Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold89
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: 5168001
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 33045 characters in sequence are not A, C, G, or T
File 12 of 27
Found at i:1738805 original size:21 final size:21
Alignment explanation
Indices: 1738763--1738835 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 21
1738753 AATAAGTATT
1738763 TTTTAAAAAATTGAT-AAA-TTA
1 TTTT-AAAAATT-ATAAAATTTA
1738784 TTTTAAAAA-TA-AATAATTTTA
1 TTTTAAAAATTATAA-AA-TTTA
* *
1738805 TATGAAAATATTATAAAATTTA
1 TTTTAAAA-ATTATAAAATTTA
1738827 TTTTAAAAA
1 TTTTAAAAA
1738836 GATATTATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
18 2 0.05
19 3 0.07
20 5 0.12
21 14 0.34
22 11 0.27
23 4 0.10
24 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
TTTTAAAAATTATAAAATTTA
Found at i:1738932 original size:23 final size:21
Alignment explanation
Indices: 1738889--1738933 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
1738879 TAATTTTTTT
1738889 ATATTTTTATTAATTAAATTA
1 ATATTTTTATTAATTAAATTA
* *
1738910 ATATTATTTAATTTATTATATTA
1 ATATT-TTT-ATTAATTAAATTA
1738933 A
1 A
1738934 ACTTAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 3 0.15
23 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATTTTTATTAATTAAATTA
Found at i:1739428 original size:17 final size:17
Alignment explanation
Indices: 1739408--1739472 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 17
1739398 TATATCGATT
*
1739408 ATATAATTATAAAAATA
1 ATATAATTATAAATATA
1739425 ATATAAATTATTAAATATA
1 ATAT-AATTA-TAAATATA
* *
1739444 TTA-AATTTTAAATATA
1 ATATAATTATAAATATA
1739460 ATTATAATATATA
1 A-TATAAT-TATA
1739473 TTAAACATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 8 0.21
17 10 0.26
18 8 0.21
19 12 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAATTATAAATATA
Found at i:1739454 original size:16 final size:17
Alignment explanation
Indices: 1739428--1739459 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1739418 AAAAATAATA
1739428 TAAATTATTAAATATAT
1 TAAATTATTAAATATAT
1739445 TAAATT-TTAAATATA
1 TAAATTATTAAATATA
1739460 ATTATAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATTATTAAATATAT
Found at i:1739476 original size:22 final size:24
Alignment explanation
Indices: 1739451--1739495 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
1739441 ATATTAAATT
*
1739451 TTAAATATAATTA-TAAT-ATATA
1 TTAAACATAATTATTAATCATATA
*
1739473 TTAAACATATTTATTAATCATAT
1 TTAAACATAATTATTAATCATAT
1739496 TTATTATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 4 0.21
24 4 0.21
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
TTAAACATAATTATTAATCATATA
Found at i:1739482 original size:13 final size:13
Alignment explanation
Indices: 1739466--1739501 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1739456 TATAATTATA
*
1739466 ATATATATTAAAC
1 ATATTTATTAAAC
*
1739479 ATATTTATTAATC
1 ATATTTATTAAAC
1739492 ATATTTATTA
1 ATATTTATTA
1739502 TATATTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (13 bp):
ATATTTATTAAAC
Found at i:1739734 original size:30 final size:30
Alignment explanation
Indices: 1739700--1739758 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1739690 TTGAAGGTAG
* *
1739700 AAATAAAT-AAGAATAAATGTTTGAAAATTC
1 AAATAAATGAA-AATAAATATTTAAAAATTC
*
1739730 AAATAGATGAAAATAAATATTTAAAAATT
1 AAATAAATGAAAATAAATATTTAAAAATT
1739759 TAATTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (30 bp):
AAATAAATGAAAATAAATATTTAAAAATTC
Found at i:1741595 original size:15 final size:16
Alignment explanation
Indices: 1741575--1741616 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
1741565 TATATAAATT
1741575 TTTAAAAATATTTT-A
1 TTTAAAAATATTTTAA
*
1741590 TTT-AAAATTTTTTAA
1 TTTAAAAATATTTTAA
1741605 TATTAAAAATAT
1 T-TTAAAAATAT
1741617 ATTTTAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.41
15 5 0.23
16 2 0.09
17 6 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAAAAATATTTTAA
Found at i:1741595 original size:23 final size:23
Alignment explanation
Indices: 1741538--1741601 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 23
1741528 TAATTATTAT
*
1741538 ATATTTTATTT-ATTTTTTAAAA
1 ATATTTTATTTAAATTTTTAAAA
* *
1741560 ATA-TATATATAAATTTTTAAAA
1 ATATTTTATTTAAATTTTTAAAA
1741582 ATATTTTATTTAAAATTTTT
1 ATATTTTATTT-AAATTTTT
1741602 TAATATTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
21 5 0.15
22 16 0.47
23 5 0.15
24 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATATTTTATTTAAATTTTTAAAA
Found at i:1742181 original size:17 final size:17
Alignment explanation
Indices: 1742161--1742206 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
1742151 AAAATTTAAT
1742161 TTAATTGATTTATATAA
1 TTAATTGATTTATATAA
* *
1742178 TTAATTGATATATGTAA
1 TTAATTGATTTATATAA
* *
1742195 TCAATTAATTTA
1 TTAATTGATTTA
1742207 AAGTTTGAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (17 bp):
TTAATTGATTTATATAA
Found at i:1742684 original size:22 final size:22
Alignment explanation
Indices: 1742654--1742710 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
1742644 ATAGAGTTAT
* **
1742654 AATATAATAATTATTTTG-TAA
1 AATAAAATAATTATTAAGATAA
*
1742675 GAATAAAAT-ATAATTAAGATAA
1 -AATAAAATAATTATTAAGATAA
1742697 AATAAAATAATTAT
1 AATAAAATAATTAT
1742711 AATAATAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (22 bp):
AATAAAATAATTATTAAGATAA
Found at i:1742896 original size:16 final size:17
Alignment explanation
Indices: 1742864--1742904 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1742854 GAAATAAAAT
*
1742864 TAAAATTAATTATTTTA
1 TAAAATTAATCATTTTA
1742881 TAAAATT-ATCATTTTA
1 TAAAATTAATCATTTTA
1742897 T-AAATTAA
1 TAAAATTAA
1742905 ATAATTATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 10 0.45
17 7 0.32
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAAATTAATCATTTTA
Found at i:1748932 original size:24 final size:24
Alignment explanation
Indices: 1748861--1748932 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
1748851 TTAATTTAAG
*
1748861 TTATTATTTAAATAATAAAAATAAT
1 TTATTATTTAAATAAT-ATAATAAT
* ** *
1748886 TTTTTATTTAAATTTTATTATAA-
1 TTATTATTTAAATAATATAATAAT
1748909 TTATTATTTCAAATAATATAATAA
1 TTATTATTT-AAATAATATAATAA
1748933 AATTTTAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
23 8 0.22
24 16 0.43
25 13 0.35
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (24 bp):
TTATTATTTAAATAATATAATAAT
Found at i:1750086 original size:13 final size:13
Alignment explanation
Indices: 1750070--1750099 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1750060 AGATATATAT
*
1750070 ATATATATGTTTA
1 ATATATATATTTA
1750083 ATATATATATTTA
1 ATATATATATTTA
1750096 ATAT
1 ATAT
1750100 TTTTAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
ATATATATATTTA
Found at i:1752424 original size:18 final size:18
Alignment explanation
Indices: 1752390--1752424 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1752380 GCAAAAGTGG
**
1752390 GAAGAAGAACAGTAACAA
1 GAAGAAGAACAACAACAA
1752408 GAAGAAGAACAACAACA
1 GAAGAAGAACAACAACA
1752425 GCAATAACAG
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:0.63, C:0.14, G:0.20, T:0.03
Consensus pattern (18 bp):
GAAGAAGAACAACAACAA
Found at i:1755100 original size:19 final size:19
Alignment explanation
Indices: 1755064--1755100 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1755054 GGTTCGTGAA
* *
1755064 GAGAGAGAAGGAAGGAAAG
1 GAGAGAGAAAGAAAGAAAG
1755083 GAGAGAGAAAGAAAGAAA
1 GAGAGAGAAAGAAAGAAA
1755101 CAAAAAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (19 bp):
GAGAGAGAAAGAAAGAAAG
Found at i:1756115 original size:16 final size:18
Alignment explanation
Indices: 1756089--1756121 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1756079 TACATTCATA
1756089 TATTCATATTAT-TTTTG
1 TATTCATATTATATTTTG
1756106 TATT-ATATTATATTTT
1 TATTCATATTATATTTT
1756122 AATTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (18 bp):
TATTCATATTATATTTTG
Found at i:1756126 original size:11 final size:12
Alignment explanation
Indices: 1756108--1756175 Score: 72
Period size: 11 Copynumber: 5.9 Consensus size: 12
1756098 TATTTTTGTA
1756108 TTATATTATATT
1 TTATATTATATT
*
1756120 TTA-ATTATTTT
1 TTATATTATATT
1756131 TTCATATTATA-T
1 TT-ATATTATATT
*
1756143 TTATATCATATT
1 TTATATTATATT
*
1756155 TCA-ATT-TATT
1 TTATATTATATT
1756165 TTATATTATAT
1 TTATATTATAT
1756176 ATAATTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
10 6 0.13
11 21 0.47
12 13 0.29
13 5 0.11
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.63
Consensus pattern (12 bp):
TTATATTATATT
Found at i:1756147 original size:35 final size:33
Alignment explanation
Indices: 1756108--1756175 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 33
1756098 TATTTTTGTA
* * *
1756108 TTATATTATATTTTAATTATTTTTTCATATTATAT
1 TTATATCATATTTCAATT-TATTTT-ATATTATAT
1756143 TTATATCATATTTCAATTTATTTTATATTATAT
1 TTATATCATATTTCAATTTATTTTATATTATAT
1756176 ATAATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 9 0.30
34 5 0.17
35 16 0.53
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.63
Consensus pattern (33 bp):
TTATATCATATTTCAATTTATTTTATATTATAT
Found at i:1756267 original size:30 final size:28
Alignment explanation
Indices: 1756197--1756267 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 28
1756187 TGTGATTAAA
*
1756197 TTTTAATTTTAAATTTATTTTATAAATAT
1 TTTTAA-TTAAAATTTATTTTATAAATAT
* *
1756226 TTTTAAATAAAATTTATTAATTAT-AATTT
1 TTTTAATTAAAATTTATT--TTATAAATAT
1756255 TATTTAATTAAAA
1 T-TTTAATTAAAA
1756268 AATTTGTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 10 0.29
29 11 0.31
30 14 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTTAATTAAAATTTATTTTATAAATAT
Found at i:1757565 original size:14 final size:13
Alignment explanation
Indices: 1757548--1757590 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
1757538 TTTTAAATAT
1757548 ATTAAAAATATTTA
1 ATTAAAAAT-TTTA
*
1757562 ATT-ATAATTTTA
1 ATTAAAAATTTTA
1757574 ATATAAAAATTTTA
1 AT-TAAAAATTTTA
1757588 ATT
1 ATT
1757591 TATTAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 6 0.24
13 6 0.24
14 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATTAAAAATTTTA
Found at i:1757623 original size:30 final size:30
Alignment explanation
Indices: 1757589--1757645 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1757579 AAAATTTTAA
*
1757589 TTTATTAA-ATATATAATAAAATATAATATT
1 TTTATTAATATA-ATAAAAAAATATAATATT
*
1757619 TTTATTAATATAATAAAAAAATCTAAT
1 TTTATTAATATAATAAAAAAATATAAT
1757646 CAATCTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (30 bp):
TTTATTAATATAATAAAAAAATATAATATT
Found at i:1773244 original size:20 final size:20
Alignment explanation
Indices: 1773207--1773251 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1773197 CTCAACAAGA
*
1773207 AAAAATATTTACAAAACTAT
1 AAAAATATATACAAAACTAT
* * *
1773227 AAAAATATATATATAACTTT
1 AAAAATATATACAAAACTAT
1773247 AAAAA
1 AAAAA
1773252 AAAAAGGTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAATATATACAAAACTAT
Found at i:1777570 original size:64 final size:64
Alignment explanation
Indices: 1777435--1777558 Score: 189
Period size: 64 Copynumber: 2.0 Consensus size: 64
1777425 TAAATTTAAA
* * * *
1777435 TATATAAATAATCAAACATTTTGTATGCAACATAGATACGTAGTTGTAGCAATAATGATTTATC
1 TATATAAATAATCAAACAGTTTATATGCAACATAGATACGTAGTTGTAGCAATAATAATTAATC
*
1777499 TATATAAATAATCAAACAGTTTATATGCAACATAGATACGTGGTTGTAGC-ATAA-AATTAA
1 TATATAAATAATCAAACAGTTTATATGCAACATAGATACGTAGTTGTAGCAATAATAATTAA
1777559 ATTATAAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 4 0.07
63 4 0.07
64 47 0.85
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (64 bp):
TATATAAATAATCAAACAGTTTATATGCAACATAGATACGTAGTTGTAGCAATAATAATTAATC
Found at i:1777632 original size:2 final size:2
Alignment explanation
Indices: 1777625--1777656 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1777615 TTTAATTTTA
1777625 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
1777657 TAAGAGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1793333 original size:28 final size:28
Alignment explanation
Indices: 1793283--1793378 Score: 86
Period size: 28 Copynumber: 3.3 Consensus size: 28
1793273 ATGATATAAC
* * *
1793283 ATAAAAATTATTAATATATAATATAAATAT
1 ATAAATATTTTTAA-AT-TAATATAAAAAT
1793313 ATAAATATTTTTAAATTAATATAAAAAT
1 ATAAATATTTTTAAATTAATATAAAAAT
* * * *
1793341 ATTAAA-ATATTAAAATTTATAAAAAAAT
1 A-TAAATATTTTTAAATTAATATAAAAAT
1793369 ATAATATATT
1 ATAA-ATATT
1793379 AAATATAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
27 3 0.05
28 32 0.58
29 8 0.15
30 12 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATAAATATTTTTAAATTAATATAAAAAT
Found at i:1793370 original size:36 final size:37
Alignment explanation
Indices: 1793295--1793385 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 37
1793285 AAAAATTATT
* * **
1793295 AATATATAATA-T-AAATATATAAATATTTTTAAATT
1 AATATAAAATATTAAAATATATAAATATTTATAAAAA
1793330 AATATAAAAATATTAAAATAT-TAAA-ATTTATAAAAA
1 AATAT-AAAATATTAAAATATATAAATATTTATAAAAA
*
1793366 AATATAATATATT-AAATATA
1 AATATAAAATATTAAAATATA
1793386 ATTATAACAC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
34 6 0.13
35 12 0.26
36 18 0.38
37 5 0.11
38 6 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (37 bp):
AATATAAAATATTAAAATATATAAATATTTATAAAAA
Found at i:1793441 original size:40 final size:38
Alignment explanation
Indices: 1793345--1793445 Score: 114
Period size: 40 Copynumber: 2.6 Consensus size: 38
1793335 AAAAATATTA
*
1793345 AAATATTAAAATTTATAAAAAAATATAATATATTAAATAT
1 AAATA-TAAAAATTA-AAAAAAATATAATATATTAAATAT
* * *
1793385 AATTATAACACA-TAAAAATAATATAATATGATGTAAATAT
1 AAATATAA-AAATTAAAAAAAATATAATAT-AT-TAAATAT
1793425 AAATATAAAAATTAAAAAAAA
1 AAATATAAAAATTAAAAAAAA
1793446 AATCTCATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
38 14 0.28
39 9 0.18
40 27 0.54
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (38 bp):
AAATATAAAAATTAAAAAAAATATAATATATTAAATAT
Found at i:1794315 original size:13 final size:13
Alignment explanation
Indices: 1794297--1794321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1794287 TATTGCAAGT
1794297 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
1794310 AAAAAAGAAAAA
1 AAAAAAGAAAAA
1794322 GAAGGAGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:1796338 original size:31 final size:31
Alignment explanation
Indices: 1796300--1796369 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
1796290 TGGAATTTCA
1796300 GCCATTGCAGCTATGTCCCAATTTCTAGACC
1 GCCATTGCAGCTATGTCCCAATTTCTAGACC
*
1796331 GCCATTGCAGCTATGTCCCAATTTCTTGACC
1 GCCATTGCAGCTATGTCCCAATTTCTAGACC
1796362 GCCATTGC
1 GCCATTGC
1796370 CGAGATTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.20, C:0.33, G:0.17, T:0.30
Consensus pattern (31 bp):
GCCATTGCAGCTATGTCCCAATTTCTAGACC
Found at i:1805237 original size:38 final size:38
Alignment explanation
Indices: 1805186--1805260 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
1805176 TCCCAAAAAC
*
1805186 AACAAACAGCATAAGATAGGATAAACTAGAACAAGACG
1 AACAAACAGCATAAGAAAGGATAAACTAGAACAAGACG
*
1805224 AACAAACAGCATAAGAAAGGATAAACTAGATCAAGAC
1 AACAAACAGCATAAGAAAGGATAAACTAGAACAAGAC
1805261 AAACCCATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.11
Consensus pattern (38 bp):
AACAAACAGCATAAGAAAGGATAAACTAGAACAAGACG
Found at i:1805249 original size:19 final size:19
Alignment explanation
Indices: 1805189--1805249 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
1805179 CAAAAACAAC
*
1805189 AAACAGCATAAGATAGGAT
1 AAACAGCATAAGAAAGGAT
* * * * *
1805208 AAACTAGAACAAG-ACGAAC
1 AAAC-AGCATAAGAAAGGAT
1805227 AAACAGCATAAGAAAGGAT
1 AAACAGCATAAGAAAGGAT
1805246 AAAC
1 AAAC
1805250 TAGATCAAGA
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
18 6 0.21
19 17 0.59
20 6 0.21
ACGTcount: A:0.57, C:0.15, G:0.18, T:0.10
Consensus pattern (19 bp):
AAACAGCATAAGAAAGGAT
Found at i:1809891 original size:2 final size:2
Alignment explanation
Indices: 1809884--1809914 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1809874 CAGGACTTAT
1809884 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1809915 AAAAGCCAAA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1812061 original size:15 final size:17
Alignment explanation
Indices: 1812041--1812075 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1812031 TGTATGAATT
1812041 TAAAAA-AATAAAAA-A
1 TAAAAATAATAAAAATA
1812056 TAAAAATAATAAAAATA
1 TAAAAATAATAAAAATA
1812073 TAA
1 TAA
1812076 TTTTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 8 0.44
17 4 0.22
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (17 bp):
TAAAAATAATAAAAATA
Found at i:1812613 original size:28 final size:28
Alignment explanation
Indices: 1812582--1812663 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 28
1812572 TATATTCTTT
1812582 TTTATTAAAGTTTGAATGATAATTGTTA
1 TTTATTAAAGTTTGAATGATAATTGTTA
* *
1812610 TTTA-CATCA-TTT---T-ATAATTG--A
1 TTTATTA-AAGTTTGAATGATAATTGTTA
*
1812631 ATTATTAAAGTTTGAATGATAATTGTTA
1 TTTATTAAAGTTTGAATGATAATTGTTA
1812659 TTTAT
1 TTTAT
1812664 ATCATTAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 18
0.62 0.10 0.29
Matches are distributed among these distances:
21 5 0.13
22 4 0.10
23 7 0.18
24 1 0.03
25 1 0.03
26 7 0.18
27 4 0.10
28 10 0.26
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.51
Consensus pattern (28 bp):
TTTATTAAAGTTTGAATGATAATTGTTA
Found at i:1812688 original size:45 final size:47
Alignment explanation
Indices: 1812583--1812699 Score: 193
Period size: 49 Copynumber: 2.5 Consensus size: 47
1812573 ATATTCTTTT
1812583 TTATTAAAGTTTGAATGATAATTGTTATTTACATCATTTTATAATTGAA
1 TTATTAAAGTTTGAATGATAATTGTTATTTACATCA--TTATAATTGAA
*
1812632 TTATTAAAGTTTGAATGATAATTGTTATTTATATCA-T-TAATTGAA
1 TTATTAAAGTTTGAATGATAATTGTTATTTACATCATTATAATTGAA
1812677 TTATTAAAGTTTGAATGATAATT
1 TTATTAAAGTTTGAATGATAATT
1812700 CATACTCAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
45 31 0.46
46 1 0.01
49 35 0.52
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.49
Consensus pattern (47 bp):
TTATTAAAGTTTGAATGATAATTGTTATTTACATCATTATAATTGAA
Found at i:1819374 original size:2 final size:2
Alignment explanation
Indices: 1819369--1819402 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1819359 AAAAGGAGGG
1819369 TA 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
1819403 ATCAAAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1820809 original size:17 final size:18
Alignment explanation
Indices: 1820787--1820832 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
1820777 TTATAATATG
1820787 AATATAATATATTAAT-A
1 AATATAATATATTAATAA
* *
1820804 AATATAAAAAATTAATAA
1 AATATAATATATTAATAA
*
1820822 AATTTAATATA
1 AATATAATATA
1820833 AAATATTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATATAATATATTAATAA
Found at i:1820844 original size:15 final size:15
Alignment explanation
Indices: 1820824--1820876 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1820814 ATTAATAAAA
1820824 TTTAATATAAAATAT
1 TTTAATATAAAATAT
* *
1820839 TTTAATATATATTAT
1 TTTAATATAAAATAT
*
1820854 ATTAATA-ATAAATAT
1 TTTAATATA-AAATAT
*
1820869 TTAAATAT
1 TTTAATAT
1820877 TTTATATTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
14 1 0.03
15 28 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTAATATAAAATAT
Found at i:1820881 original size:28 final size:30
Alignment explanation
Indices: 1820825--1820884 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
1820815 TTAATAAAAT
1820825 TTAATATAAAATATTTTAATATATATTATA
1 TTAATATAAAATATTTTAATATATATTATA
*
1820855 TTAATA-ATAAATA-TTTAA-ATATTTTATA
1 TTAATATA-AAATATTTTAATATATATTATA
1820883 TT
1 TT
1820885 TTTTATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 11 0.39
29 6 0.21
30 11 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TTAATATAAAATATTTTAATATATATTATA
Found at i:1821084 original size:18 final size:18
Alignment explanation
Indices: 1821063--1821119 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
1821053 ATAATATTTA
1821063 AAATTTTTATAATTATAT
1 AAATTTTTATAATTATAT
1821081 AAA--TTT-TAA-TATAT
1 AAATTTTTATAATTATAT
* * *
1821095 TAATATTTAAAATTATAT
1 AAATTTTTATAATTATAT
1821113 AAATTTT
1 AAATTTT
1821120 AAGATATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 7 0.23
15 3 0.10
16 6 0.19
17 2 0.06
18 13 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AAATTTTTATAATTATAT
Found at i:1821137 original size:17 final size:19
Alignment explanation
Indices: 1821100--1821148 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 19
1821090 TATATTAATA
*
1821100 TTTAAAAT-TA-TATAAAT
1 TTTAAAATATATTTTAAAT
*
1821117 TTTAAGATAT-TTTTAAA-
1 TTTAAAATATATTTTAAAT
1821134 TTTAAAATATATTTT
1 TTTAAAATATATTTT
1821149 TATTTTTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTAAAATATATTTTAAAT
Found at i:1827267 original size:24 final size:25
Alignment explanation
Indices: 1827214--1827269 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
1827204 TTTGATAATT
*
1827214 TATAAAAAAATATGAATATCATAAA
1 TATAAAAAAATATGAAAATCATAAA
1827239 T-TAAAAAAATATGAAAAT-A-AAA
1 TATAAAAAAATATGAAAATCATAAA
1827261 TAATAAAAA
1 T-ATAAAAA
1827270 TATAATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 4 0.14
23 1 0.04
24 22 0.79
25 1 0.04
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (25 bp):
TATAAAAAAATATGAAAATCATAAA
Found at i:1827619 original size:5 final size:5
Alignment explanation
Indices: 1827609--1827633 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1827599 AATAGGCAAA
1827609 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
1827634 CATATTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1830695 original size:2 final size:2
Alignment explanation
Indices: 1830679--1830713 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1830669 AAGGTTATTA
*
1830679 AT AT AT AA AT A- 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
1830714 GATACAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1831101 original size:15 final size:15
Alignment explanation
Indices: 1831075--1831135 Score: 56
Period size: 14 Copynumber: 4.1 Consensus size: 15
1831065 ATCATGATCA
1831075 ATAAAA-ATAAAAAT
1 ATAAAATATAAAAAT
1831089 ATAAAATATAAAAAT
1 ATAAAATATAAAAAT
*
1831104 -TAAATTA-AATAAAT
1 ATAAAATATAA-AAAT
* *
1831118 ATTAATTATATAAAAT
1 ATAAAATATA-AAAAT
1831134 AT
1 AT
1831136 TATAAAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
13 2 0.05
14 16 0.40
15 14 0.35
16 7 0.17
17 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAAAATATAAAAAT
Found at i:1831115 original size:16 final size:16
Alignment explanation
Indices: 1831079--1831137 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 16
1831069 TGATCAATAA
1831079 AAATAAAAATATAAA--
1 AAATAAAAAT-TAAATT
*
1831094 ATATAAAAATTAAATT
1 AAATAAAAATTAAATT
*
1831110 AAATAAATATT-AATT
1 AAATAAAAATTAAATT
*
1831125 ATATAAAATATTA
1 AAATAAAA-ATTA
1831138 TAAAAATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 4 0.11
15 19 0.54
16 12 0.34
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATAAAAATTAAATT
Found at i:1831145 original size:31 final size:30
Alignment explanation
Indices: 1831075--1831153 Score: 76
Period size: 31 Copynumber: 2.6 Consensus size: 30
1831065 ATCATGATCA
* *
1831075 ATAAAAATAAAAATATAA-AATATAAAAATT
1 ATAAAAATAAATAT-TAATTATATAAAAATT
1831105 A-AATTAAATAAATATTAATTATATAAAATATT
1 ATAA--AAATAAATATTAATTATATAAAA-ATT
1831137 ATAAAAAT-AAT-TTAATT
1 ATAAAAATAAATATTAATT
1831154 TTAAGTTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
29 8 0.19
30 7 0.17
31 21 0.50
32 4 0.10
33 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (30 bp):
ATAAAAATAAATATTAATTATATAAAAATT
Found at i:1831146 original size:16 final size:15
Alignment explanation
Indices: 1831075--1831146 Score: 51
Period size: 16 Copynumber: 4.7 Consensus size: 15
1831065 ATCATGATCA
1831075 ATAAAAATAAAAA-T
1 ATAAAAATAAAAATT
1831089 ATAAAATATAAAAATT
1 ATAAAA-ATAAAAATT
*
1831105 A-AATTAAATAAATATT
1 ATAA--AAATAAAAATT
* *
1831121 A-ATTATATAAAATATT
1 ATA-AAAATAAAA-ATT
1831137 ATAAAAATAA
1 ATAAAAATAA
1831147 TTTAATTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
14 6 0.13
15 15 0.33
16 21 0.47
17 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAAAAATAAAAATT
Found at i:1832174 original size:22 final size:24
Alignment explanation
Indices: 1832135--1832201 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 24
1832125 TAAAATATTA
* *
1832135 AATATATATAAATTTTATAAA-TT
1 AATATATTTATATTTTATAAATTT
1832158 AATA-ATTTATATTTTATAAATTTT
1 AATATATTTATATTTTATAAA-TTT
1832182 AATATATTTATATATTTATA
1 AATATATTTATAT-TTTATA
1832202 TTATATAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 14 0.37
23 4 0.11
24 6 0.16
25 8 0.21
26 6 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATATATTTATATTTTATAAATTT
Found at i:1832176 original size:31 final size:33
Alignment explanation
Indices: 1832139--1832209 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
1832129 ATATTAAATA
1832139 TATATAAATTTT-ATAAATTAATA-ATTTATAT
1 TATATAAATTTTAATAAATTAATATATTTATAT
* * *
1832170 TTTATAAATTTTAATATATTTATATATTTATAT
1 TATATAAATTTTAATAAATTAATATATTTATAT
1832203 TATATAA
1 TATATAA
1832210 TCATATTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 11 0.32
32 9 0.26
33 14 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
TATATAAATTTTAATAAATTAATATATTTATAT
Found at i:1832196 original size:8 final size:8
Alignment explanation
Indices: 1832148--1832202 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
1832138 ATATATAAAT
*
1832148 TTTATAAA
1 TTTATATA
*
1832156 TTAATA-A
1 TTTATATA
1832163 TTTATAT-
1 TTTATATA
*
1832170 TTTATAAA
1 TTTATATA
1832178 TTTTAATATA
1 -TTT-ATATA
1832188 TTTATATA
1 TTTATATA
1832196 TTTATAT
1 TTTATAT
1832203 TATATAATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 12 0.31
8 17 0.44
9 6 0.15
10 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TTTATATA
Found at i:1832199 original size:17 final size:17
Alignment explanation
Indices: 1832122--1832199 Score: 58
Period size: 17 Copynumber: 4.8 Consensus size: 17
1832112 TCATAATTAG
1832122 ATTTA-AAATATTAA-AT
1 ATTTATAAAT-TTAATAT
* * *
1832138 ATATATAAATTTTATAA
1 ATTTATAAATTTAATAT
*
1832155 ATTAAT-AATTT-ATAT
1 ATTTATAAATTTAATAT
1832170 -TTTATAAATTTTAATAT
1 ATTTATAAA-TTTAATAT
*
1832187 ATTTATATATTTA
1 ATTTATAAATTTA
1832200 TATTATATAA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
14 4 0.08
15 5 0.10
16 15 0.31
17 17 0.35
18 7 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATAAATTTAATAT
Found at i:1832206 original size:19 final size:18
Alignment explanation
Indices: 1832136--1832207 Score: 55
Period size: 18 Copynumber: 4.2 Consensus size: 18
1832126 AAAATATTAA
*
1832136 ATATATATAAATTTTA-T
1 ATATTTATAAATTTTATT
* *
1832153 AAATTAAT-AA-TTTA-T
1 ATATTTATAAATTTTATT
*
1832168 AT-TTTATAAATTTTAAT
1 ATATTTATAAATTTTATT
*
1832185 ATATTTATATATTTATATT
1 ATATTTATAAATTT-TATT
1832204 ATAT
1 ATAT
1832208 AATCATATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
14 4 0.09
15 8 0.19
16 6 0.14
17 8 0.19
18 10 0.23
19 7 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATTTATAAATTTTATT
Found at i:1834314 original size:19 final size:18
Alignment explanation
Indices: 1834286--1834333 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
1834276 ATAAATATAA
* *
1834286 TAATAAATATAAAATATT
1 TAATATATATAAAACATT
* *
1834304 TAATATTATATCACACATT
1 TAATA-TATATAAAACATT
1834323 TAATATATATA
1 TAATATATATA
1834334 TTTAATAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATATATATAAAACATT
Found at i:1834983 original size:13 final size:11
Alignment explanation
Indices: 1834927--1834978 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
1834917 TTTATAATTT
*
1834927 TAAATATAATT
1 TAAATATAATA
*
1834938 TAACATAAATATA
1 TAA-ATATA-ATA
* *
1834951 TAAAAATTATA
1 TAAATATAATA
1834962 TAAATATAATA
1 TAAATATAATA
1834973 TAAATA
1 TAAATA
1834979 CATAAATTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
11 21 0.66
12 6 0.19
13 5 0.16
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
TAAATATAATA
Found at i:1834983 original size:19 final size:19
Alignment explanation
Indices: 1834940--1834985 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1834930 ATATAATTTA
1834940 ACATAAATATATAAAAATT
1 ACATAAATATATAAAAATT
* *
1834959 ATATAAATATAATATAAA-T
1 ACATAAATAT-ATAAAAATT
1834978 ACATAAAT
1 ACATAAAT
1834986 TATTAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
ACATAAATATATAAAAATT
Found at i:1846051 original size:15 final size:14
Alignment explanation
Indices: 1846033--1846091 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
1846023 AAAATTTAAA
1846033 ATTAAAACTATTTTT
1 ATTAAAA-TATTTTT
*
1846048 ATTAAATTGATTTTT
1 ATTAAAAT-ATTTTT
*
1846063 A-TATAATATTTTT
1 ATTAAAATATTTTT
* *
1846076 ATTTAAATTTTTTT
1 ATTAAAATATTTTT
1846090 AT
1 AT
1846092 AAATTAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
13 7 0.19
14 16 0.44
15 13 0.36
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (14 bp):
ATTAAAATATTTTT
Found at i:1846075 original size:14 final size:12
Alignment explanation
Indices: 1846057--1846096 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1846047 TATTAAATTG
1846057 ATTTTTATATAA
1 ATTTTTATATAA
*
1846069 TATTTTTATTTAA
1 -ATTTTTATATAA
*
1846082 ATTTTTTTATAA
1 ATTTTTATATAA
1846094 ATT
1 ATT
1846097 AAATAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTTTATATAA
Found at i:1851409 original size:25 final size:26
Alignment explanation
Indices: 1851390--1851475 Score: 92
Period size: 25 Copynumber: 3.5 Consensus size: 26
1851380 ATTTTGATTC
1851390 AAATTTAA-TTAATTTATTTTAAGTT
1 AAATTTAATTTAATTTATTTTAAGTT
*
1851415 AAATTTAATTTAATTTAATTTAA-TT
1 AAATTTAATTTAATTTATTTTAAGTT
* * * *
1851440 AAA--TAAATAAATTAATTTAAAGTT
1 AAATTTAATTTAATTTATTTTAAGTT
1851464 -AATTTAATTTAA
1 AAATTTAATTTAA
1851476 AATGTAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
23 15 0.31
24 2 0.04
25 19 0.39
26 13 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
AAATTTAATTTAATTTATTTTAAGTT
Found at i:1851421 original size:16 final size:15
Alignment explanation
Indices: 1851391--1851472 Score: 73
Period size: 16 Copynumber: 5.6 Consensus size: 15
1851381 TTTTGATTCA
1851391 AATTTAATT-AATTT
1 AATTTAATTAAATTT
*
1851405 ATTTTAAGTTAAATTT
1 AATTTAA-TTAAATTT
*
1851421 AATTTAATTTAATTT
1 AATTTAATTAAATTT
*
1851436 AA-TTAAATAAA--T
1 AATTTAATTAAATTT
* *
1851448 AAATTAATTTAAAGTT
1 AATTTAA-TTAAATTT
1851464 AATTTAATT
1 AATTTAATT
1851473 TAAAATGTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
12 3 0.05
13 4 0.07
14 17 0.31
15 13 0.24
16 18 0.33
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
AATTTAATTAAATTT
Found at i:1851422 original size:21 final size:21
Alignment explanation
Indices: 1851398--1851475 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
1851388 TCAAATTTAA
*
1851398 TTAATTTATTTTAAGTTAAAT
1 TTAATTTAATTTAAGTTAAAT
*
1851419 TTAATTTAATTTAA-TTTAAT
1 TTAATTTAATTTAAGTTAAAT
* * * * *
1851439 TAAATAAATAAATTAATTTAAAG
1 TTAAT--TTAATTTAAGTTAAAT
1851462 TTAATTTAATTTAA
1 TTAATTTAATTTAA
1851476 AATGTAAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
20 9 0.20
21 20 0.45
22 7 0.16
23 8 0.18
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
TTAATTTAATTTAAGTTAAAT
Found at i:1851424 original size:5 final size:5
Alignment explanation
Indices: 1851391--1851475 Score: 73
Period size: 5 Copynumber: 16.4 Consensus size: 5
1851381 TTTTGATTCA
* * *
1851391 AATTT AA-TT AATTT ATTTT AAGTTA AATTT AATTT AATTT AATTT AATTA
1 AATTT AATTT AATTT AATTT AA-TTT AATTT AATTT AATTT AATTT AATTT
* * *
1851441 AATAAAT AAATT AATTT AAAGTT AATTT AATTT AA
1 AAT--TT AATTT AATTT -AATTT AATTT AATTT AA
1851476 AATGTAAAAT
Statistics
Matches: 63, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
4 4 0.06
5 49 0.78
6 8 0.13
7 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (5 bp):
AATTT
Found at i:1851489 original size:33 final size:33
Alignment explanation
Indices: 1851420--1851493 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
1851410 AAGTTAAATT
* *
1851420 TAATTT-AATTTAATTTAATTAAATAAATAAAT
1 TAATTTAAAGTTAATTTAATTAAATAAATAAAA
**
1851452 TAATTTAAAGTTAATTTAATTTAAA-ATGTAAAA
1 TAATTTAAAGTTAATTTAA-TTAAATAAATAAAA
1851485 TAATTTAAA
1 TAATTTAAA
1851494 TTTTAAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 6 0.17
33 25 0.69
34 5 0.14
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (33 bp):
TAATTTAAAGTTAATTTAATTAAATAAATAAAA
Found at i:1851494 original size:43 final size:42
Alignment explanation
Indices: 1851394--1851495 Score: 100
Period size: 43 Copynumber: 2.4 Consensus size: 42
1851384 TGATTCAAAT
* ** *
1851394 TTAATTAATTTATTTTAAGTTAAATTTAATTTAATTTAATTTAA
1 TTAAATAATTTAAATTAAGTTAAAGTTAATTTAATTTAA--TAA
* *
1851438 TTAAATAA-ATAAATTAATTTAAAGTTAATTTAATTTAA-AA
1 TTAAATAATTTAAATTAAGTTAAAGTTAATTTAATTTAATAA
1851478 TGTAAAATAATTTAAATT
1 T-T-AAATAATTTAAATT
1851496 TTAAAATTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
40 3 0.06
41 1 0.02
42 6 0.12
43 31 0.65
44 7 0.15
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (42 bp):
TTAAATAATTTAAATTAAGTTAAAGTTAATTTAATTTAATAA
Found at i:1851507 original size:24 final size:23
Alignment explanation
Indices: 1851453--1851515 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 23
1851443 TAAATAAATT
*
1851453 AATTTAAAGTTAATTT-AATTTAA
1 AATTTAAA-ATAATTTAAATTTAA
*
1851476 AATGTAAAATAATTTAAATTTTAA
1 AATTTAAAATAATTTAAA-TTTAA
1851500 AATTTAAAATAATTTA
1 AATTTAAAATAATTTA
1851516 TTTCGAACCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
22 6 0.17
23 9 0.26
24 20 0.57
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (23 bp):
AATTTAAAATAATTTAAATTTAA
Found at i:1853696 original size:2 final size:2
Alignment explanation
Indices: 1853689--1853730 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1853679 TTGAACTCTT
*
1853689 TA TA TA 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
1853731 CATGATTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1857463 original size:18 final size:18
Alignment explanation
Indices: 1857443--1857479 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1857433 AATTTTAGAT
1857443 AAAATATTAAATTATTTTA
1 AAAAT-TTAAATTATTTTA
*
1857462 AAAATTTAAATTTTTTTA
1 AAAATTTAAATTATTTTA
1857480 TGTCTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATTTAAATTATTTTA
Found at i:1857540 original size:5 final size:5
Alignment explanation
Indices: 1857532--1857558 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1857522 ATTAATATAA
1857532 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
1857559 TATAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:1857884 original size:24 final size:25
Alignment explanation
Indices: 1857840--1857886 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1857830 AAATTTTATA
1857840 AATAAATATAGATAATTTTATTTTT
1 AATAAATATAGATAATTTTATTTTT
* *
1857865 AATAAA-ATATATTATTTTATTT
1 AATAAATATAGATAATTTTATTT
1857887 ACTGATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
AATAAATATAGATAATTTTATTTTT
Found at i:1859433 original size:8 final size:8
Alignment explanation
Indices: 1859417--1859499 Score: 55
Period size: 8 Copynumber: 10.0 Consensus size: 8
1859407 TATGAATAAA
1859417 AAAATAAT
1 AAAATAAT
1859425 AATAA-AAT
1 AA-AATAAT
*
1859433 ATAAT-AT
1 AAAATAAT
1859440 AAAATAAT
1 AAAATAAT
1859448 AAAATAAT
1 AAAATAAT
1859456 ATAAATATAT
1 A-AAATA-AT
**
1859466 AAATATTTT
1 AAA-ATAAT
1859475 AAAAT-AT
1 AAAATAAT
*
1859482 ATAAATATT
1 A-AAATAAT
1859491 AAATATAAT
1 AAA-ATAAT
1859500 TATAACATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
7 10 0.17
8 25 0.42
9 19 0.32
10 5 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAAATAAT
Found at i:1859436 original size:13 final size:13
Alignment explanation
Indices: 1859406--1859468 Score: 55
Period size: 13 Copynumber: 5.0 Consensus size: 13
1859396 CTAGATCAAG
1859406 ATATGAATAA-AAA
1 ATAT-AATAATAAA
1859419 A-ATAATAATAAA
1 ATATAATAATAAA
1859431 ATATAAT-ATAAA
1 ATATAATAATAAA
*
1859443 ATAATAA-AATAAT
1 AT-ATAATAATAAA
1859456 ATA-AATATATAAA
1 ATATAATA-ATAAA
1859469 TATTTTAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
11 7 0.17
12 15 0.36
13 20 0.48
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (13 bp):
ATATAATAATAAA
Found at i:1859446 original size:31 final size:31
Alignment explanation
Indices: 1859411--1859519 Score: 89
Period size: 31 Copynumber: 3.5 Consensus size: 31
1859401 TCAAGATATG
1859411 AATAAAAAAATAATAATAAAATATAATATAA
1 AATAAAAAAATAATAATAAAATATAATATAA
* *
1859442 AATAATAAAATAAT-ATAAATATATAA-ATAT
1 AATAAAAAAATAATAATAAA-ATATAATATAA
** * *
1859472 TTTAAAATATATAA-ATATTAAATATAATTATAA
1 AATAAAA-AAATAATA-ATAAAATATAA-TATAA
* *
1859505 CATAAAAAATTAATA
1 AATAAAAAAATAATA
1859520 CAAAAATGAT
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
30 12 0.20
31 30 0.51
32 8 0.14
33 9 0.15
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (31 bp):
AATAAAAAAATAATAATAAAATATAATATAA
Found at i:1859454 original size:18 final size:18
Alignment explanation
Indices: 1859411--1859486 Score: 63
Period size: 17 Copynumber: 4.3 Consensus size: 18
1859401 TCAAGATATG
1859411 AATAAAA-AA-ATAATAAT
1 AATAAAATAATATAA-AAT
*
1859428 AA-AATATAATATAAAAT
1 AATAAAATAATATAAAAT
1859445 AATAAAATAATAT-AAAT
1 AATAAAATAATATAAAAT
* *
1859462 -ATATAAATATTTTAAAAT
1 AATA-AAATAATATAAAAT
1859480 ATATAAA
1 A-ATAAA
1859487 TATTAAATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
16 6 0.12
17 20 0.42
18 17 0.35
19 2 0.04
20 3 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAAATAATATAAAAT
Found at i:1861703 original size:14 final size:14
Alignment explanation
Indices: 1861686--1861720 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1861676 CATTTTCCGG
*
1861686 TTAGTTTTTTTTTT
1 TTAGTTTTTCTTTT
*
1861700 TTAGGTTTTCTTTT
1 TTAGTTTTTCTTTT
1861714 TTAGTTT
1 TTAGTTT
1861721 AGTTTAAGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.03, G:0.11, T:0.77
Consensus pattern (14 bp):
TTAGTTTTTCTTTT
Found at i:1873572 original size:19 final size:18
Alignment explanation
Indices: 1873532--1873626 Score: 76
Period size: 18 Copynumber: 5.4 Consensus size: 18
1873522 CCTTTAAACT
1873532 TATAAATAT--AA-TTTA
1 TATAAATATAAAATTTTA
1873547 T-TAAATATTAAAATTTTA
1 TATAAATA-TAAAATTTTA
1873565 TATAAATATAAATATTTTA
1 TATAAATATAAA-ATTTTA
* * *
1873584 AATATAAT-TATAATATTA
1 TATA-AATATAAAATTTTA
*
1873602 TA-AAATATATAAATTTAA
1 TATAAATATA-AAATTTTA
1873620 TATAAAT
1 TATAAAT
1873627 TAATTAATTA
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 6 0.10
15 2 0.03
16 3 0.05
17 5 0.08
18 22 0.35
19 22 0.35
20 3 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATAAATATAAAATTTTA
Found at i:1873590 original size:21 final size:21
Alignment explanation
Indices: 1873548--1873610 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
1873538 TATAATTTAT
1873548 TAAATATTAAA-ATTTT--ATA
1 TAAATA-TAAATATTTTAAATA
1873567 TAAATATAAATATTTTAAATA
1 TAAATATAAATATTTTAAATA
* *
1873588 TAATTAT-AATATTATAAAATA
1 TAAATATAAATATT-TTAAATA
1873609 TA
1 TA
1873611 TAAATTTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 4 0.11
19 11 0.29
20 6 0.16
21 17 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATATAAATATTTTAAATA
Found at i:1874291 original size:13 final size:13
Alignment explanation
Indices: 1874273--1874315 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1874263 ATAATTTTTT
1874273 TATATTTTAAAAA
1 TATATTTTAAAAA
*
1874286 TATA-TTTAAATA
1 TATATTTTAAAAA
* *
1874298 TATATATTAAAAT
1 TATATTTTAAAAA
1874311 TATAT
1 TATAT
1874316 ATAATATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TATATTTTAAAAA
Found at i:1874307 original size:25 final size:26
Alignment explanation
Indices: 1874273--1874331 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
1874263 ATAATTTTTT
* *
1874273 TATATTTTAAAAATATATTTAA-ATA
1 TATATATTAAAAATATATATAATATA
*
1874298 TATATATTAAAATTATATATAATATA
1 TATATATTAAAAATATATATAATATA
1874324 TAATATAT
1 T-ATATAT
1874332 AATATTGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 19 0.66
26 4 0.14
27 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TATATATTAAAAATATATATAATATA
Found at i:1874316 original size:13 final size:13
Alignment explanation
Indices: 1874272--1874317 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 13
1874262 TATAATTTTT
*
1874272 TTATATTTTAAAA
1 TTATATATTAAAA
*
1874285 --ATATATTTAAA
1 TTATATATTAAAA
1874296 TATATATATTAAAA
1 T-TATATATTAAAA
1874310 TTATATAT
1 TTATATAT
1874318 AATATATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
11 9 0.33
13 7 0.26
14 11 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTATATATTAAAA
Found at i:1874324 original size:7 final size:7
Alignment explanation
Indices: 1874312--1874336 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1874302 TATTAAAATT
1874312 ATATATA
1 ATATATA
1874319 ATATATA
1 ATATATA
1874326 ATATATA
1 ATATATA
1874333 ATAT
1 ATAT
1874337 TGTATACGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATATA
Found at i:1877196 original size:21 final size:21
Alignment explanation
Indices: 1877172--1877230 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
1877162 TTAAATTATT
1877172 ATTTAATAATAAAAATATTT-A
1 ATTTAAT-ATAAAAATATTTAA
1877193 ATTTAAT-TATAAAATATTTAA
1 ATTTAATATA-AAAATATTTAA
1877214 ATATTAATATAAAAATA
1 AT-TTAATATAAAAATA
1877231 ATTTTTAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
19 2 0.06
20 9 0.26
21 10 0.29
22 11 0.32
23 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTAATATAAAAATATTTAA
Found at i:1878581 original size:23 final size:23
Alignment explanation
Indices: 1878547--1878591 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1878537 AAAGTAATGT
1878547 TTTAAATATAAA-AAATATTTAAA
1 TTTAAATATAAATAAAT-TTTAAA
1878570 TTTATAAT-TAAATAAATTTTAA
1 TTTA-AATATAAATAAATTTTAA
1878592 TTAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTAAATATAAATAAATTTTAAA
Found at i:1878594 original size:15 final size:16
Alignment explanation
Indices: 1878566--1878595 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1878556 AAAAAATATT
1878566 TAAATTTATAATTAAA
1 TAAATTTATAATTAAA
1878582 TAAATTT-TAATTAA
1 TAAATTTATAATTAA
1878596 TTTTTATAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATTTATAATTAAA
Found at i:1880636 original size:25 final size:23
Alignment explanation
Indices: 1880581--1880636 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
1880571 ATTTAAATTT
* *
1880581 AAAAAATTAATTAATTTATTTAA
1 AAAAAATCAATTAATTAATTTAA
*
1880604 ATACAAATCAATCTAATTAATTATAA
1 A-AAAAATCAAT-TAATTAATT-TAA
1880630 AAAAAAT
1 AAAAAAT
1880637 TTAATAACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 1 0.04
24 8 0.31
25 13 0.50
26 4 0.15
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAAAATCAATTAATTAATTTAA
Found at i:1880717 original size:37 final size:38
Alignment explanation
Indices: 1880676--1880774 Score: 105
Period size: 37 Copynumber: 2.7 Consensus size: 38
1880666 TCAAAATTAT
* *
1880676 TTAAATATAAAATAA-TCAAATTTGATAAATTTAAATA
1 TTAAATATAAAATAATTCAAAATTAATAAATTTAAATA
* * * *
1880713 TTAAACAT-AATTAATTTAAAATTAATTAATTTAAATA
1 TTAAATATAAAATAATTCAAAATTAATAAATTTAAATA
* *
1880750 TTAAAT-TAAAATTATTAAAAATTAA
1 TTAAATATAAAATAATTCAAAATTAA
1880775 AATGATTTAA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
36 6 0.12
37 44 0.88
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (38 bp):
TTAAATATAAAATAATTCAAAATTAATAAATTTAAATA
Found at i:1880738 original size:15 final size:16
Alignment explanation
Indices: 1880720--1880758 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 16
1880710 ATATTAAACA
1880720 TAATTAATTTAAA-AT
1 TAATTAATTTAAATAT
1880735 TAATTAATTTAAATAT
1 TAATTAATTTAAATAT
1880751 TAAATTAA
1 T-AATTAA
1880759 AATTATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 13 0.59
16 3 0.14
17 6 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAATTAATTTAAATAT
Found at i:1880790 original size:16 final size:15
Alignment explanation
Indices: 1880745--1880808 Score: 53
Period size: 16 Copynumber: 4.3 Consensus size: 15
1880735 TAATTAATTT
1880745 AAATA-TTAAA-TTA
1 AAATATTTAAACTTA
* *
1880758 AAATTATTAAAAATTA
1 AAA-TATTTAAACTTA
1880774 AAATGATTTAAACTTA
1 AAAT-ATTTAAACTTA
*
1880790 ATATATTCT-AACTTA
1 AAATATT-TAAACTTA
1880805 AAAT
1 AAAT
1880809 TAATTTAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
13 3 0.07
14 2 0.05
15 17 0.41
16 19 0.46
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (15 bp):
AAATATTTAAACTTA
Found at i:1882401 original size:29 final size:29
Alignment explanation
Indices: 1882369--1882522 Score: 83
Period size: 29 Copynumber: 5.4 Consensus size: 29
1882359 TATAAATTTA
1882369 ATTTAAATTATTATTAAATAATAAAAAAT
1 ATTTAAATTATTATTAAATAATAAAAAAT
* * *
1882398 ATTTTTAATT-TTATTTAATTATAAAAAAT
1 A-TTTAAATTATTATTAAATAATAAAAAAT
* *
1882427 ATAT-AA--A-TATT-AATATTAAAATAAT
1 ATTTAAATTATTATTAAATAATAAAA-AAT
** * *
1882452 ATTTTAATAATTAAAATTACGATAATAATAAA-
1 A-TTT-A-AATTATTATTA-AATAATAAAAAAT
* *
1882484 ATTTAAATTATTATTTAATAGT-AAAAAT
1 ATTTAAATTATTATTAAATAATAAAAAAT
1882512 -TTTAAAATTAT
1 ATTT-AAATTAT
1882523 GAGCCACCCG
Statistics
Matches: 94, Mismatches: 17, Indels: 29
0.67 0.12 0.21
Matches are distributed among these distances:
24 8 0.09
25 8 0.09
26 2 0.02
27 9 0.10
28 13 0.14
29 29 0.31
30 8 0.09
31 4 0.04
32 4 0.04
33 2 0.02
34 7 0.07
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (29 bp):
ATTTAAATTATTATTAAATAATAAAAAAT
Found at i:1883631 original size:22 final size:22
Alignment explanation
Indices: 1883606--1883649 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1883596 TTCTATAATG
* *
1883606 AAATTAAATATTAATAATATAT
1 AAATTAAATATAAATAAAATAT
*
1883628 AAATTTAATATAAATAAAATAT
1 AAATTAAATATAAATAAAATAT
1883650 GTAATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATTAAATATAAATAAAATAT
Found at i:1886098 original size:17 final size:17
Alignment explanation
Indices: 1886076--1886109 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1886066 TAAAAATATG
1886076 TAATTATATTTTTATTT
1 TAATTATATTTTTATTT
1886093 TAATTATATTTTTATTT
1 TAATTATATTTTTATTT
1886110 ATTTATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TAATTATATTTTTATTT
Found at i:1891901 original size:15 final size:16
Alignment explanation
Indices: 1891871--1891903 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
1891861 TAAATAACCC
1891871 TTATTAATTTTATTTT
1 TTATTAATTTTATTTT
1891887 TTATT-ATTTT-TTTT
1 TTATTAATTTTATTTT
1891901 TTA
1 TTA
1891904 AAAAATTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 5 0.29
16 5 0.29
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTAATTTTATTTT
Found at i:1893513 original size:2 final size:2
Alignment explanation
Indices: 1893508--1893560 Score: 65
Period size: 2 Copynumber: 27.5 Consensus size: 2
1893498 TATTTTTTAC
* * *
1893508 AT AT AT AT AT AT AT AC AT GT AT AT AT A- AT -T AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1893548 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1893561 CAAAATTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1896964 original size:3 final size:3
Alignment explanation
Indices: 1896958--1896995 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1896948 AAAAAAAAAG
1896958 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1896996 GAGGAGAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1903739 original size:188 final size:188
Alignment explanation
Indices: 1903418--1903794 Score: 709
Period size: 188 Copynumber: 2.0 Consensus size: 188
1903408 ACACGGGCAC
1903418 AGAAATAATATGTGATGATTTCAACTTTCCACTGCATTACCTTCTGGCTTTTCCATCACAAACCA
1 AGAAATAATATGTGATGATTTCAACTTTCCACTGCATTACCTTCTGGCTTTTCCATCACAAACCA
* * *
1903483 GCAGTGCACACCATGTTGACCACTATGTACACAGAGAATGTGATTAAAGCCAAAGTCATCTATAT
66 GCAGTGCACAACATGTTGACCACTATATACACAAAGAATGTGATTAAAGCCAAAGTCATCTATAT
1903548 TATTAGAAGTTAACTGATGATGTAGAAAGAAGACTATCATGTGCATTATTAGAAGTTA
131 TATTAGAAGTTAACTGATGATGTAGAAAGAAGACTATCATGTGCATTATTAGAAGTTA
1903606 AGAAATAATATGTGATGATTTCAACTTTCCACTGCATTACCTTCTGGCTTTTCCATCACAAACCA
1 AGAAATAATATGTGATGATTTCAACTTTCCACTGCATTACCTTCTGGCTTTTCCATCACAAACCA
* *
1903671 GCAGTGCACAACATGTTGACCACTATATACACAAAGAATGTGGTTAAAGCCAAAGTCATCTGTAT
66 GCAGTGCACAACATGTTGACCACTATATACACAAAGAATGTGATTAAAGCCAAAGTCATCTATAT
1903736 TATTAGAAGTTAACTGATGATGTAGAAAGAAGACTATCATGTGCATTATTAGAAGTTA
131 TATTAGAAGTTAACTGATGATGTAGAAAGAAGACTATCATGTGCATTATTAGAAGTTA
1903794 A
1 A
1903795 CTGATGATGT
Statistics
Matches: 184, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
188 184 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (188 bp):
AGAAATAATATGTGATGATTTCAACTTTCCACTGCATTACCTTCTGGCTTTTCCATCACAAACCA
GCAGTGCACAACATGTTGACCACTATATACACAAAGAATGTGATTAAAGCCAAAGTCATCTATAT
TATTAGAAGTTAACTGATGATGTAGAAAGAAGACTATCATGTGCATTATTAGAAGTTA
Found at i:1903801 original size:46 final size:46
Alignment explanation
Indices: 1903734--1903871 Score: 276
Period size: 46 Copynumber: 3.0 Consensus size: 46
1903724 AGTCATCTGT
1903734 ATTATTAGAAGTTAACTGATGATGTAGAAAGAAGACTATCATGTGC
1 ATTATTAGAAGTTAACTGATGATGTAGAAAGAAGACTATCATGTGC
1903780 ATTATTAGAAGTTAACTGATGATGTAGAAAGAAGACTATCATGTGC
1 ATTATTAGAAGTTAACTGATGATGTAGAAAGAAGACTATCATGTGC
1903826 ATTATTAGAAGTTAACTGATGATGTAGAAAGAAGACTATCATGTGC
1 ATTATTAGAAGTTAACTGATGATGTAGAAAGAAGACTATCATGTGC
1903872 CTGCATTGTA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 92 1.00
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (46 bp):
ATTATTAGAAGTTAACTGATGATGTAGAAAGAAGACTATCATGTGC
Found at i:1903804 original size:27 final size:27
Alignment explanation
Indices: 1903774--1903850 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
1903764 GAAGACTATC
1903774 ATGTGCATTATTAGAAGTTAACTGATG
1 ATGTGCATTATTAGAAGTTAACTGATG
*
1903801 ATGTAG-A--A--AGAAG---ACT-ATC
1 ATGT-GCATTATTAGAAGTTAACTGATG
1903820 ATGTGCATTATTAGAAGTTAACTGATG
1 ATGTGCATTATTAGAAGTTAACTGATG
1903847 ATGT
1 ATGT
1903851 AGAAAGAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 20
0.63 0.03 0.33
Matches are distributed among these distances:
18 1 0.03
19 7 0.18
20 3 0.08
21 1 0.03
23 10 0.26
25 1 0.03
26 3 0.08
27 11 0.29
28 1 0.03
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (27 bp):
ATGTGCATTATTAGAAGTTAACTGATG
Found at i:1905904 original size:48 final size:49
Alignment explanation
Indices: 1905757--1905985 Score: 221
Period size: 49 Copynumber: 4.7 Consensus size: 49
1905747 CCCAAACTTA
* * * *
1905757 GAATTTCAGGCATGAGG-GATATAGGTAAAACACCTCTTGCTCAAGCTAA
1 GAATTTCAGGCATG-GGAGGTGTAGGTAAAACAGCTCTTGCTCAAGCTAG
* * * ** *
1905806 GAATCTCAGGGATTGGAGAAGTAGGCAAAACAGCTCTTGCTCAAGCTAG
1 GAATTTCAGGCATGGGAGGTGTAGGTAAAACAGCTCTTGCTCAAGCTAG
* *
1905855 GAATTTCAGGCGTGGGAGGTGTAGGT-AAACAGCTCTTGCAT-AAGTTAG
1 GAATTTCAGGCATGGGAGGTGTAGGTAAAACAGCTCTTGC-TCAAGCTAG
* ** * * *
1905903 GAATTTCGGGCATGGGAGGTAAAAGTAAAACGGCTCTTGCTCAAGCTACT
1 GAATTTCAGGCATGGGAGGTGTAGGTAAAACAGCTCTTGCTCAAGCTA-G
* * *
1905953 AAATTTCAGGAATGGGAGGTGTAGGTCAAACAG
1 GAATTTCAGGCATGGGAGGTGTAGGTAAAACAG
1905986 GTTTTCCTCA
Statistics
Matches: 143, Mismatches: 32, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
48 43 0.30
49 75 0.52
50 25 0.17
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (49 bp):
GAATTTCAGGCATGGGAGGTGTAGGTAAAACAGCTCTTGCTCAAGCTAG
Found at i:1916234 original size:18 final size:18
Alignment explanation
Indices: 1916210--1916250 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1916200 GTGTTCATCT
1916210 TCATGGTCGTGGTCGTGG
1 TCATGGTCGTGGTCGTGG
* *
1916228 TCGTGGTCGTGGTCATGG
1 TCATGGTCGTGGTCGTGG
1916246 TCATG
1 TCATG
1916251 AGGCTTTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.07, C:0.17, G:0.41, T:0.34
Consensus pattern (18 bp):
TCATGGTCGTGGTCGTGG
Found at i:1916250 original size:6 final size:6
Alignment explanation
Indices: 1916213--1916247 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1916203 TTCATCTTCA
*
1916213 TGGTCG TGGTCG TGGTCG TGGTCG TGGTCA TGGTC
1 TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGTC
1916248 ATGAGGCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.03, C:0.17, G:0.46, T:0.34
Consensus pattern (6 bp):
TGGTCG
Found at i:1919716 original size:28 final size:28
Alignment explanation
Indices: 1919661--1919743 Score: 73
Period size: 28 Copynumber: 2.9 Consensus size: 28
1919651 TTTGATAGTT
**
1919661 TTATGTATAATTTATTTAATTATTTTAA
1 TTATGTATAATTTATTTAATTAAATTAA
*
1919689 TTATGTATATTTTATTTTAA-TAAATTAA
1 TTATGTATAATTTA-TTTAATTAAATTAA
*
1919717 TTTAT-TATTAAATTATTT-ATTATAATT
1 -TTATGTA-TAATTTATTTAATTA-AATT
1919744 TTTATTTATC
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
27 1 0.02
28 26 0.58
29 18 0.40
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (28 bp):
TTATGTATAATTTATTTAATTAAATTAA
Found at i:1919736 original size:15 final size:16
Alignment explanation
Indices: 1919709--1919739 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1919699 TTTATTTTAA
1919709 TAAATTAATTTATTAT
1 TAAATTAATTTATTAT
1919725 TAAATT-ATTTATTAT
1 TAAATTAATTTATTAT
1919740 AATTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TAAATTAATTTATTAT
Found at i:1923372 original size:30 final size:29
Alignment explanation
Indices: 1923303--1923372 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 29
1923293 AAAATTAAAA
* **
1923303 TTATTTAAATTATAATATTTAATTTAATT
1 TTATATAAATTATAATAAATAATTTAATT
*
1923332 TTGATTTAAATTATAATTAAATATATTTAATT
1 TT-ATATAAATTATAA-TAAATA-ATTTAATT
1923364 TT-TATAAAT
1 TTATATAAAT
1923373 GATGATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 2 0.06
30 19 0.54
31 4 0.11
32 10 0.29
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
TTATATAAATTATAATAAATAATTTAATT
Found at i:1927859 original size:17 final size:18
Alignment explanation
Indices: 1927837--1927870 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1927827 TTAAATATAC
1927837 AATTATATT-TTTATTTT
1 AATTATATTATTTATTTT
1927854 AATTATATTATTTATTT
1 AATTATATTATTTATTT
1927871 ATTAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:1928214 original size:54 final size:54
Alignment explanation
Indices: 1928156--1928263 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
1928146 TTCACATCTT
* * *
1928156 AAAATCTATTCTAAAATTTTTACCCTCTAAAATTTTTTACATCATACCAACATC
1 AAAATCTATTCTAAAACTCTTACCCTCTAAAATTTCTTACATCATACCAACATC
* * * *
1928210 AAAATTTATTCTAAAACTCTTACTCTTTAAAATTTCTTACATCATGCCAACATC
1 AAAATCTATTCTAAAACTCTTACCCTCTAAAATTTCTTACATCATACCAACATC
1928264 TCCACCATGC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.39
Consensus pattern (54 bp):
AAAATCTATTCTAAAACTCTTACCCTCTAAAATTTCTTACATCATACCAACATC
Found at i:1929921 original size:16 final size:16
Alignment explanation
Indices: 1929900--1929951 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1929890 TTTGAATAAT
1929900 TTTTGAGTTT-AAATTA
1 TTTTGA-TTTCAAATTA
*
1929916 TTTTGATTTCGAATTA
1 TTTTGATTTCAAATTA
* * *
1929932 TTTTAAATTCAAGTTA
1 TTTTGATTTCAAATTA
1929948 TTTT
1 TTTT
1929952 AGTGCCGATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 3 0.10
16 27 0.90
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.58
Consensus pattern (16 bp):
TTTTGATTTCAAATTA
Found at i:1930794 original size:15 final size:15
Alignment explanation
Indices: 1930776--1930842 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 15
1930766 TTATTAAAAA
1930776 ATTAATTATATTAAT
1 ATTAATTATATTAAT
**
1930791 ATTAAAAATATT-AT
1 ATTAATTATATTAAT
*
1930805 CATT-ATTAT-TAAAAT
1 -ATTAATTATAT-TAAT
*
1930820 ATTATTTATATTAAT
1 ATTAATTATATTAAT
1930835 A-TAATTAT
1 ATTAATTAT
1930843 TATTTAAACA
Statistics
Matches: 39, Mismatches: 8, Indels: 11
0.67 0.14 0.19
Matches are distributed among these distances:
13 1 0.03
14 14 0.36
15 23 0.59
16 1 0.03
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTAATTATATTAAT
Found at i:1930803 original size:20 final size:20
Alignment explanation
Indices: 1930780--1930833 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1930770 TAAAAAATTA
1930780 ATTATATTAATATTAAAAAT
1 ATTATATTAATATTAAAAAT
*
1930800 ATTATCATTATTATT-AAAAT
1 ATTAT-ATTAATATTAAAAAT
1930820 ATTAT-TT-ATATTAA
1 ATTATATTAATATTAA
1930834 TATAATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 4 0.13
18 3 0.10
20 15 0.50
21 8 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTATATTAATATTAAAAAT
Found at i:1931059 original size:37 final size:34
Alignment explanation
Indices: 1931018--1931085 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 34
1931008 GTTAAATACT
* *
1931018 TAAAATAATACTATTTATTATTAAACATAATTATATA
1 TAAAATAATA-TAATAATTATTAAA-AT-ATTATATA
*
1931055 TAAAATATTATAATAATTATTAAAATATTAT
1 TAAAATAATATAATAATTATTAAAATATTAT
1931086 TTCAATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 5 0.18
35 2 0.07
36 12 0.43
37 9 0.32
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (34 bp):
TAAAATAATATAATAATTATTAAAATATTATATA
Found at i:1931242 original size:25 final size:27
Alignment explanation
Indices: 1931207--1931268 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 27
1931197 AAATAAAATT
*
1931207 AATATTTATTA-ATTATTATT-AATATA
1 AATATATATTATA-TATTATTAAATATA
1931233 AATA-ATATTATATATTATTAAAATATA
1 AATATATATTATATATTATT-AAATATA
1931260 AATATATAT
1 AATATATAT
1931269 GTTTAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
25 12 0.39
26 5 0.16
27 10 0.32
28 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
AATATATATTATATATTATTAAATATA
Found at i:1931256 original size:21 final size:21
Alignment explanation
Indices: 1931218--1931257 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1931208 ATATTTATTA
1931218 ATTATTATTAATATAAATAAT
1 ATTATTATTAATATAAATAAT
*
1931239 ATTATATATTATTA-AAATA
1 ATTAT-TATTAATATAAATA
1931258 TAAATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTATTATTAATATAAATAAT
Found at i:1931267 original size:35 final size:34
Alignment explanation
Indices: 1931190--1931267 Score: 79
Period size: 35 Copynumber: 2.3 Consensus size: 34
1931180 TTTATCATTA
*
1931190 AAATA-ATAAATAAAATTAATATTTATTAATTAT
1 AAATATATAAATAAAATTAATATTTATTAAATAT
* * *
1931223 TATTAATATAAATAATATT-ATATATTATTAAAATAT
1 AAAT-ATATAAATAAAATTAATAT-TTATT-AAATAT
1931259 AAATATATA
1 AAATATATA
1931268 TGTTTAATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
33 2 0.06
34 5 0.14
35 21 0.60
36 7 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
AAATATATAAATAAAATTAATATTTATTAAATAT
Found at i:1931291 original size:14 final size:14
Alignment explanation
Indices: 1931274--1931300 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1931264 TATATGTTTA
1931274 ATAATATTAAAATT
1 ATAATATTAAAATT
1931288 ATAATATTAAAAT
1 ATAATATTAAAAT
1931301 AACTAACAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATATTAAAATT
Found at i:1933816 original size:24 final size:24
Alignment explanation
Indices: 1933764--1933819 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1933754 AAATTTTATA
* *
1933764 ATTTAAATTAATTTTATTAGAGTT
1 ATTTAAATTAATTTTATTAAAATT
*
1933788 ATTTAAATTATTATTTATTAAAATT
1 ATTTAAATTAAT-TTTATTAAAATT
1933813 -TTTAAAT
1 ATTTAAAT
1933820 ATTTTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 18 0.64
25 10 0.36
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
ATTTAAATTAATTTTATTAAAATT
Found at i:1935141 original size:22 final size:22
Alignment explanation
Indices: 1935090--1935142 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
1935080 ATGATAATTT
* *
1935090 ATATATTAT-TTTATATTTTTA
1 ATATATTATAATTATATTTTAA
*
1935111 TTATATTATAATTATATTTTAA
1 ATATATTATAATTATATTTTAA
*
1935133 ATATTTTATA
1 ATATATTATA
1935143 TTTAATTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATATATTATAATTATATTTTAA
Found at i:1935219 original size:23 final size:24
Alignment explanation
Indices: 1935187--1935237 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
1935177 ATATAAATTT
1935187 TAAATATATA-TATTATATTTTTA
1 TAAATATATACTATTATATTTTTA
* * *
1935210 TAAATTTATACGTGTTATTTTTTTA
1 TAAATATATAC-TATTATATTTTTA
1935235 TAA
1 TAA
1935238 TAACATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 9 0.39
25 14 0.61
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (24 bp):
TAAATATATACTATTATATTTTTA
Found at i:1935953 original size:21 final size:21
Alignment explanation
Indices: 1935929--1935969 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1935919 CTGCCTTAAA
1935929 ATATTTTAT-ATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
1935950 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
1935970 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:1946575 original size:11 final size:11
Alignment explanation
Indices: 1946537--1946582 Score: 53
Period size: 10 Copynumber: 4.5 Consensus size: 11
1946527 TATAATATTA
1946537 ATATAAAA-AT
1 ATATAAAATAT
*
1946547 ATTTAAAAT-T
1 ATATAAAATAT
1946557 AT-TAAAATAT
1 ATATAAAATAT
*
1946567 TTATAAAATAT
1 ATATAAAATAT
1946578 ATATA
1 ATATA
1946583 TTTAAACTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
9 6 0.20
10 12 0.40
11 12 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATATAAAATAT
Found at i:1947477 original size:22 final size:22
Alignment explanation
Indices: 1947434--1947484 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
1947424 TATGAAGTTT
1947434 AAAATTTTTTATAATATATTAA
1 AAAATTTTTTATAATATATTAA
*
1947456 ATAATTTTTTA-AAT-TGATTTAA
1 AAAATTTTTTATAATAT-A-TTAA
1947478 AAAATTT
1 AAAATTT
1947485 AGCAGTGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.04
21 4 0.16
22 20 0.80
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
AAAATTTTTTATAATATATTAA
Found at i:1949127 original size:19 final size:20
Alignment explanation
Indices: 1949092--1949133 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
1949082 ATAAAAAGTA
*
1949092 TAATTTATTTTTTAATTTTT
1 TAATTTATTTTTAAATTTTT
1949112 TAATTT-TTTTTAAATTTTT
1 TAATTTATTTTTAAATTTTT
1949131 TAA
1 TAA
1949134 AAATTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TAATTTATTTTTAAATTTTT
Done.