Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold307
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: 622582
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 5
Found at i:320229 original size:11 final size:11
Alignment explanation
Indices: 320144--320240 Score: 67
Period size: 11 Copynumber: 8.9 Consensus size: 11
320134 TTATACAATA
*
320144 ATTATATTTCT
1 ATTATATTTAT
320155 ATTAT-TTTAT
1 ATTATATTTAT
* * *
320165 ATTTTATATAA
1 ATTATATTTAT
* * *
320176 ATTTTAATATAC
1 ATTAT-ATTTAT
320188 ATT-TATTTAT
1 ATTATATTTAT
*
320198 ATTA-AATTAT
1 ATTATATTTAT
320208 ATT-TAATTTTAT
1 ATTAT-A-TTTAT
320220 ATTATATTTAT
1 ATTATATTTAT
320231 ATTATATTTA
1 ATTATATTTA
320241 AAATTATGGC
Statistics
Matches: 70, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
10 23 0.33
11 30 0.43
12 16 0.23
13 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTATATTTAT
Found at i:320234 original size:28 final size:26
Alignment explanation
Indices: 320189--320241 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 26
320179 TTAATATACA
320189 TTTATTTATATTAAATTATATTTAAT
1 TTTATTTATATTAAATTATATTTAAT
*
320215 TTTATATTATATTTATATTATATTTAA
1 TTTAT-TTATA-TTAAATTATATTTAA
320242 AATTATGGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 5 0.21
27 5 0.21
28 14 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTATTTATATTAAATTATATTTAAT
Found at i:320237 original size:16 final size:16
Alignment explanation
Indices: 320144--320238 Score: 76
Period size: 16 Copynumber: 6.2 Consensus size: 16
320134 TTATACAATA
*
320144 ATTATATTTCTATTAT
1 ATTATATTTATATTAT
*
320160 TTTATATTT-TA-TAT
1 ATTATATTTATATTAT
* *
320174 A-AAT-TTTA-ATATAC
1 ATTATATTTATAT-TAT
*
320188 ATT-TATTTATATTAA
1 ATTATATTTATATTAT
*
320203 ATTATATTTAATTTTAT
1 ATTATATTT-ATATTAT
320220 ATTATATTTATATTAT
1 ATTATATTTATATTAT
320236 ATT
1 ATT
320239 TAAAATTATG
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
12 4 0.06
13 2 0.03
14 7 0.11
15 11 0.18
16 24 0.39
17 14 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATATTTATATTAT
Found at i:320247 original size:28 final size:26
Alignment explanation
Indices: 320190--320247 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
320180 TAATATACAT
**
320190 TTATTTATATTAAATTATATTTAATT
1 TTATTTATATTAAATTATATTTAAAA
*
320216 TTATATTATATTTATATTATATTTAAAA
1 TTAT-TTATA-TTAAATTATATTTAAAA
320244 TTAT
1 TTAT
320248 GGCAATCAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 4 0.15
27 5 0.19
28 18 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TTATTTATATTAAATTATATTTAAAA
Found at i:320513 original size:11 final size:10
Alignment explanation
Indices: 320494--320574 Score: 62
Period size: 11 Copynumber: 7.8 Consensus size: 10
320484 ATAATTTTAA
320494 AAAAT-TAATT
1 AAAATATAA-T
320504 AAAATATAAT
1 AAAATATAAT
320514 AAAA-ATAAT
1 AAAATATAAT
*
320523 AATATAATAAT
1 AAAAT-ATAAT
320534 AATAATATAA-
1 AA-AATATAAT
320544 ACATAATATAATAT
1 A-A-AATAT-A-AT
320558 AAAATATAA-
1 AAAATATAAT
320567 AAAATATA
1 AAAATATA
320575 TATATATATC
Statistics
Matches: 61, Mismatches: 2, Indels: 17
0.76 0.03 0.21
Matches are distributed among these distances:
9 16 0.26
10 12 0.20
11 22 0.36
12 8 0.13
13 2 0.03
14 1 0.02
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATATAAT
Found at i:320523 original size:3 final size:3
Alignment explanation
Indices: 320509--320556 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
320499 TAATTAAAAT
*
320509 ATA ATA AAA ATA ATA AT- ATA ATA ATA ATA AT- ATA A-A CATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
320551 ATA ATA
1 ATA ATA
320557 TAAAATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 30 0.79
4 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:320528 original size:17 final size:17
Alignment explanation
Indices: 320506--320540 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
320496 AATTAATTAA
320506 AATATAATAAAAATAAT
1 AATATAATAAAAATAAT
*
320523 AATATAATAATAATAAT
1 AATATAATAAAAATAAT
320540 A
1 A
320541 TAAACATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATATAATAAAAATAAT
Found at i:320529 original size:14 final size:14
Alignment explanation
Indices: 320512--320566 Score: 65
Period size: 14 Copynumber: 3.7 Consensus size: 14
320502 TTAAAATATA
320512 ATAAAAATAATAAT
1 ATAAAAATAATAAT
*
320526 ATAATAATAATAAT
1 ATAAAAATAATAAT
*
320540 ATAAACATAATATAAT
1 ATAAAAAT-A-ATAAT
320556 ATAAAATATAA
1 ATAAAA-ATAA
320567 AAAATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
14 19 0.56
15 2 0.06
16 11 0.32
17 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
ATAAAAATAATAAT
Found at i:320566 original size:17 final size:17
Alignment explanation
Indices: 320499--320651 Score: 70
Period size: 19 Copynumber: 8.8 Consensus size: 17
320489 TTTAAAAAAT
320499 TAAT-TAAAATATAATA
1 TAATATAAAATATAATA
*
320515 -AAAATAATAATATAATAA
1 TAATATAA-AATATAAT-A
*
320533 TAATAATATAAACATAATA
1 TAAT-ATA-AAATATAATA
320552 TAATATAAAATATAA-A
1 TAATATAAAATATAATA
* *
320568 AAATAT-ATATAT-ATA
1 TAATATAAAATATAATA
* *
320583 TCAATACTTTAAATATATTTA
1 T-AATA--TAAAATATA-ATA
320604 TAATATATAAA-A-AATA
1 TAATATA-AAATATAATA
* *
320620 TAA-ATAAATTATCAAATC
1 TAATATAAAATAT--AATA
*
320638 TAATATTAAATATA
1 TAATATAAAATATA
320652 GATGGAGAGA
Statistics
Matches: 103, Mismatches: 15, Indels: 37
0.66 0.10 0.24
Matches are distributed among these distances:
14 3 0.03
15 12 0.12
16 18 0.17
17 17 0.17
18 13 0.13
19 22 0.21
20 14 0.14
21 4 0.04
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
TAATATAAAATATAATA
Found at i:320643 original size:45 final size:45
Alignment explanation
Indices: 320547--320643 Score: 108
Period size: 47 Copynumber: 2.1 Consensus size: 45
320537 AATATAAACA
* * *
320547 TAATATAATATAAAATATAAAAAATATATATATATATCAATACTT
1 TAATATAATATAAAATATAAAAAATATAAATAAATATCAATACTC
* *
320592 TAAATATATTTATAATATATAAAAAATATAAATAAATTATCAA-A-TC
1 T-AATATA-ATATAAAATATAAAAAATATAAATAAA-TATCAATACTC
320638 TAATAT
1 TAATAT
320644 TAAATATAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
45 6 0.14
46 8 0.18
47 24 0.55
48 6 0.14
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (45 bp):
TAATATAATATAAAATATAAAAAATATAAATAAATATCAATACTC
Found at i:320987 original size:38 final size:36
Alignment explanation
Indices: 320914--320991 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 36
320904 TCAATAGATT
*
320914 ATTT-TAAAAAAATTAATTTAAATATTAAATAAAAA
1 ATTTATAAAAAAATTAATTTAAATATAAAATAAAAA
* * *
320949 ATTTATAAAATAATATAATTTTTAATATAAAATTAAAA
1 ATTTATAAAAAAAT-TAA-TTTAAATATAAAATAAAAA
320987 ATTTA
1 ATTTA
320992 AACTCATCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 4 0.11
36 8 0.22
37 3 0.08
38 21 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (36 bp):
ATTTATAAAAAAATTAATTTAAATATAAAATAAAAA
Found at i:321721 original size:30 final size:29
Alignment explanation
Indices: 321687--321750 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
321677 TAAATTTAAA
321687 TAAAATATAATTATATAATATAAAAAAAT-T
1 TAAAATATAA-TATA-AATATAAAAAAATAT
* *
321717 TAAAATATAATATAAATATATAAATATAT
1 TAAAATATAATATAAATATAAAAAAATAT
321746 TAAAA
1 TAAAA
321751 GATGAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 11 0.35
29 10 0.32
30 10 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
TAAAATATAATATAAATATAAAAAAATAT
Found at i:321729 original size:35 final size:35
Alignment explanation
Indices: 321678--321744 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
321668 TGCACCCTAT
*
321678 AAATTTAAATAAAATATAATTATAT-AATATAAAA
1 AAATTTAAATAAAATATAAATATATAAATATAAAA
*
321712 AAATTTAAAATATAATATAAATATATAAATATA
1 AAATTT-AAATAAAATATAAATATATAAATATA
321745 TTAAAAGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 6 0.21
35 17 0.59
36 6 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (35 bp):
AAATTTAAATAAAATATAAATATATAAATATAAAA
Found at i:328420 original size:22 final size:25
Alignment explanation
Indices: 328379--328430 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
328369 AATTTAATAA
*
328379 TTTATTTACTTTTATTATAAT-A-GT
1 TTTATTTA-TTTTATCATAATCATGT
328403 TTTATTT-TTTTATCATAATCATGT
1 TTTATTTATTTTATCATAATCATGT
328427 TTTA
1 TTTA
328431 AATTTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 11 0.44
23 1 0.04
24 13 0.52
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTATTTATTTTATCATAATCATGT
Found at i:328436 original size:24 final size:22
Alignment explanation
Indices: 328388--328436 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
328378 ATTTATTTAC
* **
328388 TTTTATTATAATAGTTTTATTT
1 TTTTATCATAATAGTTTTAAAT
328410 TTTTATCATAATCATGTTTTAAAT
1 TTTTATCATAAT-A-GTTTTAAAT
328434 TTT
1 TTT
328437 ATATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 11 0.50
23 1 0.05
24 10 0.45
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (22 bp):
TTTTATCATAATAGTTTTAAAT
Found at i:328461 original size:17 final size:18
Alignment explanation
Indices: 328431--328470 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
328421 TCATGTTTTA
*
328431 AATTTTATATATTTATAT
1 AATTTTATATATTTAAAT
328449 AATTTTA-ATATTTAAAT
1 AATTTTATATATTTAAAT
328466 AATTT
1 AATTT
328471 AAGTCATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTTTATATATTTAAAT
Found at i:330176 original size:2 final size:2
Alignment explanation
Indices: 330171--330316 Score: 292
Period size: 2 Copynumber: 73.0 Consensus size: 2
330161 AAAAAAGAAA
330171 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
330213 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
330255 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
330297 AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG
330317 GGGCTGTTTT
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 144 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:331166 original size:18 final size:17
Alignment explanation
Indices: 331136--331170 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
331126 AAAATAGACG
*
331136 TAAAATTTTATTATATT
1 TAAAATTTCATTATATT
331153 TAAATATTTCATTATATT
1 TAAA-ATTTCATTATATT
331171 ATAATCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
TAAAATTTCATTATATT
Found at i:331395 original size:6 final size:6
Alignment explanation
Indices: 331376--331516 Score: 59
Period size: 6 Copynumber: 23.7 Consensus size: 6
331366 TACAAAAAAT
* * *
331376 AATATA AATA-A AATATA AATATA TAA-ATA TAT-TA AA-ATT TATA-A
1 AATATA AATATA AATATA AATATA -AATATA AATATA AATATA AATATA
* * *
331420 AATATA AATTATT AATAT- -ATTTA AAT-T- CATATA AATATA TAATATA
1 AATATA AA-TATA AATATA AATATA AATATA AATATA AATATA -AATATA
* *
331466 TCAATATA ATTATA ATATATA AA-ATTA ATATATA TATATA TAATATA
1 --AATATA AATATA A-ATATA AATA-TA A-ATATA AATATA -AATATA
331513 AATA
1 AATA
331517 AATAAATAAA
Statistics
Matches: 102, Mismatches: 15, Indels: 36
0.67 0.10 0.24
Matches are distributed among these distances:
4 5 0.05
5 17 0.17
6 47 0.46
7 26 0.25
8 7 0.07
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (6 bp):
AATATA
Found at i:331399 original size:19 final size:19
Alignment explanation
Indices: 331347--331526 Score: 93
Period size: 19 Copynumber: 9.2 Consensus size: 19
331337 TATGTGAAAA
331347 AAAAT-TAAATATTATATAAT
1 AAAATATAAATA-TATA-AAT
*
331367 ACAA-A-AAATAATATAAAT
1 AAAATATAAAT-ATATAAAT
331385 AAAATATAAATATATAAAT
1 AAAATATAAATATATAAAT
* * *
331404 ATATTA-AAATTTATAAAAT
1 AAAATATAAATATAT-AAAT
*
331423 ATAAATTATTAATATATTTAAAT
1 A-AAA-TA-TAA-ATATATAAAT
**
331446 -TCATATAAATATATAATAT
1 AAAATATAAATATATAA-AT
* * *
331465 ATCAATATAATTATAATATAT
1 A-AAATATAAATAT-ATAAAT
*
331486 AAAAT-TAATATATATATAT
1 AAAATATAA-ATATATAAAT
* *
331505 ATAATATAAATAAATAAAT
1 AAAATATAAATATATAAAT
331524 AAA
1 AAA
331527 TTATCATATT
Statistics
Matches: 122, Mismatches: 22, Indels: 33
0.69 0.12 0.19
Matches are distributed among these distances:
18 20 0.16
19 54 0.44
20 20 0.16
21 15 0.12
22 3 0.02
23 6 0.05
24 4 0.03
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATATAAATATATAAAT
Found at i:331401 original size:8 final size:8
Alignment explanation
Indices: 331383--331527 Score: 97
Period size: 8 Copynumber: 17.8 Consensus size: 8
331373 AATAATATAA
331383 ATAAA-AT
1 ATAAATAT
331390 ATAAATAT
1 ATAAATAT
331398 ATAAATAT
1 ATAAATAT
*
331406 ATTAAAATTT
1 A-T-AAATAT
331416 ATAAA-AT
1 ATAAATAT
331423 ATAAAT-T
1 ATAAATAT
331430 ATTAATATAT
1 A-TAA-ATAT
*
331440 TTAAATTCAT
1 ATAAA-T-AT
331450 ATAAATAT
1 ATAAATAT
331458 AT-AATAT
1 ATAAATAT
*
331465 ATCAATAT
1 ATAAATAT
331473 AATTATAATAT
1 -A-TA-AATAT
331484 ATAAA-AT
1 ATAAATAT
331491 -T-AATAT
1 ATAAATAT
*
331497 ATATATAT
1 ATAAATAT
*
331505 ATAATATAA
1 ATAA-ATAT
*
331514 ATAAATAA
1 ATAAATAT
331522 ATAAAT
1 ATAAAT
331528 TATCATATTT
Statistics
Matches: 113, Mismatches: 8, Indels: 33
0.73 0.05 0.21
Matches are distributed among these distances:
5 2 0.02
6 3 0.03
7 23 0.20
8 46 0.41
9 19 0.17
10 15 0.13
11 5 0.04
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAAATAT
Found at i:331401 original size:15 final size:15
Alignment explanation
Indices: 331369--331522 Score: 74
Period size: 15 Copynumber: 10.2 Consensus size: 15
331359 TATATAATAC
* *
331369 AAAAAATAATATAAAT
1 AAAATATAA-ATATAT
331385 AAAATATAAATATAT
1 AAAATATAAATATAT
*
331400 AAATATATTAAAATTTAT
1 AAA-ATA-T-AAATATAT
331418 AAAATATAAAT-TATT
1 AAAATATAAATATA-T
*
331433 AATATATTTAAAT-TCAT
1 AA-A-ATATAAATAT-AT
331450 ATAAATATATAATATAT
1 A-AAATATA-AATATAT
*
331467 -CAATAT-AAT-TAT
1 AAAATATAAATATAT
*
331479 AATATATAAA-AT-T
1 AAAATATAAATATAT
*
331492 --AATATATATATAT
1 AAAATATAAATATAT
* *
331505 ATAATATAAATAAAT
1 AAAATATAAATATAT
331520 AAA
1 AAA
331523 TAAATTATCA
Statistics
Matches: 108, Mismatches: 13, Indels: 35
0.69 0.08 0.22
Matches are distributed among these distances:
11 6 0.06
12 5 0.05
13 9 0.08
14 5 0.05
15 33 0.31
16 17 0.16
17 20 0.19
18 13 0.12
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATATAAATATAT
Found at i:331441 original size:26 final size:26
Alignment explanation
Indices: 331389--331459 Score: 85
Period size: 25 Copynumber: 2.7 Consensus size: 26
331379 ATAAATAAAA
331389 TATAAATATATAAATATATTAAAATT
1 TATAAATATATAAATATATTAAAATT
331415 TATAAA-ATATAAAT-TATTAATATATT
1 TATAAATATATAAATATATTAA-A-ATT
*
331441 TA-AATTCATATAAATATAT
1 TATAAAT-ATATAAATATAT
331460 AATATATCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
24 6 0.15
25 11 0.28
26 11 0.28
27 8 0.21
28 3 0.08
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (26 bp):
TATAAATATATAAATATATTAAAATT
Found at i:332115 original size:6 final size:6
Alignment explanation
Indices: 332104--332130 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
332094 TATTCCCCTA
332104 TTTTTC TTTTTC TTTTTC TTTTTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTT
332131 CTTTGAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:333411 original size:10 final size:10
Alignment explanation
Indices: 333396--333431 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
333386 TAATATATAA
333396 TGGGCAGGGC
1 TGGGCAGGGC
333406 TGGGCAGGGC
1 TGGGCAGGGC
*
333416 TGGGCCGGGC
1 TGGGCAGGGC
333426 TTGGGC
1 -TGGGC
333432 TCGGGCCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 19 0.79
11 5 0.21
ACGTcount: A:0.06, C:0.22, G:0.58, T:0.14
Consensus pattern (10 bp):
TGGGCAGGGC
Found at i:336545 original size:14 final size:14
Alignment explanation
Indices: 336526--336553 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
336516 ACTTTGTTTT
336526 TTGCAGCTGGCTAC
1 TTGCAGCTGGCTAC
336540 TTGCAGCTGGCTAC
1 TTGCAGCTGGCTAC
336554 CCTTCTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (14 bp):
TTGCAGCTGGCTAC
Found at i:341252 original size:100 final size:96
Alignment explanation
Indices: 341061--341245 Score: 246
Period size: 100 Copynumber: 1.9 Consensus size: 96
341051 AGATAAAAAG
* * *
341061 ATATATATATTATGATAATGAATGAAAACCAAAGCTATGTAAAGAAAAATATAAGAAACGAGAAA
1 ATATATATATTATGATAATGAATGAAAAACAAAACTATGTAAAGAAAAATATAAGAAACAAGAAA
341126 CTGCATTAAAAAAATAAAAAACAATGAAAACA
66 CT-CATTAAAAAAATAAAAAACAATGAAAACA
* * * *
341158 ATATGTATGTTATGATAGTGAATGAAAAAAAACAAAACTATTTAAAGAAAAATATAAGAAACAAG
1 ATATATATATTATGATAATGAATG---AAAAACAAAACTATGTAAAGAAAAATATAAGAAACAAG
*
341223 AAACT-ATATCAAAAAATAAAAAA
63 AAACTCAT-TAAAAAAATAAAAAA
341246 ATAATGATTG
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
97 21 0.28
98 2 0.03
99 14 0.18
100 39 0.51
ACGTcount: A:0.61, C:0.07, G:0.11, T:0.22
Consensus pattern (96 bp):
ATATATATATTATGATAATGAATGAAAAACAAAACTATGTAAAGAAAAATATAAGAAACAAGAAA
CTCATTAAAAAAATAAAAAACAATGAAAACA
Found at i:341843 original size:20 final size:20
Alignment explanation
Indices: 341802--341843 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
341792 CTAAATAAAT
*
341802 ATCTTAAAAATATAATCTTA
1 ATCTTAAAAATATAATCATA
*
341822 ATCTTATAATATATAAT-ATA
1 ATCTTA-AAAATATAATCATA
341842 AT
1 AT
341844 AAAATATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (20 bp):
ATCTTAAAAATATAATCATA
Found at i:342121 original size:2 final size:2
Alignment explanation
Indices: 342109--342138 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
342099 TTGATTGATA
*
342109 AT AT CT 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
342139 TTTTTTACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:342242 original size:8 final size:8
Alignment explanation
Indices: 342229--342281 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
342219 AAGAAAGAAT
342229 AAAAAAGA
1 AAAAAAGA
342237 AAAAAAGAA
1 AAAAAAG-A
342246 AAAAAAGGA
1 AAAAAA-GA
342255 GAAAAAA-A
1 -AAAAAAGA
*
342263 AGAAAAGA
1 AAAAAAGA
*
342271 AAGAAAGA
1 AAAAAAGA
342279 AAA
1 AAA
342282 TTTATATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 5 0.14
8 17 0.46
9 8 0.22
10 7 0.19
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:342243 original size:18 final size:17
Alignment explanation
Indices: 342217--342281 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 17
342207 GGTGAAAACA
342217 AAAAGAAAGAATAAAAAAG
1 AAAA-AAAGAA-AAAAAAG
342236 AAAAAAAGAAAAAAAAGG
1 AAAAAAAGAAAAAAAA-G
* *
342254 AGAAAAA-AAAGAAAAG
1 AAAAAAAGAAAAAAAAG
*
342270 AAAGAAAGAAAA
1 AAAAAAAGAAAA
342282 TTTATATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 6 0.15
17 16 0.41
18 13 0.33
19 4 0.10
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.02
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAAG
Found at i:342260 original size:21 final size:20
Alignment explanation
Indices: 342216--342274 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
342206 TGGTGAAAAC
*
342216 AAAAAGAAAGAATAAAAA-AG
1 AAAAA-AAAGAAAAAAAAGAG
342236 -AAAAAAAGAAAAAAAAGGAG
1 AAAAAAAAGAAAAAAAA-GAG
*
342256 AAAAAAAAGAAAAGAAAGA
1 AAAAAAAAGAAAAAAAAGA
342275 AAGAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 11 0.32
19 4 0.12
20 4 0.12
21 15 0.44
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (20 bp):
AAAAAAAAGAAAAAAAAGAG
Found at i:342263 original size:30 final size:30
Alignment explanation
Indices: 342224--342281 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
342214 ACAAAAAGAA
342224 AGAATAAAAAAGAAAA-AAAGAAAAAAAAGG
1 AGAA-AAAAAAGAAAAGAAAGAAAAAAAAGG
*
342254 AGAAAAAAAAGAAAAGAAAGAAAGAAAA
1 AGAAAAAAAAGAAAAGAAAGAAAAAAAA
342282 TTTATATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (30 bp):
AGAAAAAAAAGAAAAGAAAGAAAAAAAAGG
Found at i:342715 original size:16 final size:16
Alignment explanation
Indices: 342696--342728 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
342686 AAAAAGATGG
342696 AAAGAAAAAAAAGAAA
1 AAAGAAAAAAAAGAAA
*
342712 AAAGAAAAGAAAGAAA
1 AAAGAAAAAAAAGAAA
342728 A
1 A
342729 GGAGAGAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAAGAAA
Found at i:343255 original size:16 final size:16
Alignment explanation
Indices: 343218--343254 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
343208 AATTTTAAAT
343218 ATAAAATTATTATTTA
1 ATAAAATTATTATTTA
*
343234 ATAAAATT-TTATTTG
1 ATAAAATTATTATTTA
343249 ATAAAA
1 ATAAAA
343255 AAAGAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
ATAAAATTATTATTTA
Found at i:343830 original size:16 final size:17
Alignment explanation
Indices: 343803--343843 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
343793 ATTTTAAAAT
343803 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
*
343818 TAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
343835 AAATTTTAT
1 AAATTTTAT
343844 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 6 0.27
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:343961 original size:18 final size:18
Alignment explanation
Indices: 343934--343968 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
343924 TATAAAAAAG
* *
343934 TTTGATTAATAACATTTA
1 TTTGAATAATAAAATTTA
343952 TTTGAATAATAAAATTT
1 TTTGAATAATAAAATTT
343969 TAATTAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (18 bp):
TTTGAATAATAAAATTTA
Found at i:344072 original size:20 final size:19
Alignment explanation
Indices: 344047--344085 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
344037 TTAATATTTA
344047 TTTAATCGAAAAATTTAAAT
1 TTTAAT-GAAAAATTTAAAT
* *
344067 TTTAATGTAAACTTTAAAT
1 TTTAATGAAAAATTTAAAT
344086 GCATGTTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (19 bp):
TTTAATGAAAAATTTAAAT
Found at i:344350 original size:23 final size:22
Alignment explanation
Indices: 344304--344350 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
344294 TAACTCTATC
*
344304 AAAAATATTTTATTAAAGTAAA
1 AAAAATATTTTATTAAAATAAA
344326 AAAAATTATTTTATTAATAATAAA
1 AAAAA-TATTTTATTAA-AATAAA
344350 A
1 A
344351 TTTATCTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.23
23 11 0.50
24 6 0.27
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAAATATTTTATTAAAATAAA
Found at i:348076 original size:15 final size:16
Alignment explanation
Indices: 348030--348077 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
348020 GGAAGAAAAT
*
348030 AAATCAAAATTTGTTGA
1 AAATGAAAA-TTGTTGA
*
348047 AAATG-AAATTCTTGA
1 AAATGAAAATTGTTGA
348062 AAA-GAAAATTGTTGA
1 AAATGAAAATTGTTGA
348077 A
1 A
348078 CTAGAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 1 0.04
15 19 0.70
16 3 0.11
17 4 0.15
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.31
Consensus pattern (16 bp):
AAATGAAAATTGTTGA
Found at i:353757 original size:15 final size:15
Alignment explanation
Indices: 353737--353768 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
353727 TTACTTTTCC
*
353737 TCTAGTGATGATGAG
1 TCTAGTGACGATGAG
353752 TCTAGTGACGATGAG
1 TCTAGTGACGATGAG
353767 TC
1 TC
353769 ATATGATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.31, T:0.31
Consensus pattern (15 bp):
TCTAGTGACGATGAG
Found at i:354830 original size:19 final size:18
Alignment explanation
Indices: 354802--354838 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
354792 TACCCTATGT
354802 GAAATGTATCGATACATG
1 GAAATGTATCGATACATG
354820 GAAATTGTATCGATACATG
1 GAAA-TGTATCGATACATG
354839 ATAAAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.30
Consensus pattern (18 bp):
GAAATGTATCGATACATG
Found at i:357021 original size:15 final size:17
Alignment explanation
Indices: 357001--357032 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
356991 AAAATTAATT
357001 TTAATTT-TAA-ATTTA
1 TTAATTTATAATATTTA
357016 TTAATTTATAATATTTA
1 TTAATTTATAATATTTA
357033 AAATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAATTTATAATATTTA
Found at i:357031 original size:24 final size:22
Alignment explanation
Indices: 356995--357056 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
356985 AATTAAAAAA
356995 TTAATTT-T-AATTTTAAATTT
1 TTAATTTATAAATTTTAAATTT
*
357015 ATTAATTTATAATATTTAAAATTT
1 -TTAATTTATAA-ATTTTAAATTT
* *
357039 TTTATTTTTAAATTTTAA
1 TTAATTTATAAATTTTAA
357057 TTATAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
21 7 0.21
22 7 0.21
23 10 0.29
24 10 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTAATTTATAAATTTTAAATTT
Found at i:357055 original size:23 final size:22
Alignment explanation
Indices: 356998--357056 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
356988 TAAAAAATTA
356998 ATTTT-AATTTT-AAATTTATT
1 ATTTTAAATTTTAAAATTTATT
* *
357018 AATTTATAATATTTAAAATTTTTT
1 ATTTTA-AAT-TTTAAAATTTATT
357042 ATTTTTAAATTTTAA
1 A-TTTTAAATTTTAA
357057 TTATAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 4 0.13
22 3 0.10
23 8 0.26
24 12 0.39
25 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTTAAATTTTAAAATTTATT
Found at i:358542 original size:16 final size:18
Alignment explanation
Indices: 358510--358544 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
358500 TTTTTGTATG
358510 ATATAAATTACATAATAT
1 ATATAAATTACATAATAT
358528 ATATAAA-TACA-AATAT
1 ATATAAATTACATAATAT
358544 A
1 A
358545 AAAAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 4 0.24
18 7 0.41
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATAAATTACATAATAT
Found at i:358995 original size:35 final size:35
Alignment explanation
Indices: 358945--359023 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
358935 AATATATGTA
* *
358945 TATATATATAATAAATAATTAAAA-ATTAATAAAAT
1 TATATTTATAATAAATAA-TAAAATATAAATAAAAT
*
358980 TATATTTATATTAAATAATAAAATATAAATAAAAT
1 TATATTTATAATAAATAATAAAATATAAATAAAAT
*
359015 TATGTTTAT
1 TATATTTAT
359024 CGTGAATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 5 0.13
35 34 0.87
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (35 bp):
TATATTTATAATAAATAATAAAATATAAATAAAAT
Found at i:359032 original size:35 final size:34
Alignment explanation
Indices: 358945--359035 Score: 101
Period size: 35 Copynumber: 2.6 Consensus size: 34
358935 AATATATGTA
* * *
358945 TATATATATAATAAATAATTAAAAATTAATAAAAT
1 TATATTTATAGTAAATAA-TAAAAATAAATAAAAT
*
358980 TATATTTATATTAAATAATAAAATATAAATAAAAT
1 TATATTTATAGTAAATAATAAAA-ATAAATAAAAT
* * *
359015 TATGTTTATCGTGAATAATAA
1 TATATTTATAGTAAATAATAA
359036 TTAAAAATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
34 5 0.10
35 43 0.90
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (34 bp):
TATATTTATAGTAAATAATAAAAATAAATAAAAT
Found at i:359040 original size:28 final size:28
Alignment explanation
Indices: 358998--359075 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
358988 TATTAAATAA
* * *
358998 TAAAATATAAATAAAATTATGTTTATCG-
1 TAAAAAATAATTAAAATTATATTTAT-GT
* * *
359026 TGAATAATAATTAAAAATATATTTATGT
1 TAAAAAATAATTAAAATTATATTTATGT
*
359054 TAAAAAATTATTAAAATTATAT
1 TAAAAAATAATTAAAATTATAT
359076 CTATAATATA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 1 0.03
28 38 0.97
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.41
Consensus pattern (28 bp):
TAAAAAATAATTAAAATTATATTTATGT
Found at i:360346 original size:19 final size:18
Alignment explanation
Indices: 360319--360376 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 18
360309 TAATTGTTAA
360319 TTTTTTTTATTTTTTATT
1 TTTTTTTTATTTTTTATT
360337 TTTTTATTTAATTATTATTATT
1 TTTTT-TTT-ATT-TT-TTATT
*
360359 TTTTTTGATATTTTTTAT
1 TTTTTT-TTATTTTTTAT
360377 AATTATGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
18 5 0.15
19 7 0.21
20 5 0.15
21 6 0.18
22 11 0.32
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTTTTTATTTTTTATT
Found at i:360523 original size:15 final size:16
Alignment explanation
Indices: 360492--360524 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
360482 TAAGAGGTTT
360492 TAATATTAAATATTTA
1 TAATATTAAATATTTA
*
360508 TAATTTTAAA-ATTTA
1 TAATATTAAATATTTA
360523 TA
1 TA
360525 TTTATGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATATTAAATATTTA
Found at i:361913 original size:10 final size:10
Alignment explanation
Indices: 361898--361931 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
361888 ATCAAATTAG
361898 AAAAATTAAA
1 AAAAATTAAA
361908 AAAAATT--A
1 AAAAATTAAA
361916 AAAAATTAAA
1 AAAAATTAAA
361926 AAAAAT
1 AAAAAT
361932 CATTGTTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.36
10 14 0.64
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:361921 original size:18 final size:19
Alignment explanation
Indices: 361891--361931 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
361881 CAACGTTATC
361891 AAATTAGAAAAATTAAAAA
1 AAATTAGAAAAATTAAAAA
361910 AAATTA-AAAAATTAAAAA
1 AAATTAGAAAAATTAAAAA
361928 AAAT
1 AAAT
361932 CATTGTTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (19 bp):
AAATTAGAAAAATTAAAAA
Found at i:361929 original size:9 final size:9
Alignment explanation
Indices: 361891--361929 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
361881 CAACGTTATC
*
361891 AAATTAGAA
1 AAATTAAAA
361900 AAATTAAAAA
1 AAATT-AAAA
361910 AAATT-AAA
1 AAATTAAAA
361918 AAATTAAAA
1 AAATTAAAA
361927 AAA
1 AAA
361930 ATCATTGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
8 8 0.30
9 11 0.41
10 8 0.30
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATTAAAA
Found at i:370305 original size:2 final size:2
Alignment explanation
Indices: 370298--370325 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
370288 ATTATTATCT
370298 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
370326 AGAGAGAGAG
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:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:370330 original size:2 final size:2
Alignment explanation
Indices: 370325--370357 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
370315 GTGTGTGTGT
370325 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
370358 CATAGAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:377903 original size:31 final size:31
Alignment explanation
Indices: 377860--377948 Score: 160
Period size: 31 Copynumber: 2.9 Consensus size: 31
377850 ATGCATCATT
*
377860 GTAACATCTGAAAACAAGAAATAAGATCAGG
1 GTAATATCTGAAAACAAGAAATAAGATCAGG
*
377891 GTAATATCTGAAAACAAGAAATAGGATCAGG
1 GTAATATCTGAAAACAAGAAATAAGATCAGG
377922 GTAATATCTGAAAACAAGAAATAAGAT
1 GTAATATCTGAAAACAAGAAATAAGAT
377949 TCCCCTGATC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19
Consensus pattern (31 bp):
GTAATATCTGAAAACAAGAAATAAGATCAGG
Found at i:379343 original size:13 final size:13
Alignment explanation
Indices: 379325--379353 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
379315 AGCATCCCTC
379325 ATCCCTCTCTTGT
1 ATCCCTCTCTTGT
379338 ATCCCTCTCTTGT
1 ATCCCTCTCTTGT
379351 ATC
1 ATC
379354 TTTATTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.38, G:0.07, T:0.45
Consensus pattern (13 bp):
ATCCCTCTCTTGT
Found at i:380631 original size:104 final size:103
Alignment explanation
Indices: 380341--380643 Score: 366
Period size: 104 Copynumber: 3.0 Consensus size: 103
380331 CTGTACTTTA
* * * *
380341 GTTGACCGTTTCTGTTGGCATCCT---TACACAATCTCCATC-GATATTGGTGTTAGATTGATTG
1 GTTGACCGTTTCTGTTGGCACCCTGGCTACACAATCTCCACCTG-TATTGATGTGAGATTGATTG
* * *
380402 TTATACCCTAGCTTAGCTGATTGCATGATAGATCTGCAT
65 TTATACCCTACCTTAGCTGATTGTATGATACATCTGCAT
* * * * * *
380441 GTTGACTGTTTCTGTTGGCATCCCTGGCTACACAGTCTCCACATGTATTGGA-GTGAAATGGATC
1 GTTGACCGTTTCTGTTGGCA-CCCTGGCTACACAATCTCCACCTGTATT-GATGTGAGATTGATT
380505 GTTATACCCTACCTTAGCTGATTGTATGATACATCTGCAT
64 GTTATACCCTACCTTAGCTGATTGTATGATACATCTGCAT
380545 GTTGACCGTTTCTGTTGGCACCCATGGCTACACAATCTCCACCTGTATTGATGTGAGATTGATTG
1 GTTGACCGTTTCTGTTGGCACCC-TGGCTACACAATCTCCACCTGTATTGATGTGAGATTGATTG
* ** *
380610 TTATACCTTA-CTATAATTGATTGTATGATGCATC
65 TTATACCCTACCT-TAGCTGATTGTATGATACATC
380644 CGTGCGTTGA
Statistics
Matches: 171, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
100 19 0.11
101 3 0.02
103 7 0.04
104 140 0.82
105 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (103 bp):
GTTGACCGTTTCTGTTGGCACCCTGGCTACACAATCTCCACCTGTATTGATGTGAGATTGATTGT
TATACCCTACCTTAGCTGATTGTATGATACATCTGCAT
Found at i:381771 original size:27 final size:25
Alignment explanation
Indices: 381734--381783 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 25
381724 AAAATTTTAA
381734 AAATTAAAAT-ATTTATTTAAAATAT
1 AAATTAAAATAATTTA-TTAAAATAT
381759 AAATTATATAATAATTTATTAAAAT
1 AAATTA-A-AATAATTTATTAAAAT
381784 GTAAGTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 6 0.27
26 1 0.05
27 10 0.45
28 5 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATTAAAATAATTTATTAAAATAT
Found at i:382206 original size:20 final size:20
Alignment explanation
Indices: 382165--382234 Score: 67
Period size: 21 Copynumber: 3.6 Consensus size: 20
382155 AAAAAAAAAG
*
382165 AAGAAATGAAGTAAAATAAT
1 AAGAAATGAAATAAAATAAT
382185 AAGAAATGGAAATAAAAT-AT
1 AAGAAAT-GAAATAAAATAAT
* *
382205 AAAGAAGT-AAATAATA-AAT
1 -AAGAAATGAAATAAAATAAT
382224 AA-AAATGAAAT
1 AAGAAATGAAAT
382235 TACATGGATA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
17 3 0.07
18 6 0.14
19 9 0.21
20 9 0.21
21 15 0.36
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (20 bp):
AAGAAATGAAATAAAATAAT
Found at i:382517 original size:26 final size:28
Alignment explanation
Indices: 382476--382541 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
382466 TTGGTCAAAA
*
382476 ATTATA-TAAATATTAAA-AACATAATTT
1 ATTATATTAAATATTAAATAA-AAAATTT
382503 -TTATATTAAAT-TTAAATAAAAAATTT
1 ATTATATTAAATATTAAATAAAAAATTT
*
382529 ATTTTATTAAATA
1 ATTATATTAAATA
382542 AATAATTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
26 16 0.48
27 17 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTATATTAAATATTAAATAAAAAATTT
Found at i:382540 original size:21 final size:20
Alignment explanation
Indices: 382514--382552 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
382504 TATATTAAAT
382514 TTAAATAAAAAATTTATTTTA
1 TTAAATAAAAAA-TTATTTTA
*
382535 TTAAATAAATAATTATTT
1 TTAAATAAAAAATTATTT
382553 GAATCGAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAAATAAAAAATTATTTTA
Found at i:384212 original size:6 final size:6
Alignment explanation
Indices: 384182--384229 Score: 71
Period size: 6 Copynumber: 7.8 Consensus size: 6
384172 AAAATTTTGA
384182 TATATT TAATAATT TATATT T-TATT TATATT TATATT TATATT TATAT
1 TATATT T-AT-ATT TATATT TATATT TATATT TATATT TATATT TATAT
384230 GATTAATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.13
6 26 0.67
7 4 0.10
8 4 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TATATT
Found at i:386933 original size:2 final size:2
Alignment explanation
Indices: 386926--386965 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
386916 AGAAATATGC
386926 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
386966 TGCTTTCATG
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:388423 original size:21 final size:20
Alignment explanation
Indices: 388380--388417 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
388370 TATTTAATAC
388380 TTATTTAATATTAAAATTAT
1 TTATTTAATATTAAAATTAT
* *
388400 TTATTTTATATTTAAATT
1 TTATTTAATATTAAAATT
388418 TTTTTAACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATTTAATATTAAAATTAT
Found at i:389686 original size:2 final size:2
Alignment explanation
Indices: 389681--389710 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
389671 ATGCGCGCTC
389681 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
389711 AAAGAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:395262 original size:216 final size:216
Alignment explanation
Indices: 394888--395320 Score: 866
Period size: 216 Copynumber: 2.0 Consensus size: 216
394878 TTGAAGATGT
394888 AAGAGCTCACCTAATACTCTACACCCACAAAGCCGAGAGGAAGAGCTCTTTCATTATGGTGAAGT
1 AAGAGCTCACCTAATACTCTACACCCACAAAGCCGAGAGGAAGAGCTCTTTCATTATGGTGAAGT
394953 TTAAGAGCCCTTGCTCTCAGGTTTGTGGGTTTAGCGTATCCAGATGAGTTTTGGGTACCAAAATT
66 TTAAGAGCCCTTGCTCTCAGGTTTGTGGGTTTAGCGTATCCAGATGAGTTTTGGGTACCAAAATT
395018 TGTAAAACTATTCATCATCTTTGAGTATGGTGAATTTTTCTTGTCCCCTCTACCCACAAACAAAG
131 TGTAAAACTATTCATCATCTTTGAGTATGGTGAATTTTTCTTGTCCCCTCTACCCACAAACAAAG
395083 GAATAGAGTCAAACCACATAA
196 GAATAGAGTCAAACCACATAA
395104 AAGAGCTCACCTAATACTCTACACCCACAAAGCCGAGAGGAAGAGCTCTTTCATTATGGTGAAGT
1 AAGAGCTCACCTAATACTCTACACCCACAAAGCCGAGAGGAAGAGCTCTTTCATTATGGTGAAGT
395169 TTAAGAGCCCTTGCTCTCAGGTTTGTGGGTTTAGCGTATCCAGATGAGTTTTGGGTACCAAAATT
66 TTAAGAGCCCTTGCTCTCAGGTTTGTGGGTTTAGCGTATCCAGATGAGTTTTGGGTACCAAAATT
395234 TGTAAAACTATTCATCATCTTTGAGTATGGTGAATTTTTCTTGTCCCCTCTACCCACAAACAAAG
131 TGTAAAACTATTCATCATCTTTGAGTATGGTGAATTTTTCTTGTCCCCTCTACCCACAAACAAAG
395299 GAATAGAGTCAAACCACATAA
196 GAATAGAGTCAAACCACATAA
395320 A
1 A
395321 TTATTGTGTT
Statistics
Matches: 217, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
216 217 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (216 bp):
AAGAGCTCACCTAATACTCTACACCCACAAAGCCGAGAGGAAGAGCTCTTTCATTATGGTGAAGT
TTAAGAGCCCTTGCTCTCAGGTTTGTGGGTTTAGCGTATCCAGATGAGTTTTGGGTACCAAAATT
TGTAAAACTATTCATCATCTTTGAGTATGGTGAATTTTTCTTGTCCCCTCTACCCACAAACAAAG
GAATAGAGTCAAACCACATAA
Found at i:400073 original size:15 final size:16
Alignment explanation
Indices: 400053--400085 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
400043 TTATTTTAAT
*
400053 ATTTTATAAA-AAATA
1 ATTTTAAAAATAAATA
400068 ATTTTAAAAATAAATA
1 ATTTTAAAAATAAATA
400084 AT
1 AT
400086 AATAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTTTAAAAATAAATA
Found at i:400218 original size:24 final size:22
Alignment explanation
Indices: 400190--400241 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
400180 TAATTTTTTA
*
400190 ATATATTATAATATAAATATAATT
1 ATATATTATAAT-TAAA-ATAAAT
* *
400214 ATATAATATGATTAAAATAAAT
1 ATATATTATAATTAAAATAAAT
400236 ATATAT
1 ATATAT
400242 GTTAAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 10 0.42
23 4 0.17
24 10 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
ATATATTATAATTAAAATAAAT
Found at i:402694 original size:32 final size:33
Alignment explanation
Indices: 402636--402705 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 33
402626 AATAACACAC
402636 ATATAATATAAATAAATGAATATATCAAAATAT
1 ATATAATATAAATAAATGAATATATCAAAATAT
* * * *
402669 ATATAATATGAAT-TATTAATATATCAAAATTT
1 ATATAATATAAATAAATGAATATATCAAAATAT
402701 ATATA
1 ATATA
402706 TGCAATACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 21 0.64
33 12 0.36
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (33 bp):
ATATAATATAAATAAATGAATATATCAAAATAT
Found at i:403202 original size:34 final size:33
Alignment explanation
Indices: 403148--403211 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
403138 TTAATTTGTT
*
403148 ATTTTTAATTTAATAAAAATAATATTAAATATA
1 ATTTTTAATGTAATAAAAATAATATTAAATATA
*
403181 ATTTTTAA-GTAATAATCAAATAATTTTAAAT
1 ATTTTTAATGTAATAA--AAATAATATTAAAT
403212 TGATAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 6 0.22
33 8 0.30
34 13 0.48
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (33 bp):
ATTTTTAATGTAATAAAAATAATATTAAATATA
Found at i:403656 original size:19 final size:20
Alignment explanation
Indices: 403609--403673 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 20
403599 AAAAATTTTA
* *
403609 ATTTATATTAT-TATATACA
1 ATTTATATTATATTTATACT
403628 ATTTA-A-TATATTTATA-T
1 ATTTATATTATATTTATACT
* *
403645 ATTTATATTATATTAATATT
1 ATTTATATTATATTTATACT
*
403665 ATTTTTATT
1 ATTTATATT
403674 CTTTAATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 8 0.21
18 7 0.18
19 14 0.37
20 9 0.24
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTATATTATATTTATACT
Found at i:403673 original size:9 final size:9
Alignment explanation
Indices: 403609--403686 Score: 56
Period size: 9 Copynumber: 8.7 Consensus size: 9
403599 AAAAATTTTA
403609 ATTTATATT
1 ATTTATATT
**
403618 ATTATATACA
1 ATT-TATATT
403628 ATTTA-ATAT
1 ATTTATAT-T
403637 ATTTATA-T
1 ATTTATATT
403645 ATTTATATT
1 ATTTATATT
403654 ATATTAATATT
1 AT-TT-ATATT
*
403665 ATTTTTATT
1 ATTTATATT
*
403674 CTTTA-A-T
1 ATTTATATT
403681 ATTTAT
1 ATTTAT
403687 TCATTATATT
Statistics
Matches: 54, Mismatches: 8, Indels: 15
0.70 0.10 0.19
Matches are distributed among these distances:
7 5 0.09
8 10 0.19
9 20 0.37
10 12 0.22
11 7 0.13
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTTATATT
Found at i:403685 original size:14 final size:13
Alignment explanation
Indices: 403642--403698 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 13
403632 AATATATTTA
403642 TATATTTA-T-AT
1 TATATTTATTCAT
*
403653 TATA-TTAAT-AT
1 TATATTTATTCAT
* *
403664 TATTTTTATTCTT
1 TATATTTATTCAT
403677 TAATATTTATTCAT
1 T-ATATTTATTCAT
403691 TATATTTA
1 TATATTTA
403699 AAATCAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
10 3 0.08
11 10 0.27
12 4 0.11
13 9 0.24
14 11 0.30
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (13 bp):
TATATTTATTCAT
Found at i:404062 original size:14 final size:13
Alignment explanation
Indices: 404043--404076 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
404033 ATTAAAAATA
404043 ATTTATATAATTAT
1 ATTTATATAATT-T
404057 ATTTATATAATTT
1 ATTTATATAATTT
404070 -TTTATAT
1 ATTTATAT
404077 TTAAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.35
13 1 0.05
14 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTATATAATTT
Found at i:404076 original size:18 final size:18
Alignment explanation
Indices: 404053--404142 Score: 60
Period size: 18 Copynumber: 4.9 Consensus size: 18
404043 ATTTATATAA
404053 TTATATTTATATAATTTT
1 TTATATTTATATAATTTT
*
404071 TTATATTTA-A-AATATT
1 TTATATTTATATAATTTT
* * * *
404087 ATATTTTTTTATAAATTT
1 TTATATTTATATAATTTT
*
404105 TTATATACTA-ATAATTTATT
1 TTATAT-TTATATAA-TT-TT
*
404125 TTATTTTATATATAATTT
1 TTATATT-TATATAATTT
404143 ATACGAATAT
Statistics
Matches: 52, Mismatches: 13, Indels: 13
0.67 0.17 0.17
Matches are distributed among these distances:
16 11 0.21
17 2 0.04
18 21 0.40
19 3 0.06
20 11 0.21
21 4 0.08
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATTTATATAATTTT
Found at i:404079 original size:32 final size:33
Alignment explanation
Indices: 404052--404142 Score: 85
Period size: 34 Copynumber: 2.6 Consensus size: 33
404042 AATTTATATA
*
404052 ATTATA-TTTATATAATTTTTTATATTTAAAAT
1 ATTATATTTTATATAAATTTTTATATTTAAAAT
* *
404084 ATTATATTTTTTTATAAATTTTTATATACTAATAATTT
1 ATTATA-TTTTATATAAATTTTTATAT-TTAA-AA--T
*
404122 ATTTTATTTTATATATAATTT
1 ATTATATTTTATATA-AATTT
404143 ATACGAATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
32 6 0.13
34 17 0.36
35 3 0.06
36 2 0.04
37 8 0.17
38 11 0.23
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (33 bp):
ATTATATTTTATATAAATTTTTATATTTAAAAT
Found at i:404132 original size:35 final size:35
Alignment explanation
Indices: 404056--404134 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 35
404046 TATATAATTA
* *
404056 TATTTATATAATTTTTTATATTTAAAATATTATATT
1 TATTT-TATAAATTTTTATATCTAAAATATTATATT
404092 T-TTTTATAAATTTTTATATACTAATAAT-TTAT-TT
1 TATTTTATAAATTTTTATAT-CTAA-AATATTATATT
404126 TATTTTATA
1 TATTTTATA
404135 TATAATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
34 17 0.45
35 17 0.45
36 4 0.11
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (35 bp):
TATTTTATAAATTTTTATATCTAAAATATTATATT
Found at i:404666 original size:19 final size:18
Alignment explanation
Indices: 404642--404703 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
404632 TGAGAAAAGG
404642 AAAGAAAAGAGAAATA-AAT
1 AAAGAAAAGA-AAA-AGAAT
*
404661 AAAGAAAATAAAAAGAAT
1 AAAGAAAAGAAAAAGAAT
*
404679 AAAGAAAATAAAAAG-AT
1 AAAGAAAAGAAAAAGAAT
*
404696 AACGAAAA
1 AAAGAAAA
404704 AAATTTATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.25
18 21 0.52
19 9 0.22
ACGTcount: A:0.76, C:0.02, G:0.13, T:0.10
Consensus pattern (18 bp):
AAAGAAAAGAAAAAGAAT
Found at i:404671 original size:9 final size:9
Alignment explanation
Indices: 404657--404703 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
404647 AAAGAGAAAT
404657 AAATAAAGA
1 AAATAAAGA
404666 AAATAAA-A
1 AAATAAAGA
404674 AGAATAAAGA
1 A-AATAAAGA
404684 AAATAAA-A
1 AAATAAAGA
* *
404692 AGATAACGA
1 AAATAAAGA
404701 AAA
1 AAA
404704 AAATTTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
8 8 0.25
9 22 0.69
10 2 0.06
ACGTcount: A:0.77, C:0.02, G:0.11, T:0.11
Consensus pattern (9 bp):
AAATAAAGA
Found at i:404704 original size:18 final size:18
Alignment explanation
Indices: 404658--404703 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
404648 AAGAGAAATA
404658 AATAAAGAAAATAAAAAG
1 AATAAAGAAAATAAAAAG
404676 AATAAAGAAAATAAAAAG
1 AATAAAGAAAATAAAAAG
*
404694 -ATAACGAAAA
1 AATAAAGAAAA
404704 AAATTTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.76, C:0.02, G:0.11, T:0.11
Consensus pattern (18 bp):
AATAAAGAAAATAAAAAG
Found at i:405773 original size:15 final size:16
Alignment explanation
Indices: 405754--405808 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
405744 TTTTTAAAAT
405754 AAATTTTATTAATT-A
1 AAATTTTATTAATTAA
*
405769 TAATTTTATTTAATTAA
1 AAATTTTA-TTAATTAA
* *
405786 AAATTTTATAAATATTA
1 AAATTTTATTAAT-TAA
405803 AAATTT
1 AAATTT
405809 CCTAACGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 7 0.21
16 10 0.30
17 16 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATTTTATTAATTAA
Found at i:405781 original size:16 final size:17
Alignment explanation
Indices: 405754--405794 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
405744 TTTTTAAAAT
405754 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
*
405769 TAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
405786 AAATTTTAT
1 AAATTTTAT
405795 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 6 0.27
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:405892 original size:10 final size:10
Alignment explanation
Indices: 405877--405901 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
405867 AAGTAGCCAG
405877 TTTTAAAAAT
1 TTTTAAAAAT
405887 TTTTAAAAAT
1 TTTTAAAAAT
405897 TTTTA
1 TTTTA
405902 TTTAAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTTAAAAAT
Found at i:405911 original size:20 final size:22
Alignment explanation
Indices: 405888--405928 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
405878 TTTAAAAATT
405888 TTTAAAAATT-TTT-ATTTAAG
1 TTTAAAAATTATTTGATTTAAG
*
405908 TTTAAATATTATTTGATTTAA
1 TTTAAAAATTATTTGATTTAA
405929 TTTGTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 3 0.17
22 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTAAAAATTATTTGATTTAAG
Found at i:413400 original size:17 final size:17
Alignment explanation
Indices: 413380--413413 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
413370 TTAATTTTTC
413380 ATTAA-ATTTATAAATTT
1 ATTAATATTT-TAAATTT
413397 ATTAATATTTTAAATTT
1 ATTAATATTTTAAATTT
413414 TTTTAAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTAATATTTTAAATTT
Found at i:413556 original size:3 final size:3
Alignment explanation
Indices: 413548--413579 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
413538 ACATTACACG
*
413548 TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
413580 GTCAAAGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:415346 original size:28 final size:26
Alignment explanation
Indices: 415300--415369 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 26
415290 AATTTTATCA
415300 TATTAT-TTAAATAATTTTTATATTTT
1 TATTATATTAAATAATTTTTA-ATTTT
415326 TATTATATTAAATAAGTTTTTAATTTT
1 TATTATATTAAATAA-TTTTTAATTTT
*
415353 TAATTA-AATAAATAATT
1 T-ATTATATTAAATAATT
415370 AATATTTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
26 8 0.20
27 22 0.55
28 10 0.25
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (26 bp):
TATTATATTAAATAATTTTTAATTTT
Found at i:416589 original size:32 final size:33
Alignment explanation
Indices: 416553--416627 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 33
416543 ATTATAATAA
* *
416553 AATAATATATATTATA-TTAAATTTAATAATTT
1 AATAATTTATAATATATTTAAATTTAATAATTT
* *
416585 AATAATTTATAATATATTTATATTTATTAATTT
1 AATAATTTATAATATATTTAAATTTAATAATTT
416618 -ATAATTTATA
1 AATAATTTATA
416628 CAAAAGATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 24 0.63
33 14 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
AATAATTTATAATATATTTAAATTTAATAATTT
Found at i:416624 original size:7 final size:7
Alignment explanation
Indices: 416572--416627 Score: 57
Period size: 8 Copynumber: 8.1 Consensus size: 7
416562 TATTATATTA
416572 AATTTAAT
1 AATTT-AT
416580 AATTTAAT
1 AATTT-AT
416588 AATTTAT
1 AATTTAT
416595 AA--TAT
1 AATTTAT
416600 -ATTTAT
1 AATTTAT
416606 -ATTTATT
1 AATTTA-T
416613 AATTTAT
1 AATTTAT
416620 AATTTAT
1 AATTTAT
416627 A
1 A
416628 CAAAAGATGA
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
4 1 0.02
5 3 0.07
6 8 0.18
7 14 0.32
8 18 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
AATTTAT
Found at i:417015 original size:15 final size:15
Alignment explanation
Indices: 416978--417015 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
416968 TATTTAAAAA
*
416978 ATAATATTTAATATTT
1 ATAA-ATTTAATAATT
416994 A-AAATTTAATAATT
1 ATAAATTTAATAATT
417008 ATAAATTT
1 ATAAATTT
417016 TTTTATCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 11 0.55
15 8 0.40
16 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATAAATTTAATAATT
Found at i:421618 original size:16 final size:16
Alignment explanation
Indices: 421597--421627 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
421587 TGCATTCATG
421597 TTATATTTATATTATT
1 TTATATTTATATTATT
421613 TTATATTTATATTAT
1 TTATATTTATATTAT
421628 ACTTTAAAAG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATATTTATATTATT
Found at i:423569 original size:47 final size:46
Alignment explanation
Indices: 423484--423574 Score: 110
Period size: 47 Copynumber: 2.0 Consensus size: 46
423474 TGACACCCTC
* * * * * *
423484 ATAATTTATTTTATTTAATTTTGACATGTTTGTGTATTTGTGTTGT
1 ATAATTTATTTAATATAATTTTAACATATTTGGGTATTTATGTTGT
*
423530 ATAATTTATTTAATATAGATTTTAATATATTTGGGTATTTATGTT
1 ATAATTTATTTAATATA-ATTTTAACATATTTGGGTATTTATGTT
423575 ATTTTTCGCA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
46 15 0.41
47 22 0.59
ACGTcount: A:0.27, C:0.01, G:0.13, T:0.58
Consensus pattern (46 bp):
ATAATTTATTTAATATAATTTTAACATATTTGGGTATTTATGTTGT
Found at i:423994 original size:11 final size:10
Alignment explanation
Indices: 423979--424008 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
423969 TACTAAATAT
423979 ATATTTATTA
1 ATATTTATTA
423989 ATTATTTATTA
1 A-TATTTATTA
424000 ATATTTATT
1 ATATTTATT
424009 TAGTAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
ATATTTATTA
Found at i:424531 original size:16 final size:16
Alignment explanation
Indices: 424508--424542 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
424498 CACTAAGTAA
424508 TATATATTAATTATTTAT
1 TATAT-TTAA-TATTTAT
424526 TATATTTAATATTTAT
1 TATATTTAATATTTAT
424542 T
1 T
424543 TAATATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 4 0.24
18 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATATTTAATATTTAT
Found at i:424559 original size:20 final size:21
Alignment explanation
Indices: 424536--424575 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
424526 TATATTTAAT
424536 ATTTATTT-AATA-TTAAAATA
1 ATTT-TTTAAATATTTAAAATA
424556 ATTTTTTAAATATTTAAAAT
1 ATTTTTTAAATATTTAAAAT
424576 TTTACTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 8 0.44
21 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTTTTAAATATTTAAAATA
Found at i:425039 original size:15 final size:16
Alignment explanation
Indices: 425015--425047 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
425005 TATAAATATT
*
425015 ATTTATATTTATTTAA
1 ATTTATATTTATTAAA
425031 ATTTA-ATTTATTAAA
1 ATTTATATTTATTAAA
425046 AT
1 AT
425048 ATAAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTATATTTATTAAA
Found at i:425172 original size:27 final size:28
Alignment explanation
Indices: 425124--425186 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
425114 ATATTTTTTA
* *
425124 AAAT-ATTTTTTTTAAAAATTAATAT-T
1 AAATAATTTTTATTAAAAATTAAAATAT
* **
425150 TAATAATTTTTATTAAATTTTAAAATAT
1 AAATAATTTTTATTAAAAATTAAAATAT
425178 AAATAATTT
1 AAATAATTT
425187 AATATATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
26 3 0.10
27 17 0.59
28 9 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
AAATAATTTTTATTAAAAATTAAAATAT
Found at i:426252 original size:15 final size:15
Alignment explanation
Indices: 426232--426283 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 15
426222 TATCTTTATA
426232 ATATTTATATATTTT
1 ATATTTATATATTTT
*
426247 ATATTTATATAATTTG
1 ATATTTATAT-ATTTT
*
426263 ATATATTATATTATATT
1 ATAT-TTATA-TATTTT
426280 ATAT
1 ATAT
426284 AAATTTTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 10 0.32
16 8 0.26
17 12 0.39
18 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
ATATTTATATATTTT
Found at i:426281 original size:27 final size:27
Alignment explanation
Indices: 426207--426306 Score: 88
Period size: 26 Copynumber: 3.8 Consensus size: 27
426197 GGTTCATTAG
*
426207 ATTTGATA-ATT-TATGTATCTT-TATA
1 ATTTGATATATTATAT-TATATTATATA
* *
426232 ATATTTATATATTTTA-TAT-TTATATA
1 AT-TTGATATATTATATTATATTATATA
426258 ATTTGATATATTATATTATATTATATAA
1 ATTTGATATATTATATTATATTATAT-A
426286 ATTTTGATATA-TAT-TTATATT
1 A-TTTGATATATTATATTATATT
426307 TGTATTATGT
Statistics
Matches: 64, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
25 15 0.23
26 17 0.27
27 16 0.25
28 7 0.11
29 9 0.14
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (27 bp):
ATTTGATATATTATATTATATTATATA
Found at i:426325 original size:22 final size:22
Alignment explanation
Indices: 426303--426347 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
426293 TATATATTTA
*
426303 TATTTGTATTATGT-TTA-AAT
1 TATTTTTATTATGTCTTATAAT
*
426323 TATTTTTTTTATGTCTTATAAT
1 TATTTTTATTATGTCTTATAAT
426345 TAT
1 TAT
426348 GTCATGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 3 0.14
22 6 0.29
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (22 bp):
TATTTTTATTATGTCTTATAAT
Found at i:426583 original size:15 final size:15
Alignment explanation
Indices: 426563--426597 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
426553 ATTTTGTTTT
426563 TTATAAATTCAAATA
1 TTATAAATTCAAATA
*
426578 TTATAAATTTAAATA
1 TTATAAATTCAAATA
426593 TTATA
1 TTATA
426598 TATACTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
TTATAAATTCAAATA
Found at i:426766 original size:23 final size:22
Alignment explanation
Indices: 426739--426786 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
426729 ATCCAAATCA
426739 TATTT-ATTTATATATTATATTAT
1 TATTTAATTT-TATATTATATT-T
*
426762 TATTTAATTTTATATTTTATTT
1 TATTTAATTTTATATTATATTT
426784 TAT
1 TAT
426787 AAAAATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 15 0.65
24 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TATTTAATTTTATATTATATTT
Found at i:427430 original size:20 final size:19
Alignment explanation
Indices: 427391--427427 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
427381 TCTTTTCTTT
427391 CTTTTATTTTCTTTGTTTA
1 CTTTTATTTTCTTTGTTTA
* *
427410 CTTTTTTTTTTTTTGTTT
1 CTTTTATTTTCTTTGTTT
427428 TACAGAAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.05, C:0.08, G:0.05, T:0.81
Consensus pattern (19 bp):
CTTTTATTTTCTTTGTTTA
Found at i:430652 original size:3 final size:3
Alignment explanation
Indices: 430636--430692 Score: 62
Period size: 3 Copynumber: 19.3 Consensus size: 3
430626 AGAAATTTGG
* * * * *
430636 AGA AGA TGA TGA AGA AGA AGA AGA AGG AGA AGA AGA GGA A-A AGG AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
430683 AGA AGA AGA A
1 AGA AGA AGA A
430693 TTTATAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.04
Consensus pattern (3 bp):
AGA
Found at i:437419 original size:30 final size:29
Alignment explanation
Indices: 437347--437446 Score: 101
Period size: 30 Copynumber: 3.3 Consensus size: 29
437337 TATATTTTTA
*
437347 TTGCACCCAAATAAAGTCTTTAACTTTTAAT
1 TTGCACCCAAAT-AAGTCTTTATC-TTTAAT
** *
437378 TTGCATTCAAATAAGCCTTTATCATTTAAT
1 TTGCACCCAAATAAGTCTTTATC-TTTAAT
* *
437408 TTGTACCCAAATAAGATCTTAATCTTTAAT
1 TTGCACCCAAATAAG-TCTTTATCTTTAAT
*
437438 TTACACCCA
1 TTGCACCCA
437447 GAAAGACCTT
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
30 40 0.71
31 16 0.29
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (29 bp):
TTGCACCCAAATAAGTCTTTATCTTTAAT
Found at i:438000 original size:30 final size:28
Alignment explanation
Indices: 437958--438048 Score: 92
Period size: 30 Copynumber: 3.1 Consensus size: 28
437948 AAAAGGATTA
*
437958 GGTACAACTTAAAGGTTAAGGGCATATTT
1 GGTACAAATTAAAGGTTAAGGGC-TATTT
*
437987 GGATACAAATTAAAGTTTAAGGGCTCATTT
1 GG-TACAAATTAAAGGTTAAGGGCT-ATTT
* * *
438017 AGGTATAAATTAAAGGTAAAGGACTTATTT
1 -GGTACAAATTAAAGGTTAAGGGC-TATTT
438047 GG
1 GG
438049 GTGTAATAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
29 5 0.10
30 44 0.85
31 3 0.06
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (28 bp):
GGTACAAATTAAAGGTTAAGGGCTATTT
Found at i:441875 original size:16 final size:16
Alignment explanation
Indices: 441854--441884 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
441844 CTTAAAAAAA
441854 TTAATTTAAAATAATC
1 TTAATTTAAAATAATC
441870 TTAATTTAAAATAAT
1 TTAATTTAAAATAAT
441885 TATTTTGATA
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAATTTAAAATAATC
Found at i:441952 original size:17 final size:17
Alignment explanation
Indices: 441927--442006 Score: 51
Period size: 17 Copynumber: 4.6 Consensus size: 17
441917 AATTTAAAAT
*
441927 AATTCAATTAAATATTA
1 AATTTAATTAAATATTA
*
441944 AATTTAATTAATTAAAATTTA
1 AATTTAATT-A--AATA-TTA
*
441965 AA-ATAACTTAAA-ATT-
1 AATTTAA-TTAAATATTA
441980 AA-TTAATTTAAATATTA
1 AATTTAA-TTAAATATTA
441997 AATTTAATTA
1 AATTTAATTA
442007 TATGAATTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
15 10 0.20
16 5 0.10
17 14 0.28
18 7 0.14
20 7 0.14
21 7 0.14
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTTAATTAAATATTA
Found at i:441965 original size:21 final size:20
Alignment explanation
Indices: 441917--441970 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
441907 AAACTTGAAT
441917 AATTTAAAATAATTCAATTA
1 AATTTAAAATAATTCAATTA
*
441937 AATATTAAATTTAATT-AATTAA
1 AAT-TTAAA-ATAATTCAATT-A
441959 AATTTAAAATAA
1 AATTTAAAATAA
441971 CTTAAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 6 0.21
21 14 0.48
22 9 0.31
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTTAAAATAATTCAATTA
Found at i:441993 original size:53 final size:52
Alignment explanation
Indices: 441914--442050 Score: 174
Period size: 52 Copynumber: 2.6 Consensus size: 52
441904 ATTAAACTTG
441914 AATAATTTAAAA-TAATTCAA-TTAAATATTAAATTTAATTA-ATTAAAATTTAA
1 AATAATTTAAAATTAATT-AATTTAAATATTAAATTTAATTATA-T-AAATTTAA
* *
441966 AATAACTTAAAATTAATTAATTTAAATATTAAATTTAATTATATGAATTTAA
1 AATAATTTAAAATTAATTAATTTAAATATTAAATTTAATTATATAAATTTAA
* *
442018 AATAATTTAAAATTAAAATAATCTAAAT-TTAAA
1 AATAATTTAAAATT-AATTAATTTAAATATTAAA
442051 ATAATTTAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
52 38 0.50
53 37 0.49
54 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (52 bp):
AATAATTTAAAATTAATTAATTTAAATATTAAATTTAATTATATAAATTTAA
Found at i:442016 original size:14 final size:13
Alignment explanation
Indices: 441934--442034 Score: 63
Period size: 13 Copynumber: 7.9 Consensus size: 13
441924 AATAATTCAA
441934 TTAAATATTAAAT
1 TTAAATATTAAAT
*
441947 TTAATTAATTAAAAT
1 TTAAAT-ATT-AAAT
*
441962 TTAAA-A-TAACT
1 TTAAATATTAAAT
*
441973 TAAAATTAATT-AAT
1 TTAAA-T-ATTAAAT
441987 TTAAATATTAAAT
1 TTAAATATTAAAT
* *
442000 TTAATTATATGAAT
1 TTAAATAT-TAAAT
442014 TTAAA-A-T-AAT
1 TTAAATATTAAAT
442024 TTAAA-ATTAAA
1 TTAAATATTAAA
442035 ATAATCTAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
10 9 0.13
11 9 0.13
12 6 0.09
13 18 0.26
14 18 0.26
15 9 0.13
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (13 bp):
TTAAATATTAAAT
Found at i:442016 original size:27 final size:26
Alignment explanation
Indices: 441934--442018 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 26
441924 AATAATTCAA
441934 TTAAATATTAAATTTAATTAATTAAAAT
1 TTAAATATTAAATTTAATTAA-T-AAAT
* * *
441962 TTAAA-A-TAACTTAAAATTAATTAAT
1 TTAAATATTAAATT-TAATTAATAAAT
*
441987 TTAAATATTAAATTTAATTATATGAAT
1 TTAAATATTAAATTTAATTA-ATAAAT
442014 TTAAA
1 TTAAA
442019 ATAATTTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
25 8 0.17
26 12 0.26
27 22 0.47
28 5 0.11
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (26 bp):
TTAAATATTAAATTTAATTAATAAAT
Found at i:442024 original size:10 final size:10
Alignment explanation
Indices: 442011--442062 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
442001 TAATTATATG
442011 AATTTAAAAT
1 AATTTAAAAT
442021 AATTTAAAATT
1 AATTTAAAA-T
** **
442032 AAAATAATCT
1 AATTTAAAAT
442042 AAATTTAAAAT
1 -AATTTAAAAT
442053 AATTTAAAAT
1 AATTTAAAAT
442063 TCAAATGACA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
10 20 0.62
11 12 0.38
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (10 bp):
AATTTAAAAT
Found at i:442035 original size:16 final size:16
Alignment explanation
Indices: 441955--442068 Score: 104
Period size: 16 Copynumber: 6.8 Consensus size: 16
441945 ATTTAATTAA
*
441955 TTAAAATTTAAAATAAC
1 TTAAAA-TTAAAATAAT
*
441972 TTAAAATT-AATTAAT
1 TTAAAATTAAAATAAT
*
441987 TTAAATATTAAATTTAAT
1 TTAAA-ATTAAA-ATAAT
*
442005 TATATGAATTTAAAATAAT
1 T-TA--AAATTAAAATAAT
442024 TTAAAATTAAAATAAT
1 TTAAAATTAAAATAAT
* *
442040 CTAAATTTAAAATAAT
1 TTAAAATTAAAATAAT
*
442056 TTAAAATTCAAAT
1 TTAAAATTAAAAT
442069 GACAAGAATT
Statistics
Matches: 81, Mismatches: 10, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
15 10 0.12
16 41 0.51
17 8 0.10
18 8 0.10
19 7 0.09
20 5 0.06
21 2 0.02
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (16 bp):
TTAAAATTAAAATAAT
Found at i:442048 original size:32 final size:32
Alignment explanation
Indices: 441917--442068 Score: 115
Period size: 32 Copynumber: 4.8 Consensus size: 32
441907 AAACTTGAAT
*
441917 AATTTAAAATAA-TT-CAATT-AAAT-AT-TA
1 AATTTAAAATAATTTAAAATTAAAATAATCTA
*
441944 AATTT-AATTAA-TTAAAATTTAAAATAA-CTTA
1 AATTTAAAATAATTTAAAA-TTAAAATAATC-TA
* * * *
441975 AAATT-AATTAATTTAAATATTAAATTTAATTATA
1 AATTTAAAATAATTTAAA-ATTAAA-ATAA-TCTA
442009 TGAATTTAAAATAATTTAAAATTAAAATAATCTA
1 --AATTTAAAATAATTTAAAATTAAAATAATCTA
*
442043 AATTTAAAATAATTTAAAATTCAAAT
1 AATTTAAAATAATTTAAAATTAAAAT
442069 GACAAGAATT
Statistics
Matches: 101, Mismatches: 10, Indels: 23
0.75 0.07 0.17
Matches are distributed among these distances:
26 7 0.07
27 7 0.07
28 2 0.02
29 4 0.04
30 1 0.01
31 12 0.12
32 35 0.35
33 4 0.04
34 5 0.05
35 3 0.03
36 10 0.10
37 11 0.11
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (32 bp):
AATTTAAAATAATTTAAAATTAAAATAATCTA
Found at i:442633 original size:22 final size:22
Alignment explanation
Indices: 442604--442658 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
442594 ATTATAAATA
** *
442604 AAAT-TATAATAACAGTTTTAT
1 AAATATATAATAACAAATATAT
442625 AAATATAT-ATATACAAATATAT
1 AAATATATAATA-ACAAATATAT
442647 AAATATA-AATAA
1 AAATATATAATAA
442659 TATATTACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
AAATATATAATAACAAATATAT
Found at i:442642 original size:14 final size:14
Alignment explanation
Indices: 442625--442668 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
442615 ACAGTTTTAT
442625 AAATATATATATAC
1 AAATATATATATAC
* *
442639 AAATATATAAATAT
1 AAATATATATATAC
442653 AAATA-ATATATTAC
1 AAATATATATA-TAC
442667 AA
1 AA
442669 TAACAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATATATATATAC
Found at i:442677 original size:27 final size:28
Alignment explanation
Indices: 442622--442681 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
442612 ATAACAGTTT
*
442622 TATAAATATATATATACAAATATATAAA
1 TATAAATATATATATACAAATATAAAAA
442650 TATAAATA-ATATATTAC-AATA-ACAAAA
1 TATAAATATATATA-TACAAATATA-AAAA
442677 TATAA
1 TATAA
442682 TAAAATAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 1 0.03
27 17 0.59
28 11 0.38
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (28 bp):
TATAAATATATATATACAAATATAAAAA
Done.