Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012297.1 Kokia drynarioides strain JFW-HI SEQ_127298, 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: 427781
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 212 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:682 original size:15 final size:15
Alignment explanation
Indices: 662--696 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
652 TTTGCAGGTT
662 GCAGCGACGGTGGTA
1 GCAGCGACGGTGGTA
677 GCAGCGACGGTGGTA
1 GCAGCGACGGTGGTA
692 GCAGC
1 GCAGC
697 AGTGGCGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.20, C:0.23, G:0.46, T:0.11
Consensus pattern (15 bp):
GCAGCGACGGTGGTA
Found at i:960 original size:11 final size:11
Alignment explanation
Indices: 946--1016 Score: 72
Period size: 11 Copynumber: 6.4 Consensus size: 11
936 TGGACTTTTT
946 AATTTAAATTA
1 AATTTAAATTA
* *
957 AATTCAATTTA
1 AATTTAAATTA
*
968 AATTT-AATATC
1 AATTTAAAT-TA
979 AATTTAAATTTA
1 AATTTAAA-TTA
*
991 AATTTAAATCA
1 AATTTAAATTA
*
1002 AATTTAAAATA
1 AATTTAAATTA
1013 AATT
1 AATT
1017 AAAAAAGGCC
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
10 2 0.04
11 34 0.71
12 11 0.23
13 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:971 original size:6 final size:6
Alignment explanation
Indices: 946--1009 Score: 64
Period size: 6 Copynumber: 11.3 Consensus size: 6
936 TGGACTTTTT
* * *
946 AATTTA AA-TTA AA-TTC AATTTA AATTT- AATATC AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
991 AATTTA AA-TCA AATTTA AA
1 AATTTA AATTTA AATTTA AA
1010 ATAAATTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
5 17 0.35
6 31 0.65
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:980 original size:17 final size:16
Alignment explanation
Indices: 946--991 Score: 74
Period size: 17 Copynumber: 2.8 Consensus size: 16
936 TGGACTTTTT
*
946 AATTTAAATTAAATTC
1 AATTTAAATTTAATTC
962 AATTTAAATTTAATATC
1 AATTTAAATTTAAT-TC
979 AATTTAAATTTAA
1 AATTTAAATTTAA
992 ATTTAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTTAAATTTAATTC
Found at i:992 original size:23 final size:23
Alignment explanation
Indices: 946--1009 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
936 TGGACTTTTT
* *
946 AATTTAAATTAAA-TTCAATTTA
1 AATTTAAATCAAATTTAAATTTA
968 AATTTAATATC-AATTTAAATTTA
1 AATTTAA-ATCAAATTTAAATTTA
991 AATTTAAATCAAATTTAAA
1 AATTTAAATCAAATTTAAA
1010 ATAAATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
22 12 0.32
23 25 0.68
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTTAAATCAAATTTAAATTTA
Found at i:16694 original size:20 final size:20
Alignment explanation
Indices: 16671--16722 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
16661 ATAAATTGAT
16671 ATAAATCTATAAA-AATTATA
1 ATAAATC-ATAAATAATTATA
*
16691 ATAAAATCATAAATATTTATA
1 AT-AAATCATAAATAATTATA
*
16712 AAAAAT-ATAAA
1 ATAAATCATAAA
16723 AAAAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 5 0.18
20 11 0.39
21 12 0.43
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATCATAAATAATTATA
Found at i:18617 original size:9 final size:9
Alignment explanation
Indices: 18518--18706 Score: 59
Period size: 9 Copynumber: 20.1 Consensus size: 9
18508 AAATCGTTAC
18518 ATTATAAAA
1 ATTATAAAA
18527 ATTAATAAAA
1 ATT-ATAAAA
*
18537 CTTATAAATA
1 ATTATAAA-A
18547 A-TATTAAAA
1 ATTA-TAAAA
*
18556 AATATAAAAA
1 ATTAT-AAAA
*
18566 ATT-TATACA
1 ATTATA-AAA
*
18575 ATTATTAAAC
1 ATTA-TAAAA
18585 A-T-T-AAA
1 ATTATAAAA
18591 ATTGATATAAA
1 ATT-ATA-AAA
*
18602 CTTATAAAA
1 ATTATAAAA
18611 ATTATAAAAAA
1 ATTAT--AAAA
*
18622 ATCATAAAA
1 ATTATAAAA
* *
18631 ACTTATGAAT
1 A-TTATAAAA
*
18641 ATAATAAAA
1 ATTATAAAA
*
18650 ATT-TACTAA
1 ATTATA-AAA
* *
18659 GTTCTAATAAA
1 ATTAT-A-AAA
18670 ATTATAAAA
1 ATTATAAAA
18679 TATTA-AAAA
1 -ATTATAAAA
* * *
18688 AATACAAAT
1 ATTATAAAA
18697 ATTATAAAA
1 ATTATAAAA
18706 A
1 A
18707 AAAACCATTT
Statistics
Matches: 131, Mismatches: 28, Indels: 42
0.65 0.14 0.21
Matches are distributed among these distances:
6 3 0.02
7 2 0.02
8 6 0.05
9 61 0.47
10 38 0.29
11 21 0.16
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.33
Consensus pattern (9 bp):
ATTATAAAA
Found at i:19516 original size:9 final size:9
Alignment explanation
Indices: 19371--19575 Score: 109
Period size: 9 Copynumber: 21.9 Consensus size: 9
19361 AGTTTAGATG
19371 ATTTTTATTA
1 ATTTTTA-TA
*
19381 AATTTTA-A
1 ATTTTTATA
19389 ATTTTTATA
1 ATTTTTATA
19398 ATTTATTATA
1 ATTT-TTATA
19408 A-TTTTAT-
1 ATTTTTATA
*
19415 ATCATTTATA
1 AT-TTTTATA
19425 AGTTTTTCATGA
1 A-TTTTT-AT-A
*
19437 A-ATTTATA
1 ATTTTTATA
* *
19445 AATTTTAAA
1 ATTTTTATA
19454 TATGTTTTATTA
1 -AT-TTTTA-TA
19466 A-TTTTATA
1 ATTTTTATA
*
19474 ATTTTTTAGA
1 A-TTTTTATA
19484 ATTTTTATA
1 ATTTTTATA
*
19493 ATATTTATA
1 ATTTTTATA
19502 AGTTTTTATGA
1 A-TTTTTAT-A
*
19513 TTTTTTATA
1 ATTTTTATA
*
19522 TTTTTTTATA
1 -ATTTTTATA
*
19532 AGTTTATATCA
1 A-TTTTTAT-A
*
19543 A-TTTTATT
1 ATTTTTATA
*
19551 ATTTTCA-A
1 ATTTTTATA
*
19559 TTTTTTATA
1 ATTTTTATA
19568 ATTTTTAT
1 ATTTTTAT
19576 GAGAAAATAT
Statistics
Matches: 151, Mismatches: 23, Indels: 43
0.70 0.11 0.20
Matches are distributed among these distances:
7 1 0.01
8 22 0.15
9 58 0.38
10 55 0.36
11 12 0.08
12 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:19554 original size:30 final size:30
Alignment explanation
Indices: 19496--19555 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
19486 TTTTATAATA
* * *
19496 TTTATAAGTTTTTATGATTTTTTATATTTT
1 TTTATAAGTTTATATAATTTTATATATTTT
19526 TTTATAAGTTTATATCAATTTTAT-TATTTT
1 TTTATAAGTTTATAT-AATTTTATATATTTT
19556 CAATTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (30 bp):
TTTATAAGTTTATATAATTTTATATATTTT
Found at i:20240 original size:19 final size:19
Alignment explanation
Indices: 20218--20257 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
20208 AATAATTTTC
20218 AAAAATT-CAAAATATTTAT
1 AAAAATTCCAAAAT-TTTAT
20237 AAAAATTCCAAAATTTTAT
1 AAAAATTCCAAAATTTTAT
20256 AA
1 AA
20258 TTTTTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTCCAAAATTTTAT
Found at i:23504 original size:24 final size:24
Alignment explanation
Indices: 23443--23505 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
23433 TAGATTAATA
* *
23443 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAT
* ** *
23467 AGAATTTATTTGAAACAATTAAAT
1 AGAGTTTAACTGAAACAAATAAAT
23491 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
23506 GATGATTTAT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAT
Found at i:25445 original size:24 final size:24
Alignment explanation
Indices: 25417--25472 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
25407 TAGACTAATA
25417 AGAGTTTGA-CTCAAACAAATAAAC
1 AGAGTTT-ATCTCAAACAAATAAAC
* * *
25441 AGAGTTTATTTGAAACAATTAAAC
1 AGAGTTTATCTCAAACAAATAAAC
25465 AGAGTTTA
1 AGAGTTTA
25473 ATTGAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (24 bp):
AGAGTTTATCTCAAACAAATAAAC
Found at i:25477 original size:24 final size:24
Alignment explanation
Indices: 25429--25479 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
25419 AGTTTGACTC
*
25429 AAACAAATAAACAGAGTTTATTTG
1 AAACAAATAAACAGAGTTTAATTG
*
25453 AAACAATTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
25477 AAA
1 AAA
25480 TATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.08, G:0.12, T:0.27
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:27359 original size:49 final size:49
Alignment explanation
Indices: 27287--27384 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
27277 TTAAATCTTT
27287 TTTCATAGCAAGATCAGAATAAGTTCCTTTCAAGGAAACGGAAAGGCAA
1 TTTCATAGCAAGATCAGAATAAGTTCCTTTCAAGGAAACGGAAAGGCAA
27336 TTTCATAGCAAGATCAGAATAAGTTCCTTTCAAGGAAACGGAAAGGCAA
1 TTTCATAGCAAGATCAGAATAAGTTCCTTTCAAGGAAACGGAAAGGCAA
27385 CAGAGAAAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.22
Consensus pattern (49 bp):
TTTCATAGCAAGATCAGAATAAGTTCCTTTCAAGGAAACGGAAAGGCAA
Found at i:27366 original size:27 final size:27
Alignment explanation
Indices: 27287--27367 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 27
27277 TTAAATCTTT
27287 TTTCATAGCAAGATCAGAATAAGTTCC
1 TTTCATAGCAAGATCAGAATAAGTTCC
* * * *
27314 TTTCA-AGGAA-A-C-GGA-AAG-GCAA
1 TTTCATAGCAAGATCAGAATAAGTTC-C
27336 TTTCATAGCAAGATCAGAATAAGTTCC
1 TTTCATAGCAAGATCAGAATAAGTTCC
27363 TTTCA
1 TTTCA
27368 AGGAAACGGA
Statistics
Matches: 39, Mismatches: 8, Indels: 14
0.64 0.13 0.23
Matches are distributed among these distances:
21 1 0.03
22 8 0.21
23 6 0.15
24 2 0.05
25 2 0.05
26 6 0.15
27 13 0.33
28 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (27 bp):
TTTCATAGCAAGATCAGAATAAGTTCC
Found at i:30185 original size:19 final size:20
Alignment explanation
Indices: 30141--30185 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
30131 ATAAAAAAAA
*
30141 AACAA-AAGTTCAAGTAAAC
1 AACAATAAGCTCAAGTAAAC
30160 AAC-ATAAGCTCAAGT-AAC
1 AACAATAAGCTCAAGTAAAC
30178 AACAATAA
1 AACAATAA
30186 CACAAGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.58, C:0.18, G:0.09, T:0.16
Consensus pattern (20 bp):
AACAATAAGCTCAAGTAAAC
Found at i:30191 original size:18 final size:19
Alignment explanation
Indices: 30151--30191 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
30141 AACAAAAGTT
*
30151 CAAGTAAACAACATAAGCT
1 CAAGTAAACAACATAAGCA
30170 CAAGT-AACAACAATAA-CA
1 CAAGTAAACAAC-ATAAGCA
30188 CAAG
1 CAAG
30192 ATTATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.56, C:0.22, G:0.10, T:0.12
Consensus pattern (19 bp):
CAAGTAAACAACATAAGCA
Found at i:30745 original size:42 final size:42
Alignment explanation
Indices: 30698--30781 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
30688 TAAAAGAGTT
* * *
30698 GTTTATGAGTGTTATTTAAGAAT-AAAATTATATTTGAGTTTA
1 GTTTATAAGTGTTATTTAAAAATGAAAA-TATATTTGAATTTA
*
30740 GTTTATAAGTGTTTTTTAAAAATGAAAATATATTTGAATTTA
1 GTTTATAAGTGTTATTTAAAAATGAAAATATATTTGAATTTA
30782 AAAATATTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 33 0.89
43 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (42 bp):
GTTTATAAGTGTTATTTAAAAATGAAAATATATTTGAATTTA
Found at i:31210 original size:26 final size:26
Alignment explanation
Indices: 31181--31233 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
31171 TTTTTTTCCC
*
31181 TTTTTGCATTTTTTTCTCCTCTTTTT
1 TTTTTGAATTTTTTTCTCCTCTTTTT
*
31207 TTTTTGAATTTTTTTCTCTTCTTTTT
1 TTTTTGAATTTTTTTCTCCTCTTTTT
31233 T
1 T
31234 CTTGTAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75
Consensus pattern (26 bp):
TTTTTGAATTTTTTTCTCCTCTTTTT
Found at i:32458 original size:22 final size:21
Alignment explanation
Indices: 32419--32463 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
32409 TCACAAATAC
32419 AATTTTTGGATGACCGGGGGAT
1 AATTTTTGGATGACC-GGGGAT
32441 AATTTTTGGATG-CTCGGGGAT
1 AATTTTTGGATGAC-CGGGGAT
32462 AA
1 AA
32464 AATGGTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.24, C:0.09, G:0.33, T:0.33
Consensus pattern (21 bp):
AATTTTTGGATGACCGGGGAT
Found at i:32527 original size:28 final size:29
Alignment explanation
Indices: 32440--32570 Score: 117
Period size: 29 Copynumber: 4.6 Consensus size: 29
32430 GACCGGGGGA
* *
32440 TAATTTTTGGATGCTCGGGGATAAAATGG
1 TAATTTTTGGATGTTCGGGGTTAAAATGG
* * *
32469 TAATTTTTGGAT-ATCAAGCG-TAAAATGG
1 TAATTTTTGGATGTTC-GGGGTTAAAATGG
32497 TAATTTTTGGATGTTCGGGGTTAAAAT-G
1 TAATTTTTGGATGTTCGGGGTTAAAATGG
** * *
32525 TAATTTTTGGAAAATTTGGGGTTAAAAT-A
1 TAATTTTTGG-ATGTTCGGGGTTAAAATGG
*
32554 TAATTTCTGGATAGTTC
1 TAATTTTTGGAT-GTTC
32571 AGAGATCTTC
Statistics
Matches: 83, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
28 36 0.43
29 47 0.57
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (29 bp):
TAATTTTTGGATGTTCGGGGTTAAAATGG
Found at i:33395 original size:19 final size:18
Alignment explanation
Indices: 33367--33405 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
33357 CTTAGATCTG
* *
33367 TTTATCTTTTTATTTATTT
1 TTTATATTTTGATTT-TTT
33386 TTTATATTTTGATTTTTT
1 TTTATATTTTGATTTTTT
33404 TT
1 TT
33406 ATACTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTATATTTTGATTTTTT
Found at i:34306 original size:17 final size:17
Alignment explanation
Indices: 34279--34352 Score: 94
Period size: 17 Copynumber: 4.2 Consensus size: 17
34269 TATTTCAAAT
*
34279 TTTAAAATTAAAATAAA
1 TTTAAATTTAAAATAAA
*
34296 TTTAATTTTAAAAAATAAA
1 TTTAAATTT--AAAATAAA
*
34315 TTTAAATTTAAAATAAT
1 TTTAAATTTAAAATAAA
*
34332 TTTAAACTTAAAATAAA
1 TTTAAATTTAAAATAAA
34349 TTTA
1 TTTA
34353 GAATAAAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
17 33 0.67
19 16 0.33
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:34320 original size:30 final size:30
Alignment explanation
Indices: 34281--34337 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
34271 TTTCAAATTT
*
34281 TAAAATTAAA-ATAAATTTAATTTTAAAAAA
1 TAAAATTAAATATAAA-ATAATTTTAAAAAA
* *
34311 TAAATTTAAATTTAAAATAATTTTAAA
1 TAAAATTAAATATAAAATAATTTTAAA
34338 CTTAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
TAAAATTAAATATAAAATAATTTTAAAAAA
Found at i:34361 original size:17 final size:17
Alignment explanation
Indices: 34306--34362 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
34296 TTTAATTTTA
*
34306 AAAAATAAATTTAAATT
1 AAAAATAAATTTAAACT
* *
34323 TAAAATAATTTTAAACT
1 AAAAATAAATTTAAACT
*
34340 TAAAATAAATTTAGAA-T
1 AAAAATAAATTTA-AACT
34357 AAAAAT
1 AAAAAT
34363 TGGGTTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 32 0.94
18 2 0.06
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (17 bp):
AAAAATAAATTTAAACT
Found at i:35736 original size:20 final size:20
Alignment explanation
Indices: 35708--35746 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35698 ACTATTGATG
**
35708 TTGACCGTTGGCTTTTTTCA
1 TTGACCGTTAACTTTTTTCA
*
35728 TTGATCGTTAACTTTTTTC
1 TTGACCGTTAACTTTTTTC
35747 GAGAAACTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.18, G:0.15, T:0.54
Consensus pattern (20 bp):
TTGACCGTTAACTTTTTTCA
Found at i:37132 original size:16 final size:15
Alignment explanation
Indices: 37103--37136 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
37093 ATCATTTGCT
*
37103 AAAACAAAATAAAAG
1 AAAACAAAAAAAAAG
37118 AAAACCAAAAAAAAAG
1 AAAA-CAAAAAAAAAG
37134 AAA
1 AAA
37137 CTCATTGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.82, C:0.09, G:0.06, T:0.03
Consensus pattern (15 bp):
AAAACAAAAAAAAAG
Found at i:50701 original size:24 final size:24
Alignment explanation
Indices: 50656--50701 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
50646 CTCCTTTTTA
*
50656 TTTTTTAAACATCACTTCTTAATT
1 TTTTTTAAACATCACTTATTAATT
** *
50680 TTTTTTATTCATCATTTATTAA
1 TTTTTTAAACATCACTTATTAA
50702 GATAATTATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.28, C:0.13, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTTTTAAACATCACTTATTAATT
Found at i:53273 original size:23 final size:26
Alignment explanation
Indices: 53247--53296 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
53237 TTAAATATTC
53247 AAAATAT-ATTT-TT-TAATTTTATA
1 AAAATATAATTTATTATAATTTTATA
*
53270 AAAATATAATTTATTATATTTTTATA
1 AAAATATAATTTATTATAATTTTATA
53296 A
1 A
53297 TATTTATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.30
24 4 0.17
25 2 0.09
26 10 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
AAAATATAATTTATTATAATTTTATA
Found at i:53327 original size:8 final size:9
Alignment explanation
Indices: 53307--53331 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
53297 TATTTATGAA
53307 TTTTTATTT
1 TTTTTATTT
53316 TTTTTATTT
1 TTTTTATTT
53325 TTTTTAT
1 TTTTTAT
53332 AAATTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTATTT
Found at i:53368 original size:18 final size:18
Alignment explanation
Indices: 53345--53411 Score: 73
Period size: 17 Copynumber: 3.7 Consensus size: 18
53335 TTTATATCAA
*
53345 TTTTAATGTTTTTAATAT
1 TTTTAATATTTTTAATAT
* *
53363 TTTTAAT-TTTTAAAAAT
1 TTTTAATATTTTTAATAT
* *
53380 TTTTAAAATTTCTAATATT
1 TTTTAATATTTTTAATA-T
53399 TTTTAATATTTTT
1 TTTTAATATTTTT
53412 TGTGAGAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
17 14 0.36
18 13 0.33
19 12 0.31
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (18 bp):
TTTTAATATTTTTAATAT
Found at i:53412 original size:10 final size:9
Alignment explanation
Indices: 53345--53411 Score: 73
Period size: 9 Copynumber: 7.4 Consensus size: 9
53335 TTTATATCAA
*
53345 TTTTAATGT
1 TTTTAATAT
53354 TTTTAATAT
1 TTTTAATAT
53363 TTTTAAT-T
1 TTTTAATAT
* *
53371 TTTAAAAAT
1 TTTTAATAT
*
53380 TTTTAAAAT
1 TTTTAATAT
*
53389 TTCTAATATT
1 TTTTAATA-T
53399 TTTTAATAT
1 TTTTAATAT
53408 TTTT
1 TTTT
53412 TGTGAGAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
8 6 0.12
9 35 0.71
10 8 0.16
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTAATAT
Found at i:65624 original size:16 final size:17
Alignment explanation
Indices: 65592--65628 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
65582 TTATGATTAA
65592 TTTT-TGCATTTAAGTT
1 TTTTATGCATTTAAGTT
*
65608 TTTTATGCATTT-TGTT
1 TTTTATGCATTTAAGTT
65624 TTTTA
1 TTTTA
65629 ATATTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.16, C:0.05, G:0.11, T:0.68
Consensus pattern (17 bp):
TTTTATGCATTTAAGTT
Found at i:74953 original size:25 final size:23
Alignment explanation
Indices: 74918--74967 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 23
74908 ATAAATTTAA
74918 AATTTATTAATATGAAATAAATAT
1 AATTTATTAATATGAAATAAA-AT
*
74942 AATTATATTAATATTAAATAAAAT
1 AATT-TATTAATATGAAATAAAAT
74966 AA
1 AA
74968 AAATTCCCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
AATTTATTAATATGAAATAAAAT
Found at i:75253 original size:21 final size:19
Alignment explanation
Indices: 75187--75262 Score: 59
Period size: 21 Copynumber: 3.9 Consensus size: 19
75177 AGAGGAGGAG
75187 AATATTT-TAT-TTTATTT-
1 AATATTTATATATTT-TTTA
* *
75204 AATATTAATATATTTTCTA
1 AATATTTATATATTTTTTA
*
75223 AATTTGTTATATATTTTTTGAA
1 AATAT-TTATATATTTTTT--A
*
75245 AATATTTATGTATTTTTT
1 AATATTTATATATTTTTT
75263 TTGGATTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
17 6 0.13
18 5 0.11
19 7 0.15
20 11 0.24
21 12 0.26
22 5 0.11
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (19 bp):
AATATTTATATATTTTTTA
Found at i:75795 original size:18 final size:18
Alignment explanation
Indices: 75744--75805 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 18
75734 TTATTAAATG
75744 TATATAAACATT-AA-AAA
1 TATATAAA-ATTCAATAAA
*
75761 -ATATAAAAATCAAAATAAA
1 TATATAAAATTC--AATAAA
75780 TATATAAAATTCAAT--A
1 TATATAAAATTCAATAAA
75796 TATATAAAAT
1 TATATAAAAT
75806 CTAGAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
15 2 0.05
16 18 0.47
18 5 0.13
19 3 0.08
20 10 0.26
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.31
Consensus pattern (18 bp):
TATATAAAATTCAATAAA
Found at i:76108 original size:15 final size:15
Alignment explanation
Indices: 76088--76116 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
76078 ATTTTTAAAA
76088 TTTATAATTATATAT
1 TTTATAATTATATAT
76103 TTTATAATTATATA
1 TTTATAATTATATA
76117 AAAAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTATAATTATATAT
Found at i:77058 original size:29 final size:29
Alignment explanation
Indices: 77026--77082 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
77016 CATAAATTTG
*
77026 AAATCTTTACAAATATTTTG-AATTTTTAA
1 AAATATTT-CAAATATTTTGTAATTTTTAA
* *
77055 AAATATTTTAAATTTTTTGTAATTTTTA
1 AAATATTTCAAATATTTTGTAATTTTTA
77083 TTGTGAGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (29 bp):
AAATATTTCAAATATTTTGTAATTTTTAA
Found at i:77068 original size:19 final size:19
Alignment explanation
Indices: 77021--77071 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
77011 TAAAACATAA
* * *
77021 ATTTGAAATCTTTACAAAT
1 ATTTTAAATTTTTAAAAAT
*
77040 ATTTTGAATTTTTAAAAAT
1 ATTTTAAATTTTTAAAAAT
77059 ATTTTAAATTTTT
1 ATTTTAAATTTTT
77072 TGTAATTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (19 bp):
ATTTTAAATTTTTAAAAAT
Found at i:78113 original size:22 final size:23
Alignment explanation
Indices: 78088--78134 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
78078 AAATTACGTT
*
78088 TTGATTGCTCAATT-TTTAAAAG
1 TTGATTACTCAATTATTTAAAAG
* *
78110 TTGATTATTGAATTATTTAAAAG
1 TTGATTACTCAATTATTTAAAAG
78133 TT
1 TT
78135 TTAATTTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (23 bp):
TTGATTACTCAATTATTTAAAAG
Found at i:79737 original size:31 final size:32
Alignment explanation
Indices: 79679--79738 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
79669 TAATATGTGT
*
79679 ATATTAAAATATTTATAAACATCAAAGTAATG
1 ATATTAAAAAATTTATAAACATCAAAGTAATG
*
79711 ATATTAAATAAATTT-TAAATAT-AAAGTA
1 ATATTAAA-AAATTTATAAACATCAAAGTA
79739 TAAAATACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 6 0.24
32 14 0.56
33 5 0.20
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (32 bp):
ATATTAAAAAATTTATAAACATCAAAGTAATG
Found at i:81452 original size:20 final size:21
Alignment explanation
Indices: 81409--81457 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
81399 AAAATATTGC
* * *
81409 TTTTTGTTGTTGTTTTCATTA
1 TTTTTTTTGCTGTTTTCATCA
81430 TTTTTTTTGCTGTTTT-ATCA
1 TTTTTTTTGCTGTTTTCATCA
81450 TTTTTTTT
1 TTTTTTTT
81458 TGTGTCGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.08, C:0.06, G:0.10, T:0.76
Consensus pattern (21 bp):
TTTTTTTTGCTGTTTTCATCA
Found at i:81467 original size:23 final size:23
Alignment explanation
Indices: 81409--81458 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
81399 AAAATATTGC
* *
81409 TTTTTGTTGTTGTTTTCATTATTT
1 TTTTTGCTGTT-TTATCATTATTT
81433 TTTTTGCTGTTTTATCATT-TTT
1 TTTTTGCTGTTTTATCATTATTT
81455 TTTT
1 TTTT
81459 GTGTCGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.29
23 7 0.29
24 10 0.42
ACGTcount: A:0.08, C:0.06, G:0.10, T:0.76
Consensus pattern (23 bp):
TTTTTGCTGTTTTATCATTATTT
Found at i:82544 original size:17 final size:17
Alignment explanation
Indices: 82524--82567 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
82514 AAATAGAAAT
82524 AAATATAAAAAATTCCA
1 AAATATAAAAAATTCCA
* * **
82541 AAATATATATAATTTTA
1 AAATATAAAAAATTCCA
82558 AAATATAAAA
1 AAATATAAAA
82568 TCATAAAAGT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATATAAAAAATTCCA
Found at i:85272 original size:14 final size:14
Alignment explanation
Indices: 85253--85297 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
85243 TAAAGTACAA
85253 ATTATATTTATAAT
1 ATTATATTTATAAT
*
85267 ATTATA--AATAA-
1 ATTATATTTATAAT
85278 ATTATATTTATAAT
1 ATTATATTTATAAT
85292 ATTATA
1 ATTATA
85298 AATAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 6 0.23
12 4 0.15
13 4 0.15
14 12 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTATATTTATAAT
Found at i:85280 original size:25 final size:25
Alignment explanation
Indices: 85251--85312 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
85241 GTTAAAGTAC
85251 AAATTATATTTATAATATTATAAAT
1 AAATTATATTTATAATATTATAAAT
85276 AAATTATATTTATAATATTATAAAT
1 AAATTATATTTATAATATTATAAAT
85301 AAATTATATTTA
1 AAATTATATTTA
85313 AAAAGTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AAATTATATTTATAATATTATAAAT
Found at i:86040 original size:1 final size:1
Alignment explanation
Indices: 86034--86064 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
86024 NNNNNNNNNN
86034 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
86065 GAATAACCGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:91332 original size:21 final size:21
Alignment explanation
Indices: 91306--91347 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
91296 ATCGAAGGTT
*
91306 TCTGGTTCACATAAATCAAAA
1 TCTGGTACACATAAATCAAAA
91327 TCTGGTACACATAAATCAAAA
1 TCTGGTACACATAAATCAAAA
91348 CCTTGCTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (21 bp):
TCTGGTACACATAAATCAAAA
Found at i:100399 original size:24 final size:24
Alignment explanation
Indices: 100341--100401 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
100331 AATTTACTTT
100341 ATTATAAAC-AATAAATTTAAAAAA
1 ATTA-AAACAAATAAATTTAAAAAA
* *
100365 ATTATATCAAATAAATTTAAAAAA
1 ATTAAAACAAATAAATTTAAAAAA
100389 ATTAAAACAAATA
1 ATTAAAACAAATA
100402 CTAAAACAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 2 0.06
24 30 0.94
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTAAAACAAATAAATTTAAAAAA
Found at i:100418 original size:28 final size:28
Alignment explanation
Indices: 100384--100446 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
100374 AATAAATTTA
100384 AAAAAATTAAAA-CAAATACTAAAACAAC
1 AAAAAATTAAAATC-AATACTAAAACAAC
* * *
100412 ATAAAATTAAAATCGATATTAAAACAAC
1 AAAAAATTAAAATCAATACTAAAACAAC
100440 AAAAAAT
1 AAAAAAT
100447 ATTTATGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.19
Consensus pattern (28 bp):
AAAAAATTAAAATCAATACTAAAACAAC
Found at i:102457 original size:24 final size:24
Alignment explanation
Indices: 102406--102461 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
102396 TCTTTCAGTT
* *
102406 AAACTCTGTTTATTTGTTTAAATT
1 AAACTCTATTTATTTGTTTAAATC
* *
102430 AAACTCTATTTATTTGTTTGAGTC
1 AAACTCTATTTATTTGTTTAAATC
102454 AAACTCTA
1 AAACTCTA
102462 ATTAGTCTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (24 bp):
AAACTCTATTTATTTGTTTAAATC
Found at i:109058 original size:60 final size:60
Alignment explanation
Indices: 108985--109109 Score: 234
Period size: 60 Copynumber: 2.1 Consensus size: 60
108975 AACCCATACC
*
108985 TAAG-TCATATAAATCATTTATAGGGAACACTTGAGCTAGCTAGGCCAAGACCCTTGCCA
1 TAAGCTCATATAAATAATTTATAGGGAACACTTGAGCTAGCTAGGCCAAGACCCTTGCCA
109044 TAAGCTCATATAAATAATTTATAGGGAACACTTGAGCTAGCTAGGCCAAGACCCTTGCCA
1 TAAGCTCATATAAATAATTTATAGGGAACACTTGAGCTAGCTAGGCCAAGACCCTTGCCA
109104 TAAGCT
1 TAAGCT
109110 TGCTTTTCAG
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
59 4 0.06
60 60 0.94
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (60 bp):
TAAGCTCATATAAATAATTTATAGGGAACACTTGAGCTAGCTAGGCCAAGACCCTTGCCA
Found at i:136360 original size:176 final size:176
Alignment explanation
Indices: 136066--136409 Score: 600
Period size: 176 Copynumber: 2.0 Consensus size: 176
136056 TGCCAAGCAA
136066 AAAGACCAAAAGGATATCTGTATGCCTAGGAAGAGACTAGAAGGGTGACTTAGGTGGTAATCCGT
1 AAAGACCAAAAGGATATCTGTATGCCTAGGAAGAGACTAGAAGGGTGACTTAGGTGGTAATCCGT
136131 AATGAAGATGAACTGAGAGGGTAGTCATAGCTAAGGGTGATAAATAATTTAATTGATGATAGTTA
66 AATGAAGATGAACTGAGAGGGTAGTCATAGCTAAGGGTGATAAATAATTTAATTGATGATAGTTA
*
136196 ATTATTTAATTAAATAACCAGAGATTTAATTGATCATACCAAGCGG
131 ATTATTTAATTAAATAACCAGAGATTTAATCGATCATACCAAGCGG
* *
136242 AAAGACCAAAAGGGTATCTGTATGCCTAGGAAGAGACTAGAAGGGTGACTTAGGTGGTAATCCTT
1 AAAGACCAAAAGGATATCTGTATGCCTAGGAAGAGACTAGAAGGGTGACTTAGGTGGTAATCCGT
* *
136307 AATGAAGATGAA-TCGGGAGGGTAGTCGTAGCTAAGGGTGATAAATAATTTAATTGATGATAGTT
66 AATGAAGATGAACT-GAGAGGGTAGTCATAGCTAAGGGTGATAAATAATTTAATTGATGATAGTT
** *
136371 AATTATTTAATTAAATAATTAGGGATTTAATCGATCATA
130 AATTATTTAATTAAATAACCAGAGATTTAATCGATCATA
136410 GGTTAGAGGC
Statistics
Matches: 159, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
175 1 0.01
176 158 0.99
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.28
Consensus pattern (176 bp):
AAAGACCAAAAGGATATCTGTATGCCTAGGAAGAGACTAGAAGGGTGACTTAGGTGGTAATCCGT
AATGAAGATGAACTGAGAGGGTAGTCATAGCTAAGGGTGATAAATAATTTAATTGATGATAGTTA
ATTATTTAATTAAATAACCAGAGATTTAATCGATCATACCAAGCGG
Found at i:138438 original size:38 final size:38
Alignment explanation
Indices: 138387--138459 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
138377 GGGGAAATTA
138387 GGTAGTGGAAGTATGAATATTTAATTGTTATTTAAGAG
1 GGTAGTGGAAGTATGAATATTTAATTGTTATTTAAGAG
138425 GGTAGTGGAAGTATGAATATTTAATTGTTATTTAA
1 GGTAGTGGAAGTATGAATATTTAATTGTTATTTAA
138460 CAATATTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (38 bp):
GGTAGTGGAAGTATGAATATTTAATTGTTATTTAAGAG
Found at i:138466 original size:21 final size:21
Alignment explanation
Indices: 138440--138482 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
138430 TGGAAGTATG
138440 AATATTTAATTGTTATTTAAC
1 AATATTTAATTGTTATTTAAC
138461 AATATTTAATTGTTATTTAAC
1 AATATTTAATTGTTATTTAAC
138482 A
1 A
138483 GGGATTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (21 bp):
AATATTTAATTGTTATTTAAC
Found at i:139704 original size:21 final size:19
Alignment explanation
Indices: 139667--139706 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
139657 TCAGTATATG
*
139667 ATTTTAAAATTATTAAAAT
1 ATTTTAAAAATATTAAAAT
139686 ATTTTAAAAAATATATAAAAT
1 ATTTT-AAAAATAT-TAAAAT
139707 TATTAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 7 0.39
21 6 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTTAAAAATATTAAAAT
Found at i:139732 original size:28 final size:30
Alignment explanation
Indices: 139671--139748 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 30
139661 TATATGATTT
139671 TAAAATTATTAA-AATATTTTAAAAAATATA
1 TAAAATTATTAATAAT-TTTTAAAAAATATA
**
139701 TAAAATTATTAATAATTTTT-TGAAATA-A
1 TAAAATTATTAATAATTTTTAAAAAATATA
139729 TAAAATTATTAAATAATTTT
1 TAAAATTATT-AATAATTTT
139749 AATTTTTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 11 0.25
29 14 0.32
30 16 0.36
31 3 0.07
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (30 bp):
TAAAATTATTAATAATTTTTAAAAAATATA
Found at i:140450 original size:28 final size:28
Alignment explanation
Indices: 140419--140486 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 28
140409 ATTAAAAATT
*
140419 AAAATTATTTAATAATTTTATTATTTCAAA
1 AAAATAATTTAATAATTTTATT-TTT-AAA
140449 AAAATAATTTTAATAATTTTATTTTT-AA
1 AAAATAA-TTTAATAATTTTATTTTTAAA
140477 AAAATAATTT
1 AAAATAATTT
140487 TAAAATCATT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 3 0.08
28 9 0.25
30 9 0.25
31 15 0.42
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (28 bp):
AAAATAATTTAATAATTTTATTTTTAAA
Found at i:140487 original size:28 final size:30
Alignment explanation
Indices: 140426--140489 Score: 105
Period size: 28 Copynumber: 2.2 Consensus size: 30
140416 ATTAAAATTA
140426 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTATTATTT-AAAAAAATAAT
140457 TTTAATAATTTTATT-TTT-AAAAAATAAT
1 TTTAATAATTTTATTATTTAAAAAAATAAT
140485 TTTAA
1 TTTAA
140490 AATCATTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 15 0.45
30 3 0.09
31 15 0.45
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTAATAATTTTATTATTTAAAAAAATAAT
Found at i:145156 original size:24 final size:24
Alignment explanation
Indices: 145095--145157 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
145085 TAGACTAATA
* * *
145095 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAACAAAC
*
145119 AGAGTTTAATTGAAACAAACAAAC
1 AGAGTTTAACTGAAACAAACAAAC
145143 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
145158 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.13, G:0.14, T:0.22
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAACAAAC
Found at i:148717 original size:29 final size:29
Alignment explanation
Indices: 148680--148737 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
148670 TGATAAAAAA
*
148680 ATCCTCTTGCAGATAATATTCATTTATGG
1 ATCCACTTGCAGATAATATTCATTTATGG
* *
148709 ATCCACTTGTAGATAATCTTCATTTATGG
1 ATCCACTTGCAGATAATATTCATTTATGG
148738 TGAAAATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (29 bp):
ATCCACTTGCAGATAATATTCATTTATGG
Found at i:154696 original size:19 final size:19
Alignment explanation
Indices: 154672--154708 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
154662 CATGAAAAAT
154672 TTAACTTTGTAATTAATTG
1 TTAACTTTGTAATTAATTG
154691 TTAACTTTGTAATTAATT
1 TTAACTTTGTAATTAATT
154709 TTTCTTAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.54
Consensus pattern (19 bp):
TTAACTTTGTAATTAATTG
Found at i:159870 original size:28 final size:30
Alignment explanation
Indices: 159819--159874 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
159809 AATAATTTTT
*
159819 TAATATAAATTCAACACTTGTAAAATTTAG
1 TAATAAAAATTCAACACTTGTAAAATTTAG
159849 TAATAAAAATTCAACA-TT-TAAAATTT
1 TAATAAAAATTCAACACTTGTAAAATTT
159875 CAATTTATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 8 0.32
29 2 0.08
30 15 0.60
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.38
Consensus pattern (30 bp):
TAATAAAAATTCAACACTTGTAAAATTTAG
Found at i:161805 original size:92 final size:93
Alignment explanation
Indices: 161562--161811 Score: 229
Period size: 96 Copynumber: 2.7 Consensus size: 93
161552 AACTTGTGGA
* * * * * * *
161562 AAAAGAGCTTGAAAATGTGATAGAAAACTATCAACTTAAACGAAAACGACTATCAT-TGTCATTG
1 AAAAGAGCTTGAAAACGTAATAGAAAGCTATAAACTTAAACGAAAACGCCTATCGTCT-TCATCG
*
161626 AAACCTGAAAAGGAGATTAGTAAACCCGAAG
65 AAACCAGAAAAGGAGATTAGTAAACCC--AG
* * * * *
161657 AAGAAGAGCTTGAAAACATAATAGATAGGTATAAACTTGAACGAAAGCGGCC-ATCGTCTTCATC
1 AA-AAGAGCTTGAAAACGTAATAGAAAGCTATAAACTTAAACGAAAAC-GCCTATCGTCTTCATC
* * *
161721 GAAGCCCAG-AAAGGAGATTGGTAAACTC-G
64 GAA-ACCAGAAAAGGAGATTAGTAAACCCAG
* * * * *
161750 AAAAGCGCTTGAAAAGGTTATAGAAAGCTATAAACTTCAACAAAAACGCCTATCGTCTTCAT
1 AAAAGAGCTTGAAAACGTAATAGAAAGCTATAAACTTAAACGAAAACGCCTATCGTCTTCAT
161812 GGGAAATCGA
Statistics
Matches: 125, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
91 3 0.02
92 47 0.38
93 3 0.02
95 2 0.02
96 64 0.51
97 6 0.05
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (93 bp):
AAAAGAGCTTGAAAACGTAATAGAAAGCTATAAACTTAAACGAAAACGCCTATCGTCTTCATCGA
AACCAGAAAAGGAGATTAGTAAACCCAG
Found at i:162129 original size:57 final size:57
Alignment explanation
Indices: 162064--162182 Score: 231
Period size: 57 Copynumber: 2.1 Consensus size: 57
162054 AGGTCCCTAA
162064 TTTT-AGTCAAAAGTTAAAAATATCATTTCAACAATCTGCTAGTGAATTAACAGATT
1 TTTTAAGTCAAAAGTTAAAAATATCATTTCAACAATCTGCTAGTGAATTAACAGATT
162120 TTTTAAGTCAAAAGTTAAAAATATCATTTCAACAATCTGCTAGTGAATTAACAGATT
1 TTTTAAGTCAAAAGTTAAAAATATCATTTCAACAATCTGCTAGTGAATTAACAGATT
162177 TTTTAA
1 TTTTAA
162183 CGGTAGTGAT
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 4 0.06
57 58 0.94
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (57 bp):
TTTTAAGTCAAAAGTTAAAAATATCATTTCAACAATCTGCTAGTGAATTAACAGATT
Found at i:164489 original size:6 final size:6
Alignment explanation
Indices: 164478--164515 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
164468 CATACATACG
*
164478 TATAGA TATAGA TATAGA TATAGA TATAGG TATAGA TA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TA
164516 CAGGCATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34
Consensus pattern (6 bp):
TATAGA
Found at i:168657 original size:1 final size:1
Alignment explanation
Indices: 168651--168676 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
168641 NNNNNNNNNN
168651 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
168677 ATGTTGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:172140 original size:31 final size:32
Alignment explanation
Indices: 172091--172151 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
172081 TTGGTATCTA
172091 AACTTGATATTTTTTTTCCTAATTTGGTACTTG
1 AACTTGATA-TTTTTTTCCTAATTTGGTACTTG
*
172124 AACTTGATA-TTTTTTCCTACTTTGGTAC
1 AACTTGATATTTTTTTCCTAATTTGGTAC
172152 CTAATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 18 0.67
33 9 0.33
ACGTcount: A:0.21, C:0.15, G:0.11, T:0.52
Consensus pattern (32 bp):
AACTTGATATTTTTTTCCTAATTTGGTACTTG
Found at i:185880 original size:23 final size:25
Alignment explanation
Indices: 185849--185894 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
185839 TAAAATCCAA
185849 AAATATAAAAAATTAAAG-TTGACC
1 AAATATAAAAAATTAAAGATTGACC
**
185873 AAAT-TAAAGTATTAAAGATTGA
1 AAATATAAAAAATTAAAGATTGA
185895 ATAATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.28
Consensus pattern (25 bp):
AAATATAAAAAATTAAAGATTGACC
Found at i:189843 original size:14 final size:14
Alignment explanation
Indices: 189826--189852 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
189816 TGGGGTTATT
189826 GGTTATGAGTTTGG
1 GGTTATGAGTTTGG
189840 GGTTATGAGTTTG
1 GGTTATGAGTTTG
189853 ATGTTTGGAG
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:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (14 bp):
GGTTATGAGTTTGG
Found at i:189863 original size:14 final size:14
Alignment explanation
Indices: 189855--189899 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
189845 TGAGTTTGAT
189855 GTTTGGAGTTCAAG
1 GTTTGGAGTTCAAG
*
189869 GTTTGGAGTTCTAG
1 GTTTGGAGTTCAAG
*
189883 G-TTCGAGATTCAAG
1 GTTTGGAG-TTCAAG
189897 GTT
1 GTT
189900 GAGGGTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 5 0.19
14 20 0.77
15 1 0.04
ACGTcount: A:0.20, C:0.09, G:0.33, T:0.38
Consensus pattern (14 bp):
GTTTGGAGTTCAAG
Found at i:194727 original size:11 final size:11
Alignment explanation
Indices: 194708--194738 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
194698 TCTTGACATG
194708 TAAAACCCTAT
1 TAAAACCCTAT
*
194719 TACAACCCTAT
1 TAAAACCCTAT
194730 TAAAACCCT
1 TAAAACCCT
194739 TAATTTAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (11 bp):
TAAAACCCTAT
Found at i:197153 original size:79 final size:79
Alignment explanation
Indices: 197018--197313 Score: 393
Period size: 79 Copynumber: 3.8 Consensus size: 79
197008 AACTTACATA
* * *
197018 GTCAGTTTAACTGACTAGAGCTGGGCTCATATTTGCGGTTTATCCGCTAGGTACTGGGTGTCAGG
1 GTCAGTTTAACTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGGGTGACAGG
197083 ATTTGACGGACGTT
66 ATTTGACGGACGTT
* *
197097 GTCAGTTTAACTGACTAGAGCTGGGCTCATATTTGCGGTTTATCCGCTAGGCACTGGGTGCCAGG
1 GTCAGTTTAACTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGGGTGACAGG
197162 ATTTGACGGACGTT
66 ATTTGACGGACGTT
* *
197176 GTCAGTTTAACTGACTAGAGCT-GGCTCACATTTGTC-GTTTATCCGCTAAGCACTAGGT-ACTA
1 GTCAGTTTAACTGACTAGAGCTGGGCTCACATTTG-CGGTTTATCCGCTAGGCACTGGGTGAC-A
* **
197238 AGATTTGACGGATATT
64 GGATTTGACGGACGTT
* ** * * *
197254 GTTAG-TTAATCCAACTAGAGCTGGGCTCACAATTGCAGTTTATTCGCTAGGCACTGGGTG
1 GTCAGTTTAA-CTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGGGTG
197314 CCATAACTGT
Statistics
Matches: 195, Mismatches: 16, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
77 5 0.03
78 60 0.31
79 130 0.67
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (79 bp):
GTCAGTTTAACTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGGGTGACAGG
ATTTGACGGACGTT
Found at i:197305 original size:157 final size:158
Alignment explanation
Indices: 197018--197316 Score: 408
Period size: 157 Copynumber: 1.9 Consensus size: 158
197008 AACTTACATA
* * * * * *
197018 GTCAGTTTAACTGACTAGAGCTGGGCTCATATTTGCGGTTTATCCGCTAGGTACTGGGTGTCAGG
1 GTCAGTTTAACTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAAGCACTAGGTCTCAAG
* ** * * *
197083 ATTTGACGGACGTTGTCAGTTTAACTGACTAGAGCTGGGCTCATATTTGCGGTTTATCCGCTAGG
66 ATTTGACGGACATTGTCAGTTTAACCAACTAGAGCTGGGCTCACAATTGCAGTTTATCCGCTAGG
197148 CACTGGGTGCCAGGATTTGACGGACGTT
131 CACTGGGTGCCAGGATTTGACGGACGTT
197176 GTCAGTTTAACTGACTAGAGCT-GGCTCACATTTGTC-GTTTATCCGCTAAGCACTAGGTACT-A
1 GTCAGTTTAACTGACTAGAGCTGGGCTCACATTTG-CGGTTTATCCGCTAAGCACTAGGT-CTCA
* * *
197238 AGATTTGACGGATATTGTTAG-TTAATCCAACTAGAGCTGGGCTCACAATTGCAGTTTATTCGCT
64 AGATTTGACGGACATTGTCAGTTTAA-CCAACTAGAGCTGGGCTCACAATTGCAGTTTATCCGCT
197302 AGGCACTGGGTGCCA
128 AGGCACTGGGTGCCA
197317 TAACTGTCAA
Statistics
Matches: 123, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
156 4 0.03
157 95 0.77
158 24 0.20
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (158 bp):
GTCAGTTTAACTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAAGCACTAGGTCTCAAG
ATTTGACGGACATTGTCAGTTTAACCAACTAGAGCTGGGCTCACAATTGCAGTTTATCCGCTAGG
CACTGGGTGCCAGGATTTGACGGACGTT
Found at i:200546 original size:19 final size:20
Alignment explanation
Indices: 200534--200580 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
200524 TTTTTATTAA
200534 TATTTTGAA-TTTTAAAAAT
1 TATTTTGAATTTTTAAAAAT
200553 TATTTTGAATTTTT-AAAAT
1 TATTTTGAATTTTTAAAAAT
*
200572 TAGTTTGAA
1 TATTTTGAA
200581 AATTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 22 0.85
20 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (20 bp):
TATTTTGAATTTTTAAAAAT
Found at i:200586 original size:20 final size:20
Alignment explanation
Indices: 200537--200586 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
200527 TTATTAATAT
*
200537 TTTG-AATTTTAAAAATTAT
1 TTTGAAATTTTAAAAATTAG
*
200556 TTTG-AATTTTTAAAATTAG
1 TTTGAAATTTTAAAAATTAG
200575 TTTGAAAATTTT
1 TTTG-AAATTTT
200587 TTTTTTTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 21 0.78
21 6 0.22
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
TTTGAAATTTTAAAAATTAG
Found at i:202359 original size:60 final size:60
Alignment explanation
Indices: 202292--202437 Score: 265
Period size: 60 Copynumber: 2.4 Consensus size: 60
202282 TTTTTTTTTA
* *
202292 TCACTCAACTATGAAAAGTTACAAAATTATCGCCCAACTATTAGTAAAGTTCTTTTTCGG
1 TCACTCAACTATGAAAAGTTACAAAATGATCGCCCAACTATTAGTAAAGTTATTTTTCGG
*
202352 TCACTCAACTATGAAAAGTTACAAAATGATCGTCCAACTATTAGTAAAGTTATTTTTCGG
1 TCACTCAACTATGAAAAGTTACAAAATGATCGCCCAACTATTAGTAAAGTTATTTTTCGG
202412 TCACTCAACTATGAAAAGTTACAAAA
1 TCACTCAACTATGAAAAGTTACAAAA
202438 CAGTCACCAA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 83 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (60 bp):
TCACTCAACTATGAAAAGTTACAAAATGATCGCCCAACTATTAGTAAAGTTATTTTTCGG
Found at i:202361 original size:31 final size:31
Alignment explanation
Indices: 202326--202423 Score: 78
Period size: 31 Copynumber: 3.2 Consensus size: 31
202316 AATTATCGCC
202326 CAACTATTAGTAAAGTTCTTTTTCGGTCACT
1 CAACTATTAGTAAAGTTCTTTTTCGGTCACT
* **** * *
202357 CAACTA-T-GAAAAGTTACAAAAT-GATC-GT
1 CAACTATTAGTAAAGTT-CTTTTTCGGTCACT
*
202385 CCAACTATTAGTAAAGTTATTTTTCGGTCACT
1 -CAACTATTAGTAAAGTTCTTTTTCGGTCACT
202417 CAACTAT
1 CAACTAT
202424 GAAAAGTTAC
Statistics
Matches: 46, Mismatches: 15, Indels: 12
0.63 0.21 0.16
Matches are distributed among these distances:
28 1 0.02
29 16 0.35
30 5 0.11
31 23 0.50
32 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (31 bp):
CAACTATTAGTAAAGTTCTTTTTCGGTCACT
Found at i:203175 original size:23 final size:24
Alignment explanation
Indices: 203144--203192 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
203134 TACTTGAATT
*
203144 TTTTAAAAATATTTATGAAA-AATA
1 TTTTAAAAAT-TTTATCAAATAATA
203168 TTTT-AAAATTTTATCAAATAATA
1 TTTTAAAAATTTTATCAAATAATA
203191 TT
1 TT
203193 AAAAAAACGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 11 0.48
24 4 0.17
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTTAAAAATTTTATCAAATAATA
Found at i:203198 original size:23 final size:23
Alignment explanation
Indices: 203148--203198 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
203138 TGAATTTTTT
* *
203148 AAAAATATTTATGAAAAATATTT
1 AAAAATATTTATCAAAAATATTA
*
203171 TAAAAT-TTTATCAAATAATATTA
1 AAAAATATTTATCAAA-AATATTA
203194 AAAAA
1 AAAAA
203199 ACGTAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (23 bp):
AAAAATATTTATCAAAAATATTA
Found at i:203490 original size:22 final size:23
Alignment explanation
Indices: 203456--203505 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
203446 TTTCAGGAAG
*
203456 AAAAAGCTGAAAATCAAGAGAAA
1 AAAAAGCTAAAAATCAAGAGAAA
*
203479 AAAAAGCTAAAAATCAAGAGGAA
1 AAAAAGCTAAAAATCAAGAGAAA
203502 AAAA
1 AAAA
203506 TATGATTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (23 bp):
AAAAAGCTAAAAATCAAGAGAAA
Found at i:207068 original size:24 final size:24
Alignment explanation
Indices: 207038--207098 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
207028 GATGCAAGAT
*
207038 AAGTATCGGTAGTTCTACTCATAG
1 AAGTATCGGTAGTTCTACTAATAG
* *
207062 AAGTATCGATAGTTTTACTAATAG
1 AAGTATCGGTAGTTCTACTAATAG
*
207086 AAGTATTGGTAGT
1 AAGTATCGGTAGT
207099 CTATGAACTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (24 bp):
AAGTATCGGTAGTTCTACTAATAG
Found at i:221880 original size:31 final size:30
Alignment explanation
Indices: 221842--222013 Score: 111
Period size: 31 Copynumber: 5.6 Consensus size: 30
221832 TTAATATAAC
*
221842 ATTTGGTACCTGAACTTTACACTTTTTCCTA
1 ATTTGGTACCTAAACTTT-CACTTTTTCCTA
*** *
221873 ATTTGGTACCTAAACTTTTTTTTTTTGACCCA
1 ATTTGGTACCTAAACTTTCACTTTTT--CCTA
* * *
221905 ATTTGGTACTTGAA-TTTGACACTTTCTCCTA
1 ATTTGGTACCTAAACTTT--CACTTTTTCCTA
* *
221936 ATTTGGTACCTAAACTTT---TTTTGGACCCA
1 ATTTGGTACCTAAACTTTCACTTTT--TCCTA
* * *
221965 ATTTGGTACTTGAA-TTTGGCATTTTTTCCTA
1 ATTTGGTACCTAAACTTT--CACTTTTTCCTA
221996 ATTTGGTACCTAAACTTT
1 ATTTGGTACCTAAACTTT
222014 TTTTAGATTC
Statistics
Matches: 105, Mismatches: 23, Indels: 25
0.69 0.15 0.16
Matches are distributed among these distances:
27 3 0.03
28 3 0.03
29 15 0.14
30 5 0.05
31 50 0.48
32 21 0.20
33 8 0.08
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.47
Consensus pattern (30 bp):
ATTTGGTACCTAAACTTTCACTTTTTCCTA
Found at i:221941 original size:63 final size:63
Alignment explanation
Indices: 221842--222017 Score: 270
Period size: 60 Copynumber: 2.8 Consensus size: 63
221832 TTAATATAAC
* *
221842 ATTTGGTACCTGAACTTT-ACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTTTTTGACCCA
1 ATTTGGTACTTGAA-TTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTTTTGGACCCA
*
221905 ATTTGGTACTTGAATTTGACACTTTCTCCTAATTTGGTACCTAAAC---TTTTTTTGGACCCA
1 ATTTGGTACTTGAATTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTTTTGGACCCA
* *
221965 ATTTGGTACTTGAATTTGGCATTTTTTCCTAATTTGGTACCTAAACTTTTTTT
1 ATTTGGTACTTGAATTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTT
222018 AGATTCAATT
Statistics
Matches: 103, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
60 56 0.54
62 3 0.03
63 44 0.43
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.48
Consensus pattern (63 bp):
ATTTGGTACTTGAATTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTTTTGGACCCA
Found at i:221973 original size:29 final size:28
Alignment explanation
Indices: 221935--222038 Score: 84
Period size: 29 Copynumber: 3.5 Consensus size: 28
221925 ACTTTCTCCT
221935 AATTTGGTACCTAAACTTTTTTTGGACCC
1 AATTTGGTACCTAAACTTTTTTT-GACCC
* * ** *
221964 AATTTGGTACTTGAA-TTTGGCATTTTTTCCT
1 AATTTGGTACCTAAACTTT----TTTTGACCC
**
221995 AATTTGGTACCTAAACTTTTTTTAGATTC
1 AATTTGGTACCTAAACTTTTTTT-GACCC
222024 AATTTGGTACCTAAA
1 AATTTGGTACCTAAA
222039 TTTATTAAAT
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
28 7 0.12
29 28 0.49
31 15 0.26
32 7 0.12
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (28 bp):
AATTTGGTACCTAAACTTTTTTTGACCC
Found at i:222041 original size:60 final size:60
Alignment explanation
Indices: 221842--222041 Score: 249
Period size: 60 Copynumber: 3.3 Consensus size: 60
221832 TTAATATAAC
* *
221842 ATTTGGTACCTGAACTTT-ACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTTTTTGACCCA
1 ATTTGGTACCT-AAATTTGACACTTTTTCCTAATTTGGTACCTAAAC---TTTTTTTAGACCCA
* * * *
221905 ATTTGGTACTTGAATTTGACACTTTCTCCTAATTTGGTACCTAAACTTTTTTTGGACCCA
1 ATTTGGTACCTAAATTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTAGACCCA
* * * * **
221965 ATTTGGTACTTGAATTTGGCATTTTTTCCTAATTTGGTACCTAAACTTTTTTTAGATTCA
1 ATTTGGTACCTAAATTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTAGACCCA
222025 ATTTGGTACCTAAATTT
1 ATTTGGTACCTAAATTT
222042 ATTAAATATT
Statistics
Matches: 123, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
60 82 0.67
62 4 0.03
63 37 0.30
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.47
Consensus pattern (60 bp):
ATTTGGTACCTAAATTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTAGACCCA
Found at i:222332 original size:59 final size:59
Alignment explanation
Indices: 222269--222435 Score: 246
Period size: 59 Copynumber: 2.8 Consensus size: 59
222259 AAAAAGTGTC
222269 AAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTT-GAGTACCAAATTGGACCAAAAA
1 AAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTTAG-GTACCAAATTGGACCAAAAA
* * **
222328 AAGTTTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACCCCAAA
1 AAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTTAGGTACCAAATTGGACCAAAAA
* * **
222387 AAGTTTAAGTACCAACTTAAAAAAAAGTGTCAAGTTTAGGTACCAAATT
1 AAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTTAGGTACCAAATT
222436 AGGAAAAAGT
Statistics
Matches: 97, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 96 0.99
60 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.24
Consensus pattern (59 bp):
AAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTTAGGTACCAAATTGGACCAAAAA
Found at i:222340 original size:90 final size:90
Alignment explanation
Indices: 222183--222376 Score: 282
Period size: 90 Copynumber: 2.2 Consensus size: 90
222173 TTAAAAAAAA
**
222183 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACCCCAAAAAGTTTAAGT
1 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACCAAAAAAAGTTTAAGT
* *
222248 ACCAACTTAAAAAAAAGTGTCAAGT
66 ACCAAATTAAAAAAAAGAGTCAAGT
* * *
222273 TTAGGTACCAAATTAGGAAAAAGTGTCAAGTT-TGAGTACCAAATTGGACCAAAAAAAGTTTAGG
1 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAG-GTACCAAATTGGACCAAAAAAAGTTTAAG
**
222337 TACCAAATTAGGAAAAAGAGTCAAGT
65 TACCAAATTAAAAAAAAGAGTCAAGT
*
222363 TCAGGTACCAAATT
1 TTAGGTACCAAATT
222377 GGACCCCAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
89 1 0.01
90 92 0.99
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (90 bp):
TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACCAAAAAAAGTTTAAGT
ACCAAATTAAAAAAAAGAGTCAAGT
Found at i:222340 original size:149 final size:149
Alignment explanation
Indices: 222175--222524 Score: 666
Period size: 149 Copynumber: 2.4 Consensus size: 149
222165 AATTAATATT
*
222175 AAAAAAA-ATTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACCCCAAAA
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACCCCAAAA
222239 AGTTTAAGTACCAACTTAAAAAAAAGTGTCAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGT
66 AGTTTAAGTACCAACTTAAAAAAAAGTGTCAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGT
222304 TTGAGTACCAAATTGGACC
131 TTGAGTACCAAATTGGACC
222323 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACCCCAAAA
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACCCCAAAA
222388 AGTTTAAGTACCAACTTAAAAAAAAGTGTCAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGT
66 AGTTTAAGTACCAACTTAAAAAAAAGTGTCAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGT
222453 TTGAGTACCAAATTGGACC
131 TTGAGTACCAAATTGGACC
* *
222472 AAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTCAGGTACCAAAT
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAAT
222525 GTTATATTAA
Statistics
Matches: 198, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
148 7 0.04
149 191 0.96
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (149 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACCCCAAAA
AGTTTAAGTACCAACTTAAAAAAAAGTGTCAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGT
TTGAGTACCAAATTGGACC
Found at i:222422 original size:90 final size:90
Alignment explanation
Indices: 222328--222524 Score: 306
Period size: 90 Copynumber: 2.2 Consensus size: 90
222318 GGACCAAAAA
**
222328 AAGTTTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAG-GTACCAAATTGGACCCCAAAAAGTT
1 AAGTTTAGGTACCAAATTAGGAAAAAGAGTCAAGTT-AGAGTACCAAATTGGACCAAAAAAAGTT
*
222392 TAAGTACCAACTTAAAAAAAAGTGTC
65 TAAGTACCAAATTAAAAAAAAGTGTC
* *
222418 AAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTTGAGTACCAAATTGGACCAAAAAAAGTTT
1 AAGTTTAGGTACCAAATTAGGAAAAAGAGTCAAGTTAGAGTACCAAATTGGACCAAAAAAAGTTT
* *
222483 AGGTACCAAATTAAGAAAAAGTGTC
66 AAGTACCAAATTAAAAAAAAGTGTC
*
222508 AAGTTCAGGTACCAAAT
1 AAGTTTAGGTACCAAAT
222525 GTTATATTAA
Statistics
Matches: 98, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 1 0.01
90 97 0.99
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (90 bp):
AAGTTTAGGTACCAAATTAGGAAAAAGAGTCAAGTTAGAGTACCAAATTGGACCAAAAAAAGTTT
AAGTACCAAATTAAAAAAAAGTGTC
Found at i:229855 original size:40 final size:40
Alignment explanation
Indices: 229788--229872 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
229778 AAAAATTAAC
*
229788 AAAATTTTTAAGCTTTCCCCAAAATTTCTAAGGATTTACT
1 AAAATTTTTAAGCTTTCACCAAAATTTCTAAGGATTTACT
* * *
229828 AAAATTTTTAAG-TATTTACCAATATTTCTTAGGATTTACT
1 AAAATTTTTAAGCT-TTCACCAAAATTTCTAAGGATTTACT
*
229868 TAAAT
1 AAAAT
229873 ATCCAAGGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 1 0.03
40 38 0.97
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (40 bp):
AAAATTTTTAAGCTTTCACCAAAATTTCTAAGGATTTACT
Found at i:229922 original size:20 final size:20
Alignment explanation
Indices: 229806--229944 Score: 91
Period size: 20 Copynumber: 7.0 Consensus size: 20
229796 TAAGCTTTCC
*
229806 CCAAAATTTCTAAGGATTTA
1 CCAAAATTTCTAAGAATTTA
* * *
229826 CTAAAATTTTTAAGTATTTA
1 CCAAAATTTCTAAGAATTTA
* * *
229846 CCAATATTTCTTAGGATTTA
1 CCAAAATTTCTAAGAATTTA
** * * *
229866 CTTAAATATCCAAGGA-TTA
1 CCAAAATTTCTAAGAATTTA
* * * *
229885 TCAAAATATATGAGAATTTA
1 CCAAAATTTCTAAGAATTTA
*
229905 CCAATATTTCTAAGAATTTA
1 CCAAAATTTCTAAGAATTTA
* * *
229925 TCAAAATATCTAAAAATTTA
1 CCAAAATTTCTAAGAATTTA
229945 TCAATATTTT
Statistics
Matches: 88, Mismatches: 30, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
19 12 0.14
20 76 0.86
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (20 bp):
CCAAAATTTCTAAGAATTTA
Found at i:231028 original size:14 final size:14
Alignment explanation
Indices: 230985--231029 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
230975 ACAATGTAAT
230985 AACATAAATTATTTA
1 AACATAAATTA-TTA
*
231000 AACATGATATT-TTA
1 AACAT-AAATTATTA
231014 AACATAAATTATTA
1 AACATAAATTATTA
231028 AA
1 AA
231030 ATATAAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 4 0.15
14 13 0.50
15 5 0.19
16 4 0.15
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (14 bp):
AACATAAATTATTA
Found at i:232907 original size:120 final size:119
Alignment explanation
Indices: 232673--232911 Score: 370
Period size: 120 Copynumber: 2.0 Consensus size: 119
232663 CAGGGACTAA
* *
232673 GGGATGGAGAAGGTTGTCTCATCTAATATTATGTGATTTTAGGATTAAGTCTAAATGATTCTGTA
1 GGGATGGAGAAGGTCGTCTCATCTAATATTATGTAATTTTAGGATTAAGTCTAAATGATTCTGTA
* * * *
232738 TTCATTGCTTATTAATAGATGACCGGTATATTTATATATCTTCAGAAATGGAAT
66 TTCATTGCTTATTAATAGATAACCGGAAGATTTATATATCTTCACAAATGGAAT
* *
232792 GGGATGGAGAAGGTCGTCTCATCTAATATTATGTAATTTTAGGATTTGAGTGTAAATGATTCTGT
1 GGGATGGAGAAGGTCGTCTCATCTAATATTATGTAATTTTAGGA-TTAAGTCTAAATGATTCTGT
* * *
232857 ATTCATTGCTTATTATTAGATAACGGGAAGATTTGTATATCTTCACAAATGGAAT
65 ATTCATTGCTTATTAATAGATAACCGGAAGATTTATATATCTTCACAAATGGAAT
232912 TTATTCTGTC
Statistics
Matches: 108, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
119 42 0.39
120 66 0.61
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (119 bp):
GGGATGGAGAAGGTCGTCTCATCTAATATTATGTAATTTTAGGATTAAGTCTAAATGATTCTGTA
TTCATTGCTTATTAATAGATAACCGGAAGATTTATATATCTTCACAAATGGAAT
Found at i:234924 original size:105 final size:105
Alignment explanation
Indices: 234726--234917 Score: 262
Period size: 105 Copynumber: 1.8 Consensus size: 105
234716 AAGAACTGTT
* *
234726 GTTCAAATGACCAGGAAAGACTAATCATGCATTAAATCCAAATTTTTGGATGATTACAAAGGTTC
1 GTTCAAATGACCAGGAAAAACTAATCATGCAATAAATCCAAATTTTTGGATGATTACAAAGGTTC
*
234791 CTGTAGCAGGCATGCAATTTCTTGAAGGATCAAATGGGCA
66 CTGCAGCAGGCATGCAATTTCTTGAAGGATCAAATGGGCA
** * *
234831 GTTCAAATGATTAGGAAAAACTGAA-CATGCAATAAATCCAAGTTTTTGGATGATTACAAATGTT
1 GTTCAAATGACCAGGAAAAACT-AATCATGCAATAAATCCAAATTTTTGGATGATTACAAAGGTT
* * *
234895 TCTGCGGTAGGCACT-CAATTTCT
65 CCTGCAGCAGGCA-TGCAATTTCT
234918 GAAAGGACCT
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
105 72 0.96
106 3 0.04
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (105 bp):
GTTCAAATGACCAGGAAAAACTAATCATGCAATAAATCCAAATTTTTGGATGATTACAAAGGTTC
CTGCAGCAGGCATGCAATTTCTTGAAGGATCAAATGGGCA
Found at i:238472 original size:21 final size:22
Alignment explanation
Indices: 238441--238488 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
238431 AAAAACATTA
* *
238441 ATTTTATTAAACATTAAATGAT
1 ATTTTATTAAACATAAAATGAG
*
238463 ATTTT-TTAAATATAAAATGAG
1 ATTTTATTAAACATAAAATGAG
238484 ATTTT
1 ATTTT
238489 CACTCAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (22 bp):
ATTTTATTAAACATAAAATGAG
Found at i:240121 original size:14 final size:14
Alignment explanation
Indices: 240097--240143 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
240087 ATAAATTATG
*
240097 TTAAAATTTAAAGTA
1 TTAAAAATTAAA-TA
240112 -TAAAAATTAAATA
1 TTAAAAATTAAATA
*
240125 TTAAATATTAAAT-
1 TTAAAAATTAAATA
240138 TTAAAA
1 TTAAAA
240144 TTTGAATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 7 0.25
14 21 0.75
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
TTAAAAATTAAATA
Found at i:240141 original size:20 final size:20
Alignment explanation
Indices: 240100--240142 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
240090 AATTATGTTA
240100 AAATTTAAAGTATAAAAATT
1 AAATTTAAAGTATAAAAATT
* *
240120 AAATATTAAA-TATTAAATTT
1 AAAT-TTAAAGTATAAAAATT
240140 AAA
1 AAA
240143 ATTTGAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATTTAAAGTATAAAAATT
Found at i:240948 original size:15 final size:16
Alignment explanation
Indices: 240928--240957 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
240918 GACATTAAGC
240928 AAAAAA-TCATAAAAA
1 AAAAAAGTCATAAAAA
240943 AAAAAAGTCATAAAA
1 AAAAAAGTCATAAAA
240958 CATGGGTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.77, C:0.07, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAAAGTCATAAAAA
Found at i:256761 original size:57 final size:58
Alignment explanation
Indices: 256700--256813 Score: 176
Period size: 58 Copynumber: 2.0 Consensus size: 58
256690 ATCAACAAAC
* *
256700 TAAACTCAAATATTTTTAAA-CCAAATATAATTTCATTCTTAAAAAACACTCATAAAT
1 TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAAT
* * *
256757 TAAACCCAAATATTTTTAAACCCAAATATAGTTTTATTCCTAAATAACACTCATAAA
1 TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAA
256814 CAATTCCTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 19 0.37
58 32 0.63
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (58 bp):
TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAAT
Found at i:257158 original size:18 final size:19
Alignment explanation
Indices: 257135--257170 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
257125 GTTGTGTTAT
*
257135 TGTTG-TTACTTGGACTTA
1 TGTTGTTTACTTGAACTTA
257153 TGTTGTTTACTTGAACTT
1 TGTTGTTTACTTGAACTT
257171 TTTCTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.17, C:0.11, G:0.19, T:0.53
Consensus pattern (19 bp):
TGTTGTTTACTTGAACTTA
Found at i:261631 original size:5 final size:5
Alignment explanation
Indices: 261621--261645 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
261611 TTTGGCTCTT
261621 CCTTC CCTTC CCTTC CCTTC CCTTC
1 CCTTC CCTTC CCTTC CCTTC CCTTC
261646 TTATAAGCAT
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:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
CCTTC
Found at i:266020 original size:17 final size:17
Alignment explanation
Indices: 265995--266028 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
265985 TTTATCTACA
265995 ATTAATATAAAAATAAC
1 ATTAATATAAAAATAAC
* *
266012 ATTACTATAAAATTAAC
1 ATTAATATAAAAATAAC
266029 TATTGTAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (17 bp):
ATTAATATAAAAATAAC
Found at i:274146 original size:38 final size:40
Alignment explanation
Indices: 274090--274176 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
274080 ACTCAATAGG
* * *
274090 CACCTTTTGAAGAGTCACAA-CC-TTACATATTTGATGGA
1 CACCTTTTGAAAAATCACAACCCTTTACATATTGGATGGA
*
274128 CACCTTTTGAAAAATCACAACCCTTTTCATATTGGATGGA
1 CACCTTTTGAAAAATCACAACCCTTTACATATTGGATGGA
274168 CACCTTTTG
1 CACCTTTTG
274177 GAAGAGACTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 18 0.42
39 2 0.05
40 23 0.53
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (40 bp):
CACCTTTTGAAAAATCACAACCCTTTACATATTGGATGGA
Found at i:274231 original size:19 final size:18
Alignment explanation
Indices: 274207--274244 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
274197 CATTGGATGA
*
274207 TAAATCATCATTTTTCAAT
1 TAAATCATCACTTTT-AAT
274226 TAAATCATCACTTTTAAT
1 TAAATCATCACTTTTAAT
274244 T
1 T
274245 TGCAATCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATCATCACTTTTAAT
Found at i:277272 original size:6 final size:6
Alignment explanation
Indices: 277263--277298 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
277253 TCAAACCTTT
277263 AAACCC AAACCC AAACCC AAA-CC AAA-CC AAACCC AA
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AA
277299 TTGAACCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.56, C:0.44, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACCC
Found at i:277369 original size:14 final size:14
Alignment explanation
Indices: 277352--277438 Score: 72
Period size: 14 Copynumber: 6.4 Consensus size: 14
277342 ATGTTGACCA
*
277352 TTGACCATTGATCG
1 TTGACCGTTGATCG
*
277366 TTGACAGTTGA-CGG
1 TTGACCGTTGATC-G
* *
277380 TTGGCCGTTGACCG
1 TTGACCGTTGATCG
* *
277394 TTGACTGTTGA-CT
1 TTGACCGTTGATCG
*
277407 TTGACCGTTGATCA
1 TTGACCGTTGATCG
*
277421 TTGA-CTTTGATCG
1 TTGACCGTTGATCG
277434 TTGAC
1 TTGAC
277439 TTTTTCGAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
13 23 0.40
14 34 0.59
15 1 0.02
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (14 bp):
TTGACCGTTGATCG
Found at i:277388 original size:21 final size:21
Alignment explanation
Indices: 277364--277403 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
277354 GACCATTGAT
277364 CGTTGACAGTTGACGGTTGGC
1 CGTTGACAGTTGACGGTTGGC
* *
277385 CGTTGACCGTTGACTGTTG
1 CGTTGACAGTTGACGGTTG
277404 ACTTTGACCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.20, G:0.35, T:0.33
Consensus pattern (21 bp):
CGTTGACAGTTGACGGTTGGC
Found at i:277412 original size:20 final size:21
Alignment explanation
Indices: 277387--277439 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
277377 CGGTTGGCCG
*
277387 TTGACCGTTGACT-GTTGACT
1 TTGACCGTTGACTCATTGACT
277407 TTGACCGTTGA-TCATTGACT
1 TTGACCGTTGACTCATTGACT
*
277427 TTGATCGTTGACT
1 TTGACCGTTGACT
277440 TTTTCGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.42
Consensus pattern (21 bp):
TTGACCGTTGACTCATTGACT
Found at i:284691 original size:14 final size:14
Alignment explanation
Indices: 284674--284716 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 14
284664 ACTGTTGACG
284674 GTTGGCCGTTGATC
1 GTTGGCCGTTGATC
284688 GTTGACCGGCCGTTGATC
1 GTT----GGCCGTTGATC
284706 GTTGGCCGTTG
1 GTTGGCCGTTG
284717 GCCGTTGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.44
18 14 0.56
ACGTcount: A:0.07, C:0.23, G:0.37, T:0.33
Consensus pattern (14 bp):
GTTGGCCGTTGATC
Found at i:284691 original size:32 final size:32
Alignment explanation
Indices: 284652--284725 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
284642 GCCGTTGACC
* *
284652 GATCGTTGATCGACTGTTGA-CGGTTGGCCGTT
1 GATCGTTGACCGACCGTTGATC-GTTGGCCGTT
*
284684 GATCGTTGACCGGCCGTTGATCGTTGGCCGTT
1 GATCGTTGACCGACCGTTGATCGTTGGCCGTT
**
284716 GGCCGTTGAC
1 GATCGTTGAC
284726 TTTGATTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
32 35 0.97
33 1 0.03
ACGTcount: A:0.11, C:0.23, G:0.35, T:0.31
Consensus pattern (32 bp):
GATCGTTGACCGACCGTTGATCGTTGGCCGTT
Found at i:284741 original size:20 final size:20
Alignment explanation
Indices: 284712--284758 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
284702 GATCGTTGGC
*
284712 CGTTGGCCGTTGACTTTGAT
1 CGTTGACCGTTGACTTTGAT
* *
284732 TGTTGACCGTTGTCTTTGAT
1 CGTTGACCGTTGACTTTGAT
284752 CGTTGAC
1 CGTTGAC
284759 TTTTTTCGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.19, G:0.28, T:0.43
Consensus pattern (20 bp):
CGTTGACCGTTGACTTTGAT
Found at i:285642 original size:6 final size:6
Alignment explanation
Indices: 285633--285687 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
285623 ATTGATTTTG
** *
285633 AATTTA AATTT- GTTTTA AAATTTA AATTT- AATTTA AATTTA GATTTA
1 AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA AATTTA
*
285680 TATTTA AA
1 AATTTA AA
285688 ACTTATTATA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
5 8 0.21
6 27 0.69
7 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (6 bp):
AATTTA
Found at i:285672 original size:17 final size:17
Alignment explanation
Indices: 285600--285687 Score: 88
Period size: 17 Copynumber: 5.0 Consensus size: 17
285590 TTAAACCCAT
285600 TTTAAGATTTATTTTAAGA
1 TTTAA-ATTTATTTTAA-A
* *
285619 -TTAAATTGATTTTGAA
1 TTTAAATTTATTTTAAA
*
285635 TTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
*
285653 TTTAAATTTAATTTAAA
1 TTTAAATTTATTTTAAA
*
285670 TTTAGATTTATATTTAAA
1 TTTAAATTTAT-TTTAAA
285688 ACTTATTATA
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
16 1 0.02
17 32 0.56
18 24 0.42
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:285684 original size:12 final size:11
Alignment explanation
Indices: 285651--285686 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
285641 TTTGTTTTAA
285651 AATTTAAATTT
1 AATTTAAATTT
285662 AATTTAAATTT
1 AATTTAAATTT
*
285673 AGATTTATATTT
1 A-ATTTAAATTT
285685 AA
1 AA
285687 AACTTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:286372 original size:12 final size:12
Alignment explanation
Indices: 286340--286373 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
286330 AAACGTATTT
* *
286340 AATAATAAGATT
1 AATAATAATATC
286352 AATAATAATATC
1 AATAATAATATC
286364 AATAATAATA
1 AATAATAATA
286374 ATGACGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (12 bp):
AATAATAATATC
Found at i:286388 original size:21 final size:20
Alignment explanation
Indices: 286364--286417 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
286354 TAATAATATC
* **
286364 AATAATAATAATGACGTTTTT
1 AATAATAATAATG-CCTTACT
286385 AATAATAATAACTGCCTTACT
1 AATAATAATAA-TGCCTTACT
286406 AATAATAATAAT
1 AATAATAATAAT
286418 AATATTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 26 0.90
22 2 0.07
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (20 bp):
AATAATAATAATGCCTTACT
Found at i:287493 original size:59 final size:55
Alignment explanation
Indices: 287409--287568 Score: 185
Period size: 58 Copynumber: 2.8 Consensus size: 55
287399 AAACTGTTTG
** *
287409 AAAATTCCATTTTTACCCTGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCT
1 AAAATTCCATTTTTACCCAAAACTTCCAAAAATTCCATTTTT-ACCCCAAAA-GTCT
**
287466 AAAAGTTCCATTTTTATCCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAAGTCT
1 AAAA-TTCCATTTTTA-CCCAAAACTTCCAAAAATTCCATTTTTACCCCAAAAGTCT
* *
287523 AAAATTTCCATTTTTGACCTCAAAATTTCCCAAAATTACCATTTTT
1 AAAA-TTCCATTTTT-ACC-CAAAACTTCCAAAAATT-CCATTTTT
287569 CCCTCGGGTA
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
57 23 0.26
58 34 0.38
59 33 0.37
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (55 bp):
AAAATTCCATTTTTACCCAAAACTTCCAAAAATTCCATTTTTACCCCAAAAGTCT
Found at i:287531 original size:28 final size:29
Alignment explanation
Indices: 287409--287568 Score: 162
Period size: 29 Copynumber: 5.5 Consensus size: 29
287399 AAACTGTTTG
**
287409 AAAATTCCATTTTTA-CCCTGAACTTCCA
1 AAAATTCCATTTTTACCCCAAAACTTCCA
*
287437 AAAATTCCATTTTTGACCCCAAAACTTCTA
1 AAAATTCCATTTTT-ACCCCAAAACTTCCA
* *
287467 AAAGTTCCATTTTTATCCCAAAACTTCCA
1 AAAATTCCATTTTTACCCCAAAACTTCCA
** * *
287496 AAAATTCCATTTTTACCCCCGAA-GTCTA
1 AAAATTCCATTTTTACCCCAAAACTTCCA
* * * *
287524 AAATTTCCATTTTTGACCTCAAAATTTCCC
1 AAAATTCCATTTTT-ACCCCAAAACTTCCA
287554 AAAATTACCATTTTT
1 AAAATT-CCATTTTT
287569 CCCTCGGGTA
Statistics
Matches: 107, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
28 30 0.28
29 39 0.36
30 30 0.28
31 8 0.07
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCCAAAACTTCCA
Found at i:293519 original size:18 final size:18
Alignment explanation
Indices: 293493--293528 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
293483 TGATGCTCAA
*
293493 GGGAATGAATCTGGGTAT
1 GGGAATGAACCTGGGTAT
*
293511 GGGAGTGAACCTGGGTAT
1 GGGAATGAACCTGGGTAT
293529 CGTGGGGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.08, G:0.42, T:0.25
Consensus pattern (18 bp):
GGGAATGAACCTGGGTAT
Done.