Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold392
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: 803515
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
File 4 of 6
Found at i:351401 original size:3 final size:3
Alignment explanation
Indices: 351393--351439 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
351383 GTTTAAGATG
351393 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
351440 GAGGTGATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:352037 original size:32 final size:32
Alignment explanation
Indices: 351991--352051 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
351981 TAAATATAAA
351991 TATAATAAATATATTAAATATATCATATTAAT
1 TATAATAAATATATTAAATATATCATATTAAT
* * *
352023 TATATTAATTATATTAATTATATCATATT
1 TATAATAAATATATTAAATATATCATATT
352052 TGTATTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (32 bp):
TATAATAAATATATTAAATATATCATATTAAT
Found at i:352496 original size:23 final size:25
Alignment explanation
Indices: 352453--352498 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
352443 AATATTATAA
352453 TTATTAATTTATAATTTATAATTTT
1 TTATTAATTTATAATTTATAATTTT
352478 TTATT-ATTTAT-ATTTATAATT
1 TTATTAATTTATAATTTATAATT
352499 ATTAATGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 10 0.48
24 6 0.29
25 5 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATTAATTTATAATTTATAATTTT
Found at i:352532 original size:46 final size:44
Alignment explanation
Indices: 352447--352534 Score: 106
Period size: 46 Copynumber: 2.0 Consensus size: 44
352437 CACCGTAATA
* ** *
352447 TTATAATTATTAATTTATAATTTATAATTTTTTATTATTTATAT
1 TTATAATTATTAATTTATAATATATAATTTAATAATATTTATAT
352491 TTATAATTATTAATGTTTATAATA-ATTAATTTAATAATATTTAT
1 TTATAATTATTAA--TTTATAATATA-TAATTTAATAATATTTAT
352535 TATATTCATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 13 0.35
45 1 0.03
46 23 0.62
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (44 bp):
TTATAATTATTAATTTATAATATATAATTTAATAATATTTATAT
Found at i:353222 original size:14 final size:14
Alignment explanation
Indices: 353192--353238 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
353182 ATATTAAAAC
*
353192 TAATAATTTTAAATA
1 TAATAAATTT-AATA
353207 TAATACAA-TTAATA
1 TAATA-AATTTAATA
353221 TAATAAATTTAATA
1 TAATAAATTTAATA
353235 -AATA
1 TAATA
353239 TTTTATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 6 0.21
14 15 0.52
15 7 0.24
16 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATAAATTTAATA
Found at i:353286 original size:23 final size:24
Alignment explanation
Indices: 353260--353305 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
353250 TATTTAAAAT
353260 TTTAA-TATA-TTATAATAATTATG
1 TTTAATTATATTTAT-ATAATTATG
353283 TTTAATTTATATTTATATAATTA
1 TTTAA-TTATATTTATATAATTA
353306 ATAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.25
25 11 0.55
26 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTAATTATATTTATATAATTATG
Found at i:353307 original size:42 final size:40
Alignment explanation
Indices: 353216--353310 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 40
353206 ATAATACAAT
353216 TAATATAATAAATTTAATAAATATTTTATATTTATATTTAA
1 TAAT-TAATAAATTTAATAAATATTTTATATTTATATTTAA
* *
353257 -AATTTTAATATATTATAATAATTATGTTTA-ATTTATATTTATA
1 TAA--TTAATAAATT-TAATAAATAT-TTTATATTTATATTTA-A
353300 TAATTAATAAA
1 TAATTAATAAA
353311 AAATTAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
40 2 0.04
41 8 0.18
42 28 0.62
43 5 0.11
44 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (40 bp):
TAATTAATAAATTTAATAAATATTTTATATTTATATTTAA
Found at i:354622 original size:16 final size:16
Alignment explanation
Indices: 354603--354633 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
354593 TTTTTAATTC
354603 TAATTATTTTATGTTT
1 TAATTATTTTATGTTT
354619 TAATTATTTTATGTT
1 TAATTATTTTATGTT
354634 CGAATTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
TAATTATTTTATGTTT
Found at i:354639 original size:16 final size:16
Alignment explanation
Indices: 354604--354639 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
354594 TTTTAATTCT
**
354604 AATTATTTTATGTTTT
1 AATTATTTTATGTTCG
354620 AATTATTTTATGTTCG
1 AATTATTTTATGTTCG
354636 AATT
1 AATT
354640 GTTAGCTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.61
Consensus pattern (16 bp):
AATTATTTTATGTTCG
Found at i:360284 original size:3 final size:3
Alignment explanation
Indices: 360278--360314 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
360268 TAAAAATTTT
360278 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
360315 ATACATTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:360671 original size:14 final size:14
Alignment explanation
Indices: 360648--360687 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
360638 AAAAATAAAA
360648 ATTTATAAATTTAAT
1 ATTTA-AAATTTAAT
360663 ATTTAAAATTTAAT
1 ATTTAAAATTTAAT
* *
360677 AATTACAATTT
1 ATTTAAAATTT
360688 TTTTATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTAAAATTTAAT
Found at i:360751 original size:114 final size:111
Alignment explanation
Indices: 360597--360813 Score: 278
Period size: 114 Copynumber: 1.9 Consensus size: 111
360587 TTAAAATAAA
* *
360597 TTAAAATTTTAATTAATTTAATTAATTTATATTATTATTTAAAAAATAAAAATTT-ATAAA-TTT
1 TTAAAAGTTTAATTAATTCAATTAATTTATATTATTATTTAAAAAAT-AAAATTTAATAAATTTT
*
360660 AATATTTAAA-ATTTAATAATTACAATTTTTTTATTTTTAAACTCTTACT
65 AA-ATTTAAATA-TTAAT-ATTACAATATTTTTATTTTTAAACTCTTACT
* * * *
360709 TTAAAAGTTTAAGTTTAATTCATTTAATTTATATTTTTATTTAAAATATAATATTTAATAAATTT
1 TTAAAAGTTTAA--TTAATTCAATTAATTTATATTATTATTTAAAAAATAAAATTTAATAAATTT
**
360774 TAAATTTAAATATTAATATTTTAATATTTTTATTTTTAAA
64 TAAATTTAAATATTAATATTACAATATTTTTATTTTTAAA
360814 TTATTATCGT
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
112 11 0.12
113 26 0.29
114 48 0.53
115 6 0.07
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (111 bp):
TTAAAAGTTTAATTAATTCAATTAATTTATATTATTATTTAAAAAATAAAATTTAATAAATTTTA
AATTTAAATATTAATATTACAATATTTTTATTTTTAAACTCTTACT
Found at i:360778 original size:23 final size:23
Alignment explanation
Indices: 360747--360791 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
360737 TTATATTTTT
360747 ATTTAAAATAT-AATATTTAATAA
1 ATTTAAAATATAAATA-TTAATAA
* *
360770 ATTTTAAATTTAAATATTAATA
1 ATTTAAAATATAAATATTAATA
360792 TTTTAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTAAAATATAAATATTAATAA
Found at i:360802 original size:29 final size:27
Alignment explanation
Indices: 360735--360808 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 27
360725 AATTCATTTA
*
360735 ATTT-ATATTTTTATTTAAAATATAAT
1 ATTTAATATTTTAATTTAAAATATAAT
360761 ATTTAATAAATTTTAAATTT-AAATATTAAT
1 ATTTAAT--ATTTT-AATTTAAAATA-TAAT
*
360791 ATTTTAATATTTTTATTT
1 A-TTTAATATTTTAATTT
360809 TTAAATTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
26 4 0.10
27 2 0.05
28 4 0.10
29 15 0.38
30 9 0.22
31 6 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTTAATATTTTAATTTAAAATATAAT
Found at i:360805 original size:30 final size:28
Alignment explanation
Indices: 360735--360819 Score: 77
Period size: 30 Copynumber: 2.9 Consensus size: 28
360725 AATTCATTTA
360735 ATTT-ATATTTTT-ATTTAAA-ATATAAT
1 ATTTAATATTTTTAATTTAAATAT-TAAT
*
360761 ATTTAATAAATTTTAAATTTAAATATTAAT
1 ATTTAAT--ATTTTTAATTTAAATATTAAT
*
360791 ATTTTAATATTTTTATTTTTAAATTATTA
1 A-TTTAATATTTTTA-ATTTAAA-TATTA
360820 TCGTAAACTT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
26 4 0.08
27 2 0.04
29 11 0.23
30 18 0.38
31 13 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTTAATATTTTTAATTTAAATATTAAT
Found at i:360859 original size:15 final size:16
Alignment explanation
Indices: 360836--360875 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
360826 ACTTAACAAT
*
360836 TTATATATTTATATTA
1 TTATATATTTATAATA
360852 TT-TATA-TTATAATA
1 TTATATATTTATAATA
360866 TTATATATTT
1 TTATATATTT
360876 TTATAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 9 0.43
15 8 0.38
16 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATATATTTATAATA
Found at i:361111 original size:32 final size:32
Alignment explanation
Indices: 361067--361129 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
361057 CACAATCTAT
* *
361067 TTAATTTATATTTTGACTTATAAA-ATTTAATA
1 TTAATTTATA-TTTAAATTATAAATATTTAATA
*
361099 TTAATTTTTATTTAAATTATAAATATTTAAT
1 TTAATTTATATTTAAATTATAAATATTTAAT
361130 TTCATCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (32 bp):
TTAATTTATATTTAAATTATAAATATTTAATA
Found at i:361201 original size:14 final size:14
Alignment explanation
Indices: 361184--361225 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
361174 TTATTTAATT
361184 TAATTTTATTAAAA
1 TAATTTTATTAAAA
*
361198 TAATTTTAATAAAA
1 TAATTTTATTAAAA
361212 -AA-TTTACTTAAAA
1 TAATTTTA-TTAAAA
361225 T
1 T
361226 TCATACGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 4 0.17
13 7 0.29
14 13 0.54
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATTTTATTAAAA
Found at i:363012 original size:129 final size:132
Alignment explanation
Indices: 362801--363038 Score: 297
Period size: 129 Copynumber: 1.8 Consensus size: 132
362791 TTCTATTGTT
* *
362801 TATTAAAAAAATTACATTATTGGATCCTAAAAGAATTACTTTGACATATAATTGGCACATTTAAA
1 TATTAAAAAAATTACATTATTGGATCCTAAAAGAATTACTTTAACATATAATTGACACATTTAAA
*** * * * *
362866 TGAAAATGGGACGAAATTGATGACTAATTGAAATTC-ATTACTTCAATCTCAAATACCCATTTTT
66 TGAAAATAAAACAAAATTGATCACCAATTGAAATACAATTACTTCAATCTCAAATACCCATTTTT
362930 TC
131 TC
* * *
362932 TATT-AAAAAATATACATTATTGGGT-TTAAAA-AATTA-TTTAAACATATAATTGACATATTTA
1 TATTAAAAAAAT-TACATTATTGGATCCTAAAAGAATTACTTT-AACATATAATTGACACATTTA
* *
362993 AGTGAAAATAAAACAAAATTGATCACCCATTGAAATACAATTACTT
64 AATGAAAATAAAACAAAATTGATCACCAATTGAAATACAATTACTT
363039 TGCTCCCAAA
Statistics
Matches: 90, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
128 3 0.03
129 52 0.58
130 19 0.21
131 16 0.18
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (132 bp):
TATTAAAAAAATTACATTATTGGATCCTAAAAGAATTACTTTAACATATAATTGACACATTTAAA
TGAAAATAAAACAAAATTGATCACCAATTGAAATACAATTACTTCAATCTCAAATACCCATTTTT
TC
Found at i:363343 original size:16 final size:16
Alignment explanation
Indices: 363314--363368 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
363304 AGACCTTACG
*
363314 AAATAATT-ATATAAT
1 AAATAATTAATATAAA
363329 AAA-AATATAATATAAA
1 AAATAAT-TAATATAAA
*
363345 AAATAATTAATATATA
1 AAATAATTAATATAAA
*
363361 ATATAATT
1 AAATAATT
363369 TAAAAAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 3 0.09
15 4 0.12
16 24 0.71
17 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATAATTAATATAAA
Found at i:363383 original size:25 final size:23
Alignment explanation
Indices: 363324--363389 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 23
363314 AAATAATTAT
* *
363324 ATAATAAAAATATAATATAAAAA
1 ATAATTAATATATAATATAAAAA
363347 ATAATTAATATATAATATAATTTAAA
1 ATAATTAATATATAATATAA---AAA
363373 A-AATTAATATA-AATATA
1 ATAATTAATATATAATATA
363390 TAAATATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
23 18 0.47
24 6 0.16
25 10 0.26
26 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
ATAATTAATATATAATATAAAAA
Found at i:363388 original size:29 final size:28
Alignment explanation
Indices: 363314--363403 Score: 92
Period size: 31 Copynumber: 3.0 Consensus size: 28
363304 AGACCTTACG
* *
363314 AAATAATTATATAATAAAAATATAATATAAA
1 AAATAATTA-AT-AT-ATAATATAATTTAAA
363345 AAATAATTAATATATAATATAATTTAAA
1 AAATAATTAATATATAATATAATTTAAA
*
363373 AAATTAATATAAATATATAA-ATATTTTAAA
1 AAA-TAAT-T-AATATATAATATAATTTAAA
363403 A
1 A
363404 TTTGAACAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
28 16 0.30
29 6 0.11
30 13 0.25
31 18 0.34
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
AAATAATTAATATATAATATAATTTAAA
Found at i:363667 original size:19 final size:20
Alignment explanation
Indices: 363640--363678 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
363630 TTATAATTAA
363640 ATTTAAATAAAAATA-TATT
1 ATTTAAATAAAAATACTATT
*
363659 ATTTTAATAAAAATACTATT
1 ATTTAAATAAAAATACTATT
363679 TTAAATCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTAAATAAAAATACTATT
Found at i:366410 original size:16 final size:16
Alignment explanation
Indices: 366389--366420 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
366379 TTTCATATGC
*
366389 ATATATTTATATTAAT
1 ATATATATATATTAAT
366405 ATATATATATATTAAT
1 ATATATATATATTAAT
366421 CAGTTTTTAT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATATATATATTAAT
Found at i:369018 original size:17 final size:17
Alignment explanation
Indices: 368996--369034 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
368986 CTATATTAAA
368996 AAATATATCA-TTTAATT
1 AAATATAT-ATTTTAATT
*
369013 AAATATATATTTTTATT
1 AAATATATATTTTAATT
369030 AAATA
1 AAATA
369035 CTAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATATATATTTTAATT
Found at i:369397 original size:13 final size:13
Alignment explanation
Indices: 369374--369440 Score: 50
Period size: 13 Copynumber: 5.3 Consensus size: 13
369364 TTTTAATTTT
369374 TTTAT-ATTAATA
1 TTTATAATTAATA
369386 TTTATAATTAATA
1 TTTATAATTAATA
* *
369399 TATATTA-TAATAA
1 TTTATAATTAAT-A
* *
369412 ATTATAA-TAAGA
1 TTTATAATTAATA
* *
369424 TTCATTATTAATA
1 TTTATAATTAATA
369437 TTTA
1 TTTA
369441 GTATAATTAA
Statistics
Matches: 41, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
12 14 0.34
13 27 0.66
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (13 bp):
TTTATAATTAATA
Found at i:373272 original size:251 final size:251
Alignment explanation
Indices: 372829--373331 Score: 997
Period size: 251 Copynumber: 2.0 Consensus size: 251
372819 TACAGTCGCT
372829 GTATGATCATGGGGGAGATAGTATTTGACTGCTATGATTGCATTCCTAGAAATGTATTCTGTAAT
1 GTATGATCATGGGGGAGATAGTATTTGACTGCTATGATTGCATTCCTAGAAATGTATTCTGTAAT
372894 TGATAATTCTGAACCATCTCCATTGGCCCCAAGTTTGCCTTCTTTTCCAAGTGAACATTTTAGTC
66 TGATAATTCTGAACCATCTCCATTGGCCCCAAGTTTGCCTTCTTTTCCAAGTGAACATTTTAGTC
372959 ATGGGTGGCATTCAAATTTCAATGTCTTAATGAATGGTCTCATGGTAGAAAACTTTATCATGTGT
131 ATGGGTGGCATTCAAATTTCAATGTCTTAATGAATGGTCTCATGGTAGAAAACTTTATCATGTGT
373024 GAAGATTGATTCAGAGAGTAAAACATCATGCATTTGAAATTTTAGATTTGATTGTA
196 GAAGATTGATTCAGAGAGTAAAACATCATGCATTTGAAATTTTAGATTTGATTGTA
*
373080 GTATGATCGTGGGGGAGATAGTATTTGACTGCTATGATTGCATTCCTAGAAATGTATTCTGTAAT
1 GTATGATCATGGGGGAGATAGTATTTGACTGCTATGATTGCATTCCTAGAAATGTATTCTGTAAT
373145 TGATAATTCTGAACCATCTCCATTGGCCCCAAGTTTGCCTTCTTTTCCAAGTGAACATTTTAGTC
66 TGATAATTCTGAACCATCTCCATTGGCCCCAAGTTTGCCTTCTTTTCCAAGTGAACATTTTAGTC
373210 ATGGGTGGCATTCAAATTTCAATGTCTTAATGAATGGTCTCATGGTAGAAAACTTTATCATGTGT
131 ATGGGTGGCATTCAAATTTCAATGTCTTAATGAATGGTCTCATGGTAGAAAACTTTATCATGTGT
373275 GAAGATTGATTCAGAGAGTAAAACATCATGCATTTGAAATTTTAGATTTGATTGTA
196 GAAGATTGATTCAGAGAGTAAAACATCATGCATTTGAAATTTTAGATTTGATTGTA
373331 G
1 G
373332 GGTGAGTAAC
Statistics
Matches: 251, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
251 251 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (251 bp):
GTATGATCATGGGGGAGATAGTATTTGACTGCTATGATTGCATTCCTAGAAATGTATTCTGTAAT
TGATAATTCTGAACCATCTCCATTGGCCCCAAGTTTGCCTTCTTTTCCAAGTGAACATTTTAGTC
ATGGGTGGCATTCAAATTTCAATGTCTTAATGAATGGTCTCATGGTAGAAAACTTTATCATGTGT
GAAGATTGATTCAGAGAGTAAAACATCATGCATTTGAAATTTTAGATTTGATTGTA
Found at i:374924 original size:3 final size:3
Alignment explanation
Indices: 374916--374941 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
374906 ATTTAAAATA
374916 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
374942 AATAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:379001 original size:22 final size:22
Alignment explanation
Indices: 378942--379004 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 22
378932 TAATAGATAT
378942 ATATATTTAACACG-GTTATTTTTA
1 ATATATTTAA-A-GAGTT-TTTTTA
**
378966 ATAT-TTTTTA-AGTTTTTTTA
1 ATATATTTAAAGAGTTTTTTTA
378986 ATATATTTAAAGAGTTTTT
1 ATATATTTAAAGAGTTTTT
379005 GAAAAGTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 10 0.31
21 7 0.22
22 8 0.25
23 3 0.09
24 4 0.12
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.57
Consensus pattern (22 bp):
ATATATTTAAAGAGTTTTTTTA
Found at i:379433 original size:25 final size:24
Alignment explanation
Indices: 379394--379468 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 24
379384 AATGTTACGT
* *
379394 AATATTATACTATATATAATATAA
1 AATAATATACAATATATAATATAA
*
379418 ATTACATAATAC-ATAT-TAAATATAAA
1 AATA-AT-ATACAATATAT-AATAT-AA
379444 AATAATATACAATATATAAT-TAA
1 AATAATATACAATATATAATATAA
379467 AA
1 AA
379469 AAGAGTTCAG
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
23 4 0.10
24 9 0.21
25 19 0.45
26 10 0.24
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (24 bp):
AATAATATACAATATATAATATAA
Found at i:379724 original size:3 final size:3
Alignment explanation
Indices: 379716--379740 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
379706 CTCTAAAGTT
379716 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
379741 CCCTAATGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:380894 original size:22 final size:22
Alignment explanation
Indices: 380869--380912 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
380859 AATTTATTTT
*
380869 ATATTTAAAT-TTAATTATAAAA
1 ATATATAAATATTAATTA-AAAA
380891 ATATATAAATATTAATTAAAAA
1 ATATATAAATATTAATTAAAAA
380913 TAAATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATATAAATATTAATTAAAAA
Found at i:382859 original size:7 final size:6
Alignment explanation
Indices: 382820--382884 Score: 55
Period size: 6 Copynumber: 10.8 Consensus size: 6
382810 ATCAATTCAA
* *
382820 TTAAAT TTAAAT TT-AAT TT-AAT TAAAAATT TTATAAT TTAAAT TTAAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT T-TAAA-T TTA-AAT TTAAAT TTAAAT
*
382869 AT-AAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAA
382885 ATAATCAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
5 12 0.25
6 25 0.52
7 7 0.15
8 4 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:382887 original size:16 final size:16
Alignment explanation
Indices: 382852--383045 Score: 81
Period size: 16 Copynumber: 12.0 Consensus size: 16
382842 TAAAAATTTT
382852 ATAATTTAAATTTAAAA
1 ATAATTTAAATTT-AAA
382869 ATAATTTAAATTT--A
1 ATAATTTAAATTTAAA
*
382883 A-AA--T-AA-TCAAA
1 ATAATTTAAATTTAAA
*
382894 AT-ATCTTAAACTTAAA
1 ATAAT-TTAAATTTAAA
382910 ATAATTTAAATTTAAA
1 ATAATTTAAATTTAAA
* *
382926 ATGA-TTCAATTTAAA
1 ATAATTTAAATTTAAA
*
382941 ATAA-TTAAACTCGATAAA
1 ATAATTTAAA-T--TTAAA
*
382959 ATTAATTATTAAAATT-AA
1 A-TAA-T-TTAAATTTAAA
*
382977 TTAATTTTAAATTT-AA
1 ATAA-TTTAAATTTAAA
*
382993 TTAATTTAAATATTCAATTCGA
1 ATAATTTAAAT-TT-AA----A
*
383015 CTAA-TTAAATTTAAA
1 ATAATTTAAATTTAAA
383030 ATAATTTAAATTTAAA
1 ATAATTTAAATTTAAA
383046 TTGATACGAG
Statistics
Matches: 139, Mismatches: 14, Indels: 49
0.69 0.07 0.24
Matches are distributed among these distances:
9 1 0.01
10 2 0.01
11 4 0.03
13 2 0.01
14 3 0.02
15 30 0.22
16 46 0.33
17 20 0.14
18 8 0.06
19 6 0.04
20 2 0.01
21 6 0.04
22 9 0.06
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (16 bp):
ATAATTTAAATTTAAA
Found at i:382902 original size:25 final size:25
Alignment explanation
Indices: 382866--382914 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
382856 TTTAAATTTA
*
382866 AAAATAATTTAAATTTAAAATAATC
1 AAAATAATTTAAACTTAAAATAATC
382891 AAAAT-ATCTTAAACTTAAAATAAT
1 AAAATAAT-TTAAACTTAAAATAAT
382915 TTAAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (25 bp):
AAAATAATTTAAACTTAAAATAATC
Found at i:382971 original size:13 final size:13
Alignment explanation
Indices: 382955--382979 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
382945 TTAAACTCGA
382955 TAAAATTAATTAT
1 TAAAATTAATTAT
382968 TAAAATTAATTA
1 TAAAATTAATTA
382980 ATTTTAAATT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAAAATTAATTAT
Found at i:386349 original size:13 final size:12
Alignment explanation
Indices: 386314--386349 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
386304 AATTTTAAAA
386314 AAATAAATATA-
1 AAATAAATATAT
386325 AAATAAATATAT
1 AAATAAATATAT
386337 AATATAAATATAT
1 AA-ATAAATATAT
386350 TAACATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.48
12 2 0.09
13 10 0.43
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATAAATATAT
Found at i:386832 original size:21 final size:22
Alignment explanation
Indices: 386804--386849 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
386794 TTATAATTTG
386804 TTATATTT-ATTAATAAAAATAAA
1 TTAT-TTTAATTAA-AAAAATAAA
386827 TTATTTTAAATTAAAAAAATAAA
1 TTATTTT-AATTAAAAAAATAAA
386850 AATAAAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 3 0.14
23 13 0.62
24 5 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TTATTTTAATTAAAAAAATAAA
Found at i:387022 original size:47 final size:47
Alignment explanation
Indices: 386926--387049 Score: 114
Period size: 46 Copynumber: 2.6 Consensus size: 47
386916 TTTAATTTTT
* * *
386926 TAAT-AAATAAAATAATA-ATTTTTTA-TTTTTTTTAATCATAACAAA
1 TAATAAAATAAAA-AATATTTTTTTTACTTTTTTTAAACCATAACAAA
* *
386971 TAAT-AAGTGAAAAAATATTTTTTTTACTTTTTTTAAACCA-AATAAA
1 TAATAAAAT-AAAAAATATTTTTTTTACTTTTTTTAAACCATAACAAA
*
387017 CTAATAAAAATAAAAAATATTTCTTTTATCTTT
1 -TAAT-AAAATAAAAAATATTTTTTTTA-CTTT
387050 CTCACTTTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
45 11 0.17
46 16 0.25
47 15 0.23
48 16 0.25
49 7 0.11
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (47 bp):
TAATAAAATAAAAAATATTTTTTTTACTTTTTTTAAACCATAACAAA
Found at i:387089 original size:17 final size:16
Alignment explanation
Indices: 387056--387086 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
387046 CTTTCTCACT
*
387056 TTTTTTCAATTTTTTA
1 TTTTTTAAATTTTTTA
387072 TTTTTTAAATTTTTT
1 TTTTTTAAATTTTTT
387087 TATCGTACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTAAATTTTTTA
Found at i:387779 original size:39 final size:41
Alignment explanation
Indices: 387705--387785 Score: 96
Period size: 39 Copynumber: 2.0 Consensus size: 41
387695 ATTACGTATA
* ** *
387705 AATTTTAAAAATATATATTATATATTTTATTATTTTATAAT
1 AATTTTAAAAATATATATTATATATTTAAAAATTTTAAAAT
387746 AATTTTAAAAATAT-T-TTATAT-TTATAAAAATTTTAAAAT
1 AATTTTAAAAATATATATTATATATT-TAAAAATTTTAAAAT
387785 A
1 A
387786 TTTATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
38 2 0.06
39 18 0.51
40 1 0.03
41 14 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (41 bp):
AATTTTAAAAATATATATTATATATTTAAAAATTTTAAAAT
Found at i:387783 original size:27 final size:28
Alignment explanation
Indices: 387726--387794 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
387716 TATATATTAT
*
387726 ATATTTTATTATTTTATAATAATTTTAAAA
1 ATATTTTA-TA-TTTATAAAAATTTTAAAA
387756 ATATTTTATATTTATAAAAATTTT-AAA
1 ATATTTTATATTTATAAAAATTTTAAAA
387783 ATA-TTTATATTT
1 ATATTTTATATTT
387795 TATCTCATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
26 9 0.24
27 6 0.16
28 13 0.34
29 2 0.05
30 8 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
ATATTTTATATTTATAAAAATTTTAAAA
Found at i:387796 original size:27 final size:28
Alignment explanation
Indices: 387730--387797 Score: 95
Period size: 27 Copynumber: 2.4 Consensus size: 28
387720 TATTATATAT
*
387730 TTTATTATTTTATAATAATTTTAAAAATA
1 TTTA-TATTTTATAAAAATTTTAAAAATA
387759 TTT-TATATTTATAAAAATTTT-AAAATA
1 TTTATAT-TTTATAAAAATTTTAAAAATA
387786 TTTATATTTTAT
1 TTTATATTTTAT
387798 CTCATGTGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
27 17 0.47
28 16 0.44
29 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTATATTTTATAAAAATTTTAAAAATA
Found at i:387909 original size:14 final size:14
Alignment explanation
Indices: 387890--387923 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
387880 TTAATATTTA
387890 AATATAATTAATAT
1 AATATAATTAATAT
*
387904 AATATATTTAATAT
1 AATATAATTAATAT
387918 ACATAT
1 A-ATAT
387924 TTTTATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATAATTAATAT
Found at i:388360 original size:2 final size:2
Alignment explanation
Indices: 388343--388386 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
388333 AAATCTTTTC
*
388343 TA TA CTA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
388386 T
1 T
388387 TTCAACTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:389035 original size:22 final size:22
Alignment explanation
Indices: 388992--389035 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
388982 ATTATTATTT
**
388992 TATATATATAAATATATGTATG
1 TATATATATAAATATAAATATG
* *
389014 TATATATTTAAATTTAAATATG
1 TATATATATAAATATAAATATG
389036 GGTTATGATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TATATATATAAATATAAATATG
Found at i:389877 original size:14 final size:15
Alignment explanation
Indices: 389845--389887 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
389835 TTATTATTTA
*
389845 AAAATA-TTAAATAT
1 AAAATATTTATATAT
*
389859 AAAATATTTTTATAT
1 AAAATATTTATATAT
389874 -AAATATTTATATAT
1 AAAATATTTATATAT
389888 TTTATAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAATATTTATATAT
Found at i:390707 original size:27 final size:27
Alignment explanation
Indices: 390656--390712 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
390646 AAAAATTTTA
* *
390656 TATATTTGAATGATTATATTTTATATT
1 TATATTTGAATGATTATATTATATAAT
390683 TATATTTGAAT-A-TATATTAAATATAAT
1 TATATTTGAATGATTATATT--ATATAAT
390710 TAT
1 TAT
390713 TTTTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 6 0.23
26 1 0.04
27 19 0.73
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.54
Consensus pattern (27 bp):
TATATTTGAATGATTATATTATATAAT
Found at i:391236 original size:21 final size:21
Alignment explanation
Indices: 391212--391253 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
391202 AAATATTTTA
391212 ATATAAAT-TTAATTATAAAAT
1 ATATAAATATTAA-TATAAAAT
391233 ATATAAATATTAATATAAAAT
1 ATATAAATATTAATATAAAAT
391254 TATTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATAAATATTAATATAAAAT
Found at i:391685 original size:21 final size:21
Alignment explanation
Indices: 391661--391700 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
391651 AATATTTTTA
*
391661 ATATAATTATAATAAAAATTT
1 ATATAAATATAATAAAAATTT
*
391682 ATATAAATATAATATAAAT
1 ATATAAATATAATAAAAAT
391701 ACACGCTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATAAATATAATAAAAATTT
Found at i:391698 original size:11 final size:11
Alignment explanation
Indices: 391659--391701 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
391649 ATAATATTTT
*
391659 TAATATAATTA
1 TAATATAAATA
*
391670 TAATAAAAAT-
1 TAATATAAATA
*
391680 TTATATAAATA
1 TAATATAAATA
391691 TAATATAAATA
1 TAATATAAATA
391702 CACGCTAACG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAATATAAATA
Found at i:395657 original size:17 final size:17
Alignment explanation
Indices: 395635--395673 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
395625 AAATAATAAA
*
395635 ATAAATTAACTTAATTT
1 ATAAATAAACTTAATTT
*
395652 ATAAATAAATTTAATTT
1 ATAAATAAACTTAATTT
395669 A-AAAT
1 ATAAAT
395674 GACACATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAATAAACTTAATTT
Found at i:397283 original size:12 final size:12
Alignment explanation
Indices: 397266--397290 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
397256 AGTATATAGG
397266 TATAAGTTATGA
1 TATAAGTTATGA
397278 TATAAGTTATGA
1 TATAAGTTATGA
397290 T
1 T
397291 CTTTCAAATA
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:0.16, T:0.44
Consensus pattern (12 bp):
TATAAGTTATGA
Found at i:400874 original size:24 final size:25
Alignment explanation
Indices: 400833--400883 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
400823 TAAGTTGAGT
* *
400833 TTAAAATTTTTATTATA-TAATATA
1 TTAAAATTTTTATGATATTAAAATA
400857 TTAAAA-TTTTATCGATATTAAAATA
1 TTAAAATTTTTAT-GATATTAAAATA
400882 TT
1 TT
400884 TTTTTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 6 0.26
24 9 0.39
25 8 0.35
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (25 bp):
TTAAAATTTTTATGATATTAAAATA
Found at i:400911 original size:15 final size:17
Alignment explanation
Indices: 400883--400920 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
400873 ATTAAAATAT
400883 TTTTTTAATATTATTAA
1 TTTTTTAATATTATTAA
*
400900 TTTTTTATTTATTA-TAA
1 TTTTTTA-ATATTATTAA
400917 TTTT
1 TTTT
400921 AAAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTAATATTATTAA
Found at i:400942 original size:14 final size:13
Alignment explanation
Indices: 400923--400972 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 13
400913 ATAATTTTAA
400923 AAAATATAATAATT
1 AAAATATAA-AATT
*
400937 AAAATATTAAATTT
1 AAAATA-TAAAATT
400951 AATAATATAAAAATT
1 AA-AATAT-AAAATT
400966 AAAATAT
1 AAAATAT
400973 TTTTTCATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 17 0.55
15 14 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATATAAAATT
Found at i:400953 original size:21 final size:21
Alignment explanation
Indices: 400924--400968 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
400914 TAATTTTAAA
400924 AAATATAATAAT-TAAAATATT
1 AAATATAATAATATAAAA-ATT
*
400945 AAATTTAATAATATAAAAATT
1 AAATATAATAATATAAAAATT
400966 AAA
1 AAA
400969 ATATTTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATATAATAATATAAAAATT
Found at i:401257 original size:13 final size:13
Alignment explanation
Indices: 401229--401285 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 13
401219 TATATAATAT
401229 ATTTATTTT-T-A
1 ATTTATTTTATAA
401240 ATTTATTTTATAAA
1 ATTTATTTTAT-AA
*
401254 TTTATTTATTTTATTA
1 ---ATTTATTTTATAA
401270 ATTTATTTTATAA
1 ATTTATTTTATAA
401283 ATT
1 ATT
401286 AGATAAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
11 9 0.24
12 1 0.03
13 15 0.39
14 1 0.03
16 1 0.03
17 11 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTATTTTATAA
Found at i:401262 original size:17 final size:17
Alignment explanation
Indices: 401240--401277 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
401230 TTTATTTTTA
401240 ATTTATTTTATAAATTT
1 ATTTATTTTATAAATTT
*
401257 ATTTATTTTATTAATTT
1 ATTTATTTTATAAATTT
401274 ATTT
1 ATTT
401278 TATAAATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTATTTTATAAATTT
Found at i:401273 original size:30 final size:28
Alignment explanation
Indices: 401219--401285 Score: 98
Period size: 30 Copynumber: 2.3 Consensus size: 28
401209 TAAATAAAAA
*
401219 TATATAATATATTTATTTTTAATTTATTT
1 TATA-AATTTATTTATTTTTAATTTATTT
401248 TATAAATTTATTTATTTTATTAATTTATTT
1 TATAAATTTATTTA-TTT-TTAATTTATTT
401278 TATAAATT
1 TATAAATT
401286 AGATAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 9 0.26
29 7 0.20
30 19 0.54
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TATAAATTTATTTATTTTTAATTTATTT
Found at i:401286 original size:17 final size:17
Alignment explanation
Indices: 401237--401286 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
401227 ATATTTATTT
401237 TTAATTTATTTTATAAA
1 TTAATTTATTTTATAAA
*
401254 TTTATTTA-TTT-T--A
1 TTAATTTATTTTATAAA
401267 TTAATTTATTTTATAAA
1 TTAATTTATTTTATAAA
401284 TTA
1 TTA
401287 GATAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
13 8 0.30
14 3 0.11
15 2 0.07
16 3 0.11
17 11 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTAATTTATTTTATAAA
Found at i:401297 original size:30 final size:30
Alignment explanation
Indices: 401233--401298 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
401223 TAATATATTT
* *
401233 ATTT-TTAATTTATTTTATAAATTTATTTA
1 ATTTATTAATTTATTTTATAAATTTAATAA
*
401262 TTTTATTAATTTATTTTATAAA-TTAGATAA
1 ATTTATTAATTTATTTTATAAATTTA-ATAA
401292 ATTTATT
1 ATTTATT
401299 TACCGGTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (30 bp):
ATTTATTAATTTATTTTATAAATTTAATAA
Found at i:401327 original size:17 final size:17
Alignment explanation
Indices: 401240--401327 Score: 52
Period size: 17 Copynumber: 4.9 Consensus size: 17
401230 TTTATTTTTA
* *
401240 ATTTATTTTATAAATTT
1 ATTTATCTTATTAATTT
*
401257 ATTTATTTTATTAATTT
1 ATTTATCTTATTAATTT
* *
401274 ATTTTATAAATTAGATAAATTT
1 A-TTTAT--CTT--ATTAATTT
***
401296 ATTTA-CCGGTTAATTT
1 ATTTATCTTATTAATTT
401312 ATTTATCTTATTAATT
1 ATTTATCTTATTAATT
401328 AAATTAAATT
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
16 11 0.20
17 24 0.44
18 5 0.09
20 2 0.04
21 4 0.07
22 8 0.15
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (17 bp):
ATTTATCTTATTAATTT
Found at i:401841 original size:16 final size:16
Alignment explanation
Indices: 401814--401861 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
401804 CAAAAAAAGT
401814 ATTTACTTATTTTTTTA
1 ATTTA-TTATTTTTTTA
**
401831 ATTTATTATTTTTAAA
1 ATTTATTATTTTTTTA
*
401847 ATTCA-TATTTTTTTA
1 ATTTATTATTTTTTTA
401862 TAATGAAACA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 8 0.31
16 13 0.50
17 5 0.19
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTATTATTTTTTTA
Found at i:403185 original size:20 final size:21
Alignment explanation
Indices: 403149--403206 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 21
403139 AAAATATAAA
403149 ATATTAA-AAA-T-TAATTTT
1 ATATTAATAAATTATAATTTT
*
403167 ATATTAAT-ATTTATAATTTT
1 ATATTAATAAATTATAATTTT
* *
403187 TTATTATTAAATTATAATTT
1 ATATTAATAAATTATAATTT
403207 AAGTTAGATG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 8 0.25
19 1 0.03
20 13 0.41
21 10 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTAATAAATTATAATTTT
Found at i:403201 original size:21 final size:22
Alignment explanation
Indices: 403163--403206 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
403153 TAAAAATTAA
403163 TTTTATATTAATATTTATAATT
1 TTTTATATTAATATTTATAATT
403185 TTTTATTATTAA-A-TTATAATT
1 TTTTA-TATTAATATTTATAATT
403206 T
1 T
403207 AAGTTAGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.43
22 6 0.29
23 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTATATTAATATTTATAATT
Found at i:406190 original size:26 final size:26
Alignment explanation
Indices: 406114--406242 Score: 84
Period size: 27 Copynumber: 4.8 Consensus size: 26
406104 TATAATTGTT
* **
406114 TATTTATATTATAATTAAATATTTTA
1 TATTTATATAATTTTTAAATATTTTA
* *
406140 TTATATAATAATTATTTTTTAAAATATTTTA
1 -TAT-TTAT-A-TAATTTTT-AAATATTTTA
* *
406171 TATTTATATAAATTTT-AA-ATTATA
1 TATTTATATAATTTTTAAATATTTTA
* ** *
406195 TATTT-TATTATTTTTATTGTATGTTA
1 TATTTATATAATTTTTA-AATATTTTA
406221 TATTTATATAATTTTTAAATAT
1 TATTTATATAATTTTTAAATAT
406243 GAAGTTTACG
Statistics
Matches: 76, Mismatches: 18, Indels: 17
0.68 0.16 0.15
Matches are distributed among these distances:
23 8 0.11
24 10 0.13
25 2 0.03
26 12 0.16
27 19 0.25
28 4 0.05
29 4 0.05
30 7 0.09
31 10 0.13
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (26 bp):
TATTTATATAATTTTTAAATATTTTA
Found at i:406193 original size:50 final size:50
Alignment explanation
Indices: 406139--406240 Score: 125
Period size: 50 Copynumber: 2.0 Consensus size: 50
406129 TAAATATTTT
*
406139 ATTATATA-ATAATTATTTTTTAAAATATTTTATATTTATATAAATTTTAA
1 ATTATATATATAATTA-TTTTTAAAATATGTTATATTTATATAAATTTTAA
* * *** *
406189 ATTATATATTTTATTATTTTTATTGTATGTTATATTTATATAATTTTTAA
1 ATTATATATATAATTATTTTTAAAATATGTTATATTTATATAAATTTTAA
406239 AT
1 AT
406241 ATGAAGTTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 39 0.89
51 5 0.11
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (50 bp):
ATTATATATATAATTATTTTTAAAATATGTTATATTTATATAAATTTTAA
Found at i:406243 original size:26 final size:26
Alignment explanation
Indices: 406155--406243 Score: 85
Period size: 26 Copynumber: 3.5 Consensus size: 26
406145 TAATAATTAT
*
406155 TTTTTAAAATATTTTATATTTATATAA
1 TTTTT-AAATATGTTATATTTATATAA
* * *
406182 ATTTTAAAT-T-ATATATTT-TATTA
1 TTTTTAAATATGTTATATTTATATAA
**
406205 TTTTTATTGTATGTTATATTTATATAA
1 TTTTTA-AATATGTTATATTTATATAA
406232 TTTTTAAATATG
1 TTTTTAAATATG
406244 AAGTTTACGT
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
23 9 0.19
24 8 0.17
25 2 0.04
26 15 0.31
27 14 0.29
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (26 bp):
TTTTTAAATATGTTATATTTATATAA
Found at i:408649 original size:51 final size:50
Alignment explanation
Indices: 408478--408647 Score: 252
Period size: 50 Copynumber: 3.4 Consensus size: 50
408468 GTTGATTATC
*
408478 CTTCACCTACCTTTGACAATAGAGAGAGGTGGTCATAATTG-TGAACGATT
1 CTTCACCAACCTTTGACAATAGAGAGAGGTGGTCATAATTGTTG-ACGATT
* * *
408528 CTTCACCAACCTTTGACAATAGAGAGAAGTGGTCATAACTGTTCACGATT
1 CTTCACCAACCTTTGACAATAGAGAGAGGTGGTCATAATTGTTGACGATT
* * *
408578 CTTCACCAACCTTTGACAAATGGAGAGAGGTGGCCATTATTGTTGACGATT
1 CTTCACCAACCTTTGAC-AATAGAGAGAGGTGGTCATAATTGTTGACGATT
408629 CTTCACCAACCTTTGACAA
1 CTTCACCAACCTTTGACAA
408648 ATATGGCCAT
Statistics
Matches: 108, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
50 63 0.58
51 45 0.42
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (50 bp):
CTTCACCAACCTTTGACAATAGAGAGAGGTGGTCATAATTGTTGACGATT
Found at i:413149 original size:50 final size:50
Alignment explanation
Indices: 413071--413353 Score: 422
Period size: 50 Copynumber: 5.6 Consensus size: 50
413061 AGTTGTTGCC
* * * ** *
413071 ATTGTTGACTATCCTTCACCAACTTTTGACAATAGAGAGAGGTGATCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
413121 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* * * *
413171 ATTGTTGATGATTCTTCATCAACCTTTGACAATAGAGAGAGGTGGCTATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
413221 ATTGTTGATGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* * *
413271 ATTGTTGACGATTCTTTACCAACCTTTGACAAATGGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGAC-AATAGAGAGAGGTGGCCATA
413322 ATTGTTGACGATTCTTCACCAACCTTTGACAA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAA
413354 ATGTGGCCAT
Statistics
Matches: 214, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
50 167 0.78
51 47 0.22
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:414181 original size:2 final size:2
Alignment explanation
Indices: 414174--414213 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
414164 CATGAAATGA
414174 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
414214 CAGATTATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:415470 original size:15 final size:14
Alignment explanation
Indices: 415450--415489 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
415440 AATATTTTAA
*
415450 ATAAAATAATAATAT
1 ATAAAATAATAA-AC
415465 ATAAAATATATAAAC
1 ATAAAATA-ATAAAC
415480 ATAAAATAAT
1 ATAAAATAAT
415490 TACACAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 2 0.09
15 17 0.74
16 4 0.17
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAAATAATAAAC
Found at i:415471 original size:20 final size:21
Alignment explanation
Indices: 415431--415472 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
415421 AATTTATATA
* *
415431 AAAATATATAATATTTTAAAT
1 AAAATATATAATATATAAAAT
415452 AAAATA-ATAATATATAAAAT
1 AAAATATATAATATATAAAAT
415472 A
1 A
415473 TATAAACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAATATATAATATATAAAAT
Found at i:416286 original size:17 final size:18
Alignment explanation
Indices: 416252--416287 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
416242 ATTATATTTT
*
416252 TATATTTACATTTAAATA
1 TATATTTACATATAAATA
416270 TATATTTA-ATATAAATA
1 TATATTTACATATAAATA
416287 T
1 T
416288 TAAATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TATATTTACATATAAATA
Found at i:416293 original size:13 final size:13
Alignment explanation
Indices: 416263--416312 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
416253 ATATTTACAT
416263 TTAAATAT--ATA
1 TTAAATATAAATA
*
416274 TTTAATATAAATA
1 TTAAATATAAATA
416287 TTAAATATAAATAAA
1 TTAAATATAAAT--A
416302 TTAAA-ATAAAT
1 TTAAATATAAAT
416313 CTGTAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 7 0.21
13 14 0.42
14 6 0.18
15 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TTAAATATAAATA
Found at i:422060 original size:160 final size:161
Alignment explanation
Indices: 421789--422106 Score: 514
Period size: 160 Copynumber: 2.0 Consensus size: 161
421779 CTTTCGGAGA
* * * *
421789 AATAAGTCTTCCCTACAATAAAATTAACTCTGAAAAACTAGATCGGCTATCTAGGCTAGTGCTCC
1 AATAAATCTTCCCTAAAATAAAATTAACTCTGAAAAACTAGATCAGCTATCTAGGCTAGTGCTCA
* * *
421854 TACGGCCAGCTAATCATTTCCACTCGTGGAGTTGACAAGAAGAGGACCAAGGGGTTGGTTAACAG
66 TACAGCCAGCTAACCATTTCCACTCGTGGAATTGACAAGAAGAGGACCAAGGGGTTGGTTAACAG
421919 AGTTAATAGGAAGTTTCCTTGAGTAGGGGAT
131 AGTTAATAGGAAGTTTCCTTGAGTAGGGGAT
421950 AATAAATCTTCCCTAAAATAAAATTAACTCTGAAAAACTAGATCAGCT-TCTAGGCTAGTGCTCA
1 AATAAATCTTCCCTAAAATAAAATTAACTCTGAAAAACTAGATCAGCTATCTAGGCTAGTGCTCA
** *
422014 TACAGCCAGCTAACCATTTCCACTCGTGGAATTGGA-TTGGAGAGGACCAAGGGGTTGGTTAACA
66 TACAGCCAGCTAACCATTTCCACTCGTGGAATT-GACAAGAAGAGGACCAAGGGGTTGGTTAACA
*
422078 GAGTTAATAGGAAGTTTCTTTGAGTAGGG
130 GAGTTAATAGGAAGTTTCCTTGAGTAGGG
422107 CCATGAAAGA
Statistics
Matches: 145, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
160 98 0.68
161 47 0.32
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (161 bp):
AATAAATCTTCCCTAAAATAAAATTAACTCTGAAAAACTAGATCAGCTATCTAGGCTAGTGCTCA
TACAGCCAGCTAACCATTTCCACTCGTGGAATTGACAAGAAGAGGACCAAGGGGTTGGTTAACAG
AGTTAATAGGAAGTTTCCTTGAGTAGGGGAT
Found at i:422348 original size:14 final size:14
Alignment explanation
Indices: 422253--422348 Score: 52
Period size: 14 Copynumber: 6.5 Consensus size: 14
422243 TTTAATATGT
422253 TATTAATTTAAGTTA
1 TATTAATTTAA-TTA
* *
422268 TATAAATTTTGA-TA
1 TATTAA-TTTAATTA
* * *
422282 TATTTATATATTTA
1 TATTAATTTAATTA
*
422296 TATTGATTTTTGAATTA
1 TATT-A-ATTT-AATTA
*
422313 TATTACATTTAAATA
1 TATTA-ATTTAATTA
422328 T-TATAATTTAATTA
1 TAT-TAATTTAATTA
422342 TATTAAT
1 TATTAAT
422349 ATTATATTTA
Statistics
Matches: 59, Mismatches: 15, Indels: 15
0.66 0.17 0.17
Matches are distributed among these distances:
13 2 0.03
14 26 0.44
15 13 0.22
16 10 0.17
17 8 0.14
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (14 bp):
TATTAATTTAATTA
Found at i:422382 original size:36 final size:35
Alignment explanation
Indices: 422312--422384 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 35
422302 TTTTTGAATT
422312 ATATTACATTTAAATATTATAATTTAATTATATTA
1 ATATTACATTTAAATATTATAATTTAATTATATTA
* * *
422347 ATATTATATTTAAA-ATTATCGAATTTATTTTTATTA
1 ATATTACATTTAAATATTAT--AATTTAATTATATTA
422383 AT
1 AT
422385 TTTTAGTGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 5 0.15
35 13 0.39
36 15 0.45
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.53
Consensus pattern (35 bp):
ATATTACATTTAAATATTATAATTTAATTATATTA
Found at i:423557 original size:27 final size:26
Alignment explanation
Indices: 423527--423596 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
423517 TATATTGAGT
423527 TTAAGTATAATTTTTTTATAATTTAAA
1 TTAA-TATAATTTTTTTATAATTTAAA
* ** *
423554 TTAATTTAATTTAAATTATTATTTAAA
1 TTAATATAATTT-TTTTATAATTTAAA
*
423581 -TAATATAAATTTTTTA
1 TTAATATAATTTTTTTA
423597 ATTAAATTTA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
25 3 0.09
26 16 0.47
27 15 0.44
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
TTAATATAATTTTTTTATAATTTAAA
Found at i:430456 original size:2 final size:2
Alignment explanation
Indices: 430449--430485 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
430439 GGTTTCAAGT
430449 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
430486 ATCTGACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:433002 original size:2 final size:2
Alignment explanation
Indices: 432995--433019 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
432985 TTATAAGCAC
432995 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
433020 TTAGAACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:433419 original size:17 final size:17
Alignment explanation
Indices: 433384--433425 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
433374 GTTCAAAAAT
*
433384 TTTAATATAATTAATTA
1 TTTAATTTAATTAATTA
433401 TTTAATTTAATATAA-TA
1 TTTAATTTAAT-TAATTA
433418 TTATAATT
1 TT-TAATT
433426 CTCAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATTTAATTAATTA
Found at i:434354 original size:2 final size:2
Alignment explanation
Indices: 434347--434374 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
434337 TTAATGTTAA
434347 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
434375 TCTATTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:436131 original size:21 final size:23
Alignment explanation
Indices: 436091--436142 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
436081 AAAAGTGGTT
*
436091 AAATTTTTTAATTATTTTTTAAA
1 AAATATTTTAATTATTTTTTAAA
*
436114 AAATATTTTAATT-TTTTTAAAA
1 AAATATTTTAATTATTTTTTAAA
436136 ATAATAT
1 A-AATAT
436143 AATAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATATTTTAATTATTTTTTAAA
Found at i:436145 original size:20 final size:20
Alignment explanation
Indices: 436104--436145 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
436094 TTTTTTAATT
* *
436104 ATTTTTTAAAAAATATTTTA
1 ATTTTTTAAAAAATAATATA
*
436124 ATTTTTTTAAAAATAATATA
1 ATTTTTTAAAAAATAATATA
436144 AT
1 AT
436146 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTTTTAAAAAATAATATA
Found at i:436508 original size:15 final size:15
Alignment explanation
Indices: 436484--436513 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
436474 ACTTTGACTT
436484 GGATCAACTTGGAAA
1 GGATCAACTTGGAAA
*
436499 GGATCTACTTGGAAA
1 GGATCAACTTGGAAA
436514 TCCAACCCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.23
Consensus pattern (15 bp):
GGATCAACTTGGAAA
Found at i:438587 original size:2 final size:2
Alignment explanation
Indices: 438580--438622 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
438570 GCTATATGTG
*
438580 TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
438622 T
1 T
438623 GAGTTTGCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:438763 original size:16 final size:18
Alignment explanation
Indices: 438736--438768 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
438726 ACTTGTTTGG
438736 TTTGAGAATAAT-GATTT
1 TTTGAGAATAATCGATTT
438753 TTTGA-AATAATCGATT
1 TTTGAGAATAATCGATT
438769 CTGATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.45
Consensus pattern (18 bp):
TTTGAGAATAATCGATTT
Found at i:441118 original size:28 final size:28
Alignment explanation
Indices: 441082--441139 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
441072 TTGACATGTC
**
441082 ATCCAAAAAGGGTACGATTAGATCTCAT
1 ATCCAAAAAGGGTAAAATTAGATCTCAT
441110 ATCCAAAAAGGGTAAAATTAGATCTCAT
1 ATCCAAAAAGGGTAAAATTAGATCTCAT
441138 AT
1 AT
441140 ATGGGCTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (28 bp):
ATCCAAAAAGGGTAAAATTAGATCTCAT
Found at i:445996 original size:43 final size:43
Alignment explanation
Indices: 445901--446012 Score: 110
Period size: 43 Copynumber: 2.7 Consensus size: 43
445891 TTTTTAAAAA
* *
445901 ATTATATTAAAAATTTTAAAATATAA-AATTACCTTTAATAACT
1 ATTATATTAAAAATATTAAAA-ATAATATTTACCTTTAATAACT
* ** *
445944 ATT-TTTTAAAATATATTAAAAATAATATTTATTTTTAAT-ATT
1 ATTATATTAAAA-ATATTAAAAATAATATTTACCTTTAATAACT
445986 ATTATATTAAAAATA--AAAAA-AATATTT
1 ATTATATTAAAAATATTAAAAATAATATTT
446013 TTTAATCATC
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
39 7 0.12
40 5 0.08
42 19 0.32
43 28 0.47
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.46
Consensus pattern (43 bp):
ATTATATTAAAAATATTAAAAATAATATTTACCTTTAATAACT
Found at i:447635 original size:23 final size:23
Alignment explanation
Indices: 447608--447656 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
447598 GTGAACTTTT
* *
447608 CAGTAAGATGGATTTGGTGCCGC
1 CAGTAAAACGGATTTGGTGCCGC
447631 CAGTAAAACGGATTTGGTGCCGC
1 CAGTAAAACGGATTTGGTGCCGC
447654 CAG
1 CAG
447657 AAGCTGCTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.22
Consensus pattern (23 bp):
CAGTAAAACGGATTTGGTGCCGC
Found at i:448067 original size:17 final size:18
Alignment explanation
Indices: 448031--448076 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
448021 TAATAATTTG
*
448031 TATAT-TTTTATTATATT
1 TATATATTTTATTATAAT
448048 TATATATTTTATTA-AAT
1 TATATATTTTATTATAAT
448065 TATA-ATTTTATT
1 TATATATTTTATT
448077 TAAAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 8 0.30
17 11 0.41
18 8 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATATATTTTATTATAAT
Found at i:448105 original size:17 final size:17
Alignment explanation
Indices: 448083--448137 Score: 71
Period size: 16 Copynumber: 3.4 Consensus size: 17
448073 TATTTAAAAT
448083 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
*
448100 ATTTTA-ATTTATTATTA
1 ATTTTATATTTA-TATAA
448117 A-TTTATA-TTATATAA
1 ATTTTATATTTATATAA
448132 ATTTTA
1 ATTTTA
448138 AAATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
15 5 0.15
16 16 0.48
17 12 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:448144 original size:16 final size:16
Alignment explanation
Indices: 448092--448146 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
448082 TATTTTATAT
*
448092 TTATATAAATTTTAAT
1 TTATATAAATTTTAAA
* *
448108 TTATTATTAA-TTTATA
1 TTA-TATAAATTTTAAA
448124 TTATATAAATTTTAAA
1 TTATATAAATTTTAAA
*
448140 ATATATA
1 TTATATA
448147 TTTTTATTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 5 0.16
16 21 0.68
17 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATATAAATTTTAAA
Found at i:452757 original size:2 final size:2
Alignment explanation
Indices: 452750--452780 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
452740 GTAGGACAGC
452750 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
452781 GTTTTTAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:454938 original size:2 final size:2
Alignment explanation
Indices: 454931--454957 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
454921 CACAAACAGA
454931 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
454958 AGCAACCTTT
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:456847 original size:23 final size:22
Alignment explanation
Indices: 456821--456868 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
456811 TAATTTTATG
*
456821 ATATAAAAAATAATTAAAATATA
1 ATATAAAAAATAATAAAAATA-A
*
456844 ATATAAAATATAATAAAAATAA
1 ATATAAAAAATAATAAAAATAA
456866 ATA
1 ATA
456869 AATATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
ATATAAAAAATAATAAAAATAA
Found at i:456852 original size:12 final size:12
Alignment explanation
Indices: 456821--456868 Score: 66
Period size: 11 Copynumber: 4.2 Consensus size: 12
456811 TAATTTTATG
*
456821 ATATAAAAAATA
1 ATATAAAATATA
456833 AT-TAAAATATA
1 ATATAAAATATA
456844 ATATAAAATATA
1 ATATAAAATATA
456856 ATA-AAAATA-A
1 ATATAAAATATA
456866 ATA
1 ATA
456869 AATATATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
10 4 0.12
11 16 0.47
12 14 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
ATATAAAATATA
Found at i:456853 original size:21 final size:21
Alignment explanation
Indices: 456827--456881 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 21
456817 TATGATATAA
456827 AAAATA-ATTAAAATATAATAT
1 AAAATATATTAAAATATAA-AT
*
456848 AAAATATAATAAAA-ATAAAT
1 AAAATATATTAAAATATAAAT
456868 -AAATATATTAAAAT
1 AAAATATATTAAAAT
456882 TTATGAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 12 0.40
20 2 0.07
21 10 0.33
22 6 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAATATATTAAAATATAAAT
Found at i:456861 original size:10 final size:10
Alignment explanation
Indices: 456823--456881 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
456813 ATTTTATGAT
*
456823 ATAAAAAATA
1 ATAAAATATA
456833 ATTAAAATATAA
1 A-TAAAATAT-A
456845 TATAAAATATA
1 -ATAAAATATA
456856 ATAAAA-ATA
1 ATAAAATATA
456865 A-ATAAATATA
1 ATA-AAATATA
*
456875 TTAAAAT
1 ATAAAAT
456882 TTATGAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
8 1 0.02
9 7 0.17
10 14 0.34
11 9 0.22
12 9 0.22
13 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
ATAAAATATA
Found at i:457628 original size:32 final size:32
Alignment explanation
Indices: 457551--457640 Score: 87
Period size: 32 Copynumber: 2.8 Consensus size: 32
457541 ATAATATTTA
* *
457551 AAATATTTTATATTTATATAATTTTAATATAT
1 AAATTTTTTATATTTATATAATTTTAAAATAT
* **
457583 -TATTAGTTA-ATATTATATAAATTTTAAAATAT
1 AAATTTTTTATAT-TTATAT-AATTTTAAAATAT
457615 AAATTTTTTATATTT-TAATAATTTTA
1 AAATTTTTTATATTTAT-ATAATTTTA
457641 TTAATATTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
30 2 0.04
31 11 0.24
32 20 0.44
33 10 0.22
34 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (32 bp):
AAATTTTTTATATTTATATAATTTTAAAATAT
Found at i:458194 original size:22 final size:22
Alignment explanation
Indices: 458169--458223 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
458159 ATGAATAAAA
*
458169 TATTTTATAATATAAT-ATAATT
1 TATTTTATAAT-TAATAAAAATT
*
458191 TATTATT-TTATTAATAAAAATT
1 TATT-TTATAATTAATAAAAATT
458213 TATTTTA-AATT
1 TATTTTATAATT
458224 TAAATTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
21 9 0.33
22 16 0.59
23 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTTTATAATTAATAAAAATT
Found at i:458931 original size:24 final size:24
Alignment explanation
Indices: 458895--458940 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
458885 AATAAAAATT
458895 AGCCACAAATTTTGACAAACAATA
1 AGCCACAAATTTTGACAAACAATA
* *
458919 AGCCATAATTTTTGACAAACAA
1 AGCCACAAATTTTGACAAACAA
458941 AAAGAAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.20, G:0.09, T:0.24
Consensus pattern (24 bp):
AGCCACAAATTTTGACAAACAATA
Found at i:458992 original size:27 final size:27
Alignment explanation
Indices: 458930--458998 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
458920 GCCATAATTT
* * * *
458930 TTGACAAACAAAAAGAAACCACTATTT
1 TTGACAAATACAAAGAAACCACCATTG
*
458957 TTGACAAATACAAAGTAACCACCATTG
1 TTGACAAATACAAAGAAACCACCATTG
458984 TTGACAAATACAAAG
1 TTGACAAATACAAAG
458999 GGTGACTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.49, C:0.19, G:0.10, T:0.22
Consensus pattern (27 bp):
TTGACAAATACAAAGAAACCACCATTG
Found at i:464817 original size:52 final size:52
Alignment explanation
Indices: 464669--464797 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
464659 CGAAATATGA
464669 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
464721 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
464773 AAATTTGCCTGCATATATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
464798 AAAATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:464824 original size:13 final size:13
Alignment explanation
Indices: 464806--464830 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
464796 CAAAAATCAG
464806 TGTATCGATACAA
1 TGTATCGATACAA
464819 TGTATCGATACA
1 TGTATCGATACA
464831 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:464893 original size:13 final size:13
Alignment explanation
Indices: 464875--464958 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
464865 AGCTTCGTAG
464875 CGATACATTGTAT
1 CGATACATTGTAT
464888 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
464907 CGATACATTGTAT
1 CGATACATTGTAT
464920 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
464939 CGATACATTGTAT
1 CGATACATTGTAT
464952 CGATACA
1 CGATACA
464959 ACACTTATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 26 0.44
14 1 0.02
15 2 0.03
16 8 0.14
17 2 0.03
18 1 0.02
19 19 0.32
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:464907 original size:19 final size:18
Alignment explanation
Indices: 464883--464979 Score: 88
Period size: 19 Copynumber: 5.8 Consensus size: 18
464873 AGCGATACAT
464883 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
464902 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
464915 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
464934 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
464947 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
464966 TGTATCAATACAAA
1 TGTATCGATACAAA
464980 TCGTTGAAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 25
0.71 0.01 0.27
Matches are distributed among these distances:
13 22 0.34
14 2 0.03
16 4 0.06
18 3 0.05
19 34 0.52
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:464916 original size:32 final size:32
Alignment explanation
Indices: 464875--464977 Score: 188
Period size: 32 Copynumber: 3.2 Consensus size: 32
464865 AGCTTCGTAG
*
464875 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
464907 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
464939 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
464971 CAATACA
1 CGATACA
464978 AATCGTTGAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:467197 original size:27 final size:28
Alignment explanation
Indices: 467151--467217 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
467141 ATAACTAATA
**
467151 ATTTTTGACAAATAAAAAAAAAATTACC
1 ATTTTTGACAAATAAAAAAAAAACCACC
* *
467179 ATTTTTGACAAAT-ACAAAATAACCACC
1 ATTTTTGACAAATAAAAAAAAAACCACC
*
467206 ATTGTTGACAAA
1 ATTTTTGACAAA
467218 CATAAAAGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 21 0.62
28 13 0.38
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (28 bp):
ATTTTTGACAAATAAAAAAAAAACCACC
Found at i:472753 original size:2 final size:2
Alignment explanation
Indices: 472748--472773 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
472738 CAGAGCGAGC
472748 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
472774 TTAGTTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:472993 original size:2 final size:2
Alignment explanation
Indices: 472986--473019 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
472976 AATTAAGGAC
*
472986 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
473020 CATGTTAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:477870 original size:18 final size:17
Alignment explanation
Indices: 477834--477866 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
477824 ATTAAAAAAA
477834 TTAAATTAATTTTTTAT
1 TTAAATTAATTTTTTAT
477851 TTAAA-TAATTTTTTAT
1 TTAAATTAATTTTTTAT
477867 ATTTTCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTAAATTAATTTTTTAT
Found at i:477904 original size:23 final size:24
Alignment explanation
Indices: 477844--477904 Score: 61
Period size: 29 Copynumber: 2.4 Consensus size: 24
477834 TTAAATTAAT
*
477844 TTTTTATTTAAATAATTTTTTATA
1 TTTTTATTTAAATAAATTTTTATA
477868 TTTTCATTATATTTAAATAAATTTTTATA
1 --TT--TT-TATTTAAATAAATTTTTATA
477897 -TTTTATTT
1 TTTTTATTT
477905 GTATAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
23 5 0.16
24 2 0.06
26 3 0.10
28 2 0.06
29 19 0.61
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTTTATTTAAATAAATTTTTATA
Found at i:477977 original size:30 final size:30
Alignment explanation
Indices: 477943--478013 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
477933 AAAGATTAAG
* * * *
477943 ATTTATTTATATATAACTTATAGGTTAAAA
1 ATTTATTTAAAGATAACTTAAAAGTTAAAA
*
477973 ATTTATTTAAAGATAATTTAAAAGTTAAAA
1 ATTTATTTAAAGATAACTTAAAAGTTAAAA
478003 ATTTATTTAAA
1 ATTTATTTAAA
478014 TGTAATAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (30 bp):
ATTTATTTAAAGATAACTTAAAAGTTAAAA
Found at i:478033 original size:30 final size:30
Alignment explanation
Indices: 477967--478044 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
477957 AACTTATAGG
*
477967 TTAAAAATTTATTTAAA-GATAATTTAAAAG
1 TTAAAAATTTATTTAAATGATAA-TTAAAAA
477997 TTAAAAATTTATTTAAATG-TAA-TAAAAA
1 TTAAAAATTTATTTAAATGATAATTAAAAA
*
478025 TATAAAAAAATTATTTAAAT
1 T-T-AAAAATTTATTTAAAT
478045 AAAAAGATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
28 6 0.14
29 1 0.02
30 35 0.81
31 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (30 bp):
TTAAAAATTTATTTAAATGATAATTAAAAA
Found at i:478527 original size:17 final size:17
Alignment explanation
Indices: 478474--478528 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 17
478464 TATCTATTTA
478474 TATTAT-AT-TTTAATT
1 TATTATAATATTTAATT
*
478489 TATTATATATTTTATATAATT
1 TATTATA-A---TATTTAATT
478510 TATTATAATATTTAATT
1 TATTATAATATTTAATT
478527 TA
1 TA
478529 AAAAAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
15 6 0.19
17 11 0.34
20 2 0.06
21 13 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATAATATTTAATT
Found at i:478643 original size:17 final size:20
Alignment explanation
Indices: 478617--478663 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 20
478607 TTTTATTTTA
*
478617 TATAAAATTTA-A-CATA-T
1 TATAATATTTATATCATATT
478634 TATAATATTTATATCATATT
1 TATAATATTTATATCATATT
*
478654 TATATTATTT
1 TATAATATTT
478664 TTATATCGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 10 0.40
18 1 0.04
19 4 0.16
20 10 0.40
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
TATAATATTTATATCATATT
Found at i:478931 original size:6 final size:6
Alignment explanation
Indices: 478920--478945 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
478910 TTGTTTATTA
478920 ATTAAT ATTAAT ATTAAT ATTAAT AT
1 ATTAAT ATTAAT ATTAAT ATTAAT AT
478946 AATTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTAAT
Done.