Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000913.1 Hibiscus syriacus cultivar Beakdansim tig00001818_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: 1610646
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1456098 original size:19 final size:18
Alignment explanation
Indices: 1456053--1456105 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
1456043 GCCCTAAATT
1456053 AAAAAAAAAG-AAAAAGA
1 AAAAAAAAAGAAAAAAGA
*
1456070 ACAAAGAAAAGAAAAAAGA
1 A-AAAAAAAAGAAAAAAGA
1456089 GAAAATAAAAAGAAAAA
1 -AAAA-AAAAAGAAAAA
1456106 TAAGGTGGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 1 0.03
18 8 0.27
19 10 0.33
20 11 0.37
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAAGA
Found at i:1456100 original size:25 final size:25
Alignment explanation
Indices: 1456056--1456104 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1456046 CTAAATTAAA
1456056 AAAAAAGAAAAAGAACAAAGAAAAG
1 AAAAAAGAAAAAGAACAAAGAAAAG
*
1456081 AAAAAAGAGAAAATAA-AAAGAAAA
1 AAAAAAGA-AAAAGAACAAAGAAAA
1456105 ATAAGGTGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (25 bp):
AAAAAAGAAAAAGAACAAAGAAAAG
Found at i:1456108 original size:12 final size:11
Alignment explanation
Indices: 1456053--1456105 Score: 61
Period size: 13 Copynumber: 4.4 Consensus size: 11
1456043 GCCCTAAATT
1456053 AAAAAAAAAGA
1 AAAAAAAAAGA
1456064 AAAAGAACAAAGA
1 AAAA-AA-AAAGA
1456077 AAAGAAAAAAGA
1 AAA-AAAAAAGA
1456089 GAAAATAAAAAGA
1 -AAAA-AAAAAGA
1456102 AAAA
1 AAAA
1456106 TAAGGTGGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
11 4 0.11
12 12 0.32
13 20 0.54
14 1 0.03
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:1457406 original size:120 final size:120
Alignment explanation
Indices: 1457241--1457516 Score: 381
Period size: 120 Copynumber: 2.3 Consensus size: 120
1457231 TTACATAAGA
*
1457241 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGATCAACTTCACAATGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGATCAACTTCACAACGAAGGGGCCAT
* * *
1457306 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATACAATAC
66 CCACGATTTCAACTTCACAACGAAGGATATCGTGCCCACAAGCAACATACAATAC
* * *
1457361 TTGGATTTCAACTTCACGATGAATGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGATCAACTTCACAACGAAGGGGCCAT
* * * * ** *
1457426 CCACGATTTCAATTTCACAATGAATGATATCGTGCCCACAAGCATCATCCATCTCTAGA
66 CCACGATTTCAACTTCACAACGAAGGATATCGTGCCCACAAGCAACAT--A-CAATA-C
*
1457485 TTGGATTTCAACTTCACGACGTAGGATATCCA
1 TTGGATTTCAACTTCACGACGAAGGATATCCA
1457517 GCTCAAAGAA
Statistics
Matches: 135, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
120 102 0.76
122 1 0.01
123 3 0.02
124 29 0.21
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (120 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGATCAACTTCACAACGAAGGGGCCAT
CCACGATTTCAACTTCACAACGAAGGATATCGTGCCCACAAGCAACATACAATAC
Found at i:1459033 original size:10 final size:9
Alignment explanation
Indices: 1459008--1459032 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1458998 TCGTTTTGAT
1459008 TATTTTTAC
1 TATTTTTAC
1459017 TATTTTTAC
1 TATTTTTAC
1459026 TATTTTT
1 TATTTTT
1459033 TTATTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (9 bp):
TATTTTTAC
Found at i:1459192 original size:26 final size:24
Alignment explanation
Indices: 1459140--1459187 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1459130 TTTATTTATA
1459140 TATGTATATATATTTACTAATTTT
1 TATGTATATATATTTACTAATTTT
* *
1459164 TATGTGTATATATTTA-TTATTTT
1 TATGTATATATATTTACTAATTTT
1459187 T
1 T
1459188 CTTATTATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.62
Consensus pattern (24 bp):
TATGTATATATATTTACTAATTTT
Found at i:1459274 original size:16 final size:15
Alignment explanation
Indices: 1459244--1459302 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
1459234 ATATATATTA
*
1459244 TTTATATTC-TTTTT
1 TTTATTTTCATTTTT
1459258 TTTATTTTACA-TTTT
1 TTTATTTT-CATTTTT
*
1459273 TTTATTTTTATTTTT
1 TTTATTTTCATTTTT
1459288 GTTTATGTTTC-TTTT
1 -TTTAT-TTTCATTTT
1459303 CTATTTTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 8 0.22
15 17 0.46
16 9 0.24
17 3 0.08
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (15 bp):
TTTATTTTCATTTTT
Found at i:1459287 original size:15 final size:16
Alignment explanation
Indices: 1459252--1459302 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1459242 TATTTATATT
1459252 CTTTTTTTTA-TTTTA
1 CTTTTTTTTATTTTTA
*
1459267 CATTTTTTTATTTTTA
1 CTTTTTTTTATTTTTA
*
1459283 -TTTTTGTTTATGTTT-
1 CTTTTT-TTTATTTTTA
1459298 CTTTT
1 CTTTT
1459303 CTATTTTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 13 0.43
16 17 0.57
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.78
Consensus pattern (16 bp):
CTTTTTTTTATTTTTA
Found at i:1459312 original size:12 final size:11
Alignment explanation
Indices: 1459272--1459353 Score: 60
Period size: 12 Copynumber: 7.2 Consensus size: 11
1459262 TTTTACATTT
*
1459272 TTTTATTTTTA
1 TTTTCTTTTTA
*
1459283 TTTT-TGTTTA
1 TTTTCTTTTTA
1459293 TGTTTCTTTTCTA
1 T-TTTCTTTT-TA
1459306 TTTTCTTTTTA
1 TTTTCTTTTTA
* *
1459317 GTTTCATTTTTG
1 TTTTC-TTTTTA
1459329 TTTTCTTCTCTT-
1 TTTTCTT-T-TTA
*
1459341 TTTTATTTTTA
1 TTTTCTTTTTA
1459352 TT
1 TT
1459354 CTTTTATTCT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
10 8 0.14
11 18 0.31
12 27 0.47
13 5 0.09
ACGTcount: A:0.10, C:0.09, G:0.05, T:0.77
Consensus pattern (11 bp):
TTTTCTTTTTA
Found at i:1459316 original size:40 final size:40
Alignment explanation
Indices: 1459271--1459349 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
1459261 ATTTTACATT
* * *
1459271 TTTTTATTTTTATTTTTGTTTATGTT-TCTTTTCTATTTTC
1 TTTTTAGTTTCATTTTTGTTT-TCTTCTCTTTTCTATTTTC
*
1459311 TTTTTAGTTTCATTTTTGTTTTCTTCTCTTTTTTATTTT
1 TTTTTAGTTTCATTTTTGTTTTCTTCTCTTTTCTATTTT
1459350 TATTCTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.09
40 31 0.91
ACGTcount: A:0.09, C:0.09, G:0.05, T:0.77
Consensus pattern (40 bp):
TTTTTAGTTTCATTTTTGTTTTCTTCTCTTTTCTATTTTC
Found at i:1459320 original size:23 final size:24
Alignment explanation
Indices: 1459276--1459335 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
1459266 ACATTTTTTT
*
1459276 ATTTTTATTTT-TGTTTATGTTTC
1 ATTTTTATTTTCTTTTTATGTTTC
1459299 -TTTTCTATTTTCTTTTTA-GTTTC
1 ATTTT-TATTTTCTTTTTATGTTTC
*
1459322 ATTTTTGTTTTCTT
1 ATTTTTATTTTCTT
1459336 CTCTTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 4 0.12
23 19 0.59
24 9 0.28
ACGTcount: A:0.10, C:0.08, G:0.07, T:0.75
Consensus pattern (24 bp):
ATTTTTATTTTCTTTTTATGTTTC
Found at i:1465271 original size:2 final size:2
Alignment explanation
Indices: 1465266--1465302 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1465256 GCTAAAATTC
1465266 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1465303 GCGTATTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1466184 original size:6 final size:6
Alignment explanation
Indices: 1466175--1466199 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1466165 AAATAAAAAG
1466175 GAGAAT GAGAAT GAGAAT GAGAAT G
1 GAGAAT GAGAAT GAGAAT GAGAAT G
1466200 GCAGAATGTG
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:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (6 bp):
GAGAAT
Found at i:1467569 original size:31 final size:31
Alignment explanation
Indices: 1467531--1467598 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1467521 GGGTGATCAC
*
1467531 ATCTTAATTAAATCAAAACGAAAAA-GACCAT
1 ATCTTAATTAAATAAAAAC-AAAAATGACCAT
*
1467562 ATCTTAATTAAATAAAAACAAAAATGATCAT
1 ATCTTAATTAAATAAAAACAAAAATGACCAT
1467593 ATCTTA
1 ATCTTA
1467599 TGTTTTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 5 0.15
31 29 0.85
ACGTcount: A:0.54, C:0.13, G:0.04, T:0.28
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAAAAATGACCAT
Found at i:1468983 original size:40 final size:40
Alignment explanation
Indices: 1468928--1469007 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
1468918 ATGAAGTATG
* *
1468928 TTTGCATAAAAGGATGTAAATGAGACGAGAAATATAGTAA
1 TTTGCATAAAAGGATGTAAATGAGACAAGAAAGATAGTAA
* *
1468968 TTTGCGTAAAGGGATGTAAATGAGACAAGAAAGATAGTAA
1 TTTGCATAAAAGGATGTAAATGAGACAAGAAAGATAGTAA
1469008 GTTACTCGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.46, C:0.05, G:0.25, T:0.24
Consensus pattern (40 bp):
TTTGCATAAAAGGATGTAAATGAGACAAGAAAGATAGTAA
Found at i:1471116 original size:152 final size:153
Alignment explanation
Indices: 1470924--1471213 Score: 564
Period size: 152 Copynumber: 1.9 Consensus size: 153
1470914 TTGATAGAAC
1470924 TTTATATATATATATTTTTATAAAATTTATGCTGAGCATACACTTATTTTATTTTAAATTTATTA
1 TTTATATATATATATTTTTATAAAATTTATGCTGAGCATACACTTATTTTATTTTAAATTTATTA
1470989 TGAACATGTAATGATTATTTTGTATATAATTTCAACATTTAAAATATATTTGATATATTTAAATT
66 TGAACATGTAATGATTATTTTGTATATAATTTCAACATTTAAAATATATTTGATATATTTAAATT
1471054 AAATTTTATTTTATTTTATAATA
131 AAATTTTATTTTATTTTATAATA
*
1471077 TTTATATATATAT-TTTTTATAATATTTATGCTGAGCATACACTTATTTTATTTTAAATTTATTA
1 TTTATATATATATATTTTTATAAAATTTATGCTGAGCATACACTTATTTTATTTTAAATTTATTA
1471141 TGAACATGTAATGATTATTTTGTATATAATTTCAACATTTAAAATATATTTGATATATTTAAATT
66 TGAACATGTAATGATTATTTTGTATATAATTTCAACATTTAAAATATATTTGATATATTTAAATT
1471206 AAATTTTA
131 AAATTTTA
1471214 CAAATAATAT
Statistics
Matches: 136, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
152 123 0.90
153 13 0.10
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.52
Consensus pattern (153 bp):
TTTATATATATATATTTTTATAAAATTTATGCTGAGCATACACTTATTTTATTTTAAATTTATTA
TGAACATGTAATGATTATTTTGTATATAATTTCAACATTTAAAATATATTTGATATATTTAAATT
AAATTTTATTTTATTTTATAATA
Found at i:1479437 original size:25 final size:24
Alignment explanation
Indices: 1479403--1479465 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 24
1479393 GGGCAATATT
*
1479403 TTTTTC-AAATTTTTTGATTAAATA
1 TTTTTCAAAATTTTTTAATT-AATA
*
1479427 TTTTTCAAAATTCTTTTAATTGATA
1 TTTTTCAAAATT-TTTTAATTAATA
1479452 TTTTTCAAAATTTT
1 TTTTTCAAAATTTT
1479466 AAACTCAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 8 0.23
25 20 0.57
26 7 0.20
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (24 bp):
TTTTTCAAAATTTTTTAATTAATA
Found at i:1480578 original size:25 final size:24
Alignment explanation
Indices: 1480550--1480613 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
1480540 GGGCAATATT
*
1480550 TTTTTTCAAATTTTTTGATTAAAT-A
1 TTTTTTCAAAATTTTT--TTAAATGA
*
1480575 -TTTTTCAAAATTCTTTTAAATGA
1 TTTTTTCAAAATTTTTTTAAATGA
1480598 TATTTTTCAAAATTTT
1 T-TTTTTCAAAATTTT
1480614 AAACTCAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 6 0.18
23 1 0.03
24 13 0.39
25 13 0.39
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (24 bp):
TTTTTTCAAAATTTTTTTAAATGA
Found at i:1480773 original size:24 final size:24
Alignment explanation
Indices: 1480729--1480775 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1480719 AATATAGACA
**
1480729 ATTTATGGGGTTGCTCTATTGGAC
1 ATTTATGGGGTTAATCTATTGGAC
1480753 ATTTATGGGGTATAATC-ATTGGA
1 ATTTATGGGGT-TAATCTATTGGA
1480776 TGTGTTGGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.23, C:0.09, G:0.28, T:0.40
Consensus pattern (24 bp):
ATTTATGGGGTTAATCTATTGGAC
Found at i:1488306 original size:20 final size:20
Alignment explanation
Indices: 1488281--1488330 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1488271 GGTCCTACCA
1488281 GTATCGATACTATGCTCATG
1 GTATCGATACTATGCTCATG
1488301 GTATCGATACTATGCTCATG
1 GTATCGATACTATGCTCATG
1488321 GTATCGATAC
1 GTATCGATAC
1488331 CACTATGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (20 bp):
GTATCGATACTATGCTCATG
Found at i:1490214 original size:13 final size:15
Alignment explanation
Indices: 1490183--1490218 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1490173 TAAACTCAAC
1490183 TTTATAAAAAGCATT
1 TTTATAAAAAGCATT
1490198 TTTATAAAAA-C-TT
1 TTTATAAAAAGCATT
1490211 TTTA-AAAA
1 TTTATAAAA
1490219 GTAATTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.19
13 6 0.29
14 1 0.05
15 10 0.48
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (15 bp):
TTTATAAAAAGCATT
Found at i:1497850 original size:16 final size:16
Alignment explanation
Indices: 1497826--1497865 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
1497816 AATGACTTGG
*
1497826 CACTGACTTGGATGTC
1 CACTAACTTGGATGTC
1497842 CACTAACTTGGATGTC
1 CACTAACTTGGATGTC
1497858 CACTAACT
1 CACTAACT
1497866 GTCATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (16 bp):
CACTAACTTGGATGTC
Found at i:1498430 original size:30 final size:29
Alignment explanation
Indices: 1498386--1498465 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 29
1498376 AGAAATCTTT
*
1498386 AAAAAGATGAAATTAAAGGAGTAAAATAG
1 AAAAAGATAAAATTAAAGGAGTAAAATAG
* *
1498415 AAAAAGCATAAAATTAAAGGAGTACAATAAT
1 AAAAAG-ATAAAATTAAAGGAGTAAAAT-AG
1498446 AATAATAGA-AAAATTAAAGG
1 AA-AA-AGATAAAATTAAAGG
1498466 GCTAAAGCTC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
29 6 0.14
30 19 0.43
31 14 0.32
32 3 0.07
33 2 0.05
ACGTcount: A:0.62, C:0.03, G:0.16, T:0.19
Consensus pattern (29 bp):
AAAAAGATAAAATTAAAGGAGTAAAATAG
Found at i:1498465 original size:31 final size:30
Alignment explanation
Indices: 1498386--1498443 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
1498376 AGAAATCTTT
*
1498386 AAAAAG-ATGAAATTAAAGGAGTAAAATAG
1 AAAAAGCATAAAATTAAAGGAGTAAAATAG
*
1498415 AAAAAGCATAAAATTAAAGGAGTACAATA
1 AAAAAGCATAAAATTAAAGGAGTAAAATA
1498444 ATAATAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.62, C:0.03, G:0.17, T:0.17
Consensus pattern (30 bp):
AAAAAGCATAAAATTAAAGGAGTAAAATAG
Found at i:1499889 original size:3 final size:3
Alignment explanation
Indices: 1499869--1499934 Score: 89
Period size: 3 Copynumber: 22.0 Consensus size: 3
1499859 TGCAAACATT
* *
1499869 ATA ATA ATT ATA ATTA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1499915 ACA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
1499935 TTTTTTTAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 2 0.04
3 50 0.91
4 3 0.05
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1500344 original size:131 final size:131
Alignment explanation
Indices: 1500181--1500478 Score: 339
Period size: 131 Copynumber: 2.3 Consensus size: 131
1500171 ATGAAACTGT
* * ** * *
1500181 TCCTACATGATGAGGAGATCTGGTTGTGGGATGACATAGTTCCTACGTGATGAGAATGA-CAGGC
1 TCCTACGTGATGAGGAGATCTGGTCGAAGGATGACACAGTTCCTACATGATGAGAAT-ATCAGGC
* * ** * * *
1500245 AATCATTATGGATGATAACATGGTTCCTACGTGATGACGACGGCTGATTATCTAAGGTTGACACG
65 AATCATTAGGGATGATAACACGACTCCTAAGTGATGACGACGGCTGATTATCTAAGGTTAACACA
1500310 AC
130 AC
* * *
1500312 TCCTACGTGATGAGGAGATCTGGTCGAAGGATGACACAGTTCCTACATGATGAGGATATCATGCC
1 TCCTACGTGATGAGGAGATCTGGTCGAAGGATGACACAGTTCCTACATGATGAGAATATCAGGCA
** * * *
1500377 ATTGTTAGGGATGATAACACGACTCCTAAGTGATGAGGACGGCTGGTTATCTAAGGTTAACATAA
66 ATCATTAGGGATGATAACACGACTCCTAAGTGATGACGACGGCTGATTATCTAAGGTTAACACAA
*
1500442 T
131 C
* * *
1500443 TTCTACGTGATGAGGAGGTTTGGTC-AATGGATGACA
1 TCCTACGTGATGAGGAGATCTGGTCGAA-GGATGACA
1500479 AATTATTGTG
Statistics
Matches: 140, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
130 3 0.02
131 137 0.98
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (131 bp):
TCCTACGTGATGAGGAGATCTGGTCGAAGGATGACACAGTTCCTACATGATGAGAATATCAGGCA
ATCATTAGGGATGATAACACGACTCCTAAGTGATGACGACGGCTGATTATCTAAGGTTAACACAA
C
Found at i:1500660 original size:60 final size:59
Alignment explanation
Indices: 1500512--1500864 Score: 348
Period size: 60 Copynumber: 5.7 Consensus size: 59
1500502 TATAGCTTCA
* * * * *
1500512 AAATTGACTTTAAGTTGGATATCCTTCATTGTGAAGTTGAAATCCAATCTTGTAAATTTCACC
1 AAATTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATATTG----GTTCACC
1500575 AAATTGGCTTTGAGTTGGATATCCTTCGTCT-TGAAGTTGAAATCCAAGTATTGGTTCACC
1 AAATTGGCTTTGAGTTGGATATCCTTCGT-TGTGAAGTTGAAATCCAA-TATTGGTTCACC
* *
1500635 AAATTGGTTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTGTTCCACC
1 AAATTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATATTG-GTT-CACC
* * * * * **
1500696 AAATCGGCTTTGAGTTAGATATCATTCGCTGTGAAGTTGAAATTCAAGTATTTCTTCACC
1 AAATTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAA-TATTGGTTCACC
* * * ** * *
1500756 GAATTGACTTTAAGTTGGATATCCTTCAATATGAAGTTGAAATCCAATCTTATGTAAGTTTCACC
1 AAATTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAA---TAT-T--GGTTCACC
* * *
1500821 AAATTGGTTTTGAGTTGGATATCATTCGTTGTGAAATTGAAATC
1 AAATTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATC
1500865 AAATCTCAAG
Statistics
Matches: 241, Mismatches: 38, Indels: 20
0.81 0.13 0.07
Matches are distributed among these distances:
59 5 0.02
60 94 0.39
61 47 0.20
62 6 0.02
63 43 0.18
64 5 0.02
65 41 0.17
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (59 bp):
AAATTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATATTGGTTCACC
Found at i:1500754 original size:121 final size:122
Alignment explanation
Indices: 1500512--1500864 Score: 485
Period size: 121 Copynumber: 2.9 Consensus size: 122
1500502 TATAGCTTCA
*
1500512 AAATTGACTTTAAGTTGGATATCCTTCATTGTGAAGTTGAAATCCAATCTTGTAAATTTCACCAA
1 AAATTGACTTTAAGTTGGATATCCTTCATTGTGAAGTTGAAATCCAATCTTGT-AGTTTCACCAA
* *
1500577 ATTGGCTTTGAGTTGGATATCCTTCGTCT-TGAAGTTGAAATCCAAGTATTGGTTCACC
65 ATTGGCTTTGAGTTGGATATCATTCG-CTGTGAAGTTGAAATCCAAGTATTGCTTCACC
** * * *
1500635 AAATTGGTTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGT-GTTCCACCAAA
1 AAATTGACTTTAAGTTGGATATCCTTCATTGTGAAGTTGAAATCCAATCTTGTAGTTTCACCAAA
* * * *
1500699 TCGGCTTTGAGTTAGATATCATTCGCTGTGAAGTTGAAATTCAAGTATTTCTTCACC
66 TTGGCTTTGAGTTGGATATCATTCGCTGTGAAGTTGAAATCCAAGTATTGCTTCACC
* * *
1500756 GAATTGACTTTAAGTTGGATATCCTTCAATATGAAGTTGAAATCCAATCTTATGTAAGTTTCACC
1 AAATTGACTTTAAGTTGGATATCCTTCATTGTGAAGTTGAAATCCAATC-T-TGT-AGTTTCACC
* * *
1500821 AAATTGGTTTTGAGTTGGATATCATTCGTTGTGAAATTGAAATC
63 AAATTGGCTTTGAGTTGGATATCATTCGCTGTGAAGTTGAAATC
1500865 AAATCTCAAG
Statistics
Matches: 199, Mismatches: 26, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
120 2 0.01
121 99 0.50
122 1 0.01
123 52 0.26
125 45 0.23
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (122 bp):
AAATTGACTTTAAGTTGGATATCCTTCATTGTGAAGTTGAAATCCAATCTTGTAGTTTCACCAAA
TTGGCTTTGAGTTGGATATCATTCGCTGTGAAGTTGAAATCCAAGTATTGCTTCACC
Found at i:1505157 original size:30 final size:30
Alignment explanation
Indices: 1505115--1505200 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
1505105 GAAATCTTTA
* *
1505115 AAAAG-ATGAAATTAAAGGAGTAAAATAGC
1 AAAAGTATAAAATTAAAGGACTAAAATAGC
* *
1505144 AAAAGTATAAAATTAAATGACTAAAATAGT
1 AAAAGTATAAAATTAAAGGACTAAAATAGC
* *
1505174 AATAA-TATAAAAAGTAAAGGGCTAAAA
1 AA-AAGTAT-AAAATTAAAGGACTAAAA
1505201 CACAAATATA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 5 0.11
30 25 0.53
31 17 0.36
ACGTcount: A:0.60, C:0.03, G:0.15, T:0.21
Consensus pattern (30 bp):
AAAAGTATAAAATTAAAGGACTAAAATAGC
Found at i:1506608 original size:3 final size:3
Alignment explanation
Indices: 1506602--1506670 Score: 106
Period size: 3 Copynumber: 23.7 Consensus size: 3
1506592 TAATTGTAAT
* *
1506602 TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1506650 TAA T-A TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
1506671 TTTTTTAAGT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 4 0.07
3 56 0.93
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1509477 original size:11 final size:11
Alignment explanation
Indices: 1509461--1509499 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1509451 TTTTAAATAA
1509461 ATATATTTTGT
1 ATATATTTTGT
* *
1509472 ATATA-TGTAT
1 ATATATTTTGT
1509482 ATATATTTTGT
1 ATATATTTTGT
1509493 ATATATT
1 ATATATT
1509500 ATTACTTTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (11 bp):
ATATATTTTGT
Found at i:1513405 original size:115 final size:115
Alignment explanation
Indices: 1513203--1513428 Score: 443
Period size: 115 Copynumber: 2.0 Consensus size: 115
1513193 TCCAAAGTCC
1513203 AAGTTAGTAGCATATTGCTCTTTGATGAATTAAAATCCAAGGAGTTTAGAATTCAAAGTATTAAG
1 AAGTTAGTAGCATATTGCTCTTTGATGAATTAAAATCCAAGGAGTTTAGAATTCAAAGTATTAAG
*
1513268 TAAAAATACCTGCGTGAAAGAGCATCAGTGACGATGTTATCTTTTCGTCT
66 TAAAAATACATGCGTGAAAGAGCATCAGTGACGATGTTATCTTTTCGTCT
1513318 AAGTTAGTAGCATATTGCTCTTTGATGAATTAAAATCCAAGGAGTTTAGAATTCAAAGTATTAAG
1 AAGTTAGTAGCATATTGCTCTTTGATGAATTAAAATCCAAGGAGTTTAGAATTCAAAGTATTAAG
1513383 TAAAAATACATGCGTGAAAGAGCATCAGTGACGATGTTATCTTTTC
66 TAAAAATACATGCGTGAAAGAGCATCAGTGACGATGTTATCTTTTC
1513429 CTTTCTTATA
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 110 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (115 bp):
AAGTTAGTAGCATATTGCTCTTTGATGAATTAAAATCCAAGGAGTTTAGAATTCAAAGTATTAAG
TAAAAATACATGCGTGAAAGAGCATCAGTGACGATGTTATCTTTTCGTCT
Found at i:1519894 original size:38 final size:40
Alignment explanation
Indices: 1519836--1519923 Score: 153
Period size: 38 Copynumber: 2.2 Consensus size: 40
1519826 AACGCTTGAG
1519836 AAATGAATACAAGTAAGCACAAGTAGTGTTCTTAGAAAGA
1 AAATGAATACAAGTAAGCACAAGTAGTGTTCTTAGAAAGA
1519876 AAATG-ATAC-AGTAAGCACAAGTAGTGTTCTTAGAAAGAA
1 AAATGAATACAAGTAAGCACAAGTAGTGTTCTTAGAAAG-A
1519915 AAATGAATA
1 AAATGAATA
1519924 TTGATGAATG
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
38 28 0.61
39 10 0.22
40 8 0.17
ACGTcount: A:0.49, C:0.09, G:0.19, T:0.23
Consensus pattern (40 bp):
AAATGAATACAAGTAAGCACAAGTAGTGTTCTTAGAAAGA
Found at i:1520223 original size:20 final size:20
Alignment explanation
Indices: 1520198--1520269 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
1520188 GGAAAGCAAC
1520198 AGTATCGATACCGTCCAAGG
1 AGTATCGATACCGTCCAAGG
* * ** *
1520218 AGTATCGTTACTACTTATAA-T
1 AGTATCGATAC--CGTCCAAGG
*
1520239 AGTATCGATACCGTCCATGG
1 AGTATCGATACCGTCCAAGG
*
1520259 AGTATTGATAC
1 AGTATCGATAC
1520270 TACTATATAG
Statistics
Matches: 37, Mismatches: 12, Indels: 6
0.67 0.22 0.11
Matches are distributed among these distances:
19 3 0.08
20 20 0.54
21 10 0.27
22 4 0.11
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTATCGATACCGTCCAAGG
Found at i:1520255 original size:41 final size:42
Alignment explanation
Indices: 1520198--1520292 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 42
1520188 GGAAAGCAAC
*
1520198 AGTATCGATACCGTCCAAGGAGTATCGTTACTACT-TATAAT
1 AGTATCGATACCGTCCAAGGAGTATCGATACTACTATATAAT
* * *
1520239 AGTATCGATACCGTCCATGGAGTATTGATACTACTATATAGT
1 AGTATCGATACCGTCCAAGGAGTATCGATACTACTATATAAT
1520281 AGTATCGATACC
1 AGTATCGATACC
1520293 AGACAATGGT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 32 0.65
42 17 0.35
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (42 bp):
AGTATCGATACCGTCCAAGGAGTATCGATACTACTATATAAT
Found at i:1520993 original size:12 final size:12
Alignment explanation
Indices: 1520976--1521001 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1520966 AATCTTATAA
1520976 ATAAAATCAAAC
1 ATAAAATCAAAC
1520988 ATAAAATCAAAC
1 ATAAAATCAAAC
1521000 AT
1 AT
1521002 CCAAAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.19
Consensus pattern (12 bp):
ATAAAATCAAAC
Found at i:1523037 original size:22 final size:23
Alignment explanation
Indices: 1523011--1523056 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
1523001 TCGGTATTGG
1523011 ATGAACAATATCGATACTA-ACT
1 ATGAACAATATCGATACTAGACT
1523033 ATGAACAATATCGATACTAGACT
1 ATGAACAATATCGATACTAGACT
1523056 A
1 A
1523057 GTAGTATCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (23 bp):
ATGAACAATATCGATACTAGACT
Found at i:1530884 original size:14 final size:14
Alignment explanation
Indices: 1530865--1530892 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1530855 CTACTTAGAG
1530865 TGTTCATGTAGTAT
1 TGTTCATGTAGTAT
1530879 TGTTCATGTAGTAT
1 TGTTCATGTAGTAT
1530893 CGACACTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.50
Consensus pattern (14 bp):
TGTTCATGTAGTAT
Found at i:1532248 original size:20 final size:18
Alignment explanation
Indices: 1532211--1532259 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
1532201 TCTAAATCCT
*
1532211 TTTTCAAAATTTCATTTTG
1 TTTTCAAAA-TCCATTTTG
1532230 ATTTTCAAAATCCATTTTTG
1 -TTTTCAAAATCCA-TTTTG
*
1532250 CTTTCAAAAT
1 TTTTCAAAAT
1532260 AAATCATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.31, C:0.14, G:0.04, T:0.51
Consensus pattern (18 bp):
TTTTCAAAATCCATTTTG
Found at i:1537981 original size:21 final size:22
Alignment explanation
Indices: 1537955--1537995 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
1537945 CCAGGACAGG
1537955 GAGTATCGGTACT-CCTTTAAT
1 GAGTATCGGTACTACCTTTAAT
1537976 GAGTATCGGTACTACCTTTA
1 GAGTATCGGTACTACCTTTA
1537996 TAATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (22 bp):
GAGTATCGGTACTACCTTTAAT
Found at i:1539344 original size:23 final size:22
Alignment explanation
Indices: 1539310--1539353 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1539300 TTTTGTTTTG
* *
1539310 ATTATTTAATTATTTTTTAATC
1 ATTATTAAATTATGTTTTAATC
1539332 ATTATTAACATTATGTTTTAAT
1 ATTATTAA-ATTATGTTTTAAT
1539354 TTTATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (22 bp):
ATTATTAAATTATGTTTTAATC
Found at i:1539932 original size:18 final size:18
Alignment explanation
Indices: 1539909--1539948 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1539899 TCAATGAAGA
1539909 CAACTTAGATTCCTTGTT
1 CAACTTAGATTCCTTGTT
1539927 CAACTTAGATTCCTTGTT
1 CAACTTAGATTCCTTGTT
1539945 CAAC
1 CAAC
1539949 CCAGATTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (18 bp):
CAACTTAGATTCCTTGTT
Found at i:1539954 original size:18 final size:18
Alignment explanation
Indices: 1539915--1539956 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1539905 AAGACAACTT
**
1539915 AGATTCCTTGTTCAACTT
1 AGATTCCTTGTTCAACCC
1539933 AGATTCCTTGTTCAACCC
1 AGATTCCTTGTTCAACCC
1539951 AGATTC
1 AGATTC
1539957 AAAACTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (18 bp):
AGATTCCTTGTTCAACCC
Found at i:1546243 original size:112 final size:112
Alignment explanation
Indices: 1546046--1546263 Score: 373
Period size: 112 Copynumber: 1.9 Consensus size: 112
1546036 TCAAGGTGTC
* * * *
1546046 GTTTGGTTTATATAGATGATAAGTGTTTAATTTAATTAATATTTTCCTTTTAAATTACTCTTTAA
1 GTTTGGTTTACATAGATAATAAGTGCTTAATTTAATTAATATTTTCCTTTTAAATTACTCATTAA
*
1546111 TCATTGGTTTTTGTGATTTATTTGTTCGTTTTGATTCATTTGGTTTG
66 TCATTGGTTTTTGTGATTTATTTATTCGTTTTGATTCATTTGGTTTG
*
1546158 GTTTGGTTTACATAGATAATAAGTGCTTAATTTAATTAATATTTTGCTTTTAAATTACTCATTAA
1 GTTTGGTTTACATAGATAATAAGTGCTTAATTTAATTAATATTTTCCTTTTAAATTACTCATTAA
*
1546223 TCATTGGTTTTTGTGGTTTATTTATTCGTTTTGATTCATTT
66 TCATTGGTTTTTGTGATTTATTTATTCGTTTTGATTCATTT
1546264 TTTATACAGG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 99 1.00
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (112 bp):
GTTTGGTTTACATAGATAATAAGTGCTTAATTTAATTAATATTTTCCTTTTAAATTACTCATTAA
TCATTGGTTTTTGTGATTTATTTATTCGTTTTGATTCATTTGGTTTG
Found at i:1547363 original size:12 final size:12
Alignment explanation
Indices: 1547336--1547382 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
1547326 CATTATCCCA
*
1547336 ATTTAGTTATTTT
1 ATTTAATTA-TTT
*
1547349 ATTTAATTGTTT
1 ATTTAATTATTT
1547361 ATTTAATTATTT
1 ATTTAATTATTT
*
1547373 ATTTGATTAT
1 ATTTAATTAT
1547383 ACTTCTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 23 0.77
13 7 0.23
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (12 bp):
ATTTAATTATTT
Found at i:1547459 original size:19 final size:20
Alignment explanation
Indices: 1547437--1547485 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
1547427 TTAATATTTA
*
1547437 TTATTTTATTATTTTCT-TT
1 TTATTTTATTATTATCTATT
1547456 TTA-TTTATTATTATCTATT
1 TTATTTTATTATTATCTATT
*
1547475 TTATTTAATTA
1 TTATTTTATTA
1547486 AATCTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 12 0.46
19 8 0.31
20 6 0.23
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATTTTATTATTATCTATT
Found at i:1547490 original size:19 final size:18
Alignment explanation
Indices: 1547441--1547495 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
1547431 TATTTATTAT
**
1547441 TTTATTATTTTCTTTTTA
1 TTTATTATAATCTTTTTA
*
1547459 TTTATTATTATCTATTTTA
1 TTTATTATAATCT-TTTTA
1547478 TTTAATTA-AATCTTTTTA
1 TTT-ATTATAATCTTTTTA
1547496 ACTTTACCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 17 0.52
19 12 0.36
20 4 0.12
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTATAATCTTTTTA
Found at i:1550293 original size:45 final size:45
Alignment explanation
Indices: 1550235--1550425 Score: 278
Period size: 45 Copynumber: 4.2 Consensus size: 45
1550225 ATAATTCACC
* * *
1550235 ATTATACATTTTAATTATGGCAT-CTCTTCATGCCCTTTTATACGCT
1 ATTATACATTTCAATTATGACATCCT-TTCATG-CCTTTTATACACT
*
1550281 ATTATACATTT-AATTTATGCCATCCTTTCATGCCTTTTATACACT
1 ATTATACATTTCAA-TTATGACATCCTTTCATGCCTTTTATACACT
* *
1550326 ATTATACATTTCATTTATGACATCCTTTCATGTCTTTTATACACT
1 ATTATACATTTCAATTATGACATCCTTTCATGCCTTTTATACACT
*
1550371 ATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATACACT
1 ATTATACATTTCAATTATGACATCCTTTCATGCCTTTTATACACT
1550416 ATTATACATT
1 ATTATACATT
1550426 GTTATACATC
Statistics
Matches: 136, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
45 108 0.79
46 26 0.19
47 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.05, T:0.47
Consensus pattern (45 bp):
ATTATACATTTCAATTATGACATCCTTTCATGCCTTTTATACACT
Found at i:1550365 original size:22 final size:22
Alignment explanation
Indices: 1550294--1550410 Score: 71
Period size: 22 Copynumber: 5.2 Consensus size: 22
1550284 ATACATTTAA
* *
1550294 TTTATGCCATCCTTTCATGCCT
1 TTTATGACATCCTTTCATGTCT
* * *
1550316 TTTAT-ACA-CTATTATACATTTCA
1 TTTATGACATC-CTT-T-CATGTCT
1550339 TTTATGACATCCTTTCATGTCT
1 TTTATGACATCCTTTCATGTCT
* * *
1550361 TTTAT-ACA-CTATTATACATTTCA
1 TTTATGACATC-CTT-T-CATGTCT
*
1550384 TTTATGACATCCTTTCATGCCT
1 TTTATGACATCCTTTCATGTCT
1550406 TTTAT
1 TTTAT
1550411 ACACTATTAT
Statistics
Matches: 70, Mismatches: 15, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
20 2 0.03
21 9 0.13
22 26 0.37
23 21 0.30
24 10 0.14
25 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (22 bp):
TTTATGACATCCTTTCATGTCT
Found at i:1551428 original size:54 final size:54
Alignment explanation
Indices: 1550806--1551426 Score: 803
Period size: 54 Copynumber: 11.5 Consensus size: 54
1550796 AAACTAATGT
* * *
1550806 TGAATTCTGTGAAATGCACACTTAGTGCCGAAACGGTTATTTATCCACATAGGA
1 TGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGA
** * * *
1550860 TGAATTATGTGGAATGCACACTTAGTGTCGAAATGGTTATTCATCCACATATGA
1 TGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGA
* * ** *
1550914 TGAATTTCGTGGAATGCACACTTAGTGTCGAAACAATTATTCATCCATATAGGA
1 TGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGA
* * * * * *
1550968 TGAATTCTGTGATATGCACACTCAGTGTCGAAACAGTTATTCATCCAAATAGGG
1 TGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGA
* * *
1551022 TGAATTCTGT-AGAATGCACACTTAGTGTCAAAATGGTTATTCATCCACATAGGA
1 TGAATTCCGTGA-AATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGA
* * * *
1551076 TAAATTCCGTGAAGTGCACACTAAGTGTCGAAATGGTTATTCATCCACATAGGA
1 TGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGA
*
1551130 TGAATTCCGTGAAATGCACACTTAGTGTCGAAACGATTATTCATCCACATAGGA
1 TGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGA
* *
1551184 TGAATTCCGTGAAATGCACACTTAGTATCGAAACGGTTATTCATCCACAAAGGA
1 TGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGA
** *
1551238 TGAATTCCGTGAAATGCACACTTAGTACCGAAACGATTATTCATCCACATAGGA
1 TGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGA
* * * * * * *
1551292 TAAATTCTGTCAAATGCACACTTAGTGCCGAAATGGTTATTCATCCGCATCGGA
1 TGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGA
* * * *
1551346 TGAATTCCGTGAAATGCACAATTAGTGCCAAAACAGTTATTCATCCACATAGGA
1 TGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGA
* * * *
1551400 TGAATTCCATAAAATGAATACTTAGTG
1 TGAATTCCGTGAAATGCACACTTAGTG
1551427 CCTATTTGGT
Statistics
Matches: 499, Mismatches: 66, Indels: 4
0.88 0.12 0.01
Matches are distributed among these distances:
53 1 0.00
54 497 1.00
55 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (54 bp):
TGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGA
Found at i:1554951 original size:45 final size:45
Alignment explanation
Indices: 1554861--1555043 Score: 296
Period size: 45 Copynumber: 4.0 Consensus size: 45
1554851 ACCATTATGT
* * **
1554861 ATTTCAATTATGGCATCCCTTCATGCCCTTTTATACGTTATTATAC
1 ATTTCATTTATGGCATCCTTTCATG-CCTTTTATACACTATTATAC
*
1554907 ATTTCATTTATGGAATCCTTTCATGCCTTTTATACACTATTATAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTTATACACTATTATAC
1554952 ATTTCATTTATGGCATCCTTT-ACTGCCTTTTATACACTATTATAC
1 ATTTCATTTATGGCATCCTTTCA-TGCCTTTTATACACTATTATAC
1554997 ATTTCATTTATGGCATCCTTTCATGCCTTTTATACACTATTATAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTTATACACTATTATAC
1555042 AT
1 AT
1555044 ATAGTCTTTT
Statistics
Matches: 129, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
44 1 0.01
45 105 0.81
46 23 0.18
ACGTcount: A:0.25, C:0.22, G:0.07, T:0.46
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTTATACACTATTATAC
Found at i:1555229 original size:81 final size:81
Alignment explanation
Indices: 1555048--1555282 Score: 323
Period size: 81 Copynumber: 2.9 Consensus size: 81
1555038 ATACATATAG
* * * *
1555048 TCTTTTAATCAAAGGCATTTAACCTTTCATCTAACTGGCATGATTGACACATTTTTGTCAAAAT-
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGT-AAAATG
*
1555112 -ATAGCTA-GCTATTAA
65 CACAGCTAGGCTATTAA
* ** *
1555127 TCTTTTACTCGAAGGTATTTAAATTTTCATCTAACTGGCATAATTGACACATTTCTGTTAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTAAAATGC
*
1555192 ACAACTAGGCTATTAA
66 ACAGCTAGGCTATTAA
* * *
1555208 TCTTTTACTCAAAGGTATTTAACCTTTCATCTATCTGGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTAAAATGC
1555273 ACAGCTAGGC
66 ACAGCTAGGC
1555283 CTCAAAGGCA
Statistics
Matches: 136, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
78 4 0.03
79 51 0.38
80 5 0.04
81 76 0.56
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTAAAATGC
ACAGCTAGGCTATTAA
Found at i:1555356 original size:67 final size:68
Alignment explanation
Indices: 1555215--1555418 Score: 293
Period size: 67 Copynumber: 3.0 Consensus size: 68
1555205 TAATCTTTTA
* * * * * * *
1555215 CTCAAAGGTATTTAACCTTTCATCTATCTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTA
1 CTCAAAGGCACTTAGCCTTTCATTTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTA
1555280 GGC
66 GGC
* *
1555283 CTCAAAGGCACTTAGCCTTTCATTTAACTGGCATAATTGA-ACTTTTCTGTCAAATGCACAATTA
1 CTCAAAGGCACTTAGCCTTTCATTTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTA
1555347 GGC
66 GGC
* * *
1555350 CTCAAAGGCACTTAGCCTTTCACTTAACTGGCATAATAGACACATTTCTGTCAAATGCACAGCTA
1 CTCAAAGGCACTTAGCCTTTCATTTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTA
1555415 GGC
66 GGC
1555418 C
1 C
1555419 ATTAATCTTT
Statistics
Matches: 122, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
67 62 0.51
68 60 0.49
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.30
Consensus pattern (68 bp):
CTCAAAGGCACTTAGCCTTTCATTTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTA
GGC
Found at i:1555780 original size:54 final size:54
Alignment explanation
Indices: 1555641--1556170 Score: 712
Period size: 54 Copynumber: 9.9 Consensus size: 54
1555631 TCGTGCCTAT
* * *
1555641 ACGGTTATTCATCAAC-TAATGATGAATTCCATGAAATGCACACTTAGTG-C---
1 ACGGTTATTCATCCACAT-AGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* * * *
1555691 ACGGTTATTCATCCATATAGGATGAATTCCGTGGAATGCACACTTAGTGCCAAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* * * * * *
1555745 ACGGGTATTCATCCACATAGGATAAATTTCATGGAATGCACACTTAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* * * *
1555799 ACAGTTATTCATCCACATAGGATGAATGT-GGTAAAATGCACATTTAGTGTCGAA
1 ACGGTTATTCATCCACATAGGATGAAT-TCCGTGAAATGCACACTTAGTGTCGAA
* * * *
1555853 ACAGTTATTCATCCACATAGGATAAATTCTGTGGAATGCACACTTAGTGTCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* *
1555907 ACGGTTATTCATCTACATAGGATGAATTCCATGAAATGCACACTTAGTGTCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
*
1555961 ACGGTTATTCATCCACATATGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* * *
1556015 ACGATTATTCATCCACATATGATGAATTTCGTGAAATGCACACTTAGTGTCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* *
1556069 ACGATTATTCATCCACATAGGATGAATTCCGTAAAATGCACACTTAGTGTCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* * *
1556123 ATGGTTATTCATCCACTTAGGATGAATTCCGTAAAATGCACACTTAGT
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGT
1556171 CCCTATTTGG
Statistics
Matches: 431, Mismatches: 42, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
50 42 0.10
51 2 0.00
53 1 0.00
54 385 0.89
55 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (54 bp):
ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
Found at i:1556166 original size:27 final size:27
Alignment explanation
Indices: 1556086--1556169 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
1556076 TTCATCCACA
1556086 TAGGATGAATTCCGTAAAATGCACACT
1 TAGGATGAATTCCGTAAAATGCACACT
* * * *
1556113 TAGTG-TCGAAAT-GGT--TATTCATCCACT
1 TAG-GAT-GAATTCCGTAAAATGCA--CACT
1556140 TAGGATGAATTCCGTAAAATGCACACT
1 TAGGATGAATTCCGTAAAATGCACACT
1556167 TAG
1 TAG
1556170 TCCCTATTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 16
0.63 0.12 0.25
Matches are distributed among these distances:
25 4 0.10
26 5 0.12
27 23 0.56
28 5 0.12
29 4 0.10
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (27 bp):
TAGGATGAATTCCGTAAAATGCACACT
Found at i:1556236 original size:16 final size:15
Alignment explanation
Indices: 1556210--1556239 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1556200 TAAACAGTTA
1556210 TACATATATAATTAG
1 TACATATATAATTAG
1556225 TACATCATATAATTA
1 TACAT-ATATAATTA
1556240 CACAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (15 bp):
TACATATATAATTAG
Found at i:1564935 original size:17 final size:17
Alignment explanation
Indices: 1564912--1564952 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1564902 CCCTAAGTTT
1564912 CGAGTTCGAGCATAATG
1 CGAGTTCGAGCATAATG
*
1564929 TGAGTTCGAGCATAATG
1 CGAGTTCGAGCATAATG
1564946 CGAGTTC
1 CGAGTTC
1564953 AAGTAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (17 bp):
CGAGTTCGAGCATAATG
Found at i:1568040 original size:21 final size:21
Alignment explanation
Indices: 1568010--1568082 Score: 56
Period size: 23 Copynumber: 3.3 Consensus size: 21
1568000 GATAGATACT
* * *
1568010 TTACAATATAAGCATTACCTA
1 TTACATTATAAACACTACCTA
*
1568031 TTACATTATATAAACGCTACCTA
1 TTACA-T-TATAAACACTACCTA
**
1568054 TTACATTATATAAGTGCTACCTA
1 TTACATTATA-AA-CACTACCTA
1568077 TTACAT
1 TTACAT
1568083 CATATTTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 9 0.21
22 3 0.07
23 31 0.72
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.37
Consensus pattern (21 bp):
TTACATTATAAACACTACCTA
Found at i:1568051 original size:23 final size:23
Alignment explanation
Indices: 1568025--1568087 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1568015 ATATAAGCAT
1568025 TACCTATTACATTATATAAACGC
1 TACCTATTACATTATATAAACGC
**
1568048 TACCTATTACATTATATAAGTGC
1 TACCTATTACATTATATAAACGC
*
1568071 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1568088 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGC
Found at i:1568861 original size:200 final size:200
Alignment explanation
Indices: 1568518--1569207 Score: 1263
Period size: 200 Copynumber: 3.5 Consensus size: 200
1568508 AAGCAATACC
1568518 TATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC
1 TATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC
* **
1568583 TTTATGGTTGCATCCTGTTTTTCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTG
66 TTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTG
* *
1568648 TCGACACATTATTTAGACCTATTCTCTCATAAAACTGGTATACTTGTACCGGTTAGATTGAAAAA
131 TCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAA
1568713 TTACA
196 TTACA
*
1568718 TATTACATTATACTTTTAGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC
1 TATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC
1568783 TTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTG
66 TTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTG
1568848 TCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAA
131 TCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAA
1568913 TTACA
196 TTACA
*
1568918 TATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC
1 TATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC
* *
1568983 TGTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACTACAAAAGTG
66 TTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTG
*
1569048 TCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAAAA
131 TCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAA
*
1569113 TTACC
196 TTACA
1569118 TATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC
1 TATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC
* *
1569183 TTTATTGTTGCACTCTGTTTGCCAT
66 TTTATGGTTGCACCCTGTTTGCCAT
1569208 ATTGTAAATT
Statistics
Matches: 474, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
200 474 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (200 bp):
TATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC
TTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTG
TCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAA
TTACA
Found at i:1569331 original size:18 final size:18
Alignment explanation
Indices: 1569308--1569368 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
1569298 TCTCATTCAT
*
1569308 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
1569326 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
1569345 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
1569364 AATTA
1 AATTA
1569369 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:1569344 original size:19 final size:19
Alignment explanation
Indices: 1569320--1569368 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1569310 TTATATTCAC
1569320 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
1569339 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1569358 ATACAAAATTA
1 ATACAAAATTA
1569369 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1571193 original size:33 final size:33
Alignment explanation
Indices: 1571156--1571221 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1571146 CATCTTAATA
* *
1571156 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTCCACCACT
* *
1571189 TCACCCCTCAACACCTCTACTTCTTCCACCACT
1 TCACCCCTCAACACCCCAACTTCTTCCACCACT
1571222 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.50, G:0.00, T:0.27
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTCCACCACT
Found at i:1571280 original size:21 final size:21
Alignment explanation
Indices: 1571255--1571319 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1571245 CCCCTTATGC
* *
1571255 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1571276 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1571297 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1571318 CT
1 CT
1571320 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1573399 original size:17 final size:18
Alignment explanation
Indices: 1573377--1573419 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1573367 ATATATCTGG
1573377 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1573394 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
1573414 TATCAT
1 TATCAT
1573420 ATTTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1573577 original size:161 final size:162
Alignment explanation
Indices: 1573405--1573742 Score: 489
Period size: 161 Copynumber: 2.1 Consensus size: 162
1573395 ATCATTTTGA
* * *
1573405 TACCGGTTTTATCATATTTTTACATGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCG
1 TACCGGTTTTATCATATTTTTACATGGTATATCGTTGTGGATCGATACATTTTTTAAAAGTATCG
* * *
1573470 ACACATTATAGGCGCTAAAATTGCTTCTCTTTTAAATTCACAAAGTGTAGATCCTTATA-TAAAG
66 ACACATTATAGGAGCTAAAACTGCTTCTATTTTAAATTCACAAAGTGTAGATCCTTATATTAAAG
* * *
1573534 TATCGACACTTTCAATATATCCGGTAACGTTT
131 TACCGACACTTTAAATATATCCGGTAACGCTT
* * * *
1573566 TACCGGTTTTATCATATTTTTACCTGGTATATCGTTTTGGATCGATACGTTTTTTAAAATTATCG
1 TACCGGTTTTATCATATTTTTACATGGTATATCGTTGTGGATCGATACATTTTTTAAAAGTATCG
* ** * *
1573631 ACACTTTATAGGATTTAAAACTGCTTCTATTTTAAATTCACGAAGTGTCGATCCTTATATTAAAG
66 ACACATTATAGGAGCTAAAACTGCTTCTATTTTAAATTCACAAAGTGTAGATCCTTATATTAAAG
* *
1573696 TACCGACACTTTAAATGTATCCGGTAGCGCTT
131 TACCGACACTTTAAATATATCCGGTAACGCTT
1573728 TACCGGTTTTATCAT
1 TACCGGTTTTATCAT
1573743 TTCAATACTG
Statistics
Matches: 156, Mismatches: 20, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
161 109 0.70
162 47 0.30
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.41
Consensus pattern (162 bp):
TACCGGTTTTATCATATTTTTACATGGTATATCGTTGTGGATCGATACATTTTTTAAAAGTATCG
ACACATTATAGGAGCTAAAACTGCTTCTATTTTAAATTCACAAAGTGTAGATCCTTATATTAAAG
TACCGACACTTTAAATATATCCGGTAACGCTT
Found at i:1574004 original size:69 final size:70
Alignment explanation
Indices: 1573892--1574031 Score: 273
Period size: 69 Copynumber: 2.0 Consensus size: 70
1573882 TTGGGAAAGT
1573892 CCAATTCATGTGGTTCCTAAGAAAACGGGAGTCACAGTGGTCGAAAATCAAGAAGAGGAGTTAGT
1 CCAATTCATGTGGTTCCTAAGAAAACGGGAGTCACAGTGGTCGAAAATCAAGAAGAGGAGTTAGT
1573957 GCCCA
66 GCCCA
1573962 CCAATTCATGT-GTTCCTAAGAAAACGGGAGTCACAGTGGTCGAAAATCAAGAAGAGGAGTTAGT
1 CCAATTCATGTGGTTCCTAAGAAAACGGGAGTCACAGTGGTCGAAAATCAAGAAGAGGAGTTAGT
1574026 GCCCA
66 GCCCA
1574031 C
1 C
1574032 AAGGGTTAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
69 59 0.84
70 11 0.16
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.20
Consensus pattern (70 bp):
CCAATTCATGTGGTTCCTAAGAAAACGGGAGTCACAGTGGTCGAAAATCAAGAAGAGGAGTTAGT
GCCCA
Found at i:1582194 original size:17 final size:17
Alignment explanation
Indices: 1582167--1582210 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
1582157 CCCTAAGTTT
*
1582167 CGAGATCGAGCATAATG
1 CGAGTTCGAGCATAATG
*
1582184 TGAGTTCGAGCATAATG
1 CGAGTTCGAGCATAATG
1582201 CGAGTTCGAG
1 CGAGTTCGAG
1582211 TAAAATGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.23
Consensus pattern (17 bp):
CGAGTTCGAGCATAATG
Found at i:1582217 original size:17 final size:17
Alignment explanation
Indices: 1582167--1582217 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
1582157 CCCTAAGTTT
* *
1582167 CGAGATCGAGCATAATG
1 CGAGTTCGAGCAAAATG
* *
1582184 TGAGTTCGAGCATAATG
1 CGAGTTCGAGCAAAATG
*
1582201 CGAGTTCGAGTAAAATG
1 CGAGTTCGAGCAAAATG
1582218 ATTACAAGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (17 bp):
CGAGTTCGAGCAAAATG
Found at i:1585256 original size:20 final size:20
Alignment explanation
Indices: 1585226--1585272 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
1585216 GATAGATACT
*
1585226 TTACAATATAAGCACTACCTA
1 TTAC-ATATAAACACTACCTA
*
1585247 TTACATATAAACGCTACCTA
1 TTACATATAAACACTACCTA
1585267 TTACAT
1 TTACAT
1585273 TATATAAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.32
Consensus pattern (20 bp):
TTACATATAAACACTACCTA
Found at i:1585287 original size:23 final size:22
Alignment explanation
Indices: 1585231--1585300 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 22
1585221 ATACTTTACA
*
1585231 ATATAAGCACTACCTATTACA-T
1 ATATAA-CGCTACCTATTACATT
1585253 ATA-AACGCTACCTATTACATT
1 ATATAACGCTACCTATTACATT
* * *
1585274 ATATAAGTGTTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
1585297 ATAT
1 ATAT
1585301 TTTTACCTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 13 0.32
21 6 0.15
22 5 0.12
23 17 0.41
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.36
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:1585727 original size:20 final size:20
Alignment explanation
Indices: 1585702--1585771 Score: 77
Period size: 22 Copynumber: 3.3 Consensus size: 20
1585692 GATAGATACT
**
1585702 TTACATATAAGTACTACCTA
1 TTACATATAAGCGCTACCTA
*
1585722 TTACATTTATAAACGCTACCTA
1 TTACA--TATAAGCGCTACCTA
1585744 TTACATATATAAGCGCTACCTA
1 TTAC--ATATAAGCGCTACCTA
1585766 TTACAT
1 TTACAT
1585772 CATATTTTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
20 7 0.17
22 34 0.81
24 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.36
Consensus pattern (20 bp):
TTACATATAAGCGCTACCTA
Found at i:1585740 original size:22 final size:22
Alignment explanation
Indices: 1585715--1585776 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
1585705 CATATAAGTA
*
1585715 CTACCTATTACATTTATAAACG
1 CTACCTATTACATATATAAACG
*
1585737 CTACCTATTACATATATAAGCG
1 CTACCTATTACATATATAAACG
1585759 CTACCTATTACATCATAT
1 CTACCTATTACAT-ATAT
1585777 TTTACTATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 33 0.89
23 4 0.11
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.35
Consensus pattern (22 bp):
CTACCTATTACATATATAAACG
Found at i:1585947 original size:475 final size:479
Alignment explanation
Indices: 1584835--1586208 Score: 2262
Period size: 475 Copynumber: 2.9 Consensus size: 479
1584825 TTATAATATG
*
1584835 TTGAAAGTGTCTATACTTTTTATAAAAAAAGATCGATACTTTTTTTAAAG-TTGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTAT--AAAAAGATCGATACTTTTTTTAAAGTTTGTAATTTATGTT
1584899 TCAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
64 TCAATTTTTTTAAT-GT-TTT--T-TTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
1584963 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
124 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
* *
1585028 AACCAAAGATAATAATAAATATGTAATATATATGTT-TTGTTTTTAATTTAATGATAATATATAC
189 AACCAAAGATAATAATAAATATGTAATATATATGTTATTGTTTTTAATTTAATAATAATATATAT
* * ** * *
1585092 CGTAACATAAAAAATAATCATTAGATACATATAATTACTAAATTGATATCTTAAAACTCACTCAA
254 CGTAACGTAAAAAAAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
* *
1585157 AAGATAACCTTAAATTAATGTTTTCCACAGTG-AATAAGTATGCACACTTTTATAAAAAGGATAG
319 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
* *
1585221 ATACTTTACAATATAAGCACTACCTATTACA--TATAAACGCTACCTATTACATTATATAAGTGT
384 ATACTTTACAATATAAGCACTACCTATTACATTTATAAACGCTACCTATTACATTATATAAGCGC
1585284 TACCTATTACATCATATTTTTACCTATTATA
449 TACCTATTACATCATATTTTTACCTATTATA
*
1585315 TTGAAAGTGTCCATACTTTTTA-AAAAATTATCGATACTTTTTTTAAAGTTTTGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAA-GATCGATACTTTTTTTAAAG-TTTGTAATTTATGTT
1585379 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
64 TCAATTTTTTTAAT-GT-TTT--T-TTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
1585444 AAAAAATTA-TTGATTGTTTTG--A--TTATAAAATAATATTTAGAATTTAAA-TTAACAATATT
124 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
*
1585503 AACCAAATATAATAATAAATATGTAATATAT-TGTTATTGTTTTTAATTTAATAATAATATATAT
189 AACCAAAGATAATAATAAATATGTAATATATATGTTATTGTTTTTAATTTAATAATAATATATAT
1585567 CGTAACGTAAAAAAAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
254 CGTAACGTAAAAAAAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
1585632 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
319 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
*
1585697 ATACTTTAC-ATATAAGTACTACCTATTACATTTATAAACGCTACCTATTACA-TATATAAGCGC
384 ATACTTTACAATATAAGCACTACCTATTACATTTATAAACGCTACCTATTACATTATATAAGCGC
1585760 TACCTATTACATCATA-TTTTA-CTATTATA
449 TACCTATTACATCATATTTTTACCTATTATA
*
1585789 TTGAAAGTGTCCATACTTTTTATAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGATCGATACTTTTTTTAAAGTT-TGTAATTTATGTTT
1585854 CAATTTTTTTAATGTTTGTTTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAA
65 CAATTTTTTTAATGTTT-TTTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAA
1585919 ATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCA
129 ATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCA
1585984 AAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTA
194 AAGATAATAATAAATATGTAATATATATG-TTATTGTTTTTAATTTAATAATAATATATATCGTA
*
1586049 ACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAT
258 ACGTAAAAAA-AAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAG
* *
1586114 ATAACCTTAAATTAATGTTTTCCACAGTTAAAAAAGTATGGACACTTTTATAAAAATGATAGATA
322 ATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATA
* *
1586179 CATTACAATATAAGCAATACCTATTACATT
387 CTTTACAATATAAGCACTACCTATTACATT
1586209 ATACTTTTGG
Statistics
Matches: 848, Mismatches: 25, Indels: 42
0.93 0.03 0.05
Matches are distributed among these distances:
470 49 0.06
471 13 0.02
472 2 0.00
473 6 0.01
474 80 0.09
475 213 0.25
476 131 0.15
477 27 0.03
478 65 0.08
479 121 0.14
480 72 0.08
481 69 0.08
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (479 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGATCGATACTTTTTTTAAAGTTTGTAATTTATGTTTC
AATTTTTTTAATGTTTTTTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAAT
TATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAA
GATAATAATAAATATGTAATATATATGTTATTGTTTTTAATTTAATAATAATATATATCGTAACG
TAAAAAAAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAA
CCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTT
ACAATATAAGCACTACCTATTACATTTATAAACGCTACCTATTACATTATATAAGCGCTACCTAT
TACATCATATTTTTACCTATTATA
Found at i:1586711 original size:200 final size:199
Alignment explanation
Indices: 1586199--1586883 Score: 1200
Period size: 196 Copynumber: 3.5 Consensus size: 199
1586189 TAAGCAATAC
1586199 CTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACA
1 CTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACA
* *
1586264 CTTTATGGTTGCAGCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGT
66 CTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGT
* * *
1586329 GTCGACACATTATTTAGACATATTCTCTCATAAAACTGGTATACTTGTACCGGTTAGATTGAAAA
131 GTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAA
1586394 A-TA
196 ATTA
*
1586397 C-A-TACATTATACTTTTAGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACA
1 CTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACA
*
1586460 CTTTATGGTTGCATCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGT
66 CTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGT
1586525 GTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAA
131 GTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAA
1586590 ATTA
196 ATTA
*
1586594 CATATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGAC
1 C-TATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGAC
* *
1586659 ACTGTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACTACAAAAG
65 ACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAG
*
1586724 TGTCGATACATTATTTAGACCTATTCTCTC--AAAACCGGTATACTTGTACCGATTAGATTGAAA
130 TGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
1586787 AATTA
195 AATTA
1586792 CCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGAC
1 -CTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGAC
* *
1586857 ACTTTATTGTTGCACTCTGTTTGCCAT
65 ACTTTATGGTTGCACCCTGTTTGCCAT
1586884 ATTGTAAATT
Statistics
Matches: 466, Mismatches: 16, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
196 186 0.40
197 4 0.01
198 124 0.27
199 2 0.00
200 150 0.32
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (199 bp):
CTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACA
CTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGT
GTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAA
ATTA
Found at i:1587005 original size:18 final size:18
Alignment explanation
Indices: 1586982--1587042 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
1586972 TCTCATTCAT
*
1586982 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
1587000 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
1587019 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
1587038 AATTA
1 AATTA
1587043 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:1587018 original size:19 final size:19
Alignment explanation
Indices: 1586994--1587042 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1586984 TTATATTCAC
1586994 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
1587013 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1587032 ATACAAAATTA
1 ATACAAAATTA
1587043 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1588862 original size:33 final size:33
Alignment explanation
Indices: 1588825--1588890 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1588815 CATCTTAATA
* *
1588825 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTCCACCACT
* *
1588858 TCACCCCTCAACACCTCTACTTCTTCCACCACT
1 TCACCCCTCAACACCCCAACTTCTTCCACCACT
1588891 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.50, G:0.00, T:0.27
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTCCACCACT
Found at i:1588949 original size:21 final size:21
Alignment explanation
Indices: 1588924--1588988 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1588914 CCCCTTATGC
* *
1588924 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1588945 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1588966 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1588987 CT
1 CT
1588989 TGATGTCTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1591232 original size:17 final size:18
Alignment explanation
Indices: 1591210--1591252 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1591200 ATATATCTGG
1591210 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1591227 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
1591247 TATCAT
1 TATCAT
1591253 ATTTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1591427 original size:20 final size:20
Alignment explanation
Indices: 1591402--1591457 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
1591392 AACGTTTTAT
1591402 CGGTTTTATCATTTTGTTAC
1 CGGTTTTATCATTTTGTTAC
1591422 CGGTTTTATCATATTT-TTAC
1 CGGTTTTATCAT-TTTGTTAC
*
1591442 CTGG-TATATCATTTTG
1 C-GGTTTTATCATTTTG
1591458 GATCGATACA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 3 0.09
20 24 0.75
21 5 0.16
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.54
Consensus pattern (20 bp):
CGGTTTTATCATTTTGTTAC
Found at i:1591656 original size:181 final size:181
Alignment explanation
Indices: 1591182--1591654 Score: 640
Period size: 181 Copynumber: 2.6 Consensus size: 181
1591172 CGTACTTACG
* * *
1591182 AAAGTATCGACACTTTCAATATATCTGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
1591247 TATCATATTTTTACATGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* * *
1591312 AGGCGCTAAAATTACTTCTCTTTTAAATTCACAAAGTGTCAATCCTTATAT
131 AGGAGCTAAAACTACTTCTATTTTAAATTCACAAAGTGTCAATCCTTATAT
* * *
1591363 AAAGTATCGACACTTTCAATATATTCGGTAACGTTTTATCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
1591428 TATCATATTTTTACCTGGTATATCATTTTGGATCGATACATTTTTTAAAATTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** * * *
1591493 AGGATTTAAAACTGCTTCTATTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTACTTCTATTTTAAATTCACAAAGTGTCAATCCTTATA-T
* * * * * ** *
1591545 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACTGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
1591610 TGTCATAATTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
1591655 AATTTGGATC
Statistics
Matches: 253, Mismatches: 38, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
181 158 0.62
182 95 0.38
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTACTTCTATTTTAAATTCACAAAGTGTCAATCCTTATAT
Found at i:1599606 original size:17 final size:17
Alignment explanation
Indices: 1599579--1599622 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
1599569 CCCTAAGTTT
*
1599579 CGAGATCGAGCATAATG
1 CGAGTTCGAGCATAATG
*
1599596 TGAGTTCGAGCATAATG
1 CGAGTTCGAGCATAATG
1599613 CGAGTTCGAG
1 CGAGTTCGAG
1599623 TAAAATGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.23
Consensus pattern (17 bp):
CGAGTTCGAGCATAATG
Found at i:1599629 original size:17 final size:17
Alignment explanation
Indices: 1599579--1599629 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
1599569 CCCTAAGTTT
* *
1599579 CGAGATCGAGCATAATG
1 CGAGTTCGAGCAAAATG
* *
1599596 TGAGTTCGAGCATAATG
1 CGAGTTCGAGCAAAATG
*
1599613 CGAGTTCGAGTAAAATG
1 CGAGTTCGAGCAAAATG
1599630 ATTACAAGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (17 bp):
CGAGTTCGAGCAAAATG
Found at i:1602686 original size:21 final size:21
Alignment explanation
Indices: 1602656--1602728 Score: 56
Period size: 23 Copynumber: 3.3 Consensus size: 21
1602646 GATAGATACT
* * *
1602656 TTACAATATAAGCATTACCTA
1 TTACATTATAAACACTACCTA
*
1602677 TTACATTATATAAACGCTACCTA
1 TTACA-T-TATAAACACTACCTA
**
1602700 TTACATTATATAAGTGCTACCTA
1 TTACATTATA-AA-CACTACCTA
1602723 TTACAT
1 TTACAT
1602729 CATATTTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 9 0.21
22 3 0.07
23 31 0.72
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.37
Consensus pattern (21 bp):
TTACATTATAAACACTACCTA
Found at i:1602697 original size:23 final size:23
Alignment explanation
Indices: 1602671--1602733 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1602661 ATATAAGCAT
1602671 TACCTATTACATTATATAAACGC
1 TACCTATTACATTATATAAACGC
**
1602694 TACCTATTACATTATATAAGTGC
1 TACCTATTACATTATATAAACGC
*
1602717 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1602734 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGC
Found at i:1603510 original size:196 final size:199
Alignment explanation
Indices: 1603157--1603840 Score: 1207
Period size: 200 Copynumber: 3.5 Consensus size: 199
1603147 AAGCAATACC
1603157 TATTACATTATACTTTTGGG-TTCGATGTTTATGGGATCGACAC-TTTTATATATGGATCGACAC
1 TATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC
* *
1603220 TTTATGGTTGCATCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTG
66 TTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACC-AAAATATCGACACAAACTACAAAAGTG
* *
1603285 TCGACACATTATTTAGACCTATTCTCTCATAAAACTGGTATACTTGTACCGGTTAGATTGAAAAA
130 TCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAA
1603350 TTACA
195 TTACA
*
1603355 TATTACATTATAC-TTTAGG-TTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC
1 TATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC
1603418 TTTATGGTTGCA-CCTGTTTGCCATTCATTCTGGACCAAAATATCGACACAAACTACAAAAGTGT
66 TTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAATATCGACACAAACTACAAAAGTGT
1603482 CGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAAT
131 CGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAAT
1603547 TACA
196 TACA
*
1603551 TATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC
1 TATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC
*
1603616 TGTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACTACAAAAGTG
66 TTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCA-AAATATCGACACAAACTACAAAAGTG
* *
1603681 TCGATACATTATTTAGACCAATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAAAA
130 TCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAA
*
1603746 TTACC
195 TTACA
1603751 TATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC
1 TATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC
* *
1603816 TTTATTGTTGCACTCTGTTTGCCAT
66 TTTATGGTTGCACCCTGTTTGCCAT
1603841 ATTGTAAATT
Statistics
Matches: 467, Mismatches: 14, Indels: 8
0.96 0.03 0.02
Matches are distributed among these distances:
196 108 0.23
197 55 0.12
198 100 0.21
199 25 0.05
200 179 0.38
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (199 bp):
TATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC
TTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAATATCGACACAAACTACAAAAGTGT
CGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAAT
TACA
Found at i:1603980 original size:19 final size:19
Alignment explanation
Indices: 1603952--1603999 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1603942 TTATATTCAC
1603952 ATAC-AAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
1603970 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1603989 ATACAAAATTA
1 ATACAAAATTA
1604000 ACCCTACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1605811 original size:33 final size:33
Alignment explanation
Indices: 1605774--1605839 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1605764 CATCTTAATA
* *
1605774 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTCCACCACT
* *
1605807 TCACCCCTCAACACCTCTACTTCTTCCACCACT
1 TCACCCCTCAACACCCCAACTTCTTCCACCACT
1605840 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.50, G:0.00, T:0.27
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTCCACCACT
Found at i:1605898 original size:21 final size:21
Alignment explanation
Indices: 1605873--1605937 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1605863 CCCCTTATGC
* *
1605873 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1605894 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1605915 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1605936 CT
1 CT
1605938 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1608174 original size:17 final size:18
Alignment explanation
Indices: 1608152--1608194 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1608142 ATATATCTGG
1608152 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1608169 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
1608189 TATCAT
1 TATCAT
1608195 ATTTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1608368 original size:20 final size:20
Alignment explanation
Indices: 1608338--1608388 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1608328 TCCGGTAACG
*
1608338 TTTTACCGGTTTTATCAT-T
1 TTTTACTGGTTTTATCATAT
1608357 TTGTTACTGGTTTTATCATAT
1 TT-TTACTGGTTTTATCATAT
1608378 TTTTACCTGGT
1 TTTTA-CTGGT
1608389 ATATCGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 2 0.07
20 18 0.64
21 8 0.29
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.57
Consensus pattern (20 bp):
TTTTACTGGTTTTATCATAT
Found at i:1608428 original size:181 final size:182
Alignment explanation
Indices: 1608124--1608596 Score: 669
Period size: 181 Copynumber: 2.6 Consensus size: 182
1608114 CGTACTTACG
* * * *
1608124 AAAGTATCGACACTTTCAATATATCTGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACTGGTTT
* * * *
1608189 TATCATATTTTTACATGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* * *
1608254 AGGCGCTAAAATTGCTTCTCTTTTAAATTCACAAAGTGTAGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTATTTTAAATTCACAAAGTGTAGATCCTTATATT
*
1608305 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACTGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACTGGTTT
* * * *
1608370 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACGTTTTTTAAAATTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** * *
1608435 AGGATTTAAAACTGCTTCTATTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTATTTTAAATTCACAAAGTGTAGATCCTTATATT
* * * * * **
1608487 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACTGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACTGGTTT
* * *
1608552 TGTCATAATTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
1608597 AATTTGGATC
Statistics
Matches: 258, Mismatches: 33, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
181 160 0.62
182 98 0.38
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACTGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTATTTTAAATTCACAAAGTGTAGATCCTTATATT
Done.