Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006588.1 Hibiscus syriacus cultivar Beakdansim tig00016153_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 150208
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5327 original size:57 final size:57
Alignment explanation
Indices: 5263--5506 Score: 411
Period size: 57 Copynumber: 4.3 Consensus size: 57
5253 ATGGCACTGA
*
5263 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGGATTTTCGTATGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTT
5320 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTT
* *
5377 GTGTGCAATAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGTACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTT
* * *
5434 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCATATGGACAC--T
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTT
*
5489 GTGTGCAAAAAGCTAAGA
1 GTGTGCAAAAAGTTAAGA
5507 GTGTGAATTT
Statistics
Matches: 178, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
55 18 0.10
57 160 0.90
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (57 bp):
GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTT
Found at i:5611 original size:27 final size:27
Alignment explanation
Indices: 5527--5617 Score: 71
Period size: 27 Copynumber: 3.4 Consensus size: 27
5517 CCATAAGGGC
5527 ACTATGTGTGCAAACTAAGAAATTCAT
1 ACTATGTGTGCAAACTAAGAAATTCAT
** * ***
5554 ACTAAGTGTGTG-AATTTACGTAAGGGC--
1 ACT-A-TGTGTGCAAACTAAG-AAATTCAT
5581 ACTATGTGTGCAAACTAAGAAATTCAT
1 ACTATGTGTGCAAACTAAGAAATTCAT
*
5608 ACTAAGTGTG
1 ACTATGTGTG
5618 TGAATTTTCG
Statistics
Matches: 45, Mismatches: 13, Indels: 12
0.64 0.19 0.17
Matches are distributed among these distances:
25 9 0.20
26 6 0.13
27 15 0.33
28 6 0.13
29 9 0.20
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (27 bp):
ACTATGTGTGCAAACTAAGAAATTCAT
Found at i:5685 original size:55 final size:54
Alignment explanation
Indices: 5501--5684 Score: 271
Period size: 54 Copynumber: 3.4 Consensus size: 54
5491 GTGCAAAAAG
* * *
5501 CTAAGAGTGTGAATTTCCATAAGGGCACTATGTGTGCAAACTAAGAAATTCATA
1 CTAAGTGTGTGAATTTTCGTAAGGGCACTATGTGTGCAAACTAAGAAATTCATA
*
5555 CTAAGTGTGTGAATTTACGTAAGGGCACTATGTGTGCAAACTAAGAAATTCATA
1 CTAAGTGTGTGAATTTTCGTAAGGGCACTATGTGTGCAAACTAAGAAATTCATA
* * *
5609 CTAAGTGTGTGAATTTTCGTATGGGAACTATATGTGCAAACATAAGAAATTCATA
1 CTAAGTGTGTGAATTTTCGTAAGGGCACTATGTGTGCAAAC-TAAGAAATTCATA
*
5664 ATAAGTAG-GTGAATTTTCGTA
1 CTAAGT-GTGTGAATTTTCGTA
5685 TTAGTAGTGG
Statistics
Matches: 120, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
54 88 0.73
55 31 0.26
56 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (54 bp):
CTAAGTGTGTGAATTTTCGTAAGGGCACTATGTGTGCAAACTAAGAAATTCATA
Found at i:6855 original size:20 final size:20
Alignment explanation
Indices: 6830--6870 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
6820 CCAAACCACC
*
6830 AAATGCAACTATATGATCCT
1 AAATGCAACTAAATGATCCT
*
6850 AAATGCATCTAAATGATCCT
1 AAATGCAACTAAATGATCCT
6870 A
1 A
6871 CATGTGCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (20 bp):
AAATGCAACTAAATGATCCT
Found at i:7949 original size:18 final size:18
Alignment explanation
Indices: 7926--7964 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
7916 TTACAGTTAC
7926 AATCCTAATTTGATTAAA
1 AATCCTAATTTGATTAAA
*
7944 AATCCTAGTTTGATTAAA
1 AATCCTAATTTGATTAAA
7962 AAT
1 AAT
7965 AGATAACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (18 bp):
AATCCTAATTTGATTAAA
Found at i:13724 original size:39 final size:39
Alignment explanation
Indices: 13658--13780 Score: 149
Period size: 39 Copynumber: 3.2 Consensus size: 39
13648 GGAATACCAA
* *
13658 CCATCCACT-CCATGCATGTGAACACCAACCGTACACTT
1 CCATGCACTACCATGCATGTGAACACCAACCATACACTT
* * *
13696 CCATGCACTGCCCTGCATGTGAACACCAACCATCCACTT
1 CCATGCACTACCATGCATGTGAACACCAACCATACACTT
* * * * *
13735 CCGTGAACTACCATGCTTGTGAACACCAACCATGCACTA
1 CCATGCACTACCATGCATGTGAACACCAACCATACACTT
13774 CCATGCA
1 CCATGCA
13781 TGTGAACTGG
Statistics
Matches: 71, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
38 8 0.11
39 63 0.89
ACGTcount: A:0.28, C:0.38, G:0.13, T:0.20
Consensus pattern (39 bp):
CCATGCACTACCATGCATGTGAACACCAACCATACACTT
Found at i:21274 original size:2 final size:2
Alignment explanation
Indices: 21267--21299 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
21257 TAGAAAAACA
21267 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21300 CAATGCCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25154 original size:14 final size:14
Alignment explanation
Indices: 25135--25203 Score: 95
Period size: 14 Copynumber: 4.9 Consensus size: 14
25125 AAGTCAACAT
25135 GTTGACTCAGACGA
1 GTTGACTCAGACGA
* *
25149 GTTGACTCAGAAGG
1 GTTGACTCAGACGA
25163 GTTGACTCAGACCGA
1 GTTGACTCAGA-CGA
25178 GTTGACTCAGAC-A
1 GTTGACTCAGACGA
25191 GGTTGACTCAGAC
1 -GTTGACTCAGAC
25204 CGAATCAGGC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
13 1 0.02
14 36 0.73
15 12 0.24
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.22
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:25186 original size:29 final size:29
Alignment explanation
Indices: 25135--25206 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 29
25125 AAGTCAACAT
25135 GTTGACTCAGA-CGAGTTGACTCAGA-AGG
1 GTTGACTCAGACCGAGTTGACTCAGACA-G
25163 GTTGACTCAGACCGAGTTGACTCAGACAG
1 GTTGACTCAGACCGAGTTGACTCAGACAG
25192 GTTGACTCAGACCGA
1 GTTGACTCAGACCGA
25207 ATCAGGCAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
28 11 0.26
29 30 0.71
30 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.21
Consensus pattern (29 bp):
GTTGACTCAGACCGAGTTGACTCAGACAG
Found at i:26496 original size:13 final size:13
Alignment explanation
Indices: 26496--26529 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
26486 CCGTTGACCC
26496 GACCCGACCCGTT
1 GACCCGACCCGTT
*
26509 TACCCGACCCGTT
1 GACCCGACCCGTT
26522 GACCCGAC
1 GACCCGAC
26530 TCGACCCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.47, G:0.21, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:26497 original size:18 final size:18
Alignment explanation
Indices: 26474--26543 Score: 87
Period size: 18 Copynumber: 4.2 Consensus size: 18
26464 ACCGGTCACA
26474 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
26492 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
26509 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
26523 ACCCGACTCGACCCGTTG
1 ACCCGACCCGACCCGTTG
26541 ACC
1 ACC
26544 GTTGACCCGT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
13 12 0.27
18 32 0.73
ACGTcount: A:0.17, C:0.49, G:0.20, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:26517 original size:31 final size:31
Alignment explanation
Indices: 26478--26558 Score: 117
Period size: 31 Copynumber: 2.5 Consensus size: 31
26468 GTCACAACCC
26478 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* *
26509 TACCCGACCCGTTGACCCGACTCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
26540 GACCGTTGACCCGTTGACC
1 GACC--CGACCCGTTGACC
26559 GTTGACCGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 32 0.73
33 12 0.27
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.17
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:26525 original size:8 final size:8
Alignment explanation
Indices: 26514--26565 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
26504 CCGTTTACCC
26514 GACCCGTT
1 GACCCGTT
*
26522 GACCCGACTC
1 GACCCG--TT
26532 GACCCGTT
1 GACCCGTT
26540 GA-CCGTT
1 GACCCGTT
26547 GACCCGTT
1 GACCCGTT
26555 GA-CCGTT
1 GACCCGTT
26562 GACC
1 GACC
26566 GGAGTTGACC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 14 0.37
8 17 0.45
10 7 0.18
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:26547 original size:7 final size:7
Alignment explanation
Indices: 26535--26566 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
26525 CCGACTCGAC
26535 CCGTTGA
1 CCGTTGA
26542 CCGTTGA
1 CCGTTGA
26549 CCCGTTGA
1 -CCGTTGA
26557 CCGTTGA
1 CCGTTGA
26564 CCG
1 CCG
26567 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:26552 original size:15 final size:15
Alignment explanation
Indices: 26532--26565 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
26522 GACCCGACTC
26532 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
26547 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
26562 GACC
1 GACC
26566 GGAGTTGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:29124 original size:24 final size:24
Alignment explanation
Indices: 29028--29136 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
29018 GAATATTTTA
* * *
29028 TCTGATTTCTGATTTGAATTCTAT
1 TCTGATATCTGATCTGAATTCTGT
* * *
29052 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * * *
29076 TCTGAT-TCCTAACCTGGATTTTGT
1 TCTGATAT-CTGATCTGAATTCTGT
*
29100 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTCTGT
* *
29124 TTTGATTTCTGAT
1 TCTGATATCTGAT
29137 ATCTCCGTTT
Statistics
Matches: 64, Mismatches: 19, Indels: 4
0.74 0.22 0.05
Matches are distributed among these distances:
23 1 0.02
24 62 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.16, T:0.49
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:31286 original size:13 final size:13
Alignment explanation
Indices: 31286--31319 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
31276 CCGTTGACCC
31286 GACCCGACCCGTT
1 GACCCGACCCGTT
*
31299 TACCCGACCCGTT
1 GACCCGACCCGTT
31312 GACCCGAC
1 GACCCGAC
31320 TCGACCCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.47, G:0.21, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:31287 original size:18 final size:18
Alignment explanation
Indices: 31264--31333 Score: 87
Period size: 18 Copynumber: 4.2 Consensus size: 18
31254 ACCGGTCACA
31264 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
31282 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
31299 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
31313 ACCCGACTCGACCCGTTG
1 ACCCGACCCGACCCGTTG
31331 ACC
1 ACC
31334 GTTGACCCGT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
13 12 0.27
18 32 0.73
ACGTcount: A:0.17, C:0.49, G:0.20, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:31307 original size:31 final size:31
Alignment explanation
Indices: 31268--31348 Score: 117
Period size: 31 Copynumber: 2.5 Consensus size: 31
31258 GTCACAACCC
31268 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* *
31299 TACCCGACCCGTTGACCCGACTCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
31330 GACCGTTGACCCGTTGACC
1 GACC--CGACCCGTTGACC
31349 GTTGACCGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 32 0.73
33 12 0.27
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.17
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:31315 original size:8 final size:8
Alignment explanation
Indices: 31304--31355 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
31294 CCGTTTACCC
31304 GACCCGTT
1 GACCCGTT
*
31312 GACCCGACTC
1 GACCCG--TT
31322 GACCCGTT
1 GACCCGTT
31330 GA-CCGTT
1 GACCCGTT
31337 GACCCGTT
1 GACCCGTT
31345 GA-CCGTT
1 GACCCGTT
31352 GACC
1 GACC
31356 GGAGTTGACC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 14 0.37
8 17 0.45
10 7 0.18
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:31337 original size:7 final size:7
Alignment explanation
Indices: 31325--31356 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
31315 CCGACTCGAC
31325 CCGTTGA
1 CCGTTGA
31332 CCGTTGA
1 CCGTTGA
31339 CCCGTTGA
1 -CCGTTGA
31347 CCGTTGA
1 CCGTTGA
31354 CCG
1 CCG
31357 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:31342 original size:15 final size:15
Alignment explanation
Indices: 31322--31355 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
31312 GACCCGACTC
31322 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
31337 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
31352 GACC
1 GACC
31356 GGAGTTGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:33909 original size:24 final size:24
Alignment explanation
Indices: 33813--33921 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
33803 GAATATTTTA
* * *
33813 TCTGATTTCTGATTTGAATTCTAT
1 TCTGATATCTGATCTGAATTCTGT
* * *
33837 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * * *
33861 TCTGAT-TCCTAACCTGGATTTTGT
1 TCTGATAT-CTGATCTGAATTCTGT
*
33885 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTCTGT
* *
33909 TTTGATTTCTGAT
1 TCTGATATCTGAT
33922 ATCTCCGTTT
Statistics
Matches: 64, Mismatches: 19, Indels: 4
0.74 0.22 0.05
Matches are distributed among these distances:
23 1 0.02
24 62 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.16, T:0.49
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:38761 original size:15 final size:15
Alignment explanation
Indices: 38727--38779 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
38717 AAAGTCAACC
* *
38727 GGTTGACTCGGA-CT
1 GGTTGACTCAGACCG
38741 GGTTGACTCAGACCG
1 GGTTGACTCAGACCG
*
38756 GGTTGACTCAAACCG
1 GGTTGACTCAGACCG
38771 GGTTGACTC
1 GGTTGACTC
38780 GGACTGGCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
14 11 0.31
15 24 0.69
ACGTcount: A:0.19, C:0.25, G:0.32, T:0.25
Consensus pattern (15 bp):
GGTTGACTCAGACCG
Found at i:38791 original size:29 final size:30
Alignment explanation
Indices: 38741--38800 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
38731 GACTCGGACT
*
38741 GGTTGACTCAGACCGGGTTGACTCAAACCG
1 GGTTGACTCAGACCGGGCTGACTCAAACCG
* * *
38771 GGTTGACTCGGA-CTGGCTGACTCGAACCG
1 GGTTGACTCAGACCGGGCTGACTCAAACCG
38800 G
1 G
38801 ACCAGGCGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.20, C:0.27, G:0.33, T:0.20
Consensus pattern (30 bp):
GGTTGACTCAGACCGGGCTGACTCAAACCG
Found at i:38830 original size:18 final size:19
Alignment explanation
Indices: 38792--38832 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
38782 ACTGGCTGAC
*
38792 TCGAACCGGACCAGGCGGG
1 TCGAACCGGACCAGACGGG
*
38811 TCGAATCGGA-CAGACGGG
1 TCGAACCGGACCAGACGGG
38829 TCGA
1 TCGA
38833 GTTGATTCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.24, C:0.27, G:0.39, T:0.10
Consensus pattern (19 bp):
TCGAACCGGACCAGACGGG
Found at i:49297 original size:31 final size:32
Alignment explanation
Indices: 49261--49326 Score: 87
Period size: 35 Copynumber: 2.0 Consensus size: 32
49251 CGTCACTTCC
* *
49261 AGTAAGGCCTTGAGCACACAGCCTAGGAACCAGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACC---A
49296 AGTAAGGCCCTGAGCACACAGCCGAGGAACC
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACC
49327 TCCAGGTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.33, C:0.29, G:0.27, T:0.11
Consensus pattern (32 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCA
Found at i:49425 original size:24 final size:24
Alignment explanation
Indices: 49415--49529 Score: 178
Period size: 24 Copynumber: 4.8 Consensus size: 24
49405 CATAATTCAC
* * *
49415 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
49439 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
49463 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
49487 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
49511 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
49530 ATCAAATCAA
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
23 2 0.02
24 81 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:49546 original size:48 final size:49
Alignment explanation
Indices: 49391--49546 Score: 165
Period size: 48 Copynumber: 3.2 Consensus size: 49
49381 AAACAGATAT
* * * * * *
49391 ATCAAAAATCAAATCATAATTCACGTCAAGTATCATATCA-AAATCCAG
1 ATCAAAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAAATCCAA
* ** *
49439 GTCAAGTATCAGATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCAT
1 ATCAAAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAAATCCAA
* * * *
49487 GTCAGATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAAT-CAA
1 ATCAAAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAAATCCAA
49535 ATCAAAAATCAG
1 ATCAAAAATCAG
49547 TTAAAATATT
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
48 87 0.97
49 3 0.03
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (49 bp):
ATCAAAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAAATCCAA
Found at i:49546 original size:72 final size:72
Alignment explanation
Indices: 49391--49546 Score: 190
Period size: 72 Copynumber: 2.2 Consensus size: 72
49381 AAACAGATAT
* * * *
49391 ATCAAAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAG
1 ATCAAAAATCAGATCAGAATCCACGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCAGATCAG
49456 AATCCAA
66 AATCCAA
* ** * * *
49463 GTCAAGTATCAGATCAGAATCCATGTC-AGATATCAGATCAGAATCCATGTCAAGTATCAGATCA
1 ATCAAAAATCAGATCAGAATCCACGTCAAG-TATCAGATCAAAATCCAGGTCAAGTATCAGATCA
49527 GAAAT-CAA
65 G-AATCCAA
49535 ATCAAAAATCAG
1 ATCAAAAATCAG
49547 TTAAAATATT
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
71 2 0.03
72 64 0.93
73 3 0.04
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (72 bp):
ATCAAAAATCAGATCAGAATCCACGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCAGATCAG
AATCCAA
Found at i:54326 original size:24 final size:24
Alignment explanation
Indices: 54202--54316 Score: 169
Period size: 24 Copynumber: 4.8 Consensus size: 24
54192 CATAATTCAC
* *
54202 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAA
54226 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
54250 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
*
54274 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
*
54298 GTCAAGTTTCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
54317 ATCAAATCAA
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
23 2 0.02
24 81 0.95
25 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:54333 original size:48 final size:48
Alignment explanation
Indices: 54178--54333 Score: 161
Period size: 48 Copynumber: 3.2 Consensus size: 48
54168 AAACGAATAT
* * * * * *
54178 ATCAAAAATCAAATCATAATTCACGTCAAGTATCATATCAGAATCCAG
1 ATCAAAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* ** *
54226 GTCAAGTATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAT
1 ATCAAAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* * * * *
54274 GTCAGATATCAGATCAGAATCCATGTCAAGTTTCAGATCAGAAAT-CAA
1 ATCAAAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCAA
54322 ATCAAAAATCAG
1 ATCAAAAATCAG
54334 GTAAAATATT
Statistics
Matches: 90, Mismatches: 17, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
48 87 0.97
49 3 0.03
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (48 bp):
ATCAAAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
Found at i:54333 original size:72 final size:72
Alignment explanation
Indices: 54178--54333 Score: 190
Period size: 72 Copynumber: 2.2 Consensus size: 72
54168 AAACGAATAT
* * * *
54178 ATCAAAAATCAAATCATAATTCACGTCAAGTATCATATCAGAATCCAGGTCAAGTATCAGATCAG
1 ATCAAAAATCAGATCAGAATCCACGTCAAGTATCAGATCAGAATCCAGGTCAAGTATCAGATCAG
54243 AATCCAA
66 AATCCAA
* ** * * *
54250 GTCAAGTATCAGATCAGAATCCATGTC-AGATATCAGATCAGAATCCATGTCAAGTTTCAGATCA
1 ATCAAAAATCAGATCAGAATCCACGTCAAG-TATCAGATCAGAATCCAGGTCAAGTATCAGATCA
54314 GAAAT-CAA
65 G-AATCCAA
54322 ATCAAAAATCAG
1 ATCAAAAATCAG
54334 GTAAAATATT
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
71 2 0.03
72 64 0.93
73 3 0.04
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (72 bp):
ATCAAAAATCAGATCAGAATCCACGTCAAGTATCAGATCAGAATCCAGGTCAAGTATCAGATCAG
AATCCAA
Found at i:57685 original size:22 final size:22
Alignment explanation
Indices: 57660--57702 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
57650 AATATATTTA
57660 TTATAAAACATAT-TATAAAATG
1 TTATAAAA-ATATATATAAAATG
*
57682 TTATAAAAATATATCTAAAAT
1 TTATAAAAATATATATAAAAT
57703 TAATTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (22 bp):
TTATAAAAATATATATAAAATG
Found at i:57817 original size:16 final size:18
Alignment explanation
Indices: 57791--57837 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
57781 GTGAAAATAT
*
57791 AATAAAATATACA-T-TA
1 AATATAATATACATTATA
* *
57807 ATTATAATATAAATTATA
1 AATATAATATACATTATA
57825 AATATAATATACA
1 AATATAATATACA
57838 AATATATTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
16 10 0.42
17 1 0.04
18 13 0.54
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (18 bp):
AATATAATATACATTATA
Found at i:57835 original size:23 final size:20
Alignment explanation
Indices: 57786--57835 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 20
57776 ATAGAGTGAA
*
57786 AATATAATAAAATATACATT
1 AATATAATAAAATATAAATT
57806 AATTATAATATAAATTATAAATAT
1 AA-TATAATA-AAA-TATAAAT-T
57830 AATATA
1 AATATA
57836 CAAATATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 2 0.08
21 7 0.28
22 3 0.12
23 10 0.40
24 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAATAAAATATAAATT
Found at i:59048 original size:30 final size:31
Alignment explanation
Indices: 58996--59055 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
58986 CTTAGCTTTA
**
58996 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
59026 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
59056 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:59908 original size:19 final size:20
Alignment explanation
Indices: 59884--59934 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
59874 CGGCCAAGAG
* *
59884 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
59903 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
59923 CATGTATTTTCA
1 CATGTATTTTCA
59935 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:62766 original size:20 final size:20
Alignment explanation
Indices: 62741--62793 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
62731 GCGAGAGCTT
62741 GGCTCAGTGGAGTTCTTTCA
1 GGCTCAGTGGAGTTCTTTCA
62761 GGCTCAGTGGAGTTCTTTCA
1 GGCTCAGTGGAGTTCTTTCA
* *
62781 GACTCAATGGAGT
1 GGCTCAGTGGAGT
62794 CTTGGGCGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (20 bp):
GGCTCAGTGGAGTTCTTTCA
Found at i:63615 original size:21 final size:21
Alignment explanation
Indices: 63589--63631 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
63579 GCTTCACTGT
* *
63589 AAGATTTTATGGCCTCGACAA
1 AAGATTTCATGGCCTCAACAA
*
63610 AAGATTTCATGGCTTCAACAA
1 AAGATTTCATGGCCTCAACAA
63631 A
1 A
63632 GACTTTGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (21 bp):
AAGATTTCATGGCCTCAACAA
Found at i:76333 original size:2 final size:2
Alignment explanation
Indices: 76326--76356 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
76316 TTGGCTAGAC
76326 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
76357 TTGTATATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:83171 original size:65 final size:62
Alignment explanation
Indices: 83090--83234 Score: 177
Period size: 61 Copynumber: 2.3 Consensus size: 62
83080 ATAGGTTTAT
* *
83090 ATTAGCACTAGTGTGTAAGGACACTAAGTGCT-GGTGGTGGGCACAACCTTATATGTCATATCCA
1 ATTAGCACTAGAGTGTAA-GACA-T-AGTG-TAGATGGTGGGCACAACCTTATATGTCATATCCA
83154 G
62 G
* * * *
83155 ATTAGCACTAGAGTGTAA-ACATAGTGTAGATGGTGGGCACAACCTTGTGTGTCATATTCGG
1 ATTAGCACTAGAGTGTAAGACATAGTGTAGATGGTGGGCACAACCTTATATGTCATATCCAG
*
83216 ATTAGCACTAGAGCGTAAG
1 ATTAGCACTAGAGTGTAAG
83235 TTTAGTGTAG
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
60 1 0.01
61 49 0.69
62 1 0.01
63 3 0.04
65 17 0.24
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.28
Consensus pattern (62 bp):
ATTAGCACTAGAGTGTAAGACATAGTGTAGATGGTGGGCACAACCTTATATGTCATATCCAG
Found at i:89363 original size:20 final size:20
Alignment explanation
Indices: 89335--89388 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
89325 AATTGTTGGG
89335 CAGTGGTATCGATA-CTCAGT
1 CAGTGGTATCGATACCT-AGT
*
89355 CAGTTGTATCGATACCTAGT
1 CAGTGGTATCGATACCTAGT
89375 CAGTGGTATCGATA
1 CAGTGGTATCGATA
89389 TCGGGGTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
CAGTGGTATCGATACCTAGT
Found at i:89629 original size:3 final size:3
Alignment explanation
Indices: 89621--89665 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
89611 TCATCTCGAC
89621 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
89666 TATTGTATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:91969 original size:130 final size:131
Alignment explanation
Indices: 91720--92082 Score: 511
Period size: 130 Copynumber: 2.8 Consensus size: 131
91710 ATTAATATTG
* * * * *
91720 AAAATAGTAATATCTTTTCATTTCGGGTT-GAGTAGTAAATGACTGCTTAAAGGCATGAGAGGTC
1 AAAATAGTGATATCTCTTCATTTC-GATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTC
91784 ATTTATTCTCGATTGGAAATAATTAGATATT-TCGGTTTTCTCTCGAAACAATATTGAATTTTAA
65 ATTTATTCTCGATTGGAAATAATTAGATATTATC-GTTTTCTCTCGAAACAATATTGAATTTTAA
91848 GAC
129 GAC
* *
91851 AAAATAGTGATA-CTCTTCATTTCGATTGGACTAATAAATGACTGCTTTAAGGAATGAGAGGTCA
1 AAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
* *
91915 -TTATTTCTCGATTAGAAATAATTAGATATTATCGTTTTCTCTC-AAAGCAATATTGCATTTTAA
66 TTTA-TTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCGAAA-CAATATTGAATTTTAA
*
91978 GAT
129 GAC
* * * * *
91981 GAAATAGTGATATATCTTCATTTCGATTGTAGTAATAAATGACTGCTTTAAGGCATTAGATGTCA
1 AAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
*
92046 TTTATTCTCGATTGGAAATAATTAGATATTATAGTTT
66 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTT
92083 CCTTTTTTAA
Statistics
Matches: 207, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
129 9 0.04
130 105 0.51
131 90 0.43
132 3 0.01
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.39
Consensus pattern (131 bp):
AAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCGAAACAATATTGAATTTTAAGA
C
Found at i:103246 original size:90 final size:89
Alignment explanation
Indices: 103093--103267 Score: 278
Period size: 90 Copynumber: 2.0 Consensus size: 89
103083 CCTAACACAC
* * * * *
103093 CCTTTTATAGCCAAGTTACCCTAGTTATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAAGGATTTTATTATTTCAAATTAATTAAATCTAT
*
103158 ATTTAATTAATTAGAATTTAATAAT
66 ATTTAATTAATT-GAAATTAATAAT
*
103183 CCTTTTATATCCAAGTTACCCTAATCATATCAAGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAAGGATTTTATTATTTCAAATTAATTAAATCTAT
103248 ATTTAATTAATTGAAATTAA
66 ATTTAATTAATTGAAATTAA
103268 ATATTAGGGA
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 7 0.09
90 71 0.91
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAAGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAATAAT
Found at i:103257 original size:20 final size:20
Alignment explanation
Indices: 103232--103311 Score: 58
Period size: 20 Copynumber: 3.9 Consensus size: 20
103222 TATTATTTCA
103232 AATTAATTAAATCTATATTT
1 AATTAATTAAATCTATATTT
*
103252 AATTAATTGAAAT-TAAATATT
1 AATTAATT-AAATCTATAT-TT
* *
103273 AGGGATT-ATTAAA-ATATATAT
1 A---ATTAATTAAATCTATATTT
*
103294 AATTAATTAACTCTATAT
1 AATTAATTAAATCTATAT
103312 ATATTTTAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
18 3 0.06
19 5 0.11
20 17 0.36
21 9 0.19
22 7 0.15
23 3 0.06
24 3 0.06
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (20 bp):
AATTAATTAAATCTATATTT
Found at i:104423 original size:22 final size:22
Alignment explanation
Indices: 104381--104425 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
104371 TTCACCTGAA
**
104381 AAAAGAAAAATGATGAAAAAAG
1 AAAAGAAAAATGAAAAAAAAAG
104403 AAAAGAAAAA-GAAAAATAAAAG
1 AAAAGAAAAATGAAAAA-AAAAG
104425 A
1 A
104426 GAATAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.07
Consensus pattern (22 bp):
AAAAGAAAAATGAAAAAAAAAG
Found at i:105391 original size:133 final size:134
Alignment explanation
Indices: 105148--105396 Score: 385
Period size: 133 Copynumber: 1.9 Consensus size: 134
105138 TTCCCAAAAC
* *
105148 TTTCAGATTTGATCTTCCCTGAAGAAGCAGTGGAACAAGTCTACCTCGATTCAATTTTCCTTGAA
1 TTTCAGATTTGATCTTCCCTGAAGAAGCAGTGGAACAACTCTACCTCGATTCAATTTTCCCTGAA
* * * * * * *
105213 GAACTGTGGAATGAATCAACGTTTCCAGATCTGGTTTTCCCTGAAGAAGCAGCGGAATAAATCCC
66 GAACAGTGAAATGAATCAACATTTCCAGATATGATCTACCCTGAAGAAGCAGCGGAATAAATCCC
105278 CTCT
131 CTCT
105282 TTTCAGATTTGATCTTCCCTG-AGTAA-CAGTGGAACAACTCTACCTCGATTCAATTTTCCCTGA
1 TTTCAGATTTGATCTTCCCTGAAG-AAGCAGTGGAACAACTCTACCTCGATTCAATTTTCCCTGA
*
105345 AGAACAGTGAAATGAATCAACATTTCCAGATATGATCTACCTTGAAGAAGCA
65 AGAACAGTGAAATGAATCAACATTTCCAGATATGATCTACCCTGAAGAAGCA
105397 ATAGAGCATA
Statistics
Matches: 104, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
133 81 0.78
134 23 0.22
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (134 bp):
TTTCAGATTTGATCTTCCCTGAAGAAGCAGTGGAACAACTCTACCTCGATTCAATTTTCCCTGAA
GAACAGTGAAATGAATCAACATTTCCAGATATGATCTACCCTGAAGAAGCAGCGGAATAAATCCC
CTCT
Found at i:105607 original size:3 final size:3
Alignment explanation
Indices: 105599--105780 Score: 364
Period size: 3 Copynumber: 60.7 Consensus size: 3
105589 TCATCCTGAC
105599 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
105647 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
105695 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
105743 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
105781 AAGCATTTAC
Statistics
Matches: 179, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 179 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:107176 original size:18 final size:18
Alignment explanation
Indices: 107145--107182 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 18
107135 AAATAAAAGT
107145 AATTAAATAATAATTTAAA
1 AATTAAATAATAA-TTAAA
107164 AATTAAA-AATAATTAAA
1 AATTAAATAATAATTAAA
107181 AA
1 AA
107183 GGTTATGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATTAAATAATAATTAAA
Found at i:107360 original size:33 final size:33
Alignment explanation
Indices: 107318--107381 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
107308 GTTTAGGTAA
107318 TAAATATGTAGTTTACCCTTCACTTTTTCGTAC
1 TAAATATGTAGTTTACCCTTCACTTTTTCGTAC
*
107351 TAAATATGTAGTTTACCCTTTACTTTTTCGT
1 TAAATATGTAGTTTACCCTTCACTTTTTCGT
107382 TCAACCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.09, T:0.48
Consensus pattern (33 bp):
TAAATATGTAGTTTACCCTTCACTTTTTCGTAC
Found at i:111741 original size:170 final size:170
Alignment explanation
Indices: 111442--111762 Score: 498
Period size: 170 Copynumber: 1.9 Consensus size: 170
111432 GAAATTACAT
* *
111442 ATAAATAATGAAAATTCTAAAGCTAAATTTAATTACAAATAATCAATAGAATAATTGAAAATTTG
1 ATAAATAATGAAAAGTCTAAAGCTAAATTTAATTACAAATAATCAATAGAACAATTGAAAATTTG
* *
111507 TAACAAATTAAAATTCTCATATTGGACTCGTATTCAATTTTTTGCATGTACAATCTTCACTAAAA
66 TAACAAATTAAAATTCTCATATTGGACTCGTATTCAATTTTATGCACGTACAATCTTCACTAAAA
*
111572 TAAGCATATGTTGAGTTCCTGATATATTAAATTACCATAA
131 TAAGCATATCTTGAGTTCCTGATATATTAAATTACCATAA
* * *
111612 ATAAATAATGAAAAGTCTAAAGTTGAATTTAATTACAAATAATCAATAGAACAATTGAAATTTTG
1 ATAAATAATGAAAAGTCTAAAGCTAAATTTAATTACAAATAATCAATAGAACAATTGAAAATTTG
** * * * ** *
111677 TAACAAATTAAAATTCTTGTGTTGGACTCGTATTCAATTTTATGTACGTTCGGTCTTTACTAAAA
66 TAACAAATTAAAATTCTCATATTGGACTCGTATTCAATTTTATGCACGTACAATCTTCACTAAAA
111742 TAAGCATATCTTGAGTTCCTG
131 TAAGCATATCTTGAGTTCCTG
111763 GTATCCGATT
Statistics
Matches: 135, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
170 135 1.00
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (170 bp):
ATAAATAATGAAAAGTCTAAAGCTAAATTTAATTACAAATAATCAATAGAACAATTGAAAATTTG
TAACAAATTAAAATTCTCATATTGGACTCGTATTCAATTTTATGCACGTACAATCTTCACTAAAA
TAAGCATATCTTGAGTTCCTGATATATTAAATTACCATAA
Found at i:122874 original size:18 final size:18
Alignment explanation
Indices: 122848--122886 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
122838 TGAACTTATA
* *
122848 TTATTGTTTTAAATTGTT
1 TTATAGTTTTAAATAGTT
122866 TTATAGTTTTAAATAGTT
1 TTATAGTTTTAAATAGTT
122884 TTA
1 TTA
122887 CAAAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (18 bp):
TTATAGTTTTAAATAGTT
Found at i:129016 original size:21 final size:20
Alignment explanation
Indices: 128990--129056 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
128980 ATCTTTAATG
*
128990 TGGATACTAGTTCATCTGGTA
1 TGGATACCAGTTCATCT-GTA
*
129011 TGGATACCAG-TCCTCCTGTA
1 TGGATACCAGTTCAT-CTGTA
* *
129031 TGGATACCAGTTTATCCCGTA
1 TGGATACCAGTTCAT-CTGTA
129052 TGGAT
1 TGGAT
129057 GTCAGAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
20 16 0.41
21 23 0.59
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.34
Consensus pattern (20 bp):
TGGATACCAGTTCATCTGTA
Found at i:133036 original size:14 final size:15
Alignment explanation
Indices: 133019--133047 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
133009 TATTATCAAT
133019 AAAAAAT-TAAAATA
1 AAAAAATCTAAAATA
133033 AAAAAATCTAAAATA
1 AAAAAATCTAAAATA
133048 TATGGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAAATCTAAAATA
Found at i:133485 original size:81 final size:81
Alignment explanation
Indices: 133339--133498 Score: 218
Period size: 81 Copynumber: 2.0 Consensus size: 81
133329 ATTATTTTGG
* * * *
133339 ATTAAGACTAATTTGATATAATGTATAAGTTTTAGAGACTAAATATATATTATACGCATGTCACA
1 ATTAAGACTAATTTGATACAATGTATAAGTATTAGAGACTAAATATATAATATACGCATGCCACA
133404 TCAC-CTTTTCCGTTGA
66 TCACGC-TTTCCGTTGA
* *
133420 ATTAGGACTAATTTGATACAATGTATAAGTATTAGAGACTAAA-ACTATAATATATC-CGTGCCA
1 ATTAAGACTAATTTGATACAATGTATAAGTATTAGAGACTAAATA-TATAATATA-CGCATGCCA
133483 CATCACGCTTTCCGTT
64 CATCACGCTTTCCGTT
133499 AAGTCAGCTA
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
80 1 0.01
81 67 0.96
82 2 0.03
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (81 bp):
ATTAAGACTAATTTGATACAATGTATAAGTATTAGAGACTAAATATATAATATACGCATGCCACA
TCACGCTTTCCGTTGA
Found at i:135393 original size:22 final size:22
Alignment explanation
Indices: 135347--135393 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
135337 GAGAGCAAGA
* *
135347 AAACAGCAACCAAGCAATAGAG
1 AAACAGCAACCAACCAATACAG
* *
135369 AAACATCAACCAACCAATACTG
1 AAACAGCAACCAACCAATACAG
135391 AAA
1 AAA
135394 ATAGAGAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.55, C:0.26, G:0.11, T:0.09
Consensus pattern (22 bp):
AAACAGCAACCAACCAATACAG
Found at i:136057 original size:19 final size:18
Alignment explanation
Indices: 136015--136059 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
136005 TAATTTACAT
136015 TTTAAT-TTATATAATAA
1 TTTAATATTATATAATAA
*
136032 TTT--TATTAGTATAGTAA
1 TTTAATATTA-TATAATAA
136049 TTTAATATTAT
1 TTTAATATTAT
136060 TTTGAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
15 1 0.04
16 3 0.13
17 13 0.57
18 1 0.04
19 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
TTTAATATTATATAATAA
Found at i:147430 original size:36 final size:36
Alignment explanation
Indices: 147381--147485 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
147371 TTCTCAAGTT
147381 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
* *
147417 AATCAAGCATTCACAAAAGAGTAGTGAAACAATGCA
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
147453 AATCAAGCCTTCACAAAAAGAGTAGTGAAGCAA
1 AATCAAGCCTTCAC-AAAAGAGTAGTGAAGCAA
147486 GATCAGATTA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 47 0.73
37 17 0.27
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.16
Consensus pattern (36 bp):
AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
Found at i:148933 original size:19 final size:18
Alignment explanation
Indices: 148891--148935 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
148881 TATTTTACAT
148891 TTTAAT-TTATATAATAA
1 TTTAATATTATATAATAA
*
148908 TTT--TATTAGTATAGTAA
1 TTTAATATTA-TATAATAA
148925 TTTAATATTAT
1 TTTAATATTAT
148936 TTTGAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
15 1 0.04
16 3 0.13
17 13 0.57
18 1 0.04
19 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
TTTAATATTATATAATAA
Done.