Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 26 of 32
Found at i:4553722 original size:18 final size:17
Alignment explanation
Indices: 4553683--4553755 Score: 76
Period size: 17 Copynumber: 4.2 Consensus size: 17
4553673 TTAATTTTTT
* *
4553683 AATTTTTACTTAATTAA
1 AATTTTTATTTAAATAA
**
4553700 GTTTTTTATTTAAATAA
1 AATTTTTATTTAAATAA
4553717 AATTTTTATTTAAATTAA
1 AATTTTTATTTAAA-TAA
*
4553735 AA-ATTTATTTAAATATA
1 AATTTTTATTTAAATA-A
4553752 AATT
1 AATT
4553756 AAATATTATG
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
16 2 0.04
17 38 0.84
18 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (17 bp):
AATTTTTATTTAAATAA
Found at i:4558403 original size:19 final size:21
Alignment explanation
Indices: 4558337--4558406 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
4558327 CAAATAATTA
* *
4558337 TTTAATAAAAAAATATTTAAA-
1 TTTAAT-ATAAAATATATAAAT
4558358 TTTAATTATAAAATATATAAAT
1 TTTAA-TATAAAATATATAAAT
*
4558380 ATTAATATAAAA-ATA-AAAT
1 TTTAATATAAAATATATAAAT
4558399 TTTAATAT
1 TTTAATAT
4558407 TATTGTATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
19 11 0.26
20 3 0.07
21 24 0.56
22 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTAATATAAAATATATAAAT
Found at i:4560992 original size:3 final size:3
Alignment explanation
Indices: 4560984--4561017 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
4560974 CATTTTCAAC
*
4560984 AGA AGA AGA AGA CGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
4561018 TATTCACCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.03, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:4561132 original size:39 final size:39
Alignment explanation
Indices: 4561081--4561163 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
4561071 AGAAGAAGAT
* *
4561081 GAAGAAGATTCACTCATGCA-ATCATCATTTTCAAGGGAA
1 GAAGAAGATTCACCCA-GAAGATCATCATTTTCAAGGGAA
* * * *
4561120 GAAGAATATTCACCCAGAAGATCGTCTTTTTCAATGGAA
1 GAAGAAGATTCACCCAGAAGATCATCATTTTCAAGGGAA
4561159 GAAGA
1 GAAGA
4561164 TCGAATTGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
38 2 0.05
39 35 0.95
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (39 bp):
GAAGAAGATTCACCCAGAAGATCATCATTTTCAAGGGAA
Found at i:4564053 original size:19 final size:21
Alignment explanation
Indices: 4564023--4564062 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
4564013 TAAAAGCTTA
4564023 AATATATTTAATTAT-ATTTT
1 AATATATTTAATTATAATTTT
4564043 AATAT-TTTAATTATAATTTT
1 AATATATTTAATTATAATTTT
4564063 TATTATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AATATATTTAATTATAATTTT
Found at i:4573423 original size:19 final size:21
Alignment explanation
Indices: 4573387--4573433 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 21
4573377 TTTATATTAA
4573387 TATATTTTTATATTTAAAATA-T
1 TATA-TTTTATA-TTAAAATATT
4573409 TATATTTTATA-TAAAATATT
1 TATATTTTATATTAAAATATT
4573429 TATAT
1 TATAT
4573434 ATTAATAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.29
20 6 0.25
21 7 0.29
22 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATATTTTATATTAAAATATT
Found at i:4573979 original size:17 final size:17
Alignment explanation
Indices: 4573917--4573981 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 17
4573907 CGTTTTTATG
*
4573917 TTTGTATCATATTTATTT
1 TTTGTAT-ATTTTTATTT
* *
4573935 TTATATTATATTTTAATTAT
1 TT-T-GTATATTTTTATT-T
*
4573955 TTT-CATATTTTTATTT
1 TTTGTATATTTTTATTT
4573971 TTTGTATATTT
1 TTTGTATATTT
4573982 AAAGTAGTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
16 4 0.11
17 16 0.43
18 2 0.05
19 9 0.24
20 6 0.16
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTGTATATTTTTATTT
Found at i:4574346 original size:18 final size:19
Alignment explanation
Indices: 4574306--4574349 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
4574296 TTATTATTTA
*
4574306 ATAAAATTTATTTTATAAT
1 ATAAAATTTATTTAATAAT
*
4574325 -TAAATTTTA-TTAATAAT
1 ATAAAATTTATTTAATAAT
4574342 ATAAAATT
1 ATAAAATT
4574350 AACTATATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATAAAATTTATTTAATAAT
Found at i:4574460 original size:16 final size:16
Alignment explanation
Indices: 4574439--4574485 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
4574429 AAAGATGCAA
4574439 AGAAAAAAAAGAAAAG
1 AGAAAAAAAAGAAAAG
* *
4574455 AG-AAAAAAGGAGAGAG
1 AGAAAAAAAAGA-AAAG
*
4574471 AGAAATAAAAGAAAA
1 AGAAAAAAAAGAAAA
4574486 TTTTAATGTG
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
15 8 0.33
16 9 0.38
17 7 0.29
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (16 bp):
AGAAAAAAAAGAAAAG
Found at i:4574555 original size:18 final size:18
Alignment explanation
Indices: 4574532--4574568 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4574522 TATTATTTAA
*
4574532 AGTATTATAAATTTATAT
1 AGTATTATAAATATATAT
*
4574550 AGTATTATACATATATAT
1 AGTATTATAAATATATAT
4574568 A
1 A
4574569 TTTATATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (18 bp):
AGTATTATAAATATATAT
Found at i:4574626 original size:23 final size:21
Alignment explanation
Indices: 4574596--4574653 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 21
4574586 TCGTGACATA
4574596 TTTA-TTTTTATATTATGTTT
1 TTTATTTTTTATATTATGTTT
* *
4574616 TAATTATTTTTTATGTCATGTTT
1 T--TTATTTTTTATATTATGTTT
4574639 TTTATTTTTTATATT
1 TTTATTTTTTATATT
4574654 TAAAGTAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 12 0.39
22 3 0.10
23 15 0.48
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (21 bp):
TTTATTTTTTATATTATGTTT
Found at i:4574643 original size:21 final size:19
Alignment explanation
Indices: 4574596--4574650 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 19
4574586 TCGTGACATA
4574596 TTTATTTTTATATTATGTTT
1 TTTATTTTT-TATTATGTTT
4574616 TAATTATTTTTTATGTCATGTTT
1 T--TTATTTTTTAT-T-ATGTTT
4574639 TTTATTTTTTAT
1 TTTATTTTTTAT
4574651 ATTTAAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
20 1 0.03
21 14 0.45
22 9 0.29
23 7 0.23
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (19 bp):
TTTATTTTTTATTATGTTT
Found at i:4574873 original size:16 final size:17
Alignment explanation
Indices: 4574849--4574881 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4574839 ATTTTTATTA
*
4574849 AAAATAATTTAAAATAT
1 AAAATAATTAAAAATAT
4574866 AAAA-AATTAAAAATAT
1 AAAATAATTAAAAATAT
4574882 TATTAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATAATTAAAAATAT
Found at i:4575772 original size:12 final size:13
Alignment explanation
Indices: 4575748--4575785 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
4575738 AATTACATAA
4575748 ATATATTTA-ATT
1 ATATATTTATATT
4575760 ATAT-TTTATATT
1 ATATATTTATATT
4575772 ATATATTTAATATT
1 ATATATTT-ATATT
4575786 TTTATGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.17
12 11 0.48
13 3 0.13
14 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATATATTTATATT
Found at i:4577495 original size:18 final size:18
Alignment explanation
Indices: 4577472--4577527 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 18
4577462 ATTTAAGTAA
4577472 TATTTAAAGTTAAAAATT
1 TATTTAAAGTTAAAAATT
*
4577490 TATTT-AAG-T-ATAATT
1 TATTTAAAGTTAAAAATT
*
4577505 TA---AAAATTAAAAATT
1 TATTTAAAGTTAAAAATT
4577520 TATTTAAA
1 TATTTAAA
4577528 TATAAGTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 12
0.66 0.07 0.27
Matches are distributed among these distances:
13 2 0.07
14 1 0.03
15 14 0.48
16 1 0.03
17 3 0.10
18 8 0.28
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (18 bp):
TATTTAAAGTTAAAAATT
Found at i:4577517 original size:30 final size:29
Alignment explanation
Indices: 4577462--4577552 Score: 114
Period size: 30 Copynumber: 3.1 Consensus size: 29
4577452 TTAAGAGTTC
*
4577462 ATTTAAGTA-ATATTTAAAGTTAAAAATTT
1 ATTTAAGTATA-ATTTAAAATTAAAAATTT
4577491 ATTTAAGTATAATTTAAAAATTAAAAATTT
1 ATTTAAGTATAATTT-AAAATTAAAAATTT
* *
4577521 ATTTAAATATAAGTTTAATATT-AAAATTT
1 ATTTAAGTATAA-TTTAAAATTAAAAATTT
4577550 ATT
1 ATT
4577553 GATATAAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
29 23 0.41
30 30 0.54
31 3 0.05
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (29 bp):
ATTTAAGTATAATTTAAAATTAAAAATTT
Found at i:4579167 original size:19 final size:19
Alignment explanation
Indices: 4579145--4579181 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4579135 ATATGATTTG
* *
4579145 ATTTATTAATTATGAATAA
1 ATTTATAAATTATCAATAA
4579164 ATTTATAAATTATCAATA
1 ATTTATAAATTATCAATA
4579182 TAAAATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTTATAAATTATCAATAA
Found at i:4580771 original size:17 final size:17
Alignment explanation
Indices: 4580744--4580786 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
4580734 TTATTTAAAT
4580744 TTAATTATAAATTATATA
1 TTAA-TATAAATTATATA
*
4580762 TTAATATAAATTATATT
1 TTAATATAAATTATATA
4580779 TTAA-ATAA
1 TTAATATAA
4580787 TAATTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAATATAAATTATATA
Found at i:4580831 original size:30 final size:30
Alignment explanation
Indices: 4580787--4580854 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
4580777 TTTTAAATAA
* *
4580787 TAAT-TAAAATTTTAAAATTA-ATTTTAATT
1 TAATATAAAATTTT-AAATCAGAATTTAATT
4580816 TAA-ATAAACATTTTAAATCAGAATTTAATT
1 TAATATAAA-ATTTTAAATCAGAATTTAATT
4580846 TAATATAAA
1 TAATATAAA
4580855 TGCTCCTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 12 0.36
30 16 0.48
31 5 0.15
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (30 bp):
TAATATAAAATTTTAAATCAGAATTTAATT
Found at i:4581686 original size:2 final size:2
Alignment explanation
Indices: 4581679--4581706 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4581669 ATATGCCTAT
4581679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4581707 GTACAACGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4582504 original size:17 final size:17
Alignment explanation
Indices: 4582463--4582506 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
4582453 TTGAAATAAA
*
4582463 ATATTTTAGATCCAAATT
1 ATATTTTA-ATCAAAATT
*
4582481 AGA-TTTAATCAAAATT
1 ATATTTTAATCAAAATT
4582497 ATATTTTAAT
1 ATATTTTAAT
4582507 TTAATTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 10 0.45
17 10 0.45
18 2 0.09
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (17 bp):
ATATTTTAATCAAAATT
Found at i:4583746 original size:25 final size:25
Alignment explanation
Indices: 4583703--4583751 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
4583693 TGCTTTAAAC
* *
4583703 ATATCTATAATCATGATAAATTTAA
1 ATATCTATAACCATAATAAATTTAA
* *
4583728 ATATCTATCACCATAATAATTTTA
1 ATATCTATAACCATAATAAATTTA
4583752 TTTGTTAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (25 bp):
ATATCTATAACCATAATAAATTTAA
Found at i:4587649 original size:42 final size:42
Alignment explanation
Indices: 4587549--4587650 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
4587539 TATTTGATTC
* * *
4587549 AATCTGATTAGGAGATTCAAAAAGCTTTACCGGGATGGGTTA
1 AATCTGATTAGGAGATTCAAAAAGATATACCGGGATAGGTTA
* * * * *
4587591 AATCCGGTTAGAAGATTCAAAAAGATATATCGGTATAGGTTA
1 AATCTGATTAGGAGATTCAAAAAGATATACCGGGATAGGTTA
*
4587633 AATCTAATTAGGAGATTC
1 AATCTGATTAGGAGATTC
4587651 TGTTATTTGA
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (42 bp):
AATCTGATTAGGAGATTCAAAAAGATATACCGGGATAGGTTA
Found at i:4587696 original size:58 final size:58
Alignment explanation
Indices: 4587618--4587730 Score: 174
Period size: 58 Copynumber: 1.9 Consensus size: 58
4587608 CAAAAAGATA
*
4587618 TATCGGTATAGGTTAAATCTAATTAGGAGATTCTGTTA-TTTGAATTGATTCAACCCTT
1 TATCGGTATAGGTTAAATCTAATTAAGAGATTCTG-TAGTTTGAATTGATTCAACCCTT
* * *
4587676 TATCGGTATGGGTTAAATCTACTTAAGAGATTTTGTAGTTTGAATTGATTCAACC
1 TATCGGTATAGGTTAAATCTAATTAAGAGATTCTGTAGTTTGAATTGATTCAACC
4587731 ACATCTAGTC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
57 2 0.04
58 48 0.96
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41
Consensus pattern (58 bp):
TATCGGTATAGGTTAAATCTAATTAAGAGATTCTGTAGTTTGAATTGATTCAACCCTT
Found at i:4589969 original size:2 final size:2
Alignment explanation
Indices: 4589962--4589986 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4589952 GGGGAGGCAC
4589962 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
4589987 CTAGGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4591198 original size:8 final size:8
Alignment explanation
Indices: 4591185--4591213 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
4591175 TTGGAAGAAT
4591185 TGTCGTGA
1 TGTCGTGA
4591193 TGTCGTGA
1 TGTCGTGA
4591201 TGTCGTGA
1 TGTCGTGA
4591209 TGTCG
1 TGTCG
4591214 ATTCTTTGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.14, G:0.38, T:0.38
Consensus pattern (8 bp):
TGTCGTGA
Found at i:4594751 original size:5 final size:5
Alignment explanation
Indices: 4594743--4594767 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4594733 CCCCCCGGCG
4594743 GACTC GACTC GACTC GACTC GACTC
1 GACTC GACTC GACTC GACTC GACTC
4594768 AAGTTTTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (5 bp):
GACTC
Found at i:4595562 original size:2 final size:2
Alignment explanation
Indices: 4595555--4595597 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
4595545 TCAATTGTTA
4595555 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4595597 T
1 T
4595598 TTAATTTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:4600389 original size:2 final size:2
Alignment explanation
Indices: 4600384--4600413 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4600374 TATATATATA
4600384 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
4600414 CACGTCGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:4601024 original size:11 final size:9
Alignment explanation
Indices: 4600993--4601085 Score: 57
Period size: 9 Copynumber: 9.9 Consensus size: 9
4600983 TTATTAATAT
4600993 AATATA-AA
1 AATATATAA
*
4601001 AAAAT-TAA
1 AATATATAA
4601009 AATATGATATA
1 AATAT-ATA-A
4601020 AATATATAA
1 AATATATAA
*
4601029 AATATAATGTA
1 AATAT-AT-AA
4601040 AA-ATATAA
1 AATATATAA
* *
4601048 AATATTTTA
1 AATATATAA
*
4601057 AATAAAATAA
1 AAT-ATATAA
4601067 TAATATTATAA
1 -AATA-TATAA
4601078 AATATATA
1 AATATATA
4601086 TATAAAATAA
Statistics
Matches: 65, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
8 13 0.20
9 19 0.29
10 17 0.26
11 16 0.25
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (9 bp):
AATATATAA
Found at i:4601045 original size:21 final size:22
Alignment explanation
Indices: 4600988--4601046 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
4600978 TAATATTATT
*
4600988 AATATAATATAAAA-AAATTAA
1 AATATAATATAAAATATATTAA
*
4601009 AATATGATAT-AAATATA-TAA
1 AATATAATATAAAATATATTAA
*
4601029 AATATAATGTAAAATATA
1 AATATAATATAAAATATA
4601047 AAATATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (22 bp):
AATATAATATAAAATATATTAA
Found at i:4601047 original size:19 final size:19
Alignment explanation
Indices: 4600988--4601098 Score: 79
Period size: 20 Copynumber: 5.8 Consensus size: 19
4600978 TAATATTATT
*
4600988 AATATAATATAAAAAAATTAA
1 AATATAATAT-AAAATA-TAA
*
4601009 AATATGATATAAATATATAA
1 AATATAATATAAA-ATATAA
*
4601029 AATATAATGTAAAATATAA
1 AATATAATATAAAATATAA
*
4601048 AATATTTTAA-ATAAAATA-AT
1 AATA---TAATATAAAATATAA
4601068 AATAT--TATAAAATAT-A
1 AATATAATATAAAATATAA
* *
4601084 TATATAAAATAAAAT
1 AATATAATATAAAAT
4601099 TTACCCTCAA
Statistics
Matches: 73, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
16 12 0.16
17 1 0.01
18 7 0.10
19 10 0.14
20 22 0.30
21 18 0.25
22 3 0.04
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AATATAATATAAAATATAA
Found at i:4601060 original size:48 final size:50
Alignment explanation
Indices: 4600993--4601094 Score: 120
Period size: 48 Copynumber: 2.1 Consensus size: 50
4600983 TTATTAATAT
** *
4600993 AATATAAAAAAATTAAAATATGAT-ATAA-ATATATAAAATATA-ATGTAA
1 AATATAAAAAAATTAAAATAAAATAATAATAT-TATAAAATATATATATAA
* * *
4601041 AATATAAAATATTTTAAATAAAATAATAATATTATAAAATATATATATAA
1 AATATAAAAAAATTAAAATAAAATAATAATATTATAAAATATATATATAA
4601091 AATA
1 AATA
4601095 AAATTTACCC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
48 19 0.42
49 15 0.33
50 11 0.24
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (50 bp):
AATATAAAAAAATTAAAATAAAATAATAATATTATAAAATATATATATAA
Found at i:4601062 original size:21 final size:22
Alignment explanation
Indices: 4601038--4601094 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
4601028 AAATATAATG
*
4601038 TAAAATATAAAATATT-TTAAA
1 TAAAATATAAAATATTATAAAA
*
4601059 TAAAATA-ATAATATTATAAAA
1 TAAAATATAAAATATTATAAAA
*
4601080 TATATATATAAAATA
1 TA-AAATATAAAATA
4601095 AAATTTACCC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 7 0.24
21 13 0.45
22 4 0.14
23 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAATATAAAATATTATAAAA
Found at i:4601077 original size:16 final size:14
Alignment explanation
Indices: 4601042--4601095 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
4601032 ATAATGTAAA
* *
4601042 ATATAAAATATTTT
1 ATATAAAATAATAT
*
4601056 AAATAAAATAATAAT
1 ATATAAAATAAT-AT
4601071 ATTATAAAAT-ATAT
1 A-TATAAAATAATAT
4601085 ATATAAAATAA
1 ATATAAAATAA
4601096 AATTTACCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 8 0.24
14 14 0.42
15 4 0.12
16 7 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATAAAATAATAT
Found at i:4605870 original size:24 final size:24
Alignment explanation
Indices: 4605843--4605889 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4605833 AAATAATAAA
4605843 ATATTTAAAT-TTAATTATAAATAT
1 ATATTTAAATATT-ATTATAAATAT
**
4605867 ATATTTTTATATTATTATAAATA
1 ATATTTAAATATTATTATAAATA
4605890 ATAAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATTTAAATATTATTATAAATAT
Found at i:4606296 original size:13 final size:13
Alignment explanation
Indices: 4606263--4606315 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
4606253 TTTTTTTTAT
*
4606263 TATTATTTTTTAA
1 TATTATTTATTAA
*
4606276 TA-TATTTATCAA
1 TATTATTTATTAA
4606288 TATTATTTA-TATA
1 TATTATTTATTA-A
*
4606301 TATTAATTATTAA
1 TATTATTTATTAA
4606314 TA
1 TA
4606316 AATAATAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 11 0.33
13 20 0.61
14 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATTTATTAA
Found at i:4606333 original size:38 final size:37
Alignment explanation
Indices: 4606291--4606362 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
4606281 TTATCAATAT
*
4606291 TATTTATATA-TATTAATTATTAATAAATAATAAAATTA
1 TATTTATAAATTA-TAATTA-TAATAAATAATAAAATTA
* *
4606329 TATTTTTAAATTATAATTATATTAAATAATAAAA
1 TATTTATAAATTATAATTATAATAAATAATAAAA
4606363 AAATTAAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
37 14 0.47
38 14 0.47
39 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (37 bp):
TATTTATAAATTATAATTATAATAAATAATAAAATTA
Found at i:4606766 original size:13 final size:13
Alignment explanation
Indices: 4606748--4606778 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4606738 AAGGGATTAC
4606748 ATTGATTTTTTTT
1 ATTGATTTTTTTT
4606761 ATTGATTTTTTTT
1 ATTGATTTTTTTT
*
4606774 CTTGA
1 ATTGA
4606779 ATGATGTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.03, G:0.10, T:0.71
Consensus pattern (13 bp):
ATTGATTTTTTTT
Found at i:4615979 original size:59 final size:59
Alignment explanation
Indices: 4615887--4616063 Score: 327
Period size: 59 Copynumber: 3.0 Consensus size: 59
4615877 CTTAGAGTTA
4615887 TTGCAAATATCTTGACACAATACTGGCATAATCATGCAAATCCTATTAGGACTTTGTAT
1 TTGCAAATATCTTGACACAATACTGGCATAATCATGCAAATCCTATTAGGACTTTGTAT
4615946 TTGCAAATATCTTGACACAATACTGGCATAATCATGCAAATCCTATTAGGACTTTGTAT
1 TTGCAAATATCTTGACACAATACTGGCATAATCATGCAAATCCTATTAGGACTTTGTAT
* * *
4616005 TTGCAAATATCTTGACAAAATACTGACATAATCATGAAAATCCTATTAGGACTTTGTAT
1 TTGCAAATATCTTGACACAATACTGGCATAATCATGCAAATCCTATTAGGACTTTGTAT
4616064 GGTTAGTTTG
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 115 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.34
Consensus pattern (59 bp):
TTGCAAATATCTTGACACAATACTGGCATAATCATGCAAATCCTATTAGGACTTTGTAT
Found at i:4618642 original size:2 final size:2
Alignment explanation
Indices: 4618635--4618664 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4618625 TATTAGGCAA
4618635 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4618665 GATACACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4621135 original size:3 final size:3
Alignment explanation
Indices: 4621121--4621151 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
4621111 CAATAAATAC
*
4621121 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4621152 GAAAGGCCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:4622267 original size:17 final size:19
Alignment explanation
Indices: 4622235--4622269 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
4622225 TTTTTTTATC
4622235 AAAATAATATATTAAAATT
1 AAAATAATATATTAAAATT
4622254 AAAA-AATA-ATTAAAAT
1 AAAATAATATATTAAAAT
4622270 ATTTTAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAATAATATATTAAAATT
Found at i:4622756 original size:32 final size:34
Alignment explanation
Indices: 4622720--4622784 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 34
4622710 ATATTTTTTT
4622720 AATTTTATAAT-ATTAATA-ATT-TATATTATATA
1 AATTTTA-AATAATTAATATATTATATATTATATA
*
4622752 AATTTTAAATAATTTATATATTATATATTATAT
1 AATTTTAAATAATTAATATATTATATATTATAT
4622785 TTATATTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 3 0.10
32 13 0.45
33 3 0.10
34 10 0.34
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
AATTTTAAATAATTAATATATTATATATTATATA
Found at i:4622791 original size:11 final size:11
Alignment explanation
Indices: 4622768--4622805 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
4622758 AAATAATTTA
4622768 TATATTATATAT
1 TATATT-TATAT
4622780 TATATTTATAT
1 TATATTTATAT
*
4622791 TATATTTATGT
1 TATATTTATAT
4622802 TATA
1 TATA
4622806 GTAATTGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 19 0.76
12 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (11 bp):
TATATTTATAT
Found at i:4622796 original size:16 final size:16
Alignment explanation
Indices: 4622702--4622805 Score: 53
Period size: 16 Copynumber: 6.8 Consensus size: 16
4622692 TAATATTTAA
*
4622702 ATTAT-TTTATATTTT
1 ATTATATTTATATTAT
* *
4622717 TTTA-ATTT-TATAAT
1 ATTATATTTATATTAT
4622731 ATTAATAATTTATATTAT
1 ATT-AT-ATTTATATTAT
* * *
4622749 A-TAAATTTTAAATAAT
1 ATTATA-TTTATATTAT
*
4622765 -TTATATAT-TA-TAT
1 ATTATATTTATATTAT
4622778 ATTATATTTATATTAT
1 ATTATATTTATATTAT
4622794 ATT-TATGTTATA
1 ATTATAT-TTATA
4622806 GTAATTGTGT
Statistics
Matches: 65, Mismatches: 13, Indels: 21
0.66 0.13 0.21
Matches are distributed among these distances:
13 2 0.03
14 14 0.22
15 15 0.23
16 23 0.35
17 5 0.08
18 6 0.09
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (16 bp):
ATTATATTTATATTAT
Found at i:4623507 original size:131 final size:130
Alignment explanation
Indices: 4623241--4623476 Score: 364
Period size: 131 Copynumber: 1.8 Consensus size: 130
4623231 AAGCAATGCC
* * *
4623241 TTTTTTTTAAATATTTATGGTTAATAAAGTCTTTTTAAATATACTTATTTAATAATTTGCTCTTA
1 TTTTTTTTAAATATTTATGGCTAATAAAGTCTTTTGAAATAGACTTATTTAATAATTTGCTCTTA
* * ** *
4623306 GTCAACTTTAATAATTTTTGATTAAATCATGCATTTATTTATTTATTAAACAATTATGCATTTGC
66 GCCAACTTTAATAATTTTTGATTAAACCATGCATTTAAATATTTATTAAACAATTATCCATTT-C
*
4623371 T
130 A
*
4623372 TTTTTTTTTAATATTTATGGCTAATAAAGTCTTTTGAAATAGACTTATTTAATAATTTGCTCTTA
1 TTTTTTTTAAATATTTATGGCTAATAAAGTCTTTTGAAATAGACTTATTTAATAATTTGCTCTTA
*
4623437 GCCAACTTTAATAATTTTTTATTAAACCATGCATTTAAAT
66 GCCAACTTTAATAATTTTTGATTAAACCATGCATTTAAAT
4623477 CTTTGATCTG
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
131 96 1.00
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.50
Consensus pattern (130 bp):
TTTTTTTTAAATATTTATGGCTAATAAAGTCTTTTGAAATAGACTTATTTAATAATTTGCTCTTA
GCCAACTTTAATAATTTTTGATTAAACCATGCATTTAAATATTTATTAAACAATTATCCATTTCA
Found at i:4623574 original size:19 final size:18
Alignment explanation
Indices: 4623548--4623589 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
4623538 TTTTGTAAAT
4623548 AATAATTAAAA-TTATATA
1 AATAATTAAAAGTTA-ATA
4623566 AATATATTAAAAGTTAATA
1 AATA-ATTAAAAGTTAATA
4623585 AATAA
1 AATAA
4623590 AAAAAATCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.23
19 14 0.64
20 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AATAATTAAAAGTTAATA
Found at i:4624147 original size:43 final size:43
Alignment explanation
Indices: 4624077--4624167 Score: 164
Period size: 43 Copynumber: 2.1 Consensus size: 43
4624067 CCTAGCTCTT
* *
4624077 GTTTCGATTCCTCCAACGTCAGATCTTCTTCCCAAGTGCTTCA
1 GTTTTGATCCCTCCAACGTCAGATCTTCTTCCCAAGTGCTTCA
4624120 GTTTTGATCCCTCCAACGTCAGATCTTCTTCCCAAGTGCTTCA
1 GTTTTGATCCCTCCAACGTCAGATCTTCTTCCCAAGTGCTTCA
4624163 GTTTT
1 GTTTT
4624168 ATCTCTCAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.18, C:0.31, G:0.14, T:0.37
Consensus pattern (43 bp):
GTTTTGATCCCTCCAACGTCAGATCTTCTTCCCAAGTGCTTCA
Found at i:4625527 original size:2 final size:2
Alignment explanation
Indices: 4625520--4625559 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4625510 GATCATCTTG
4625520 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4625560 CTTTTTTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4627199 original size:14 final size:14
Alignment explanation
Indices: 4627180--4627206 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4627170 ATTCACACGT
4627180 CATTATGATAACGC
1 CATTATGATAACGC
4627194 CATTATGATAACG
1 CATTATGATAACG
4627207 TAGATGTAAA
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:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (14 bp):
CATTATGATAACGC
Found at i:4633382 original size:26 final size:26
Alignment explanation
Indices: 4633345--4633395 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
4633335 TTTTTTATTA
*
4633345 TTAAATATT-AAATATACTAAATTAAT
1 TTAAATATTAAAATATA-AAAATTAAT
4633371 TTAAAT-TATAAAATATAAAAATTAA
1 TTAAATAT-TAAAATATAAAAATTAA
4633396 AAATATTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 1 0.05
26 14 0.64
27 7 0.32
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
TTAAATATTAAAATATAAAAATTAAT
Found at i:4634076 original size:18 final size:19
Alignment explanation
Indices: 4634040--4634077 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
4634030 ATAAAAATAA
* *
4634040 TTTATTTTTTATCTTAATT
1 TTTATTTTTAATCTAAATT
4634059 TTTATTTTTAAT-TAAATT
1 TTTATTTTTAATCTAAATT
4634077 T
1 T
4634078 ATTTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTATTTTTAATCTAAATT
Found at i:4634195 original size:17 final size:19
Alignment explanation
Indices: 4634159--4634199 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
4634149 AATTTGATCA
4634159 TAAATAAATATTAAATAAT
1 TAAATAAATATTAAATAAT
*
4634178 TAAA-AAATATT-TATAAT
1 TAAATAAATATTAAATAAT
4634195 TAAAT
1 TAAAT
4634200 TTAATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 9 0.45
18 7 0.35
19 4 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAATAAATATTAAATAAT
Found at i:4634231 original size:27 final size:27
Alignment explanation
Indices: 4634162--4634232 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
4634152 TTGATCATAA
4634162 ATAAATATTAA-ATAATTAAAAAATAT
1 ATAAATATTAATATAATTAAAAAATAT
* * * *
4634188 TTATAAT-TAAATTTAATTATAAAATAT
1 ATA-AATATTAATATAATTAAAAAATAT
4634215 ATAAATATTAATATAATT
1 ATAAATATTAATATAATT
4634233 TTTTAAATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
26 8 0.23
27 27 0.77
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
ATAAATATTAATATAATTAAAAAATAT
Found at i:4634463 original size:19 final size:20
Alignment explanation
Indices: 4634439--4634487 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
4634429 TTCATTATAT
4634439 TATTAAA-ATATAAATTTTA
1 TATTAAATATATAAATTTTA
* *
4634458 TATTAATATTTATATATTTTA
1 TATTAA-ATATATAAATTTTA
4634479 TAATTAAAT
1 T-ATTAAAT
4634488 TTAAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 6 0.24
20 1 0.04
21 13 0.52
22 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTAAATATATAAATTTTA
Found at i:4634476 original size:21 final size:21
Alignment explanation
Indices: 4634447--4634490 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4634437 ATTATTAAAA
4634447 TATAAATTTTAT-ATTAATATT
1 TATAAATTTTATAATTAA-ATT
*
4634468 TATATATTTTATAATTAAATT
1 TATAAATTTTATAATTAAATT
4634489 TA
1 TA
4634491 AATAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATAAATTTTATAATTAAATT
Found at i:4634777 original size:2 final size:2
Alignment explanation
Indices: 4634772--4634805 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4634762 ATGAAGAGAA
4634772 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4634806 TCTCTAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4636284 original size:3 final size:3
Alignment explanation
Indices: 4636276--4636306 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4636266 TGGATCCGAC
4636276 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
4636307 GTCATCATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:4638199 original size:18 final size:19
Alignment explanation
Indices: 4638178--4638219 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
4638168 TTGCCTAAAG
4638178 ATTTTATTT-TTAAAATTT
1 ATTTTATTTATTAAAATTT
*
4638196 A-TTTATTTATTTAAATTT
1 ATTTTATTTATTAAAATTT
*
4638214 TTTTTA
1 ATTTTA
4638220 AAATAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 7 0.35
18 9 0.45
19 4 0.20
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTTTATTTATTAAAATTT
Found at i:4642750 original size:16 final size:15
Alignment explanation
Indices: 4642727--4642802 Score: 65
Period size: 13 Copynumber: 5.4 Consensus size: 15
4642717 TTATAAAATT
4642727 TTTAATTAAATAAAA
1 TTTAATTAAATAAAA
4642742 TTATAATT-AATAAAA
1 TT-TAATTAAATAAAA
* **
4642757 TTTATTTAAA-ATTA
1 TTTAATTAAATAAAA
4642771 TTTAA-TAAAT-AAA
1 TTTAATTAAATAAAA
*
4642784 TTTAA--AATTAAAA
1 TTTAATTAAATAAAA
4642797 TTTAAT
1 TTTAAT
4642803 CATAAAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
12 3 0.06
13 18 0.37
14 10 0.20
15 13 0.27
16 5 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAATTAAATAAAA
Found at i:4642755 original size:15 final size:16
Alignment explanation
Indices: 4642719--4642795 Score: 56
Period size: 14 Copynumber: 5.1 Consensus size: 16
4642709 TAAAATTTTT
*
4642719 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
4642736 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
*
4642751 ATAAAATT-TATTTAA
1 ATAAAATTATAATTAA
**
4642766 A-ATTATT-TAA-TAA
1 ATAAAATTATAATTAA
* *
4642779 ATAAATTTAAAATTAA
1 ATAAAATTATAATTAA
4642795 A
1 A
4642796 ATTTAATCAT
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
13 4 0.09
14 13 0.28
15 13 0.28
16 11 0.23
17 6 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:4642786 original size:23 final size:25
Alignment explanation
Indices: 4642737--4642793 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 25
4642727 TTTAATTAAA
**
4642737 TAAAATTATAATTAATAAAATTTATT
1 TAAAATTAT-ATTAATAAAATAAATT
4642763 TAAAATTAT-TTAAT-AAATAAATT
1 TAAAATTATATTAATAAAATAAATT
4642786 TAAAATTA
1 TAAAATTA
4642794 AAATTTAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 15 0.52
24 5 0.17
26 9 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TAAAATTATATTAATAAAATAAATT
Found at i:4642793 original size:43 final size:43
Alignment explanation
Indices: 4642696--4642794 Score: 132
Period size: 43 Copynumber: 2.3 Consensus size: 43
4642686 CACATTTATA
*
4642696 AAAATTAAAA-AAATAAAATTTTTATAAAATTTTTAATTAAAT
1 AAAATTAAAATTAATAAAATTTTTATAAAATTTTTAATTAAAT
*
4642738 AAAATTATAATTAATAAAATTTATT-TAAAATTATTTAA-TAAAT
1 AAAATTAAAATTAATAAAATTT-TTATAAAATT-TTTAATTAAAT
*
4642781 AAATTTAAAATTAA
1 AAAATTAAAATTAA
4642795 AATTTAATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
42 9 0.18
43 34 0.68
44 7 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (43 bp):
AAAATTAAAATTAATAAAATTTTTATAAAATTTTTAATTAAAT
Found at i:4642812 original size:14 final size:13
Alignment explanation
Indices: 4642770--4642822 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
4642760 ATTTAAAATT
4642770 ATTTAATA-AATAA
1 ATTTAATATAA-AA
* *
4642783 ATTTAAAATTAAA
1 ATTTAATATAAAA
4642796 ATTTAATCATAAAA
1 ATTTAAT-ATAAAA
*
4642810 ATTTTATATAAAA
1 ATTTAATATAAAA
4642823 TATAAGATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
13 21 0.64
14 12 0.36
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTTAATATAAAA
Found at i:4642840 original size:17 final size:17
Alignment explanation
Indices: 4642818--4642850 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4642808 AAATTTTATA
4642818 TAAAATATAAGATAAAT
1 TAAAATATAAGATAAAT
*
4642835 TAAAATATAATATAAA
1 TAAAATATAAGATAAA
4642851 CATAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
TAAAATATAAGATAAAT
Found at i:4642860 original size:24 final size:23
Alignment explanation
Indices: 4642815--4642873 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
4642805 TAAAAATTTT
* *
4642815 ATATAAAATATAAGATAAATTAAA
1 ATATAATATA-AACATAAATTAAA
4642839 ATATAATATAAACATAATATTAAA
1 ATATAATATAAACATAA-ATTAAA
*
4642863 AAATAAT-TAAA
1 ATATAATATAAA
4642874 ATACACTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.32
24 21 0.68
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (23 bp):
ATATAATATAAACATAAATTAAA
Found at i:4643007 original size:15 final size:15
Alignment explanation
Indices: 4642987--4643027 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
4642977 TAAAAAATAA
*
4642987 TATAAACATAATGTT
1 TATAAACATAATATT
4643002 TATAAA-A-AATATT
1 TATAAACATAATATT
4643015 TA-AAACATAATAT
1 TATAAACATAATAT
4643028 GAAAATGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
12 3 0.13
13 8 0.35
14 6 0.26
15 6 0.26
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (15 bp):
TATAAACATAATATT
Found at i:4643044 original size:22 final size:21
Alignment explanation
Indices: 4643019--4643067 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
4643009 AATATTTAAA
*
4643019 ACATAATATGAAAATGATATAC
1 ACATAATACGAAAAT-ATATAC
*
4643041 ACATAATACGAATATATATAC
1 ACATAATACGAAAATATATAC
*
4643062 ATATAA
1 ACATAA
4643068 AAATATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.55, C:0.10, G:0.06, T:0.29
Consensus pattern (21 bp):
ACATAATACGAAAATATATAC
Found at i:4643219 original size:29 final size:29
Alignment explanation
Indices: 4643166--4643226 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
4643156 AATACATAAA
* *
4643166 TTTTTCTCTTTTTCTTGCTTTTTTTTCTT
1 TTTTTCTCTTTTTCTTGATTTTTTTTATT
*
4643195 TTTTTCTC-TTTTCTTTATTTCTTTTTATT
1 TTTTTCTCTTTTTCTTGATTT-TTTTTATT
4643224 TTT
1 TTT
4643227 CCAGCTTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (29 bp):
TTTTTCTCTTTTTCTTGATTTTTTTTATT
Found at i:4643221 original size:10 final size:9
Alignment explanation
Indices: 4643166--4643226 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
4643156 AATACATAAA
*
4643166 TTTTTCTCT
1 TTTTTTTCT
*
4643175 TTTTCTTGCT
1 TTTT-TTTCT
4643185 TTTTTTTCT
1 TTTTTTTCT
4643194 TTTTTTCTCT
1 TTTTTT-TCT
* *
4643204 TTTCTTTAT
1 TTTTTTTCT
*
4643213 TTCTTTTTAT
1 TT-TTTTTCT
4643223 TTTT
1 TTTT
4643227 CCAGCTTTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 20 0.47
10 23 0.53
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:4644705 original size:4 final size:4
Alignment explanation
Indices: 4644698--4644739 Score: 75
Period size: 4 Copynumber: 10.2 Consensus size: 4
4644688 TTTTTTTCTC
4644698 CTTT CTTT CTTT CTTT CTTT CTTTT CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT CTTT C
4644740 CTGCCCCCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 33 0.89
5 4 0.11
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:4644724 original size:21 final size:21
Alignment explanation
Indices: 4644699--4644739 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
4644689 TTTTTTCTCC
4644699 TTTCTTTCTTTCTTTCTTTCT
1 TTTCTTTCTTTCTTTCTTTCT
4644720 TTTCTTTCTTTCTTTCTTTC
1 TTTCTTTCTTTCTTTCTTTC
4644740 CTGCCCCCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTCTTTCTTTCTTTCTTTCT
Found at i:4645074 original size:41 final size:39
Alignment explanation
Indices: 4645015--4645098 Score: 98
Period size: 41 Copynumber: 2.1 Consensus size: 39
4645005 ATAATTTTTA
*
4645015 ATTTTATATAATTTTTATATAATTTAAATAAAAAAT-ATT
1 ATTTTATATAATATTTATAT-ATTTAAATAAAAAATAATT
* * *
4645054 ATTTTAGTATTAATATTTATATATTTTATTTAAAAATAATT
1 ATTTTA-TA-TAATATTTATATATTTAAATAAAAAATAATT
4645095 ATTT
1 ATTT
4645099 ATTAAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
39 6 0.16
40 14 0.37
41 18 0.47
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (39 bp):
ATTTTATATAATATTTATATATTTAAATAAAAAATAATT
Found at i:4645101 original size:45 final size:42
Alignment explanation
Indices: 4645005--4645101 Score: 94
Period size: 41 Copynumber: 2.3 Consensus size: 42
4644995 TATTATAATT
*
4645005 ATAATT-TTTAATTTTATATAATTTTTATATAATTTAAATAAA
1 ATAATTATTT-ATTTTATATAATATTTATATAATTTAAATAAA
* **
4645047 A-AA-TA-TTATTTTAGTATTAATATTTATATATTTTATTTAAAA
1 ATAATTATTTATTTTA-TA-TAATATTTATATAATTTAAAT-AAA
4645089 ATAATTATTTATT
1 ATAATTATTTATT
4645102 AAAAAATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
39 6 0.14
40 5 0.11
41 19 0.43
42 5 0.11
43 2 0.05
44 2 0.05
45 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (42 bp):
ATAATTATTTATTTTATATAATATTTATATAATTTAAATAAA
Found at i:4649425 original size:21 final size:20
Alignment explanation
Indices: 4649401--4649441 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
4649391 TTACTATTTT
4649401 GCTTGCTTGATATGGAGTTTG
1 GCTTGCTTGATATGG-GTTTG
4649422 GCTTGCTTGATATGGGTTTG
1 GCTTGCTTGATATGGGTTTG
4649442 AATGAATCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.12, C:0.10, G:0.34, T:0.44
Consensus pattern (20 bp):
GCTTGCTTGATATGGGTTTG
Found at i:4653452 original size:3 final size:3
Alignment explanation
Indices: 4653444--4653472 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4653434 TCGCTAAAGC
4653444 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
4653473 TTTTATAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:4664037 original size:10 final size:11
Alignment explanation
Indices: 4664023--4664052 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
4664013 CAGCATATAT
4664023 TTATATATTTA
1 TTATATATTTA
4664034 -TATATATTTA
1 TTATATATTTA
4664044 TTATATATT
1 TTATATATT
4664053 AATAACTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTATATATTTA
Found at i:4664990 original size:21 final size:23
Alignment explanation
Indices: 4664966--4665013 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
4664956 TAAAATTATC
*
4664966 ATTATTATTAT-GAAATATAAA-
1 ATTATTATTATAAAAATATAAAT
4664987 ATTA-TATTATAAAAATATAAAT
1 ATTATTATTATAAAAATATAAAT
4665009 ATTAT
1 ATTAT
4665014 AATAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 13 0.57
22 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTATTATTATAAAAATATAAAT
Found at i:4665018 original size:20 final size:20
Alignment explanation
Indices: 4664978--4665020 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
4664968 TATTATTATG
4664978 AAATATAAAATTATATTATAA
1 AAATATAAAATTATA-TATAA
4664999 AAATATAAATATTATA-ATAA
1 AAATATAAA-ATTATATATAA
4665019 AA
1 AA
4665021 TATTTAAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 9 0.43
22 6 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATATAAAATTATATATAA
Found at i:4665101 original size:17 final size:17
Alignment explanation
Indices: 4665079--4665119 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
4665069 GGTTGGTTAT
*
4665079 TTTTTTAAATGAATTTA
1 TTTTTTAAATGAATTAA
**
4665096 TTTTTTATCTGAATTAA
1 TTTTTTAAATGAATTAA
4665113 TTTTTTA
1 TTTTTTA
4665120 TTTTTAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.63
Consensus pattern (17 bp):
TTTTTTAAATGAATTAA
Found at i:4665120 original size:17 final size:17
Alignment explanation
Indices: 4665088--4665120 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4665078 TTTTTTTAAA
*
4665088 TGAATTTATTTTTTATC
1 TGAATTAATTTTTTATC
4665105 TGAATTAATTTTTTAT
1 TGAATTAATTTTTTAT
4665121 TTTTAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (17 bp):
TGAATTAATTTTTTATC
Found at i:4665132 original size:14 final size:15
Alignment explanation
Indices: 4665109--4665137 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4665099 TTTATCTGAA
4665109 TTAAT-TTTTTATTT
1 TTAATATTTTTATTT
4665123 TTAATATTTTTATTT
1 TTAATATTTTTATTT
4665138 AAATTTCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTAATATTTTTATTT
Found at i:4665488 original size:2 final size:2
Alignment explanation
Indices: 4665481--4665505 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4665471 ACATGCATAC
4665481 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 A
4665506 AACCAAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4665839 original size:23 final size:23
Alignment explanation
Indices: 4665809--4665852 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
4665799 GATCGAAGCC
4665809 AGAACCAGCAAACTCATACTGCT
1 AGAACCAGCAAACTCATACTGCT
4665832 AGAACCAGCAAACTCATACTG
1 AGAACCAGCAAACTCATACTG
4665853 TTGGAGCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.30, G:0.14, T:0.16
Consensus pattern (23 bp):
AGAACCAGCAAACTCATACTGCT
Found at i:4675650 original size:45 final size:45
Alignment explanation
Indices: 4675599--4675684 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
4675589 GGTAATGAAA
4675599 CCCCATTAAAAGAAAAGAAAAGCGACAGAACGTTATGAAAAGCGT
1 CCCCATTAAAAGAAAAGAAAAGCGACAGAACGTTATGAAAAGCGT
* *
4675644 CCCCATTAAAAGAAGAGAAAAGCGACAGAACTTTATGAAAA
1 CCCCATTAAAAGAAAAGAAAAGCGACAGAACGTTATGAAAA
4675685 AGGTTCCAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.50, C:0.17, G:0.19, T:0.14
Consensus pattern (45 bp):
CCCCATTAAAAGAAAAGAAAAGCGACAGAACGTTATGAAAAGCGT
Found at i:4678417 original size:30 final size:30
Alignment explanation
Indices: 4678348--4678422 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
4678338 GTAAAAATAA
** * *
4678348 ATAAAATAAAAATTAAATATAATAATTATT
1 ATAAAATTTAAATTAAATAAAATAAATATT
*
4678378 TTAATAATTTAAATT-AATAAAATAAAATATT
1 ATAA-AATTTAAATTAAATAAAAT-AAATATT
4678409 ATAAAATTTAAATT
1 ATAAAATTTAAATT
4678423 TTTTAAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
30 20 0.54
31 17 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
ATAAAATTTAAATTAAATAAAATAAATATT
Found at i:4678433 original size:31 final size:33
Alignment explanation
Indices: 4678359--4678434 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 33
4678349 TAAAATAAAA
*
4678359 ATTAAATATAATAATTATTTTAATAATTTAAATT
1 ATTAAA-ATAATAATTATTATAATAATTTAAATT
*
4678393 AATAAAATAA-AA-TATTATAA-AATTTAAATTT
1 ATTAAAATAATAATTATTATAATAATTTAAA-TT
*
4678424 TTTAAAATAAT
1 ATTAAAATAAT
4678435 TTATATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 8 0.22
31 17 0.47
32 2 0.06
33 4 0.11
34 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
ATTAAAATAATAATTATTATAATAATTTAAATT
Found at i:4679425 original size:3 final size:3
Alignment explanation
Indices: 4679411--4679443 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
4679401 CCTCTTATCT
*
4679411 TTA TTG TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4679444 AACACACACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:4680311 original size:20 final size:20
Alignment explanation
Indices: 4680262--4680312 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
4680252 ATAAAAAGAG
4680262 ATATTTTAATTTTTTATATT
1 ATATTTTAATTTTTTATATT
*
4680282 ATTAAATTTAATTTTTTAT-TAT
1 A-T-ATTTTAATTTTTTATAT-T
4680304 ATATTTTAA
1 ATATTTTAA
4680313 AAATTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 7 0.27
21 3 0.12
22 16 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATATTTTAATTTTTTATATT
Found at i:4680375 original size:47 final size:43
Alignment explanation
Indices: 4680306--4680418 Score: 113
Period size: 47 Copynumber: 2.5 Consensus size: 43
4680296 TTTATTATAT
*
4680306 ATTTTAAAAATT-ATAATAAATAAAAATAATTAGTAATAAT-TAAA
1 ATTTTAAATATTAATAA-AAATAAAAATAATTA-T-ATAATATAAA
** *
4680350 TATTATTTAAATATTAATAAAAATAATTATAATTATATGATATAAA
1 -A-T-TTTAAATATTAATAAAAATAAAAATAATTATATAATATAAA
4680396 ATTTTAAATATTATATAAAAATA
1 ATTTTAAATATTA-ATAAAAATA
4680419 TATTTAAATT
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
43 11 0.19
44 10 0.17
45 6 0.10
46 6 0.10
47 22 0.37
48 4 0.07
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (43 bp):
ATTTTAAATATTAATAAAAATAAAAATAATTATATAATATAAA
Found at i:4680376 original size:41 final size:43
Alignment explanation
Indices: 4680324--4680418 Score: 115
Period size: 41 Copynumber: 2.2 Consensus size: 43
4680314 AATTATAATA
* **
4680324 AATAAAAATAATTAGTAA-TA-ATTAAATATTA-TTTAAATATT
1 AATAAAAATAATTA-TAATTATATGAAATAAAATTTTAAATATT
*
4680365 AATAAAAATAATTATAATTATATGATATAAAATTTTAAATATT
1 AATAAAAATAATTATAATTATATGAAATAAAATTTTAAATATT
4680408 ATATAAAAATA
1 A-ATAAAAATA
4680419 TATTTAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 3 0.07
41 16 0.35
42 7 0.15
43 11 0.24
44 9 0.20
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (43 bp):
AATAAAAATAATTATAATTATATGAAATAAAATTTTAAATATT
Found at i:4680423 original size:24 final size:23
Alignment explanation
Indices: 4680355--4680427 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 23
4680345 TTAAATATTA
4680355 TTTAAATATTA-ATAAAAATAAT
1 TTTAAATATTATATAAAAATAAT
* * *
4680377 TATAATTA-TATGAT-ATAA-AAT
1 TTTAAATATTAT-ATAAAAATAAT
4680398 TTTAAATATTATATAAAAAT-AT
1 TTTAAATATTATATAAAAATAAT
4680420 ATTTAAAT
1 -TTTAAAT
4680428 TACAATTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
21 13 0.33
22 17 0.44
23 9 0.23
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (23 bp):
TTTAAATATTATATAAAAATAAT
Found at i:4687826 original size:20 final size:21
Alignment explanation
Indices: 4687788--4687826 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
4687778 ATGAAGTAGA
* *
4687788 AACCTAGCAAAGAACAAAAAG
1 AACCTAGCAAAAAAAAAAAAG
4687809 AACCT-GCAAAAAAAAAAA
1 AACCTAGCAAAAAAAAAAA
4687827 GAAAAAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.67, C:0.18, G:0.10, T:0.05
Consensus pattern (21 bp):
AACCTAGCAAAAAAAAAAAAG
Found at i:4687827 original size:19 final size:21
Alignment explanation
Indices: 4687788--4687829 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
4687778 ATGAAGTAGA
*
4687788 AACCTAGCAAAGAACAAAAAG
1 AACCTAGCAAAGAAAAAAAAG
4687809 AACCT-GCAAA-AAAAAAAAG
1 AACCTAGCAAAGAAAAAAAAG
4687828 AA
1 AA
4687830 AAAAGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 5 0.25
21 5 0.25
ACGTcount: A:0.67, C:0.17, G:0.12, T:0.05
Consensus pattern (21 bp):
AACCTAGCAAAGAAAAAAAAG
Found at i:4691212 original size:15 final size:14
Alignment explanation
Indices: 4691185--4691215 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
4691175 TAATTATAAT
4691185 TATAATAAATAAAA
1 TATAATAAATAAAA
4691199 TATAATATAATAAAA
1 TATAATA-AATAAAA
4691214 TA
1 TA
4691216 CGTTACTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TATAATAAATAAAA
Found at i:4691529 original size:2 final size:2
Alignment explanation
Indices: 4691522--4691564 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
4691512 AGGATAGCGC
* *
4691522 AG AG AG AG AG AA AG AG AG CG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4691564 A
1 A
4691565 ATGGTAAACC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4702493 original size:23 final size:23
Alignment explanation
Indices: 4702463--4702512 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
4702453 AGTGTTCAAG
4702463 TGCAGAAAGTTTTATAATCCGTC
1 TGCAGAAAGTTTTATAATCCGTC
4702486 TGCAGAAAGTTTTATAATCCGTC
1 TGCAGAAAGTTTTATAATCCGTC
4702509 TGCA
1 TGCA
4702513 TAAATCATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (23 bp):
TGCAGAAAGTTTTATAATCCGTC
Found at i:4703993 original size:16 final size:15
Alignment explanation
Indices: 4703972--4704018 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
4703962 AATTTGATCA
4703972 TTTAAAGTAAAAAATT
1 TTTAAA-TAAAAAATT
*
4703988 TTTAAA-ATAAAATT
1 TTTAAATAAAAAATT
*
4704002 TTTAAAATTAAAAATT
1 TTT-AAATAAAAAATT
4704018 T
1 T
4704019 AATTTTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 10 0.38
15 3 0.12
16 13 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
TTTAAATAAAAAATT
Found at i:4703999 original size:14 final size:15
Alignment explanation
Indices: 4703982--4704014 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
4703972 TTTAAAGTAA
4703982 AAAATTTTTAAAA-T
1 AAAATTTTTAAAATT
4703996 AAAATTTTTAAAATT
1 AAAATTTTTAAAATT
4704011 AAAA
1 AAAA
4704015 ATTTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATTTTTAAAATT
Found at i:4704014 original size:20 final size:19
Alignment explanation
Indices: 4703989--4704035 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
4703979 TAAAAAATTT
4703989 TTAAAATAAAATTTTTAAAA
1 TTAAAATAAAA-TTTTAAAA
**
4704009 TTAAAAATTTAATTTTAAAA
1 TT-AAAATAAAATTTTAAAA
4704029 -TAAAATA
1 TTAAAATA
4704036 TTTTTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 5 0.22
19 1 0.04
20 10 0.43
21 7 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAAATAAAATTTTAAAA
Found at i:4704038 original size:20 final size:20
Alignment explanation
Indices: 4704001--4704038 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4703991 AAAATAAAAT
4704001 TTTTAAAATTAAAAATTTAA
1 TTTTAAAATTAAAAATTTAA
4704021 TTTTAAAA-TAAAATATTT
1 TTTTAAAATTAAAA-ATTT
4704039 TTTTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTTAAAATTAAAAATTTAA
Found at i:4704665 original size:25 final size:23
Alignment explanation
Indices: 4704601--4704673 Score: 60
Period size: 25 Copynumber: 3.0 Consensus size: 23
4704591 ATATTTATTC
*
4704601 TTTATATAATAAATACTACATTA
1 TTTATATAATAAAAACTACATTA
*
4704624 TGTATATAAATACAAAACTA-ATATA
1 TTTATAT-AATA-AAAACTACAT-TA
*
4704649 TATTATATAATTAAAAA-TATATTA
1 T-TTATATAA-TAAAAACTACATTA
4704673 T
1 T
4704674 ACCAAATTCG
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
23 6 0.15
24 11 0.27
25 17 0.41
26 7 0.17
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.41
Consensus pattern (23 bp):
TTTATATAATAAAAACTACATTA
Found at i:4706513 original size:45 final size:42
Alignment explanation
Indices: 4706453--4706539 Score: 102
Period size: 45 Copynumber: 2.0 Consensus size: 42
4706443 TATTATTTAA
* * **
4706453 AAATAAAAATAATTTATATATACTTTTATAATTAAATTTAAAT
1 AAATAAAAATAATTTAAATAAAAATTTATAATTAAA-TTAAAT
*
4706496 AAATATAAAATATATTTAAATAAAAATTTATATTTAAATTAAAT
1 AAATA-AAAATA-ATTTAAATAAAAATTTATAATTAAATTAAAT
4706540 TTATCAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 5 0.14
44 12 0.32
45 20 0.54
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (42 bp):
AAATAAAAATAATTTAAATAAAAATTTATAATTAAATTAAAT
Found at i:4706515 original size:17 final size:18
Alignment explanation
Indices: 4706495--4706543 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
4706485 TAAATTTAAA
4706495 TAAATATAAAA-TATATT
1 TAAATATAAAATTATATT
4706512 TAAATA-AAAATTTATATT
1 TAAATATAAAA-TTATATT
*
4706530 TAAAT-TAAATTTAT
1 TAAATATAAAATTAT
4706544 CAAATTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 4 0.14
17 10 0.36
18 14 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATATAAAATTATATT
Found at i:4706748 original size:17 final size:18
Alignment explanation
Indices: 4706728--4706761 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4706718 AAACTATTAA
*
4706728 TATCT-TCTTTTTTTTAT
1 TATCTCTCTTATTTTTAT
4706745 TATCTCTCTTATTTTTA
1 TATCTCTCTTATTTTTA
4706762 GATATTCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (18 bp):
TATCTCTCTTATTTTTAT
Found at i:4707470 original size:22 final size:21
Alignment explanation
Indices: 4707427--4707502 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
4707417 AAAGAATTTT
* *
4707427 ATTAATAAATATTTTTTTAAA
1 ATTAATTAATATTTATTTAAA
4707448 ATTAATTAATATATTATTTAAA
1 ATTAATTAATAT-TTATTTAAA
*
4707470 AATAA-TAATA-TTATATTAAA
1 ATTAATTAATATTTAT-TTAAA
*
4707490 TTTAA-T-ATATTTA
1 ATTAATTAATATTTA
4707503 ATGAATATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
19 7 0.15
20 12 0.26
21 16 0.34
22 12 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAATTAATATTTATTTAAA
Found at i:4707499 original size:19 final size:18
Alignment explanation
Indices: 4707451--4707500 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
4707441 TTTTAAAATT
4707451 AATTAATATATTATTTAA
1 AATTAATATATTATTTAA
*
4707469 AAATAATAATATTATATTAA
1 AATTAAT-ATATTAT-TTAA
*
4707489 ATTTAATATATT
1 AATTAATATATT
4707501 TAATGAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.22
19 12 0.44
20 9 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTAATATATTATTTAA
Found at i:4708162 original size:45 final size:44
Alignment explanation
Indices: 4708100--4708184 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 44
4708090 ATTGTAATAA
* *
4708100 TTTTTTAATAATATAATCTTTTATTAA-TTTAAAATAATATAAAC
1 TTTTTTAATAATATAATCTTATAATAATTTTAAAA-AATATAAAC
*
4708144 TTTTATTAATAATCTAATCTTATAATAATTTTAAAAAATAT
1 TTTT-TTAATAATATAATCTTATAATAATTTTAAAAAATAT
4708185 TAATATAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 4 0.11
45 25 0.69
46 7 0.19
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (44 bp):
TTTTTTAATAATATAATCTTATAATAATTTTAAAAAATATAAAC
Found at i:4712228 original size:103 final size:104
Alignment explanation
Indices: 4712103--4712296 Score: 354
Period size: 103 Copynumber: 1.9 Consensus size: 104
4712093 CACCATTTTA
*
4712103 AATAACCAAAGTAACATCATTCAGTAAGGAACTCTATATAAGATATATGATCAAGCCCCAAA-AG
1 AATAACCAAAGTAACATCATTCAGTAAGGAACTCTATATAAGATAAATGATCAAGCCCCAAACAG
4712167 AGGAATTGAAGATCACTTCTCTTGATAAGATAAATGAAC
66 AGGAATTGAAGATCACTTCTCTTGATAAGATAAATGAAC
*
4712206 AATAACCAAAGTAACATCATTCAGTAAGGAACTCTATATTAGATAAATGATCAAGCCCCAAACAG
1 AATAACCAAAGTAACATCATTCAGTAAGGAACTCTATATAAGATAAATGATCAAGCCCCAAACAG
*
4712271 AGGAATTGAAGATCATTTCTCTTGAT
66 AGGAATTGAAGATCACTTCTCTTGAT
4712297 CTGCAGCAAA
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
103 60 0.69
104 27 0.31
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.25
Consensus pattern (104 bp):
AATAACCAAAGTAACATCATTCAGTAAGGAACTCTATATAAGATAAATGATCAAGCCCCAAACAG
AGGAATTGAAGATCACTTCTCTTGATAAGATAAATGAAC
Found at i:4714321 original size:15 final size:15
Alignment explanation
Indices: 4714282--4714329 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
4714272 TATGTCTATT
* *
4714282 ATTTTAAAAGTATTA
1 ATTTTAAAAATTTTA
* *
4714297 TTTTTCAAAATTTTA
1 ATTTTAAAAATTTTA
4714312 ATTTTAAAAATTTATA
1 ATTTTAAAAATTT-TA
4714328 AT
1 AT
4714330 AAATAGATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTTTAAAAATTTTA
Found at i:4714399 original size:22 final size:23
Alignment explanation
Indices: 4714348--4714388 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
4714338 TACAAAATTT
4714348 TTAATTTTATAATAATATTATTA
1 TTAATTTTATAATAATATTATTA
4714371 TT-ATTTTATAA-AA-ATTAT
1 TTAATTTTATAATAATATTAT
4714389 CTTGTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 9 0.50
23 2 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAATTTTATAATAATATTATTA
Found at i:4715016 original size:2 final size:2
Alignment explanation
Indices: 4715009--4715042 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4714999 TAAAAAGCGC
4715009 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4715043 TTAGTTGCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4716717 original size:23 final size:22
Alignment explanation
Indices: 4716674--4716720 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
4716664 TTTTATATAT
4716674 TAATTATAAAATTTTAAATTTTA
1 TAATTATAAAATTTT-AATTTTA
*
4716697 TAATTATTAAATATTTTATTTTTA
1 TAATTA-TAAA-ATTTTAATTTTA
4716721 AAAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 10 0.48
25 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TAATTATAAAATTTTAATTTTA
Found at i:4719483 original size:5 final size:5
Alignment explanation
Indices: 4719473--4719497 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4719463 AGGGGGGAAA
4719473 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
4719498 CGGGCATGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:4720225 original size:2 final size:2
Alignment explanation
Indices: 4720214--4720249 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4720204 TGACTTTAAG
4720214 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4720250 CGCCAGTCTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4721807 original size:2 final size:2
Alignment explanation
Indices: 4721800--4721855 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
4721790 GCCATCTGAA
4721800 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4721842 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
4721856 GAAGGAAAGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4722304 original size:12 final size:12
Alignment explanation
Indices: 4722278--4722310 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4722268 TTAGAATAGG
4722278 AATAAATAT-TA
1 AATAAATATATA
4722289 AATAAATATATA
1 AATAAATATATA
*
4722301 AATAATTATA
1 AATAAATATA
4722311 AAGTTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AATAAATATATA
Found at i:4733208 original size:8 final size:10
Alignment explanation
Indices: 4733182--4733220 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
4733172 GAGCGAGGAA
4733182 GAAAGAGAGG
1 GAAAGAGAGG
4733192 GAAAGAGAGG
1 GAAAGAGAGG
*
4733202 GAAAGAGAGA
1 GAAAGAGAGG
*
4733212 GAGAGAGAG
1 GAAAGAGAG
4733221 ACTGATTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (10 bp):
GAAAGAGAGG
Found at i:4736228 original size:17 final size:16
Alignment explanation
Indices: 4736182--4736228 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
4736172 TAGGGCGGGA
*
4736182 AGAAAATTAGGAAGATG
1 AGAAAATTA-GAAGAGG
*
4736199 A-AAAATTAAAAGAGG
1 AGAAAATTAGAAGAGG
4736214 AGAAAAGTTAGAAGA
1 AGAAAA-TTAGAAGA
4736229 TAGGAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 6 0.24
16 11 0.44
17 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.15
Consensus pattern (16 bp):
AGAAAATTAGAAGAGG
Done.