACTGGAACAAG
1 ACCGATACATGCATGGGTTCTACTAGAACAAG
15351 TATGCAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (32 bp):
ACCGATACATGCATGGGTTCTACTAGAACAAG
Found at i:21317 original size:79 final size:83
Alignment explanation
Indices: 21171--21324 Score: 190
Period size: 79 Copynumber: 1.9 Consensus size: 83
21161 TTAATTTTTT
* *
21171 GTTTGGAAACTAAATCAAAATCAAATCAAATCTATTGAACGACGAGAATAAATCCCGAAATAAAA
1 GTTTGGAAACTAAATCAAAATCAAA-CAAATCTATTGAACGACGAGAATAAATCCCAAAACAAAA
*
21236 TTATTTAATTCTAATTCTC
65 TTATTCAATTCTAATTCTC
* * * ** *
21255 GTTTGGAAACTAAATCAAAAT-AAA-ATAT-T-TTGAATGACGGGAATAAATTTCAAAACAGAAT
1 GTTTGGAAACTAAATCAAAATCAAACAAATCTATTGAACGACGAGAATAAATCCCAAAACAAAAT
21316 TATTCAATT
66 TATTCAATT
21325 AGTTCTTATT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
79 33 0.54
80 1 0.02
81 3 0.05
83 3 0.05
84 21 0.34
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (83 bp):
GTTTGGAAACTAAATCAAAATCAAACAAATCTATTGAACGACGAGAATAAATCCCAAAACAAAAT
TATTCAATTCTAATTCTC
Found at i:21863 original size:13 final size:13
Alignment explanation
Indices: 21847--21873 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21837 GTTTATATAA
21847 AAACACCATATTT
1 AAACACCATATTT
21860 AAACACCATATTT
1 AAACACCATATTT
21873 A
1 A
21874 TATTTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAACACCATATTT
Found at i:24408 original size:21 final size:23
Alignment explanation
Indices: 24366--24409 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
24356 TTAGGTTAAT
*
24366 TTTAGATTAAATAATTTCATTAG
1 TTTAGATTAAATAATTTAATTAG
*
24389 TTTA-ATT-AATACTTTAATTAG
1 TTTAGATTAAATAATTTAATTAG
24410 GATCGACACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 3 0.16
23 4 0.21
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (23 bp):
TTTAGATTAAATAATTTAATTAG
Found at i:26215 original size:19 final size:20
Alignment explanation
Indices: 26188--26226 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
26178 AAATATTTTG
*
26188 TTTTGATTAACTTATTCAAA
1 TTTTGATTAACTGATTCAAA
26208 TTTT-ATTAACTGATTCAAA
1 TTTTGATTAACTGATTCAAA
26227 AGTTAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTTGATTAACTGATTCAAA
Found at i:27648 original size:24 final size:24
Alignment explanation
Indices: 27601--27649 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
27591 TGATCCAATT
* * * *
27601 AATATAGAGATAGACGTAGTCATA
1 AATATAGACATAGAAGAAGACATA
27625 AATATAGACATAGAAGAAGACATA
1 AATATAGACATAGAAGAAGACATA
27649 A
1 A
27650 TCACTAGCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.20
Consensus pattern (24 bp):
AATATAGACATAGAAGAAGACATA
Found at i:28826 original size:12 final size:12
Alignment explanation
Indices: 28809--28902 Score: 68
Period size: 12 Copynumber: 7.9 Consensus size: 12
28799 ATAACATCCA
28809 AACAACCAAAAT
1 AACAACCAAAAT
*
28821 AACAACCAAACT
1 AACAACCAAAAT
* * *
28833 AGCAGCAAAAAT
1 AACAACCAAAAT
*
28845 AACAA-CAAAAC
1 AACAACCAAAAT
*
28856 AACAACAAAAAT
1 AACAACCAAAAT
*
28868 AGCAACAACAAAA-
1 AACAAC--CAAAAT
*
28881 AAAAACCAAAAT
1 AACAACCAAAAT
*
28893 AGC-ACCAAAA
1 AACAACCAAAA
28903 CAATTAAAAA
Statistics
Matches: 61, Mismatches: 17, Indels: 9
0.70 0.20 0.10
Matches are distributed among these distances:
11 21 0.34
12 32 0.52
13 4 0.07
14 4 0.07
ACGTcount: A:0.67, C:0.23, G:0.04, T:0.05
Consensus pattern (12 bp):
AACAACCAAAAT
Found at i:28844 original size:24 final size:23
Alignment explanation
Indices: 28809--28938 Score: 84
Period size: 22 Copynumber: 5.6 Consensus size: 23
28799 ATAACATCCA
* *
28809 AACAACCAAAATAACAACCAAAC
1 AACAACAAAAATAACAACAAAAC
* *
28832 TAGCAGCAAAAATAACAACAAAAC
1 -AACAACAAAAATAACAACAAAAC
28856 AACAACAAAAATAGCAACAACAAAA-
1 AACAACAAAAAT---AACAACAAAAC
* * * *
28881 AAAAACCAAAATAGCACCAAAAC
1 AACAACAAAAATAACAACAAAAC
** * *
28904 AATTA-AAAAATAGCACCAAAAC
1 AACAACAAAAATAACAACAAAAC
* *
28926 AATAACCAAAATA
1 AACAACAAAAATA
28939 GTAAAAAACC
Statistics
Matches: 86, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
22 28 0.33
23 19 0.22
24 19 0.22
25 10 0.12
26 10 0.12
ACGTcount: A:0.66, C:0.22, G:0.04, T:0.08
Consensus pattern (23 bp):
AACAACAAAAATAACAACAAAAC
Found at i:32473 original size:52 final size:51
Alignment explanation
Indices: 32416--32527 Score: 143
Period size: 52 Copynumber: 2.2 Consensus size: 51
32406 TCTCATTCCT
* * **
32416 ATTTTACCTATAATAAAATTTTGATGATTTTATGCCTAGTAAAATTATGACA
1 ATTTTACCCATAATAAAATTTTGACGATTTTACCCCTA-TAAAATTATGACA
* * *
32468 ATTTTACCCCTAATAAAATTTTGACGATTTTACCCCTATAAAATTTTGATA
1 ATTTTACCCATAATAAAATTTTGACGATTTTACCCCTATAAAATTATGACA
*
32519 AATTTACCC
1 ATTTTACCC
32528 CAGGTAACAT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 19 0.37
52 33 0.63
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (51 bp):
ATTTTACCCATAATAAAATTTTGACGATTTTACCCCTATAAAATTATGACA
Found at i:32514 original size:25 final size:25
Alignment explanation
Indices: 32428--32516 Score: 115
Period size: 26 Copynumber: 3.5 Consensus size: 25
32418 TTTACCTATA
* **
32428 ATAAAATTTTGATGATTTTATGCCT
1 ATAAAATTTTGACGATTTTACCCCT
* *
32453 AGTAAAATTATGACAATTTTACCCCT
1 A-TAAAATTTTGACGATTTTACCCCT
32479 AATAAAATTTTGACGATTTTACCCCT
1 -ATAAAATTTTGACGATTTTACCCCT
32505 ATAAAATTTTGA
1 ATAAAATTTTGA
32517 TAAATTTACC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
25 13 0.24
26 41 0.75
27 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.40
Consensus pattern (25 bp):
ATAAAATTTTGACGATTTTACCCCT
Found at i:32524 original size:25 final size:25
Alignment explanation
Indices: 32428--32528 Score: 112
Period size: 26 Copynumber: 4.0 Consensus size: 25
32418 TTTACCTATA
** **
32428 ATAAAATTTTGATGATTTTATGCCT
1 ATAAAATTTTGACAATTTTACCCCT
*
32453 AGTAAAATTATGACAATTTTACCCCT
1 A-TAAAATTTTGACAATTTTACCCCT
*
32479 AATAAAATTTTGACGATTTTACCCCT
1 -ATAAAATTTTGACAATTTTACCCCT
* *
32505 ATAAAATTTTGATAAATTTACCCC
1 ATAAAATTTTGACAATTTTACCCC
32529 AGGTAACATT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
25 22 0.34
26 41 0.64
27 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.40
Consensus pattern (25 bp):
ATAAAATTTTGACAATTTTACCCCT
Found at i:32684 original size:26 final size:26
Alignment explanation
Indices: 32612--32692 Score: 119
Period size: 26 Copynumber: 3.2 Consensus size: 26
32602 AATTTTCAAG
* *
32612 AAAATTATGACGATTTTACCACTAGT
1 AAAATTATGACGATTTTACCCCTAAT
32638 AAAATTATGACGATTTTACCCCTAAT
1 AAAATTATGACGATTTTACCCCTAAT
* *
32664 AAAATTATGACGGTTTTACCCAT-AT
1 AAAATTATGACGATTTTACCCCTAAT
32689 AAAA
1 AAAA
32693 ATTTGACAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 6 0.12
26 45 0.88
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (26 bp):
AAAATTATGACGATTTTACCCCTAAT
Found at i:32748 original size:182 final size:182
Alignment explanation
Indices: 32451--32789 Score: 534
Period size: 182 Copynumber: 1.9 Consensus size: 182
32441 GATTTTATGC
* * *
32451 CTAGTAAAATTATGACAATTTTACCCCTAATAAAATTTTGACGATTTTACCCCTATAAAATTTTG
1 CTAGTAAAATTATGACAATTTTACCCCTAATAAAATTATGACGATTTTACCCATATAAAAATTTG
* * * * *
32516 ATAAATTTACCCCAGGTAACATTTCAAGAAAATATGTTAAATATTTCATAACTCAACATTCTCAC
66 ACAAACTTACCCCAGATAAAATTTCAAGAAAATATGTTAAATATTTCATAACACAACATTCTCAC
* *
32581 TATAATTGGATGGTTTATTTTAATTTTCAAGAAAATTATGACGATTTTACCA
131 TATAACTGGATGATTTATTTTAATTTTCAAGAAAATTATGACGATTTTACCA
* *
32633 CTAGTAAAATTATGACGATTTTACCCCTAATAAAATTATGACGGTTTTACCCATATAAAAATTTG
1 CTAGTAAAATTATGACAATTTTACCCCTAATAAAATTATGACGATTTTACCCATATAAAAATTTG
* * *
32698 ACAAACTTACCCCCGATAAAATTTCAAGAAAATATGTTTAATATTTCATAACACAACTTTCTCAC
66 ACAAACTTACCCCAGATAAAATTTCAAGAAAATATGTTAAATATTTCATAACACAACATTCTCAC
*
32763 TGTAACTGGATGATTTATTTTAATTTT
131 TATAACTGGATGATTTATTTTAATTTT
32790 TTAGCTTTAA
Statistics
Matches: 141, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
182 141 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (182 bp):
CTAGTAAAATTATGACAATTTTACCCCTAATAAAATTATGACGATTTTACCCATATAAAAATTTG
ACAAACTTACCCCAGATAAAATTTCAAGAAAATATGTTAAATATTTCATAACACAACATTCTCAC
TATAACTGGATGATTTATTTTAATTTTCAAGAAAATTATGACGATTTTACCA
Found at i:49210 original size:20 final size:20
Alignment explanation
Indices: 49172--49210 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
49162 TCTTTGTCTA
*
49172 CTTCAATGCCCTGACAATGC
1 CTTCAATGCCATGACAATGC
49192 CTTCAATTGCCATGA-AATG
1 CTTCAA-TGCCATGACAATG
49211 ACATTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
CTTCAATGCCATGACAATGC
Found at i:51476 original size:17 final size:19
Alignment explanation
Indices: 51448--51482 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
51438 TCTGTTATGG
51448 TTGCATTCTAGCT-TGTGA
1 TTGCATTCTAGCTATGTGA
51466 TTGCA-TCTAGCTATGTG
1 TTGCATTCTAGCTATGTG
51483 TCTGCATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (19 bp):
TTGCATTCTAGCTATGTGA
Found at i:57957 original size:17 final size:18
Alignment explanation
Indices: 57935--57982 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
57925 TATCATGTAG
*
57935 TTGTCATCACATTTTTA-
1 TTGTCAACACATTTTTAT
*
57952 TTGTCACCACA-TTTTAT
1 TTGTCAACACATTTTTAT
57969 TTGTCAACACATTT
1 TTGTCAACACATTT
57983 GCATTGTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 5 0.19
17 20 0.74
18 2 0.07
ACGTcount: A:0.25, C:0.21, G:0.06, T:0.48
Consensus pattern (18 bp):
TTGTCAACACATTTTTAT
Found at i:58595 original size:2 final size:2
Alignment explanation
Indices: 58590--58619 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
58580 AGAAAATCTA
58590 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58620 CTAAATGTTG
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:65979 original size:14 final size:14
Alignment explanation
Indices: 65960--65990 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
65950 TTATCATAAA
65960 TTTTTTTCTTCTTT
1 TTTTTTTCTTCTTT
65974 TTTTTTTCTTCTTT
1 TTTTTTTCTTCTTT
65988 TTT
1 TTT
65991 CTCATTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTTTCTTCTTT
Found at i:67103 original size:21 final size:21
Alignment explanation
Indices: 67058--67101 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
67048 CTTCATGTCA
* *
67058 TTCTCTTCTTCTTTTTCTTCT
1 TTCTCTTCCTCTTCTTCTTCT
67079 TTCTCTTCCTCTTCCTTCTTCT
1 TTCTCTTCCTCTT-CTTCTTCT
67101 T
1 T
67102 CTGGTCATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (21 bp):
TTCTCTTCCTCTTCTTCTTCT
Found at i:76574 original size:31 final size:32
Alignment explanation
Indices: 76538--76611 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 32
76528 TATTCGAGTT
76538 AAGACTAAAATTTTA-AAATTCAAAAAGTACA
1 AAGACTAAAATTTTACAAATTCAAAAAGTACA
* *
76569 AAGACTAAAA-TTTACCAATTCTAAAAGTACA
1 AAGACTAAAATTTTACAAATTCAAAAAGTACA
*
76600 ATGACTAAAATT
1 AAGACTAAAATT
76612 AATCAAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.11
31 33 0.87
32 1 0.03
ACGTcount: A:0.54, C:0.12, G:0.07, T:0.27
Consensus pattern (32 bp):
AAGACTAAAATTTTACAAATTCAAAAAGTACA
Found at i:76631 original size:29 final size:31
Alignment explanation
Indices: 76560--76637 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 31
76550 TTAAAATTCA
* * *
76560 AAAAGTACAAAGACTAAAATTTACCAATTCT
1 AAAAGTACAATGACTAAAATTAACCAAATCT
*
76591 AAAAGTACAATGACTAAAATTAATCAAAT-T
1 AAAAGTACAATGACTAAAATTAACCAAATCT
*
76621 -AAAGTACAATGGCTAAA
1 AAAAGTACAATGACTAAA
76638 CCCAAAACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 16 0.38
30 1 0.02
31 25 0.60
ACGTcount: A:0.54, C:0.13, G:0.09, T:0.24
Consensus pattern (31 bp):
AAAAGTACAATGACTAAAATTAACCAAATCT
Found at i:77244 original size:20 final size:20
Alignment explanation
Indices: 77212--77252 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
77202 TAAAGAAATT
77212 TATATATTAAAATATTTTCA
1 TATATATTAAAATATTTTCA
77232 TATA-ATTACAAATATTTTCA
1 TATATATTA-AAATATTTTCA
77252 T
1 T
77253 CTCTTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (20 bp):
TATATATTAAAATATTTTCA
Found at i:78006 original size:13 final size:13
Alignment explanation
Indices: 77988--78040 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
77978 TAGGTTTTTT
77988 AATTTAATATTTA
1 AATTTAATATTTA
*
78001 AATTTAATATTTTT
1 AATTTAATA-TTTA
* ** *
78015 AAGTTCGTATTTG
1 AATTTAATATTTA
78028 AATTTAATATTTA
1 AATTTAATATTTA
78041 TTTTTAATTT
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
13 21 0.70
14 9 0.30
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (13 bp):
AATTTAATATTTA
Found at i:85411 original size:16 final size:17
Alignment explanation
Indices: 85379--85412 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
85369 GAAATTCTTA
85379 ACAAACATAAACTGAAC
1 ACAAACATAAACTGAAC
*
85396 ACAAACA-AACCTGAAC
1 ACAAACATAAACTGAAC
85412 A
1 A
85413 GAAATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.59, C:0.26, G:0.06, T:0.09
Consensus pattern (17 bp):
ACAAACATAAACTGAAC
Found at i:102143 original size:34 final size:34
Alignment explanation
Indices: 102100--102170 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
102090 GAAAAATAAA
102100 ATATAATCCGATTTTTAGCACGAAAATATTCATC
1 ATATAATCCGATTTTTAGCACGAAAATATTCATC
*
102134 ATATAATCCGATTTTTAGCATGAAAATATTCATC
1 ATATAATCCGATTTTTAGCACGAAAATATTCATC
102168 ATA
1 ATA
102171 CTTTTATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.37
Consensus pattern (34 bp):
ATATAATCCGATTTTTAGCACGAAAATATTCATC
Found at i:103771 original size:15 final size:15
Alignment explanation
Indices: 103751--103781 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
103741 TGCCTTTACA
103751 AAATTTGACTGTAGC
1 AAATTTGACTGTAGC
103766 AAATTTGACTGTAGC
1 AAATTTGACTGTAGC
103781 A
1 A
103782 TTGCTTTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (15 bp):
AAATTTGACTGTAGC
Found at i:105477 original size:97 final size:98
Alignment explanation
Indices: 105310--105505 Score: 358
Period size: 97 Copynumber: 2.0 Consensus size: 98
105300 ATTTCATTTC
* *
105310 TCATTTCTCCATTTAAAAAAGATAAGAATGACGTAAAATCACAATTTCATACTATCCTTACTCAT
1 TCATTTCTCCATTTAAAAAAAATAAGAATGACGTAAAATCACAATTTCATACCATCCTTACTCAT
*
105375 GTTTTCAATTTATTAAATGCTGCTTCTAATCAG
66 GTTTTCAATTTATTAAATGCTACTTCTAATCAG
105408 TCATTTCTCCA-TTAAAAAAAATAAGAATGACGTAAAATCACAATTTCATACCATCCTTACTCAT
1 TCATTTCTCCATTTAAAAAAAATAAGAATGACGTAAAATCACAATTTCATACCATCCTTACTCAT
105472 GTTTTCAATTTATTAAATGCTACTTCTAATCAG
66 GTTTTCAATTTATTAAATGCTACTTCTAATCAG
105505 T
1 T
105506 GACAGCACAA
Statistics
Matches: 95, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
97 84 0.88
98 11 0.12
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (98 bp):
TCATTTCTCCATTTAAAAAAAATAAGAATGACGTAAAATCACAATTTCATACCATCCTTACTCAT
GTTTTCAATTTATTAAATGCTACTTCTAATCAG
Found at i:106607 original size:3 final size:3
Alignment explanation
Indices: 106599--106654 Score: 87
Period size: 3 Copynumber: 18.7 Consensus size: 3
106589 TTTTCTGTGT
106599 TTC TTC TTC -TC TTTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
106644 TTC TTC CTC TT
1 TTC TTC TTC TT
106655 GTTTGGCAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.92
4 2 0.04
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:111296 original size:40 final size:40
Alignment explanation
Indices: 111243--111376 Score: 214
Period size: 40 Copynumber: 3.4 Consensus size: 40
111233 GAGGATATGT
** *
111243 TTAAAAAGGAAGACTTGGGACTCGATAGAGCATAAGATTG
1 TTAAAAAGGAAGACTTATGACTCGGTAGAGCATAAGATTG
*
111283 TTAAAAGGGAAGACTTATGACTCGGTAGAGCATAAGATTG
1 TTAAAAAGGAAGACTTATGACTCGGTAGAGCATAAGATTG
* *
111323 TTAAAAAGGAAGACGTATGACTCGGTAGAGCATAGGATTG
1 TTAAAAAGGAAGACTTATGACTCGGTAGAGCATAAGATTG
111363 TTAAAAAGGAAGAC
1 TTAAAAAGGAAGAC
111377 ACATGAACCT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.40, C:0.10, G:0.28, T:0.22
Consensus pattern (40 bp):
TTAAAAAGGAAGACTTATGACTCGGTAGAGCATAAGATTG
Found at i:112076 original size:21 final size:21
Alignment explanation
Indices: 112052--112096 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
112042 TTAGTATCAG
*
112052 TAGAAGTAAAACTTGTATCGA
1 TAGAACTAAAACTTGTATCGA
***
112073 TAGAACTGTCACTTGTATCGA
1 TAGAACTAAAACTTGTATCGA
112094 TAG
1 TAG
112097 TAATTTGCAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (21 bp):
TAGAACTAAAACTTGTATCGA
Found at i:118768 original size:15 final size:15
Alignment explanation
Indices: 118728--118777 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
118718 TTAGTCACTT
*
118728 GAAAAAGAA-AAATGA
1 GAAAAAGAAGAAA-AA
118743 GAAAAAGGAAGAAAAA
1 GAAAAA-GAAGAAAAA
118759 GAAAAAGAAGAAAAA
1 GAAAAAGAAGAAAAA
118774 -AAAA
1 GAAAA
118778 TTTAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
14 4 0.12
15 15 0.47
16 10 0.31
17 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (15 bp):
GAAAAAGAAGAAAAA
Found at i:131791 original size:17 final size:18
Alignment explanation
Indices: 131752--131795 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
131742 ATGCATCTCA
* *
131752 TTTAGTTGTCATTGCATT
1 TTTATTTGTCACTGCATT
131770 TTTATTTGTCACTGCA-T
1 TTTATTTGTCACTGCATT
131787 TTTATTTGT
1 TTTATTTGT
131796 TAGTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.16, C:0.11, G:0.14, T:0.59
Consensus pattern (18 bp):
TTTATTTGTCACTGCATT
Found at i:132399 original size:18 final size:18
Alignment explanation
Indices: 132373--132415 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
132363 AATCACGTAT
132373 AAAAA-AAAGAAAAGAAG
1 AAAAAGAAAGAAAAGAAG
*
132390 AAAAAGAAAGCAAAGAAG
1 AAAAAGAAAGAAAAGAAG
132408 -AAAAGAAA
1 AAAAAGAAA
132416 AGCAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAGAAAAGAAG
Found at i:132417 original size:18 final size:17
Alignment explanation
Indices: 132373--132429 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 17
132363 AATCACGTAT
*
132373 AAAAAAAAGAAAAGAAG
1 AAAAAAAAGCAAAGAAG
132390 AAAAAGAAAGCAAAGAAG
1 AAAAA-AAAGCAAAGAAG
132408 AAAAGAAAAGCAAA-AA-
1 AAAA-AAAAGCAAAGAAG
132424 AAAAAA
1 AAAAAA
132430 TATTGCAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
15 2 0.05
16 4 0.11
17 7 0.19
18 23 0.62
19 1 0.03
ACGTcount: A:0.81, C:0.04, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGCAAAGAAG
Found at i:136903 original size:40 final size:40
Alignment explanation
Indices: 136858--137031 Score: 267
Period size: 40 Copynumber: 4.3 Consensus size: 40
136848 GAGGATATGT
136858 TTAAAAAGGAAGACTTATGACTCGGTAGAGCATAAGATTG
1 TTAAAAAGGAAGACTTATGACTCGGTAGAGCATAAGATTG
* * * *
136898 TTAAAAGGGAAGACTTATGACTCAGTATAGCATATGATTG
1 TTAAAAAGGAAGACTTATGACTCGGTAGAGCATAAGATTG
*** * *
136938 TTAAATTTGAAGACTTATGAGTCGGTAGAGCATAAGATTA
1 TTAAAAAGGAAGACTTATGACTCGGTAGAGCATAAGATTG
136978 TTAAAAAGGAAGACTTATGACTCGGTAGAGCATAAGATTG
1 TTAAAAAGGAAGACTTATGACTCGGTAGAGCATAAGATTG
137018 TTAAAAAGGAAGAC
1 TTAAAAAGGAAGAC
137032 ACATGAACCT
Statistics
Matches: 117, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 117 1.00
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (40 bp):
TTAAAAAGGAAGACTTATGACTCGGTAGAGCATAAGATTG
Found at i:140941 original size:22 final size:22
Alignment explanation
Indices: 140913--140956 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
140903 ATACATGGCA
140913 GGTTTGACTTCTCTTTAAGATT
1 GGTTTGACTTCTCTTTAAGATT
140935 GGTTTGACTTCTCTTTAAGATT
1 GGTTTGACTTCTCTTTAAGATT
140957 AATTCCCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.50
Consensus pattern (22 bp):
GGTTTGACTTCTCTTTAAGATT
Found at i:141906 original size:25 final size:25
Alignment explanation
Indices: 141873--141920 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
141863 GACAAAAGAC
*
141873 AAAAATGCTATAGAGGAGCATACGA
1 AAAAATGCTACAGAGGAGCATACGA
*
141898 AAAAATGCTACAGATGAGCATAC
1 AAAAATGCTACAGAGGAGCATAC
141921 TAGTTTTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.21, T:0.17
Consensus pattern (25 bp):
AAAAATGCTACAGAGGAGCATACGA
Found at i:142775 original size:56 final size:56
Alignment explanation
Indices: 142689--142809 Score: 233
Period size: 56 Copynumber: 2.2 Consensus size: 56
142679 CTTAATGCAT
142689 TAGTTGTTTGAACACGTAGGTGAAATGTAACAACCCGTTTTCAGTGGTGTCGAAAA
1 TAGTTGTTTGAACACGTAGGTGAAATGTAACAACCCGTTTTCAGTGGTGTCGAAAA
142745 TAGTTGTTTGAACACGTAGGTGAAATGTAACAACCCGTTTTCAGTGGTGTCGAAAA
1 TAGTTGTTTGAACACGTAGGTGAAATGTAACAACCCGTTTTCAGTGGTGTCGAAAA
*
142801 TAGTGGTTT
1 TAGTTGTTT
142810 TGAGACCACG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (56 bp):
TAGTTGTTTGAACACGTAGGTGAAATGTAACAACCCGTTTTCAGTGGTGTCGAAAA
Found at i:143853 original size:14 final size:16
Alignment explanation
Indices: 143834--143866 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
143824 CTCGAACTCT
143834 TTATTTTA-TT-TTAA
1 TTATTTTACTTGTTAA
143848 TTATTTTACTTGTTAA
1 TTATTTTACTTGTTAA
143864 TTA
1 TTA
143867 ATATTTAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 2 0.12
16 7 0.41
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (16 bp):
TTATTTTACTTGTTAA
Found at i:147832 original size:23 final size:23
Alignment explanation
Indices: 147804--147876 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 23
147794 GGTCCCTGCA
147804 TTTTTATATTGTTTTAA-TTTAAT
1 TTTTTAT-TTGTTTTAATTTTAAT
*
147827 TTTTTATTCTGTTTTTTAATTTTAAC
1 TTTTTATT-TG--TTTTAATTTTAAT
* *
147853 CTTTAATTTGTTTTAATTTTAAT
1 TTTTTATTTGTTTTAATTTTAAT
147876 T
1 T
147877 AAGTCCTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
22 1 0.02
23 21 0.51
25 8 0.20
26 11 0.27
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.68
Consensus pattern (23 bp):
TTTTTATTTGTTTTAATTTTAAT
Found at i:147997 original size:26 final size:25
Alignment explanation
Indices: 147968--148028 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
147958 TTATTGTTTG
147968 TTTTTATTTGT-TTTTATATTTATT-
1 TTTTTATTT-TATTTTATATTTATTA
*
147992 TATTTTATTATTATTTTATGTTTATTA
1 T-TTTTATT-TTATTTTATATTTATTA
*
148019 TGTTTATTTT
1 TTTTTATTTT
148029 CTTTAGTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
24 1 0.03
25 10 0.32
26 19 0.61
27 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (25 bp):
TTTTTATTTTATTTTATATTTATTA
Found at i:148003 original size:16 final size:16
Alignment explanation
Indices: 147970--148019 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
147960 ATTGTTTGTT
*
147970 TTTATTTGTTTT-TATA
1 TTTATTTATTTTAT-TA
147986 TTTATTTATTTTATTA
1 TTTATTTATTTTATTA
148002 -TTATTTTATGTTTATTA
1 TTTA-TTTAT-TTTATTA
148019 T
1 T
148020 GTTTATTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 3 0.10
16 18 0.62
17 8 0.28
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (16 bp):
TTTATTTATTTTATTA
Found at i:148044 original size:35 final size:34
Alignment explanation
Indices: 147976--148044 Score: 79
Period size: 35 Copynumber: 2.0 Consensus size: 34
147966 TGTTTTTATT
*
147976 TGTTTTTATATTTATTTATTTTATTATTATTTTA
1 TGTTTTTATATTTATTTATTTTATAATTATTTTA
*
148010 TGTTTATTATGTTTATTT-TCTTTAGTAATT-TTTTA
1 TGTTT-TTATATTTATTTAT-TTTA-TAATTATTTTA
148045 GTTCATACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
34 6 0.20
35 20 0.67
36 4 0.13
ACGTcount: A:0.22, C:0.01, G:0.06, T:0.71
Consensus pattern (34 bp):
TGTTTTTATATTTATTTATTTTATAATTATTTTA
Found at i:151844 original size:15 final size:13
Alignment explanation
Indices: 151820--151858 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 13
151810 TGCATATGCA
151820 TACATGCATTCAT
1 TACATGCATTCAT
151833 TAGCATTGCATTTCAT
1 TA-CA-TGCA-TTCAT
151849 TACATGCATT
1 TACATGCATT
151859 TAAAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 4 0.17
14 6 0.26
15 6 0.26
16 7 0.30
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (13 bp):
TACATGCATTCAT
Found at i:154025 original size:15 final size:15
Alignment explanation
Indices: 153984--154018 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
153974 AATTTCACCC
153984 AAAAAAAGAAAAGAA
1 AAAAAAAGAAAAGAA
* *
153999 AAGAAAACAAAAGAA
1 AAAAAAAGAAAAGAA
154014 AAAAA
1 AAAAA
154019 TAAAAAAAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAGAA
Found at i:155071 original size:102 final size:102
Alignment explanation
Indices: 154892--155518 Score: 697
Period size: 102 Copynumber: 6.2 Consensus size: 102
154882 AAACAATTCT
* ** * **
154892 TATATCTCTGAAGTTGTAGTGGAAT-GGAGAAAAAC-AGCAGTAGCAGATCTCAATCTCTTTGAA
1 TATATCCCTGAAGTTGTAGTGG-ATCGGATTAAAACTAACAGTAGCAGATCTCAATCTCCCTGAA
* *
154955 GTTACAGTGAAATGGAGTGAAGCCACAACACCAAATCC
65 GTTGCAGTGGAATGGAGTGAAGCCACAACACCAAATCC
* * ** * * *
154993 TATATTCCTAAAGTTACAGTGGATTGGATTAAAACTAATAGTAGCAGATCTCAATCTTCCTGAAG
1 TATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTAACAGTAGCAGATCTCAATCTCCCTGAAG
* * * * *
155058 TTACATTGGAATGGAATGAATCCACAACACCAAATCA
66 TTGCAGTGGAATGGAGTGAAGCCACAACACCAAATCC
* * * * * *
155095 TATATCCCTGAAGTTGCAGTGAATCAGATTAAAACTAACAATA-CTAGATCTTAGTCTCCCTGAA
1 TATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTAACAGTAGC-AGATCTCAATCTCCCTGAA
* *
155159 GTTGTAATGGAATGGAGTGAAGCCACAACACCAAATCC
65 GTTGCAGTGGAATGGAGTGAAGCCACAACACCAAATCC
* * * *
155197 TATATCCCTGAAGTTATTGTGGATCGGATCAAAACTAACAGTAGCAGATCTCAATCTCCCTAAAG
1 TATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTAACAGTAGCAGATCTCAATCTCCCTGAAG
* * * *
155262 TTGCAGTGGAATGGAGTGAAACTACAACACCAAAACG
66 TTGCAGTGGAATGGAGTGAAGCCACAACACCAAATCC
* * *
155299 TATGTCCCTGAAGTTGTAGTGGATCGGATTAAAACTAACAGTAGCAAATCTCAAACTCCCTGAAG
1 TATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTAACAGTAGCAGATCTCAATCTCCCTGAAG
**
155364 TTGCAGTGGAATGGAGTGAAGTTACAACACCAAATCC
66 TTGCAGTGGAATGGAGTGAAGCCACAACACCAAATCC
* * * * *
155401 TATGTCCCTGAGGTTGTAGTGGATCAGATTAAAACTGACAATAGC-GAATCTCAATCTCCCTGAA
1 TATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTAACAGTAGCAG-ATCTCAATCTCCCTGAA
* * * ** *
155465 GCTGTAGTGGAATGAAGTGAAGTTATAA-ACCCAAATCC
65 GTTGCAGTGGAATGGAGTGAAGCCACAACA-CCAAATCC
* *
155503 TATATTCTTGAAGTTG
1 TATATCCCTGAAGTTG
155519 CATAAATAAG
Statistics
Matches: 445, Mismatches: 75, Indels: 11
0.84 0.14 0.02
Matches are distributed among these distances:
100 2 0.00
101 27 0.06
102 415 0.93
103 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (102 bp):
TATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTAACAGTAGCAGATCTCAATCTCCCTGAAG
TTGCAGTGGAATGGAGTGAAGCCACAACACCAAATCC
Found at i:155320 original size:50 final size:49
Alignment explanation
Indices: 155046--155485 Score: 215
Period size: 50 Copynumber: 8.7 Consensus size: 49
155036 GCAGATCTCA
* ** * * * *
155046 ATCTTCCTGAAGTTACATTGGAATGGAATGAATCCACAACACCAAATCAT
1 ATCTCCCTGAAGTTGTAGTGGAATGGAGTGAAACTACAACACCAAATC-T
* * * * * * * *
155096 ATATCCCTGAAGTTGCAGT-GAATCAGATTAAAACTAACAATACTAGATCTT
1 ATCTCCCTGAAGTTGTAGTGGAAT-GGAGTGAAACT-ACAACACCAAATC-T
* * *
155147 AGTCTCCCTGAAGTTGTAATGGAATGGAGTGAAGCCACAACACCAAATCCT
1 A-TCTCCCTGAAGTTGTAGTGGAATGGAGTGAAACTACAACACCAAAT-CT
* * * * ** * *
155198 ATATCCCTGAAGTTATTGTGG-ATCGGA-TCAAAACTAACAGTAGCAGATCT
1 ATCTCCCTGAAGTTGTAGTGGAAT-GGAGT-GAAACT-ACAACACCAAATCT
* * *
155248 CAATCTCCCTAAAGTTGCAGTGGAATGGAGTGAAACTACAACACCAAAACGT
1 --ATCTCCCTGAAGTTGTAGTGGAATGGAGTGAAACTACAACACCAAATC-T
* * * ** *
155300 ATGTCCCTGAAGTTGTAGTGG-ATCGGATTAAAACTAACAGTAGCAAATCT
1 ATCTCCCTGAAGTTGTAGTGGAAT-GGAGTGAAACT-ACAACACCAAATCT
* * **
155350 CAAACTCCCTGAAGTTGCAGTGGAATGGAGTGAAGTTACAACACCAAATCCT
1 --ATCTCCCTGAAGTTGTAGTGGAATGGAGTGAAACTACAACACCAAAT-CT
* * * * * * * *
155402 ATGTCCCTGAGGTTGTAGTGG-ATCAGATTAAAACTGACAATAGCGAATCT
1 ATCTCCCTGAAGTTGTAGTGGAAT-GGAGTGAAACT-ACAACACCAAATCT
* *
155452 CAATCTCCCTGAAGCTGTAGTGGAATGAAGTGAA
1 --ATCTCCCTGAAGTTGTAGTGGAATGGAGTGAA
155486 GTTATAAACC
Statistics
Matches: 282, Mismatches: 84, Indels: 46
0.68 0.20 0.11
Matches are distributed among these distances:
49 11 0.04
50 98 0.35
51 66 0.23
52 96 0.34
53 11 0.04
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (49 bp):
ATCTCCCTGAAGTTGTAGTGGAATGGAGTGAAACTACAACACCAAATCT
Found at i:155486 original size:306 final size:306
Alignment explanation
Indices: 154929--155517 Score: 770
Period size: 306 Copynumber: 1.9 Consensus size: 306
154919 AGAAAAACAG
** * * *
154929 CAGTAGCAGATCTCAATCTCTTTGAAGTTACAGTGAAATGGAGTGAAGCCACAACACCAAATCCT
1 CAGTAGCAGATCTCAATCTCCCTAAAGTTACAGTGAAATGGAGTGAAACCACAACACCAAAACCT
* * * * * *
154994 ATATTCCTAAAGTTACAGTGGATTGGATTAAAACTAATAGTAGCAGATCTCAATCTTCCTGAAGT
66 ATATCCCTAAAGTTACAGTGGATCGGATTAAAACTAACAGTAGCAAATCTCAAACTCCCTGAAGT
*
155059 TACATTGGAATGGAATGAATCCACAACACCAAATCATATATCCCTGAAGTTGCAGTGAATCAGAT
131 TACAGTGGAATGGAATGAATCCACAACACCAAATCATATATCCCTGAAGTTGCAGTGAATCAGAT
* * * * *
155124 TAAAACTAACAATACTAGATCTTAGTCTCCCTGAAGTTGTAATGGAATGGAGTGAAGCCAC-AAC
196 TAAAACTAACAATACGAGATCTCAATCTCCCTGAAGCTGTAATGGAATGAAGTGAAGCCACAAAC
155188 ACCAAATCCTATATCCCTGAAGTTATTGTGGATCGGATCAAAACTAA
261 -CCAAATCCTATATCCCTGAAGTTATTGTGGATCGGATCAAAACTAA
* * * *
155235 CAGTAGCAGATCTCAATCTCCCTAAAGTTGCAGTGGAATGGAGTGAAACTACAACACCAAAACGT
1 CAGTAGCAGATCTCAATCTCCCTAAAGTTACAGTGAAATGGAGTGAAACCACAACACCAAAACCT
* * **
155300 ATGTCCCTGAAGTTGTAGTGGATCGGATTAAAACTAACAGTAGCAAATCTCAAACTCCCTGAAGT
66 ATATCCCTAAAGTTACAGTGGATCGGATTAAAACTAACAGTAGCAAATCTCAAACTCCCTGAAGT
* * * * * * * *
155365 TGCAGTGGAATGGAGTGAAGT-TACAACACCAAATCCTATGTCCCTGAGGTTGTAGTGGATCAGA
131 TACAGTGGAATGGAATGAA-TCCACAACACCAAATCATATATCCCTGAAGTTGCAGTGAATCAGA
* * ** *
155429 TTAAAACTGACAATAGCGA-ATCTCAATCTCCCTGAAGCTGTAGTGGAATGAAGTGAAGTTATAA
195 TTAAAACTAACAATA-CGAGATCTCAATCTCCCTGAAGCTGTAATGGAATGAAGTGAAGCCACAA
* *
155493 ACCCAAATCCTATATTCTTGAAGTT
259 ACCCAAATCCTATATCCCTGAAGTT
155518 GCATAAATAA
Statistics
Matches: 240, Mismatches: 40, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
306 234 0.98
307 6 0.03
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (306 bp):
CAGTAGCAGATCTCAATCTCCCTAAAGTTACAGTGAAATGGAGTGAAACCACAACACCAAAACCT
ATATCCCTAAAGTTACAGTGGATCGGATTAAAACTAACAGTAGCAAATCTCAAACTCCCTGAAGT
TACAGTGGAATGGAATGAATCCACAACACCAAATCATATATCCCTGAAGTTGCAGTGAATCAGAT
TAAAACTAACAATACGAGATCTCAATCTCCCTGAAGCTGTAATGGAATGAAGTGAAGCCACAAAC
CCAAATCCTATATCCCTGAAGTTATTGTGGATCGGATCAAAACTAA
Found at i:156149 original size:13 final size:13
Alignment explanation
Indices: 156131--156182 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
156121 CTCAAACACC
156131 CAAACCCAAAATA
1 CAAACCCAAAATA
*
156144 CAAACCC-AAATT
1 CAAACCCAAAATA
156156 CAAAACCCAAAATTA
1 C-AAACCCAAAA-TA
156171 CACAAGCCCAAA
1 CA-AA-CCCAAA
156183 TTTAAAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
12 5 0.16
13 13 0.41
14 4 0.12
15 4 0.12
16 6 0.19
ACGTcount: A:0.56, C:0.33, G:0.02, T:0.10
Consensus pattern (13 bp):
CAAACCCAAAATA
Found at i:156183 original size:29 final size:26
Alignment explanation
Indices: 156132--156189 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 26
156122 TCAAACACCC
156132 AAACCCAAAATACAAACCCAAATTCA
1 AAACCCAAAATACAAACCCAAATTCA
*
156158 AAACCCAAAATTACACAAGCCCAAATTTA
1 AAACCCAAAA-TACA-AA-CCCAAATTCA
156187 AAA
1 AAA
156190 TGACAAGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 10 0.36
27 4 0.14
28 2 0.07
29 12 0.43
ACGTcount: A:0.57, C:0.28, G:0.02, T:0.14
Consensus pattern (26 bp):
AAACCCAAAATACAAACCCAAATTCA
Found at i:159312 original size:26 final size:25
Alignment explanation
Indices: 159283--159343 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
159273 TTATTGTTTG
159283 TTTTTATTTGT-TTTTATATTTATT-
1 TTTTTATTT-TATTTTATATTTATTA
*
159307 TATTTTATTATTATTTTATGTTTATTA
1 T-TTTTATT-TTATTTTATATTTATTA
*
159334 TGTTTATTTT
1 TTTTTATTTT
159344 CTTTAGTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
24 1 0.03
25 10 0.32
26 19 0.61
27 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (25 bp):
TTTTTATTTTATTTTATATTTATTA
Found at i:159318 original size:16 final size:16
Alignment explanation
Indices: 159285--159334 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
159275 ATTGTTTGTT
*
159285 TTTATTTGTTTT-TATA
1 TTTATTTATTTTAT-TA
159301 TTTATTTATTTTATTA
1 TTTATTTATTTTATTA
159317 -TTATTTTATGTTTATTA
1 TTTA-TTTAT-TTTATTA
159334 T
1 T
159335 GTTTATTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 3 0.10
16 18 0.62
17 8 0.28
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (16 bp):
TTTATTTATTTTATTA
Found at i:161172 original size:37 final size:35
Alignment explanation
Indices: 161095--161172 Score: 86
Period size: 37 Copynumber: 2.2 Consensus size: 35
161085 TTTAAAATTA
* *
161095 AATTTTTAAATATAAAATTATTAATATTACTATAT
1 AATTTTTAAATAAAAAATTATTAATATTACTAAAT
* *
161130 TATTTTTCAAAATAAAAAATTATTACA-ATTATTAAAT
1 AATTTTT--AAATAAAAAATTATTA-ATATTACTAAAT
161167 AATTTT
1 AATTTT
161173 AATTTCATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 6 0.17
37 28 0.80
38 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (35 bp):
AATTTTTAAATAAAAAATTATTAATATTACTAAAT
Found at i:161963 original size:7 final size:7
Alignment explanation
Indices: 161953--161978 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
161943 TAAAAAAAGA
161953 TTGAAAC
1 TTGAAAC
161960 TTGAAAC
1 TTGAAAC
161967 TTGAAAC
1 TTGAAAC
161974 TTGAA
1 TTGAA
161979 GATGAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (7 bp):
TTGAAAC
Done.