Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397260.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_51.0, 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: 10072460
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 70252 characters in sequence are not A, C, G, or T
File 20 of 20
Found at i:9512202 original size:33 final size:32
Alignment explanation
Indices: 9512146--9512322 Score: 190
Period size: 33 Copynumber: 5.6 Consensus size: 32
9512136 CTAATATGTA
*
9512146 ATAATAATAAGCAAAA-TTCATTGCTTGAATTAT
1 ATAATAA-AAGTAAAAGTT-ATTGCTTGAATTAT
9512179 ATAATTAAAAGTAAAAGTTATTGCTTGAA-T-T
1 ATAA-TAAAAGTAAAAGTTATTGCTTGAATTAT
*
9512210 A-AATAAGAA-TAAAATTTATTGCTTGAATTAT
1 ATAATAA-AAGTAAAAGTTATTGCTTGAATTAT
9512241 ATAATAAAAAGTAAAAGTTATTGCTTGAATTAT
1 ATAAT-AAAAGTAAAAGTTATTGCTTGAATTAT
* * *
9512274 AT-A-AGAA-TGAAACTTATTGCTTGAATTAT
1 ATAATAAAAGTAAAAGTTATTGCTTGAATTAT
*
9512303 ATAATAATAAGTAAAGGTTA
1 ATAATAA-AAGTAAAAGTTA
9512323 CGAAATTATA
Statistics
Matches: 122, Mismatches: 10, Indels: 24
0.78 0.06 0.15
Matches are distributed among these distances:
29 42 0.34
30 9 0.07
31 5 0.04
32 9 0.07
33 52 0.43
34 5 0.04
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (32 bp):
ATAATAAAAGTAAAAGTTATTGCTTGAATTAT
Found at i:9512232 original size:29 final size:29
Alignment explanation
Indices: 9512190--9512312 Score: 147
Period size: 29 Copynumber: 4.1 Consensus size: 29
9512180 TAATTAAAAG
9512190 TAAAAGTTATTGCTTGAATTAAATAAGAA
1 TAAAAGTTATTGCTTGAATTAAATAAGAA
* *
9512219 TAAAATTTATTGCTTGAATTATATAATAAAAA
1 TAAAAGTTATTGCTTGAA-T-TA-AATAAGAA
*
9512251 GTAAAAGTTATTGCTTGAATTATATAAGAA
1 -TAAAAGTTATTGCTTGAATTAAATAAGAA
* * * *
9512281 TGAAACTTATTGCTTGAATTATATAATAA
1 TAAAAGTTATTGCTTGAATTAAATAAGAA
9512310 TAA
1 TAA
9512313 GTAAAGGTTA
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
29 45 0.56
30 7 0.09
31 4 0.05
32 8 0.10
33 17 0.21
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.38
Consensus pattern (29 bp):
TAAAAGTTATTGCTTGAATTAAATAAGAA
Found at i:9512235 original size:62 final size:62
Alignment explanation
Indices: 9512158--9512322 Score: 260
Period size: 62 Copynumber: 2.7 Consensus size: 62
9512148 AATAATAAGC
*
9512158 AAAATTCATTGCTTGAATTATATAATTAAAAGTAAAAGTTATTGCTTGAATTAAATAAGAAT
1 AAAATTTATTGCTTGAATTATATAATTAAAAGTAAAAGTTATTGCTTGAATTAAATAAGAAT
* *
9512220 AAAATTTATTGCTTGAATTATATAATAAAAAGTAAAAGTTATTGCTTGAATTATATAAGAAT
1 AAAATTTATTGCTTGAATTATATAATTAAAAGTAAAAGTTATTGCTTGAATTAAATAAGAAT
* * *
9512282 GAAACTTATTGCTTGAATTATATAA-TAATAAGTAAAGGTTA
1 AAAATTTATTGCTTGAATTATATAATTAA-AAGTAAAAGTTA
9512323 CGAAATTATA
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
61 2 0.02
62 93 0.98
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (62 bp):
AAAATTTATTGCTTGAATTATATAATTAAAAGTAAAAGTTATTGCTTGAATTAAATAAGAAT
Found at i:9523177 original size:33 final size:34
Alignment explanation
Indices: 9523092--9523177 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 34
9523082 AAACAAATTA
* *
9523092 AAATAAAATATATAATATA-AAAAATATATTAAAG
1 AAATAAAA-ATAAAATATATAAAAATATAATAAAG
* * *
9523126 AAATGAAAATAAAATATATAAAATTATAAT-AAT
1 AAATAAAAATAAAATATATAAAAATATAATAAAG
9523159 AAATAAAAATAAAATATAT
1 AAATAAAAATAAAATATAT
9523178 GACATTAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 29 0.64
34 16 0.36
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (34 bp):
AAATAAAAATAAAATATATAAAAATATAATAAAG
Found at i:9523192 original size:87 final size:88
Alignment explanation
Indices: 9523095--9523262 Score: 204
Period size: 87 Copynumber: 1.9 Consensus size: 88
9523085 CAAATTAAAA
*
9523095 TAAAATATATAATATAAAAAAT-ATATTA-A-AGAAATGAA-AATAAAATATATAAAATTATAAT
1 TAAAATATAT-ATATAAAAAATGATATTATATAAAAATGAATAATAAAA-ATAT-AAA-TATAAT
9523156 AATAAATAAAA-ATAAAATATATGACAT
62 AA-AAATAAAATATAAAATATATGACAT
* * * *
9523183 TAAAA-ATATATTTAAAATATGATATTATATAAAAATTAATAATAAAAATATAAATATATTAAAA
1 TAAAATATATATATAAAAAATGATATTATATAAAAATGAATAATAAAAATATAAATATAATAAAA
9523247 ATAAAATATAAAATAT
66 ATAAAATATAAAATAT
9523263 TATAATAATA
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
86 17 0.24
87 26 0.37
88 9 0.13
89 11 0.16
90 7 0.10
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (88 bp):
TAAAATATATATATAAAAAATGATATTATATAAAAATGAATAATAAAAATATAAATATAATAAAA
ATAAAATATAAAATATATGACAT
Found at i:9523271 original size:113 final size:113
Alignment explanation
Indices: 9523131--9523358 Score: 424
Period size: 113 Copynumber: 2.0 Consensus size: 113
9523121 TAAAGAAATG
9523131 AAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
9523196 AA-AATATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
66 AAGAA-ATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
9523244 AAAATAAAATATA-AAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATT
1 AAAATAAAATATATAAA-ATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATT
9523308 TAAGAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
65 TAAGAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
9523357 AA
1 AA
9523359 CTTATATTTT
Statistics
Matches: 113, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
112 3 0.03
113 108 0.96
114 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (113 bp):
AAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
AAGAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
Found at i:9523523 original size:15 final size:15
Alignment explanation
Indices: 9523503--9523547 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
9523493 TGTTATTTTC
*
9523503 CTTGCAATCACATTG
1 CTTGCAATCACATTA
9523518 CTTGCAATCACATTA
1 CTTGCAATCACATTA
*
9523533 CTTACAATCACATTA
1 CTTGCAATCACATTA
9523548 TCTGTAATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (15 bp):
CTTGCAATCACATTA
Found at i:9525448 original size:10 final size:8
Alignment explanation
Indices: 9525420--9525459 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
9525410 CTTTCTCGTT
9525420 TCTCTCTTA
1 TCTCTC-TA
*
9525429 TCTCTCTC
1 TCTCTCTA
*
9525437 TCTCTCCA
1 TCTCTCTA
9525445 TCTCTCTA
1 TCTCTCTA
9525453 TCTCTCT
1 TCTCTCT
9525460 GGGTGTACCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
8 21 0.78
9 6 0.22
ACGTcount: A:0.07, C:0.42, G:0.00, T:0.50
Consensus pattern (8 bp):
TCTCTCTA
Found at i:9537733 original size:47 final size:47
Alignment explanation
Indices: 9537664--9537759 Score: 156
Period size: 47 Copynumber: 2.0 Consensus size: 47
9537654 TGTGTTTCCC
*
9537664 TCAGCCTGGTTTTGGCAGCCCTTCTCTTCAATTTTATGGATAAACTA
1 TCAGCCTGGTTTTGACAGCCCTTCTCTTCAATTTTATGGATAAACTA
* **
9537711 TCAGCCTGGTTTTGATAGCCCTTCTCTTGGATTTTATGGATAAACTA
1 TCAGCCTGGTTTTGACAGCCCTTCTCTTCAATTTTATGGATAAACTA
9537758 TC
1 TC
9537760 TGTTGGCAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.40
Consensus pattern (47 bp):
TCAGCCTGGTTTTGACAGCCCTTCTCTTCAATTTTATGGATAAACTA
Found at i:9548767 original size:22 final size:23
Alignment explanation
Indices: 9548739--9548799 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
9548729 AAAAAATTAT
9548739 TAATATTTATATTATATA-TGAA
1 TAATATTTATATTATATATTGAA
* *
9548761 TAATATTTATATAAAATATATTGCA
1 TAATATTTATAT--TATATATTGAA
9548786 T-ATATTTATATTAT
1 TAATATTTATATTAT
9548800 GTTTAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 14 0.42
24 15 0.45
25 4 0.12
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (23 bp):
TAATATTTATATTATATATTGAA
Found at i:9570505 original size:6 final size:6
Alignment explanation
Indices: 9570494--9570518 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9570484 CTTGTTTAGT
9570494 ACAATC ACAATC ACAATC ACAATC A
1 ACAATC ACAATC ACAATC ACAATC A
9570519 TACTTACTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (6 bp):
ACAATC
Found at i:9572917 original size:22 final size:22
Alignment explanation
Indices: 9572869--9572917 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
9572859 TATTACGTTC
*
9572869 AATTAAACATATATATTTTTAT
1 AATTAAACAGATATATTTTTAT
*
9572891 -TTTAAATCAGATA-ATTTTTAT
1 AATTAAA-CAGATATATTTTTAT
9572912 AATTAA
1 AATTAA
9572918 TAGTTAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (22 bp):
AATTAAACAGATATATTTTTAT
Found at i:9590025 original size:13 final size:13
Alignment explanation
Indices: 9590007--9590034 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
9589997 TTCACATTAC
9590007 TGTGGATGTGATG
1 TGTGGATGTGATG
9590020 TGTGGATGTGATG
1 TGTGGATGTGATG
9590033 TG
1 TG
9590035 AACTGTAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.46, T:0.39
Consensus pattern (13 bp):
TGTGGATGTGATG
Found at i:9597219 original size:13 final size:13
Alignment explanation
Indices: 9597201--9597226 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9597191 TATATATATA
9597201 TATTTATTTATTG
1 TATTTATTTATTG
9597214 TATTTATTTATTG
1 TATTTATTTATTG
9597227 AAAGGGAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (13 bp):
TATTTATTTATTG
Found at i:9612726 original size:43 final size:44
Alignment explanation
Indices: 9612678--9612769 Score: 132
Period size: 43 Copynumber: 2.1 Consensus size: 44
9612668 CCTGACATTC
* *
9612678 TTTTACGATGCTAATCATGTAATTGCTACATTCACAAAAGCC-A
1 TTTTACAATGCCAATCATGTAATTGCTACATTCACAAAAGCCAA
* * *
9612721 TTTTACAATGCCAATTATGTACTTGCTACATTTACAAAAGCCAA
1 TTTTACAATGCCAATCATGTAATTGCTACATTCACAAAAGCCAA
9612765 TTTTA
1 TTTTA
9612770 GATTTATTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 37 0.86
44 6 0.14
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.36
Consensus pattern (44 bp):
TTTTACAATGCCAATCATGTAATTGCTACATTCACAAAAGCCAA
Found at i:9638108 original size:25 final size:25
Alignment explanation
Indices: 9638080--9638156 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 25
9638070 ATGTGAGCTT
9638080 TCATATTGTTCTGATGAGATCTTGG
1 TCATATTGTTCTGATGAGATCTTGG
* * * * *
9638105 TCATGTGGATGTGATGTGATCTT--
1 TCATATTGTTCTGATGAGATCTTGG
* *
9638128 TCACATTGTTCTGGTGAGATCTTGG
1 TCATATTGTTCTGATGAGATCTTGG
9638153 TCAT
1 TCAT
9638157 GTGGATGTGA
Statistics
Matches: 37, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
23 16 0.43
25 21 0.57
ACGTcount: A:0.18, C:0.13, G:0.26, T:0.43
Consensus pattern (25 bp):
TCATATTGTTCTGATGAGATCTTGG
Found at i:9638136 original size:48 final size:48
Alignment explanation
Indices: 9638069--9638170 Score: 177
Period size: 48 Copynumber: 2.1 Consensus size: 48
9638059 GCACCAGTTC
*
9638069 GATGTGAGCTTTCATATTGTTCTGATGAGATCTTGGTCATGTGGATGT
1 GATGTGAGCTTTCACATTGTTCTGATGAGATCTTGGTCATGTGGATGT
* *
9638117 GATGTGATCTTTCACATTGTTCTGGTGAGATCTTGGTCATGTGGATGT
1 GATGTGAGCTTTCACATTGTTCTGATGAGATCTTGGTCATGTGGATGT
9638165 GATGTG
1 GATGTG
9638171 TGACCTTGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.18, C:0.11, G:0.30, T:0.41
Consensus pattern (48 bp):
GATGTGAGCTTTCACATTGTTCTGATGAGATCTTGGTCATGTGGATGT
Found at i:9638397 original size:53 final size:53
Alignment explanation
Indices: 9638334--9638436 Score: 197
Period size: 53 Copynumber: 1.9 Consensus size: 53
9638324 TTTTTGAGTT
9638334 CCAAAGTTGGAACCAAAGACTCTGAAGGAGAGGTGAAGAAGATCAACCAAGGG
1 CCAAAGTTGGAACCAAAGACTCTGAAGGAGAGGTGAAGAAGATCAACCAAGGG
*
9638387 CCAAAGTTGGAACCAAAGACTTTGAAGGAGAGGTGAAGAAGATCAACCAA
1 CCAAAGTTGGAACCAAAGACTCTGAAGGAGAGGTGAAGAAGATCAACCAA
9638437 AGACTTTGAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.43, C:0.17, G:0.28, T:0.13
Consensus pattern (53 bp):
CCAAAGTTGGAACCAAAGACTCTGAAGGAGAGGTGAAGAAGATCAACCAAGGG
Found at i:9638440 original size:34 final size:34
Alignment explanation
Indices: 9638397--9638461 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
9638387 CCAAAGTTGG
9638397 AACCAAAGACTTTGAAGGAGAGGTGAAGAAGATC
1 AACCAAAGACTTTGAAGGAGAGGTGAAGAAGATC
9638431 AACCAAAGACTTTGAAGGAGAGGTGAAGAAG
1 AACCAAAGACTTTGAAGGAGAGGTGAAGAAG
9638462 TTTAATCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.45, C:0.11, G:0.31, T:0.14
Consensus pattern (34 bp):
AACCAAAGACTTTGAAGGAGAGGTGAAGAAGATC
Found at i:9638591 original size:44 final size:44
Alignment explanation
Indices: 9638528--9638612 Score: 170
Period size: 44 Copynumber: 1.9 Consensus size: 44
9638518 CCCTTTGGAA
9638528 AAACTCTTAATTATACTTTATTATTAAAGCATATATAATAATCC
1 AAACTCTTAATTATACTTTATTATTAAAGCATATATAATAATCC
9638572 AAACTCTTAATTATACTTTATTATTAAAGCATATATAATAA
1 AAACTCTTAATTATACTTTATTATTAAAGCATATATAATAA
9638613 CAATCCTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (44 bp):
AAACTCTTAATTATACTTTATTATTAAAGCATATATAATAATCC
Found at i:9648790 original size:2 final size:2
Alignment explanation
Indices: 9648783--9648808 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9648773 CCCAAAACAT
9648783 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
9648809 CCGGATTATT
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):
TA
Found at i:9651847 original size:10 final size:10
Alignment explanation
Indices: 9651816--9651847 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
9651806 ACAGCATATA
9651816 TATGTGTGTG
1 TATGTGTGTG
*
9651826 TGTGTGTGTG
1 TATGTGTGTG
9651836 TATGTGTGTG
1 TATGTGTGTG
9651846 TA
1 TA
9651848 CTGACTTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.09, C:0.00, G:0.41, T:0.50
Consensus pattern (10 bp):
TATGTGTGTG
Found at i:9653531 original size:23 final size:23
Alignment explanation
Indices: 9653505--9653552 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
9653495 GGTGCAAAGG
9653505 GAGAACTGTCATGTAACAAAACA
1 GAGAACTGTCATGTAACAAAACA
9653528 GAGAACTGTCATGTAACAAAACA
1 GAGAACTGTCATGTAACAAAACA
9653551 GA
1 GA
9653553 ATCATCTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.48, C:0.17, G:0.19, T:0.17
Consensus pattern (23 bp):
GAGAACTGTCATGTAACAAAACA
Found at i:9656996 original size:21 final size:21
Alignment explanation
Indices: 9656971--9657025 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
9656961 AACAGCAAGC
9656971 CCAGCGCTGCAGCTCAAGCTT
1 CCAGCGCTGCAGCTCAAGCTT
9656992 CCAGCGCTGCAGCTCAAGCTT
1 CCAGCGCTGCAGCTCAAGCTT
9657013 CCAGCGCTGCAGC
1 CCAGCGCTGCAGC
9657026 ACCGTCCTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.18, C:0.40, G:0.25, T:0.16
Consensus pattern (21 bp):
CCAGCGCTGCAGCTCAAGCTT
Found at i:9678484 original size:3 final size:3
Alignment explanation
Indices: 9678472--9678506 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
9678462 AAAATGAAAT
9678472 GAA G-A GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
9678507 TAAATCGTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:9686639 original size:3 final size:3
Alignment explanation
Indices: 9686633--9686667 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
9686623 AGAAAAAAAG
*
9686633 TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9686668 TATTTTTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:9699702 original size:47 final size:47
Alignment explanation
Indices: 9699633--9699729 Score: 176
Period size: 47 Copynumber: 2.1 Consensus size: 47
9699623 TTTTTTGTTA
* *
9699633 TGATGAACAGATTTGTAGGAATATTTCTAATGTGTTCTTGACTACAT
1 TGATGAACAGATTTGTAGGAATAATTCTAACGTGTTCTTGACTACAT
9699680 TGATGAACAGATTTGTAGGAATAATTCTAACGTGTTCTTGACTACAT
1 TGATGAACAGATTTGTAGGAATAATTCTAACGTGTTCTTGACTACAT
9699727 TGA
1 TGA
9699730 CTCAGATTCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (47 bp):
TGATGAACAGATTTGTAGGAATAATTCTAACGTGTTCTTGACTACAT
Found at i:9706482 original size:12 final size:12
Alignment explanation
Indices: 9706442--9706476 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
9706432 AACCAAGGGA
*
9706442 AAGGAAAAGAAG
1 AAGGAGAAGAAG
*
9706454 AAGAAGAAGAAG
1 AAGGAGAAGAAG
9706466 AAGGAGAAGAA
1 AAGGAGAAGAA
9706477 AGAGGATTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
AAGGAGAAGAAG
Found at i:9723097 original size:35 final size:35
Alignment explanation
Indices: 9723029--9723097 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
9723019 TTCAGTGGCT
*
9723029 TCAGGATGGCAGCTTCTTTCCAGATTTCAGCATTG
1 TCAGGATGGCAGCTTCTTTCCAGATTGCAGCATTG
*
9723064 TCAGGATGGCAGCTTCTTTCCAGATTGCTGCATT
1 TCAGGATGGCAGCTTCTTTCCAGATTGCAGCATT
9723098 ATCACCACTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (35 bp):
TCAGGATGGCAGCTTCTTTCCAGATTGCAGCATTG
Found at i:9731949 original size:69 final size:71
Alignment explanation
Indices: 9731855--9731985 Score: 196
Period size: 69 Copynumber: 1.9 Consensus size: 71
9731845 CCAACAGGTG
* *
9731855 CGCACAGCATGGGCGAGCGGCACGCAGGCTC-GGGC-CGTCGGCCCAGCAGGGGTGCGCGGCGCG
1 CGCACAGCATGGGCGAGCGGCACGCAGGCTCAGGGCTCGCCGGCCCAGCAGGGGTGCACGGCGCG
9731918 CGGGGA
66 CGGGGA
* *
9731924 CGCAGAGCATGGGCGCA-CGGTACGCAGGCTCAGGGCTCGCCGGCCCAGCAGGGGTGCACGGC
1 CGCACAGCATGGGCG-AGCGGCACGCAGGCTCAGGGCTCGCCGGCCCAGCAGGGGTGCACGGC
9731986 ACGCAGGTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
69 27 0.49
70 5 0.09
71 23 0.42
ACGTcount: A:0.15, C:0.34, G:0.45, T:0.07
Consensus pattern (71 bp):
CGCACAGCATGGGCGAGCGGCACGCAGGCTCAGGGCTCGCCGGCCCAGCAGGGGTGCACGGCGCG
CGGGGA
Found at i:9741517 original size:26 final size:25
Alignment explanation
Indices: 9741480--9741543 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 25
9741470 TGTTATGTAC
9741480 AAAAATCTATTACACGTCATGGTT-AA
1 AAAAAT-TATTACACGTCAT-GTTGAA
*
9741506 GAAAAATTATTACACGTGATGTTGAA
1 -AAAAATTATTACACGTCATGTTGAA
9741532 AAAATATTATTA
1 AAAA-ATTATTA
9741544 TTACATGCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
25 7 0.21
26 21 0.62
27 6 0.18
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.33
Consensus pattern (25 bp):
AAAAATTATTACACGTCATGTTGAA
Found at i:9760422 original size:2 final size:2
Alignment explanation
Indices: 9760417--9760441 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9760407 CTCTGGTTTT
9760417 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 T
9760442 TATTCTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9761260 original size:4 final size:4
Alignment explanation
Indices: 9761251--9761305 Score: 51
Period size: 4 Copynumber: 13.5 Consensus size: 4
9761241 AAGATTAAAA
* *
9761251 ATTT ATTT ATGTA ATTT ATTT ATTT ATTT A--T ATTT GATGTT ATTC ATTT
1 ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT -AT-TT ATTT ATTT
9761300 ATTT AT
1 ATTT AT
9761306 AACATGTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
2 2 0.05
4 31 0.74
5 7 0.17
6 2 0.05
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.65
Consensus pattern (4 bp):
ATTT
Found at i:9761268 original size:13 final size:13
Alignment explanation
Indices: 9761250--9761301 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
9761240 AAAGATTAAA
9761250 AATTTATTTATGT
1 AATTTATTTATGT
*
9761263 AATTTATTTATTT
1 AATTTATTTATGT
*
9761276 ATTTATATTTGATGT
1 AATT-TATTT-ATGT
* *
9761291 TATTCATTTAT
1 AATTTATTTAT
9761302 TTATAACATG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
13 17 0.55
14 9 0.29
15 5 0.16
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (13 bp):
AATTTATTTATGT
Found at i:9763609 original size:5 final size:5
Alignment explanation
Indices: 9763599--9763640 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
9763589 AGATGTCCTC
9763599 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AA
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AA
9763641 CTTACCCGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:9796218 original size:2 final size:2
Alignment explanation
Indices: 9796211--9796236 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9796201 TCATTAGTAG
9796211 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
9796237 GTGGTGAGTA
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:9806752 original size:2 final size:2
Alignment explanation
Indices: 9806745--9806773 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9806735 CTGCAATAAC
9806745 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 T
9806774 CACATACAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9827325 original size:222 final size:222
Alignment explanation
Indices: 9826928--9827371 Score: 676
Period size: 222 Copynumber: 2.0 Consensus size: 222
9826918 TTTTGGTTCA
*
9826928 CAGGTTGGTTACCATCCTGACTTTGAAGGCTCAAGATGTTTGTTCATAGTTCGAAAAGATGGAGA
1 CAGGTTGGTTACCATCCTGACTTTGAAGGCTCAAGATGTTTGTTCATAGTTCGAAAAGACGGAGA
*
9826993 AATGGTTGACTTTTCTTACTGGAAATGCATCAAAGGCCTGATCAGAAAAAACTATCCTCTATATG
66 AATGGTTGACTGTTCTTACTGGAAATGCATCAAAGGCCTGATCAGAAAAAACTATCCTCTATATG
* * * *
9827058 CGGACAGCTTCATTCTCAGACATTTTCGACGGCGTAGACGGAGTTGATGAGGGTAATA-TTCTGA
131 CAGACAGCTTCATTCTCAGACATTTTCGACAGCATAGACGGAGTTGACGAGGGTAATACTT-TGA
9827122 ACTTGTCAACCACTTTATGTTATTATGT
195 ACTTGTCAACCACTTTATGTTATTATGT
* * * *
9827150 CAGGTTGGTTGCCATCCTGACTTTGAAGGCTTAAGATGTTTGTTCATAGTTTGGAAAGACGGAGA
1 CAGGTTGGTTACCATCCTGACTTTGAAGGCTCAAGATGTTTGTTCATAGTTCGAAAAGACGGAGA
* * * *
9827215 ACTGGTTGACTGTTCTTGCTGGAAATGCATCAAAGGCCTGATCAGGAAAAACTATCCTCTCTATG
66 AATGGTTGACTGTTCTTACTGGAAATGCATCAAAGGCCTGATCAGAAAAAACTATCCTCTATATG
* * * * *
9827280 TAGACTGCTTTATTCTCAGACA-TTTCTGACAGCATAGATGGAGTTGACGAGGTTAATACTTTGA
131 CAGACAGCTTCATTCTCAGACATTTTC-GACAGCATAGACGGAGTTGACGAGGGTAATACTTTGA
*
9827344 ACTTGTCAACCACTTTATGTTGTTATGT
195 ACTTGTCAACCACTTTATGTTATTATGT
9827372 TTAGAGGATT
Statistics
Matches: 200, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
221 4 0.02
222 194 0.97
223 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (222 bp):
CAGGTTGGTTACCATCCTGACTTTGAAGGCTCAAGATGTTTGTTCATAGTTCGAAAAGACGGAGA
AATGGTTGACTGTTCTTACTGGAAATGCATCAAAGGCCTGATCAGAAAAAACTATCCTCTATATG
CAGACAGCTTCATTCTCAGACATTTTCGACAGCATAGACGGAGTTGACGAGGGTAATACTTTGAA
CTTGTCAACCACTTTATGTTATTATGT
Found at i:9832865 original size:15 final size:15
Alignment explanation
Indices: 9832845--9832873 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9832835 AAAAATTGGT
9832845 TGCTGCTGTTGCTGG
1 TGCTGCTGTTGCTGG
9832860 TGCTGCTGTTGCTG
1 TGCTGCTGTTGCTG
9832874 TTGAGTTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.21, G:0.38, T:0.41
Consensus pattern (15 bp):
TGCTGCTGTTGCTGG
Found at i:9857873 original size:2 final size:2
Alignment explanation
Indices: 9857863--9857898 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
9857853 GGGGAGAGAA
*
9857863 AT AT GT 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
9857899 TCCTTTAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9859535 original size:2 final size:2
Alignment explanation
Indices: 9859530--9859554 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9859520 AGCCATTTCC
9859530 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 T
9859555 CTAAAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9863290 original size:2 final size:2
Alignment explanation
Indices: 9863267--9863308 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
9863257 AATAAAATAA
*
9863267 AT AT TT AT AT -T AT AT CAT 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
9863309 GATCTTATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:9883731 original size:2 final size:2
Alignment explanation
Indices: 9883724--9883763 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
9883714 ATGATGCTGA
*
9883724 CT CT CT CT CT CT CT CA CT -T CAT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT CT CT CT
9883764 ATATATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.05, C:0.47, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:9897502 original size:23 final size:24
Alignment explanation
Indices: 9897466--9897514 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 24
9897456 ATAAAGATGA
9897466 TTTTAAATTCAAATT-ATTAAATT
1 TTTTAAATTCAAATTAATTAAATT
9897489 TTTTAAAATT-AAATTAAATTAAATT
1 TTTT-AAATTCAAATT-AATTAAATT
9897514 T
1 T
9897515 GAATGAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 9 0.39
24 5 0.22
25 9 0.39
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTTAAATTCAAATTAATTAAATT
Found at i:9921988 original size:15 final size:14
Alignment explanation
Indices: 9921967--9922001 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
9921957 TTCTCAAGAA
9921967 AAGAAAGAGAGAAAG
1 AAGAAAGAGA-AAAG
*
9921982 GAGAAAGAGAAAAG
1 AAGAAAGAGAAAAG
9921996 AAGAAA
1 AAGAAA
9922002 ACAAAAACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (14 bp):
AAGAAAGAGAAAAG
Found at i:9922405 original size:31 final size:31
Alignment explanation
Indices: 9922370--9922453 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 31
9922360 TACTTATATT
**
9922370 TTCTGAAGGAAAATTCCTGATAATTTGATTC
1 TTCTGAAGGAAAATTCCTGATAATTAAATTC
* * *
9922401 TTCTGAAGCAAAACTGCATGATAATTAAATTC
1 TTCTGAAGGAAAA-TTCCTGATAATTAAATTC
* *
9922433 TTCCGAA-GCAAATTCCTGATA
1 TTCTGAAGGAAAATTCCTGATA
9922454 TTAGCACATG
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
30 7 0.17
31 15 0.36
32 20 0.48
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (31 bp):
TTCTGAAGGAAAATTCCTGATAATTAAATTC
Found at i:9926300 original size:17 final size:17
Alignment explanation
Indices: 9926280--9926318 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
9926270 ATTTTATATA
9926280 ATTAAAT-ATATAAAATT
1 ATTAAATAAT-TAAAATT
9926297 ATTAAATAATTAAAATT
1 ATTAAATAATTAAAATT
9926314 ATTAA
1 ATTAA
9926319 TTTTTTTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAAATAATTAAAATT
Found at i:9926303 original size:8 final size:8
Alignment explanation
Indices: 9926260--9926318 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
9926250 CATTAGTAAC
9926260 TAAATTAT
1 TAAATTAT
9926268 T-AATT-T
1 TAAATTAT
* *
9926274 TATATAAT
1 TAAATTAT
9926282 TAAATATAT
1 TAAAT-TAT
*
9926291 AAAATTAT
1 TAAATTAT
*
9926299 TAAATAAT
1 TAAATTAT
9926307 TAAAATTAT
1 T-AAATTAT
9926316 TAA
1 TAA
9926319 TTTTTTTCTA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
6 2 0.05
7 6 0.15
8 18 0.46
9 13 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
TAAATTAT
Found at i:9932733 original size:5 final size:5
Alignment explanation
Indices: 9932723--9932749 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
9932713 AAGGGGCTGC
9932723 TGGCA TGGCA TGGCA TGGCA TGGCA TG
1 TGGCA TGGCA TGGCA TGGCA TGGCA TG
9932750 AGCGTGTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.41, T:0.22
Consensus pattern (5 bp):
TGGCA
Found at i:9933601 original size:2 final size:2
Alignment explanation
Indices: 9933594--9933618 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9933584 TTCCTTTCTT
9933594 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 T
9933619 TGTGCAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9935762 original size:2 final size:2
Alignment explanation
Indices: 9935755--9935784 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9935745 AAATTAAAGA
9935755 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
9935785 TCTTCAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9938534 original size:5 final size:5
Alignment explanation
Indices: 9938524--9938550 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
9938514 TTGCATTACT
9938524 TTCCC TTCCC TTCCC TTCCC TTCCC TT
1 TTCCC TTCCC TTCCC TTCCC TTCCC TT
9938551 TGTGTAGTGC
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:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (5 bp):
TTCCC
Found at i:9946348 original size:2 final size:2
Alignment explanation
Indices: 9946341--9946366 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9946331 TACAACTATC
9946341 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
9946367 AACCCTCCGT
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):
TA
Found at i:9948156 original size:2 final size:2
Alignment explanation
Indices: 9948149--9948179 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
9948139 TTTTGAAATA
*
9948149 TG TG TG TG TG TG TG TG TG TG TG TT TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
9948180 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55
Consensus pattern (2 bp):
TG
Found at i:9954824 original size:2 final size:2
Alignment explanation
Indices: 9954817--9954846 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
9954807 CCCTCTCCCC
9954817 CT CT CT CT CT CT CT CT CT CT CT CT -T CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
9954847 CTTTGAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:9968049 original size:10 final size:9
Alignment explanation
Indices: 9968027--9968052 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
9968017 TTGCTGTAGG
9968027 AAAAAGGGT
1 AAAAAGGGT
9968036 AAAAAGGGT
1 AAAAAGGGT
9968045 AAAAAGGG
1 AAAAAGGG
9968053 AAAGAGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.35, T:0.08
Consensus pattern (9 bp):
AAAAAGGGT
Found at i:9987960 original size:16 final size:16
Alignment explanation
Indices: 9987941--9987975 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9987931 AATTATTACG
9987941 TAAAAATAAAATAAAA
1 TAAAAATAAAATAAAA
* *
9987957 TAAAAATATAATATAA
1 TAAAAATAAAATAAAA
9987973 TAA
1 TAA
9987976 TTATTACGTA
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAAATAAAATAAAA
Found at i:9988006 original size:43 final size:44
Alignment explanation
Indices: 9987926--9988025 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 44
9987916 TGATCTGAAT
* *
9987926 AAAACAATTATTACGTAAAAATAAAATAAAATAAAAATATAAT-
1 AAAATAATTATTACGTAAAAATAAAATAAAATAAAAATAAAATA
* * *
9987969 ATAATAATTATTACGTAAATCGATACAAT-AAAT-AAAATAAAATA
1 AAAATAATTATTACGTAAA--AATAAAATAAAATAAAAATAAAATA
9988013 AAAATAATTATTA
1 AAAATAATTATTA
9988026 TGATTTATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
43 26 0.54
44 16 0.33
45 6 0.12
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (44 bp):
AAAATAATTATTACGTAAAAATAAAATAAAATAAAAATAAAATA
Found at i:9988142 original size:101 final size:102
Alignment explanation
Indices: 9988037--9988248 Score: 220
Period size: 101 Copynumber: 2.1 Consensus size: 102
9988027 GATTTATTAC
* *
9988037 AATATTTAATTAATAATAATAATT-TTAAAATAAAAAATAA-AAAAATTAAATTACT-TTTTATT
1 AATATTTAATTAAT-ATAATAATTATTAAAAT-AAAAATAATAAAAATTAAATTA-TAATTTA-A
*
9988099 ATA-TA-TATTATTATTTTATTTATTTTATTTTT-AAATATT
62 ATACTACTATGATTATTTT-TTTATTTTATTTTTAAAATATT
* * ** * * * * *
9988138 AATATTTTATTTATATTTTAATTATTAATATTAAAATAATAATATTTAATTTATAATTTAAATAC
1 AATATTTAATTAATATAATAATTATTAAAATAAAAATAATAAAAATTAAATTATAATTTAAATAC
9988203 TACTATGATTATTTTTTTATTTTATTTTTAAAATATT
66 TACTATGATTATTTTTTTATTTTATTTTTAAAATATT
9988240 AATAATTTA
1 AAT-ATTTA
9988249 TATTTTATTT
Statistics
Matches: 91, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
100 18 0.20
101 48 0.53
102 21 0.23
103 4 0.04
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (102 bp):
AATATTTAATTAATATAATAATTATTAAAATAAAAATAATAAAAATTAAATTATAATTTAAATAC
TACTATGATTATTTTTTTATTTTATTTTTAAAATATT
Found at i:9988146 original size:26 final size:26
Alignment explanation
Indices: 9988117--9988169 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
9988107 TATTATTTTA
9988117 TTTATTT-TATTTTTAAATATTAATAT
1 TTTATTTATA-TTTTAAATATTAATAT
*
9988143 TTTATTTATATTTTAATTATTAATAT
1 TTTATTTATATTTTAAATATTAATAT
9988169 T
1 T
9988170 AAAATAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTATTTATATTTTAAATATTAATAT
Found at i:9988193 original size:14 final size:14
Alignment explanation
Indices: 9988137--9988194 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
9988127 TTTTAAATAT
*
9988137 TAATATTTTATTTA
1 TAATATTTAATTTA
9988151 T-AT-TTTAA-TTA
1 TAATATTTAATTTA
* * *
9988162 TTAATATTAAAATAA
1 -TAATATTTAATTTA
9988177 TAATATTTAATTTA
1 TAATATTTAATTTA
9988191 TAAT
1 TAAT
9988195 TTAAATACTA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
11 3 0.09
12 5 0.15
13 4 0.12
14 20 0.59
15 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAATATTTAATTTA
Found at i:9988248 original size:22 final size:21
Alignment explanation
Indices: 9988223--9988339 Score: 53
Period size: 22 Copynumber: 5.3 Consensus size: 21
9988213 ATTTTTTTAT
9988223 TTTATTTTTAAAATATTAATAA
1 TTTATTTTTAAAATATTAAT-A
*
9988245 TTTATATTTTATTTATAATATAAATAA
1 TTTAT-TTTTA---A-AATATTAAT-A
* ** * *
9988272 TCTATCATTTAAATATTAGTA
1 TTTATTTTTAAAATATTAATA
* *
9988293 -TT-TTATTATAA-ATTAAT-
1 TTTATTTTTAAAATATTAATA
9988310 TATTATTTTTTAAAATATTAATA
1 T-TTA-TTTTTAAAATATTAATA
9988333 TTTATTT
1 TTTATTT
9988340 ATAATTTAAA
Statistics
Matches: 70, Mismatches: 14, Indels: 23
0.65 0.13 0.21
Matches are distributed among these distances:
18 5 0.07
19 8 0.11
20 1 0.01
21 11 0.16
22 21 0.30
23 7 0.10
26 3 0.04
27 14 0.20
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (21 bp):
TTTATTTTTAAAATATTAATA
Found at i:9988259 original size:27 final size:28
Alignment explanation
Indices: 9988220--9988281 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
9988210 ATTATTTTTT
* *
9988220 TATTTTATTTTTAAAATATTAATAATTTA
1 TATTTTA-TTTTAAAATATAAATAATCTA
*
9988249 TATTTTA-TTTATAATATAAATAATCTA
1 TATTTTATTTTAAAATATAAATAATCTA
9988276 TCATTT
1 T-ATTT
9988282 AAATATTAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 18 0.62
28 4 0.14
29 7 0.24
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.56
Consensus pattern (28 bp):
TATTTTATTTTAAAATATAAATAATCTA
Found at i:9988323 original size:19 final size:19
Alignment explanation
Indices: 9988278--9988345 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
9988268 ATAATCTATC
*
9988278 ATTTAAA-TATTAGTATTTT
1 ATTTAAATTATTAATA-TTT
*
9988297 ATTATAAATTAATTATTATTT
1 ATT-TAAATT-ATTAATATTT
*
9988318 -TTTAAAATATTAATATTT
1 ATTTAAATTATTAATATTT
9988336 ATTTATAATT
1 ATTTA-AATT
9988346 TAAATTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
18 9 0.22
19 12 0.30
20 9 0.22
21 4 0.10
22 6 0.15
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (19 bp):
ATTTAAATTATTAATATTT
Found at i:9988334 original size:18 final size:18
Alignment explanation
Indices: 9988282--9988353 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 18
9988272 TCTATCATTT
*
9988282 AAATATTAGTATTTTATTA
1 AAATATTAATATTTT-TTA
*
9988301 TAAATTAATTATTATTTTTTA
1 -AAA-T-ATTAATATTTTTTA
9988322 AAATATTAATATTTATTTA
1 AAATATTAATATTT-TTTA
*
9988341 TAAT-TTAA-ATTTT
1 AAATATTAATATTTT
9988354 ATTATGATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
16 1 0.02
17 4 0.09
18 13 0.28
19 8 0.17
20 6 0.13
21 4 0.09
22 10 0.22
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (18 bp):
AAATATTAATATTTTTTA
Found at i:9988354 original size:18 final size:18
Alignment explanation
Indices: 9988236--9988356 Score: 50
Period size: 18 Copynumber: 6.2 Consensus size: 18
9988226 ATTTTTAAAA
* *
9988236 TATTAATAATTTATATTT
1 TATTTATAATTTAAATTT
*
9988254 TATTTATAATATAAATAATCT
1 TATTTATAATTTAAAT--T-T
*
9988275 ATCATTTA-AATATTAGTATTT
1 -T-ATTTATAAT-TTA-AATTT
*
9988296 TA-TTATAAATTAATTATTAT
1 TATTTATAATTTAA--ATT-T
* *
9988316 TTTTTAAAATATT-AATATT
1 TATTTATAAT-TTAAAT-TT
9988335 TATTTATAATTTAAATTT
1 TATTTATAATTTAAATTT
9988353 TATT
1 TATT
9988357 ATGATTATTT
Statistics
Matches: 76, Mismatches: 12, Indels: 30
0.64 0.10 0.25
Matches are distributed among these distances:
18 27 0.36
19 20 0.26
20 5 0.07
21 8 0.11
22 7 0.09
23 7 0.09
24 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (18 bp):
TATTTATAATTTAAATTT
Found at i:9988362 original size:150 final size:150
Alignment explanation
Indices: 9988128--9988591 Score: 535
Period size: 151 Copynumber: 3.0 Consensus size: 150
9988118 TTATTTTATT
* *
9988128 TTTAAATATTAATATTTTATTTATATTTTAATTATTA-ATATTAAAATAATAATATTTAATTTAT
1 TTTAAATATTAATATTTTATTTATAATTTAATTATTATATTTTAAAATAATAATATTT-ATTTAT
* * *
9988192 AATTTAAATACTACTATGATTATT-TTTTTATTTTATTTTTAAAATATTAATAATTTATATTTTA
65 AATTTAAATATTATTATGATTATTATTTTTATTTTATTTTTTAAATATTAATAATTTATA-TTTA
*
9988256 TTTATAATATAAATAATCT-ATCA
129 TTTA-AATATTAATAAT-TGATCA
* * * *
9988279 TTTAAATATTAGTATTTTA-TTATAAATTAATTATTATTTTTTAAAATATTAATATTTATTTATA
1 TTTAAATATTAATATTTTATTTATAATTTAATTATTATATTTTAAAATAATAATATTTATTTATA
* *
9988343 ATTTAAATTTTATTATGATTATTTATTTTTATTTAATTTAATTTTTTTAATATTAATAATTTATA
66 ATTTAAATATTATTATGATTA-TTATTTTTA--T--TTT-ATTTTTTAAATATTAATAATTTATA
*
9988408 -TT-TTTAAATATTAATAATTGATTA
125 TTTATTTAAATATTAATAATTGATCA
* * * * * *
9988432 TTTAAGTATTAATATGTTATTTATAATTTAATCATTAATATTATAAAATACTACTATTTTATTTA
1 TTTAAATATTAATATTTTATTTATAATTTAATTATT-ATATTTTAAAATAATAATA-TTTATTTA
* *
9988497 TAATTTAAATGTTATTATGATTTTTTATTTTTATTTTATTTTTTAAATATTAATAATTTATAATT
64 TAATTTAAATATTATTATGA-TTATTATTTTTATTTTATTTTTTAAATATTAATAATTTAT-ATT
* * *
9988562 GATTTAAAATATTAATAATTGGTAA
127 TATTT-AAATATTAATAATTGATCA
9988587 TTTAA
1 TTTAA
9988592 TTTATAATTT
Statistics
Matches: 268, Mismatches: 28, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
150 40 0.15
151 60 0.22
152 11 0.04
153 31 0.12
154 23 0.09
155 39 0.15
156 39 0.15
157 25 0.09
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (150 bp):
TTTAAATATTAATATTTTATTTATAATTTAATTATTATATTTTAAAATAATAATATTTATTTATA
ATTTAAATATTATTATGATTATTATTTTTATTTTATTTTTTAAATATTAATAATTTATATTTATT
TAAATATTAATAATTGATCA
Found at i:9988414 original size:22 final size:21
Alignment explanation
Indices: 9988376--9988453 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 21
9988366 TATTTTTATT
9988376 TAATTTAATTTTTTTAATATTAA
1 TAATTT-A-TTTTTTAATATTAA
9988399 TAATTTATATTTTTAAATATTAA
1 TAATTTAT-TTTTT-AATATTAA
* *
9988422 TAATTGATTATTTAAGTATTAA
1 TAATTTATTTTTTAA-TATTAA
9988444 T-ATGTTATTT
1 TAAT-TTATTT
9988454 ATAATTTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
21 5 0.11
22 21 0.45
23 21 0.45
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
TAATTTATTTTTTAATATTAA
Found at i:9988454 original size:19 final size:22
Alignment explanation
Indices: 9988391--9988445 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
9988381 TAATTTTTTT
* *
9988391 AATATTAATAATTTATATTTTTA
1 AATATTAATAATTGAT-TATTTA
9988414 AATATTAATAATTGATTATTTA
1 AATATTAATAATTGATTATTTA
*
9988436 AGTATTAATA
1 AATATTAATA
9988446 TGTTATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
AATATTAATAATTGATTATTTA
Found at i:9988603 original size:27 final size:26
Alignment explanation
Indices: 9988538--9988603 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
9988528 TATTTTATTT
* *
9988538 TTTAAATATTAATAATTTATAATTGA
1 TTTAAATATTAATAATTGATAATTAA
*
9988564 TTTAAAATATTAATAATTGGTAATTTAA
1 TTT-AAATATTAATAATTGATAA-TTAA
9988592 TTTATAAT-TTAA
1 TTTA-AATATTAA
9988604 ATATTATTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 3 0.09
27 22 0.65
28 9 0.26
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (26 bp):
TTTAAATATTAATAATTGATAATTAA
Found at i:9988875 original size:27 final size:29
Alignment explanation
Indices: 9988825--9988881 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
9988815 TTAAAATATG
* *
9988825 AAAATATTAATTTTTTTAATTTTAA-TTT
1 AAAATATTAATTTTTATAAGTTTAAGTTT
9988853 AAAATATTAA-TTTTATAAGTTTAAGTTT
1 AAAATATTAATTTTTATAAGTTTAAGTTT
9988881 A
1 A
9988882 TAATTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (29 bp):
AAAATATTAATTTTTATAAGTTTAAGTTT
Found at i:9989390 original size:15 final size:15
Alignment explanation
Indices: 9989372--9989439 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
9989362 ATATTTGTAA
9989372 ATAAAATATTAATAT
1 ATAAAATATTAATAT
9989387 ATAAAAATATTAATA-
1 AT-AAAATATTAATAT
* *
9989402 AT-TAA-ATT-ATAA
1 ATAAAATATTAATAT
9989414 ATAAAATATTAATAT
1 ATAAAATATTAATAT
* *
9989429 TTAAATTATTA
1 ATAAAATATTA
9989440 CTTATTCATA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
11 3 0.07
12 5 0.12
13 4 0.09
14 3 0.07
15 16 0.37
16 12 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAAAATATTAATAT
Found at i:9989450 original size:22 final size:24
Alignment explanation
Indices: 9989420--9989463 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
9989410 ATAAATAAAA
9989420 TATTAATA-TTTAAAT-TATTACT
1 TATTAATATTTTAAATATATTACT
*
9989442 TATTCATATTTTAAATATATTA
1 TATTAATATTTTAAATATATTA
9989464 TAAAGTGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTAATATTTTAAATATATTACT
Found at i:9989457 original size:42 final size:42
Alignment explanation
Indices: 9989357--9989458 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 42
9989347 ATCCTCCCTA
9989357 TATTAATATTTGTAAATAAAATATTAATATATAAAAATATTAAT
1 TATT-ATATTT-TAAATAAAATATTAATATATAAAAATATTAAT
* * * * * *
9989401 AATTAAATTATAAATAAAATATTAATAT-TTAAATTATTACT
1 TATTATATTTTAAATAAAATATTAATATATAAAAATATTAAT
9989442 TATTCATATTTTAAATA
1 TATT-ATATTTTAAATA
9989459 TATTATAAAG
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
41 13 0.27
42 28 0.58
43 4 0.08
44 3 0.06
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (42 bp):
TATTATATTTTAAATAAAATATTAATATATAAAAATATTAAT
Found at i:9989809 original size:27 final size:28
Alignment explanation
Indices: 9989770--9989828 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
9989760 TATTAATATT
* * *
9989770 TAAATGATGAATTATTAATAT-TATAAA
1 TAAATAATCAATTATTAATATATAAAAA
9989797 TAAATAATCAATTATTAATATATAAAAA
1 TAAATAATCAATTATTAATATATAAAAA
9989825 TAAA
1 TAAA
9989829 ATAAAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (28 bp):
TAAATAATCAATTATTAATATATAAAAA
Found at i:9989847 original size:189 final size:188
Alignment explanation
Indices: 9989516--9989882 Score: 456
Period size: 189 Copynumber: 1.9 Consensus size: 188
9989506 AGACTAACAT
* * * * *
9989516 TTAAATAATCAATAAAATATTAGTATTTTATAAAATTATTAAATTATTAATAAAATATTAATATT
1 TTAAATAATAAATAAAATATGAATACTTTATAAAATTATTAAATTATAAATAAAATATTAATATT
* * * *
9989581 TAAATGATCTATTATTAATATTTTAAATAAATTATTCCCATTTAAACAATAAAATAAAATAAAAA
66 TAAATGATCAATTATTAATATTATAAATAAATTAATCCAATTTAAACAATAAAATAAAATAAAAA
* * *
9989646 TAAATAATCATAATAAAATTTTAATTATAAATAAAATATTAGTGTTTAAAAAATTAATGA
131 TAAATAATCATAATAAAA-TTTAAAT-TAAATAAAATATTAATATTTAAAAAATTAATGA
*
9989706 TTAAATTATAAATAAAATATGAATACTTTATAAACA-TA-TAAATTATAAATAAAATATTAATAT
1 TTAAATAATAAATAAAATATGAATACTTTATAAA-ATTATTAAATTATAAATAAAATATTAATAT
* * *
9989769 TTAAATGATGAATTATTAATATTATAAATAAA-TAAT-CAATTATTAATATATAAAAATAAAAT-
65 TTAAATGATCAATTATTAATATTATAAATAAATTAATCCAATT-TAAACA-AT-AAAATAAAATA
** * * *
9989831 AAAATATTTGATCATAATAATATTTAAATTAAATTAAATATTAATATTTAAA
127 AAAATAAATAATCATAATAAAATTTAAATTAAATAAAATATTAATATTTAAA
9989883 TGATCAATTA
Statistics
Matches: 152, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
187 24 0.16
188 13 0.09
189 73 0.48
190 41 0.27
191 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (188 bp):
TTAAATAATAAATAAAATATGAATACTTTATAAAATTATTAAATTATAAATAAAATATTAATATT
TAAATGATCAATTATTAATATTATAAATAAATTAATCCAATTTAAACAATAAAATAAAATAAAAA
TAAATAATCATAATAAAATTTAAATTAAATAAAATATTAATATTTAAAAAATTAATGA
Found at i:9989883 original size:19 final size:22
Alignment explanation
Indices: 9989859--9989906 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
9989849 AATATTTAAA
9989859 TTAAAT-T-AAATATTAATA-T
1 TTAAATATCAAATATTAATATT
*
9989878 TTAAATGATCAATTATTAATATT
1 TTAAAT-ATCAAATATTAATATT
9989901 TTAAAT
1 TTAAAT
9989907 GCATTATCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 6 0.25
21 1 0.04
22 10 0.42
23 7 0.29
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTAAATATCAAATATTAATATT
Found at i:9990087 original size:22 final size:24
Alignment explanation
Indices: 9990025--9990129 Score: 103
Period size: 22 Copynumber: 4.4 Consensus size: 24
9990015 AAATGAAATA
*
9990025 AATA-TTAA-TATTATAAAATATT
1 AATATTTAATTATTATAAATTATT
* *
9990047 AATGA-TAAATTATAAATAAATTATT
1 AAT-ATTTAATTAT-TATAAATTATT
9990072 AATATTTAA-T-TTATAAATTATT
1 AATATTTAATTATTATAAATTATT
9990094 AATATTTTAATTAAGTTATAAATTATT
1 AATA-TTTAATT-A-TTATAAATTATT
9990121 AATATTTAA
1 AATATTTAA
9990130 AAATAAAATA
Statistics
Matches: 69, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
22 17 0.25
23 10 0.14
24 6 0.09
25 15 0.22
26 5 0.07
27 16 0.23
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
AATATTTAATTATTATAAATTATT
Found at i:9990112 original size:27 final size:23
Alignment explanation
Indices: 9990062--9990127 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 23
9990052 TAAATTATAA
9990062 ATAAATTATTAATA-TTTAATTT
1 ATAAATTATTAATATTTTAATTT
9990084 ATAAATTATTAATATTTTAATTAAGTT
1 ATAAATTATTAATATTTTAA-T---TT
9990111 ATAAATTATTAATATTT
1 ATAAATTATTAATATTT
9990128 AAAAATAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
22 14 0.36
23 5 0.13
24 1 0.03
27 19 0.49
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATAAATTATTAATATTTTAATTT
Found at i:9990138 original size:22 final size:23
Alignment explanation
Indices: 9990062--9990138 Score: 77
Period size: 22 Copynumber: 3.3 Consensus size: 23
9990052 TAAATTATAA
**
9990062 ATAAATTATTAATATTT-AATTT
1 ATAAATTATTAATATTTAAAAAT
*
9990084 ATAAATTATTAATATTTTAATTAAGTT
1 ATAAATTATTAATA-TTTAA--AA-AT
9990111 ATAAATTATTAATATTTAAAAAT
1 ATAAATTATTAATATTTAAAAAT
9990134 A-AAAT
1 ATAAAT
9990139 AAAATAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
22 18 0.38
23 5 0.10
24 3 0.06
26 6 0.12
27 16 0.33
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (23 bp):
ATAAATTATTAATATTTAAAAAT
Found at i:9990143 original size:27 final size:27
Alignment explanation
Indices: 9990083--9990170 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
9990073 ATATTTAATT
* * **
9990083 TATAAATTATTAATATTTTAATTAAGT
1 TATAAATTATTAATATTTAAAATAAAA
9990110 TATAAATTATTAATATTTAAAAATAAAA
1 TATAAATTATTAATATTT-AAAATAAAA
* * *
9990138 TA-AAATAAATAATCATATATATAATAAAA
1 TATAAATTATTAAT-AT-T-TAAAATAAAA
9990167 TATA
1 TATA
9990171 TTTTTATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
27 27 0.55
28 9 0.18
29 11 0.22
30 2 0.04
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (27 bp):
TATAAATTATTAATATTTAAAATAAAA
Found at i:9999432 original size:21 final size:21
Alignment explanation
Indices: 9999408--9999451 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
9999398 CCAATTATTA
*
9999408 AACTTGAATTGTTACAAATGG
1 AACTTGAATCGTTACAAATGG
9999429 AACTTGAATCGTTACAAATGG
1 AACTTGAATCGTTACAAATGG
9999450 AA
1 AA
9999452 AGGTAAGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (21 bp):
AACTTGAATCGTTACAAATGG
Found at i:9999948 original size:52 final size:51
Alignment explanation
Indices: 9999838--9999971 Score: 151
Period size: 52 Copynumber: 2.6 Consensus size: 51
9999828 CTTCATCAGA
* * * *
9999838 AAGAAAAACGTTTAAGCATTTTGAGCATTTCGGAGTAATTCTTGATACGTC
1 AAGAAAAACCTTTAAGCATTTTAAGCATTTTGGAGTAATTCTTGATACATC
* * * * * *
9999889 AAAAAAAACTTTTGAGCATTTTTAAGCATTTTGGAGTAATTTTTGATATATG
1 AAGAAAAACCTTTAAGCA-TTTTAAGCATTTTGGAGTAATTCTTGATACATC
* *
9999941 AAGAAAAACCTTTAAACATTTTAAACATTTT
1 AAGAAAAACCTTTAAGCATTTTAAGCATTTT
9999972 TTGTTAAATA
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
51 27 0.40
52 41 0.60
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.37
Consensus pattern (51 bp):
AAGAAAAACCTTTAAGCATTTTAAGCATTTTGGAGTAATTCTTGATACATC
Found at i:10000097 original size:22 final size:22
Alignment explanation
Indices: 10000072--10000115 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
10000062 GCTTTGATGC
* * *
10000072 TTTTTAAGTATTGCGTGACTAA
1 TTTTTAAGCATTACGGGACTAA
10000094 TTTTTAAGCATTACGGGACTAA
1 TTTTTAAGCATTACGGGACTAA
10000116 CTTTAGATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (22 bp):
TTTTTAAGCATTACGGGACTAA
Found at i:10000151 original size:23 final size:22
Alignment explanation
Indices: 10000125--10000177 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
10000115 ACTTTAGATG
*
10000125 TTACGTGACTGATTGATATGGCA
1 TTACGTGACTGATTG-TAAGGCA
* *
10000148 TTACATGACTTATTGTAAGGCA
1 TTACGTGACTGATTGTAAGGCA
*
10000170 TTGCGTGA
1 TTACGTGA
10000178 GGGATTGTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (22 bp):
TTACGTGACTGATTGTAAGGCA
Found at i:10005232 original size:29 final size:28
Alignment explanation
Indices: 10005192--10005249 Score: 64
Period size: 29 Copynumber: 2.0 Consensus size: 28
10005182 GATGAAATTT
*
10005192 AAAAAAGAAGAA-GAAAAAAGCAAAAGAA
1 AAAAAAAAAGAACGAAAAAAGC-AAAGAA
**
10005220 AAAAAAAACAGAACTCAAAAAGCAAAGAA
1 AAAAAAAA-AGAACGAAAAAAGCAAAGAA
10005249 A
1 A
10005250 GAATGTGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 7 0.28
29 11 0.44
30 7 0.28
ACGTcount: A:0.76, C:0.09, G:0.14, T:0.02
Consensus pattern (28 bp):
AAAAAAAAAGAACGAAAAAAGCAAAGAA
Found at i:10010235 original size:20 final size:20
Alignment explanation
Indices: 10010210--10010247 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10010200 TATTATTTTT
10010210 AAAAATTAA-TAATGAAAACA
1 AAAAATTAAGTAAT-AAAACA
10010230 AAAAATTAAGTAATAAAA
1 AAAAATTAAGTAATAAAA
10010248 AACGTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAAATTAAGTAATAAAACA
Found at i:10020809 original size:2 final size:2
Alignment explanation
Indices: 10020802--10020834 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
10020792 TTTCCCTAAT
10020802 TA TA TA TA TA TA TA TA TA TA TA TA -A TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10020835 GTATGTTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:10032199 original size:20 final size:21
Alignment explanation
Indices: 10032160--10032199 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10032150 TTTCTTCTTT
*
10032160 ATCTGTTTCTTTTCAGAAGCA
1 ATCTGTTTCTTTCCAGAAGCA
10032181 ATCTGTTTCTTTCCA-AAGC
1 ATCTGTTTCTTTCCAGAAGC
10032200 CTTTTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (21 bp):
ATCTGTTTCTTTCCAGAAGCA
Found at i:10048547 original size:2 final size:2
Alignment explanation
Indices: 10048540--10048571 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10048530 CTCTTTCATC
10048540 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
10048572 TGCCTCAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10056528 original size:15 final size:15
Alignment explanation
Indices: 10056508--10056537 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10056498 AAACAAGTGG
10056508 AATAGAGAGAAGAGA
1 AATAGAGAGAAGAGA
*
10056523 AATAGAGGGAAGAGA
1 AATAGAGAGAAGAGA
10056538 CCAGAAAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.37, T:0.07
Consensus pattern (15 bp):
AATAGAGAGAAGAGA
Found at i:10067269 original size:29 final size:31
Alignment explanation
Indices: 10067223--10067294 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 31
10067213 TGTAATAAAA
* * *
10067223 TTTTTTCACCATAGCGTATAATAA-CAT-TT
1 TTTTTTCAACATAACGTATAATAATAATATT
*
10067252 TTTTTTCAATATAACGTATAATAATAATATT
1 TTTTTTCAACATAACGTATAATAATAATATT
*
10067283 TTTTTTCTACAT
1 TTTTTTCAACAT
10067295 GATTTGTAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 21 0.60
30 2 0.06
31 12 0.34
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.50
Consensus pattern (31 bp):
TTTTTTCAACATAACGTATAATAATAATATT
Found at i:10067974 original size:17 final size:18
Alignment explanation
Indices: 10067947--10067992 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
10067937 TAAAAAACTC
10067947 TTTAAAAAA-AATATTTTTT
1 TTTAAAAAATAA-A-TTTTT
10067966 TTTAAAAAATAAATTTTT
1 TTTAAAAAATAAATTTTT
10067984 TTTAAAAAA
1 TTTAAAAAA
10067993 AGAGCTTCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.54
19 10 0.38
20 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTAAAAAATAAATTTTT
Found at i:10067974 original size:18 final size:19
Alignment explanation
Indices: 10067947--10067993 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
10067937 TAAAAAACTC
*
10067947 TTTAAAAAAA-ATATTTTT
1 TTTAAAAAAATAAATTTTT
*
10067965 TTTTAAAAAATAAATTTTT
1 TTTAAAAAAATAAATTTTT
10067984 TTTAAAAAAA
1 TTTAAAAAAA
10067994 GAGCTTCAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTAAAAAAATAAATTTTT
Done.