Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009025.1 Corchorus capsularis cultivar CVL-1 contig09046, 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: 46614
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Found at i:261 original size:42 final size:42
Alignment explanation
Indices: 208--294 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
198 AATTAATCTA
208 AAACAGCTTGCATAGACAAATAGGTTAATTTAAAAAATTATT
1 AAACAGCTTGCATAGACAAATAGGTTAATTTAAAAAATTATT
*
250 AAACAGTTTGCATAGACAAATAGGTTAATTTAAAAAATTATT
1 AAACAGCTTGCATAGACAAATAGGTTAATTTAAAAAATTATT
292 AAA
1 AAA
295 AAGTGAACCT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.31
Consensus pattern (42 bp):
AAACAGCTTGCATAGACAAATAGGTTAATTTAAAAAATTATT
Found at i:569 original size:14 final size:14
Alignment explanation
Indices: 550--579 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
540 TTTAACTGTG
550 AGGTTTGTAAGGTA
1 AGGTTTGTAAGGTA
564 AGGTTTGTAAGGTA
1 AGGTTTGTAAGGTA
578 AG
1 AG
580 TGATAATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (14 bp):
AGGTTTGTAAGGTA
Found at i:3177 original size:48 final size:48
Alignment explanation
Indices: 3116--3212 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
3106 AACTATTTTG
* *
3116 ATTCATGAGTGTTATGATTTGCTCTAATCTCATAATATTTTTGTATTA
1 ATTCATAAGTGTTATGATTTGCTCTAATCTCATAATATTTTGGTATTA
3164 ATTCATAAGTGTTATGATTTGCTCTAATCTCATAATATTTTGGTATTA
1 ATTCATAAGTGTTATGATTTGCTCTAATCTCATAATATTTTGGTATTA
3212 A
1 A
3213 ATTAACGTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.48
Consensus pattern (48 bp):
ATTCATAAGTGTTATGATTTGCTCTAATCTCATAATATTTTGGTATTA
Found at i:3205 original size:21 final size:21
Alignment explanation
Indices: 3133--3205 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 21
3123 AGTGTTATGA
3133 TTTGCTCTAATCTCATAATATT
1 TTTGCTCTAATCTCATAATA-T
*
3155 TTTG-TATTAAT-TCATAAGTGTTAT
1 TTTGCT-CTAATCTCATAA----TAT
3179 GATTTGCTCTAATCTCATAATAT
1 --TTTGCTCTAATCTCATAATAT
3202 TTTG
1 TTTG
3206 GTATTAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 19
0.66 0.03 0.31
Matches are distributed among these distances:
21 11 0.28
22 8 0.20
23 3 0.08
24 1 0.03
25 2 0.05
26 8 0.20
27 7 0.17
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (21 bp):
TTTGCTCTAATCTCATAATAT
Found at i:3296 original size:24 final size:24
Alignment explanation
Indices: 3269--3338 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
3259 GTCATGGTTT
3269 TATTTCTAACCAAAATACTTTTTC
1 TATTTCTAACCAAAATACTTTTTC
*
3293 TA--T-T-A--AAAATAAATTTTT-
1 TATTTCTAACCAAAAT-ACTTTTTC
*
3311 TAATTCTAACCAAAATACTTTTTC
1 TATTTCTAACCAAAATACTTTTTC
3335 TATT
1 TATT
3339 AAAAATCAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 16
0.65 0.06 0.30
Matches are distributed among these distances:
18 7 0.20
19 6 0.17
20 2 0.06
21 2 0.06
22 2 0.06
23 6 0.17
24 10 0.29
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (24 bp):
TATTTCTAACCAAAATACTTTTTC
Found at i:3301 original size:18 final size:19
Alignment explanation
Indices: 3287--3356 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 19
3277 ACCAAAATAC
3287 TTTTTCTATTAAAAATAAA
1 TTTTTCTATTAAAAATAAA
*
3306 TTTTT-TAATTCTAACCAAA-ATAC
1 TTTTTCT-A-T-TAA--AAATA-AA
*
3329 TTTTTCTATTAAAAATCAA
1 TTTTTCTATTAAAAATAAA
3348 TTTTTCTAT
1 TTTTTCTAT
3357 GAACACGGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 16
0.68 0.05 0.27
Matches are distributed among these distances:
18 1 0.03
19 19 0.47
20 1 0.03
21 6 0.15
22 2 0.05
23 10 0.25
24 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTTCTATTAAAAATAAA
Found at i:3312 original size:42 final size:42
Alignment explanation
Indices: 3266--3352 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
3256 AGTGTCATGG
*
3266 TTTTATTTCTAACCAAAATACTTTTTCTATTAAAAATAAATT
1 TTTTAATTCTAACCAAAATACTTTTTCTATTAAAAATAAATT
*
3308 TTTTAATTCTAACCAAAATACTTTTTCTATTAAAAATCAATT
1 TTTTAATTCTAACCAAAATACTTTTTCTATTAAAAATAAATT
3350 TTT
1 TTT
3353 CTATGAACAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (42 bp):
TTTTAATTCTAACCAAAATACTTTTTCTATTAAAAATAAATT
Found at i:8385 original size:12 final size:12
Alignment explanation
Indices: 8368--8392 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8358 AGCTGAAAAA
8368 TCCAAAGCTAAC
1 TCCAAAGCTAAC
8380 TCCAAAGCTAAC
1 TCCAAAGCTAAC
8392 T
1 T
8393 TTAGGTAATT
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:0.32, G:0.08, T:0.20
Consensus pattern (12 bp):
TCCAAAGCTAAC
Found at i:22416 original size:2 final size:2
Alignment explanation
Indices: 22398--22473 Score: 51
Period size: 2 Copynumber: 41.0 Consensus size: 2
22388 ACATATAAAT
*
22398 TA TA TA T- TA TA -A T- TA TA TA TA T- TA TA TA TA TA CT- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
22436 TA -A CTT TA T- TT TA TA TA TA TA TA TA TA TA -A TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22474 AATAAATAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
1 8 0.13
2 51 0.85
3 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:22473 original size:9 final size:9
Alignment explanation
Indices: 22383--22474 Score: 57
Period size: 9 Copynumber: 10.4 Consensus size: 9
22373 TTTTTTAAAA
*
22383 ATAATACAT
1 ATAATATAT
22392 ATAA-ATTAT
1 ATAATA-TAT
*
22401 ATATTATA-
1 ATAATATAT
*
22409 ATTATATAT
1 ATAATATAT
*
22418 ATTATATAT
1 ATAATATAT
* *
22427 ATACT-TTT
1 ATAATATAT
*
22435 ATAACTTTAT
1 ATAA-TATAT
* *
22445 TTTATATAT
1 ATAATATAT
22454 AT-ATATAT
1 ATAATATAT
22462 ATAATATAT
1 ATAATATAT
22471 ATAA
1 ATAA
22475 ATAAATAACC
Statistics
Matches: 64, Mismatches: 13, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
8 20 0.31
9 39 0.61
10 5 0.08
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (9 bp):
ATAATATAT
Found at i:22473 original size:13 final size:13
Alignment explanation
Indices: 22390--22478 Score: 51
Period size: 13 Copynumber: 6.6 Consensus size: 13
22380 AAAATAATAC
22390 ATATA-AAT-TAT
1 ATATATAATATAT
22401 ATATTATAAT-TAT
1 ATA-TATAATATAT
22414 ATATATTATATATAT
1 ATATA-TA-ATATAT
* *
22429 ACTTTTATAACTTTAT
1 A--TATATAA-TATAT
*
22445 -TTTATATATATAT
1 ATATATA-ATATAT
22458 ATATATAATATAT
1 ATATATAATATAT
*
22471 ATAAATAA
1 ATATATAA
22479 ATAACCCGAC
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
11 3 0.05
12 4 0.06
13 34 0.54
14 8 0.13
15 5 0.08
16 6 0.10
17 3 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATATAATATAT
Found at i:22482 original size:17 final size:17
Alignment explanation
Indices: 22448--22482 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
22438 ACTTTATTTT
* *
22448 ATATATATATATATATA
1 ATATATATAAATAAATA
22465 ATATATATAAATAAATA
1 ATATATATAAATAAATA
22482 A
1 A
22483 CCCGACCCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATATATAAATAAATA
Found at i:22588 original size:48 final size:48
Alignment explanation
Indices: 22517--22614 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
22507 GGAACCGACA
22517 AGGTCATATGTAGGTGCCTTATGGACCATGTGAACAGCATCAAGCTTG
1 AGGTCATATGTAGGTGCCTTATGGACCATGTGAACAGCATCAAGCTTG
22565 AGGTCATATGTAGGTGCCTTATGGACCATGTGAACAGCATCAAGCTTG
1 AGGTCATATGTAGGTGCCTTATGGACCATGTGAACAGCATCAAGCTTG
22613 AG
1 AG
22615 CGCACCTACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.27
Consensus pattern (48 bp):
AGGTCATATGTAGGTGCCTTATGGACCATGTGAACAGCATCAAGCTTG
Found at i:23732 original size:201 final size:198
Alignment explanation
Indices: 23366--23739 Score: 550
Period size: 201 Copynumber: 1.9 Consensus size: 198
23356 CATATTTGCG
* *
23366 TTTGATCCTAAAAAGTTAATTTGGATTAAATTCTAATTTCATCGCGGTTAAATAGTAGTTAAATT
1 TTTGATCCTAAAAAGTTAATTTGGATTAAATTCTAATTTCATCCCAGTTAAATAGTAGTTAAATT
** *
23431 AGCAATACTGCTCAACTAGGATTACCAAATTGACCATAACATTCTTTATACAAACTGGTTCTAAC
66 AGCAATACCACTCAACTAGGATTACCAAATTGACAATAACATTCTTTATACAAACTGGTTCTAAC
* * *
23496 CTCTCAAATTCAACATAAAGAATAGAAGGAAACCCTGGCCTCCTCAATGCCCTGGAAACATATTC
131 CTCTCAAATTCAACATAAAGAAGAGAAGAAAACCCTAGCCTCCTCAATGCCCTGGAAACATATTC
23561 AGC
196 AGC
* *
23564 TTTGATCCATATAAAAGTTTACTTTGGATTAAATTCTAATTTGATCCCAGTTAAATAGTAGTTAA
1 TTTGATCC-TA-AAAAG-TTAATTTGGATTAAATTCTAATTTCATCCCAGTTAAATAGTAGTTAA
* * * * * *
23629 ATTGGCAATACCACTCAATTAGGGTTACCAAATTGACAATAGCATTTTTTATACAAAGTGGTTCT
63 ATTAGCAATACCACTCAACTAGGATTACCAAATTGACAATAACATTCTTTATACAAACTGGTTCT
** *
23694 AACCTCTTGAATTCAACATAAGGAAGAGAAGAAAACCCTAGCCTCC
128 AACCTCTCAAATTCAACATAAAGAAGAGAAGAAAACCCTAGCCTCC
23740 ATAACGCCTT
Statistics
Matches: 154, Mismatches: 19, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
198 8 0.05
199 2 0.01
200 5 0.03
201 139 0.90
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (198 bp):
TTTGATCCTAAAAAGTTAATTTGGATTAAATTCTAATTTCATCCCAGTTAAATAGTAGTTAAATT
AGCAATACCACTCAACTAGGATTACCAAATTGACAATAACATTCTTTATACAAACTGGTTCTAAC
CTCTCAAATTCAACATAAAGAAGAGAAGAAAACCCTAGCCTCCTCAATGCCCTGGAAACATATTC
AGC
Found at i:26301 original size:13 final size:14
Alignment explanation
Indices: 26272--26301 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
26262 TAATTAAATC
26272 AATAATCTCCTATA
1 AATAATCTCCTATA
26286 AATAATCTCC-ATA
1 AATAATCTCCTATA
26299 AAT
1 AAT
26302 CACTGCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAATCTCCTATA
Found at i:26521 original size:70 final size:70
Alignment explanation
Indices: 26427--26568 Score: 275
Period size: 70 Copynumber: 2.0 Consensus size: 70
26417 TACAAATATG
26427 ATGTTGTGCATGTAACCTCCAAATTAATAAATATCTTGAAGAAACGTTACAAGCATTTGTAACCG
1 ATGTTGTGCATGTAACCTCCAAATTAATAAATATCTTGAAGAAACGTTACAAGCATTTGTAACCG
26492 CCCAA
66 CCCAA
*
26497 ATGTTGTGCATGTAACCTCCAAATTAGTAAATATCTTGAAGAAACGTTACAAGCATTTGTAACCG
1 ATGTTGTGCATGTAACCTCCAAATTAATAAATATCTTGAAGAAACGTTACAAGCATTTGTAACCG
26562 CCCAA
66 CCCAA
26567 AT
1 AT
26569 ATGATATTGT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Consensus pattern (70 bp):
ATGTTGTGCATGTAACCTCCAAATTAATAAATATCTTGAAGAAACGTTACAAGCATTTGTAACCG
CCCAA
Found at i:26651 original size:113 final size:115
Alignment explanation
Indices: 26499--26709 Score: 327
Period size: 113 Copynumber: 1.9 Consensus size: 115
26489 CCGCCCAAAT
* * * *
26499 GTTGTGCATGTAACCTCCAAATTAGTAAATATCTTGAAGAAACGTTACAAGCATTTGTAACCGCC
1 GTTGTGCATGCAACCTCCAAATTACTAAATACCTTGAAGAAACGTTAAAAGCATTTGTAACCGCC
* *
26564 CAAATATGATATTGTGTATGTAACCTCC-CAATTACTGAATACCTTAAAA
66 CAAATATGATATTGTGCATATAACCTCCACAATTACTGAATACCTTAAAA
*
26613 GTTGTGCATGCAACCTCC-AATTACTAAATACCTTGAAGAAACGTTAAAAGTATTTGTAACCGCC
1 GTTGTGCATGCAACCTCCAAATTACTAAATACCTTGAAGAAACGTTAAAAGCATTTGTAACCGCC
* *
26677 TAAATATGATGTTGTGCATATAACCTCCACAAT
66 CAAATATGATATTGTGCATATAACCTCCACAAT
26710 ATTAAATACC
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
113 66 0.76
114 21 0.24
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (115 bp):
GTTGTGCATGCAACCTCCAAATTACTAAATACCTTGAAGAAACGTTAAAAGCATTTGTAACCGCC
CAAATATGATATTGTGCATATAACCTCCACAATTACTGAATACCTTAAAA
Found at i:26756 original size:113 final size:113
Alignment explanation
Indices: 26510--26757 Score: 252
Period size: 113 Copynumber: 2.2 Consensus size: 113
26500 TTGTGCATGT
* * * *
26510 AACCTCCAAATTAGTAAATATCTTGAAGAAACGTTACAAGCATTTGTAACCGCCCAAATATGATA
1 AACCT-CAAAATACTAAATACCTTGAAGAAACGTTAAAAGCATTTGTAACCGCCCAAATATGATA
* * * ** * *
26575 TTGTGTATGTAACCTCCCAATTACTGAATACCTTAAAAGTTGTGCATGC
65 TTGTGCATATAACCTCCCAATTACTAAATACCTTAAAAGACGTACAAGC
* * * * *
26624 AACCTCCAATTACTAAATACCTTGAAGAAACGTTAAAAGTATTTGTAACCGCCTAAATATGATGT
1 AACCTCAAAATACTAAATACCTTGAAGAAACGTTAAAAGCATTTGTAACCGCCCAAATATGATAT
* *
26689 TGTGCATATAACCTCCACAA-TATTAAATACCTTGAATAGACGTTACAAG-
66 TGTGCATATAACCTCC-CAATTACTAAATACCTT-AAAAGACG-TACAAGC
*
26738 TACCGTCAAAATA-T-AATACC
1 AACC-TCAAAATACTAAATACC
26758 ATGTATGTAA
Statistics
Matches: 111, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
113 84 0.76
114 17 0.15
115 10 0.09
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.29
Consensus pattern (113 bp):
AACCTCAAAATACTAAATACCTTGAAGAAACGTTAAAAGCATTTGTAACCGCCCAAATATGATAT
TGTGCATATAACCTCCCAATTACTAAATACCTTAAAAGACGTACAAGC
Found at i:28704 original size:16 final size:16
Alignment explanation
Indices: 28683--28717 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28673 AGTATGAAAA
28683 AGACAAGAGAATAGAG
1 AGACAAGAGAATAGAG
* *
28699 AGACAATAGAATATAG
1 AGACAAGAGAATAGAG
28715 AGA
1 AGA
28718 AGAAGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.26, T:0.11
Consensus pattern (16 bp):
AGACAAGAGAATAGAG
Found at i:29381 original size:21 final size:20
Alignment explanation
Indices: 29357--29635 Score: 128
Period size: 21 Copynumber: 14.1 Consensus size: 20
29347 ACTCTTTGAA
*
29357 TTACTGATCACCTTTTACTC
1 TTACTGATTACCTTTTACTC
*
29377 TTTACTGATTACTATTTTACTC
1 -TTACTGATTAC-CTTTTACTC
* * *
29399 TTACTAATTACCACTTTGCTC
1 TTACTGATTACC-TTTTACTC
29420 TTACTGATTA-CTGTTTAACTC
1 TTACTGATTACCT-TTT-ACTC
* *
29441 TTACTAATTACCTTTTACTGA
1 TTACTGATTACCTTTTACT-C
29462 TTACT-A-T---TTTT-CTC
1 TTACTGATTACCTTTTACTC
29476 TTTACTGATTACC--TTA---
1 -TTACTGATTACCTTTTACTC
*
29492 -TACTGATTACTATTTTACTC
1 TTACTGATTAC-CTTTTACTC
29512 TTACTGATTACC---T--T-
1 TTACTGATTACCTTTTACTC
* *
29526 TTGCTGATTACTATTTTACTC
1 TTACTGATTAC-CTTTTACTC
*
29547 TTTACTGATTACCTTCTTACTTT
1 -TTACTGATTACCTT-TTAC-TC
*
29570 TTACTGATTACTATTTTACTC
1 TTACTGATTAC-CTTTTACTC
* *
29591 TTTACTTATTACCATTTTGCTC
1 -TTACTGATTACC-TTTTACTC
* * *
29613 TCATTGATTACCATTTTGCTC
1 TTACTGATTACC-TTTTACTC
29634 TT
1 TT
29636 TTTACTGATT
Statistics
Matches: 197, Mismatches: 28, Indels: 66
0.68 0.10 0.23
Matches are distributed among these distances:
14 20 0.10
15 8 0.04
16 5 0.03
17 5 0.03
18 3 0.02
19 1 0.01
20 9 0.05
21 87 0.44
22 56 0.28
23 3 0.02
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.51
Consensus pattern (20 bp):
TTACTGATTACCTTTTACTC
Found at i:29424 original size:35 final size:35
Alignment explanation
Indices: 29371--29559 Score: 200
Period size: 35 Copynumber: 5.1 Consensus size: 35
29361 TGATCACCTT
* *
29371 TTACTCTTTACTGATTACTATTTTACTCTTACTAA
1 TTACCCTTTACTGATTACTATTTTACTCTTACTGA
* * *
29406 TTACCACTTTGCTCTTACTGATTACTGTTTAACTCTTACTAA
1 TTA-C-C----CT-TTACTGATTACTATTTTACTCTTACTGA
* *
29448 TTACCTTTTACTGATTACTATTTTTCTCTTTACTGA
1 TTACCCTTTACTGATTACTATTTTACTC-TTACTGA
29484 TTA-CCTTATACTGATTACTATTTTACTCTTACTGA
1 TTACCCTT-TACTGATTACTATTTTACTCTTACTGA
* *
29519 TTACCTTTTGCTGATTACTATTTTACTCTTTACTGA
1 TTACCCTTTACTGATTACTATTTTACTC-TTACTGA
29555 TTACC
1 TTACC
29560 TTCTTACTTT
Statistics
Matches: 131, Mismatches: 12, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
35 53 0.40
36 45 0.34
40 1 0.01
41 3 0.02
42 29 0.22
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.50
Consensus pattern (35 bp):
TTACCCTTTACTGATTACTATTTTACTCTTACTGA
Found at i:29481 original size:22 final size:22
Alignment explanation
Indices: 29454--29646 Score: 119
Period size: 22 Copynumber: 8.5 Consensus size: 22
29444 CTAATTACCT
*
29454 TTTACTGATTACTATTTTTCTC
1 TTTACTGATTACTATTTTACTC
*
29476 TTTACTGATTACCTTATACTGATTACTAT
1 TTTACTGATTA-C-TAT--T--TTACT-C
*
29505 TTTACT-CTTACTGA--TTAC-C
1 TTTACTGATTACT-ATTTTACTC
*
29524 TTTTGCTGATTACTATTTTACTC
1 -TTTACTGATTACTATTTTACTC
* *
29547 TTTACTGATTACCT-TCTTACTT
1 TTTACTGATTA-CTATTTTACTC
29569 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
* * *
29591 TTTACTTATTACCATTTTGCTC
1 TTTACTGATTACTATTTTACTC
* * * *
29613 -TCATTGATTACCATTTTGCTC
1 TTTACTGATTACTATTTTACTC
29634 TTTTTACTGATTA
1 --TTTACTGATTA
29647 TCATTACTTT
Statistics
Matches: 134, Mismatches: 19, Indels: 34
0.72 0.10 0.18
Matches are distributed among these distances:
20 6 0.04
21 29 0.22
22 67 0.50
23 4 0.03
24 11 0.08
26 2 0.01
27 2 0.01
28 7 0.05
29 6 0.04
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.53
Consensus pattern (22 bp):
TTTACTGATTACTATTTTACTC
Found at i:29522 original size:71 final size:71
Alignment explanation
Indices: 29421--29561 Score: 237
Period size: 71 Copynumber: 2.0 Consensus size: 71
29411 ACTTTGCTCT
* *
29421 TACTGATTACTGTTTAACTCTTACTAATTACCTTTTACTGATTACTATTTTTCTCTTTACTGATT
1 TACTGATTACTATTTAACTCTTACTAATTACCTTTTACTGATTACTATTTTACTCTTTACTGATT
29486 ACCTTA
66 ACCTTA
* * *
29492 TACTGATTACTATTTTACTCTTACTGATTACCTTTTGCTGATTACTATTTTACTCTTTACTGATT
1 TACTGATTACTATTTAACTCTTACTAATTACCTTTTACTGATTACTATTTTACTCTTTACTGATT
29557 ACCTT
66 ACCTT
29562 CTTACTTTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.51
Consensus pattern (71 bp):
TACTGATTACTATTTAACTCTTACTAATTACCTTTTACTGATTACTATTTTACTCTTTACTGATT
ACCTTA
Found at i:29581 original size:71 final size:71
Alignment explanation
Indices: 29418--29581 Score: 224
Period size: 71 Copynumber: 2.3 Consensus size: 71
29408 ACCACTTTGC
* *
29418 TCTTACTGATTACTGTTTAACTCTTACTAATTACCTTTTACTGATTACTATTTTTCTCTTTACTG
1 TCTTACTGATTACTGATT-ACTCTTACTAATTACCTTTTACTGATTACTATTTTACTCTTTACTG
29483 ATTACCT
65 ATTACCT
* * *
29490 T-ATACTGATTACT-ATTTTACTCTTACTGATTACCTTTTGCTGATTACTATTTTACTCTTTACT
1 TCTTACTGATTACTGA--TTACTCTTACTAATTACCTTTTACTGATTACTATTTTACTCTTTACT
29553 GATTACCT
64 GATTACCT
**
29561 TCTTACTTTTTACTGATTACT
1 TCTTACTGATTACTGATTACT
29582 ATTTTACTCT
Statistics
Matches: 80, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
71 67 0.84
72 12 0.15
73 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.52
Consensus pattern (71 bp):
TCTTACTGATTACTGATTACTCTTACTAATTACCTTTTACTGATTACTATTTTACTCTTTACTGA
TTACCT
Found at i:29582 original size:44 final size:44
Alignment explanation
Indices: 29519--29603 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
29509 CTCTTACTGA
*
29519 TTACCTTTTGCTGATTACTATTTTACTCTTTACTGATTACCTTC
1 TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACCTTC
* *
29563 TTACTTTTTACTGATTACTATTTTACTCTTTACTTATTACC
1 TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACC
29604 ATTTTGCTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.20, C:0.21, G:0.05, T:0.54
Consensus pattern (44 bp):
TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACCTTC
Found at i:29675 original size:22 final size:21
Alignment explanation
Indices: 29519--29676 Score: 95
Period size: 22 Copynumber: 7.2 Consensus size: 21
29509 CTCTTACTGA
* * *
29519 TTACCTTTTGCTGATTACTATT
1 TTACTTTTTACTGATTAC-CTT
*
29541 TTACTCTTTACTGATTACCTT
1 TTACTTTTTACTGATTACCTT
*
29562 CTTACTTTTTACTGATTACTATT
1 -TTACTTTTTACTGATTAC-CTT
* *
29585 TTACTCTTTACTTATTACCATT
1 TTACTTTTTACTGATTACC-TT
* * * *
29607 TTGC-TCTCATTGATTACCATT
1 TTACTTTTTACTGATTACC-TT
* * *
29628 TTGCTCTTTTTACTGATTATC-A
1 TT--ACTTTTTACTGATTACCTT
*
29650 TTACTTTTTTATTGATTACCTT
1 TTAC-TTTTTACTGATTACCTT
29672 TTACT
1 TTACT
29677 ATTTCATTCT
Statistics
Matches: 103, Mismatches: 25, Indels: 17
0.71 0.17 0.12
Matches are distributed among these distances:
20 1 0.01
21 30 0.29
22 59 0.57
23 3 0.03
24 10 0.10
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.55
Consensus pattern (21 bp):
TTACTTTTTACTGATTACCTT
Found at i:29711 original size:22 final size:23
Alignment explanation
Indices: 29686--29745 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
29676 TATTTCATTC
29686 TTTACTGATTATCTTTTTAC-TT
1 TTTACTGATTATCTTTTTACTTT
*
29708 TTTACTGATTATC--ATTACTTT
1 TTTACTGATTATCTTTTTACTTT
* *
29729 TTTATTGATTACCTTTT
1 TTTACTGATTATCTTTT
29746 ACTGATTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 4 0.13
21 13 0.42
22 13 0.42
23 1 0.03
ACGTcount: A:0.20, C:0.13, G:0.05, T:0.62
Consensus pattern (23 bp):
TTTACTGATTATCTTTTTACTTT
Found at i:29745 original size:14 final size:15
Alignment explanation
Indices: 29721--29759 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
29711 ACTGATTATC
* *
29721 ATTACTTTTTTATTG
1 ATTACTCTTTTACTG
29736 ATTAC-CTTTTACTG
1 ATTACTCTTTTACTG
29750 ATTACTCTTT
1 ATTACTCTTT
29760 ACTTTTTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.21, C:0.15, G:0.05, T:0.59
Consensus pattern (15 bp):
ATTACTCTTTTACTG
Found at i:29747 original size:22 final size:22
Alignment explanation
Indices: 29686--29748 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
29676 TATTTCATTC
*
29686 TTTACTGATTATCTTTTTAC-TT
1 TTTACTGATTA-CCTTTTACTTT
* *
29708 TTTACTGATTATC-ATTACTTT
1 TTTACTGATTACCTTTTACTTT
*
29729 TTTATTGATTACCTTTTACT
1 TTTACTGATTACCTTTTACT
29749 GATTACTCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 4 0.12
21 13 0.39
22 16 0.48
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (22 bp):
TTTACTGATTACCTTTTACTTT
Found at i:29767 original size:35 final size:34
Alignment explanation
Indices: 29635--29803 Score: 146
Period size: 35 Copynumber: 4.8 Consensus size: 34
29625 ATTTTGCTCT
*
29635 TTTTACTGATTATCATTACTTTTTTATTGATTACC
1 TTTTACTGATTATCTTTAC-TTTTTATTGATTACC
** ** *
29670 TTTTACT-ATTTCATTCTTTACTGATTATCTTTTTACT
1 TTTTACTGA-TT-A-TCTTTACTTTTTAT-TGATTACC
*
29707 TTTTACTGATTATCATTACTTTTTTATTGATTACC
1 TTTTACTGATTATCTTTAC-TTTTTATTGATTACC
**
29742 TTTTACTGATTACTCTTTACTTTTTA-CCATT-CTTC
1 TTTTACTGATTA-TCTTTACTTTTTATTGATTAC--C
29777 TTTTACTGATTACTCTTTACTTTTTAT
1 TTTTACTGATTA-TCTTTACTTTTTAT
29804 CATTGTACTC
Statistics
Matches: 109, Mismatches: 15, Indels: 19
0.76 0.10 0.13
Matches are distributed among these distances:
33 1 0.01
34 4 0.04
35 65 0.60
36 18 0.17
37 20 0.18
38 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.04, T:0.59
Consensus pattern (34 bp):
TTTTACTGATTATCTTTACTTTTTATTGATTACC
Found at i:29836 original size:50 final size:49
Alignment explanation
Indices: 29779--29874 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 49
29769 CATTCTTCTT
* * *
29779 TTACTGATTACTCTTTACTTTTTATCATTGTACTCTTTACTAATTACACC
1 TTACTGATTACTCTTTACTCTTTACCATT-TACCCTTTACTAATTACACC
* * *
29829 TTACTGATTATTCTTTACTCTTTACCATTTTCCCTTTACTGATTAC
1 TTACTGATTACTCTTTACTCTTTACCATTTACCCTTTACTAATTAC
29875 TAATTTTACT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
49 14 0.35
50 26 0.65
ACGTcount: A:0.22, C:0.23, G:0.04, T:0.51
Consensus pattern (49 bp):
TTACTGATTACTCTTTACTCTTTACCATTTACCCTTTACTAATTACACC
Found at i:30131 original size:55 final size:53
Alignment explanation
Indices: 30055--30161 Score: 178
Period size: 55 Copynumber: 2.0 Consensus size: 53
30045 AATTTACTTA
* *
30055 ATTAATCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTGACTCTG
1 ATTAATCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTG
30108 ATTAATCTATTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCT
1 ATTAATC--TTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCT
30162 TAACTATCAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
53 7 0.14
55 43 0.86
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.50
Consensus pattern (53 bp):
ATTAATCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTG
Found at i:30184 original size:71 final size:71
Alignment explanation
Indices: 30108--30311 Score: 390
Period size: 71 Copynumber: 2.9 Consensus size: 71
30098 CTTGACTCTG
*
30108 ATTAATCTATTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATCAAT
1 ATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATCAAT
30173 TTACTA
66 TTACTA
30179 ATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATCAAT
1 ATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATCAAT
30244 TTACTA
66 TTACTA
*
30250 ATTAATCTCTTTTTACTTAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACTATC
1 ATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATC
30312 TCTTTTACTT
Statistics
Matches: 131, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 131 1.00
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.46
Consensus pattern (71 bp):
ATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATCAAT
TTACTA
Found at i:30195 original size:55 final size:53
Alignment explanation
Indices: 30055--30182 Score: 158
Period size: 55 Copynumber: 2.4 Consensus size: 53
30045 AATTTACTTA
* *
30055 ATTAATCT-T-TTTACTTTATTACTGATTTACTGATTACTATTACCTTGACTC
1 ATTAATCTATATTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTC
*
30106 TGATTAATCTATTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTC
1 --ATTAATCTATATTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTC
30161 -TTAA-CTATCAATTTAC-TAATTA
1 ATTAATCTAT--ATTTACTTAATTA
30183 ATCTCTTTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
51 4 0.06
52 10 0.15
53 13 0.19
54 1 0.01
55 40 0.59
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.48
Consensus pattern (53 bp):
ATTAATCTATATTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTC
Found at i:30232 original size:126 final size:124
Alignment explanation
Indices: 29994--30232 Score: 351
Period size: 126 Copynumber: 1.9 Consensus size: 124
29984 ATTACTATCG
* * *
29994 TTTTACTTAATTGCTGATTTACTGATTACTACTTTTACTCCATTAATTATCAATTTACTTAATTA
1 TTTTACTTAATTACCGATTTACTGATTACTACTTTTACTCCATTAACTATCAATTTACTTAATTA
* *
30059 ATCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTAT
66 ATCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTGATTAATCTAT
30118 TTTTACTTAATTACCGATTTACTGATTACTA-TTACCTTGACT-C-TTAACTATCAATTTAC-TA
1 TTTTACTTAATTACCGATTTACTGATTACTACTT---TT-ACTCCATTAACTATCAATTTACTTA
30179 ATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCT
62 ATTAA--TCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCT
30233 TAACTATCAA
Statistics
Matches: 104, Mismatches: 5, Indels: 10
0.87 0.04 0.08
Matches are distributed among these distances:
123 2 0.02
124 36 0.35
125 15 0.14
126 48 0.46
127 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (124 bp):
TTTTACTTAATTACCGATTTACTGATTACTACTTTTACTCCATTAACTATCAATTTACTTAATTA
ATCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTGATTAATCTAT
Found at i:30334 original size:54 final size:55
Alignment explanation
Indices: 30254--30365 Score: 181
Period size: 54 Copynumber: 2.1 Consensus size: 55
30244 TTACTAATTA
*
30254 ATCTCTTTTTACTTAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACT
1 ATCTCTTTTTACTTAATTACCAATTTACTGACTACTATTACCTTGACTCTTAACT
* * *
30309 ATCTC-TTTTACTTACTTACTAATTTACTGATTACTATTACCTTGACTCTTAACT
1 ATCTCTTTTTACTTAATTACCAATTTACTGACTACTATTACCTTGACTCTTAACT
30363 ATC
1 ATC
30366 AATTTACTGA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
54 48 0.91
55 5 0.09
ACGTcount: A:0.26, C:0.23, G:0.04, T:0.46
Consensus pattern (55 bp):
ATCTCTTTTTACTTAATTACCAATTTACTGACTACTATTACCTTGACTCTTAACT
Found at i:30359 original size:196 final size:195
Alignment explanation
Indices: 29954--30422 Score: 583
Period size: 196 Copynumber: 2.4 Consensus size: 195
29944 CTTACTATTT
* ** * * *
29954 TTACCTTGACTCTTAATTATTGATTTACTGATTACTATCGTTTTACTTAATTGCTGATTTACTGA
1 TTACCTTGACTCTTAACTATCAATTTACTGATTAATATCGTTTTACTTAATTACCGATTTACTGA
* * *
30019 TTACTACTTTTACTCCATTAATTATCAATTTACTTAATTAATCTTTTTACTTTATTACTGATTTA
66 TTACTACTTTTACTCCATTAACTATCAATTTACTTAATTAATCTTTTTACTTAATTACCGATTTA
* * * * *
30084 CTGATTACTATTACCTTGACTCTGATTAATCTATTTTTACTTAATTACCGATTTACTGATTACTA
131 CTGACTACTATTACCTTGACTCTAACTAATCTACTTTTACTTAATTACCAATTTACTGATTACTA
* * *
30149 TTACCTTGACTCTTAACTATCAATTTACTAATTAATCTCTTTTTACTTAATTACCGATTTACTGA
1 TTACCTTGACTCTTAACTATCAATTTACTGATTAATATCGTTTTACTTAATTACCGATTTACTGA
30214 TTACTA-TTACCTTGACT-C-TTAACTATCAATTTAC-TAATTAATCTCTTTTTACTTAATTACC
66 TTACTACTT---TT-ACTCCATTAACTATCAATTTACTTAATTAA--TCTTTTTACTTAATTACC
* *
30275 GATTTACTGACTACTATTACCTTGACTCTTAACT-ATCT-CTTTTACTTACTTACTAATTTACTG
125 GATTTACTGACTACTATTACCTTGACTC-TAACTAATCTACTTTTACTTAATTACCAATTTACTG
30338 ATTACTA
189 ATTACTA
* * * * *
30345 TTACCTTGACTCTTAACTATCAATTTACTGATTACTATC-TTTGACTCTTAACTATCAATTTACT
1 TTACCTTGACTCTTAACTATCAATTTACTGATTAATATCGTTTTA--CTTAATTACCGATTTACT
30409 GATTACTATCTTTT
64 GATTACTA-CTTTT
30423 TACTTAATTG
Statistics
Matches: 237, Mismatches: 26, Indels: 21
0.83 0.09 0.07
Matches are distributed among these distances:
194 2 0.01
195 73 0.31
196 81 0.34
197 73 0.31
198 6 0.03
199 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.48
Consensus pattern (195 bp):
TTACCTTGACTCTTAACTATCAATTTACTGATTAATATCGTTTTACTTAATTACCGATTTACTGA
TTACTACTTTTACTCCATTAACTATCAATTTACTTAATTAATCTTTTTACTTAATTACCGATTTA
CTGACTACTATTACCTTGACTCTAACTAATCTACTTTTACTTAATTACCAATTTACTGATTACTA
Found at i:30396 original size:35 final size:35
Alignment explanation
Indices: 30329--30421 Score: 159
Period size: 35 Copynumber: 2.6 Consensus size: 35
30319 CTTACTTACT
*
30329 AATTTACTGATTACTATTACCTTGACTCTTAACTATC
1 AATTTACTGATTACTA-T-CTTTGACTCTTAACTATC
30366 AATTTACTGATTACTATCTTTGACTCTTAACTATC
1 AATTTACTGATTACTATCTTTGACTCTTAACTATC
30401 AATTTACTGATTACTATCTTT
1 AATTTACTGATTACTATCTTT
30422 TTACTTAATT
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
35 38 0.69
36 1 0.02
37 16 0.29
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.46
Consensus pattern (35 bp):
AATTTACTGATTACTATCTTTGACTCTTAACTATC
Found at i:30399 original size:54 final size:54
Alignment explanation
Indices: 30276--30381 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
30266 TTAATTACCG
* ** *
30276 ATTTACTGACTACTATTACCTTGACTCTTAACTATCTCTTTTACTTACTTACTA
1 ATTTACTGATTACTATTACCTTGACTCTTAACTATCTAATTTACTGACTTACTA
30330 ATTTACTGATTACTATTACCTTGACTCTTAACTATC-AATTTACTGA-TTACTA
1 ATTTACTGATTACTATTACCTTGACTCTTAACTATCTAATTTACTGACTTACTA
30382 TCTTTGACTC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 6 0.12
53 7 0.15
54 35 0.73
ACGTcount: A:0.28, C:0.22, G:0.05, T:0.45
Consensus pattern (54 bp):
ATTTACTGATTACTATTACCTTGACTCTTAACTATCTAATTTACTGACTTACTA
Found at i:30426 original size:18 final size:17
Alignment explanation
Indices: 30368--30422 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
30358 TAACTATCAA
30368 TTTACTGATTACTATCT
1 TTTACTGATTACTATCT
* * *
30385 TTGACT-CTTAACTATCAA
1 TTTACTGATT-ACTATC-T
30403 TTTACTGATTACTATCT
1 TTTACTGATTACTATCT
30420 TTT
1 TTT
30423 TACTTAATTG
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
16 2 0.07
17 14 0.48
18 11 0.38
19 2 0.07
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.51
Consensus pattern (17 bp):
TTTACTGATTACTATCT
Found at i:30489 original size:69 final size:68
Alignment explanation
Indices: 30367--30520 Score: 204
Period size: 69 Copynumber: 2.2 Consensus size: 68
30357 TTAACTATCA
*
30367 ATTTACTGATTACTATCTTTGACTCTTAACTATCAATTTACTGATTACTATCTTTTTACTTAATT
1 ATTTACTGATTACTATCTTTGACTCTTAACTATCAATTTACTAATTAC-ATCTTTTTACTTAATT
*
30432 GCTG
65 ACTG
* * * *
30436 ATTTATTGATTACTA-CTTTTACTCCCTTAATTATCAATTTACTTAATTA-ATCTTTTTACTTTA
1 ATTTACTGATTACTATCTTTGACT--CTTAACTATCAATTTAC-TAATTACATCTTTTTACTTAA
30499 TTACTG
63 TTACTG
30505 ATTTACTGATTACTAT
1 ATTTACTGATTACTAT
30521 TTCCTTGACT
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
68 7 0.09
69 46 0.62
70 16 0.22
71 5 0.07
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.51
Consensus pattern (68 bp):
ATTTACTGATTACTATCTTTGACTCTTAACTATCAATTTACTAATTACATCTTTTTACTTAATTA
CTG
Found at i:30565 original size:229 final size:230
Alignment explanation
Indices: 30134--30586 Score: 630
Period size: 229 Copynumber: 2.0 Consensus size: 230
30124 TTAATTACCG
*
30134 ATTTACTGATTACTATTACCTTGACTCTTAACTATCAATTTACTAATTAATCTCTTTTTACTTAA
1 ATTTACTGATTACTATTACCTTGACTCTTAACTATCAATTTACTAATTAATATCTTTTTACTTAA
30199 TTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATCAATTTACTAATTAATCTCTTTTT
66 TTACCGATTTACTGATTACTATT--CTTGACTCTTAACTATCAATTTACTAATTAA-CTCTTTTT
*
30264 ACTTAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACTATCTCTTTTACTTACTTACT
128 ACTTAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACTATCTCTTTTACTTAATTACT
30329 AATTTACTGATTACTATTACCTTGACTCTTAACTATCA
193 AATTTACTGATTACTATTACCTTGACTCTTAACTATCA
* * *
30367 ATTTACTGATTACTA-T-CTTTGACTCTTAACTATCAATTTACTGATTACTATCTTTTTACTTAA
1 ATTTACTGATTACTATTACCTTGACTCTTAACTATCAATTTACTAATTAATATCTTTTTACTTAA
* * * *
30430 TTGCTGATTTATTGATTACTACTT-TT-ACTCCCTTAATTATCAATTTACTTAATTAA-TCTTTT
66 TTACCGATTTACTGATTACTA-TTCTTGACT--CTTAACTATCAATTTAC-TAATTAACTCTTTT
* * * * * *
30492 TACTTTATTACTGATTTACTGATTACTATTTCCTTGACTC-TGATTAATCTCTTTTACTTAATTA
127 TACTTAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACT-ATCTCTTTTACTTAATTA
* * *
30556 GTGATTTACTGATTACTATTTCCTTGACTCT
191 CTAATTTACTGATTACTATTACCTTGACTCT
30587 GATTAATCTT
Statistics
Matches: 197, Mismatches: 18, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
228 6 0.03
229 89 0.45
230 16 0.08
231 68 0.35
232 3 0.02
233 15 0.08
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.48
Consensus pattern (230 bp):
ATTTACTGATTACTATTACCTTGACTCTTAACTATCAATTTACTAATTAATATCTTTTTACTTAA
TTACCGATTTACTGATTACTATTCTTGACTCTTAACTATCAATTTACTAATTAACTCTTTTTACT
TAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACTATCTCTTTTACTTAATTACTAAT
TTACTGATTACTATTACCTTGACTCTTAACTATCA
Found at i:30638 original size:55 final size:54
Alignment explanation
Indices: 30481--30641 Score: 252
Period size: 54 Copynumber: 3.0 Consensus size: 54
30471 AATTTACTTA
*
30481 ATTAATC-TTTTTACTTTATTACTGATTTACTGATTACTATTTCCTTGACTCTG
1 ATTAATCTTTTTTACTTAATTACTGATTTACTGATTACTATTTCCTTGACTCTG
* *
30534 ATTAATCTCTTTTACTTAATTAGTGATTTACTGATTACTATTTCCTTGACTCTG
1 ATTAATCTTTTTTACTTAATTACTGATTTACTGATTACTATTTCCTTGACTCTG
* * *
30588 ATTAATCTTTTTTCACTTAATTACCGATTTACTGATTACTATTACTTTGACTCT
1 ATTAATCTTTTTT-ACTTAATTACTGATTTACTGATTACTATTTCCTTGACTCT
30642 TAATTACTTA
Statistics
Matches: 98, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 7 0.07
54 55 0.56
55 36 0.37
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.51
Consensus pattern (54 bp):
ATTAATCTTTTTTACTTAATTACTGATTTACTGATTACTATTTCCTTGACTCTG
Found at i:30646 original size:37 final size:37
Alignment explanation
Indices: 30603--30683 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
30593 TCTTTTTTCA
* *
30603 CTTAATTACCGATTTACTGATTACTATTACTTTGACT
1 CTTAATTACCGAATTACTGATTACCATTACTTTGACT
** *
30640 CTTAATTACTTAATTACTGATTACCGTTACTTTGACT
1 CTTAATTACCGAATTACTGATTACCATTACTTTGACT
30677 CTTAATT
1 CTTAATT
30684 TATTGGAGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.47
Consensus pattern (37 bp):
CTTAATTACCGAATTACTGATTACCATTACTTTGACT
Found at i:34322 original size:59 final size:59
Alignment explanation
Indices: 34250--34369 Score: 213
Period size: 59 Copynumber: 2.0 Consensus size: 59
34240 AAGGACTTAA
*
34250 GCTCTATGATTAAAATGCAACACTACTAAATTACTAAATGAAAAGAAACCATGCCATAT
1 GCTCTATGATTAAAATGCAACACTACTAAATTACTAAATGAAAAGAAACCATGCAATAT
* *
34309 GCTCTATGATTAAAATGCAACACTACTAAATTACTTAATGAAAAGAAATCATGCAATAT
1 GCTCTATGATTAAAATGCAACACTACTAAATTACTAAATGAAAAGAAACCATGCAATAT
34368 GC
1 GC
34370 GAAAATGCTA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (59 bp):
GCTCTATGATTAAAATGCAACACTACTAAATTACTAAATGAAAAGAAACCATGCAATAT
Found at i:34933 original size:43 final size:43
Alignment explanation
Indices: 34886--34984 Score: 146
Period size: 43 Copynumber: 2.3 Consensus size: 43
34876 TTTGCTAATA
* *
34886 GCTAAAAATTGAGAGACCTGTTCTGAAGTTGA-TTTGGATAACT
1 GCTAAAAATTGAGAGACCTATTCTAAAGTTGACTTT-GATAACT
34929 GCTAAAAATTGAGAGACCTATTCTAAAGTTGACTTTGATAACT
1 GCTAAAAATTGAGAGACCTATTCTAAAGTTGACTTTGATAACT
*
34972 GCTGAAAACTTGA
1 GCT-AAAAATTGA
34985 TGATTTGAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
43 40 0.78
44 11 0.22
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (43 bp):
GCTAAAAATTGAGAGACCTATTCTAAAGTTGACTTTGATAACT
Found at i:35050 original size:22 final size:22
Alignment explanation
Indices: 35022--35098 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
35012 AGAATTACGG
35022 CCCGGAGGCTTCTGATTTCATA
1 CCCGGAGGCTTCTGATTTCATA
* * *
35044 CCCGGAGGCTGCCAGAATT-ACTA
1 CCCGGAGGCT-TCTGATTTCA-TA
* * **
35067 CCCGGAGGTTTCTGATATCACG
1 CCCGGAGGCTTCTGATTTCATA
35089 CCCGGAGGCT
1 CCCGGAGGCT
35099 ATCAGGAATT
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
22 24 0.59
23 17 0.41
ACGTcount: A:0.19, C:0.30, G:0.27, T:0.23
Consensus pattern (22 bp):
CCCGGAGGCTTCTGATTTCATA
Found at i:35124 original size:46 final size:46
Alignment explanation
Indices: 34998--35134 Score: 127
Period size: 45 Copynumber: 3.0 Consensus size: 46
34988 TTTGAAGTAT
* * ** * * *
34998 GCCCGGAGGCAATCAGAATTACGGCCCGGAGGCTT-CTGATTTCAT
1 GCCCGGAGGCTACCAGAATTACTACCCGGAGGTTTCCTGATATCAC
* *
35043 ACCCGGAGGCTGCCAGAATTACTACCCGGAGGTTT-CTGATATCAC
1 GCCCGGAGGCTACCAGAATTACTACCCGGAGGTTTCCTGATATCAC
* * *
35088 GCCCGGAGGCTATCAGGAATTGCTACCCGG-GTGTTTCCTGATTTCAC
1 GCCCGGAGGCTACCA-GAATTACTACCCGGAG-GTTTCCTGATATCAC
35135 TAAAAACATC
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
45 49 0.65
46 17 0.23
47 9 0.12
ACGTcount: A:0.21, C:0.28, G:0.27, T:0.24
Consensus pattern (46 bp):
GCCCGGAGGCTACCAGAATTACTACCCGGAGGTTTCCTGATATCAC
Found at i:36923 original size:26 final size:25
Alignment explanation
Indices: 36889--36937 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
36879 AGGCTGAGTT
*
36889 TTTTCTTTTTCCTCCTTCTTCTTTTA
1 TTTTATTTTTCCTCCTT-TTCTTTTA
*
36915 TTTTATTTTTCTTCCTTTTCTTT
1 TTTTATTTTTCCTCCTTTTCTTT
36938 GAGTTGAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTATTTTTCCTCCTTTTCTTTTA
Found at i:37442 original size:22 final size:22
Alignment explanation
Indices: 37416--37770 Score: 236
Period size: 22 Copynumber: 16.2 Consensus size: 22
37406 TTACTCTTGT
*
37416 TGATTACCTTCTTACTTTTTAC
1 TGATTACCTTTTTACTTTTTAC
*
37438 TGATTACCATTTTACTCTTTTAC
1 TGATTACCTTTTTACT-TTTTAC
* *
37461 TGATTACTATTTTCTGCTCCTTTTTTAC
1 TGATTAC--CTTT-T--TAC-TTTTTAC
*
37489 TGATTA-CTCTTTTAGTTTTTAC
1 TGATTACCT-TTTTACTTTTTAC
* *
37511 TGATTACC-TTTTGCGTTTTAC
1 TGATTACCTTTTTACTTTTTAC
*
37532 TGATTACCTTTTTA-TTTCTTGC
1 TGATTACCTTTTTACTTT-TTAC
* *
37554 TGATTAGCTTTTTACTCTTTAC
1 TGATTACCTTTTTACTTTTTAC
** *
37576 TGACCACCTTTTTAC-TCTTAC
1 TGATTACCTTTTTACTTTTTAC
* *
37597 TGATTTCC-TTTTACTTCTTAC
1 TGATTACCTTTTTACTTTTTAC
* *
37618 TTATTA-CTTTTTAC-TCTTAC
1 TGATTACCTTTTTACTTTTTAC
*
37638 TGATTA-CTATTTACTTTTTAC
1 TGATTACCTTTTTACTTTTTAC
*
37659 TGACTA-CTATTTTA-TTCTTGT-C
1 TGATTACCT-TTTTACTT-TT-TAC
* *
37681 -GATTACCTTCTTACTTTTTAA
1 TGATTACCTTTTTACTTTTTAC
*
37702 TGATTA-CTATTTTACTCTTTAC
1 TGATTACCT-TTTTACTTTTTAC
* * **
37724 TAATTACCATTTTACCCTTT-C
1 TGATTACCTTTTTACTTTTTAC
* *
37745 AG-GTACCTTTTTACTTTTTAC
1 TGATTACCTTTTTACTTTTTAC
37766 TGATT
1 TGATT
37771 GCATGCTATT
Statistics
Matches: 258, Mismatches: 49, Indels: 52
0.72 0.14 0.14
Matches are distributed among these distances:
20 39 0.15
21 74 0.29
22 104 0.40
23 19 0.07
25 4 0.02
26 3 0.01
28 14 0.05
29 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.54
Consensus pattern (22 bp):
TGATTACCTTTTTACTTTTTAC
Found at i:37467 original size:15 final size:15
Alignment explanation
Indices: 37449--37502 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
37439 GATTACCATT
37449 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
37464 TTACTATTTT-CTG-
1 TTACTCTTTTACTGA
* * *
37477 CTCCTTTTTTACTGA
1 TTACTCTTTTACTGA
37492 TTACTCTTTTA
1 TTACTCTTTTA
37503 GTTTTTACTG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 7 0.23
14 6 0.20
15 17 0.57
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:37530 original size:43 final size:41
Alignment explanation
Indices: 37483--37738 Score: 173
Period size: 43 Copynumber: 6.0 Consensus size: 41
37473 TCTGCTCCTT
*
37483 TTTTACTGATTACTCTTTTAGTTTTTACTGATTACCTTTTGC
1 TTTTACTGATTACTCTTTTA-TTTTTACTGATTACCTTTTAC
* *
37525 GTTTTACTGATTAC-CTTTTTATTTCTTGCTGATTAGCTTTTTAC
1 -TTTTACTGATTACTC-TTTTATTT-TTACTGATTA-CCTTTTAC
** * * *
37569 TCTTTACTGACCAC-CTTTTTACTCTTACTGATTTCCTTTTAC
1 T-TTTACTGATTACTC-TTTTATTTTTACTGATTACCTTTTAC
* * *
37611 TTCTTACTTATTACT-TTTTACTCTTACTGATTA-CTATTTAC
1 TT-TTACTGATTACTCTTTTATTTTTACTGATTACCT-TTTAC
* *
37652 TTTTTACTGACTACTATTTTATTCTTGT-C-GATTACCTTCTTAC
1 -TTTTACTGATTACTCTTTTATT-TT-TACTGATTACCTT-TTAC
* * * *
37695 TTTTTAATGATTACTATTTTACTCTTTACTAATTACCATTTTAC
1 -TTTTACTGATTACTCTTTTA-TTTTTACTGATTACC-TTTTAC
37739 CCTTTCAGGT
Statistics
Matches: 174, Mismatches: 22, Indels: 33
0.76 0.10 0.14
Matches are distributed among these distances:
40 2 0.01
41 33 0.19
42 35 0.20
43 66 0.38
44 36 0.21
45 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.55
Consensus pattern (41 bp):
TTTTACTGATTACTCTTTTATTTTTACTGATTACCTTTTAC
Found at i:38016 original size:55 final size:55
Alignment explanation
Indices: 37955--38150 Score: 338
Period size: 55 Copynumber: 3.6 Consensus size: 55
37945 CATTTTAACT
* *
37955 CTTAATTATCGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
38010 CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
*
38065 CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCCCTTTTTA
1 CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
** *
38120 CTTAATTATTGATTTACTGATTTCTATTACT
1 CTTAATTACCGATTTACTGATTACTATTACT
38151 CTTTACTGAT
Statistics
Matches: 135, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 135 1.00
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (55 bp):
CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
Found at i:38206 original size:22 final size:22
Alignment explanation
Indices: 38146--38207 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
38136 CTGATTTCTA
**
38146 TTACTCTTTACTGATTATCACT
1 TTACTCTTTACTGATTGCCACT
*
38168 TTACTCTTTACTGATTGCCATT
1 TTACTCTTTACTGATTGCCACT
38190 TTAC-CTTTTACTGATTGC
1 TTACTC-TTTACTGATTGC
38208 ATCTTTCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 1 0.03
22 35 0.97
ACGTcount: A:0.19, C:0.23, G:0.08, T:0.50
Consensus pattern (22 bp):
TTACTCTTTACTGATTGCCACT
Found at i:42126 original size:27 final size:27
Alignment explanation
Indices: 42088--42155 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
42078 GAATGTGCAA
* *
42088 AATGACCAAAATGCCCCTTAGTCTAAG
1 AATGACCAAAATGCCCCTAAATCTAAG
* *
42115 AATGACCAAAATACCCCTAAATGTAAG
1 AATGACCAAAATGCCCCTAAATCTAAG
*
42142 AAAGACCAAAATGC
1 AATGACCAAAATGC
42156 TAATTAGACC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.46, C:0.24, G:0.13, T:0.18
Consensus pattern (27 bp):
AATGACCAAAATGCCCCTAAATCTAAG
Found at i:42817 original size:14 final size:13
Alignment explanation
Indices: 42792--42849 Score: 64
Period size: 14 Copynumber: 4.3 Consensus size: 13
42782 TAAAAACTCA
42792 AAAACT-TTTTTG
1 AAAACTATTTTTG
42804 AAAACTCATTTTTG
1 AAAACT-ATTTTTG
*
42818 AAAACTTTTTCTTG
1 AAAACTATTT-TTG
*
42832 AAAACAATTTTTTG
1 AAAACTA-TTTTTG
42846 AAAA
1 AAAA
42850 ATATCTCTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
12 6 0.15
13 3 0.08
14 27 0.69
15 3 0.08
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (13 bp):
AAAACTATTTTTG
Found at i:42842 original size:26 final size:25
Alignment explanation
Indices: 42792--42842 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
42782 TAAAAACTCA
*
42792 AAAACTTTTTTGAAAACTCATTTTTG
1 AAAACTTTTTTGAAAAC-CAATTTTG
42818 AAAACTTTTTCTTGAAAA-CAATTTT
1 AAAAC-TTTT-TTGAAAACCAATTTT
42843 TTGAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 11 0.50
27 4 0.18
28 7 0.32
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (25 bp):
AAAACTTTTTTGAAAACCAATTTTG
Found at i:42843 original size:28 final size:26
Alignment explanation
Indices: 42792--42849 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 26
42782 TAAAAACTCA
*
42792 AAAACTTTTTTGAAAACTCATTTTTG
1 AAAACTTTTTTGAAAACTAATTTTTG
42818 AAAACTTTTTCTTGAAAAC-AATTTTTTG
1 AAAAC-TTTT-TTGAAAACTAA-TTTTTG
42846 AAAA
1 AAAA
42850 ATATCTCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 5 0.18
27 5 0.18
28 18 0.64
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (26 bp):
AAAACTTTTTTGAAAACTAATTTTTG
Found at i:45564 original size:22 final size:22
Alignment explanation
Indices: 45539--45684 Score: 165
Period size: 22 Copynumber: 6.7 Consensus size: 22
45529 TATTTATTAC
*
45539 TACTCTTTACTAATTACTATTT
1 TACTCTTTACTGATTACTATTT
*
45561 TACTCTTTACTGATTACCT-TCT
1 TACTCTTTACTGATTA-CTATTT
*
45583 TACTTTTTACTGATTACTATTT
1 TACTCTTTACTGATTACTATTT
*
45605 TACTCTTTACTGATTACCATTT
1 TACTCTTTACTGATTACTATTT
* * * *
45627 TGCTC-TCATTGATTACCATTT
1 TACTCTTTACTGATTACTATTT
*
45648 TGCTC-TTACTGATTACTATTT
1 TACTCTTTACTGATTACTATTT
45669 TAC-CTTTTACTGATTA
1 TACTC-TTTACTGATTA
45685 TCATTACTTT
Statistics
Matches: 107, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
20 1 0.01
21 36 0.34
22 68 0.64
23 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.52
Consensus pattern (22 bp):
TACTCTTTACTGATTACTATTT
Found at i:45641 original size:21 final size:21
Alignment explanation
Indices: 45591--45669 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
45581 CTTACTTTTT
* * *
45591 ACTGATTACTATTTTACTCTTT
1 ACTGATTACCATTTTGCTC-TC
45613 ACTGATTACCATTTTGCTCTC
1 ACTGATTACCATTTTGCTCTC
* *
45634 ATTGATTACCATTTTGCTCTT
1 ACTGATTACCATTTTGCTCTC
*
45655 ACTGATTACTATTTT
1 ACTGATTACCATTTT
45670 ACCTTTTACT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 33 0.66
22 17 0.34
ACGTcount: A:0.22, C:0.20, G:0.08, T:0.51
Consensus pattern (21 bp):
ACTGATTACCATTTTGCTCTC
Found at i:45702 original size:64 final size:65
Alignment explanation
Indices: 45588--45783 Score: 199
Period size: 72 Copynumber: 2.9 Consensus size: 65
45578 CTTCTTACTT
* * *
45588 TTTACTGATTACTATTTTA-CTCTTTACTGATTACCATT--TTGCTCTCATTGATTACCATTTTG
1 TTTACTGATTACTATTTTACCT-TTTACTGATTATCATTACTT--TTTTATTGATTACCATTTT-
45650 C-TC
62 CATC
45653 -TTACTGATTACTATTTTACCTTTTACTGATTATCATTACTTTTTTATTGATTACCTTTTACTAT
1 TTTACTGATTACTATTTTACCTTTTACTGATTATCATTACTTTTTTATTGATTACC----A-T-T
45717 TTCATTC
60 TTCA-TC
*
45724 TTTACTGATTATCT-TTTTACTTTTTACTGATTATCATTACTTTTTTATTGATTACC-TTTT
1 TTTACTGATTA-CTATTTTACCTTTTACTGATTATCATTACTTTTTTATTGATTACCATTTT
45784 ACTGATTACT
Statistics
Matches: 114, Mismatches: 4, Indels: 26
0.79 0.03 0.18
Matches are distributed among these distances:
64 45 0.39
65 5 0.04
66 3 0.03
68 1 0.01
69 2 0.02
70 3 0.03
71 2 0.02
72 51 0.45
73 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.06, T:0.56
Consensus pattern (65 bp):
TTTACTGATTACTATTTTACCTTTTACTGATTATCATTACTTTTTTATTGATTACCATTTTCATC
Found at i:45707 original size:35 final size:35
Alignment explanation
Indices: 45668--45804 Score: 163
Period size: 35 Copynumber: 3.8 Consensus size: 35
45658 GATTACTATT
45668 TTACCTTTTACTGATTATCATTACTTTTTTATTGA
1 TTACCTTTTACTGATTATCATTACTTTTTTATTGA
**
45703 TTACCTTTTACT-ATT-TCATT-CTTTACTGATTATCTTT
1 TTACCTTTTACTGATTATCATTACTTT--T--TTAT-TGA
*
45740 TTACTTTTTACTGATTATCATTACTTTTTTATTGA
1 TTACCTTTTACTGATTATCATTACTTTTTTATTGA
*
45775 TTACCTTTTACTGATTACTCTTTACTTTTT
1 TTACCTTTTACTGATTA-TCATTACTTTTT
45805 ACCATTCTTC
Statistics
Matches: 86, Mismatches: 7, Indels: 17
0.78 0.06 0.15
Matches are distributed among these distances:
32 4 0.05
33 5 0.06
34 4 0.05
35 29 0.34
36 19 0.22
37 12 0.14
38 4 0.05
39 5 0.06
40 4 0.05
ACGTcount: A:0.20, C:0.16, G:0.04, T:0.59
Consensus pattern (35 bp):
TTACCTTTTACTGATTATCATTACTTTTTTATTGA
Found at i:45742 original size:72 final size:72
Alignment explanation
Indices: 45653--45839 Score: 249
Period size: 72 Copynumber: 2.6 Consensus size: 72
45643 CATTTTGCTC
45653 TTACTGATTACTATTTTACCTTTTACTGATTATCATTACTTTTTTATTGATTACCTTTTACTATT
1 TTACTGATTACTATTTTACCTTTTACTGATTATCATTACTTTTTTATTGATTACCTTTTACTATT
45718 TCATTCT
66 TCATTCT
*
45725 TTACTGATTATCT-TTTTACTTTTTACTGATTATCATTACTTTTTTATTGATTACCTTTTACTGA
1 TTACTGATTA-CTATTTTACCTTTTACTGATTATCATTACTTTTTTATTGATTACCTTTTACT-A
*
45789 -TT-ACTCT
64 TTTCATTCT
** * *
45796 TTACTTTTTACCATTCTT--CTTTTACTGATTACTCTTTACTTTTT
1 TTACTGATTACTATT-TTACCTTTTACTGATTA-TCATTACTTTTT
45840 ATCATTGTAC
Statistics
Matches: 103, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
70 13 0.13
71 25 0.24
72 62 0.60
73 3 0.03
ACGTcount: A:0.20, C:0.17, G:0.04, T:0.58
Consensus pattern (72 bp):
TTACTGATTACTATTTTACCTTTTACTGATTATCATTACTTTTTTATTGATTACCTTTTACTATT
TCATTCT
Found at i:45749 original size:22 final size:23
Alignment explanation
Indices: 45724--45783 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
45714 TATTTCATTC
45724 TTTACTGATTATCTTTTTAC-TT
1 TTTACTGATTATCTTTTTACTTT
*
45746 TTTACTGATTATC--ATTACTTT
1 TTTACTGATTATCTTTTTACTTT
* *
45767 TTTATTGATTACCTTTT
1 TTTACTGATTATCTTTT
45784 ACTGATTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 4 0.13
21 13 0.42
22 13 0.42
23 1 0.03
ACGTcount: A:0.20, C:0.13, G:0.05, T:0.62
Consensus pattern (23 bp):
TTTACTGATTATCTTTTTACTTT
Found at i:45783 original size:14 final size:15
Alignment explanation
Indices: 45759--45797 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
45749 ACTGATTATC
* *
45759 ATTACTTTTTTATTG
1 ATTACTCTTTTACTG
45774 ATTAC-CTTTTACTG
1 ATTACTCTTTTACTG
45788 ATTACTCTTT
1 ATTACTCTTT
45798 ACTTTTTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.21, C:0.15, G:0.05, T:0.59
Consensus pattern (15 bp):
ATTACTCTTTTACTG
Found at i:45785 original size:22 final size:22
Alignment explanation
Indices: 45724--45786 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
45714 TATTTCATTC
*
45724 TTTACTGATTATCTTTTTAC-TT
1 TTTACTGATTA-CCTTTTACTTT
* *
45746 TTTACTGATTATC-ATTACTTT
1 TTTACTGATTACCTTTTACTTT
*
45767 TTTATTGATTACCTTTTACT
1 TTTACTGATTACCTTTTACT
45787 GATTACTCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 4 0.12
21 13 0.39
22 16 0.48
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (22 bp):
TTTACTGATTACCTTTTACTTT
Found at i:45805 original size:35 final size:34
Alignment explanation
Indices: 45668--45841 Score: 156
Period size: 35 Copynumber: 4.9 Consensus size: 34
45658 GATTACTATT
*
45668 TTACCTTTTACTGATTATCATTACTTTTTTATTGA
1 TTACCTTTTACTGATTATCTTTAC-TTTTTATTGA
** **
45703 TTACCTTTTACT-ATTTCATTCTTTACTGATTATCTTT
1 TTACCTTTTACTGA-TT-A-TCTTTACTTTTTAT-TGA
* *
45740 TTACTTTTTACTGATTATCATTACTTTTTTATTGA
1 TTACCTTTTACTGATTATCTTTAC-TTTTTATTGA
**
45775 TTACCTTTTACTGATTACTCTTTACTTTTTA-CCA
1 TTACCTTTTACTGATTA-TCTTTACTTTTTATTGA
45809 TT-CTTCTTTTACTGATTACTCTTTACTTTTTAT
1 TTAC--CTTTTACTGATTA-TCTTTACTTTTTAT
45842 CATTGTACTC
Statistics
Matches: 114, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
33 1 0.01
34 4 0.04
35 70 0.61
36 18 0.16
37 20 0.18
38 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.04, T:0.59
Consensus pattern (34 bp):
TTACCTTTTACTGATTATCTTTACTTTTTATTGA
Found at i:45874 original size:50 final size:49
Alignment explanation
Indices: 45817--45912 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 49
45807 CATTCTTCTT
* * *
45817 TTACTGATTACTCTTTACTTTTTATCATTGTACTCTTTACTAATTACACC
1 TTACTGATTACTCTTTACTCTTTACCATT-TACCCTTTACTAATTACACC
* * *
45867 TTACTGATTATTCTTTACTCTTTACCATTTTCCCTTTACTGATTAC
1 TTACTGATTACTCTTTACTCTTTACCATTTACCCTTTACTAATTAC
45913 TAATATTACT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
49 14 0.35
50 26 0.65
ACGTcount: A:0.22, C:0.23, G:0.04, T:0.51
Consensus pattern (49 bp):
TTACTGATTACTCTTTACTCTTTACCATTTACCCTTTACTAATTACACC
Found at i:46027 original size:40 final size:36
Alignment explanation
Indices: 45957--46133 Score: 122
Period size: 34 Copynumber: 5.0 Consensus size: 36
45947 GATTAATCCA
* *
45957 TTTACTT--TTAATTACTGATTTGCTGCTTACTATT
1 TTTACTTACTTAATTACTGATTTACTGATTACTATT
* *
45991 TTTACCTTGACTCTTAATTATTGATTTACTGATTACTATC
1 TTTA-CTT-A--CTTAATTACTGATTTACTGATTACTATT
* *
46031 TTT--TTACTTAATTGCTGATTTACTGATTACTACT
1 TTTACTTACTTAATTACTGATTTACTGATTACTATT
* * * *
46065 TTTAC-TCCATTAATTA-TCAATTTACTTAATTA--ATC
1 TTTACTTAC-TTAATTACT-GATTTAC-TGATTACTATT
*
46100 TTT--TTACTTTATTACTGATTTACTGATTACTATT
1 TTTACTTACTTAATTACTGATTTACTGATTACTATT
46134 ACCTTGACTC
Statistics
Matches: 109, Mismatches: 19, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
32 5 0.05
33 12 0.11
34 36 0.33
35 10 0.09
36 13 0.12
37 7 0.06
40 26 0.24
ACGTcount: A:0.25, C:0.15, G:0.06, T:0.53
Consensus pattern (36 bp):
TTTACTTACTTAATTACTGATTTACTGATTACTATT
Found at i:46169 original size:55 final size:53
Alignment explanation
Indices: 46093--46199 Score: 178
Period size: 55 Copynumber: 2.0 Consensus size: 53
46083 AATTTACTTA
* *
46093 ATTAATCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTGACTCTG
1 ATTAATCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTG
46146 ATTAATCTATTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCT
1 ATTAATC--TTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCT
46200 TAACTATCAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
53 7 0.14
55 43 0.86
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.50
Consensus pattern (53 bp):
ATTAATCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTG
Found at i:46233 original size:55 final size:53
Alignment explanation
Indices: 46093--46220 Score: 158
Period size: 55 Copynumber: 2.4 Consensus size: 53
46083 AATTTACTTA
* *
46093 ATTAATCT-T-TTTACTTTATTACTGATTTACTGATTACTATTACCTTGACTC
1 ATTAATCTATATTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTC
*
46144 TGATTAATCTATTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTC
1 --ATTAATCTATATTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTC
46199 -TTAA-CTATCAATTTAC-TAATTA
1 ATTAATCTAT--ATTTACTTAATTA
46221 ATCTCTTTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
51 4 0.06
52 10 0.15
53 13 0.19
54 1 0.01
55 40 0.59
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.48
Consensus pattern (53 bp):
ATTAATCTATATTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTC
Found at i:46303 original size:126 final size:127
Alignment explanation
Indices: 46072--46417 Score: 351
Period size: 126 Copynumber: 2.7 Consensus size: 127
46062 ACTTTTACTC
* *
46072 CATTAATTATCAATTTACTTAATTAA--TCTTTTTACTTTATTACTGATTTACTGATTACTATTA
1 CATTAACTATCAATTTAC-TAATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTA
* * *
46135 CCTTGACTCTGATTAATCTAT--TTTTACTTAATT-ACCGATTTAC-TGATTA-CTA-TTACCTT
65 CCTTGACTC---TTAA-CTATCAATTTAC-TAATTAACCGATTTACTTAATTACCGATTTA-C-T
46194 GACT-
123 GACTA
*
46198 C-TTAACTATCAATTTACTAATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTAC
1 CATTAACTATCAATTTACTAATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTAC
**
46262 CTTGACTCTTAACTATCAATTTACTAATTAATCTCTTTTTACTTAATTACCGATTTACTGACTA
66 CTTGACTCTTAACTATCAATTTACTAATTAA-C-CGATTTACTTAATTACCGATTTACTGACTA
* * * * * * *
46326 CTATTACCT-TGACTCT--TAACT-ATCTCTTTTTACTTACTTACTAATTTACTGATTACTATTA
1 C-ATTAACTATCAATTTACTAATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTA
*
46387 CCTTGACTCTTAACTATCAATTTACTGATTA
65 CCTTGACTCTTAACTATCAATTTACTAATTA
46418 CTATCTTTGA
Statistics
Matches: 190, Mismatches: 17, Indels: 26
0.82 0.07 0.11
Matches are distributed among these distances:
122 4 0.02
123 9 0.05
124 13 0.07
125 16 0.08
126 118 0.62
127 14 0.07
128 4 0.02
129 7 0.04
130 5 0.03
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.47
Consensus pattern (127 bp):
CATTAACTATCAATTTACTAATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTAC
CTTGACTCTTAACTATCAATTTACTAATTAACCGATTTACTTAATTACCGATTTACTGACTA
Found at i:46351 original size:55 final size:55
Alignment explanation
Indices: 46292--46404 Score: 190
Period size: 55 Copynumber: 2.1 Consensus size: 55
46282 TTACTAATTA
*
46292 ATCTCTTTTTACTTAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACT
1 ATCTCTTTTTACTTAATTACCAATTTACTGACTACTATTACCTTGACTCTTAACT
* * *
46347 ATCTCTTTTTACTTACTTACTAATTTACTGATTACTATTACCTTGACTCTTAACT
1 ATCTCTTTTTACTTAATTACCAATTTACTGACTACTATTACCTTGACTCTTAACT
46402 ATC
1 ATC
46405 AATTTACTGA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.26, C:0.23, G:0.04, T:0.47
Consensus pattern (55 bp):
ATCTCTTTTTACTTAATTACCAATTTACTGACTACTATTACCTTGACTCTTAACT
Found at i:46375 original size:71 final size:71
Alignment explanation
Indices: 46146--46349 Score: 390
Period size: 71 Copynumber: 2.9 Consensus size: 71
46136 CTTGACTCTG
*
46146 ATTAATCTATTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATCAAT
1 ATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATCAAT
46211 TTACTA
66 TTACTA
46217 ATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATCAAT
1 ATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATCAAT
46282 TTACTA
66 TTACTA
*
46288 ATTAATCTCTTTTTACTTAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACTATC
1 ATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATC
46350 TCTTTTTACT
Statistics
Matches: 131, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 131 1.00
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.46
Consensus pattern (71 bp):
ATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATCAAT
TTACTA
Found at i:46383 original size:197 final size:194
Alignment explanation
Indices: 45992--46456 Score: 616
Period size: 197 Copynumber: 2.4 Consensus size: 194
45982 CTTACTATTT
* ** * *
45992 TTACCTTGACTCTTAATTATTGATTTACTGATTACTATCTTTTTACTTAATTGCTGATTTACTGA
1 TTACCTTGACTCTTAACTATCAATTTACTGATTACTATCTTTTTACTTAATTACCGATTTACTGA
* * *
46057 TTACTACTTTTACTCCATTAATTATCAATTTACTTAATTAATCTTTTTACTTTATTACTGATTTA
66 TTACTA-TTTTACTCCATTAACTATCAATTTACTTAATTAATCTTTTTACTTAATTACCGATTTA
* * * *
46122 CTGATTACTATTACCTTGACTCTGATTAATCTATTTTTACTTAATTACCGATTTACTGATTACTA
130 CTGACTACTATTACCTTGACTCTAACTAATCTATTTTTACTTAATTACCAATTTACTGATTACTA
* * *
46187 TTACCTTGACTCTTAACTATCAATTTACTAATTAATCTCTTTTTACTTAATTACCGATTTACTGA
1 TTACCTTGACTCTTAACTATCAATTTACTGATTACTATCTTTTTACTTAATTACCGATTTACTGA
46252 TTACTATTACCTTGACT-C-TTAACTATCAATTTAC-TAATTAATCTCTTTTTACTTAATTACCG
66 TTACTATT---TT-ACTCCATTAACTATCAATTTACTTAATTAA--TCTTTTTACTTAATTACCG
* * *
46314 ATTTACTGACTACTATTACCTTGACTCTTAACT-ATCTCTTTTTACTTACTTACTAATTTACTGA
125 ATTTACTGACTACTATTACCTTGACTC-TAACTAATCTATTTTTACTTAATTACCAATTTACTGA
46378 TTACTA
189 TTACTA
* * *
46384 TTACCTTGACTCTTAACTATCAATTTACTGATTACTATCTTTGATT-CTTAACTATCAATTTACT
1 TTACCTTGACTCTTAACTATCAATTTACTGATTACTATCTTT--TTACTTAATTACCGATTTACT
46448 GATTACTAT
64 GATTACTAT
46457 CTTTTTACTT
Statistics
Matches: 237, Mismatches: 24, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
194 2 0.01
195 70 0.30
196 15 0.06
197 118 0.50
198 30 0.13
199 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.48
Consensus pattern (194 bp):
TTACCTTGACTCTTAACTATCAATTTACTGATTACTATCTTTTTACTTAATTACCGATTTACTGA
TTACTATTTTACTCCATTAACTATCAATTTACTTAATTAATCTTTTTACTTAATTACCGATTTAC
TGACTACTATTACCTTGACTCTAACTAATCTATTTTTACTTAATTACCAATTTACTGATTACTA
Found at i:46425 original size:126 final size:126
Alignment explanation
Indices: 46221--46456 Score: 357
Period size: 126 Copynumber: 1.9 Consensus size: 126
46211 TTACTAATTA
*
46221 ATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATCAATTTAC
1 ATCTCTTTTTACTTAATTACCAATTTACTGATTACTATTACCTTGACTCTTAACTATCAATTTAC
* * *
46286 TAATTAATCTCTTT-TTACTTAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACT
66 TAATTAATATCTTTATT-CTTAACTACCAATTTACTGACTACTATTACCTTGACTCTTAACT
* *
46347 ATCTCTTTTTACTTACTTACTAATTTACTGATTACTATTACCTTGACTCTTAACTATCAATTTAC
1 ATCTCTTTTTACTTAATTACCAATTTACTGATTACTATTACCTTGACTCTTAACTATCAATTTAC
* * * *
46412 TGATTACTATCTTTGATTCTTAACTATCAATTTACTGATTACTAT
66 TAATTAATATCTTT-ATTCTTAACTACCAATTTACTGACTACTAT
46457 CTTTTTACTT
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
126 73 0.74
127 23 0.23
128 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (126 bp):
ATCTCTTTTTACTTAATTACCAATTTACTGATTACTATTACCTTGACTCTTAACTATCAATTTAC
TAATTAATATCTTTATTCTTAACTACCAATTTACTGACTACTATTACCTTGACTCTTAACT
Found at i:46440 original size:35 final size:35
Alignment explanation
Indices: 46368--46460 Score: 150
Period size: 35 Copynumber: 2.6 Consensus size: 35
46358 CTTACTTACT
*
46368 AATTTACTGATTACTATTACCTTGACTCTTAACTATC
1 AATTTACTGATTACTA-T-CTTTGACTCTTAACTATC
*
46405 AATTTACTGATTACTATCTTTGATTCTTAACTATC
1 AATTTACTGATTACTATCTTTGACTCTTAACTATC
46440 AATTTACTGATTACTATCTTT
1 AATTTACTGATTACTATCTTT
46461 TTACTTAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
35 37 0.69
36 1 0.02
37 16 0.30
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.47
Consensus pattern (35 bp):
AATTTACTGATTACTATCTTTGACTCTTAACTATC
Found at i:46463 original size:18 final size:18
Alignment explanation
Indices: 46407--46465 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
46397 TAACTATCAA
46407 TTTACTGATTACTATCTT
1 TTTACTGATTACTATCTT
* **
46425 TGATT-CT--TAACTATCAA
1 T--TTACTGATTACTATCTT
46442 TTTACTGATTACTATCTT
1 TTTACTGATTACTATCTT
46460 TTTACT
1 TTTACT
46466 TAATTGCTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
15 2 0.07
16 2 0.07
17 8 0.27
18 14 0.47
19 2 0.07
20 2 0.07
ACGTcount: A:0.25, C:0.17, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTACTGATTACTATCTT
Found at i:46486 original size:69 final size:70
Alignment explanation
Indices: 46406--46559 Score: 208
Period size: 69 Copynumber: 2.2 Consensus size: 70
46396 TTAACTATCA
* *
46406 ATTTACTGATTACTATCTTTGA-T-TCTTAACTATCAATTTAC-TGATTACTATCTTTTTACTTA
1 ATTTACTGATTACTATCTTTGACTCCCTTAACTATCAATTTACTTAATTA--ATCTTTTTACTTA
*
46468 ATTGCTG
64 ATTACTG
* * *
46475 ATTTACTGATTACTA-CTTTTACTCCCTTAATTATCAATTTACTTAATTAATCTTTTTACTTTAT
1 ATTTACTGATTACTATCTTTGACTCCCTTAACTATCAATTTACTTAATTAATCTTTTTACTTAAT
46539 TACTG
66 TACTG
46544 ATTTACTGATTACTAT
1 ATTTACTGATTACTAT
46560 TTCCTTGACT
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
68 5 0.07
69 49 0.65
70 16 0.21
71 5 0.07
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.51
Consensus pattern (70 bp):
ATTTACTGATTACTATCTTTGACTCCCTTAACTATCAATTTACTTAATTAATCTTTTTACTTAAT
TACTG
Found at i:46605 original size:230 final size:231
Alignment explanation
Indices: 46172--46614 Score: 628
Period size: 230 Copynumber: 1.9 Consensus size: 231
46162 TTAATTACCG
*
46172 ATTTACTGATTACTATTACCTTGACTCTTAACTATCAATTTACTAATTAATCTCTTTTTACTTAA
1 ATTTACTGATTACTATTACCTTGACTCTTAACTATCAATTTACTAATTAATATCTTTTTACTTAA
46237 TTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATCAATTTACTAATTAATCTCTTTTT
66 TTACCGATTTACTGATTACTATT--CTTGACTCTTAACTATCAATTTACTAATTAA-CTCTTTTT
*
46302 ACTTAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACTATCTCTTTTTACTTACTTAC
128 ACTTAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACTATCTCTTTTTACTTAATTAC
46367 TAATTTACTGATTACTATTACCTTGACTCTTAACTATCA
193 TAATTTACTGATTACTATTACCTTGACTCTTAACTATCA
* * * *
46406 ATTTACTGATTACTA-T-CTTTGATTCTTAACTATCAATTTACTGATTACTATCTTTTTACTTAA
1 ATTTACTGATTACTATTACCTTGACTCTTAACTATCAATTTACTAATTAATATCTTTTTACTTAA
* * *
46469 TTGCTGATTTACTGATTACTACTT-TT-ACTCCCTTAATTATCAATTTACTTAATTAA-TCTTTT
66 TTACCGATTTACTGATTACTA-TTCTTGACT--CTTAACTATCAATTTAC-TAATTAACTCTTTT
* * * * * *
46531 TACTTTATTACTGATTTACTGATTACTATTTCCTTGACTC-TGATTAATCTCTTTTTACTTAATT
127 TACTTAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACT-ATCTCTTTTTACTTAATT
*
46595 ACTGATTTACTGATTACTAT
191 ACTAATTTACTGATTACTAT
Statistics
Matches: 188, Mismatches: 16, Indels: 14
0.86 0.07 0.06
Matches are distributed among these distances:
229 6 0.03
230 80 0.43
231 16 0.09
232 68 0.36
233 3 0.02
234 15 0.08
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.49
Consensus pattern (231 bp):
ATTTACTGATTACTATTACCTTGACTCTTAACTATCAATTTACTAATTAATATCTTTTTACTTAA
TTACCGATTTACTGATTACTATTCTTGACTCTTAACTATCAATTTACTAATTAACTCTTTTTACT
TAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACTATCTCTTTTTACTTAATTACTAA
TTTACTGATTACTATTACCTTGACTCTTAACTATCA
Done.