Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014583.1 Kokia drynarioides strain JFW-HI SEQ_129622, 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: 323357
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 84 characters in sequence are not A, C, G, or T
Found at i:15249 original size:5 final size:5
Alignment explanation
Indices: 15239--15291 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
15229 GATTCAGTTG
* * * *
15239 TTAAT TTAAT TTAAT TTAAAT TGATT TTAAAT TTAAT TGAAT TTAAT ATAAT
1 TTAAT TTAAT TTAAT TT-AAT TTAAT TT-AAT TTAAT TTAAT TTAAT TTAAT
15291 T
1 T
15292 ATTAAATATT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
5 30 0.79
6 8 0.21
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (5 bp):
TTAAT
Found at i:15260 original size:16 final size:16
Alignment explanation
Indices: 15239--15284 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
15229 GATTCAGTTG
*
15239 TTAATTTAATTT-AAT
1 TTAATTGAATTTAAAT
*
15254 TTAAATTGATTTTAAAT
1 TT-AATTGAATTTAAAT
15271 TTAATTGAATTTAA
1 TTAATTGAATTTAA
15285 TATAATTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 2 0.08
16 19 0.73
17 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (16 bp):
TTAATTGAATTTAAAT
Found at i:16469 original size:2 final size:2
Alignment explanation
Indices: 16462--16488 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16452 CAAATGGTTG
16462 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
16489 ATAGGGGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38232 original size:21 final size:21
Alignment explanation
Indices: 38172--38246 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
38162 GGAGTTTTTA
38172 GTATCGGTAGAAGCATG--ACTT
1 GTATCGGTAGAA--ATGTCACTT
* *
38193 GTTTCGGTAGAAATTTCACTT
1 GTATCGGTAGAAATGTCACTT
* * **
38214 GTATCAGTAGAACTGTCACAG
1 GTATCGGTAGAAATGTCACTT
38235 GTATCGGTAGAA
1 GTATCGGTAGAA
38247 GCCTGCACTG
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 2 0.05
21 41 0.95
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAATGTCACTT
Found at i:41461 original size:5 final size:5
Alignment explanation
Indices: 41451--41482 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
41441 GCTCGTATTC
41451 CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT CT
1 CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT CT
41483 ATAGTTTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (5 bp):
CTCTT
Found at i:47048 original size:41 final size:40
Alignment explanation
Indices: 46951--47027 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 40
46941 AGAATTTTCA
46951 TAATTAAATATTTTTTCTGTCACATCAATTGAAAAAAAATT
1 TAATTAAA-ATTTTTTCTGTCACATCAATTGAAAAAAAATT
* *
46992 TAACTGAAATTTTTTTCTGTCACATCAATT-AAAAAA
1 TAA-TTAAAATTTTTTCTGTCACATCAATTGAAAAAA
47028 GTTTTCGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 6 0.18
41 23 0.70
42 4 0.12
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (40 bp):
TAATTAAAATTTTTTCTGTCACATCAATTGAAAAAAAATT
Found at i:48153 original size:29 final size:31
Alignment explanation
Indices: 48121--48185 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
48111 TAAAAAAATG
* *
48121 TGTATA-A-TTGAATCAAAATTAAAGTTTCA
1 TGTATACATTTGAACCAAAATTAAAGATTCA
48150 TGTATACATTTGAACCAAAATTAAAGATTCA
1 TGTATACATTTGAACCAAAATTAAAGATTCA
48181 TGTAT
1 TGTAT
48186 TAAATTGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 6 0.19
30 1 0.03
31 25 0.78
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (31 bp):
TGTATACATTTGAACCAAAATTAAAGATTCA
Found at i:50839 original size:96 final size:96
Alignment explanation
Indices: 50651--50841 Score: 228
Period size: 96 Copynumber: 2.0 Consensus size: 96
50641 ATTTTGGGAA
** *
50651 AAGGATATTCAATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCAATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
* *
50716 GAATCGAAGATAAAGAAACATTGCCTCGATC
66 GAAGCGAAGATAAAGAAACATTACCTCGATC
* * * *
50747 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGTACCTAGTAAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCAATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTC
*
50811 -GAAACGCGAA-ATAAACG-AATATTACCTCGAT
65 AG-AA-GCGAAGATAAA-GAAACATTACCTCGAT
50842 TTTAAAGTCT
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
95 2 0.02
96 74 0.91
97 5 0.06
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (96 bp):
AAGGATATTCAATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAAGCGAAGATAAAGAAACATTACCTCGATC
Found at i:51172 original size:29 final size:29
Alignment explanation
Indices: 51140--51300 Score: 71
Period size: 29 Copynumber: 5.6 Consensus size: 29
51130 AATTCAGAGT
51140 TAAAAATGGAATTTTTAAACATTCGGGGG
1 TAAAAATGGAATTTTTAAACATTCGGGGG
* * * * *
51169 T-AAAAGGGTAATTTTGAGAGC-TTCGAGGT
1 TAAAAATGG-AATTTTTA-AACATTCGGGGG
* * ** *
51198 TGAAAATGGAGTTTTTGGACATTCAGGGG
1 TAAAAATGGAATTTTTAAACATTCGGGGG
* * * **
51227 -CAAAATGGTAATTTTTGGAA-GTTTTGGGG
1 TAAAAATGG-AATTTTT-AAACATTCGGGGG
* *
51256 TTAAAATGGAATTTTTAGAA-GTTCGGGGG
1 TAAAAATGGAATTTTTA-AACATTCGGGGG
**
51285 TAAAAATATAATTTTT
1 TAAAAATGGAATTTTT
51301 GGAAGTTTTA
Statistics
Matches: 97, Mismatches: 27, Indels: 16
0.69 0.19 0.11
Matches are distributed among these distances:
28 14 0.14
29 66 0.68
30 17 0.18
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (29 bp):
TAAAAATGGAATTTTTAAACATTCGGGGG
Found at i:51207 original size:58 final size:58
Alignment explanation
Indices: 51107--51305 Score: 163
Period size: 58 Copynumber: 3.4 Consensus size: 58
51097 GGATTATCGA
* * * **
51107 GGGTGAAATGGTAATTTTGGGAAAATTC-AGAGTTAAAAATGGAATTTTTAAACATTCGG
1 GGGTAAAAGGGTAATTTTTGGAAGCTTCGAG-GTT-AAAATGGAATTTTTAAACATTCGG
* ** *
51166 GGGTAAAAGGGTAA-TTTT-GAGAGCTTCGAGGTTGAAAATGGAGTTTTTGGACATTCAG
1 GGGTAAAAGGGTAATTTTTGGA-AGCTTCGAGGTT-AAAATGGAATTTTTAAACATTCGG
* * * * * *
51224 GGGCAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAATGGAATTTTTAGAA-GTTCGG
1 GGGTAAAAGGGTAATTTTTGGAAGCTTCGAGGTTAAAATGGAATTTTTA-AACATTCGG
***
51282 GGGTAAAAATATAATTTTTGGAAG
1 GGGTAAAAGGGTAATTTTTGGAAG
51306 TTTTAAGGTA
Statistics
Matches: 111, Mismatches: 24, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
57 2 0.02
58 79 0.71
59 28 0.25
60 2 0.02
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (58 bp):
GGGTAAAAGGGTAATTTTTGGAAGCTTCGAGGTTAAAATGGAATTTTTAAACATTCGG
Found at i:51305 original size:29 final size:28
Alignment explanation
Indices: 51200--51546 Score: 247
Period size: 29 Copynumber: 11.9 Consensus size: 28
51190 TTCGAGGTTG
* *
51200 AAAATGGAGTTTTTGGACA-TTCAGGGG-C
1 AAAATGGAATTTTTGGA-AGTTC-GGGGTA
* *
51228 AAAATGGTAATTTTTGGAAGTTTTGGGGTT
1 AAAATGG-AATTTTTGGAAG-TTCGGGGTA
*
51258 AAAATGGAATTTTTAGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTC-GGGGTA
** ***
51287 AAAATATAATTTTTGGAAGTTTTAAGGTAA
1 AAAATGGAATTTTTGGAAG-TTCGGGGT-A
51317 AAAAT-GAGATTTTTGGAAGTTCGGGAGTA
1 AAAATGGA-ATTTTTGGAAGTTCGGG-GTA
* * *
51346 AATATGGGATTTTTGGAAGTTCAAGGGTA
1 AAAATGGAATTTTTGGAAGTTC-GGGGTA
* *
51375 AAAAT-GAGATTTTTGGGAGTTTCGGGGTCT
1 AAAATGGA-ATTTTTGGAAG-TTCGGGGT-A
*
51405 AAAATGGAATTTTTCGAAGTTCGGGGGT-
1 AAAATGGAATTTTTGGAAGTTC-GGGGTA
* *
51433 AAAATGGAATTTTTGGGAGTTTCTGGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGGGGT-A
* * *
51463 AAAATGGAATTTTCGAAAGTTCGGTGTA
1 AAAATGGAATTTTTGGAAGTTCGGGGTA
* * *
51491 AAATTTGAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGGGGT-A
*
51521 AAATTCGG-ATTTTTGGAAGTTTCGGG
1 AAAAT-GGAATTTTTGGAAG-TTCGGG
51547 ACCTCTTGTG
Statistics
Matches: 255, Mismatches: 42, Indels: 42
0.75 0.12 0.12
Matches are distributed among these distances:
28 48 0.19
29 110 0.43
30 94 0.37
31 3 0.01
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCGGGGTA
Found at i:51330 original size:59 final size:58
Alignment explanation
Indices: 51235--51388 Score: 177
Period size: 59 Copynumber: 2.6 Consensus size: 58
51225 GGCAAAATGG
** * *
51235 TAATTTTTGGAAGTTTTGGGGTTAAAATG-GAATTTTTAGAAGTTCGGGGGTAAAAATA
1 TAATTTTTGGAAGTTTTAAGGTAAAAATGAG-ATTTTTAGAAGTTCGGGAGTAAAAATA
* * *
51293 TAATTTTTGGAAGTTTTAAGGTAAAAAATGAGATTTTTGGAAGTTCGGGAGTAAATATG
1 TAATTTTTGGAAGTTTTAAGGT-AAAAATGAGATTTTTAGAAGTTCGGGAGTAAAAATA
** *
51352 GGATTTTTGGAAG-TTCAAGGGTAAAAATGAGATTTTT
1 TAATTTTTGGAAGTTTTAA-GGTAAAAATGAGATTTTT
51389 GGGAGTTTCG
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
58 39 0.47
59 43 0.52
60 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.38
Consensus pattern (58 bp):
TAATTTTTGGAAGTTTTAAGGTAAAAATGAGATTTTTAGAAGTTCGGGAGTAAAAATA
Found at i:51475 original size:88 final size:85
Alignment explanation
Indices: 51142--51541 Score: 255
Period size: 88 Copynumber: 4.6 Consensus size: 85
51132 TTCAGAGTTA
* * * * *
51142 AAAATGGAATTTTT-AAACATTCGGGGGTAAAAGGGTAA-TTTT-GAGAGCTTCGAGGTTGAAAA
1 AAAATGGAATTTTTGGAA-GTTCGGGGGTAAAATGG-AATTTTTGGA-AG-TTC-AGGGTAAAAA
* **
51204 TGGAGTTTTT-GGACATTCAGGGG-C
61 TGGAATTTTTGGGAGTTTC-GGGGTC
* * * * *
51228 AAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATA
1 AAAATGG-AATTTTTGGAAG-TTCGGGGGTAAAATGGAATTTTTGGAAGTTC-AGGGTAAAAATG
* * *** *
51293 TAATTTTTGGAAGTTTTAAGGTAA
63 GAATTTTTGGGAGTTTCGGGGT-C
* *
51317 AAAAT-GAGATTTTTGGAAGTTCGGGAGTAAATATGGGATTTTTGGAAGTTCAAGGGTAAAAAT-
1 AAAATGGA-ATTTTTGGAAGTTCGGGGGTAAA-ATGGAATTTTTGGAAGTTC-AGGGTAAAAATG
51380 GAGATTTTTGGGAGTTTCGGGGTC
63 GA-ATTTTTGGGAGTTTCGGGGTC
* * *
51404 TAAAATGGAATTTTTCGAAGTTCGGGGGTAAAATGGAATTTTTGGGAGTTTCTGGGTCAAAAATG
1 -AAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGGAATTTTTGGAAG-TTCAGGGT-AAAAATG
* ** *
51469 GAATTTTCGAAAG-TTCGGTGT-
63 GAATTTTTGGGAGTTTCGGGGTC
* *
51490 AAAATTTGAATTTTTGGAAGTTTC-GAGGTCAAAATTCGG-ATTTTTGGAAGTT
1 AAAA-TGGAATTTTTGGAAG-TTCGGGGGT-AAAA-T-GGAATTTTTGGAAGTT
51542 TCGGGACCTC
Statistics
Matches: 249, Mismatches: 44, Indels: 41
0.75 0.13 0.12
Matches are distributed among these distances:
85 4 0.02
86 24 0.10
87 74 0.30
88 134 0.54
89 13 0.05
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.35
Consensus pattern (85 bp):
AAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGGAATTTTTGGAAGTTCAGGGTAAAAATGGAA
TTTTTGGGAGTTTCGGGGTC
Found at i:53350 original size:17 final size:17
Alignment explanation
Indices: 53325--53414 Score: 65
Period size: 17 Copynumber: 5.1 Consensus size: 17
53315 GGACTTTTAA
* **
53325 TTAAGTTTTAAATCCAT
1 TTAAATTTTAAATAAAT
*
53342 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
*
53359 TTAAA-TTTAAAGCAAAT
1 TTAAATTTTAAA-TAAAT
*
53376 TTAAATTTAAAAGATAAAT
1 TTAAATTT-TAA-ATAAAT
* *
53395 CTAAATTTAAAAATAAAT
1 TTAAATTT-TAAATAAAT
53413 TT
1 TT
53415 GAATCAATTT
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
16 5 0.08
17 27 0.46
18 9 0.15
19 17 0.29
20 1 0.02
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.42
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:53354 original size:6 final size:6
Alignment explanation
Indices: 53340--53405 Score: 55
Period size: 6 Copynumber: 11.2 Consensus size: 6
53330 TTTTAAATCC
* **
53340 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA
** *
53387 AGATAA ATCTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA A
53406 AATAAATTTG
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
5 7 0.15
6 35 0.76
7 4 0.09
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:53412 original size:18 final size:18
Alignment explanation
Indices: 53340--53414 Score: 82
Period size: 17 Copynumber: 4.2 Consensus size: 18
53330 TTTTAAATCC
* *
53340 ATTTAAATTT-TAATTAA
1 ATTTAAATTTAAAAATAA
**
53357 ATTTAAATTT-AAAGCAA
1 ATTTAAATTTAAAAATAA
53374 ATTTAAATTTAAAAGATAA
1 ATTTAAATTTAAAA-ATAA
*
53393 ATCTAAATTTAAAAATAA
1 ATTTAAATTTAAAAATAA
53411 ATTT
1 ATTT
53415 GAATCAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
17 24 0.49
18 10 0.20
19 15 0.31
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTTAAATTTAAAAATAA
Found at i:57616 original size:10 final size:9
Alignment explanation
Indices: 57603--57774 Score: 86
Period size: 9 Copynumber: 18.4 Consensus size: 9
57593 ATTTTAATTT
57603 TTTTTATAA
1 TTTTTATAA
57612 GTTTTTA-AGA
1 -TTTTTATA-A
57622 TTTTTATAAA
1 TTTTTAT-AA
* *
57632 ATTTTAAATA
1 TTTTTATA-A
57642 TATTTTATTAA
1 T-TTTTA-TAA
57653 -TTTTATAAA
1 TTTTTAT-AA
*
57662 ATTTTATAA
1 TTTTTATAA
*
57671 GTTTTTATTA
1 -TTTTTATAA
57681 TTTTT-TATA
1 TTTTTATA-A
*
57690 TTTTAATAA
1 TTTTTATAA
*
57699 GTTTATATAA
1 -TTTTTATAA
*
57709 -TTTTATTA
1 TTTTTATAA
*
57717 TTTTTAAAA
1 TTTTTATAA
*
57726 TATTTT-TAG
1 T-TTTTATAA
57735 TTTTTAGTAA
1 TTTTTA-TAA
*
57745 TTTTTATAC
1 TTTTTATAA
* *
57754 TCTTT-TGA
1 TTTTTATAA
57762 TTTTTATAA
1 TTTTTATAA
57771 TTTT
1 TTTT
57775 CCTTGTGTTC
Statistics
Matches: 122, Mismatches: 23, Indels: 35
0.68 0.13 0.19
Matches are distributed among these distances:
8 17 0.14
9 49 0.40
10 48 0.39
11 7 0.06
12 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:57685 original size:19 final size:18
Alignment explanation
Indices: 57593--57751 Score: 74
Period size: 19 Copynumber: 8.4 Consensus size: 18
57583 GTTCATATCG
* *
57593 ATTTTAATTTTTTTTATA
1 ATTTTTATTATTTTTATA
**
57611 AGTTTTTAAGATTTTTATAAA
1 A-TTTTTATTATTTTTAT--A
* *
57632 ATTTTAAATATATTTTATTA
1 ATTTTTATTAT-TTTTA-TA
* *
57652 A-TTTTATAAAATTTTATA
1 ATTTTTAT-TATTTTTATA
57670 AGTTTTTATTATTTTT-TA
1 A-TTTTTATTATTTTTATA
* * *
57688 TATTTTAATAAGTTTATATA
1 -ATTTTTATTA-TTTTTATA
*
57708 A-TTTTATTATTTTTAAA
1 ATTTTTATTATTTTTATA
*
57725 ATATTT-TTAGTTTTTAGTA
1 ATTTTTATTA-TTTTTA-TA
57744 ATTTTTAT
1 ATTTTTAT
57752 ACTCTTTTGA
Statistics
Matches: 104, Mismatches: 22, Indels: 28
0.68 0.14 0.18
Matches are distributed among these distances:
17 10 0.10
18 28 0.27
19 38 0.37
20 20 0.19
21 7 0.07
22 1 0.01
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (18 bp):
ATTTTTATTATTTTTATA
Found at i:57721 original size:28 final size:28
Alignment explanation
Indices: 57645--57723 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
57635 TTAAATATAT
* *
57645 TTTAT-TAATTTTATAAAATTTT-ATAAG
1 TTTATATAATTTTAT-TATTTTTAATAAG
* *
57672 TTTTTATTATTTT-TTATATTTTAATAAG
1 TTTATATAATTTTATTAT-TTTTAATAAG
57700 TTTATATAATTTTATTATTTTTAA
1 TTTATATAATTTTATTATTTTTAA
57724 AATATTTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
26 1 0.02
27 9 0.21
28 28 0.67
29 4 0.10
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (28 bp):
TTTATATAATTTTATTATTTTTAATAAG
Found at i:57740 original size:46 final size:46
Alignment explanation
Indices: 57640--57733 Score: 118
Period size: 46 Copynumber: 2.0 Consensus size: 46
57630 AAATTTTAAA
* * **
57640 TATATTTTATTAATTTTATAAAATTTTATAAGTTTTTATTATTTTT
1 TATATTTTAATAAGTTTATAAAATTTTATAAGTTTTTAAAATTTTT
* *
57686 TATATTTTAATAAGTTTATATAATTTTATTA-TTTTTAAAATATTTT
1 TATATTTTAATAAGTTTATAAAATTTTATAAGTTTTTAAAAT-TTTT
57732 TA
1 TA
57734 GTTTTTAGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 8 0.20
46 33 0.80
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (46 bp):
TATATTTTAATAAGTTTATAAAATTTTATAAGTTTTTAAAATTTTT
Found at i:57746 original size:36 final size:35
Alignment explanation
Indices: 57624--57748 Score: 85
Period size: 38 Copynumber: 3.4 Consensus size: 35
57614 TTTTAAGATT
* * * *
57624 TTTATAAAATTTTAAATATATTTTATTAATTTTATAAAA
1 TTTATATAATTTT-ATTAT-TTTTAAT-ATTTTAT-AAG
*
57663 TTT-TATAAGTTTTTATTATTTTTTATATTTTAATAAG
1 TTTATATAA--TTTTATTATTTTTAATATTTT-ATAAG
57700 TTTATATAATTTTATTATTTTTAAAATATTTT-T-AG
1 TTTATATAATTTTATTATTTTT--AATATTTTATAAG
*
57735 TTTTTAGTAATTTT
1 TTTATA-TAATTTT
57749 TATACTCTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
35 7 0.10
36 21 0.29
37 10 0.14
38 23 0.32
39 7 0.10
40 4 0.06
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (35 bp):
TTTATATAATTTTATTATTTTTAATATTTTATAAG
Found at i:61588 original size:35 final size:35
Alignment explanation
Indices: 61549--61620 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
61539 AGAACAACAA
61549 AAGCAGGTGGAGTTCCAGATTGATCCAGTATCTAC
1 AAGCAGGTGGAGTTCCAGATTGATCCAGTATCTAC
61584 AAGCAGGTGGAGTTCCAGATTGATCCAGTATCTAC
1 AAGCAGGTGGAGTTCCAGATTGATCCAGTATCTAC
61619 AA
1 AA
61621 CAGAGTTAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (35 bp):
AAGCAGGTGGAGTTCCAGATTGATCCAGTATCTAC
Found at i:62296 original size:17 final size:17
Alignment explanation
Indices: 62274--62310 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
62264 AGGTGAAAAA
* *
62274 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
62291 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
62308 CTT
1 CTT
62311 ATCAAGGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.14, G:0.24, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:62396 original size:41 final size:41
Alignment explanation
Indices: 62302--62397 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
62292 TTGTTCGTAG
* * * *
62302 AGAATTCTTATCAAGGTGGAGATTGTTAGAATTTGGTGACT
1 AGAATTCTTGTTAAGGTAGAGATTGTTAGAAATTGGTGACT
**
62343 AGAATTAATGTTAAGGTAGAGATTGTTA-AAATTGAGTGACT
1 AGAATTCTTGTTAAGGTAGAGATTGTTAGAAATTG-GTGACT
62384 AGAATTCTTGTTAA
1 AGAATTCTTGTTAA
62398 AATAAAATTC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 5 0.11
41 41 0.89
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTAGAGATTGTTAGAAATTGGTGACT
Found at i:75854 original size:3 final size:3
Alignment explanation
Indices: 75846--75874 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
75836 TGTTTCACAC
75846 TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
75875 AATTGGAACT
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:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:78728 original size:2 final size:2
Alignment explanation
Indices: 78723--78755 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
78713 AAAAGCTTTG
78723 TC TC TC -C 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
78756 CTCCTCTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:87239 original size:38 final size:38
Alignment explanation
Indices: 87146--87251 Score: 110
Period size: 38 Copynumber: 2.8 Consensus size: 38
87136 TTTATATATC
*
87146 TAAT-TATCTTAAA-TTTAAATTTAAATTAAATAATGCA
1 TAATATAT-TTAAATTTTAAATTTAAATTAAATAATGAA
* * * * *
87183 TATTTTATTATAATTTTTAAATTT-GATTAAATAATTAA
1 TAATATATT-TAAATTTTAAATTTAAATTAAATAATGAA
87221 TAATATAGTTTAAATTTTAAATTTAAATTAA
1 TAATATA-TTTAAATTTTAAATTTAAATTAA
87252 TTTATAATGA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
37 4 0.07
38 35 0.64
39 16 0.29
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (38 bp):
TAATATATTTAAATTTTAAATTTAAATTAAATAATGAA
Found at i:87272 original size:39 final size:36
Alignment explanation
Indices: 87154--87273 Score: 93
Period size: 39 Copynumber: 3.1 Consensus size: 36
87144 TCTAATTATC
87154 TTAAA-TTTAAATTTAAATTAA-ATAATGCATATTTT
1 TTAAATTTTAAATTTAAATTAATATAATG-ATATTTT
* * **
87189 ATTATAATTTTTAAATTT-GATTAAATAATTAATAATATAGT
1 -TTA-AA-TTTTAAATTTAAATT-AAT-A-TAATGATATTTT
87230 TTAAATTTTAAATTTAAATTAATTTATAATGATAATTTT
1 TTAAATTTTAAATTTAAATTAA--TATAATGAT-ATTTT
87269 TTAAA
1 TTAAA
87274 ATATAATGAT
Statistics
Matches: 65, Mismatches: 8, Indels: 19
0.71 0.09 0.21
Matches are distributed among these distances:
36 3 0.05
37 2 0.03
38 21 0.32
39 25 0.38
40 4 0.06
41 6 0.09
42 4 0.06
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (36 bp):
TTAAATTTTAAATTTAAATTAATATAATGATATTTT
Found at i:87296 original size:21 final size:21
Alignment explanation
Indices: 87254--87316 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 21
87244 TAAATTAATT
**
87254 TATAATGAT-AATTTTTTAAAA
1 TATAATGATAAAAATTTT-AAA
87275 TATAATGATAAAAATTTTAAA
1 TATAATGATAAAAATTTTAAA
87296 TATTAA-GATAAATAATATTTA
1 TA-TAATGATAAA-AAT-TTTA
87317 TCTTAATGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
21 20 0.56
22 12 0.33
23 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (21 bp):
TATAATGATAAAAATTTTAAA
Found at i:87335 original size:27 final size:27
Alignment explanation
Indices: 87305--87357 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
87295 ATATTAAGAT
* *
87305 AAATAATATTTATCTTAATGATAATTA
1 AAATAATATCTATATTAATGATAATTA
*
87332 AAATAATATCTATATTTATGATAATT
1 AAATAATATCTATATTAATGATAATT
87358 TTATATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (27 bp):
AAATAATATCTATATTAATGATAATTA
Found at i:88454 original size:29 final size:28
Alignment explanation
Indices: 88416--88494 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
88406 TTTTGAACAT
*
88416 TTCGGA-GCAAAATGGTAACTTTTGGATG
1 TTCGGAGGCAAAATGGTAA-TTTTGGATA
* *
88444 TTCGGGGGCAAAATGATAATTTTGGATA
1 TTCGGAGGCAAAATGGTAATTTTGGATA
*
88472 TTCGGAGGTAAAATGGTAATTTT
1 TTCGGAGGCAAAATGGTAATTTT
88495 TTTAGTACAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
28 33 0.75
29 11 0.25
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.34
Consensus pattern (28 bp):
TTCGGAGGCAAAATGGTAATTTTGGATA
Found at i:88537 original size:29 final size:30
Alignment explanation
Indices: 88504--88644 Score: 159
Period size: 29 Copynumber: 4.9 Consensus size: 30
88494 TTTTAGTACA
* *
88504 AGGGTAAAAATGTAGTTTTTAAAAGTTCAG
1 AGGGTAAAAATGTAATTTTTAGAAGTTCAG
* *
88534 -GGGTAAAAATGTGATTTTTAGAAGTTTAG
1 AGGGTAAAAATGTAATTTTTAGAAGTTCAG
* * *
88563 -GGG-CAAAATGTAATTTTGAGAAGTT-TG
1 AGGGTAAAAATGTAATTTTTAGAAGTTCAG
*
88590 AGGGTAAAAATGTAATTTTTGGAAGTTC-G
1 AGGGTAAAAATGTAATTTTTAGAAGTTCAG
88619 AGGGT-AAAATGTAATTTTTGAGAAGT
1 AGGGTAAAAATGTAATTTTT-AGAAGT
88645 CTAGGGGTCA
Statistics
Matches: 95, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
27 1 0.01
28 36 0.38
29 58 0.61
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (30 bp):
AGGGTAAAAATGTAATTTTTAGAAGTTCAG
Found at i:88571 original size:57 final size:57
Alignment explanation
Indices: 88510--88680 Score: 177
Period size: 57 Copynumber: 3.0 Consensus size: 57
88500 TACAAGGGTA
* *
88510 AAAATGTAGTTTTTAAAAGTTCAGGGGTAAAAATGTGATTTTTAGAAGTTTAGGGGC
1 AAAATGTAATTTTTAGAAGTTCAGGGGTAAAAATGTGATTTTTAGAAGTTTAGGGGC
* * * * * *
88567 AAAATGTAATTTTGAGAAGTT-TGAGGGTAAAAATGTAATTTTTGGAAG-TTCGAGGGT
1 AAAATGTAATTTTTAGAAGTTCAG-GGGTAAAAATGTGATTTTTAGAAGTTTAG-GGGC
* * *
88624 AAAATGTAATTTTTGAGAAG-TCTAGGGGTCAAAATATGATTTCTAGATAGTTTAGGG
1 AAAATGTAATTTTT-AGAAGTTC-AGGGGTAAAAATGTGATTTTTAGA-AGTTTAGGG
88681 ACCTTTTGGA
Statistics
Matches: 91, Mismatches: 16, Indels: 12
0.76 0.13 0.10
Matches are distributed among these distances:
56 4 0.04
57 57 0.63
58 22 0.24
59 5 0.05
60 3 0.03
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (57 bp):
AAAATGTAATTTTTAGAAGTTCAGGGGTAAAAATGTGATTTTTAGAAGTTTAGGGGC
Found at i:89531 original size:3 final size:3
Alignment explanation
Indices: 89514--89547 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
89504 AAAAGGGTCT
89514 TTA TTCA TT- TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA T
89548 ATTTGTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:89739 original size:11 final size:10
Alignment explanation
Indices: 89723--89786 Score: 58
Period size: 11 Copynumber: 6.0 Consensus size: 10
89713 CGATTTCTTT
89723 TTATTTATTCA
1 TTATTTATT-A
89734 TTATTTATATA
1 TTATTTAT-TA
89745 TATATTTATTAA
1 T-TATTTATT-A
*
89757 TTATTTATGA
1 TTATTTATTA
*
89767 CTATGTT-TTA
1 TTAT-TTATTA
89777 TTATTTATTA
1 TTATTTATTA
89787 ATTTAATATC
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
9 2 0.05
10 12 0.27
11 20 0.45
12 10 0.23
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (10 bp):
TTATTTATTA
Found at i:90451 original size:6 final size:6
Alignment explanation
Indices: 90442--90523 Score: 61
Period size: 6 Copynumber: 14.5 Consensus size: 6
90432 TGGACTTTTA
* *
90442 AAATTT AAATTT AAA-TT AAA-AT AAATTT AAATTT -AATTT AAA-AT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
90486 AAATTC AAACTT AAA--T -AATTT AAAATTT AAAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT -AAATTT -AAATTT AAA
90524 ATTGGATTCT
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
3 2 0.03
4 1 0.02
5 19 0.31
6 28 0.45
7 12 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (6 bp):
AAATTT
Found at i:90467 original size:22 final size:22
Alignment explanation
Indices: 90442--90523 Score: 94
Period size: 22 Copynumber: 3.7 Consensus size: 22
90432 TGGACTTTTA
90442 AAATTTAAATTTAAATTAAAAT
1 AAATTTAAATTTAAATTAAAAT
*
90464 AAATTTAAATTTAATTTAAAAT
1 AAATTTAAATTTAAATTAAAAT
* * **
90486 AAATTCAAACTTAAA-TAATTT
1 AAATTTAAATTTAAATTAAAAT
90507 AAAATTTAAAATTTAAA
1 -AAATTT-AAATTTAAA
90524 ATTGGATTCT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
21 4 0.08
22 38 0.76
23 8 0.16
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATTTAAATTTAAATTAAAAT
Found at i:90515 original size:16 final size:16
Alignment explanation
Indices: 90476--90526 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
90466 ATTTAAATTT
* *
90476 AATTTAAAATAAATTCA
1 AATTT-AAATAATTTAA
*
90493 AACTTAAATAATTTAA
1 AATTTAAATAATTTAA
90509 AATTT-AA-AATTTAA
1 AATTTAAATAATTTAA
90523 AATT
1 AATT
90527 GGATTCTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 11 0.37
15 2 0.07
16 13 0.43
17 4 0.13
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTTAAATAATTTAA
Found at i:92284 original size:5 final size:5
Alignment explanation
Indices: 92274--92298 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
92264 AAATTTGATA
92274 AGATT AGATT AGATT AGATT AGATT
1 AGATT AGATT AGATT AGATT AGATT
92299 TAATTGTGTA
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:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
AGATT
Found at i:95607 original size:14 final size:14
Alignment explanation
Indices: 95572--95618 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 14
95562 TTTGAAACAA
95572 TAAATATTATATTTAT
1 TAAA-ATTAT-TTTAT
*
95588 TGAAATTTATTTT-T
1 T-AAAATTATTTTAT
95602 TAAAATTATTTTAT
1 TAAAATTATTTTAT
95616 TAA
1 TAA
95619 TACAATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 10 0.37
14 6 0.22
15 3 0.11
16 5 0.19
17 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TAAAATTATTTTAT
Found at i:99280 original size:14 final size:14
Alignment explanation
Indices: 99261--99298 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
99251 TCACAATTTC
99261 ATTCTCAATTTATT
1 ATTCTCAATTTATT
*
99275 ATTCTCGATTTATT
1 ATTCTCAATTTATT
*
99289 ATTCTTAATT
1 ATTCTCAATT
99299 GTCAATTCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.03, T:0.58
Consensus pattern (14 bp):
ATTCTCAATTTATT
Found at i:99306 original size:28 final size:28
Alignment explanation
Indices: 99275--99333 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
99265 TCAATTTATT
* * *
99275 ATTCTCGATTTATTATTCTTAATTGTCA
1 ATTCTCGATTTATTATGCTAAATTCTCA
*
99303 ATTCTCGATTTTTTATGCTAAATTCTCA
1 ATTCTCGATTTATTATGCTAAATTCTCA
99331 ATT
1 ATT
99334 TTTTTTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (28 bp):
ATTCTCGATTTATTATGCTAAATTCTCA
Found at i:99345 original size:21 final size:21
Alignment explanation
Indices: 99302--99352 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
99292 CTTAATTGTC
*
99302 AATTCTCGATTTTTTATGCTA
1 AATTCTCAATTTTTTATGCTA
* **
99323 AATTCTCAATTTTTTTTTTTA
1 AATTCTCAATTTTTTATGCTA
99344 AATTCTCAA
1 AATTCTCAA
99353 ATCTAAATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.14, G:0.04, T:0.55
Consensus pattern (21 bp):
AATTCTCAATTTTTTATGCTA
Found at i:110154 original size:15 final size:16
Alignment explanation
Indices: 110134--110163 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
110124 GAATTTGAAT
110134 AATAAAT-TTTTAAAA
1 AATAAATCTTTTAAAA
110149 AATAAATCTTTTAAA
1 AATAAATCTTTTAAA
110164 TGGGTTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAAATCTTTTAAAA
Found at i:110679 original size:14 final size:14
Alignment explanation
Indices: 110639--110685 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
110629 TAAAATTAAA
*
110639 AAATTATAAAAACT
1 AAATTATAAAAATT
* *
110653 AAA-AATATCAAATT
1 AAATTATA-AAAATT
110667 AAATTATAAAAATT
1 AAATTATAAAAATT
110681 AAATT
1 AAATT
110686 CACAATTTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
13 3 0.12
14 20 0.77
15 3 0.12
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATTATAAAAATT
Found at i:118235 original size:51 final size:51
Alignment explanation
Indices: 118175--118277 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
118165 AATTTGATTC
*
118175 AGTAAATAATAGTTGAAGGAAAATTATAAAATAATCCAAAATATTTATATG
1 AGTAAATAATAATTGAAGGAAAATTATAAAATAATCCAAAATATTTATATG
*
118226 AGTAAATAATAATTGAAGGAAAATTATAAAATAATCTAAAATATTTATATG
1 AGTAAATAATAATTGAAGGAAAATTATAAAATAATCCAAAATATTTATATG
118277 A
1 A
118278 TTTTTATAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.54, C:0.03, G:0.11, T:0.32
Consensus pattern (51 bp):
AGTAAATAATAATTGAAGGAAAATTATAAAATAATCCAAAATATTTATATG
Found at i:126918 original size:31 final size:31
Alignment explanation
Indices: 126862--126928 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
126852 GATAACTTAT
*
126862 ATTTTTATCATTTTTAAAGGATTAAATTAAA
1 ATTTTTATCATTTTTAAAGGATTAAAGTAAA
** * *
126893 ATTTTTATCATTTTTAGCGGGTTAAAGTACA
1 ATTTTTATCATTTTTAAAGGATTAAAGTAAA
126924 ATTTT
1 ATTTT
126929 ATGTTAATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.49
Consensus pattern (31 bp):
ATTTTTATCATTTTTAAAGGATTAAAGTAAA
Found at i:132117 original size:20 final size:18
Alignment explanation
Indices: 132080--132144 Score: 78
Period size: 17 Copynumber: 3.6 Consensus size: 18
132070 AAGTTTTGAT
* *
132080 TTTAAAATTAGGTTTAAA
1 TTTAAATTTAGCTTTAAA
*
132098 TTTAAATTTATCTTTTTAAA
1 TTTAAATTTAGC--TTTAAA
132118 TTTAAATTT-GCTTTAAA
1 TTTAAATTTAGCTTTAAA
132135 TTTAAATTTA
1 TTTAAATTTA
132145 ATCAAATTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 15 0.38
18 9 0.22
19 1 0.03
20 15 0.38
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (18 bp):
TTTAAATTTAGCTTTAAA
Found at i:132464 original size:25 final size:25
Alignment explanation
Indices: 132436--132488 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
132426 AGCACCAGCA
*
132436 CCACCTCCAGCTTCAACTTG-CACTG
1 CCACCACCAGCTTCAAC-TGCCACTG
* *
132461 CCACCAGCTGCTTCAACTGCCACTG
1 CCACCACCAGCTTCAACTGCCACTG
132486 CCA
1 CCA
132489 TCGTCGAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.21, C:0.45, G:0.13, T:0.21
Consensus pattern (25 bp):
CCACCACCAGCTTCAACTGCCACTG
Found at i:132955 original size:3 final size:3
Alignment explanation
Indices: 132949--132997 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
132939 AATGTGCTAT
* * * *
132949 TAA TAA TAC TAA TAA TAA TAT TAT TAA TAA TAA TTAA TAC TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
132995 TAA
1 TAA
132998 ATAAAAAAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:134063 original size:29 final size:29
Alignment explanation
Indices: 134016--134251 Score: 253
Period size: 30 Copynumber: 8.0 Consensus size: 29
134006 TACCTTAGAG
*
134016 ACCCCGAAACTTCCCAAAATTCCATTTTT
1 ACCCCGAAACTTCCAAAAATTCCATTTTT
* * *
134045 ACCCCTAAACTTCTAAAAATTTCATTTTT
1 ACCCCGAAACTTCCAAAAATTCCATTTTT
* *
134074 AACCTCGAAACTTCCTAAAATTCCATTTTT
1 -ACCCCGAAACTTCCAAAAATTCCATTTTT
*
134104 ACCCCTG-AACTTCCAAAAATTTCATTTTT
1 ACCCC-GAAACTTCCAAAAATTCCATTTTT
* *
134133 GACCCCGAAACTTCTAAAAATTCCATCTTT
1 -ACCCCGAAACTTCCAAAAATTCCATTTTT
* *
134163 ACCCCCTAAA-TTCCAAAAATTCCATTCTTA
1 A-CCCCGAAACTTCCAAAAATTCCATT-TTT
* *
134193 ACCCCAAAACTTCCAAAAACTCCATTTTT
1 ACCCCGAAACTTCCAAAAATTCCATTTTT
* *
134222 GACCCCAAAACTTTCAAAAATTACC-TTTTT
1 -ACCCCGAAACTTCCAAAAATT-CCATTTTT
134252 GCTCTCGAAT
Statistics
Matches: 174, Mismatches: 24, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
29 74 0.43
30 98 0.56
31 2 0.01
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (29 bp):
ACCCCGAAACTTCCAAAAATTCCATTTTT
Found at i:134087 original size:30 final size:30
Alignment explanation
Indices: 134016--134347 Score: 258
Period size: 29 Copynumber: 11.3 Consensus size: 30
134006 TACCTTAGAG
*
134016 ACCCCGAAACTTCCCAAAATTCCATTTTT-
1 ACCCCGAAACTTCCAAAAATTCCATTTTTA
* * *
134045 ACCCCTAAACTTCTAAAAATTTCATTTTTA
1 ACCCCGAAACTTCCAAAAATTCCATTTTTA
* *
134075 ACCTCGAAACTTCCTAAAATTCCATTTTT-
1 ACCCCGAAACTTCCAAAAATTCCATTTTTA
* *
134104 ACCCCTG-AACTTCCAAAAATTTCATTTTTG
1 ACCCC-GAAACTTCCAAAAATTCCATTTTTA
* *
134134 ACCCCGAAACTTCTAAAAATTCCATCTTTA
1 ACCCCGAAACTTCCAAAAATTCCATTTTTA
* * *
134164 CCCCCTAAA-TTCCAAAAATTCCATTCTTA
1 ACCCCGAAACTTCCAAAAATTCCATTTTTA
* * *
134193 ACCCCAAAACTTCCAAAAACTCCATTTTTG
1 ACCCCGAAACTTCCAAAAATTCCATTTTTA
* *
134223 ACCCCAAAACTTTCAAAAATTACC-TTTTT-
1 ACCCCGAAACTTCCAAAAATT-CCATTTTTA
* * * **
134252 GCTCTCG-AA-TGTCCAAAAACTCCATTTTCG
1 AC-CCCGAAACT-TCCAAAAATTCCATTTTTA
* *
134282 ACCTCGAAAC-TCTC-AAAATTACC-CTTTTA
1 ACCCCGAAACTTC-CAAAAATT-CCATTTTTA
* * *
134311 CCCCCG--AGTGTCTAAAAATTCCATTTTTA
1 ACCCCGAAACT-TCCAAAAATTCCATTTTTA
134340 ACCCCGAA
1 ACCCCGAA
134348 TTTTCCCAAA
Statistics
Matches: 238, Mismatches: 45, Indels: 38
0.74 0.14 0.12
Matches are distributed among these distances:
27 1 0.00
28 5 0.02
29 125 0.53
30 105 0.44
31 2 0.01
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (30 bp):
ACCCCGAAACTTCCAAAAATTCCATTTTTA
Found at i:134115 original size:59 final size:58
Alignment explanation
Indices: 134016--134243 Score: 278
Period size: 59 Copynumber: 3.8 Consensus size: 58
134006 TACCTTAGAG
* *
134016 ACCCCGAAACTTCCCAAAATTCCATTTTTACCCCTAAACTTCTAAAAATTTCATTTTTA
1 ACCCCGAAACTTCCTAAAATTCCATTTTTACCCCT-AACTTCCAAAAATTTCATTTTTA
* *
134075 ACCTCGAAACTTCCTAAAATTCCATTTTTACCCCTGAACTTCCAAAAATTTCATTTTTG
1 ACCCCGAAACTTCCTAAAATTCCATTTTTACCCCT-AACTTCCAAAAATTTCATTTTTA
* * * *
134134 ACCCCGAAACTT-CTAAAAATTCCATCTTTACCCCCTAAATTCCAAAAATTCCATTCTTA
1 ACCCCGAAACTTCCT-AAAATTCCATTTTTA-CCCCTAACTTCCAAAAATTTCATTTTTA
* * * * *
134193 ACCCCAAAACTTCCAAAAACTCCATTTTTGACCCCAAAACTTTCAAAAATT
1 ACCCCGAAACTTCCTAAAATTCCATTTTT-ACCCC-TAACTTCCAAAAATT
134244 ACCTTTTTGC
Statistics
Matches: 146, Mismatches: 18, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
58 2 0.01
59 125 0.86
60 19 0.13
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (58 bp):
ACCCCGAAACTTCCTAAAATTCCATTTTTACCCCTAACTTCCAAAAATTTCATTTTTA
Found at i:136660 original size:23 final size:23
Alignment explanation
Indices: 136634--136681 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
136624 CACTAGTTTG
*
136634 ATTTTTCAAAAATAAATTA-ATAT
1 ATTTTT-AAAAACAAATTACATAT
136657 ATTTTTAAAAACAAATTACATAT
1 ATTTTTAAAAACAAATTACATAT
136680 AT
1 AT
136682 AAGCATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTTTAAAAACAAATTACATAT
Found at i:136661 original size:22 final size:23
Alignment explanation
Indices: 136636--136681 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
136626 CTAGTTTGAT
*
136636 TTTTCAAAAATAAATTA-ATATA
1 TTTTCAAAAACAAATTACATATA
*
136658 TTTTTAAAAACAAATTACATATA
1 TTTTCAAAAACAAATTACATATA
136681 T
1 T
136682 AAGCATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTTCAAAAACAAATTACATATA
Found at i:137187 original size:5 final size:5
Alignment explanation
Indices: 137177--137201 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
137167 TTTCTTCTTC
137177 TTTGG TTTGG TTTGG TTTGG TTTGG
1 TTTGG TTTGG TTTGG TTTGG TTTGG
137202 CCCCATTTGT
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:0.00, G:0.40, T:0.60
Consensus pattern (5 bp):
TTTGG
Found at i:141129 original size:28 final size:29
Alignment explanation
Indices: 141098--141164 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 29
141088 ATTTATTTTA
**
141098 TTTTACATTAA-TAAAATTAGTACAACTG
1 TTTTACATTAATTAAAATTAACACAACTG
** *
141126 TTTTA-AAAAATTAAAATTAACACAATTG
1 TTTTACATTAATTAAAATTAACACAACTG
141154 TTTTACATTAA
1 TTTTACATTAA
141165 GCTTTTTAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
27 3 0.10
28 24 0.80
29 3 0.10
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.40
Consensus pattern (29 bp):
TTTTACATTAATTAAAATTAACACAACTG
Found at i:162792 original size:9 final size:9
Alignment explanation
Indices: 162780--162805 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
162770 CAAAATGTGA
162780 AAAAAAATT
1 AAAAAAATT
162789 AAAAAAATT
1 AAAAAAATT
162798 AAAAAAAT
1 AAAAAAAT
162806 CAAACATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAAAAATT
Found at i:165787 original size:8 final size:8
Alignment explanation
Indices: 165776--165813 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
165766 TTTTTAGAAT
165776 TTATAAAA
1 TTATAAAA
165784 TTAT-AAA
1 TTATAAAA
165791 TTATTAAAA
1 TTA-TAAAA
*
165800 TAATAAAA
1 TTATAAAA
165808 TTATAA
1 TTATAA
165814 TTTTACTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 6 0.23
8 15 0.58
9 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TTATAAAA
Found at i:166219 original size:30 final size:27
Alignment explanation
Indices: 166174--166230 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 27
166164 AAAATTATGT
166174 TTTTAATTTTTTTTAAAAATAATAAAA
1 TTTTAATTTTTTTTAAAAATAATAAAA
*
166201 TTTTAATTTAATTATTTAAAAATTATAAAA
1 TTTTAATTT--TT-TTTAAAAATAATAAAA
166231 ATATGAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 9 0.35
29 2 0.08
30 15 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TTTTAATTTTTTTTAAAAATAATAAAA
Found at i:166725 original size:31 final size:30
Alignment explanation
Indices: 166672--166731 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
166662 AGGATTATGA
* *
166672 TTTTTTAAAATGTTAAATTTTTAATTTAAG
1 TTTTTTAAAATGTTAAAATTTTAAATTAAG
* *
166702 TTTTTTATAATTTATAAAATTTTAAATTAA
1 TTTTTTAAAATGT-TAAAATTTTAAATTAA
166732 TAATAGTAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (30 bp):
TTTTTTAAAATGTTAAAATTTTAAATTAAG
Found at i:167460 original size:13 final size:13
Alignment explanation
Indices: 167442--167466 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
167432 GAACTCAAGT
167442 AAAACAAAAAAAA
1 AAAACAAAAAAAA
167455 AAAACAAAAAAA
1 AAAACAAAAAAA
167467 CAAATTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAACAAAAAAAA
Found at i:169556 original size:29 final size:29
Alignment explanation
Indices: 169514--169574 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
169504 GGTCAAAGTA
169514 AGAATTCTTCTTCATCTAGACATGTGACT
1 AGAATTCTTCTTCATCTAGACATGTGACT
169543 AGAATTCTTCTTCATCTAGACATGTGACT
1 AGAATTCTTCTTCATCTAGACATGTGACT
169572 AGA
1 AGA
169575 TCCTACGCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (29 bp):
AGAATTCTTCTTCATCTAGACATGTGACT
Found at i:170187 original size:38 final size:38
Alignment explanation
Indices: 170136--170211 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
170126 TACATGTTAG
* *
170136 CTTCTTTGCTTGCTCAGTTACTTCAATTATCTTCTTAT
1 CTTCTTTGCTTGCTCAATTACTTCAATTATCTTATTAT
*
170174 CTTCTTTGCTTGCTTAATTACTTCAATTATCTTATTAT
1 CTTCTTTGCTTGCTCAATTACTTCAATTATCTTATTAT
170212 TTTGTCACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.18, C:0.21, G:0.07, T:0.54
Consensus pattern (38 bp):
CTTCTTTGCTTGCTCAATTACTTCAATTATCTTATTAT
Found at i:174599 original size:19 final size:19
Alignment explanation
Indices: 174575--174611 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
174565 TTTAATTATC
*
174575 AGAATAAAAAAGTTTAATT
1 AGAATAAAAAAGTATAATT
*
174594 AGAATAGAAAAGTATAAT
1 AGAATAAAAAAGTATAAT
174612 AAAAGTAAAA
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:0.59, C:0.00, G:0.14, T:0.27
Consensus pattern (19 bp):
AGAATAAAAAAGTATAATT
Found at i:174623 original size:19 final size:19
Alignment explanation
Indices: 174577--174623 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
174567 TAATTATCAG
* *
174577 AATAAAAAAGTTTAATTAG
1 AATAAAAAAGTATAATTAA
*
174596 AATAGAAAAGTATAA-TAA
1 AATAAAAAAGTATAATTAA
174614 AAGTAAAAAA
1 AA-TAAAAAA
174624 AAAAATTTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (19 bp):
AATAAAAAAGTATAATTAA
Found at i:182005 original size:22 final size:20
Alignment explanation
Indices: 181976--182182 Score: 209
Period size: 22 Copynumber: 9.9 Consensus size: 20
181966 AGTGCTGTTT
*
181976 TTTTTTTGCTGTTTTGGTTGC
1 TTTTTTTACTGTTTTGG-TGC
** *
181997 TATTTTTTGTTGTTTTGGTGT
1 T-TTTTTTACTGTTTTGGTGC
*
182018 TGTGTTTTTACTGTTTTGGTAC
1 T-T-TTTTTACTGTTTTGGTGC
182040 TTTTTTTACTGTTTTGGTTGC
1 TTTTTTTACTGTTTTGG-TGC
* *
182061 TATTTTTTATTGTTTTGGTGT
1 T-TTTTTTACTGTTTTGGTGC
*
182082 TGTGTTTTTACTGTTTTGGTAC
1 T-T-TTTTTACTGTTTTGGTGC
182104 TTTTTTTACTGTTTTGGTTGC
1 TTTTTTTACTGTTTTGG-TGC
*
182125 TATTTTTTATTGTTTTGGTG-
1 T-TTTTTTACTGTTTTGGTGC
* * *
182145 TTGTGTTACTGTTTTGGTAC
1 TTTTTTTACTGTTTTGGTGC
182165 TTTTTTTACTGTTTTGGT
1 TTTTTTTACTGTTTTGGT
182183 TGCTATTTTG
Statistics
Matches: 156, Mismatches: 22, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
19 14 0.09
20 47 0.30
21 19 0.12
22 76 0.49
ACGTcount: A:0.07, C:0.06, G:0.21, T:0.66
Consensus pattern (20 bp):
TTTTTTTACTGTTTTGGTGC
Found at i:182045 original size:11 final size:11
Alignment explanation
Indices: 182026--182182 Score: 59
Period size: 10 Copynumber: 15.1 Consensus size: 11
182016 GTTGTGTTTT
182026 TACTGTTTTGG
1 TACTGTTTTGG
*
182037 TACT-TTTT-T
1 TACTGTTTTGG
182046 TACTGTTTTGG
1 TACTGTTTTGG
* * *
182057 TTGCTATTTT-T
1 -TACTGTTTTGG
*
182068 TATTGTTTTGG
1 TACTGTTTTGG
** *
182079 TGTTGTGTTT-T
1 TACTGT-TTTGG
182090 TACTGTTTTGG
1 TACTGTTTTGG
*
182101 TACT-TTTT-T
1 TACTGTTTTGG
182110 TACTGTTTTGG
1 TACTGTTTTGG
* * *
182121 TTGCTATTTT-T
1 -TACTGTTTTGG
*
182132 TATTGTTTTGG
1 TACTGTTTTGG
* *
182143 ---TGTTGTGT
1 TACTGTTTTGG
182151 TACTGTTTTGG
1 TACTGTTTTGG
*
182162 TACT-TTTT-T
1 TACTGTTTTGG
182171 TACTGTTTTGG
1 TACTGTTTTGG
182182 T
1 T
182183 TGCTATTTTG
Statistics
Matches: 102, Mismatches: 29, Indels: 30
0.63 0.18 0.19
Matches are distributed among these distances:
8 6 0.06
9 12 0.12
10 39 0.38
11 28 0.27
12 17 0.17
ACGTcount: A:0.08, C:0.07, G:0.20, T:0.64
Consensus pattern (11 bp):
TACTGTTTTGG
Found at i:182052 original size:64 final size:64
Alignment explanation
Indices: 181976--182191 Score: 393
Period size: 64 Copynumber: 3.4 Consensus size: 64
181966 AGTGCTGTTT
* *
181976 TTTTTTTGCTGTTTTGGTTGCTATTTTTTGTTGTTTTGGTGTTGTGTTTTTACTGTTTTGGTAC
1 TTTTTTTACTGTTTTGGTTGCTATTTTTTATTGTTTTGGTGTTGTGTTTTTACTGTTTTGGTAC
182040 TTTTTTTACTGTTTTGGTTGCTATTTTTTATTGTTTTGGTGTTGTGTTTTTACTGTTTTGGTAC
1 TTTTTTTACTGTTTTGGTTGCTATTTTTTATTGTTTTGGTGTTGTGTTTTTACTGTTTTGGTAC
182104 TTTTTTTACTGTTTTGGTTGCTATTTTTTATTGTTTTGGTGTTGTG---TTACTGTTTTGGTAC
1 TTTTTTTACTGTTTTGGTTGCTATTTTTTATTGTTTTGGTGTTGTGTTTTTACTGTTTTGGTAC
182165 TTTTTTTACTGTTTTGGTTGCTATTTT
1 TTTTTTTACTGTTTTGGTTGCTATTTT
182192 GGTGCTATTT
Statistics
Matches: 150, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
61 42 0.28
64 108 0.72
ACGTcount: A:0.07, C:0.06, G:0.21, T:0.66
Consensus pattern (64 bp):
TTTTTTTACTGTTTTGGTTGCTATTTTTTATTGTTTTGGTGTTGTGTTTTTACTGTTTTGGTAC
Found at i:182057 original size:42 final size:42
Alignment explanation
Indices: 181977--182191 Score: 206
Period size: 42 Copynumber: 5.1 Consensus size: 42
181967 GTGCTGTTTT
* ** *
181977 TTTTTTGCTGTTTTGGTTGCTATTTTTTGTTGTTTTGGTGTTG
1 TTTTTTACTGTTTTGG-TGCTATTTTTTACTGTTTTGGTGCTG
* *
182020 TGTTTTTACTGTTTTGGTACT-TTTTTTACTGTTTTGGTTGCTA
1 T-TTTTTACTGTTTTGGTGCTATTTTTTACTGTTTTGG-TGCTG
* * * *
182063 TTTTTTATTGTTTTGGTGTTGTGTTTTTACTGTTTTGGTACT-
1 TTTTTTACTGTTTTGGTGCTAT-TTTTTACTGTTTTGGTGCTG
*
182105 TTTTTTACTGTTTTGGTTGCTATTTTTTATTGTTTTGGTG-T-
1 TTTTTTACTGTTTTGG-TGCTATTTTTTACTGTTTTGGTGCTG
* * * *
182146 TGTGTTACTGTTTTGGTACT-TTTTTTACTGTTTTGGTTGCTA
1 TTTTTTACTGTTTTGGTGCTATTTTTTACTGTTTTGG-TGCTG
182188 TTTT
1 TTTT
182192 GGTGCTATTT
Statistics
Matches: 143, Mismatches: 21, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
39 15 0.10
40 5 0.03
41 16 0.11
42 62 0.43
43 16 0.11
44 29 0.20
ACGTcount: A:0.07, C:0.07, G:0.21, T:0.66
Consensus pattern (42 bp):
TTTTTTACTGTTTTGGTGCTATTTTTTACTGTTTTGGTGCTG
Found at i:189101 original size:192 final size:192
Alignment explanation
Indices: 188773--189195 Score: 607
Period size: 192 Copynumber: 2.2 Consensus size: 192
188763 TTGGGTACCG
* * * *
188773 CATATGTTACGAGTCCTCGACAGCTCGTGTGAGTAGCATTGTGAGTCGAAAAAAAAATATGAATC
1 CATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGAGTCGAAAAAAAAATATGAATC
* *
188838 CTAAATGGATTATAGGCCCTACGATGACTGAGATTTATGCTTAAATGCATATTCTCGACAACTCA
66 CTAAATGGATTATAGGCCCTACGATGACTGAGATTTATACTTAAATGCATATTATCGACAACTCA
* * * *
188903 TGTGAGCAACATCTTTAGGGGACAGGTTACAGACAAATA-CTGTATCGATGGCTGAGGCACCA
131 TGTGAGCAACATCGTTAGGGGACAGGTTACAGACAAACACCT-TACCGATGACTGAGGCACCA
* * *
188965 CATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGAGTCGGAAAAGATATATGAATC
1 CATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGAGTCGAAAAAAAAATATGAATC
* * * * *
189030 CTAAATGGATTATAGGCCCTATGATGGCTGGGATTTATACTTAAATGCATATTATCGACAGCTCG
66 CTAAATGGATTATAGGCCCTACGATGACTGAGATTTATACTTAAATGCATATTATCGACAACTCA
* * * *
189095 TGTGAGCAGCATCGTTAGGGGACAGTTTACAGACAAACACCTTACCGATGACTGGGGTACCA
131 TGTGAGCAACATCGTTAGGGGACAGGTTACAGACAAACACCTTACCGATGACTGAGGCACCA
*
189157 CATATGTTGTGAGTCCTCGATAGCTCGTGCT-AGCAGCAT
1 CATATGTTGCGAGTCCTCGATAGCTCGTG-TGAGCAGCAT
189196 TGGGTACCGG
Statistics
Matches: 206, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
192 203 0.99
193 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (192 bp):
CATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGAGTCGAAAAAAAAATATGAATC
CTAAATGGATTATAGGCCCTACGATGACTGAGATTTATACTTAAATGCATATTATCGACAACTCA
TGTGAGCAACATCGTTAGGGGACAGGTTACAGACAAACACCTTACCGATGACTGAGGCACCA
Found at i:192564 original size:18 final size:18
Alignment explanation
Indices: 192543--192589 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
192533 TCATCCGGAT
*
192543 TGGCGAGTTCACAACAAG
1 TGGCGAGCTCACAACAAG
192561 TGGC-ATGCTCACAACAAG
1 TGGCGA-GCTCACAACAAG
192579 TGGCGAGCTCA
1 TGGCGAGCTCA
192590 TTTATTTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 1 0.04
18 24 0.92
19 1 0.04
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.17
Consensus pattern (18 bp):
TGGCGAGCTCACAACAAG
Found at i:196869 original size:7 final size:7
Alignment explanation
Indices: 196859--196899 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
196849 AAGTCAACGA
196859 TCAATGG
1 TCAATGG
196866 TCAATGG
1 TCAATGG
196873 TCAAAT--
1 TC-AATGG
*
196879 TCAACGG
1 TCAATGG
196886 TCAATGG
1 TCAATGG
196893 TCAATGG
1 TCAATGG
196900 GTCGAGTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
5 2 0.07
6 2 0.07
7 22 0.76
8 3 0.10
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (7 bp):
TCAATGG
Found at i:196882 original size:20 final size:20
Alignment explanation
Indices: 196859--196896 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
196849 AAGTCAACGA
*
196859 TCAATGGTCAATGGTCAAAT
1 TCAACGGTCAATGGTCAAAT
196879 TCAACGGTCAATGGTCAA
1 TCAACGGTCAATGGTCAA
196897 TGGGTCGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
TCAACGGTCAATGGTCAAAT
Found at i:196882 original size:27 final size:27
Alignment explanation
Indices: 196844--196899 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
196834 AAAGTTAACG
196844 GGTCAAAGTCAACGATCAATGGTCAAT
1 GGTCAAAGTCAACGATCAATGGTCAAT
* *
196871 GGTCAAATTCAACGGTCAATGGTCAAT
1 GGTCAAAGTCAACGATCAATGGTCAAT
196898 GG
1 GG
196900 GTCGAGTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (27 bp):
GGTCAAAGTCAACGATCAATGGTCAAT
Found at i:198679 original size:19 final size:21
Alignment explanation
Indices: 198626--198679 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
198616 CATGAGTTTA
* *
198626 ATATATAATTAAT-TTTTATT
1 ATATAAAAGTAATGTTTTATT
198646 ATATAAAAGTAAATGTTTTA-T
1 ATATAAAAGT-AATGTTTTATT
*
198667 ATTTAAAA-TAATG
1 ATATAAAAGTAATG
198680 AAAATAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 4 0.14
20 9 0.31
21 11 0.38
22 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (21 bp):
ATATAAAAGTAATGTTTTATT
Found at i:213759 original size:21 final size:22
Alignment explanation
Indices: 213735--213775 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
213725 GAATGGAAAG
*
213735 GAAAAAAAT-AATAAAGAAAAT
1 GAAAAAAATAAAGAAAGAAAAT
213756 GAAAAAAATAAAGAAAGAAA
1 GAAAAAAATAAAGAAAGAAA
213776 TAATTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (22 bp):
GAAAAAAATAAAGAAAGAAAAT
Found at i:213776 original size:21 final size:20
Alignment explanation
Indices: 213730--213776 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
213720 AGAGAGAATG
* *
213730 GAAAGGAAAAAAATAATAAA
1 GAAATGAAAAAAATAAGAAA
213750 GAAAATGAAAAAAATAAAGAAA
1 G-AAATGAAAAAAAT-AAGAAA
213772 GAAAT
1 GAAAT
213777 AATTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 16 0.70
22 6 0.26
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (20 bp):
GAAATGAAAAAAATAAGAAA
Found at i:217823 original size:9 final size:10
Alignment explanation
Indices: 217796--217836 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
217786 TGTAAACCAT
217796 TTTTTTTAAA
1 TTTTTTTAAA
*
217806 TCCTTTTTTCAA
1 T--TTTTTTAAA
217818 TTTTTTTAAA
1 TTTTTTTAAA
217828 TTTTTTTAA
1 TTTTTTTAA
217837 GTAATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 18 0.67
12 9 0.33
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:219953 original size:49 final size:49
Alignment explanation
Indices: 219881--219980 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
219871 ATGTTTGGAC
219881 TTGAAGCCACAAAGGTAACTCATGATGAGGGTGTATTCTCGAAGGATCT
1 TTGAAGCCACAAAGGTAACTCATGATGAGGGTGTATTCTCGAAGGATCT
219930 TTGAAGCCACAAAGGTAACTCATGATGAGGGTGTATTCTCGAAGGATCT
1 TTGAAGCCACAAAGGTAACTCATGATGAGGGTGTATTCTCGAAGGATCT
219979 TT
1 TT
219981 AAATATTTCC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (49 bp):
TTGAAGCCACAAAGGTAACTCATGATGAGGGTGTATTCTCGAAGGATCT
Found at i:231755 original size:16 final size:17
Alignment explanation
Indices: 231729--231760 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
231719 GAGAAAAATA
231729 TATACTATAAAATATTT
1 TATACTATAAAATATTT
231746 TATA-TATAAAATATT
1 TATACTATAAAATATT
231761 CGTGTGGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TATACTATAAAATATTT
Found at i:234911 original size:21 final size:23
Alignment explanation
Indices: 234859--234914 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
234849 GTTTTTTTAC
*
234859 CGAGTTAATTTTTTAGATAATTA
1 CGAGTTATTTTTTTAGATAATTA
234882 C-A-TTCATTTTTTTA-A-AATTA
1 CGAGTT-ATTTTTTTAGATAATTA
234902 CGAGTTATTTTTT
1 CGAGTTATTTTTT
234915 CAATTTAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
20 6 0.21
21 11 0.38
22 11 0.38
23 1 0.03
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (23 bp):
CGAGTTATTTTTTTAGATAATTA
Found at i:234912 original size:20 final size:23
Alignment explanation
Indices: 234859--234914 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 23
234849 GTTTTTTTAC
234859 CGAGTTAATTTTTTAGATAATTA
1 CGAGTTAATTTTTTAGATAATTA
*
234882 C-A-TTCATTTTTTTA-A-AATTA
1 CGAGTT-AATTTTTTAGATAATTA
234902 CGAGTT-ATTTTTT
1 CGAGTTAATTTTTT
234915 CAATTTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
20 12 0.43
21 4 0.14
22 11 0.39
23 1 0.04
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (23 bp):
CGAGTTAATTTTTTAGATAATTA
Found at i:238176 original size:78 final size:78
Alignment explanation
Indices: 238088--238241 Score: 299
Period size: 78 Copynumber: 2.0 Consensus size: 78
238078 TTTGAAGGGT
*
238088 TTTTTTTATATAAATAATACAAAAAAAAAATTATCTACAAAAATAATATACTCTCCCTATTATTT
1 TTTTTTTATATAAATAATACAAAAAAAAAATTATCTACAAAAATAATACACTCTCCCTATTATTT
238153 ACTAAAACGGTGA
66 ACTAAAACGGTGA
238166 TTTTTTTATATAAATAATACAAAAAAAAAATTATCTACAAAAATAATACACTCTCCCTATTATTT
1 TTTTTTTATATAAATAATACAAAAAAAAAATTATCTACAAAAATAATACACTCTCCCTATTATTT
238231 ACTAAAACGGT
66 ACTAAAACGGT
238242 ACACTTAGGA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.36
Consensus pattern (78 bp):
TTTTTTTATATAAATAATACAAAAAAAAAATTATCTACAAAAATAATACACTCTCCCTATTATTT
ACTAAAACGGTGA
Found at i:238931 original size:16 final size:16
Alignment explanation
Indices: 238903--238942 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
238893 TTGAAATTAA
238903 ATTTTTT-ACAAAAAT
1 ATTTTTTGACAAAAAT
*
238918 ATTTTTTGATAAAAAT
1 ATTTTTTGACAAAAAT
238934 -TTTTTTGAC
1 ATTTTTTGAC
238943 TAATTGATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (16 bp):
ATTTTTTGACAAAAAT
Found at i:254337 original size:29 final size:30
Alignment explanation
Indices: 254276--254340 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
254266 CCCAAAACTT
*
254276 TACATGAACTATGGTTTAATGTGCAATTGTA
1 TACATGAACTATGATTT-ATGTGCAATTGTA
* * *
254307 TACATGAACTTTGATTT-TGTGTAATTTTA
1 TACATGAACTATGATTTATGTGCAATTGTA
254336 TACAT
1 TACAT
254341 AAAATTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 15 0.50
31 15 0.50
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (30 bp):
TACATGAACTATGATTTATGTGCAATTGTA
Found at i:254354 original size:29 final size:29
Alignment explanation
Indices: 254295--254354 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
254285 TATGGTTTAA
* * *
254295 TGTGCAATTGTATACATGAACTTTGATTT
1 TGTGCAATTGTATACATAAAATTTGAATT
* * *
254324 TGTGTAATTTTATACATAAAATTTTAATT
1 TGTGCAATTGTATACATAAAATTTGAATT
254353 TG
1 TG
254355 ATCCAATTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.48
Consensus pattern (29 bp):
TGTGCAATTGTATACATAAAATTTGAATT
Found at i:254526 original size:31 final size:30
Alignment explanation
Indices: 254481--254568 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 30
254471 TCTTTAAATG
*
254481 TGTATGATTAAACCAAAATTAAAGTTTCA-A
1 TGTATAATT-AACCAAAATTAAAGTTTCACA
* *
254511 -GTATATATTTGAACCACAATTACAGTTTCACA
1 TGTATA-A-TT-AACCAAAATTAAAGTTTCACA
254543 TGTATAATTACACC-AAATTAAAGTTT
1 TGTATAATTA-ACCAAAATTAAAGTTT
254569 ATGTATACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
29 4 0.09
30 12 0.26
31 24 0.51
32 2 0.04
33 5 0.11
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (30 bp):
TGTATAATTAACCAAAATTAAAGTTTCACA
Found at i:259605 original size:25 final size:25
Alignment explanation
Indices: 259572--259621 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
259562 TTTCTTGAGA
259572 TTTTTACTAATTAACTTTTCAATGT
1 TTTTTACTAATTAACTTTTCAATGT
259597 TTTTTACTAATTAACTTTTCAATGT
1 TTTTTACTAATTAACTTTTCAATGT
259622 ATTAGATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.04, T:0.56
Consensus pattern (25 bp):
TTTTTACTAATTAACTTTTCAATGT
Found at i:262625 original size:12 final size:12
Alignment explanation
Indices: 262603--262638 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 12
262593 TTAAATTGAT
262603 TTAATTCAATTAA
1 TTAA-TCAATTAA
262616 TTAATCAATTAA
1 TTAATCAATTAA
262628 TTAATCTAATT
1 TTAATC-AATT
262639 CGATCGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 14 0.64
13 8 0.36
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (12 bp):
TTAATCAATTAA
Found at i:266790 original size:30 final size:31
Alignment explanation
Indices: 266754--266815 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
266744 TTTCAATCCC
*
266754 TCAAC-TTTGAAAATATGACAAAATAGTCCT
1 TCAACTTTTGAAAATATGACAAAACAGTCCT
*
266784 TCAACTTTTGAAAATGTGACAAAACAGTCCT
1 TCAACTTTTGAAAATATGACAAAACAGTCCT
266815 T
1 T
266816 TTCCGTCACA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (31 bp):
TCAACTTTTGAAAATATGACAAAACAGTCCT
Found at i:266939 original size:30 final size:31
Alignment explanation
Indices: 266903--266974 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 31
266893 GTTACGTTTA
* * * *
266903 ACAAAACAGTCACTCAACTT-TGGAAATGTG
1 ACAAAACAGTCACTAAAATTATCGAAAAGTG
266933 ACAAAACAGTCACTAAAATTATCGAAAAGTG
1 ACAAAACAGTCACTAAAATTATCGAAAAGTG
*
266964 ACAAAATAGTC
1 ACAAAACAGTC
266975 CTCTTGTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 18 0.50
31 18 0.50
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.21
Consensus pattern (31 bp):
ACAAAACAGTCACTAAAATTATCGAAAAGTG
Found at i:268764 original size:16 final size:16
Alignment explanation
Indices: 268739--268780 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
268729 AGGAAATTTA
* *
268739 TTTATTAAAAAGTAAT
1 TTTATAAAAAAATAAT
*
268755 TTTATAAAAAAATAGT
1 TTTATAAAAAAATAAT
268771 TTTA-AAAAAA
1 TTTATAAAAAA
268781 CTCACAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (16 bp):
TTTATAAAAAAATAAT
Found at i:274498 original size:26 final size:23
Alignment explanation
Indices: 274463--274514 Score: 59
Period size: 26 Copynumber: 2.1 Consensus size: 23
274453 AATTAATTTT
*
274463 TATATAAAAATTATTTAAAAATATAA
1 TATATAAAAAATA-TT-AAAATA-AA
*
274489 TATATTAAAAATATTAAAATAAA
1 TATATAAAAAATATTAAAATAAA
274512 TAT
1 TAT
274515 TTCTCATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.21
24 6 0.25
25 2 0.08
26 11 0.46
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TATATAAAAAATATTAAAATAAA
Found at i:284640 original size:13 final size:13
Alignment explanation
Indices: 284622--284647 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
284612 TTTTTGATGG
284622 AATGAATTCACAT
1 AATGAATTCACAT
284635 AATGAATTCACAT
1 AATGAATTCACAT
284648 TCACATTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
AATGAATTCACAT
Found at i:289264 original size:12 final size:12
Alignment explanation
Indices: 289247--289271 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
289237 TGATGAGGGC
289247 TGAAAGAGTGAG
1 TGAAAGAGTGAG
289259 TGAAAGAGTGAG
1 TGAAAGAGTGAG
289271 T
1 T
289272 ATTATGATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (12 bp):
TGAAAGAGTGAG
Found at i:290942 original size:10 final size:10
Alignment explanation
Indices: 290901--290943 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
290891 GTTTTTAATT
290901 ATTTTATTATA
1 ATTTT-TTATA
*
290912 GTTTTTTATA
1 ATTTTTTATA
*
290922 AATTTTT-TA
1 ATTTTTTATA
290931 ATTTTTTATA
1 ATTTTTTATA
290941 ATT
1 ATT
290944 CTAGAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 8 0.30
10 15 0.56
11 4 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:302648 original size:18 final size:18
Alignment explanation
Indices: 302596--302660 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
302586 AGCATTTATT
302596 TATTTTTAAAATTTAAAAA
1 TATTTTTAAAA-TTAAAAA
* *
302615 -A-TTATAAAA-AAAAAA
1 TATTTTTAAAATTAAAAA
302630 TATTTTTAAAATTAAAAA
1 TATTTTTAAAATTAAAAA
* *
302648 TAATTTTGAAATT
1 TATTTTTAAAATT
302661 TTGAAATTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
15 5 0.14
16 1 0.03
17 14 0.38
18 17 0.46
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
TATTTTTAAAATTAAAAA
Found at i:303141 original size:13 final size:14
Alignment explanation
Indices: 303115--303146 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
303105 GTCATTTGTC
303115 TCTTTTATCTTTTA
1 TCTTTTATCTTTTA
303129 TCTTTTA-CTTTTA
1 TCTTTTATCTTTTA
303142 TCTTT
1 TCTTT
303147 ATTACTTACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (14 bp):
TCTTTTATCTTTTA
Found at i:303148 original size:6 final size:7
Alignment explanation
Indices: 303115--303146 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
303105 GTCATTTGTC
303115 TCTTTTA
1 TCTTTTA
303122 TCTTTTA
1 TCTTTTA
303129 TCTTTTA
1 TCTTTTA
303136 -CTTTTA
1 TCTTTTA
303142 TCTTT
1 TCTTT
303147 ATTACTTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (7 bp):
TCTTTTA
Found at i:307800 original size:23 final size:24
Alignment explanation
Indices: 307752--307811 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
307742 ATCTACATAA
307752 ATAAATAA-TAAAATATAATAATT
1 ATAAATAATTAAAATATAATAATT
* *
307775 AT-AATCATTAAAATATTAATTA-T
1 ATAAATAATTAAAATA-TAATAATT
307798 ATAAATAATTAAAA
1 ATAAATAATTAAAA
307812 AAATATATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 4 0.13
23 12 0.39
24 15 0.48
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
ATAAATAATTAAAATATAATAATT
Found at i:309773 original size:33 final size:33
Alignment explanation
Indices: 309736--309803 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
309726 AAAATCTCAA
*
309736 GGTTTTCTTTCTTCACTTATGAAAATGGAAAAT
1 GGTTTTCTTTCTTCACTTACGAAAATGGAAAAT
*
309769 GGTTTTCTTTCTTCACTTACGACAATGGAAAAT
1 GGTTTTCTTTCTTCACTTACGAAAATGGAAAAT
309802 GG
1 GG
309804 GGAAGATGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.40
Consensus pattern (33 bp):
GGTTTTCTTTCTTCACTTACGAAAATGGAAAAT
Found at i:312322 original size:193 final size:193
Alignment explanation
Indices: 312050--312411 Score: 505
Period size: 195 Copynumber: 1.9 Consensus size: 193
312040 CTATAAATTA
** * * *
312050 TTCCCTAATGATGCTGCTCACAAGAGCTATCGAGAGTATGCATAAAGCATAGTCTCAGCCATTGT
1 TTCCCTAACAATGCTGCTCACAAGAGCTATCGAGAATATGCATAAAGCATAATCTCAGCCAGTGT
* *
312115 AGGGCCTATAATCCA-TTTAGGATTCATATCTC-TTTCCCGAGTCACGATGCTGCTTACACGAGC
66 AGGGCCTATAATCCATTTTAGGATTCATATCTCATTTCCCAACTCACGATGCTGCTTACACGAGC
* **
312178 TGTTGAGGACTCGTAACATATGTGGTACCTCAGCCATCGATACGGTATCTGTGCATATAACTG
131 TGTTGAGGACTCGCAACATATACGGTACCTCAGCCATCGATACGGTATCTGTGCATATAACTG
* * * *
312241 TTCCCTAACAATGCTGCTCACACA-AGTTGTCGAGAATATGCACTTATGCATAAATCTCAGCCAG
1 TTCCCTAACAATGCTGCTCACA-AGAGCTATCGAGAATATGCA-TAAAGCAT-AATCTCAGCCAG
* * * *
312305 TGTAGGGCCTCTAATCCATTTTTGGATTCTTTTCTCATTTCCCAACTCACGATGCTGCTTACACG
63 TGTAGGGCCTATAATCCATTTTAGGATTCATATCTCATTTCCCAACTCACGATGCTGCTTACACG
*
312370 AGCTGTTGAGGACTCGCAACATATACGGTACCTCATCCATCG
128 AGCTGTTGAGGACTCGCAACATATACGGTACCTCAGCCATCG
312412 CGTCATTTTC
Statistics
Matches: 147, Mismatches: 19, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
191 35 0.24
192 7 0.05
193 27 0.18
194 14 0.10
195 64 0.44
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (193 bp):
TTCCCTAACAATGCTGCTCACAAGAGCTATCGAGAATATGCATAAAGCATAATCTCAGCCAGTGT
AGGGCCTATAATCCATTTTAGGATTCATATCTCATTTCCCAACTCACGATGCTGCTTACACGAGC
TGTTGAGGACTCGCAACATATACGGTACCTCAGCCATCGATACGGTATCTGTGCATATAACTG
Found at i:312907 original size:16 final size:16
Alignment explanation
Indices: 312883--312914 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
312873 TCCTTACAAA
*
312883 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
312899 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
312915 AAAAATCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:315208 original size:21 final size:21
Alignment explanation
Indices: 315182--315222 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
315172 CCCTTTTCCA
* *
315182 TTTTTATTTTTGAAATTTAAT
1 TTTTTAATTTTAAAATTTAAT
315203 TTTTTAATTTTAAAATTTAA
1 TTTTTAATTTTAAAATTTAA
315223 GTTAACTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTTAATTTTAAAATTTAAT
Found at i:318905 original size:2 final size:2
Alignment explanation
Indices: 318898--318933 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
318888 CCATCCAAAC
318898 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
318934 ACCCAGAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:322704 original size:11 final size:11
Alignment explanation
Indices: 322688--322748 Score: 59
Period size: 11 Copynumber: 5.3 Consensus size: 11
322678 GGAGAACAAC
* *
322688 GAAAAATGAAG
1 GAAAAAAGAAA
322699 GAAAAAAGAAA
1 GAAAAAAGAAA
322710 GAAAAAAGAGAAA
1 G-AAAAA-AGAAA
322723 GAAAGAAAGAAA
1 GAAA-AAAGAAA
* *
322735 GAAAGAAGGAA
1 GAAAAAAGAAA
322746 GAA
1 GAA
322749 GGAGAAGAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
11 18 0.42
12 17 0.40
13 8 0.19
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:322712 original size:4 final size:4
Alignment explanation
Indices: 322699--322741 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
322689 AAAAATGAAG
*
322699 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAA
322742 GGAAGAAGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:322714 original size:21 final size:21
Alignment explanation
Indices: 322699--322740 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
322689 AAAAATGAAG
322699 GAAA-AAAGAAAGAAAAAAGA
1 GAAAGAAAGAAAGAAAAAAGA
322719 GAAAGAAAGAAAGAAAGAAAGA
1 GAAAGAAAGAAAGAAA-AAAGA
322741 AGGAAGAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAGAAAAAAGA
Found at i:322757 original size:9 final size:9
Alignment explanation
Indices: 322743--322775 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
322733 AAGAAAGAAG
322743 GAAGAAGGA
1 GAAGAAGGA
*
322752 GAAGAAGGG
1 GAAGAAGGA
322761 GAAGAAGGA
1 GAAGAAGGA
322770 GAAGAA
1 GAAGAA
322776 AAAATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (9 bp):
GAAGAAGGA
Found at i:322826 original size:16 final size:16
Alignment explanation
Indices: 322805--322844 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
322795 TATTTTTAAA
322805 TTTAATTTTAAAATAT
1 TTTAATTTTAAAATAT
322821 TTTAATTTTAAAATAT
1 TTTAATTTTAAAATAT
322837 TTTAATTT
1 TTTAATTT
322845 GTTAATTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAATTTTAAAATAT
Found at i:323178 original size:20 final size:21
Alignment explanation
Indices: 323137--323179 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
323127 TAATTTACTT
323137 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
323158 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
323178 TA
1 TA
323180 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Done.