Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001497.1 Hibiscus syriacus cultivar Beakdansim tig00002919_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: 1780709
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1408307 original size:15 final size:15
Alignment explanation
Indices: 1408279--1408325 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1408269 ATTTAATTTA
1408279 AATTTAAAATATATAT
1 AATTT-AAATATATAT
* *
1408295 AATATT-TATATATTT
1 AAT-TTAAATATATAT
1408310 AATTTAAATATATAT
1 AATTTAAATATATAT
1408325 A
1 A
1408326 TCCAGGCATG
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
14 2 0.08
15 18 0.72
16 3 0.12
17 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATTTAAATATATAT
Found at i:1415611 original size:10 final size:10
Alignment explanation
Indices: 1415596--1415624 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1415586 CTAGAAAATA
1415596 GAAAGAAAGG
1 GAAAGAAAGG
1415606 GAAAGAAAGG
1 GAAAGAAAGG
1415616 GAAAGAAAG
1 GAAAGAAAG
1415625 AAAATACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAAGAAAGG
Found at i:1424646 original size:38 final size:38
Alignment explanation
Indices: 1424595--1424671 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
1424585 TAGCAAAGGA
*
1424595 ATACAGAAACAATCTCGACCAAAGTAATAAAGATGAGC
1 ATACAGAAACAATCTCAACCAAAGTAATAAAGATGAGC
*
1424633 ATACAGAAACAATCTCAACCAAAGTAATAATGATGAGC
1 ATACAGAAACAATCTCAACCAAAGTAATAAAGATGAGC
1424671 A
1 A
1424672 GAACTAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.51, C:0.18, G:0.14, T:0.17
Consensus pattern (38 bp):
ATACAGAAACAATCTCAACCAAAGTAATAAAGATGAGC
Found at i:1425230 original size:20 final size:21
Alignment explanation
Indices: 1425197--1425236 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1425187 AGCGTCCTCT
1425197 TTTCTATAACTTTT-ATTTTA
1 TTTCTATAACTTTTCATTTTA
**
1425217 TTTCTATATTTTTTCATTTT
1 TTTCTATAACTTTTCATTTT
1425237 TATAATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTCTATAACTTTTCATTTTA
Found at i:1425690 original size:5 final size:5
Alignment explanation
Indices: 1425682--1425708 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1425672 GGACCAAAAA
1425682 CCGAC CCGAC CCGAC CCGAC CCGAC CC
1 CCGAC CCGAC CCGAC CCGAC CCGAC CC
1425709 ATCTCACCCC
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:0.63, G:0.19, T:0.00
Consensus pattern (5 bp):
CCGAC
Found at i:1427658 original size:14 final size:15
Alignment explanation
Indices: 1427635--1427667 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1427625 TTTAACCATA
*
1427635 ACAACCTTAATAAT-
1 ACAACATTAATAATG
1427649 ACAACATTAATAATG
1 ACAACATTAATAATG
1427664 ACAA
1 ACAA
1427668 ATACTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.55, C:0.18, G:0.03, T:0.24
Consensus pattern (15 bp):
ACAACATTAATAATG
Found at i:1427692 original size:2 final size:2
Alignment explanation
Indices: 1427685--1427720 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1427675 TTAAAAAGTA
*
1427685 AT AT AT AT AT AT AT AT AT AT AT GT 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
1427721 GTATGTGTGT
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:1427802 original size:56 final size:56
Alignment explanation
Indices: 1427716--1427828 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
1427706 TGTATATATA
*
1427716 TATATGTATGTGTGTAAATGGATTTTTAAGAGGGTAGGTTTATTTTCTTTAGTAAT
1 TATATGTATGTGTGTAAATGGATTTTTAAGAGGGTAGGTTTATTTTCTTTAGGAAT
1427772 TATATGTATGTGTGTAAATGGATTTTTAAGAGGGTAGGTTTATTTTCTTTAGGAAT
1 TATATGTATGTGTGTAAATGGATTTTTAAGAGGGTAGGTTTATTTTCTTTAGGAAT
1427828 T
1 T
1427829 TGGAATTCCC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.27, C:0.02, G:0.24, T:0.48
Consensus pattern (56 bp):
TATATGTATGTGTGTAAATGGATTTTTAAGAGGGTAGGTTTATTTTCTTTAGGAAT
Found at i:1430211 original size:20 final size:21
Alignment explanation
Indices: 1430169--1430211 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1430159 CGCACTAAAT
*
1430169 GCTGAACGATTCAGTATTCAGA
1 GCTGAACGATTCA-TATTAAGA
*
1430191 GCTGAATGATTC-TATTAAGA
1 GCTGAACGATTCATATTAAGA
1430211 G
1 G
1430212 GCAAACAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (21 bp):
GCTGAACGATTCATATTAAGA
Found at i:1431144 original size:29 final size:29
Alignment explanation
Indices: 1431108--1431193 Score: 136
Period size: 29 Copynumber: 3.0 Consensus size: 29
1431098 AGTGTTGGCC
* * *
1431108 GTAGGTCGTCATGCAATCCGGACGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
*
1431137 GTAGGTCGCCATGCACTTCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
1431166 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
1431194 ACCCTTGTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.16, C:0.31, G:0.30, T:0.22
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:1431348 original size:33 final size:33
Alignment explanation
Indices: 1431311--1431385 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
1431301 GCGACATACC
* *
1431311 CTCGCTCGGCTT-CCCTCGGATTCCCTCACATAG
1 CTCGCTCGG-TTGCCCTCAGATGCCCTCACATAG
*
1431344 CTCGCTCGGTTGCCCTCAGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCAGATGCCCTCACATAG
*
1431377 CTCGTTCGG
1 CTCGCTCGG
1431386 ATGGCCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 2 0.05
33 35 0.95
ACGTcount: A:0.11, C:0.40, G:0.23, T:0.27
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCAGATGCCCTCACATAG
Found at i:1431399 original size:14 final size:14
Alignment explanation
Indices: 1431377--1431409 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1431367 CCTCGCATAG
*
1431377 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
1431391 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
1431405 CTCGG
1 CTCGG
1431410 ATGCCCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:1443386 original size:60 final size:56
Alignment explanation
Indices: 1443274--1443440 Score: 158
Period size: 56 Copynumber: 2.9 Consensus size: 56
1443264 GAATTATAAC
* * * * * *
1443274 TCATTTTAAATTGGTCCTTAAATTTTTTAAGATTCTAATTTAAT-CTTCAAACTATGAATG
1 TCATTTTAAATTAGTTCTTAAACTTTTAAATATTCTAATTTTATCCTT-AAACT-T---TG
* *
1443334 TCATCTTAAATTAGTTCTTAAACTTTTAAATATTCTAATTTTATCCCTAAACTTTG
1 TCATTTTAAATTAGTTCTTAAACTTTTAAATATTCTAATTTTATCCTTAAACTTTG
** * *
1443390 TTTTTTTAAATTAG-TCTTCAAACTTTTGAATATTTTAATTTTATCCTTAAA
1 TCATTTTAAATTAGTTCTT-AAACTTTTAAATATTCTAATTTTATCCTTAAA
1443441 TTCATCCAAT
Statistics
Matches: 91, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
55 4 0.04
56 42 0.46
59 1 0.01
60 42 0.46
61 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.50
Consensus pattern (56 bp):
TCATTTTAAATTAGTTCTTAAACTTTTAAATATTCTAATTTTATCCTTAAACTTTG
Found at i:1461430 original size:25 final size:25
Alignment explanation
Indices: 1461360--1461430 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 25
1461350 TAATTCTTTT
* *
1461360 AAATATTTTAAATAACTAA-ATTATA
1 AAATATTTTAAATAA-TAATATAAAA
* ** *
1461385 AAATTTATTTAGTTAAAAATATAAAA
1 AAATAT-TTTAAATAATAATATAAAA
1461411 AAATATTTTAAATAATAATA
1 AAATATTTTAAATAATAATA
1461431 AATTTAAAAT
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
25 18 0.53
26 16 0.47
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (25 bp):
AAATATTTTAAATAATAATATAAAA
Found at i:1461438 original size:16 final size:15
Alignment explanation
Indices: 1461417--1461454 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 15
1461407 AAAAAAATAT
1461417 TTTAAATAATAATAAA
1 TTTAAATAATAA-AAA
1461433 TTTAAAATAATAAAAA
1 TTT-AAATAATAAAAA
1461449 TTTAAA
1 TTTAAA
1461455 ATTTAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.14
16 9 0.43
17 9 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTAAATAATAAAAA
Found at i:1461465 original size:16 final size:16
Alignment explanation
Indices: 1461405--1461456 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
1461395 AGTTAAAAAT
* *
1461405 ATAAAAAAATATTTTAA
1 ATAATAAAA-ATTTAAA
1461422 ATAATAATAAATTTAAA
1 ATAATAA-AAATTTAAA
1461439 ATAATAAAAATTTAAA
1 ATAATAAAAATTTAAA
1461455 AT
1 AT
1461457 TTAAAAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
16 11 0.34
17 19 0.59
18 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATAAAAATTTAAA
Found at i:1465117 original size:23 final size:23
Alignment explanation
Indices: 1465091--1465148 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
1465081 TCTTATTTAA
*
1465091 TTTAGAATTTATGGTGAATTTCT
1 TTTAGAATTTATGGTAAATTTCT
*
1465114 TTTAAAGAA--TATGGTAAATTTTT
1 TTT--AGAATTTATGGTAAATTTCT
*
1465137 TTTTGAATTTAT
1 TTTAGAATTTAT
1465149 AGACAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
21 3 0.11
23 21 0.75
25 4 0.14
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.53
Consensus pattern (23 bp):
TTTAGAATTTATGGTAAATTTCT
Found at i:1469554 original size:16 final size:16
Alignment explanation
Indices: 1469535--1469565 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1469525 GTCAAATTTT
*
1469535 AATTTTGTTTTTTACA
1 AATTTAGTTTTTTACA
1469551 AATTTAGTTTTTTAC
1 AATTTAGTTTTTTAC
1469566 TTCTAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
AATTTAGTTTTTTACA
Found at i:1471094 original size:19 final size:18
Alignment explanation
Indices: 1471070--1471110 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
1471060 TAAAAATTAC
*
1471070 TTAAAATATTAATTTTTAT
1 TTAAAATATTAATGTTT-T
1471089 TTAAAATATTAATGTTTT
1 TTAAAATATTAATGTTTT
1471107 TTAA
1 TTAA
1471111 TATTTTCGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTAAAATATTAATGTTTT
Found at i:1472804 original size:14 final size:14
Alignment explanation
Indices: 1472795--1472821 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1472785 CAAATTTCAT
1472795 AAAATGAATTATAG
1 AAAATGAATTATAG
1472809 AAAATGAATTATA
1 AAAATGAATTATA
1472822 TTTTTAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (14 bp):
AAAATGAATTATAG
Found at i:1475770 original size:22 final size:22
Alignment explanation
Indices: 1475742--1475789 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
1475732 TTTACCTTTT
1475742 GTTTTGAGCAGGTGATTTGGTG
1 GTTTTGAGCAGGTGATTTGGTG
1475764 GTTTTGAGCAGGTGATTTGGTG
1 GTTTTGAGCAGGTGATTTGGTG
1475786 GTTT
1 GTTT
1475790 GTGCGTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.12, C:0.04, G:0.40, T:0.44
Consensus pattern (22 bp):
GTTTTGAGCAGGTGATTTGGTG
Found at i:1479829 original size:20 final size:20
Alignment explanation
Indices: 1479793--1479830 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1479783 ATCCTATTCC
**
1479793 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1479813 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1479831 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1484528 original size:7 final size:7
Alignment explanation
Indices: 1484513--1484548 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
1484503 AACGAAGGGA
1484513 AAGAAAG
1 AAGAAAG
*
1484520 AATAAAG
1 AAGAAAG
1484527 AAGAAAG
1 AAGAAAG
1484534 AAGAAAG
1 AAGAAAG
1484541 AAGAAAG
1 AAGAAAG
1484548 A
1 A
1484549 TCAGGGGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (7 bp):
AAGAAAG
Found at i:1489407 original size:34 final size:34
Alignment explanation
Indices: 1489368--1489474 Score: 142
Period size: 34 Copynumber: 3.1 Consensus size: 34
1489358 TAAGTTGAAA
* * *
1489368 TTTAATGTTAAATTTCAAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
1489402 TTTAATTTTAAATTTCGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* * *
1489436 TTTTATTTTAAATTTTGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
1489470 TTTAA
1 TTTAA
1489475 AAACATTTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:1490062 original size:21 final size:21
Alignment explanation
Indices: 1489995--1490063 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
1489985 TATGGTATAA
*
1489995 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
1490016 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1490037 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1490058 AACCCT
1 AACCCT
1490064 ACGGAGATGG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.22, C:0.28, G:0.32, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1490099 original size:21 final size:21
Alignment explanation
Indices: 1490073--1490112 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1490063 TACGGAGATG
*
1490073 GCATATGAACTGGTGGGCTTT
1 GCATATGAACTGGAGGGCTTT
*
1490094 GCATATGAAGTGGAGGGCT
1 GCATATGAACTGGAGGGCT
1490113 GGGCATGTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.38, T:0.28
Consensus pattern (21 bp):
GCATATGAACTGGAGGGCTTT
Found at i:1490118 original size:21 final size:21
Alignment explanation
Indices: 1490072--1490118 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1490062 CTACGGAGAT
* *
1490072 GGCATATGAACTGGTGGGCTT
1 GGCATATGAACTGGAGGGCTG
* *
1490093 TGCATATGAAGTGGAGGGCTG
1 GGCATATGAACTGGAGGGCTG
1490114 GGCAT
1 GGCAT
1490119 GTACCCCTAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.13, G:0.40, T:0.26
Consensus pattern (21 bp):
GGCATATGAACTGGAGGGCTG
Found at i:1491735 original size:35 final size:33
Alignment explanation
Indices: 1491691--1491779 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 33
1491681 TAATAATTCT
1491691 AAATAAATAATAATTATATAAATATTATTTTAATA-A
1 AAAT-AATAATAATTATATAAATA-TA--TTAATATA
* *
1491727 AAATAATAATATTTACATAAATATATTAATATA
1 AAATAATAATAATTATATAAATATATTAATATA
* *
1491760 AAAT-ATAATAACTATTTAAA
1 AAATAATAATAATTATATAAA
1491780 AAAAATACTA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
32 18 0.39
33 5 0.11
34 2 0.04
35 17 0.37
36 4 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (33 bp):
AAATAATAATAATTATATAAATATATTAATATA
Found at i:1491746 original size:20 final size:19
Alignment explanation
Indices: 1491719--1491786 Score: 54
Period size: 20 Copynumber: 3.7 Consensus size: 19
1491709 TAAATATTAT
1491719 TTTAATAAAAATAATAATA
1 TTTAATAAAAATAATAATA
* *
1491738 TTTACATAAATATATTAATA
1 TTTA-ATAAAAATAATAATA
*
1491758 --T-A-AAATATAATAACTA
1 TTTAATAAAAATAATAA-TA
*
1491774 TTTAAAAAAAATA
1 TTTAATAAAAATA
1491787 CTAACATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
15 10 0.26
16 3 0.08
18 2 0.05
19 5 0.13
20 19 0.49
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
TTTAATAAAAATAATAATA
Found at i:1491756 original size:32 final size:35
Alignment explanation
Indices: 1491691--1491770 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 35
1491681 TAATAATTCT
*
1491691 AAATAAATAATAATTATATAAATATTATTTTAATA-A
1 AAAT-AATAATAATTACATAAATATTA-TTTAATATA
*
1491727 AAATAATAATATTTACATAAATA-TA-TTAATATA
1 AAATAATAATAATTACATAAATATTATTTAATATA
1491760 AAAT-ATAATAA
1 AAATAATAATAA
1491771 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 12 0.30
33 5 0.12
34 2 0.05
35 17 0.43
36 4 0.10
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (35 bp):
AAATAATAATAATTACATAAATATTATTTAATATA
Found at i:1491796 original size:35 final size:34
Alignment explanation
Indices: 1491723--1491799 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 34
1491713 TATTATTTTA
* * * *
1491723 ATAAAAATAATAATATTTACATAAATATATTAAT
1 ATAAAAATAATAATATTTACAAAAAAATACTAAC
1491757 ATAAAATATAATAACTATTTA-AAAAAAATACTAAC
1 ATAAAA-ATAATAA-TATTTACAAAAAAATACTAAC
1491792 ATAAAAAT
1 ATAAAAAT
1491800 GAATTTCTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 8 0.22
35 23 0.62
36 6 0.16
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (34 bp):
ATAAAAATAATAATATTTACAAAAAAATACTAAC
Found at i:1492924 original size:49 final size:49
Alignment explanation
Indices: 1492871--1493000 Score: 224
Period size: 49 Copynumber: 2.7 Consensus size: 49
1492861 GGTTGATTGG
* *
1492871 GATACCCCGGGCACCATGGAGGTCCACCCCTGGATGAGAGGTTGCCCGA
1 GATACCCCGGACTCCATGGAGGTCCACCCCTGGATGAGAGGTTGCCCGA
*
1492920 GATACCCCGGACTCCATAGAGGTCCACCCCTGGATGAGAGGTTGCCCGA
1 GATACCCCGGACTCCATGGAGGTCCACCCCTGGATGAGAGGTTGCCCGA
*
1492969 GATACCCCGGACTCCATGGAGGTCCGCCCCTG
1 GATACCCCGGACTCCATGGAGGTCCACCCCTG
1493001 CCCACCACTA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 76 1.00
ACGTcount: A:0.20, C:0.35, G:0.30, T:0.15
Consensus pattern (49 bp):
GATACCCCGGACTCCATGGAGGTCCACCCCTGGATGAGAGGTTGCCCGA
Found at i:1495826 original size:2 final size:2
Alignment explanation
Indices: 1495819--1495852 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1495809 TCGTTTTTAA
1495819 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1495853 TATTTTTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1508307 original size:25 final size:25
Alignment explanation
Indices: 1508253--1508317 Score: 62
Period size: 25 Copynumber: 2.5 Consensus size: 25
1508243 TTTAAAGTAT
*
1508253 ATTATTTTTTAATCTAAATATTCATT
1 ATTATTTTTT-ATCTAAATATTCATA
1508279 ATTATTTTTTATC-AAAGTATAT-ATA
1 ATTATTTTTTATCTAAA-TAT-TCATA
1508304 ATTATAATTTTTAT
1 ATTAT--TTTTTAT
1508318 TTTATTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
24 3 0.09
25 13 0.38
26 11 0.32
27 7 0.21
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTATTTTTTATCTAAATATTCATA
Found at i:1514237 original size:32 final size:32
Alignment explanation
Indices: 1514192--1514253 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
1514182 GATAATTTAA
1514192 ATAATTTTATTTAAAATAAAAAATTTAAAAGT
1 ATAATTTTATTTAAAATAAAAAATTTAAAAGT
**
1514224 ATAATTTCT-TTTAAAATAAAATTTTTAAAA
1 ATAATTT-TATTTAAAATAAAAAATTTAAAA
1514254 ATTTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (32 bp):
ATAATTTTATTTAAAATAAAAAATTTAAAAGT
Found at i:1515032 original size:90 final size:91
Alignment explanation
Indices: 1514863--1515033 Score: 227
Period size: 90 Copynumber: 1.9 Consensus size: 91
1514853 TAAAAAGTTT
* * * **
1514863 ATGTAACATTCTTGATTATAAATGAAATTATTATCAATTATATAATTTTTTATAGTAGACATGAC
1 ATGTAACATTCTTGATTATAAATGAAATTATTATCAATTATATAACTTTTTACAGTAGAAAAAAC
* * *
1514928 AATATTTTAGGTTAAAATCCGTCGTA
66 AACATTTGAAGTTAAAATCCGTCGTA
* * * *
1514954 ATGTAACATTCTTGATTATAACT-AAATTATTATCAATTATGTAACTTTTTACATTAGAAAAAAT
1 ATGTAACATTCTTGATTATAAATGAAATTATTATCAATTATATAACTTTTTACAGTAGAAAAAAC
1515018 AACATTTGAAGTTAAA
66 AACATTTGAAGTTAAA
1515034 TTTCATCATA
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
90 46 0.68
91 22 0.32
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (91 bp):
ATGTAACATTCTTGATTATAAATGAAATTATTATCAATTATATAACTTTTTACAGTAGAAAAAAC
AACATTTGAAGTTAAAATCCGTCGTA
Found at i:1518647 original size:2 final size:2
Alignment explanation
Indices: 1518590--1518631 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1518580 ATAAGATGAT
*
1518590 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1518632 CGAACATGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1521027 original size:18 final size:19
Alignment explanation
Indices: 1520998--1521046 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
1520988 ATTTAGATAT
*
1520998 TTTTTATATTTTATGTTAAAA
1 TTTTTAT-TTTCAT-TTAAAA
*
1521019 TTTTT-TTTTCCTTTAAAA
1 TTTTTATTTTCATTTAAAA
1521037 TTTTTATTTT
1 TTTTTATTTT
1521047 TACATCAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 11 0.44
19 8 0.32
20 1 0.04
21 5 0.20
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTTATTTTCATTTAAAA
Found at i:1521967 original size:15 final size:15
Alignment explanation
Indices: 1521947--1521980 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1521937 AGTATGGTGT
1521947 ATGTGTTTAGGAGGC
1 ATGTGTTTAGGAGGC
1521962 ATGTGTTTAGGAGGC
1 ATGTGTTTAGGAGGC
1521977 ATGT
1 ATGT
1521981 AGGTGGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.21, C:0.06, G:0.38, T:0.35
Consensus pattern (15 bp):
ATGTGTTTAGGAGGC
Found at i:1527829 original size:21 final size:22
Alignment explanation
Indices: 1527803--1527854 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
1527793 ATAGGATTTA
*
1527803 AAAAATAT-TAAGTTCATAATT
1 AAAAATATACAAGTTCATAATT
**
1527824 AAAAATATGACAAGTTCATCTTT
1 AAAAATAT-ACAAGTTCATAATT
1527847 AAAAATAT
1 AAAAATAT
1527855 GATGTTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 8 0.31
23 18 0.69
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.35
Consensus pattern (22 bp):
AAAAATATACAAGTTCATAATT
Found at i:1527838 original size:23 final size:23
Alignment explanation
Indices: 1527812--1527856 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1527802 AAAAAATATT
1527812 AAGTTCATAATTAAAAATATGAC
1 AAGTTCATAATTAAAAATATGAC
**
1527835 AAGTTCATCTTTAAAAATATGA
1 AAGTTCATAATTAAAAATATGA
1527857 TGTTAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (23 bp):
AAGTTCATAATTAAAAATATGAC
Found at i:1531679 original size:9 final size:9
Alignment explanation
Indices: 1531665--1531691 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1531655 GATTGGCCGA
1531665 TTCAACCGG
1 TTCAACCGG
1531674 TTCAACCGG
1 TTCAACCGG
1531683 TTCAACCGG
1 TTCAACCGG
1531692 GAACCGTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (9 bp):
TTCAACCGG
Found at i:1532269 original size:23 final size:22
Alignment explanation
Indices: 1532243--1532285 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1532233 TTAGCCCTAA
*
1532243 ATTTATTTTTTAATTATAATTAT
1 ATTTATTATTTAA-TATAATTAT
1532266 ATTTATTATTTAATATAATT
1 ATTTATTATTTAATATAATT
1532286 TACCTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTATTATTTAATATAATTAT
Found at i:1535482 original size:2 final size:2
Alignment explanation
Indices: 1535475--1535538 Score: 85
Period size: 2 Copynumber: 32.5 Consensus size: 2
1535465 TTTAAATAAA
* * * *
1535475 AT AT AT AT AT TT AT AT AT TT A- AT TT AA 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
1535516 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1535539 CCCAGCCCGA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1535485 original size:32 final size:33
Alignment explanation
Indices: 1535437--1535517 Score: 110
Period size: 32 Copynumber: 2.5 Consensus size: 33
1535427 ATAATTATTT
* *
1535437 ATATATATATAAATATTAATAAATTTAATTTAA
1 ATATAAATATATATATTAATAAATTTAATTTAA
* *
1535470 ATA-AAATATATATATTTATATATTTAATTTAA
1 ATATAAATATATATATTAATAAATTTAATTTAA
*
1535502 ATATATATATATATAT
1 ATATAAATATATATAT
1535518 ATATATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 28 0.67
33 14 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
ATATAAATATATATATTAATAAATTTAATTTAA
Found at i:1535571 original size:12 final size:12
Alignment explanation
Indices: 1535556--1535590 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1535546 CGATTCTCGG
1535556 CCCAATACCCGA
1 CCCAATACCCGA
* *
1535568 CCCAATACCTGG
1 CCCAATACCCGA
1535580 CCCAATACCCG
1 CCCAATACCCG
1535591 TTTAAATAAC
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:0.29, C:0.49, G:0.11, T:0.11
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:1536303 original size:31 final size:31
Alignment explanation
Indices: 1536268--1536335 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
1536258 CTTTTAAAAC
*
1536268 TTGCAATACAATCCCCTAACATTTAGTCCGT
1 TTGCAATACAATCCCCCAACATTTAGTCCGT
** *
1536299 TTGCAATATGATCCCCCAACATTTAGTCTGT
1 TTGCAATACAATCCCCCAACATTTAGTCCGT
1536330 TTGCAA
1 TTGCAA
1536336 AATAGTCCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (31 bp):
TTGCAATACAATCCCCCAACATTTAGTCCGT
Found at i:1537677 original size:31 final size:31
Alignment explanation
Indices: 1537636--1537702 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
1537626 AATACAGTCT
*
1537636 CCCAACATTTAGTATGTTTGTAATATGGTCC
1 CCCAACATTTAGTATGTTTGCAATATGGTCC
* *
1537667 CCCAATATTTAGTCTGTTTGCAATATGGTCC
1 CCCAACATTTAGTATGTTTGCAATATGGTCC
1537698 CCCAA
1 CCCAA
1537703 GCAACTGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (31 bp):
CCCAACATTTAGTATGTTTGCAATATGGTCC
Found at i:1542077 original size:27 final size:23
Alignment explanation
Indices: 1542022--1542086 Score: 58
Period size: 27 Copynumber: 2.7 Consensus size: 23
1542012 ATAAAATTAT
1542022 AAAAAATAACAAATAAAGAAAAA
1 AAAAAATAACAAATAAAGAAAAA
*
1542045 ATAAAAATACACTATAATAAAGTAAAA
1 A-AAAAATA-AC-A-AATAAAGAAAAA
* * *
1542072 GAAAAACAACGAATA
1 AAAAAATAACAAATA
1542087 TCCACAACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
23 5 0.15
24 7 0.21
25 4 0.12
26 7 0.21
27 11 0.32
ACGTcount: A:0.72, C:0.08, G:0.06, T:0.14
Consensus pattern (23 bp):
AAAAAATAACAAATAAAGAAAAA
Found at i:1542226 original size:16 final size:16
Alignment explanation
Indices: 1542205--1542235 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1542195 GAATTTTTAA
1542205 AATATTCTTTTATTTT
1 AATATTCTTTTATTTT
1542221 AATATTCTTTTATTT
1 AATATTCTTTTATTT
1542236 CTCCTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
AATATTCTTTTATTTT
Found at i:1543789 original size:19 final size:19
Alignment explanation
Indices: 1543765--1543819 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
1543755 ATGACCAACA
1543765 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
1543784 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
*
1543803 AAATCGCAACGCGATCT
1 AAATCGCAATGCGATCT
1543820 TCAGTATCGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAATGCGATCTCT
Found at i:1543860 original size:20 final size:20
Alignment explanation
Indices: 1543805--1543881 Score: 59
Period size: 20 Copynumber: 3.9 Consensus size: 20
1543795 CGATCTCTAA
*
1543805 ATCGCAACGCGATCTTCAGT
1 ATCGCAACGCGATTTTCAGT
**
1543825 ATCGCAAATC-AGTTTTCAG-
1 ATCGCAACGCGA-TTTTCAGT
* *
1543844 ATTCGCAACGCGATTTTAACT
1 A-TCGCAACGCGATTTTCAGT
**
1543865 ATCGCATTGCGATTTTC
1 ATCGCAACGCGATTTTC
1543882 CAAATTTGCG
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
19 2 0.05
20 39 0.91
21 2 0.05
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (20 bp):
ATCGCAACGCGATTTTCAGT
Found at i:1543998 original size:19 final size:19
Alignment explanation
Indices: 1543974--1544013 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1543964 CAAAATCGCA
1543974 ATGCGATTTTCAAAGCGCC
1 ATGCGATTTTCAAAGCGCC
1543993 ATGCGATTTTCAAAGCGCC
1 ATGCGATTTTCAAAGCGCC
1544012 AT
1 AT
1544014 TAGTATCGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (19 bp):
ATGCGATTTTCAAAGCGCC
Found at i:1544673 original size:20 final size:20
Alignment explanation
Indices: 1544585--1544690 Score: 90
Period size: 20 Copynumber: 5.4 Consensus size: 20
1544575 AAATCGCAAC
*
1544585 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
1544604 GCGATTTTCA-TTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
* ** **
1544623 GTGATAGTCAAATTCGCGTT
1 GCGATTTTCATTTTCGCGTT
** *
1544643 GCGATAATCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
* *
1544663 GCGATTTTCATTTTTGTGTT
1 GCGATTTTCATTTTCGCGTT
*
1544683 GCAATTTT
1 GCGATTTT
1544691 AAGTTTCAGA
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
19 24 0.33
20 48 0.67
ACGTcount: A:0.16, C:0.15, G:0.22, T:0.47
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:1546625 original size:20 final size:20
Alignment explanation
Indices: 1546602--1546650 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1546592 GAAACTTAAA
1546602 ATCGCAACGCGGAA-ATGACT
1 ATCGCAACGC-GAATATGACT
*
1546622 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATATGACT
1546642 ATCGCAACG
1 ATCGCAACG
1546651 AGATAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAATATGACT
Found at i:1546692 original size:33 final size:34
Alignment explanation
Indices: 1546642--1546717 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
1546632 GAATTTGACT
*
1546642 ATCGCAACGAGATAATCGCAATGCG-AAATAAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
* *
1546675 ATCGCAACGTGAAAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
1546709 ATCGCAACG
1 ATCGCAACG
1546718 CGAATTTAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 23 0.59
34 16 0.41
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.14
Consensus pattern (34 bp):
ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
Found at i:1546707 original size:20 final size:20
Alignment explanation
Indices: 1546684--1546721 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1546674 AATCGCAACG
*
1546684 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAACGCGAAAA
1546704 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
1546722 TTTAGTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAAA
Found at i:1546739 original size:19 final size:19
Alignment explanation
Indices: 1546717--1546759 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1546707 AAATCGCAAC
1546717 GCGA-ATTTAGTTTCGCATT
1 GCGATATTTA-TTTCGCATT
*
1546736 GCGATTTTTATTTCGCATT
1 GCGATATTTATTTCGCATT
1546755 GCGAT
1 GCGAT
1546760 TATCTTGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (19 bp):
GCGATATTTATTTCGCATT
Found at i:1546760 original size:19 final size:20
Alignment explanation
Indices: 1546722--1546760 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
1546712 GCAACGCGAA
1546722 TTTAGTTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
1546742 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
1546761 ATCTTGTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (20 bp):
TTTAGTTTCGCATTGCGATT
Found at i:1546791 original size:20 final size:20
Alignment explanation
Indices: 1546766--1546833 Score: 102
Period size: 20 Copynumber: 3.4 Consensus size: 20
1546756 CGATTATCTT
*
1546766 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAATTTCGC
1546786 GTTGCGATAGTC-ATTTCCGC
1 GTTGCGATAGTCAATTT-CGC
*
1546806 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAATTTCGC
1546826 GTTGCGAT
1 GTTGCGAT
1546834 TTTAAGTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.07
20 38 0.86
21 3 0.07
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGTCAATTTCGC
Found at i:1546843 original size:20 final size:20
Alignment explanation
Indices: 1546820--1546862 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1546810 CGATAGTCAT
1546820 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
1546840 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
1546860 TTT
1 TTT
1546863 TAGAATCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.12, G:0.23, T:0.51
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:1546850 original size:40 final size:40
Alignment explanation
Indices: 1546765--1546853 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
1546755 GCGATTATCT
*
1546765 TGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTCCG
1 TGTTGCGATAGTCAAATTCGCGTTGCGATAGTAATTTCCG
* ** **
1546805 CGTTGCGATAGTCATTTTCGCGTTGCGATTTTAAGTTT-CG
1 TGTTGCGATAGTCAAATTCGCGTTGCGATAGTAA-TTTCCG
1546845 TGTTGCGAT
1 TGTTGCGAT
1546854 TTTAAGTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 38 0.93
41 3 0.07
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.39
Consensus pattern (40 bp):
TGTTGCGATAGTCAAATTCGCGTTGCGATAGTAATTTCCG
Found at i:1547416 original size:21 final size:21
Alignment explanation
Indices: 1547392--1547450 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
1547382 CTATCATCCC
1547392 TCAAGAGTCTCCTCCCATCGT
1 TCAAGAGTCTCCTCCCATCGT
* * **
1547413 TCAAGAGGCCCCTGTCATCGT
1 TCAAGAGTCTCCTCCCATCGT
*
1547434 TGAAGAGGTCT-CTCCCA
1 TCAAGA-GTCTCCTCCCA
1547451 CCATTTAAGA
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.20, C:0.34, G:0.20, T:0.25
Consensus pattern (21 bp):
TCAAGAGTCTCCTCCCATCGT
Found at i:1547461 original size:42 final size:42
Alignment explanation
Indices: 1547339--1547450 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
1547329 GCTCGACTCA
* * * *
1547339 CCTGTCATTGTTCAAGAGGCCTCTCCTATCGTTCAGGAGGCC
1 CCTGTCATCGTTCAAGAGGTCTCTCCCATCGTTCAAGAGGCC
* **
1547381 CCTATCATCCCTCAAGA-GTCTCCTCCCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGTCT-CTCCCATCGTTCAAGAGGCC
*
1547423 CCTGTCATCGTTGAAGAGGTCTCTCCCA
1 CCTGTCATCGTTCAAGAGGTCTCTCCCA
1547451 CCATTTAAGA
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 3 0.05
42 50 0.88
43 4 0.07
ACGTcount: A:0.19, C:0.35, G:0.20, T:0.27
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGGTCTCTCCCATCGTTCAAGAGGCC
Found at i:1549016 original size:20 final size:20
Alignment explanation
Indices: 1548991--1549051 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
1548981 AACGCTAAAC
*
1548991 TCAAAATAGCAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
1549011 TCAAAATCGCAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
* *
1549031 CCAAAATCGCAACGCGAAAG
1 TCAAAATCGCAATGCGAAAG
1549051 T
1 T
1549052 AAATTCGCGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (20 bp):
TCAAAATCGCAATGCGAAAG
Found at i:1549120 original size:19 final size:19
Alignment explanation
Indices: 1549096--1549160 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
1549086 ATTTTCTCGT
*
1549096 TGCGATAGTCAACTTCCCG
1 TGCGATAGTCAAATTCCCG
* **
1549115 TGCGATAATCAAATTCACAT
1 TGCGATAGTCAAATTC-CCG
*
1549135 TGCGATAGTCAAATTCGCG
1 TGCGATAGTCAAATTCCCG
1549154 TTGCGAT
1 -TGCGAT
1549161 TTTTGCATTG
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 14 0.39
20 22 0.61
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (19 bp):
TGCGATAGTCAAATTCCCG
Found at i:1549142 original size:73 final size:74
Alignment explanation
Indices: 1549052--1549194 Score: 182
Period size: 73 Copynumber: 1.9 Consensus size: 74
1549042 ACGCGAAAGT
* * * * * * *
1549052 AAATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCT-CGTTGCGATAGTCAACTTCCCG-
1 AAATTCACATTGCGATAGTCAAATACGCGTTGCGATTTT-TGCATTGCAATAGTCAAATTCCCGT
1549115 TGCGATAATC
65 TGCGATAATC
* *
1549125 AAATTCACATTGCGATAGTCAAATTCGCGTTGCGATTTTTGCATTGCAATAGTCAAATTCGCGTT
1 AAATTCACATTGCGATAGTCAAATACGCGTTGCGATTTTTGCATTGCAATAGTCAAATTCCCGTT
1549190 GCGAT
66 GCGAT
1549195 TTTTACGTTG
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
72 1 0.02
73 52 0.88
74 6 0.10
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.34
Consensus pattern (74 bp):
AAATTCACATTGCGATAGTCAAATACGCGTTGCGATTTTTGCATTGCAATAGTCAAATTCCCGTT
GCGATAATC
Found at i:1549192 original size:54 final size:53
Alignment explanation
Indices: 1549123--1549268 Score: 132
Period size: 54 Copynumber: 2.7 Consensus size: 53
1549113 CGTGCGATAA
* * *
1549123 TCAAATTCACATTGCGATAGTCAAATTCGCGTTGCGATTTTTGCATTGCAATAG
1 TCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTCT-CATTGCAATAG
** * ** * * * * **
1549177 TCAAATTCGCGTTGCGATTTTTACGTT-GCGATAGTCAAATTCTCGTTGTGATAG
1 TCAAATTCGCGTTGCGATAGTCAAATTCGCG-TTG-CGATTTCTCATTGCAATAG
1549231 TCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 TCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1549269 ATTCAAATGA
Statistics
Matches: 67, Mismatches: 22, Indels: 7
0.70 0.23 0.07
Matches are distributed among these distances:
53 5 0.07
54 54 0.81
55 8 0.12
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (53 bp):
TCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTCTCATTGCAATAG
Found at i:1549229 original size:20 final size:20
Alignment explanation
Indices: 1549200--1549276 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
1549190 GCGATTTTTA
*
1549200 CGTTGCGATAGTCAAATTCT
1 CGTTGCGATAGTCAAATTCG
*
1549220 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1549240 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1549260 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
1549277 GAATGTGTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1549255 original size:40 final size:40
Alignment explanation
Indices: 1549044--1549276 Score: 164
Period size: 34 Copynumber: 6.3 Consensus size: 40
1549034 AAATCGCAAC
* * * *
1549044 GCGAAAGT-AAATTCGCGTTGCGATAGTCTAATACGCTTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTT
* * *
1549083 GCGAT--T----TTCTCGTTGCGATAGTCAACTTCCCG-T
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTT
* * *
1549116 GCGATAATCAAATTCACATTGCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTT
* * *
1549156 GCGAT--T----TTTGCATTGCAATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTT
** *
1549190 GCGAT--T----TTTACGTTGCGATAGTCAAATTCTCGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTT
*
1549224 GTGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTT
*
1549264 GCGATATTCAAAT
1 GCGATAGTCAAAT
1549277 GAATGTGTAA
Statistics
Matches: 157, Mismatches: 24, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
33 6 0.04
34 79 0.50
35 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 26 0.17
40 42 0.27
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.34
Consensus pattern (40 bp):
GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTT
Found at i:1549499 original size:140 final size:140
Alignment explanation
Indices: 1549247--1549529 Score: 521
Period size: 140 Copynumber: 2.0 Consensus size: 140
1549237 TCGCGTTGCG
*
1549247 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGAGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
* *
1549312 TAGTAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1549377 AATACACATA
131 AATACACATA
*
1549387 ATAGTCAAATTCGAGTTGTGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGAGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1549452 TAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
*
1549517 AATACATATA
131 AATACACATA
1549527 ATA
1 ATA
1549530 CAACGTTTGC
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 138 1.00
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGAGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:1551919 original size:24 final size:24
Alignment explanation
Indices: 1551885--1551938 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1551875 CTGAAACATC
*
1551885 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* *
1551909 ATCAAAGTCCGGGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
1551933 ATCAAA
1 ATCAAA
1551939 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:1552117 original size:22 final size:22
Alignment explanation
Indices: 1552091--1552143 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1552081 TATTGGAAAT
1552091 GTGGTGAAACAAAATTTGCTTG
1 GTGGTGAAACAAAATTTGCTTG
1552113 GTGGTGAAACAAAATTTGCTTG
1 GTGGTGAAACAAAATTTGCTTG
*
1552135 GTGATGAAA
1 GTGGTGAAA
1552144 TTGTGGTGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (22 bp):
GTGGTGAAACAAAATTTGCTTG
Found at i:1552800 original size:20 final size:20
Alignment explanation
Indices: 1552775--1552818 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1552765 GAAATTCAGT
*
1552775 GTTGCGACAGTCAGAATCGC
1 GTTGCGACAGTCAGAATCGA
*
1552795 GTTGCGATAGTCAGAATCGA
1 GTTGCGACAGTCAGAATCGA
1552815 GTTG
1 GTTG
1552819 TGATTATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (20 bp):
GTTGCGACAGTCAGAATCGA
Found at i:1552950 original size:19 final size:19
Alignment explanation
Indices: 1552926--1552964 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1552916 TTTACGATAC
* *
1552926 TAGAGATCGCGTTGCGATT
1 TAGAGATCGCATTGCAATT
1552945 TAGAGATCGCATTGCAATT
1 TAGAGATCGCATTGCAATT
1552964 T
1 T
1552965 TGTTAGTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (19 bp):
TAGAGATCGCATTGCAATT
Found at i:1563593 original size:21 final size:21
Alignment explanation
Indices: 1563567--1563606 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1563557 TTTAAGACAG
*
1563567 TTTCAACCTAAAATATTATCA
1 TTTCAACCTAAAAAATTATCA
1563588 TTTCAACCTAAAAAATTAT
1 TTTCAACCTAAAAAATTAT
1563607 ATAAATTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTCAACCTAAAAAATTATCA
Found at i:1571285 original size:17 final size:17
Alignment explanation
Indices: 1571244--1571288 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1571234 CCCTACTTGA
1571244 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** **
1571261 TTTTATATTTTTTAAAT
1 TTAAATATTTAATAAAT
1571278 TTAAATATTTA
1 TTAAATATTTA
1571289 TTTTTACATG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:1571320 original size:16 final size:16
Alignment explanation
Indices: 1571299--1571332 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1571289 TTTTTACATG
1571299 AACCAAAA-TACTATTA
1 AACCAAAATTA-TATTA
1571315 AACCAAAATTATATTA
1 AACCAAAATTATATTA
1571331 AA
1 AA
1571333 TATATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (16 bp):
AACCAAAATTATATTA
Found at i:1572680 original size:36 final size:36
Alignment explanation
Indices: 1572631--1572727 Score: 149
Period size: 36 Copynumber: 2.7 Consensus size: 36
1572621 TTTTGACGGC
*
1572631 CGATAGTCGCAAATATCTCGATTATGAATCAACGTT
1 CGATAGTCACAAATATCTCGATTATGAATCAACGTT
*
1572667 CGATAGTCACAAATATCTCGATTATGAATCGACGTT
1 CGATAGTCACAAATATCTCGATTATGAATCAACGTT
* * *
1572703 CTATAGTCACAAAGATCTCAATTAT
1 CGATAGTCACAAATATCTCGATTAT
1572728 ATCATAAGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (36 bp):
CGATAGTCACAAATATCTCGATTATGAATCAACGTT
Found at i:1581897 original size:2 final size:2
Alignment explanation
Indices: 1581890--1581921 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1581880 AAATCTTTCG
1581890 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1581922 TTTAATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1611381 original size:2 final size:2
Alignment explanation
Indices: 1611374--1611400 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1611364 TGTGATTCTT
1611374 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 T
1611401 GTAAGTGTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1624479 original size:15 final size:16
Alignment explanation
Indices: 1624451--1624484 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1624441 TGCGCTTGGT
1624451 AGGAAAGCAAAATGAG
1 AGGAAAGCAAAATGAG
1624467 AGGAAAG-AAAATGAG
1 AGGAAAGCAAAATGAG
1624482 AGG
1 AGG
1624485 GATGATAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.56, C:0.03, G:0.35, T:0.06
Consensus pattern (16 bp):
AGGAAAGCAAAATGAG
Found at i:1627790 original size:4 final size:4
Alignment explanation
Indices: 1627781--1627807 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1627771 AATAAAAGAG
1627781 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1627808 AAGGTAACGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1628276 original size:15 final size:15
Alignment explanation
Indices: 1628256--1628306 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
1628246 GATCAAAAAT
1628256 ATTTTATAATATACG
1 ATTTTATAATATACG
**
1628271 ATTTTAATCAA-A-AAT
1 ATTTT-AT-AATATACG
1628286 ATTTTATAATATACG
1 ATTTTATAATATACG
1628301 ATTTTA
1 ATTTTA
1628307 ATTCATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
13 2 0.07
14 3 0.11
15 18 0.64
16 3 0.11
17 2 0.07
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (15 bp):
ATTTTATAATATACG
Found at i:1628281 original size:30 final size:30
Alignment explanation
Indices: 1628247--1628308 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1628237 AATCTCAGTG
1628247 ATCAAAAATATTTTATAATATACGATTTTA
1 ATCAAAAATATTTTATAATATACGATTTTA
1628277 ATCAAAAATATTTTATAATATACGATTTTA
1 ATCAAAAATATTTTATAATATACGATTTTA
1628307 AT
1 AT
1628309 TCATTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (30 bp):
ATCAAAAATATTTTATAATATACGATTTTA
Found at i:1628452 original size:21 final size:21
Alignment explanation
Indices: 1628426--1628518 Score: 118
Period size: 21 Copynumber: 4.4 Consensus size: 21
1628416 ATTTTGGACT
1628426 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
1628447 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAATTTGGAATAA
* *
1628468 ATCGCAATGAATTTTGAATAA
1 ATCGCAACGAATTTGGAATAA
1628489 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
1628510 ATCGCAACG
1 ATCGCAACG
1628519 CGAACTTCGA
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
19 8 0.13
21 42 0.70
23 10 0.17
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:1628466 original size:42 final size:42
Alignment explanation
Indices: 1628419--1628558 Score: 153
Period size: 42 Copynumber: 3.3 Consensus size: 42
1628409 CGTTGCGATT
*
1628419 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTCGAATAAATCGCAACGCGAAC
* * *
1628461 TTGGACTATCGCAATGAATTTTGAATAAATCGCAA--CGAAT
1 TTGGACTATCGCAACGAATTTCGAATAAATCGCAACGCGAAC
* * *
1628501 TTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAATTTCGAATAAATCGCAACGCGAAC
1628545 TTGGACTATCGCAA
1 TTGGACTATCGCAA
1628559 TGCGAATATG
Statistics
Matches: 82, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
40 10 0.12
42 54 0.66
44 18 0.22
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTCGAATAAATCGCAACGCGAAC
Found at i:1628534 original size:21 final size:21
Alignment explanation
Indices: 1628510--1628564 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
1628500 TTTGGAATAA
1628510 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
1628531 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
1628552 ATCGCAATGCGAA
1 ATCGCAACGCGAA
1628565 TATGTAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:1628556 original size:63 final size:61
Alignment explanation
Indices: 1628419--1628558 Score: 199
Period size: 63 Copynumber: 2.2 Consensus size: 61
1628409 CGTTGCGATT
* * *
1628419 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAATGAAT
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
* *
1628480 TTTGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA--CGAAC
1628545 TTGGACTATCGCAA
1 TTGGACTATCGCAA
1628559 TGCGAATATG
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
61 5 0.07
63 55 0.81
65 8 0.12
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (61 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
Found at i:1628597 original size:21 final size:21
Alignment explanation
Indices: 1628572--1628625 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1628562 GAATATGTAA
1628572 ATCGCATTGCGATAGTCCAAG
1 ATCGCATTGCGATAGTCCAAG
* *
1628593 ATCGCGTTGCGATAGTCGAAG
1 ATCGCATTGCGATAGTCCAAG
*
1628614 TTCGCATTGCGA
1 ATCGCATTGCGA
1628626 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (21 bp):
ATCGCATTGCGATAGTCCAAG
Found at i:1636497 original size:29 final size:31
Alignment explanation
Indices: 1636429--1636497 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1636419 GCAATGTCAC
*
1636429 AGTGATCATTTTATAACAGTTAGATAAATTT
1 AGTGATTATTTTATAACAGTTAGATAAATTT
* * *
1636460 AATGATTATTTTATAACA-TTTGAT-AGTTT
1 AGTGATTATTTTATAACAGTTAGATAAATTT
1636489 AGTGATTAT
1 AGTGATTAT
1636498 AGTAACCATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 12 0.36
30 5 0.15
31 16 0.48
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.46
Consensus pattern (31 bp):
AGTGATTATTTTATAACAGTTAGATAAATTT
Found at i:1638114 original size:3 final size:3
Alignment explanation
Indices: 1638106--1638131 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1638096 GATTAAAAAT
1638106 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1638132 GAAGTTATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1638717 original size:15 final size:16
Alignment explanation
Indices: 1638683--1638718 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1638673 TTTTCACGAT
*
1638683 ATTAATATCACTTTTT
1 ATTAATATCACTTTTA
1638699 ATTAATATCA-TTTTA
1 ATTAATATCACTTTTA
1638714 ATTAA
1 ATTAA
1638719 CTATATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTAATATCACTTTTA
Found at i:1645857 original size:11 final size:11
Alignment explanation
Indices: 1645835--1645891 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
1645825 TTGTCGATTG
1645835 TTATTGTTTTTC
1 TTATT-TTTTTC
1645847 TTATTTTTTTC
1 TTATTTTTTTC
* * *
1645858 ATATTATTTCC
1 TTATTTTTTTC
1645869 TTTATTTTTTTC
1 -TTATTTTTTTC
* *
1645881 ATATTATTTTC
1 TTATTTTTTTC
1645892 CTTTATTTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
11 23 0.64
12 13 0.36
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.72
Consensus pattern (11 bp):
TTATTTTTTTC
Found at i:1645891 original size:24 final size:23
Alignment explanation
Indices: 1645847--1645900 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
1645837 ATTGTTTTTC
1645847 TTATTTTTTTCATATTATTTCCT
1 TTATTTTTTTCATATTATTTCCT
1645870 TTATTTTTTTCATATTATTTTCCT
1 TTATTTTTTTCATATTA-TTTCCT
1645894 TTATTTT
1 TTATTTT
1645901 ATGTGTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 17 0.57
24 13 0.43
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (23 bp):
TTATTTTTTTCATATTATTTCCT
Found at i:1656006 original size:21 final size:21
Alignment explanation
Indices: 1655980--1656120 Score: 169
Period size: 21 Copynumber: 6.8 Consensus size: 21
1655970 GTTTCCAGAT
* *
1655980 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
* *
1656001 TCGCAATGCAAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
1656022 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
** * *
1656043 TCGCAATATGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
1656063 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
**
1656084 TCGCAACACGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1656105 TCGCAATGCGAACTTG
1 TCGCAATGCGAACTTG
1656121 CGAACTTGGA
Statistics
Matches: 101, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
20 15 0.15
21 86 0.85
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:1656078 original size:41 final size:41
Alignment explanation
Indices: 1656021--1656164 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
1656011 AACTTCGACT
*
1656021 ATCGCAATGCGAACTTGGACTATCGCAATATGAATATGTAA
1 ATCGCAATGCGAACTTGGACTATCGCAATACGAATATGTAA
*
1656062 ATCGCAATGCGAACTTGGACTATCGCAACACGAACT-TGGACTATCGCA
1 ATCGCAATGCGAACTTGGACTATCGCAATACGAA-TAT-G--TA----A
*
1656110 AT-GCGAACTTGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGC-AA--TGCGAACTTGGACTATCGCAATACGAATATGTAA
1656153 ATCGCAATGCGA
1 ATCGCAATGCGA
1656165 TAGTCGAAGT
Statistics
Matches: 86, Mismatches: 4, Indels: 26
0.74 0.03 0.22
Matches are distributed among these distances:
41 38 0.44
42 2 0.02
43 5 0.06
44 4 0.05
47 4 0.05
48 5 0.06
49 2 0.02
50 26 0.30
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (41 bp):
ATCGCAATGCGAACTTGGACTATCGCAATACGAATATGTAA
Found at i:1656315 original size:6 final size:6
Alignment explanation
Indices: 1656304--1656346 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
1656294 GATACGTATT
* *
1656304 ACCACG ACCACG ACCACG ACCCCG ACCCCG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1656347 CGAGACGGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
5 10 0.28
6 26 0.72
ACGTcount: A:0.26, C:0.58, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1657015 original size:21 final size:21
Alignment explanation
Indices: 1656991--1657127 Score: 147
Period size: 21 Copynumber: 6.6 Consensus size: 21
1656981 TTTGGAATAA
*
1656991 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
1657012 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
* * *
1657033 ATTGCAATGC-AAATAT-GTA-A
1 ATCGCAATGCGAACT-TCG-ACT
*
1657053 ATCGCAATGCGATA-GTCGACT
1 ATCGCAATGCGA-ACTTCGACT
*
1657074 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
1657095 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
1657116 ATCGCATTGCGA
1 ATCGCAATGCGA
1657128 TTTACATATT
Statistics
Matches: 96, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
20 16 0.17
21 79 0.82
22 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:1657109 original size:83 final size:83
Alignment explanation
Indices: 1656991--1657168 Score: 236
Period size: 83 Copynumber: 2.1 Consensus size: 83
1656981 TTTGGAATAA
* * *
1656991 ATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTCGACTATTGCAATGCAAATATGTA-A-A
1 ATCGCAATGCGAACTTCGACTATCGCAACGCGAACTTCGACTATCGCAATGC-AAT-T-TACATA
1657054 -TCGCAATGCGATAGTCGACT
63 TTCGCAATGCGATAGTCGACT
* * *
1657074 ATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTC
1 ATCGCAATGCGAACTTCGACTATCGCAACGCGAACTTCGACTATCGCAATGCAATTTACATATTC
*
1657139 GCATTGCGATAGTCGACT
66 GCAATGCGATAGTCGACT
*
1657157 ATCGCATTGCGA
1 ATCGCAATGCGA
1657169 TTTACATATT
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
80 2 0.02
81 2 0.02
82 3 0.04
83 77 0.92
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (83 bp):
ATCGCAATGCGAACTTCGACTATCGCAACGCGAACTTCGACTATCGCAATGCAATTTACATATTC
GCAATGCGATAGTCGACT
Found at i:1657142 original size:20 final size:20
Alignment explanation
Indices: 1657117--1657189 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
1657107 ACTTCGACTA
1657117 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
1657137 TCGCATTGCGATAGT-CGACTA-
1 TCGCATTGCGAT-TTAC-A-TAT
1657158 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1657178 TCGCATTGCGAT
1 TCGCATTGCGAT
1657190 AGTCCAAGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
19 2 0.04
20 27 0.59
21 15 0.33
22 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1657155 original size:41 final size:41
Alignment explanation
Indices: 1657054--1657284 Score: 218
Period size: 41 Copynumber: 5.4 Consensus size: 41
1657044 AATATGTAAA
* * *
1657054 TCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGAC-TA-
1 TCGCATTGCGATAGTCGACTATCGCATTGCG-A-TT-TACATAT
** *
1657096 TCGCAACGCGA-ACTTCGACTATCGCATTGCGATTTACATAT
1 TCGCATTGCGATA-GTCGACTATCGCATTGCGATTTACATAT
1657137 TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATAT
* * * *
1657178 TCGCATTGCGATAGTCCAAGTTCGCAAGTTCGCATTGCGATAGTCCA-AGT
1 TCGCATTGCGATAGT-C--G---ACTA--TCGCATTGCGAT-TTACATA-T
1657228 TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATAT
1657269 TCGCATTGCGATAGTC
1 TCGCATTGCGATAGTC
1657285 CAAGTTCGCG
Statistics
Matches: 159, Mismatches: 15, Indels: 31
0.78 0.07 0.15
Matches are distributed among these distances:
39 2 0.01
40 4 0.03
41 73 0.46
42 41 0.26
44 3 0.02
47 3 0.02
49 14 0.09
50 19 0.12
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (41 bp):
TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATAT
Found at i:1657163 original size:21 final size:21
Alignment explanation
Indices: 1657053--1657193 Score: 91
Period size: 21 Copynumber: 6.8 Consensus size: 21
1657043 AAATATGTAA
*
1657053 ATCGCAATGCGATAGTCGACT
1 ATCGCATTGCGATAGTCGACT
* * *
1657074 ATCGCAATGCGA-ACTTGGACT
1 ATCGCATTGCGATA-GTCGACT
** *
1657095 ATCGCAACGCGA-ACTTCGACT
1 ATCGCATTGCGATA-GTCGACT
*
1657116 ATCGCATTGCGAT--T-TACAT
1 ATCGCATTGCGATAGTCGAC-T
1657135 ATTCGCATTGCGATAGTCGACT
1 A-TCGCATTGCGATAGTCGACT
*
1657157 ATCGCATTGCGAT--T-TACAT
1 ATCGCATTGCGATAGTCGAC-T
1657176 ATTCGCATTGCGATAGTC
1 A-TCGCATTGCGATAGTC
1657194 CAAGTTCGCA
Statistics
Matches: 99, Mismatches: 9, Indels: 22
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.04
19 6 0.06
20 25 0.25
21 58 0.59
22 4 0.04
23 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (21 bp):
ATCGCATTGCGATAGTCGACT
Found at i:1657203 original size:21 final size:19
Alignment explanation
Indices: 1657117--1657300 Score: 77
Period size: 21 Copynumber: 8.6 Consensus size: 19
1657107 ACTTCGACTA
*
1657117 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGT-CA-AT
*
1657137 TCGCATTGCGATAGTCGACT
1 TCGCATTGCGATAGTC-AAT
*
1657157 ATCGCATTGCGAT-TTACATAT
1 -TCGCATTGCGATAGT-CA-AT
1657178 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGT-CAA-T
1657199 TCGCAAGTTCGCATTGCGATAGTCCAAGT
1 T--C--G----CATTGCGATAGT-CAA-T
*
1657228 TCGCATTGCGATAGTCGACT
1 TCGCATTGCGATAGTC-AAT
*
1657248 ATCGCATTGCGAT-TTACATAT
1 -TCGCATTGCGATAGT-CA-AT
1657269 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGT-CAA-T
*
1657290 TCGCGTTGCGA
1 TCGCATTGCGA
1657301 ATCTGGAAAC
Statistics
Matches: 131, Mismatches: 12, Indels: 41
0.71 0.07 0.22
Matches are distributed among these distances:
20 46 0.35
21 62 0.47
23 1 0.01
25 2 0.02
27 1 0.01
29 19 0.15
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (19 bp):
TCGCATTGCGATAGTCAAT
Found at i:1657219 original size:29 final size:29
Alignment explanation
Indices: 1657177--1657232 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
1657167 GATTTACATA
1657177 TTCGCATTGCGATAGTCCAAGTTCGCAAG
1 TTCGCATTGCGATAGTCCAAGTTCGCAAG
1657206 TTCGCATTGCGATAGTCCAAGTTCGCA
1 TTCGCATTGCGATAGTCCAAGTTCGCA
1657233 TTGCGATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (29 bp):
TTCGCATTGCGATAGTCCAAGTTCGCAAG
Found at i:1662036 original size:30 final size:30
Alignment explanation
Indices: 1662002--1662074 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
1661992 CCCGAAGGAC
1662002 CTATCCAGAGGTCATAAAAATCCTCGGTAA
1 CTATCCAGAGGTCATAAAAATCCTCGGTAA
*
1662032 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAAATCCTCGGTAA
* *
1662062 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1662075 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAAATCCTCGGTAA
Found at i:1662170 original size:63 final size:61
Alignment explanation
Indices: 1662057--1662185 Score: 188
Period size: 63 Copynumber: 2.1 Consensus size: 61
1662047 AAAGATCCTC
* *
1662057 GGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
* *
1662118 GGTATACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATA
1662181 GGTAA
1 GGTAA
1662186 ACCCTCGACT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
61 5 0.08
62 25 0.41
63 31 0.51
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (61 bp):
GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
Found at i:1662180 original size:32 final size:31
Alignment explanation
Indices: 1662060--1662187 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
1662050 GATCCTCGGT
* * * *
1662060 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
1662091 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
1662122 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
1662154 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
1662185 AAC
1 AAC
1662188 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.62
32 23 0.28
33 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:1663587 original size:21 final size:21
Alignment explanation
Indices: 1663561--1663606 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1663551 ATTTTATTCG
* *
1663561 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
1663582 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
1663603 CTTG
1 CTTG
1663607 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:1667030 original size:30 final size:30
Alignment explanation
Indices: 1666996--1667068 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
1666986 CCCAAAGGAC
1666996 CTATCCAGAGGTCATAAAAATCCTCGGTAA
1 CTATCCAGAGGTCATAAAAATCCTCGGTAA
* *
1667026 CTATCCAGAGGTTATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAAATCCTCGGTAA
* *
1667056 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1667069 CCGAAGAACC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAAATCCTCGGTAA
Found at i:1667164 original size:63 final size:61
Alignment explanation
Indices: 1667051--1667179 Score: 188
Period size: 63 Copynumber: 2.1 Consensus size: 61
1667041 AAAGATCCTC
* *
1667051 GGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
* *
1667112 GGTATACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATA
1667175 GGTAA
1 GGTAA
1667180 ACCCTCGACT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
61 5 0.08
62 25 0.41
63 31 0.51
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (61 bp):
GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
Found at i:1667174 original size:32 final size:31
Alignment explanation
Indices: 1667054--1667181 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
1667044 GATCCTCGGT
* * * *
1667054 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
1667085 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
1667116 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
1667148 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
1667179 AAC
1 AAC
1667182 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.62
32 23 0.28
33 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:1668578 original size:21 final size:21
Alignment explanation
Indices: 1668552--1668597 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1668542 ATTTTATTCG
* *
1668552 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
1668573 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
1668594 CTTG
1 CTTG
1668598 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:1669612 original size:42 final size:41
Alignment explanation
Indices: 1669532--1669669 Score: 145
Period size: 42 Copynumber: 3.3 Consensus size: 41
1669522 CATCCAACGA
* * ** *
1669532 ATAAGGAGTTGGATCAACATCATCATTTTGTTATTCCATCAT
1 ATAAGGAGTTGGATAAACATCATCA-TTTGCTCGTCCATCAC
* *
1669574 ATAAGGAGTTGAATAAACATCATCATTTCGCTCGTCCATAAC
1 ATAAGGAGTTGGATAAACATCATCATTT-GCTCGTCCATCAC
* * *
1669616 ATAAGGAGTTGGATTAGCATCA-C-CTTGACTCGTCCATCAC
1 ATAAGGAGTTGGATAAACATCATCATTTG-CTCGTCCATCAC
1669656 ATAAGGAGTTGGAT
1 ATAAGGAGTTGGAT
1669670 CAGCATCACC
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 1 0.01
40 27 0.33
41 4 0.05
42 50 0.61
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (41 bp):
ATAAGGAGTTGGATAAACATCATCATTTGCTCGTCCATCAC
Found at i:1669659 original size:40 final size:40
Alignment explanation
Indices: 1669604--1669681 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
1669594 CATCATTTCG
*
1669604 CTCGTCCATAACATAAGGAGTTGGATTAGCATCACCTTGA
1 CTCGTCCATAACATAAGGAGTTGGATCAGCATCACCTTGA
*
1669644 CTCGTCCATCACATAAGGAGTTGGATCAGCATCACCTT
1 CTCGTCCATAACATAAGGAGTTGGATCAGCATCACCTT
1669682 AGGTCAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (40 bp):
CTCGTCCATAACATAAGGAGTTGGATCAGCATCACCTTGA
Found at i:1669979 original size:9 final size:9
Alignment explanation
Indices: 1669965--1669989 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1669955 TTATCCCAAA
1669965 ATGATGACG
1 ATGATGACG
1669974 ATGATGACG
1 ATGATGACG
1669983 ATGATGA
1 ATGATGA
1669990 TAATAATAAA
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:0.36, C:0.08, G:0.32, T:0.24
Consensus pattern (9 bp):
ATGATGACG
Found at i:1705789 original size:15 final size:16
Alignment explanation
Indices: 1705765--1705795 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1705755 TCAATTGTTT
1705765 AAATTAATAGTACTTA
1 AAATTAATAGTACTTA
1705781 AAATT-ATAGTACTTA
1 AAATTAATAGTACTTA
1705796 TTCAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
AAATTAATAGTACTTA
Found at i:1709407 original size:29 final size:31
Alignment explanation
Indices: 1709366--1709427 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
1709356 GTTGTCTACT
*
1709366 ACAACAGATGGTTTGA-GTATTATGAACTAG
1 ACAACAGATGGTTTGACATATTATGAACTAG
1709396 ACAACA-ATGGTTTGACATATTATGAACTAG
1 ACAACAGATGGTTTGACATATTATGAACTAG
1709426 AC
1 AC
1709428 GAGCAACATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (31 bp):
ACAACAGATGGTTTGACATATTATGAACTAG
Found at i:1712780 original size:5 final size:5
Alignment explanation
Indices: 1712770--1712801 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1712760 AGAAGGAGGT
1712770 AAGAA AAG-A AA-AA AAGAA AAGAA AAGAA AAGA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGA
1712802 GAAAAAGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 6 0.24
5 19 0.76
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:1714931 original size:2 final size:2
Alignment explanation
Indices: 1714924--1714984 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1714914 ATGTATTTGT
1714924 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1714966 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1714985 GGAGAAAATG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.