Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 12 of 24
Found at i:1646432 original size:25 final size:25
Alignment explanation
Indices: 1646404--1646469 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 25
1646394 TATTTTATTA
*
1646404 ATTATTA-TAATTATATATTAAATAT
1 ATTATTATTAATTATAT-TTAAAAAT
*
1646429 ATTA-TATTGATTATATTTAAAAAT
1 ATTATTATTAATTATATTTAAAAAT
*
1646453 ATTA-TATTTATTATATT
1 ATTATTATTAATTATATT
1646470 ATATTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 25 0.68
25 12 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
ATTATTATTAATTATATTTAAAAAT
Found at i:1646454 original size:24 final size:24
Alignment explanation
Indices: 1646413--1646469 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
1646403 AATTATTATA
*
1646413 ATTATATATTAAATATATTATATTG
1 ATTATAT-TTAAAAATATTATATTG
*
1646438 ATTATATTTAAAAATATTATATTT
1 ATTATATTTAAAAATATTATATTG
1646462 ATTATATT
1 ATTATATT
1646470 ATATTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 23 0.77
25 7 0.23
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTATATTTAAAAATATTATATTG
Found at i:1647632 original size:12 final size:12
Alignment explanation
Indices: 1647615--1647641 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1647605 TAATAACTAT
1647615 ATATAAAAAGTA
1 ATATAAAAAGTA
1647627 ATATAAAAAGTA
1 ATATAAAAAGTA
1647639 ATA
1 ATA
1647642 AATAATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (12 bp):
ATATAAAAAGTA
Found at i:1648226 original size:25 final size:24
Alignment explanation
Indices: 1648192--1648245 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
1648182 TAAAGTGTGG
1648192 AAATAATTTTTAAAT-TTAAAATTA
1 AAATAATTTTTAAATATT-AAATTA
*
1648216 AAATAACTTTTTTAATATTAAATTA
1 AAATAA-TTTTTAAATATTAAATTA
*
1648241 TAATA
1 AAATA
1648246 CGTGATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 6 0.23
25 18 0.69
26 2 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
AAATAATTTTTAAATATTAAATTA
Found at i:1648832 original size:18 final size:19
Alignment explanation
Indices: 1648809--1648848 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1648799 AAATTATATT
*
1648809 TAAAATATT-ATATATTCA
1 TAAAATATTGATATATTAA
*
1648827 TAAAATTTTGATATATTAA
1 TAAAATATTGATATATTAA
1648846 TAA
1 TAA
1648849 TTAATATTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (19 bp):
TAAAATATTGATATATTAA
Found at i:1649733 original size:16 final size:16
Alignment explanation
Indices: 1649712--1649746 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1649702 GTAGGTAGCA
1649712 TTAGACCTTGGGTACT
1 TTAGACCTTGGGTACT
* *
1649728 TTAGACCTTTGGTGCT
1 TTAGACCTTGGGTACT
1649744 TTA
1 TTA
1649747 CACAGCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (16 bp):
TTAGACCTTGGGTACT
Found at i:1650176 original size:14 final size:14
Alignment explanation
Indices: 1650131--1650179 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
1650121 AGTGAATGAA
1650131 ATATTTTAATTTTT
1 ATATTTTAATTTTT
* *
1650145 ATATTATTAA-ATTA
1 ATATT-TTAATTTTT
1650159 ATATTTTAATTTTT
1 ATATTTTAATTTTT
1650173 ATATTTT
1 ATATTTT
1650180 GAAAGTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 4 0.14
14 21 0.72
15 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATATTTTAATTTTT
Found at i:1650240 original size:31 final size:32
Alignment explanation
Indices: 1650178--1650241 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1650168 TTTTTATATT
* *
1650178 TTGAAAGTTATAGTAAATAAAAAAATGATTAA
1 TTGAAAATTATAGTAAATAAAAAAATAATTAA
1650210 TTGAAAATTATAGTAAAT-AAAAAATAATTAA
1 TTGAAAATTATAGTAAATAAAAAAATAATTAA
1650241 T
1 T
1650242 AGTGTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (32 bp):
TTGAAAATTATAGTAAATAAAAAAATAATTAA
Found at i:1650712 original size:14 final size:14
Alignment explanation
Indices: 1650693--1650723 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1650683 CATAATTTTG
1650693 TATTTATGAAATTA
1 TATTTATGAAATTA
*
1650707 TATTTATGATATTA
1 TATTTATGAAATTA
1650721 TAT
1 TAT
1650724 ATTCATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTTATGAAATTA
Found at i:1651994 original size:3 final size:3
Alignment explanation
Indices: 1651986--1652028 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1651976 TAACCAAGAT
1651986 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1652029 CTGAACAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1652369 original size:16 final size:15
Alignment explanation
Indices: 1652343--1652398 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
1652333 ATATTATAAT
1652343 TTTTATTAAATATTATA
1 TTTT-TTAAAT-TTATA
1652360 TTTTTTAAATTTA-A
1 TTTTTTAAATTTATA
*
1652374 TTTTTAATAATTTAATA
1 TTTTTTA-AATTT-ATA
1652391 TTTTTTAA
1 TTTTTTAA
1652399 GTTTTAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 7 0.21
15 8 0.24
16 8 0.24
17 11 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTTAAATTTATA
Found at i:1652385 original size:15 final size:15
Alignment explanation
Indices: 1652339--1652394 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
1652329 CTCCATATTA
*
1652339 TAATTTTTATTAAATAT
1 TAATTTTTAAT-AAT-T
*
1652356 TATATTTTTTA-AATT
1 TA-ATTTTTAATAATT
1652371 TAATTTTTAATAATT
1 TAATTTTTAATAATT
1652386 TAATATTTT
1 TAAT-TTTT
1652395 TTAAGTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 7 0.21
15 11 0.33
16 7 0.21
17 2 0.06
18 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TAATTTTTAATAATT
Found at i:1652395 original size:31 final size:32
Alignment explanation
Indices: 1652339--1652398 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
1652329 CTCCATATTA
*
1652339 TAATTTTTATTAAATATTATATTTTTTAAATT
1 TAATTTTTAATAAATATTATATTTTTTAAATT
1652371 TAATTTTTAAT-AAT-TTAATATTTTTTAA
1 TAATTTTTAATAAATATT-ATATTTTTTAA
1652399 GTTTTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 2 0.08
31 14 0.54
32 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (32 bp):
TAATTTTTAATAAATATTATATTTTTTAAATT
Found at i:1652625 original size:19 final size:18
Alignment explanation
Indices: 1652589--1652626 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1652579 TTTTTTTTCG
1652589 TTTAAATTATTTTTTAAA
1 TTTAAATTATTTTTTAAA
1652607 TTTAATATT-TTTATTTAAA
1 TTTAA-ATTATTT-TTTAAA
1652626 T
1 T
1652627 CTTTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTAAATTATTTTTTAAA
Found at i:1653044 original size:2 final size:2
Alignment explanation
Indices: 1653037--1653064 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1653027 GAATCAATAC
1653037 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
1653065 GCTAACGGAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1653224 original size:2 final size:2
Alignment explanation
Indices: 1653219--1653253 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1653209 TTTTTTGTAG
1653219 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1653254 GTGTGTGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1654991 original size:18 final size:18
Alignment explanation
Indices: 1654958--1655001 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
1654948 GATTTGATAA
1654958 ATTTAATATTTATATTAT
1 ATTTAATATTTATATTAT
1654976 ATTTATATATTT-TATTAT
1 ATTTA-ATATTTATATTAT
1654994 ATTATAAT
1 ATT-TAAT
1655002 CGTATTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTAATATTTATATTAT
Found at i:1655682 original size:11 final size:11
Alignment explanation
Indices: 1655668--1655705 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1655658 AATAAATATA
1655668 ATAAATAATTG
1 ATAAATAATTG
*
1655679 ATAAAT-ATAG
1 ATAAATAATTG
1655689 -TAAATAATTG
1 ATAAATAATTG
1655699 ATAAATA
1 ATAAATA
1655706 TATATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 5 0.22
10 6 0.26
11 12 0.52
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (11 bp):
ATAAATAATTG
Found at i:1655682 original size:20 final size:20
Alignment explanation
Indices: 1655659--1655707 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1655649 TCAATAAGTA
1655659 ATAAATATAATAAATAATTG
1 ATAAATATAATAAATAATTG
*
1655679 ATAAATATAGTAAATAATTG
1 ATAAATATAATAAATAATTG
1655699 ATAAATATA
1 ATAAATATA
1655708 TATTTTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (20 bp):
ATAAATATAATAAATAATTG
Found at i:1661011 original size:32 final size:34
Alignment explanation
Indices: 1660958--1661031 Score: 107
Period size: 32 Copynumber: 2.2 Consensus size: 34
1660948 TTTATAGTAT
*
1660958 TTTATATTTATGTAAATTTTAAAATATTAAT-TA
1 TTTATATTTATATAAATTTTAAAATATTAATGTA
*
1660991 TTTATATTT-TATAAATTTTAAAATATTTATGTA
1 TTTATATTTATATAAATTTTAAAATATTAATGTA
*
1661024 TTTTTATT
1 TTTATATT
1661032 GTCGTATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 19 0.51
33 18 0.49
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (34 bp):
TTTATATTTATATAAATTTTAAAATATTAATGTA
Found at i:1661017 original size:25 final size:23
Alignment explanation
Indices: 1660973--1661020 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
1660963 ATTTATGTAA
*
1660973 ATTTTAAAATATTAATTATTTAT
1 ATTTTAAAATATTAAATATTTAT
*
1660996 ATTTTATAAATTTTAAAATATTTAT
1 ATTTTA-AAATATT-AAATATTTAT
1661021 GTATTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 6 0.29
25 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTTAAAATATTAAATATTTAT
Found at i:1661214 original size:17 final size:17
Alignment explanation
Indices: 1661194--1661228 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1661184 AAAATTTTAA
1661194 ATATACTCATATTAAAT
1 ATATACTCATATTAAAT
* *
1661211 ATATATTCATATTCAAT
1 ATATACTCATATTAAAT
1661228 A
1 A
1661229 CTCACACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATACTCATATTAAAT
Found at i:1664324 original size:30 final size:31
Alignment explanation
Indices: 1664290--1664351 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1664280 TTTCATATTA
* *
1664290 TAATTTTTATTAA-ATATTATTTTTTAAATT
1 TAATTTTTAGTAATATAATATTTTTTAAATT
*
1664320 TAATTTTTAGTAATTTAATATTTTTTAAATT
1 TAATTTTTAGTAATATAATATTTTTTAAATT
1664351 T
1 T
1664352 TAAAATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 12 0.43
31 16 0.57
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (31 bp):
TAATTTTTAGTAATATAATATTTTTTAAATT
Found at i:1664327 original size:15 final size:16
Alignment explanation
Indices: 1664290--1664351 Score: 62
Period size: 15 Copynumber: 4.1 Consensus size: 16
1664280 TTTCATATTA
1664290 TAATTTTTATTAAATAT
1 TAATTTTTATTAAAT-T
1664307 T-A-TTTT-TTAAATT
1 TAATTTTTATTAAATT
*
1664320 TAATTTTTAGT-AATT
1 TAATTTTTATTAAATT
1664335 TAATATTTT-TTAAATT
1 TAAT-TTTTATTAAATT
1664351 T
1 T
1664352 TAAAATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
13 2 0.05
14 7 0.18
15 17 0.45
16 11 0.29
17 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TAATTTTTATTAAATT
Found at i:1664982 original size:2 final size:2
Alignment explanation
Indices: 1664975--1665022 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1664965 CTTCAAATCA
1664975 AT 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 AT
1665017 AT AT AT
1 AT AT AT
1665023 TTTGCTAATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1665407 original size:28 final size:28
Alignment explanation
Indices: 1665316--1665399 Score: 141
Period size: 28 Copynumber: 3.0 Consensus size: 28
1665306 ACAAATGCCA
*
1665316 TCCTTTGTATTTGTCAAATATGATGGTT
1 TCCTTTGTATTTGTCAAATATGGTGGTT
* *
1665344 TCCTTTATATTTGTCAAATATGGTAGTT
1 TCCTTTGTATTTGTCAAATATGGTGGTT
1665372 TCCTTTGTATTTGTCAAATATGGTGGTT
1 TCCTTTGTATTTGTCAAATATGGTGGTT
1665400 ATTTTTGTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (28 bp):
TCCTTTGTATTTGTCAAATATGGTGGTT
Found at i:1669923 original size:28 final size:28
Alignment explanation
Indices: 1669891--1669945 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1669881 CAAATGACAC
1669891 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
1669919 CCTTTGTATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
1669946 ATTTTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.11, G:0.22, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:1669952 original size:28 final size:28
Alignment explanation
Indices: 1669893--1669981 Score: 103
Period size: 28 Copynumber: 3.2 Consensus size: 28
1669883 AATGACACCC
*
1669893 TTTGTATTTGTCAAATATGGTGGTT-TCC
1 TTTGTATTTGTCAAATATGGTGGTTAT-T
1669921 TTTGTATTTGTCAAATATGGTGGTTATT
1 TTTGTATTTGTCAAATATGGTGGTTATT
* *
1669949 TTTG--TTTGTAAAAAATGGTGGCTTATT
1 TTTGTATTTGTCAAATATGGTGG-TTATT
1669976 ATTTGT
1 -TTTGT
1669982 CAAAATTGGT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
26 15 0.28
27 5 0.09
28 33 0.61
29 1 0.02
ACGTcount: A:0.21, C:0.06, G:0.21, T:0.52
Consensus pattern (28 bp):
TTTGTATTTGTCAAATATGGTGGTTATT
Found at i:1669966 original size:26 final size:28
Alignment explanation
Indices: 1669927--1669981 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
1669917 TTCCTTTGTA
* *
1669927 TTTGTCAAATATGGTGG-TTATT-TTTG
1 TTTGTAAAAAATGGTGGCTTATTATTTG
1669953 TTTGTAAAAAATGGTGGCTTATTATTTG
1 TTTGTAAAAAATGGTGGCTTATTATTTG
1669981 T
1 T
1669982 CAAAATTGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 15 0.60
27 5 0.20
28 5 0.20
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.51
Consensus pattern (28 bp):
TTTGTAAAAAATGGTGGCTTATTATTTG
Found at i:1669986 original size:24 final size:24
Alignment explanation
Indices: 1669897--1669991 Score: 66
Period size: 28 Copynumber: 3.7 Consensus size: 24
1669887 ACACCCTTTG
* *
1669897 TATTTGTCAAATATGGTGGTTTCCTTT
1 TATTTGTCAAAAATGGTGG-TT--ATT
*
1669924 GTATTTGTCAAATATGGTGGTTATTTT
1 -TATTTGTCAAAAATGGTGGTTA--TT
* *
1669951 TGTTTGTAAAAAATGGTGGCTTA-T
1 TATTTGTCAAAAATGGTGG-TTATT
*
1669975 TATTTGTCAAAATTGGT
1 TATTTGTCAAAAATGGT
1669992 AGCTAATTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
24 15 0.26
26 16 0.28
27 7 0.12
28 19 0.33
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.48
Consensus pattern (24 bp):
TATTTGTCAAAAATGGTGGTTATT
Found at i:1671349 original size:32 final size:32
Alignment explanation
Indices: 1671303--1671363 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1671293 ATCTAAATCG
1671303 TGTAGAAATGAAGTTTTGAGAAA-GAAAAGATT
1 TGTAGAAATGAAGTTTTG-GAAAGGAAAAGATT
* *
1671335 TGTAGAAGTTAAGTTTTGGAAAGGAAAAG
1 TGTAGAAATGAAGTTTTGGAAAGGAAAAG
1671364 CCGTTGACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 4 0.15
32 22 0.85
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (32 bp):
TGTAGAAATGAAGTTTTGGAAAGGAAAAGATT
Found at i:1671421 original size:2 final size:2
Alignment explanation
Indices: 1671414--1671463 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1671404 AAATCTGAAA
1671414 AT 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 AT
1671456 AT AT AT AT
1 AT AT AT AT
1671464 CTAGATAACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1672301 original size:16 final size:16
Alignment explanation
Indices: 1672280--1672313 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1672270 TGAGTTTATA
1672280 AAATTT-AATTTATTTT
1 AAATTTGAA-TTATTTT
1672296 AAATTTGAATTATTTT
1 AAATTTGAATTATTTT
1672312 AA
1 AA
1672314 GTTTTAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
AAATTTGAATTATTTT
Found at i:1674127 original size:13 final size:13
Alignment explanation
Indices: 1674109--1674133 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1674099 ATTTAATTTG
1674109 TATTGTTTTGGGC
1 TATTGTTTTGGGC
1674122 TATTGTTTTGGG
1 TATTGTTTTGGG
1674134 ATGGCAAAGC
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:0.08, C:0.04, G:0.32, T:0.56
Consensus pattern (13 bp):
TATTGTTTTGGGC
Found at i:1679057 original size:15 final size:15
Alignment explanation
Indices: 1679033--1679067 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1679023 TTTTTAGTTA
1679033 ATTTTTATTTT-AAT
1 ATTTTTATTTTAAAT
1679047 ATTTATTATTTTAAAT
1 ATTT-TTATTTTAAAT
1679063 ATTTT
1 ATTTT
1679068 GATTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.21
15 8 0.42
16 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTATTTTAAAT
Found at i:1679663 original size:15 final size:13
Alignment explanation
Indices: 1679627--1679659 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1679617 TTAGTATCTT
*
1679627 TTAA-TTTATATA
1 TTAATTTTAAATA
1679639 TTAATTTTAAATA
1 TTAATTTTAAATA
1679652 TTAATTTT
1 TTAATTTT
1679660 TTAATTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTAATTTTAAATA
Found at i:1679915 original size:2 final size:2
Alignment explanation
Indices: 1679902--1679949 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
1679892 ACTTACATAA
* ** *
1679902 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT GC AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1679944 AT AT AT
1 AT AT AT
1679950 GAATCTATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1679949 original size:10 final size:10
Alignment explanation
Indices: 1679895--1679933 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1679885 TGAGATAACT
*
1679895 TACATAAATA
1 TACATATATA
1679905 TACATATATA
1 TACATATATA
*
1679915 TATATATATA
1 TACATATATA
*
1679925 TATATATAT
1 TACATATAT
1679934 GCATATACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (10 bp):
TACATATATA
Found at i:1680500 original size:21 final size:21
Alignment explanation
Indices: 1680475--1680518 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1680465 GAATTTAAAG
* *
1680475 AAAATTGATTAAAAATAATAA
1 AAAATTAAATAAAAATAATAA
*
1680496 AAAATTAAATAAAACTAATAA
1 AAAATTAAATAAAAATAATAA
1680517 AA
1 AA
1680519 CTTTTTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (21 bp):
AAAATTAAATAAAAATAATAA
Found at i:1680637 original size:20 final size:19
Alignment explanation
Indices: 1680603--1680651 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
1680593 CATTGAATAA
*
1680603 ATTTATATTTTTATTAATT
1 ATTTATATATTTATTAATT
*
1680622 ATTTATGATATTTATTATTT
1 ATTTAT-ATATTTATTAATT
1680642 ATTTA-ATATT
1 ATTTATATATT
1680652 AAAAATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 5 0.19
19 6 0.22
20 16 0.59
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTTATATATTTATTAATT
Found at i:1680661 original size:21 final size:21
Alignment explanation
Indices: 1680635--1680675 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1680625 TATGATATTT
1680635 ATTATTTATTTAAT-ATTAAAA
1 ATTATTT-TTTAATAATTAAAA
1680656 ATTATTTTTTAATAATTAAA
1 ATTATTTTTTAATAATTAAA
1680676 TTTTTAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTATTTTTTAATAATTAAAA
Found at i:1682670 original size:8 final size:10
Alignment explanation
Indices: 1682645--1682676 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1682635 TTGTTGCAAA
1682645 ATAATTATAT
1 ATAATTATAT
1682655 ATAATTAT-T
1 ATAATTATAT
1682664 A-AATTATAT
1 ATAATTATAT
1682673 ATAA
1 ATAA
1682677 ATAAACTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 6 0.30
9 4 0.20
10 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
ATAATTATAT
Found at i:1685002 original size:2 final size:2
Alignment explanation
Indices: 1684995--1685055 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
1684985 AGATACATGT
1684995 TA TA TA TA 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 TA TA TA TA
*
1685037 TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA T
1685056 GTTGCATTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1687109 original size:7 final size:7
Alignment explanation
Indices: 1687097--1687122 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1687087 CAACTGCTGC
1687097 CAGAAAT
1 CAGAAAT
1687104 CAGAAAT
1 CAGAAAT
1687111 CAGAAAT
1 CAGAAAT
1687118 CAGAA
1 CAGAA
1687123 TGTGCTGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.12
Consensus pattern (7 bp):
CAGAAAT
Found at i:1688524 original size:27 final size:27
Alignment explanation
Indices: 1688496--1688547 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
1688486 GTTTAAAAGA
*
1688496 AAAAATAAT-TT-CTAAAGATATTTGAG
1 AAAAATAATGTTACTAAA-ATAATTGAG
1688522 AAAAATAATGTTACTAAAATAATTGA
1 AAAAATAATGTTACTAAAATAATTGA
1688548 AGATTGATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 9 0.39
27 9 0.39
28 5 0.22
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.33
Consensus pattern (27 bp):
AAAAATAATGTTACTAAAATAATTGAG
Found at i:1688551 original size:86 final size:86
Alignment explanation
Indices: 1688450--1688614 Score: 280
Period size: 86 Copynumber: 1.9 Consensus size: 86
1688440 GAATAAGAAA
*
1688450 TAAAATAATTGAAGATTAATTGAAAATTGATAGTTGGTTTAAAAGAA-AA-AATAATTTCTAAAG
1 TAAAATAATTGAAGATTAATTGAAAATTGATAATTGG-TTAAAA-AATAATAATAATTTCTAAAG
1688513 ATATTTGAGAAAAATAATGTTAC
64 ATATTTGAGAAAAATAATGTTAC
*
1688536 TAAAATAATTGAAGATTGATTGAAAATTGATAATTGGTTAAAAAATAATAATAATTTCTAAAGAT
1 TAAAATAATTGAAGATTAATTGAAAATTGATAATTGGTTAAAAAATAATAATAATTTCTAAAGAT
1688601 ATTTGAGAAAAATA
66 ATTTGAGAAAAATA
1688615 GTATTATTAA
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
84 2 0.03
85 8 0.11
86 65 0.87
ACGTcount: A:0.51, C:0.02, G:0.13, T:0.34
Consensus pattern (86 bp):
TAAAATAATTGAAGATTAATTGAAAATTGATAATTGGTTAAAAAATAATAATAATTTCTAAAGAT
ATTTGAGAAAAATAATGTTAC
Found at i:1689196 original size:12 final size:12
Alignment explanation
Indices: 1689179--1689203 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1689169 TTATCGATGC
1689179 TCGAGTACTACA
1 TCGAGTACTACA
1689191 TCGAGTACTACA
1 TCGAGTACTACA
1689203 T
1 T
1689204 AAAAAGTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (12 bp):
TCGAGTACTACA
Found at i:1689412 original size:16 final size:17
Alignment explanation
Indices: 1689391--1689428 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
1689381 ATCAATAATT
1689391 AATTTAAATATT-TTTA
1 AATTTAAATATTCTTTA
1689407 AATTT-AATATTCTTTA
1 AATTTAAATATTCTTTA
1689423 AATTTA
1 AATTTA
1689429 TGATAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTTAAATATTCTTTA
Found at i:1689560 original size:18 final size:18
Alignment explanation
Indices: 1689539--1689596 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 18
1689529 TTATTTCATA
1689539 TATTTTTAAACAATATTT
1 TATTTTTAAACAATATTT
*
1689557 TATTTTT-ATC-ATATTT
1 TATTTTTAAACAATATTT
* *
1689573 ACATTTTTAAAAAATATTAT
1 -TATTTTTAAACAATATT-T
1689593 TATT
1 TATT
1689597 ATTATTATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
16 6 0.19
17 8 0.26
18 8 0.26
19 8 0.26
20 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTTTAAACAATATTT
Found at i:1689657 original size:21 final size:19
Alignment explanation
Indices: 1689619--1689657 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
1689609 AAAAATAAAT
*
1689619 TATAATCACATTAATTAAC
1 TATAATCACATAAATTAAC
1689638 TATAATCATCTATAAATTAA
1 TATAATCA-C-ATAAATTAA
1689658 TTAATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 1 0.06
21 8 0.47
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (19 bp):
TATAATCACATAAATTAAC
Found at i:1689681 original size:20 final size:20
Alignment explanation
Indices: 1689656--1689695 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1689646 TCTATAAATT
1689656 AATTAATA-AAATATATTAAA
1 AATTAATACAAA-ATATTAAA
1689676 AATTAATACAAAATATTAAA
1 AATTAATACAAAATATTAAA
1689696 TCAAATCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTAATACAAAATATTAAA
Found at i:1690070 original size:2 final size:2
Alignment explanation
Indices: 1690065--1690090 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1690055 TGCCATCTTC
1690065 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
1690091 GTAACTACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1691650 original size:6 final size:6
Alignment explanation
Indices: 1691641--1691666 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1691631 AGAAGAAGAA
1691641 GAAGGT GAAGGT GAAGGT GAAGGT GA
1 GAAGGT GAAGGT GAAGGT GAAGGT GA
1691667 CAGTGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.50, T:0.15
Consensus pattern (6 bp):
GAAGGT
Found at i:1692587 original size:31 final size:31
Alignment explanation
Indices: 1692551--1692614 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
1692541 AAAGCATATA
* *
1692551 AAAGCTTGAACAAATTAAGTATCAAACTAAT
1 AAAGCTTGAACAAATTAAGTAACAAAATAAT
1692582 AAAGCTTGAACAAATTAAGTAACAAAATAAT
1 AAAGCTTGAACAAATTAAGTAACAAAATAAT
1692613 AA
1 AA
1692615 TTATATTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.56, C:0.11, G:0.09, T:0.23
Consensus pattern (31 bp):
AAAGCTTGAACAAATTAAGTAACAAAATAAT
Found at i:1693456 original size:13 final size:13
Alignment explanation
Indices: 1693416--1693463 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
1693406 TAATTATAAA
1693416 AAAT-ATAAATATT
1 AAATAATAAATA-T
* *
1693429 AAAATATTAATTAT
1 -AAATAATAAATAT
1693443 AAATAATAAATAT
1 AAATAATAAATAT
1693456 AAATAATA
1 AAATAATA
1693464 CTAGTGGATC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 19 0.66
14 5 0.17
15 5 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAATAATAAATAT
Found at i:1694330 original size:51 final size:51
Alignment explanation
Indices: 1694244--1694345 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 51
1694234 ACATTTGACC
* *
1694244 ATAAACCATCACTCCAAATCATTTGAAATGCGTAATAAATAGAATAGGATT
1 ATAAACCATCACTCCAAATCATTAGAAATGCGTAATAAACAGAATAGGATT
* * * * *
1694295 ATAAACCATTACTCTAAATCATTAGGAATGTGTAATAAACAGATTAGGATT
1 ATAAACCATCACTCCAAATCATTAGAAATGCGTAATAAACAGAATAGGATT
1694346 CTTATGTCCC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (51 bp):
ATAAACCATCACTCCAAATCATTAGAAATGCGTAATAAACAGAATAGGATT
Found at i:1694538 original size:15 final size:14
Alignment explanation
Indices: 1694495--1694540 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
1694485 GTATTAATAT
1694495 TATATTGTATATTTA
1 TATATT-TATATTTA
*
1694510 -ATATTT-TATATA
1 TATATTTATATTTA
1694522 TATATATTATATTTA
1 TATAT-TTATATTTA
1694537 TATA
1 TATA
1694541 ATCGTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 5 0.19
13 5 0.19
14 7 0.27
15 9 0.35
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
TATATTTATATTTA
Found at i:1695323 original size:22 final size:22
Alignment explanation
Indices: 1695298--1695339 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1695288 ATTAAAATGT
1695298 TATTATTAT-ATTAATATTTATA
1 TATTATTATAATTAA-ATTTATA
*
1695320 TATTTTTATAATTAAATTTA
1 TATTATTATAATTAAATTTA
1695340 AATAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTATTATAATTAAATTTATA
Found at i:1695483 original size:27 final size:26
Alignment explanation
Indices: 1695431--1695483 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
1695421 GACCAAAAAG
* *
1695431 AAAAAGAAATCAACAAATTAATAATT
1 AAAAACAAATCAACAAATTAAAAATT
* *
1695457 AAAAACAAATCCAACTAATTTAAAATT
1 AAAAACAAAT-CAACAAATTAAAAATT
1695484 TCTTAATGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.62, C:0.11, G:0.02, T:0.25
Consensus pattern (26 bp):
AAAAACAAATCAACAAATTAAAAATT
Found at i:1701942 original size:3 final size:3
Alignment explanation
Indices: 1701934--1701960 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1701924 AGAAATTACA
1701934 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1701961 TACATAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1704671 original size:6 final size:5
Alignment explanation
Indices: 1704632--1704660 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1704622 CTAGGTAGCT
1704632 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1704661 TTCCTTTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:1704955 original size:27 final size:25
Alignment explanation
Indices: 1704905--1704956 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
1704895 AAAATTTATT
*
1704905 TTTATAAATTATTAAAATATTAAAA
1 TTTATAAATTATTAAAATAATAAAA
*
1704930 TTTATATAATTATATAACATAATAAAA
1 TTTATA-AATTAT-TAAAATAATAAAA
1704957 AACAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 6 0.26
27 11 0.48
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
TTTATAAATTATTAAAATAATAAAA
Found at i:1706021 original size:25 final size:25
Alignment explanation
Indices: 1705966--1706015 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1705956 ATTTTTAGTT
1705966 AATTTATATTAGTTATATAATAATA
1 AATTTATATTAGTTATATAATAATA
1705991 AATTTATATTTA-TTATATAATAATA
1 AATTTATA-TTAGTTATATAATAATA
1706016 TTTTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
AATTTATATTAGTTATATAATAATA
Found at i:1706380 original size:9 final size:9
Alignment explanation
Indices: 1706360--1706411 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
1706350 TTTAATTATC
*
1706360 AATTAATTT
1 AATTAAATT
*
1706369 AATTAAAAT
1 AATTAAATT
**
1706378 AATTTTATT
1 AATTAAATT
*
1706387 AATCAAATT
1 AATTAAATT
1706396 AATTAAATT
1 AATTAAATT
*
1706405 ACTTAAA
1 AATTAAA
1706412 ATATATAATA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTAAATT
Found at i:1706388 original size:18 final size:18
Alignment explanation
Indices: 1706360--1706414 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
1706350 TTTAATTATC
*
1706360 AATTAATTTAATTAAAAT
1 AATTAAATTAATTAAAAT
** * *
1706378 AATTTTATTAATCAAATT
1 AATTAAATTAATTAAAAT
*
1706396 AATTAAATTACTTAAAAT
1 AATTAAATTAATTAAAAT
1706414 A
1 A
1706415 TATAATATGG
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTAAATTAATTAAAAT
Found at i:1706501 original size:22 final size:22
Alignment explanation
Indices: 1706471--1706513 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1706461 TTGTTAAATT
1706471 TTTTAAC-TTATTATAAATATATA
1 TTTTAACTTTATT-TAAA-ATATA
1706494 TTTT-ACTTTATTTAAAATAT
1 TTTTAACTTTATTTAAAATAT
1706514 TTGTTAGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTAACTTTATTTAAAATATA
Found at i:1706892 original size:21 final size:21
Alignment explanation
Indices: 1706840--1706905 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 21
1706830 TTAATAAAAA
* *
1706840 ATTTAATAATTTATAT-ATAT
1 ATTTAATTATTTTTATAATAT
* *
1706860 ATATCA-TATTTTATATAATA-
1 ATTTAATTATTTT-TATAATAT
*
1706880 ATTTAATTATTTTTATATTAT
1 ATTTAATTATTTTTATAATAT
1706901 ATTTA
1 ATTTA
1706906 TAATATATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
19 4 0.11
20 17 0.49
21 14 0.40
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTTAATTATTTTTATAATAT
Found at i:1706905 original size:11 final size:11
Alignment explanation
Indices: 1706853--1706913 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
1706843 TAATAATTTA
*
1706853 TATATATATAT
1 TATATTTATAT
*
1706864 CATATTTTATAT
1 TATA-TTTATAT
*
1706876 AATAATTTA-AT
1 TAT-ATTTATAT
*
1706887 TATTTTTATAT
1 TATATTTATAT
*
1706898 TATATTTATAA
1 TATATTTATAT
1706909 TATAT
1 TATAT
1706914 AACTATTTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
10 4 0.10
11 23 0.57
12 12 0.30
13 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1707801 original size:15 final size:16
Alignment explanation
Indices: 1707773--1707806 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1707763 AAAAAATTAA
1707773 TTTTGTAAATATATTT
1 TTTTGTAAATATATTT
1707789 TTTTGTAAA-ATATTT
1 TTTTGTAAATATATTT
1707804 TTT
1 TTT
1707807 AAATAAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTTGTAAATATATTT
Found at i:1707913 original size:31 final size:28
Alignment explanation
Indices: 1707878--1707945 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 28
1707868 ATTTAAAAAG
* *
1707878 TTAATAAATAATGATATATTAATTATTATTT
1 TTAATAAAAAATAATAT-TTAATTA--ATTT
1707909 TTAATAAAAAATAATATTTAATTAATTT
1 TTAATAAAAAATAATATTTAATTAATTT
1707937 TTAA-AAAAA
1 TTAATAAAAA
1707946 TTACATTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 5 0.14
28 8 0.23
30 7 0.20
31 15 0.43
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
TTAATAAAAAATAATATTTAATTAATTT
Found at i:1708045 original size:22 final size:22
Alignment explanation
Indices: 1708019--1708080 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 22
1708009 ATTATTATTT
1708019 TTTAATAAAATTAAAAATAA-TA
1 TTTAATAAAATTAAAAA-AATTA
**
1708041 TTTAATTAACTTTAAAAAAATTTA
1 TTTAA-TAAAATTAAAAAAA-TTA
1708065 TATTAAT-AAATTAAAA
1 T-TTAATAAAATTAAAA
1708081 TATTAATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
22 7 0.22
23 17 0.53
24 4 0.12
25 4 0.12
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAATAAAATTAAAAAAATTA
Found at i:1708047 original size:116 final size:109
Alignment explanation
Indices: 1707915--1708292 Score: 449
Period size: 116 Copynumber: 3.4 Consensus size: 109
1707905 ATTTTTAATA
*
1707915 AAAAATAATATTTAATTAATTTTTAAAAAAATTACATTAATAAATTAAAATATTAATTATTTTTT
1 AAAAATAATATTTAATTAA-TTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTTTTT
1707980 TAAAATAAAAATTAAATTAAAAAGAGTTTATTATTATTTTTTAATAAAATT
65 T---AT---AATTAAATTAAAAAGAGTTTATTATTATTTTTTAATAAAATT
* * *
1708031 AAAAATAATATTTAATTAACTTTAAAAAAATTTATATTAATAAATTAAAATATTAATTA----TT
1 AAAAATAATATTTAATTAATTTTAAAAAAA-TTACATTAACAAATTAAAATATTAATTATTTTTT
*
1708092 T-T--TTAAATTAAAAAGGGTTTATTATTATTATTTTTAATAAAATT
65 TATAATTAAATTAAAAAGAGTTTATTATTA-T-TTTTTAATAAAATT
1708136 AAAAATAATATTTAATTAAGTTTT-AAAAAATTACATTAACAAATTAAAATATTAATTATTATGT
1 AAAAATAATATTTAATTAA-TTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATT-T-T
*
1708200 TTTATAA--AAA-TAAAAAGTA-TTTATTA-TATTTTTTAATAAAATA
63 TTTATAATTAAATTAAAAAG-AGTTTATTATTATTTTTTAATAAAATT
* * *
1708243 AAAAATGATATTTAATTAAATTTAAAAAATTTTACATTAACAAATTAAAA
1 AAAAATAATATTTAATTAATTTTAAAAAA-ATTACATTAACAAATTAAAA
1708293 AATATTTAAA
Statistics
Matches: 235, Mismatches: 11, Indels: 40
0.82 0.04 0.14
Matches are distributed among these distances:
103 24 0.10
104 27 0.11
105 39 0.17
106 6 0.03
107 36 0.15
108 21 0.09
109 2 0.01
110 17 0.07
111 4 0.02
112 3 0.01
115 10 0.04
116 46 0.20
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (109 bp):
AAAAATAATATTTAATTAATTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTTTTTT
ATAATTAAATTAAAAAGAGTTTATTATTATTTTTTAATAAAATT
Found at i:1708097 original size:42 final size:38
Alignment explanation
Indices: 1707909--1708098 Score: 117
Period size: 41 Copynumber: 4.9 Consensus size: 38
1707899 ATTATTATTT
* * *
1707909 TTAATAAAAAATAATAT-TTAATTAATTTTTAAAAAAA
1 TTAATTAAAAATAAAATATTAATTATTTTTTAAAAAAA
1707946 TTACATTAATAAATTAAAATATTAATTATTTTTTTAAAATAAAAA
1 TTA-ATTAA-AAA-TAAAATATTAATTA-TTTTTT--AA-AAAAA
* *** *
1707991 TTAAATTAAAAAGAGTTTATT-ATTATTTTTT--AATAA
1 TT-AATTAAAAATAAAATATTAATTATTTTTTAAAAAAA
* **
1708027 --AATTAAAAATAATAT-TTAATTA-ACTTTAAAAAAA
1 TTAATTAAAAATAAAATATTAATTATTTTTTAAAAAAA
1708061 TTTATATTAATAAATTAAAATATTAATTATTTTTTAAA
1 -TTA-ATTAA-AAA-TAAAATATTAATTATTTTTTAAA
1708099 TTAAAAAGGG
Statistics
Matches: 116, Mismatches: 17, Indels: 35
0.69 0.10 0.21
Matches are distributed among these distances:
32 5 0.04
33 16 0.14
34 4 0.03
36 4 0.03
37 4 0.03
38 9 0.08
39 6 0.05
40 10 0.09
41 20 0.17
42 15 0.13
43 5 0.04
44 5 0.04
45 12 0.10
46 1 0.01
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (38 bp):
TTAATTAAAAATAAAATATTAATTATTTTTTAAAAAAA
Found at i:1708247 original size:32 final size:31
Alignment explanation
Indices: 1708176--1708246 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
1708166 TTACATTAAC
* * *
1708176 AAATTAAAA-TATTAATTATTATGTTTTATAA
1 AAATAAAAAGTATTTATTA-TATTTTTTATAA
1708207 AAATAAAAAGTATTTATTATATTTTTTA-ATA
1 AAATAAAAAGTATTTATTATATTTTTTATA-A
1708238 AAATAAAAA
1 AAATAAAAA
1708247 ATGATATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.03
31 26 0.74
32 8 0.23
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (31 bp):
AAATAAAAAGTATTTATTATATTTTTTATAA
Found at i:1708749 original size:122 final size:119
Alignment explanation
Indices: 1708581--1708925 Score: 460
Period size: 122 Copynumber: 2.9 Consensus size: 119
1708571 ATTATAATAA
* * *
1708581 TTTTTAATTTAAA-TTTTTATTTTTAAAAAACATAATAATTAATATTTAATTTATTAATGTAAAT
1 TTTTTTATTTAAATTTTTTATTTTTAAAAAACATAATAATTAATATTTAATTTGTTAATGTAATT
*
1708645 TTTTAAACTTAATTAAATATATTTTTATTTTATTAAAAATTATAATAAAAAACC
66 TTTTAAACTTAATTAAATATATTTTTATTTTATTAAAAATAATAATAAAAAACC
1708699 TTTTTTATTTTAAAATTTTTTATTTTTATAAAAACATAATAATTAATATTTGAATTTGTTAATGT
1 TTTTTTA-TTT-AAATTTTTTATTTTTA-AAAAACATAATAATTAATATTT-AATTTGTTAATGT
* *
1708764 AATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAATAATAATAATAAACT
62 AATTTTTTAAACTTAATTAAATA-TATTTTT-ATTTTATTAAAAATAATAATAAAAAACC
* *
1708824 TTTTTTATTT-AATTTTTTATTTTTAAAAAA-AT--TAA-T-A-GTTTAATTTGTTAATATATAT
1 TTTTTTATTTAAATTTTTTATTTTTAAAAAACATAATAATTAATATTTAATTTGTTAATGTA-AT
* *
1708882 TTTTTAAAGTTAATT-AA-ATATTATT-TTTTATTAAAAATAATAAT
65 TTTTTAAACTTAATTAAATATATTTTTATTTTATTAAAAATAATAAT
1708926 TAATACATTA
Statistics
Matches: 209, Mismatches: 10, Indels: 24
0.86 0.04 0.10
Matches are distributed among these distances:
110 19 0.09
112 6 0.03
113 1 0.00
114 15 0.07
115 19 0.09
116 1 0.00
117 1 0.00
118 9 0.04
119 3 0.01
120 5 0.02
121 17 0.08
122 37 0.18
123 34 0.16
124 10 0.05
125 32 0.15
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (119 bp):
TTTTTTATTTAAATTTTTTATTTTTAAAAAACATAATAATTAATATTTAATTTGTTAATGTAATT
TTTTAAACTTAATTAAATATATTTTTATTTTATTAAAAATAATAATAAAAAACC
Found at i:1708906 original size:115 final size:115
Alignment explanation
Indices: 1708617--1708925 Score: 391
Period size: 123 Copynumber: 2.7 Consensus size: 115
1708607 AAAACATAAT
* *
1708617 AATTAATATTTAATTTATTAATGTAAATTTTTAAACTTAATTAAATA-TATTTTTATTTTATTAA
1 AATTAATATTTAATTTGTTAATGTAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAA
*
1708681 AAATTATAATAAAAAACCTTTTTTATTTTAAAATTTTTTATTTTTATAAAAACATAA
66 AAATAATAATAAAAAACCTTTTTTATTTT-AAATTTTTTATTTTTAT----A-A-AA
1708738 TAATTAATATTTGAATTTGTTAATGTAATTTTTTAAACTTAATTAAATATTATTTTTAATTTTAT
1 -AATTAATATTT-AATTTGTTAATGTAATTTTTTAAACTTAATTAAATATTATTTTT-ATTTTAT
* *
1708803 TAAAAATAATAATAATAAACTTTTTTTA-TTT-AATTTTTTATTTTTA-AAAA
63 TAAAAATAATAATAAAAAACCTTTTTTATTTTAAATTTTTTATTTTTATAAAA
* *
1708853 AATTAATAGTTTAATTTGTTAATATATATTTTTTAAAGTTAATTAAATATTA---TT-TTTTATT
1 AATTAATA-TTTAATTTGTTAATGTA-ATTTTTTAAACTTAATTAAATATTATTTTTATTTTATT
1708914 AAAAATAATAAT
64 AAAAATAATAAT
1708926 TAATACATTA
Statistics
Matches: 175, Mismatches: 7, Indels: 22
0.86 0.03 0.11
Matches are distributed among these distances:
110 19 0.11
112 2 0.01
114 21 0.12
115 29 0.17
116 1 0.01
117 1 0.01
122 26 0.15
123 34 0.19
124 10 0.06
125 32 0.18
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (115 bp):
AATTAATATTTAATTTGTTAATGTAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAA
AAATAATAATAAAAAACCTTTTTTATTTTAAATTTTTTATTTTTATAAAA
Found at i:1709740 original size:177 final size:178
Alignment explanation
Indices: 1709380--1710171 Score: 813
Period size: 177 Copynumber: 4.5 Consensus size: 178
1709370 TAATGTATAA
* * *
1709380 ATTGTAAATGTCAAACTG-TAAGAAATAGACTAATGCATGGATTATATCTGAGAATC-GAATTTT
1 ATTGTAAATGTCAAACTGCAAAG-ATTAGACTAATGCATGAATTATATCTGAGAATCAG-A-TTT
* * * * * *
1709443 TTTTTTATG----AA-AAAA-TTGATTAATTGTGAATGTC-AGACTGTAAGGATTAAAATAATGC
63 TTTTTTATGAAAAAAGAAAAGTTGATTGATTGTAAATGTCAAGACTGCAAGGATTAGACTAATGT
* * * *
1709501 ATGAATTATATCTGAGAATCAATTTTTTTATTAAAAAAAAAAAGAAAAGTTGATTA
128 AAGAATTATATCTGAGAATCAATTCTTTT-TT----ATAAAAAGAAAAGTTGATTG
* * **
1709557 ATTGTAAATGTCATACTGCAAAGATTAGACTAATGCATGAATTATATCTAAGAATTGGATTTTTT
1 ATTGTAAATGTCAAACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTTTTT
1709622 TTTATGGAAAAAAAGAAAAGTTGATTGATTGTAAATGT-AAGACTGCAAGGATTAGACTAATGTA
66 TTTAT-G-AAAAAAGAAAAGTTGATTGATTGTAAATGTCAAGACTGCAAGGATTAGACTAATGTA
* *
1709686 AGAATTATATCTGATAATCAATTCTTTTTTATAGAAA-AAAA-TTGATTG
129 AGAATTATATCTGAGAATCAATTCTTTTTTATAAAAAGAAAAGTTGATTG
*
1709734 ATTGTAAATGTCAAACTGC-AAGTATTAGACTAA-GTCATGAATTATATTTGAGAATC-GATTTC
1 ATTGTAAATGTCAAACTGCAAAG-ATTAGACTAATG-CATGAATTATATCTGAGAATCAGATTT-
* * * **
1709796 TTTTTTAT-AGAAAA-AAAAGTTAACTGATTGTAAATGTCAA-ACTATAAGGATTAGACTAATGT
63 TTTTTTATGAAAAAAGAAAAGTTGATTGATTGTAAATGTCAAGACTGCAAGGATTAGACTAATGT
* * *
1709858 ATGAATTATATATGAGAATCAGATTCTTTTTTATAAAAA-AAAAGTTGACTG
128 AAGAATTATATCTGAGAATCA-ATTCTTTTTTATAAAAAGAAAAGTTGATTG
** * * * * *
1709909 ATTGTAAATGTCGGATTGCAAGGATTAGATTAATACATGAATTATATCCGAGAATCAGA--TTTT
1 ATTGTAAATGTCAAACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTTTTT
1709972 TTTATGGAAAAAAAGAAAAGTTG-TTGATTGTAAATGTCAAG-CTGCAAGGATTAGACTAATGTA
66 TTTAT-G-AAAAAAGAAAAGTTGATTGATTGTAAATGTCAAGACTGCAAGGATTAGACTAATGTA
* * *
1710035 TA-AATTATATCTGAGAATCGGATTCTTTTTTATAAAAAAAAGAAAGACTGATTG
129 -AGAATTATATCTGAGAATC-AATTCTTTTTTAT-AAAAAGA-AAAG-TTGATTG
** * * * *
1710089 ATTGTAAATACCAAACAGTAAGGATTAGACTAATGTATGAATTATATCTGAGAATCAGATTATTT
1 ATTGTAAATGTCAAACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATT-TTT
1710154 TTTATATGAAAAAAGAAA
65 TTT-TATGAAAAAAGAAA
1710172 GACAGCAAGA
Statistics
Matches: 519, Mismatches: 61, Indels: 65
0.80 0.09 0.10
Matches are distributed among these distances:
173 67 0.13
174 28 0.05
175 50 0.10
176 93 0.18
177 120 0.23
178 9 0.02
179 9 0.02
180 53 0.10
182 12 0.02
183 13 0.03
184 65 0.13
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (178 bp):
ATTGTAAATGTCAAACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTTTTT
TTTATGAAAAAAGAAAAGTTGATTGATTGTAAATGTCAAGACTGCAAGGATTAGACTAATGTAAG
AATTATATCTGAGAATCAATTCTTTTTTATAAAAAGAAAAGTTGATTG
Found at i:1710115 original size:91 final size:88
Alignment explanation
Indices: 1709380--1710171 Score: 777
Period size: 92 Copynumber: 8.9 Consensus size: 88
1709370 TAATGTATAA
* * * * *
1709380 ATTGTAAATGTCAAACTGTAAGAAATAGACTAATGCATGGATTATATCTGAGAATCGAATT-TTT
1 ATTGTAAATGTCAAACTGCAAGGATTAGACTAATGTATGAATTATATCTGAGAATCG-ATTCTTT
* ** *
1709444 TTT-T-TATGAA-AAAATTGATTA
65 TTTATAAAAAAAGAAAATTGATTG
* * * * * * * *
1709465 ATTGTGAATGTCAGACTGTAAGGATTAAAATAATGCATGAATTATATCTGAGAATCAATTTTTTT
1 ATTGTAAATGTCAAACTGCAAGGATTAGACTAATGTATGAATTATATCTGAGAATCGATTCTTTT
* *
1709530 ATTAAAAAAAAAAAGAAAAGTTGATTA
66 -TT--ATAAAAAAAGAAAA-TTGATTG
* * * * * *
1709557 ATTGTAAATGTCATACTGCAAAGATTAGACTAATGCATGAATTATATCTAAGAATTGGATTTTTT
1 ATTGTAAATGTCAAACTGCAAGGATTAGACTAATGTATGAATTATATCTGAGAA-TCGATTCTTT
1709622 TTTATGGAAAAAAAGAAAAGTTGATTG
65 TTTAT--AAAAAAAGAAAA-TTGATTG
* * *
1709649 ATTGTAAATGT-AAGACTGCAAGGATTAGACTAATGTAAGAATTATATCTGATAATCAATTCTTT
1 ATTGTAAATGTCAA-ACTGCAAGGATTAGACTAATGTATGAATTATATCTGAGAATCGATTCTTT
*
1709713 TTTAT--AGAAA-AAAATTGATTG
65 TTTATAAAAAAAGAAAATTGATTG
* *
1709734 ATTGTAAATGTCAAACTGCAAGTATTAGACTAA-GTCATGAATTATATTTGAGAATCGATTTCTT
1 ATTGTAAATGTCAAACTGCAAGGATTAGACTAATGT-ATGAATTATATCTGAGAATCGA-TTCTT
* * * *
1709798 TTTTATAGAAAAA-AAAGTTAACTG
64 TTTTATAAAAAAAGAAAATTGATTG
** *
1709822 ATTGTAAATGTCAAACTATAAGGATTAGACTAATGTATGAATTATATATGAGAATCAGATTCTTT
1 ATTGTAAATGTCAAACTGCAAGGATTAGACTAATGTATGAATTATATCTGAGAATC-GATTCTTT
* *
1709887 TTTAT-AAAAAA-AAAGTTGACTG
65 TTTATAAAAAAAGAAAATTGATTG
** * * ** *
1709909 ATTGTAAATGTCGGATTGCAAGGATTAGATTAATACATGAATTATATCCGAGAATCAGA-T-TTT
1 ATTGTAAATGTCAAACTGCAAGGATTAGACTAATGTATGAATTATATCTGAGAATC-GATTCTTT
1709972 TTTATGGAAAAAAAGAAAAGTTG-TTG
65 TTTAT--AAAAAAAGAAAA-TTGATTG
* *
1709998 ATTGTAAATGTCAAGCTGCAAGGATTAGACTAATGTATAAATTATATCTGAGAATCGGATTCTTT
1 ATTGTAAATGTCAAACTGCAAGGATTAGACTAATGTATGAATTATATCTGAGAATC-GATTCTTT
*
1710063 TTTATAAAAAAAAGAAAGACTGATTG
65 TTTAT-AAAAAAAGAAA-ATTGATTG
** * * *
1710089 ATTGTAAATACCAAACAGTAAGGATTAGACTAATGTATGAATTATATCTGAGAATCAGATTATTT
1 ATTGTAAATGTCAAACTGCAAGGATTAGACTAATGTATGAATTATATCTGAGAATC-GATTCTTT
1710154 TTTATATGAAAAAAGAAA
65 TTTATA--AAAAAAGAAA
1710172 GACAGCAAGA
Statistics
Matches: 597, Mismatches: 80, Indels: 53
0.82 0.11 0.07
Matches are distributed among these distances:
84 5 0.01
85 115 0.19
86 20 0.03
87 68 0.11
88 78 0.13
89 58 0.10
90 22 0.04
91 91 0.15
92 131 0.22
93 9 0.02
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (88 bp):
ATTGTAAATGTCAAACTGCAAGGATTAGACTAATGTATGAATTATATCTGAGAATCGATTCTTTT
TTATAAAAAAAGAAAATTGATTG
Found at i:1712766 original size:23 final size:21
Alignment explanation
Indices: 1712719--1712786 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
1712709 TTAGTTTAAT
* * *
1712719 TAATTTAAATAAATATAATTT
1 TAATTTAAATAAAAATAAATA
1712740 TAATATTAAATAAAGAATAAATA
1 TAAT-TTAAATAAA-AATAAATA
*
1712763 TAATTTATAATTAATAA-AAATA
1 TAATTTA-AA-TAAAAATAAATA
1712785 TA
1 TA
1712787 TATCTAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 4 0.10
22 19 0.49
23 13 0.33
24 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (21 bp):
TAATTTAAATAAAAATAAATA
Found at i:1717699 original size:17 final size:19
Alignment explanation
Indices: 1717664--1717699 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1717654 ATTAAATTAA
1717664 TATTGATAGTTTTTGATAT
1 TATTGATAGTTTTTGATAT
1717683 TATTG-TAGTTTTT-ATAT
1 TATTGATAGTTTTTGATAT
1717700 CAATTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 8 0.47
19 5 0.29
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (19 bp):
TATTGATAGTTTTTGATAT
Found at i:1719700 original size:3 final size:3
Alignment explanation
Indices: 1719694--1719736 Score: 68
Period size: 3 Copynumber: 13.7 Consensus size: 3
1719684 GATCGATAAG
1719694 ATA ATA ATA ATA ATTA ATA ATA ATA ATA ATA ATA ATAA ATA AT
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA AT-A ATA AT
1719737 TTTAATTATC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1719742 original size:22 final size:22
Alignment explanation
Indices: 1719694--1719736 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1719684 GATCGATAAG
*
1719694 ATAATAATAATAATTAATAATA
1 ATAATAATAATAATAAATAATA
1719716 ATAATAATAATAATAAATAAT
1 ATAATAATAATAATAAATAAT
1719737 TTTAATTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATAATAATAATAATAAATAATA
Found at i:1719830 original size:12 final size:13
Alignment explanation
Indices: 1719797--1719832 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1719787 TAATAAAAAA
1719797 TAAATTTAATTCT
1 TAAATTTAATTCT
*
1719810 TATATTTAATT-T
1 TAAATTTAATTCT
1719822 TAAATTTAATT
1 TAAATTTAATT
1719833 AAATTTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (13 bp):
TAAATTTAATTCT
Found at i:1719902 original size:69 final size:71
Alignment explanation
Indices: 1719758--1719890 Score: 155
Period size: 69 Copynumber: 1.9 Consensus size: 71
1719748 AAATTTACTT
* * * * * *
1719758 AATTAAGTTTAATTAAATTTATTTATATGTAATAAAAAATAAATTTAATTCTTATATTTAATTTT
1 AATTAAATTTAATTAAATTTATTTATATCTAATAAAAAATAAAATAAATTCTCATAATTAATTTT
*
1719823 AAATTT
66 AAATTC
* *
1719829 AATTAAATTTGATTAAGTTTA-TT-TATCTAATAAAAAATAAACATAAATT-TCATAATTAATTT
1 AATTAAATTTAATTAAATTTATTTATATCTAATAAAAAATAAA-ATAAATTCTCATAATTAATTT
1719891 CAATCTCAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
69 28 0.53
70 7 0.13
71 18 0.34
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (71 bp):
AATTAAATTTAATTAAATTTATTTATATCTAATAAAAAATAAAATAAATTCTCATAATTAATTTT
AAATTC
Found at i:1719944 original size:19 final size:21
Alignment explanation
Indices: 1719915--1719954 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1719905 TATACTCGAA
1719915 TTTAAATTATA-ATTAAAAAT
1 TTTAAATTATATATTAAAAAT
1719935 TTTAAA-TATATATTAAAAAT
1 TTTAAATTATATATTAAAAAT
1719955 AAAAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTAAATTATATATTAAAAAT
Found at i:1720113 original size:18 final size:18
Alignment explanation
Indices: 1720076--1720109 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1720066 TTATTAAATT
*
1720076 AAAAAATTGATAATATTA
1 AAAAAATTGAAAATATTA
1720094 AAAAAATT-AAAATATT
1 AAAAAATTGAAAATATT
1720110 TAAATTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
AAAAAATTGAAAATATTA
Found at i:1720143 original size:19 final size:19
Alignment explanation
Indices: 1720114--1720151 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1720104 AATATTTAAA
1720114 TTTAATTTA-TTTGATAAT
1 TTTAATTTATTTTGATAAT
1720132 TTTAACTTTATTTTGATAAT
1 TTTAA-TTTATTTTGATAAT
1720152 AATTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 4 0.22
20 9 0.50
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTAATTTATTTTGATAAT
Found at i:1720431 original size:5 final size:5
Alignment explanation
Indices: 1720421--1720450 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
1720411 ACCAAAATTT
1720421 AATCA AATCA ATATCA AATCA AATCA AATC
1 AATCA AATCA A-ATCA AATCA AATCA AATC
1720451 TTACTCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (5 bp):
AATCA
Found at i:1720436 original size:11 final size:10
Alignment explanation
Indices: 1720421--1720450 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
1720411 ACCAAAATTT
1720421 AATCAAATCA
1 AATCAAATCA
1720431 ATATCAAATCA
1 A-ATCAAATCA
1720442 AATCAAATC
1 AATCAAATC
1720451 TTACTCAAAA
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:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (10 bp):
AATCAAATCA
Found at i:1724184 original size:2 final size:2
Alignment explanation
Indices: 1724177--1724212 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1724167 TGAATGTAGG
1724177 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
1724213 CTTCTTAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1729357 original size:19 final size:18
Alignment explanation
Indices: 1729333--1729375 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1729323 AATTTAAATC
1729333 AAATTACTATTTATTAATT
1 AAATTACTATTT-TTAATT
* *
1729352 AAATTATTATTTTTATTT
1 AAATTACTATTTTTAATT
1729370 AAATTA
1 AAATTA
1729376 ATTATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATTACTATTTTTAATT
Found at i:1729625 original size:5 final size:5
Alignment explanation
Indices: 1729617--1729643 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1729607 AAAAATGGTT
1729617 AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AA
1729644 TTTGATTTGA
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:1730194 original size:20 final size:19
Alignment explanation
Indices: 1730155--1730194 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1730145 TATTATTTTT
*
1730155 TATTTTATTATATTTAAAA
1 TATTTTATTATATATAAAA
*
1730174 TATTTTATATTTATATAAAA
1 TATTTTAT-TATATATAAAA
1730194 T
1 T
1730195 TTGATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTTATTATATATAAAA
Found at i:1730306 original size:14 final size:14
Alignment explanation
Indices: 1730289--1730316 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1730279 TTTTATATTA
1730289 TATTTTATTTTAAT
1 TATTTTATTTTAAT
1730303 TATTTTATTTTAAT
1 TATTTTATTTTAAT
1730317 ATCATATAAT
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTTTATTTTAAT
Found at i:1730841 original size:14 final size:14
Alignment explanation
Indices: 1730818--1730848 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1730808 TGCAAAAAAA
1730818 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
*
1730832 AAAAAGAAAGAAAG
1 AAAAAAAAAGAAAG
1730846 AAA
1 AAA
1730849 GAAGCAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:1730845 original size:18 final size:18
Alignment explanation
Indices: 1730814--1730851 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1730804 TTTATGCAAA
1730814 AAAAAAAAAAAAAGAAAG
1 AAAAAAAAAAAAAGAAAG
* *
1730832 AAAAAGAAAGAAAGAAAG
1 AAAAAAAAAAAAAGAAAG
1730850 AA
1 AA
1730852 GCAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAGAAAG
Found at i:1732637 original size:20 final size:20
Alignment explanation
Indices: 1732608--1732651 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1732598 TTTTTAATAA
1732608 ATTAAATTAT-TAAAATATTT
1 ATTAAATTATATAAAAT-TTT
*
1732628 ATTAATTTATCATAAAATTTT
1 ATTAAATTAT-ATAAAATTTT
1732649 ATT
1 ATT
1732652 TGAGCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 6 0.29
22 6 0.29
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTAAATTATATAAAATTTT
Found at i:1733756 original size:20 final size:18
Alignment explanation
Indices: 1733740--1733822 Score: 66
Period size: 18 Copynumber: 4.6 Consensus size: 18
1733730 CATTTTATAT
1733740 TATATTTATATATTTTAA
1 TATATTTATATATTTTAA
1733758 TATA-TTATAATCATATTTAA
1 TATATTTAT-AT-AT-TTTAA
* *
1733778 AATATTT-TATATTTTTAT
1 TATATTTATATA-TTTTAA
* *
1733796 TAAATTTA-ATATATTAA
1 TATATTTATATATTTTAA
1733813 TA-ATTTATAT
1 TATATTTATAT
1733823 TATATAAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
16 5 0.10
17 12 0.23
18 19 0.37
19 5 0.10
20 9 0.17
21 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATTTATATATTTTAA
Found at i:1735319 original size:42 final size:42
Alignment explanation
Indices: 1735260--1735344 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
1735250 CTGTTAGTCT
* *
1735260 TGATATTCTGGTTTGGCTCTATACTTGCACTTATAATTTGGA
1 TGATATGCTGGTTTGGCTATATACTTGCACTTATAATTTGGA
*
1735302 TGATATGCTGGTTTGGCTATATTCTTGCACTTATAATTTGGA
1 TGATATGCTGGTTTGGCTATATACTTGCACTTATAATTTGGA
1735344 T
1 T
1735345 TGGTCAAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.21, C:0.13, G:0.20, T:0.46
Consensus pattern (42 bp):
TGATATGCTGGTTTGGCTATATACTTGCACTTATAATTTGGA
Found at i:1736589 original size:197 final size:197
Alignment explanation
Indices: 1736240--1736617 Score: 639
Period size: 197 Copynumber: 1.9 Consensus size: 197
1736230 ATACAAATAC
** *
1736240 TTTTAAGGAAAATGAAAAGTTTGGTTAATATAAGCTAGATGTGTTTATTCACTTTGTTGTTTTAT
1 TTTTAAGGAAAATGAAAAGTAAGGTTAATATAAGCTAGATGTGTTTATTCACTTTGTTGTTTAAT
*
1736305 GTTGTACTTATTTTGATTTCTTTCATTCTCTTGAGGCTAGTTGGAATTTTGATTGATGCTATGAT
66 ATTGTACTTATTTTGATTTCTTTCATTCTCTTGAGGCTAGTTGGAATTTTGATTGATGCTATGAT
* * * *
1736370 GGCTTATGTTGTTTCGACTCTTTATTTTTCTTGAAGTATTTGTGTCTAACACTCGTATCCAATAC
131 GACCTAGGGTGTTTCGACTCTTTATTTTTCTTGAAGTATTTGTGTCTAACACTCGTATCCAATAC
1736435 AA
196 AA
*
1736437 TTTTAAGGAAAATGAAAAGTAAGGTTAATATAAGCTAGATGTGTTTGTTCACTTTGTTGTTTAAT
1 TTTTAAGGAAAATGAAAAGTAAGGTTAATATAAGCTAGATGTGTTTATTCACTTTGTTGTTTAAT
* *
1736502 ATTGTTCTTATTTTGATTTCTTTCATTCTCTTGAGGCTGGTTGGAATTTTGATTGATGCTATGAT
66 ATTGTACTTATTTTGATTTCTTTCATTCTCTTGAGGCTAGTTGGAATTTTGATTGATGCTATGAT
* *
1736567 GACCTAGGGTGTTTCTACTCTTTATTTTTCTTGAAGTATTTGTGTTTAACA
131 GACCTAGGGTGTTTCGACTCTTTATTTTTCTTGAAGTATTTGTGTCTAACA
1736618 TATGTATCCG
Statistics
Matches: 168, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
197 168 1.00
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.47
Consensus pattern (197 bp):
TTTTAAGGAAAATGAAAAGTAAGGTTAATATAAGCTAGATGTGTTTATTCACTTTGTTGTTTAAT
ATTGTACTTATTTTGATTTCTTTCATTCTCTTGAGGCTAGTTGGAATTTTGATTGATGCTATGAT
GACCTAGGGTGTTTCGACTCTTTATTTTTCTTGAAGTATTTGTGTCTAACACTCGTATCCAATAC
AA
Found at i:1737041 original size:13 final size:13
Alignment explanation
Indices: 1737012--1737052 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1737002 TTATTATTAT
*
1737012 TATTT-TTTTAAA
1 TATTTGTTTTAGA
1737024 TATTTGTGTTT-GA
1 TATTTGT-TTTAGA
1737037 TATTTGTTTTAGA
1 TATTTGTTTTAGA
1737050 TAT
1 TAT
1737053 AGTCTGACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 8 0.32
13 14 0.56
14 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.63
Consensus pattern (13 bp):
TATTTGTTTTAGA
Found at i:1739251 original size:29 final size:30
Alignment explanation
Indices: 1739191--1739259 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
1739181 ATTAAGTGGC
* * ** *
1739191 AAAATTCAATTAAATTTAAAATTTAATGAT
1 AAAATTTAATTAAATTAAAAATAAAATAAT
1739221 AAAATTTAATTAAA-TAAAAATAAAATAAT
1 AAAATTTAATTAAATTAAAAATAAAATAAT
1739250 AAAATTTAAT
1 AAAATTTAAT
1739260 ATTTTGATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (30 bp):
AAAATTTAATTAAATTAAAAATAAAATAAT
Found at i:1739260 original size:13 final size:13
Alignment explanation
Indices: 1739207--1739260 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
1739197 CAATTAAATT
*
1739207 TAAAATTTAATGA
1 TAAAATTTAATAA
1739220 TAAAATTTAATTAAA
1 TAAAATTTAA-T-AA
**
1739235 TAAAAATAAAATAA
1 T-AAAATTTAATAA
1739249 TAAAATTTAATA
1 TAAAATTTAATA
1739261 TTTTGATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
13 19 0.58
14 4 0.12
15 3 0.09
16 7 0.21
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (13 bp):
TAAAATTTAATAA
Found at i:1739631 original size:22 final size:23
Alignment explanation
Indices: 1739597--1739646 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
1739587 CTTCATAGAC
* *
1739597 TTATTCATATATTTAT-ACAAAA
1 TTATTAATATATTTATAAAAAAA
* *
1739619 TTATTAATCTATTTTTAAAAAAA
1 TTATTAATATATTTATAAAAAAA
1739642 TTATT
1 TTATT
1739647 TTTTTTACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (23 bp):
TTATTAATATATTTATAAAAAAA
Found at i:1742139 original size:25 final size:25
Alignment explanation
Indices: 1742096--1742162 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
1742086 TTATAAAACC
* * *
1742096 TTAACTAAATAAATATTAAAAAAAA
1 TTAAATAAATATATTTTAAAAAAAA
* *
1742121 TTAAATAAATATATTTTAATAAATA
1 TTAAATAAATATATTTTAAAAAAAA
* *
1742146 TAAAATTAAAAATATTT
1 TTAAA-TAAATATATTT
1742163 GTATTTTTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
25 24 0.71
26 10 0.29
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (25 bp):
TTAAATAAATATATTTTAAAAAAAA
Found at i:1742241 original size:22 final size:24
Alignment explanation
Indices: 1742184--1742253 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 24
1742174 TTAAAATAAT
*
1742184 AATTATTTA-TTTATTT-TTTAAAA
1 AATTATTCACTTT-TTTATTTAAAA
1742207 AATTATTCAC-TTTTTATTTAAAA
1 AATTATTCACTTTTTTATTTAAAA
* *
1742230 AATT-TTGACTTTTTTACTTAAAA
1 AATTATTCACTTTTTTATTTAAAA
1742253 A
1 A
1742254 GACAATTAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 7 0.17
23 34 0.83
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (24 bp):
AATTATTCACTTTTTTATTTAAAA
Found at i:1743255 original size:21 final size:21
Alignment explanation
Indices: 1743213--1743256 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1743203 CACTGGTTAC
*
1743213 AATAAAATTAATTATTAAAAT
1 AATAAAATTAATAATTAAAAT
1743234 AATAAAATTAA-AATTAACAAT
1 AATAAAATTAATAATTAA-AAT
1743255 AA
1 AA
1743257 AATATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AATAAAATTAATAATTAAAAT
Found at i:1743257 original size:18 final size:19
Alignment explanation
Indices: 1743211--1743264 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
1743201 TCCACTGGTT
*
1743211 ACAATAAAATTAATTATTAAA
1 ACAATAAAATTAA-AATT-AA
*
1743232 ATAATAAAATTAAAATT-A
1 ACAATAAAATTAAAATTAA
1743250 ACAATAAAATATAAA
1 ACAATAAAAT-TAAA
1743265 TTTAGATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 10 0.34
19 4 0.14
20 3 0.10
21 12 0.41
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (19 bp):
ACAATAAAATTAAAATTAA
Found at i:1743450 original size:16 final size:15
Alignment explanation
Indices: 1743429--1743464 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1743419 CTTTTAATTT
*
1743429 TTTAATTTAAATTAA
1 TTTAATTCAAATTAA
1743444 GTTTAATTCAAATTAA
1 -TTTAATTCAAATTAA
1743460 TTTAA
1 TTTAA
1743465 AAATTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (15 bp):
TTTAATTCAAATTAA
Found at i:1743912 original size:24 final size:24
Alignment explanation
Indices: 1743881--1743942 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
1743871 AATGACACAT
1743881 TTTAAAATAAAAATAAATAATAATTA
1 TTTAAAATAAAAATAAATAAT--TTA
* *
1743907 -TT-AAATAAATATATATAATTTA
1 TTTAAAATAAAAATAAATAATTTA
1743929 TTTAAAATAAAAAT
1 TTTAAAATAAAAAT
1743943 TATACAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 3 0.10
23 2 0.06
24 24 0.77
25 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TTTAAAATAAAAATAAATAATTTA
Found at i:1743971 original size:20 final size:20
Alignment explanation
Indices: 1743897--1743973 Score: 56
Period size: 20 Copynumber: 3.9 Consensus size: 20
1743887 ATAAAAATAA
1743897 ATAATAATTA-TTAAATAAATAT
1 ATAA-AATTATTTAAAT-AAT-T
*
1743919 ATATAATTTATTT-AA-AA-T
1 ATA-AAATTATTTAAATAATT
**
1743937 A-AAAATTATACAAATAATT
1 ATAAAATTATTTAAATAATT
1743956 ATAAAATTATTTAAATAA
1 ATAAAATTATTTAAATAA
1743974 CTTCAAATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
16 6 0.14
17 3 0.07
18 4 0.09
19 2 0.05
20 16 0.37
22 9 0.21
23 3 0.07
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAATTATTTAAATAATT
Found at i:1743972 original size:35 final size:37
Alignment explanation
Indices: 1743894--1743973 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 37
1743884 AAAATAAAAA
* * *
1743894 TAAATAATAATTATTAAATAAATATATATAATTTATT
1 TAAATAAAAATTATCAAATAAATATATATAAATTATT
1743931 TAAAATAAAAATTATACAAAT-AAT-TATA-AAATTATT
1 T-AAATAAAAATTAT-CAAATAAATATATATAAATTATT
1743967 TAAATAA
1 TAAATAA
1743974 CTTCAAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
35 6 0.16
36 8 0.21
37 5 0.13
38 15 0.39
39 4 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (37 bp):
TAAATAAAAATTATCAAATAAATATATATAAATTATT
Found at i:1745463 original size:15 final size:14
Alignment explanation
Indices: 1745431--1745470 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
1745421 TTTATCGCAT
*
1745431 TATTTATTAT-TGA
1 TATTTATTATATAA
1745444 TATTTATTATAATAA
1 TATTTATTAT-ATAA
1745459 TATTTATTATAT
1 TATTTATTATAT
1745471 TAACAATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 10 0.42
14 2 0.08
15 12 0.50
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (14 bp):
TATTTATTATATAA
Found at i:1746826 original size:16 final size:17
Alignment explanation
Indices: 1746786--1746842 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
1746776 ATACTACTTG
*
1746786 ATTAAATATATATTTTT
1 ATTAAATATATATTTAT
1746803 ATTAAATATATA-TTAT
1 ATTAAATATATATTTAT
*
1746819 ATTTAATACT-TATTTAT
1 ATTAAATA-TATATTTAT
1746836 AATTAAA
1 -ATTAAA
1746843 ATTATATATC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 12 0.35
17 17 0.50
18 5 0.15
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTAAATATATATTTAT
Found at i:1747047 original size:13 final size:12
Alignment explanation
Indices: 1747015--1747048 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1747005 AAAAAAAGTT
*
1747015 AAAATATGATAA
1 AAAATATAATAA
1747027 AAAATATAATAA
1 AAAATATAATAA
1747039 AAAATTATAA
1 AAAA-TATAA
1747049 ATATGACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (12 bp):
AAAATATAATAA
Found at i:1747078 original size:18 final size:17
Alignment explanation
Indices: 1747057--1747126 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 17
1747047 AAATATGACA
1747057 TAAATACATAAAATATAT
1 TAAA-ACATAAAATATAT
* *
1747075 TAAATA-AAATAAATTTAT
1 TAAA-ACATA-AAATATAT
*
1747093 TAAAACATCAAAATTTAT
1 TAAAACAT-AAAATATAT
*
1747111 ATAAAATATAAAATAT
1 -TAAAACATAAAATAT
1747127 GACTATAACA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
17 3 0.07
18 32 0.74
19 8 0.19
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAACATAAAATATAT
Found at i:1747451 original size:14 final size:14
Alignment explanation
Indices: 1747434--1747464 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1747424 AAATCTTAAC
1747434 CAAGAAAGCATACA
1 CAAGAAAGCATACA
1747448 CAAGAAAGCATACA
1 CAAGAAAGCATACA
1747462 CAA
1 CAA
1747465 AATTAAGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (14 bp):
CAAGAAAGCATACA
Found at i:1749010 original size:4 final size:4
Alignment explanation
Indices: 1749001--1749027 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1748991 AAGATCAAAA
1749001 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1749028 ATAGAGGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1753607 original size:28 final size:28
Alignment explanation
Indices: 1753576--1753635 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
1753566 AAAAAGGAAC
* *
1753576 AAATTTAAAATTTATA-TTTTATTTTTAA
1 AAATTT-AAATTTAAATTTTTATATTTAA
* *
1753604 AAATTTTATTTTAAATTTTTATATTTAA
1 AAATTTAAATTTAAATTTTTATATTTAA
1753632 AAAT
1 AAAT
1753636 GACACATCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
AAATTTAAATTTAAATTTTTATATTTAA
Found at i:1753611 original size:15 final size:15
Alignment explanation
Indices: 1753591--1753635 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1753581 TAAAATTTAT
1753591 ATTTTATTTTTAAAA
1 ATTTTATTTTTAAAA
1753606 ATTTTA-TTTT-AAA
1 ATTTTATTTTTAAAA
* *
1753619 TTTTTATATTTAAAA
1 ATTTTATTTTTAAAA
1753634 AT
1 AT
1753636 GACACATCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 8 0.32
14 7 0.28
15 10 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTATTTTTAAAA
Done.