Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008029.1 Hibiscus syriacus cultivar Beakdansim tig00110505_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: 3983240
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 18
Found at i:1684369 original size:29 final size:29
Alignment explanation
Indices: 1684324--1684415 Score: 148
Period size: 29 Copynumber: 3.2 Consensus size: 29
1684314 ACCGTTGATC
* *
1684324 GGGTGTTAGTTTTGTAATTATTTTTAAAA
1 GGGTGTTAGTTTCGTAAATATTTTTAAAA
*
1684353 GGGTGCTAGTTTCGTAAATATTTTTAAAA
1 GGGTGTTAGTTTCGTAAATATTTTTAAAA
*
1684382 GGGTGTTAGTTTCGTAAATATTTTAAAAA
1 GGGTGTTAGTTTCGTAAATATTTTTAAAA
1684411 GGGTG
1 GGGTG
1684416 ATAATTGTGT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.29, C:0.03, G:0.24, T:0.43
Consensus pattern (29 bp):
GGGTGTTAGTTTCGTAAATATTTTTAAAA
Found at i:1685387 original size:42 final size:42
Alignment explanation
Indices: 1685323--1685491 Score: 277
Period size: 42 Copynumber: 4.0 Consensus size: 42
1685313 GAAGGAAGTA
*
1685323 TTCTTAGGTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGT
1 TTCTCAGGTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGT
*
1685365 TTCTCAGGTCCCTTTGCTGTGTGTAAAGGTAAGCCTTACAGT
1 TTCTCAGGTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGT
* *
1685407 TTCCCAGGTCCCTTTGCTGTGTGCAAAGGTAAGCCTTATAGT
1 TTCTCAGGTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGT
* *
1685449 TTC-CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
1 TTCTCAGGTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGT
1685490 TT
1 TT
1685492 TCCTAGGCTC
Statistics
Matches: 119, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
41 37 0.31
42 82 0.69
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (42 bp):
TTCTCAGGTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGT
Found at i:1685514 original size:84 final size:84
Alignment explanation
Indices: 1685328--1685530 Score: 257
Period size: 84 Copynumber: 2.4 Consensus size: 84
1685318 AAGTATTCTT
* * *
1685328 AGGTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGTTTCTCAGGTCCCTTTGCTGTGTGTAAAG
1 AGGTCCATCTGCTGTGTGCAAAGGTAAGCCTTACAGTTTCTCAGGTCCCTTTGCTGTGTGCAAAG
1685393 GTAAGCCTTACAGTTTCCC
66 GTAAGCCTTACAGTTTCCC
* * * * *
1685412 AGGTCCCTTTGCTGTGTGCAAAGGTAAGCCTTATAGTTTC-CAGGTTCCTTTGCTGTGTGCAAGG
1 AGGTCCATCTGCTGTGTGCAAAGGTAAGCCTTACAGTTTCTCAGGTCCCTTTGCTGTGTGCAAAG
*
1685476 GTAAGCCTTACAGTTTTCCT
66 GTAAGCCTTACAG-TTTCCC
* * *
1685496 AGG-CTCATCTGCTTTGTGCACATGTTAAGCCTTAC
1 AGGTC-CATCTGCTGTGTGCA-AAGGTAAGCCTTAC
1685531 TGGTGTACAA
Statistics
Matches: 105, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
83 35 0.33
84 59 0.56
85 11 0.10
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (84 bp):
AGGTCCATCTGCTGTGTGCAAAGGTAAGCCTTACAGTTTCTCAGGTCCCTTTGCTGTGTGCAAAG
GTAAGCCTTACAGTTTCCC
Found at i:1691463 original size:18 final size:18
Alignment explanation
Indices: 1691440--1691481 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1691430 TTGACCGGAT
*
1691440 TTGACCAGACATGACCCG
1 TTGACCAGACATAACCCG
*
1691458 TTGACCCGACATAACCCG
1 TTGACCAGACATAACCCG
1691476 TTGACC
1 TTGACC
1691482 GTTGACCGTG
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:0.26, C:0.36, G:0.19, T:0.19
Consensus pattern (18 bp):
TTGACCAGACATAACCCG
Found at i:1691539 original size:29 final size:29
Alignment explanation
Indices: 1691495--1691580 Score: 127
Period size: 29 Copynumber: 3.0 Consensus size: 29
1691485 GACCGTGTGT
* *
1691495 TAGTTTTGTAATTATTTTTAAAAGGGTGC
1 TAGTTTCGTAAATATTTTTAAAAGGGTGC
* *
1691524 TAGTTTCTTAAATATTTTTAAAAGGGTGT
1 TAGTTTCGTAAATATTTTTAAAAGGGTGC
*
1691553 TAGTTTCGTAAATATTTTAAAAAGGGTG
1 TAGTTTCGTAAATATTTTTAAAAGGGTG
1691581 ATAATTGTGT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.45
Consensus pattern (29 bp):
TAGTTTCGTAAATATTTTTAAAAGGGTGC
Found at i:1692205 original size:41 final size:42
Alignment explanation
Indices: 1692090--1692205 Score: 135
Period size: 42 Copynumber: 2.8 Consensus size: 42
1692080 GAAGGAAGTA
* * * *
1692090 TTCTCAGGTCCCTTTGTTGTGTGCAAAGATAAGTCTTACAGT
1 TTCTCAGGTCCCTTTGATGTGTGCAAAGGTAAGCCTTACACT
* * * *
1692132 TTCCCAAGTCCCTTTGCTGTGTGCAAATGTAAGCCTTACACT
1 TTCTCAGGTCCCTTTGATGTGTGCAAAGGTAAGCCTTACACT
* *
1692174 TT-TCAGGTTCCTTTGATGTGTGCAAGGGTAAG
1 TTCTCAGGTCCCTTTGATGTGTGCAAAGGTAAG
1692206 TTTACAATTT
Statistics
Matches: 61, Mismatches: 13, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
41 24 0.39
42 37 0.61
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (42 bp):
TTCTCAGGTCCCTTTGATGTGTGCAAAGGTAAGCCTTACACT
Found at i:1692238 original size:83 final size:84
Alignment explanation
Indices: 1692093--1692254 Score: 184
Period size: 83 Copynumber: 1.9 Consensus size: 84
1692083 GGAAGTATTC
* * * * *
1692093 TCAGGTCCCTTTGTTGTGTGCAAAGATAAGTCTTACAGTTTCCCAAGTCCCTTTGCTGTGTGCAA
1 TCAGGTCCCTTTGATGTGTGCAAAGATAAGTCTTACAATTTCCCAAGGCCCTCTACTGTGTGCAA
*
1692158 ATG-TAAGCCTTACACTTT
66 AGGTTAAGCCTTACACTTT
* * * * * *
1692176 TCAGGTTCCTTTGATGTGTGCAAGGGTAAGT-TTACAATTTTCCTAGGCTCCTCTACTTTGTGCA
1 TCAGGTCCCTTTGATGTGTGCAAAGATAAGTCTTACAATTTCCCAAGGC-CCTCTACTGTGTGCA
*
1692240 CAGGTTAAGCCTTAC
65 AAGGTTAAGCCTTAC
1692255 TGGTGTATAG
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
82 13 0.20
83 41 0.64
84 10 0.16
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.36
Consensus pattern (84 bp):
TCAGGTCCCTTTGATGTGTGCAAAGATAAGTCTTACAATTTCCCAAGGCCCTCTACTGTGTGCAA
AGGTTAAGCCTTACACTTT
Found at i:1693297 original size:33 final size:34
Alignment explanation
Indices: 1693241--1693304 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
1693231 GCAATCAATC
1693241 CTAATAAATAAAGTCTTAAAATAAT-ATAAAATA
1 CTAATAAATAAAGTCTTAAAATAATAATAAAATA
**
1693274 CTAATAAATAGAA-TCTTCTAATAATAATAAA
1 CTAATAAATA-AAGTCTTAAAATAATAATAAA
1693305 CTAATATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 20 0.74
34 7 0.26
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (34 bp):
CTAATAAATAAAGTCTTAAAATAATAATAAAATA
Found at i:1695798 original size:18 final size:17
Alignment explanation
Indices: 1695742--1695800 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 17
1695732 TTTGGTTTAC
*
1695742 GGAATGTAAGATTACGTTT
1 GGAATGTAACATTAC--TT
1695761 GGAAAT-T-ACATTAC-T
1 GG-AATGTAACATTACTT
1695776 GGAATGTAACATTACTAT
1 GGAATGTAACATTACT-T
1695794 GGAATGT
1 GGAATGT
1695801 TGTATTACCT
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
14 3 0.09
15 4 0.12
16 7 0.21
18 14 0.41
19 3 0.09
20 3 0.09
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (17 bp):
GGAATGTAACATTACTT
Found at i:1696226 original size:17 final size:16
Alignment explanation
Indices: 1696199--1696232 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1696189 TTAAATATTA
1696199 TTTTAAATAATTATAT
1 TTTTAAATAATTATAT
*
1696215 TTTTATAATAATTTTAT
1 TTTTA-AATAATTATAT
1696232 T
1 T
1696233 CTTTTCATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAAATAATTATAT
Found at i:1700891 original size:14 final size:14
Alignment explanation
Indices: 1700874--1700900 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1700864 TTACAATGTT
1700874 TTATTTAAGTTATA
1 TTATTTAAGTTATA
1700888 TTATTTAAGTTAT
1 TTATTTAAGTTAT
1700901 GTTTGATCAT
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:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATTTAAGTTATA
Found at i:1701144 original size:21 final size:23
Alignment explanation
Indices: 1701094--1701145 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1701084 GTTGAGGGTT
*
1701094 CTATGTGGTCCTTCGAGACAAAA
1 CTATATGGTCCTTCGAGACAAAA
* *
1701117 CTATATGGTCTTTCGGGAC-AAA
1 CTATATGGTCCTTCGAGACAAAA
1701139 -TATATGG
1 CTATATGG
1701146 CACTTCGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 7 0.27
22 3 0.12
23 16 0.62
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (23 bp):
CTATATGGTCCTTCGAGACAAAA
Found at i:1701624 original size:17 final size:18
Alignment explanation
Indices: 1701591--1701624 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1701581 TACATTTGTA
1701591 TTTATGTAAATTATTAAG
1 TTTATGTAAATTATTAAG
*
1701609 TTTATTTAAA-TATTAA
1 TTTATGTAAATTATTAA
1701625 TGTGAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
TTTATGTAAATTATTAAG
Found at i:1709063 original size:61 final size:61
Alignment explanation
Indices: 1708967--1709089 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
1708957 AAATAAATAA
1708967 TCTAATTTACAATTTCAGACCAAGTAGTATCGGTACTCTATGCCTAGTATCGATACTTCCC
1 TCTAATTTACAATTTCAGACCAAGTAGTATCGGTACTCTATGCCTAGTATCGATACTTCCC
*
1709028 TCTAATTTACAATTTCAGACCAAGTAGTATTGGTACTCTATGCCTAGTATCGATACTTCCC
1 TCTAATTTACAATTTCAGACCAAGTAGTATCGGTACTCTATGCCTAGTATCGATACTTCCC
1709089 T
1 T
1709090 TATATGATAC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.36
Consensus pattern (61 bp):
TCTAATTTACAATTTCAGACCAAGTAGTATCGGTACTCTATGCCTAGTATCGATACTTCCC
Found at i:1716416 original size:13 final size:13
Alignment explanation
Indices: 1716395--1716426 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1716385 CAAATCACTA
1716395 AAAAG-ATAAAAT
1 AAAAGAATAAAAT
1716407 AAAAGAATAAAAT
1 AAAAGAATAAAAT
1716420 AAAAGAA
1 AAAAGAA
1716427 ACTAATGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (13 bp):
AAAAGAATAAAAT
Found at i:1719813 original size:21 final size:20
Alignment explanation
Indices: 1719776--1719815 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1719766 TCATGCAAGA
**
1719776 ATTTATGGCCTTGACAAAAG
1 ATTTATGGCCTCAACAAAAG
1719796 ATTTCATGGCCTCAACAAAA
1 ATTT-ATGGCCTCAACAAAA
1719816 ACTTTGATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:1723675 original size:28 final size:30
Alignment explanation
Indices: 1723605--1723686 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 30
1723595 ACGATTAGAG
*
1723605 TTTATGAAATTTTTTTGGGATTTT-TAGGAA
1 TTTAT-AAGTTTTTTTGGGATTTTATAGGAA
*
1723635 TTTATAAG-TTTTTTGAGATTTTAT-GGAA
1 TTTATAAGTTTTTTTGGGATTTTATAGGAA
1723663 -TT-TAAGTTTTTTTTGGGAATTTTA
1 TTTATAAG-TTTTTTTGGG-ATTTTA
1723687 AAAATTTCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
26 4 0.09
27 2 0.04
28 25 0.56
29 9 0.20
30 5 0.11
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (30 bp):
TTTATAAGTTTTTTTGGGATTTTATAGGAA
Found at i:1724496 original size:24 final size:23
Alignment explanation
Indices: 1724446--1724496 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
1724436 AATCCATATA
* *
1724446 ATTTTTAAAATAAATTAATACTG
1 ATTTTTAAAATAAATAAATAATG
* *
1724469 ATTTTATAAAATATATAAATAATT
1 ATTTT-TAAAATAAATAAATAATG
1724493 ATTT
1 ATTT
1724497 AATTATCTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTTTAAAATAAATAAATAATG
Found at i:1725337 original size:151 final size:153
Alignment explanation
Indices: 1725129--1725438 Score: 516
Period size: 151 Copynumber: 2.0 Consensus size: 153
1725119 AAGACAAATT
*
1725129 TATAATTCAAATCTTAAAATTTTAAAATCCTTTTGAAGACAAAAATTTAAGATTTGAATTATAAA
1 TATAATTCAAATCTTAAAATTTTAAAATCCTTTTGAAGACAAAAATTTAAGAGTTGAATTATAAA
* * * ** *
1725194 TTTGTCTTGTGATTTAAGTTGTGTTTGTAACTTTTGATTCATTAAATAAAATTTTAATATAATTT
66 TTTGTCTTGTGATTTAAATTGTGTATGCAACTTTCAATTCATTAAACAAAATTTTAATATAATTT
* *
1725259 AATTTTTTAATATATAATTCATA
131 AATTATTTAAAATATAATTCATA
1725282 TATAATTCAAATCTT-AAATTTTAAAATCCTTTTGAAGA-AAAAATTTAAGAGTTGAATTATAAA
1 TATAATTCAAATCTTAAAATTTTAAAATCCTTTTGAAGACAAAAATTTAAGAGTTGAATTATAAA
*
1725345 TTTGTCTTGTGATTTAAATTGTGTATGCAACTTTCAATTCGTTAAACAAAATTTTAATATAATTT
66 TTTGTCTTGTGATTTAAATTGTGTATGCAACTTTCAATTCATTAAACAAAATTTTAATATAATTT
1725410 AATTATTTAAAATATAATTCATA
131 AATTATTTAAAATATAATTCATA
1725433 TATAAT
1 TATAAT
1725439 AATTGAAAAA
Statistics
Matches: 147, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
151 109 0.74
152 23 0.16
153 15 0.10
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (153 bp):
TATAATTCAAATCTTAAAATTTTAAAATCCTTTTGAAGACAAAAATTTAAGAGTTGAATTATAAA
TTTGTCTTGTGATTTAAATTGTGTATGCAACTTTCAATTCATTAAACAAAATTTTAATATAATTT
AATTATTTAAAATATAATTCATA
Found at i:1727021 original size:18 final size:18
Alignment explanation
Indices: 1726992--1727034 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
1726982 TTTAAAATAA
1726992 ATTTTGATTTAACT-TCTTT
1 ATTTT-ATTTAA-TGTCTTT
1727011 ATTTTATTTAATGTCTTT
1 ATTTTATTTAATGTCTTT
*
1727029 TTTTTA
1 ATTTTA
1727035 CTCCAGTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 16 0.73
19 5 0.23
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (18 bp):
ATTTTATTTAATGTCTTT
Found at i:1733679 original size:3 final size:3
Alignment explanation
Indices: 1733659--1733700 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
1733649 CCAACAAATG
*
1733659 TAA TAA -AA TAA TTAA TAA TAA TAA TAA TAA TATA TTA TAA TA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA
1733701 TTTTTTAAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 27 0.79
4 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1734018 original size:91 final size:91
Alignment explanation
Indices: 1733859--1734103 Score: 433
Period size: 91 Copynumber: 2.7 Consensus size: 91
1733849 AAACATTAGA
1733859 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAAC
*
1733924 TCTTCATTGGAAATATTGATGCAAGG
66 TCTTCATTGGAAATACTGATGCAAGG
* *
1733950 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTGTTGGATGAGTTCTTCTCATTATGATC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAAC
1734015 TCTTCATTGGAAATACTGATGCAAGG
66 TCTTCATTGGAAATACTGATGCAAGG
*
1734041 TTGAACAAATTCTTCTCATTATGAA---CTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAAC
1734103 T
66 T
1734104 TTCTCCTTTA
Statistics
Matches: 148, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
88 36 0.24
91 112 0.76
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.42
Consensus pattern (91 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAAC
TCTTCATTGGAAATACTGATGCAAGG
Found at i:1734090 original size:36 final size:35
Alignment explanation
Indices: 1734050--1734142 Score: 129
Period size: 35 Copynumber: 2.7 Consensus size: 35
1734040 GTTGAACAAA
*
1734050 TTCTTCTCATTATGAACTTCTTCCTCGTT-GGATGAG
1 TTCTTCTCATTATGAACTTCTTCCT--TTAGGACGAG
1734086 TTCTTCTCATTATGAACTT-TCTCCTTTAGGACGAG
1 TTCTTCTCATTATGAACTTCT-TCCTTTAGGACGAG
1734121 TTCTTCTCATTATGAAC-TCTTC
1 TTCTTCTCATTATGAACTTCTTC
1734143 TGGAAATGTT
Statistics
Matches: 53, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
34 5 0.09
35 25 0.47
36 23 0.43
ACGTcount: A:0.18, C:0.24, G:0.13, T:0.45
Consensus pattern (35 bp):
TTCTTCTCATTATGAACTTCTTCCTTTAGGACGAG
Found at i:1734129 original size:35 final size:35
Alignment explanation
Indices: 1734050--1734143 Score: 129
Period size: 36 Copynumber: 2.6 Consensus size: 35
1734040 GTTGAACAAA
*
1734050 TTCTTCTCATTATGAAC-TTCTTCCTCGTTGGATGAG
1 TTCTTCTCATTATGAACTTTC-TCCTC-TTGGACGAG
1734086 TTCTTCTCATTATGAACTTTCTCCT-TTAGGACGAG
1 TTCTTCTCATTATGAACTTTCTCCTCTT-GGACGAG
1734121 TTCTTCTCATTATGAACTCTTCT
1 TTCTTCTCATTATGAACT-TTCT
1734144 GGAAATGTTG
Statistics
Matches: 54, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
34 2 0.04
35 24 0.44
36 25 0.46
37 3 0.06
ACGTcount: A:0.18, C:0.23, G:0.13, T:0.46
Consensus pattern (35 bp):
TTCTTCTCATTATGAACTTTCTCCTCTTGGACGAG
Found at i:1734483 original size:137 final size:134
Alignment explanation
Indices: 1734185--1734546 Score: 493
Period size: 137 Copynumber: 2.7 Consensus size: 134
1734175 ATTTGGAAGG
*
1734185 AACAAG-TCTTTCTCATTATGAAC-TTTCT-CCT-TTAGGATGAATTCTTCTCATTATGAACTCT
1 AACAAGCTC-TTCTCATTATGAACTTTTCTCCCTCTTAGGATGAGTTCTTCTCATTATGAACTCT
* ** **
1734246 CT-ATTAGAAATGTCAATCCCTCAAGCTAGGCGTCACTAATTTGAAATGTCATGAATCGAGTGAT
65 -TAATTAGAAATGTCAATCCCTCAAGCGAGGCGTCACTAATTCAAAATGTCATGAATAAAGTGAT
*
1734310 AGGTCG
129 AGGTCA
1734316 AACAAGCTCTTCTCATTATGAACTTTTTCTCCCTCTGTAGGATGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAAC-TTTTCTCCCTCT-TAGGATGAGTTCTTCTCATTATGAACTC
* * *
1734381 TTAATTAAAAATGTCAATCCCTCAAGCGAGGCGCTCACTGATTCAAAATGTCGTGAATAAAGTGA
64 TTAATTAGAAATGTCAATCCCTCAAGCGAGGCG-TCACTAATTCAAAATGTCATGAATAAAGTGA
*
1734446 TATGTCA
128 TAGGTCA
1734453 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATTA-GATGAGTTCTTCTCATTATGAACT
1 AACAAGCTCTTCTCATTATGAACTT-TTCTCCCTC--TTAGGATGAGTTCTTCTCATTATGAACT
* *
1734517 CTCAATTGGAAATGTCAATCCCTCAAGCGA
63 CTTAATTAGAAATGTCAATCCCTCAAGCGA
1734547 TGAGACATTG
Statistics
Matches: 206, Mismatches: 14, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
131 20 0.10
132 2 0.01
133 5 0.02
134 3 0.01
135 2 0.01
136 58 0.28
137 113 0.55
138 2 0.01
139 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (134 bp):
AACAAGCTCTTCTCATTATGAACTTTTCTCCCTCTTAGGATGAGTTCTTCTCATTATGAACTCTT
AATTAGAAATGTCAATCCCTCAAGCGAGGCGTCACTAATTCAAAATGTCATGAATAAAGTGATAG
GTCA
Found at i:1734740 original size:81 final size:82
Alignment explanation
Indices: 1734593--1734838 Score: 343
Period size: 89 Copynumber: 2.9 Consensus size: 82
1734583 AAAAATGTCA
*
1734593 AAAACATCCA-GCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCTGA
1 AAAACAT-CATGCACTGAAGGTCTTATGGATGG-CCGAAGGACTTACAAATCAAGAAACCCCCGA
1734657 AGGCTTAGTTTCGCATTTG
64 AGGCTTAGTTTCGCATTTG
* *
1734676 AAAATATCATGCACTAAAGGTCTTAT-GATGGCCGAAGGACTTACAAATCAAGAAACCCCCGAAG
1 AAAACATCATGCACTGAAGGTCTTATGGATGGCCGAAGGACTTACAAATCAAGAAACCCCCGAAG
*
1734740 GCTTAGTTTCTAAAATCTCATTTG
66 GCTTAG--T-T----TCGCATTTG
* *
1734764 AAAACATCTTGCACTGAAGGTCTTATGGATGGCCGAAGGACTTACAAATCAAGAAAACCCCGAAG
1 AAAACATCATGCACTGAAGGTCTTATGGATGGCCGAAGGACTTACAAATCAAGAAACCCCCGAAG
1734829 GCTTAGTTTC
66 GCTTAGTTTC
1734839 TAAAAACACA
Statistics
Matches: 146, Mismatches: 8, Indels: 19
0.84 0.05 0.11
Matches are distributed among these distances:
81 38 0.26
82 9 0.06
83 22 0.15
84 1 0.01
86 1 0.01
87 1 0.01
88 31 0.21
89 43 0.29
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (82 bp):
AAAACATCATGCACTGAAGGTCTTATGGATGGCCGAAGGACTTACAAATCAAGAAACCCCCGAAG
GCTTAGTTTCGCATTTG
Found at i:1744782 original size:3 final size:3
Alignment explanation
Indices: 1744762--1744796 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
1744752 CTAACAAATG
1744762 TAA TAA -AA TAA TTAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA
1744797 TTTTTTAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1745856 original size:18 final size:17
Alignment explanation
Indices: 1745829--1745862 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1745819 TATTGTTATT
*
1745829 ATTAATTAATTAAATTAA
1 ATTAAATAA-TAAATTAA
1745847 ATTAAATAATAAATTA
1 ATTAAATAATAAATTA
1745863 TATAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAAATAATAAATTAA
Found at i:1746722 original size:28 final size:28
Alignment explanation
Indices: 1746672--1746742 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
1746662 TAAAATTATT
* * *
1746672 AAAATTCTCAAAAAAGACTTAAA-TTCTA
1 AAAAATCTCAAAAAACACCTAAATTTC-A
* *
1746700 GAAAATCTCAAAAAACTCCTAAATTTCA
1 AAAAATCTCAAAAAACACCTAAATTTCA
*
1746728 AAAAATCTTAAAAAA
1 AAAAATCTCAAAAAA
1746743 ATCATAAACT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
28 32 0.91
29 3 0.09
ACGTcount: A:0.56, C:0.15, G:0.03, T:0.25
Consensus pattern (28 bp):
AAAAATCTCAAAAAACACCTAAATTTCA
Found at i:1747157 original size:30 final size:29
Alignment explanation
Indices: 1747093--1747169 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
1747083 TTAGAGTATA
*
1747093 TGTTTTTTTTAGATTTTTAGAAATTTAGG
1 TGTTTTTTTGAGATTTTTAGAAATTTAGG
* **
1747122 AGTTTTTTTGAGATTTTCT-GGTATTTAAGG
1 TGTTTTTTTGAGATTTT-TAGAAATTT-AGG
*
1747152 TG-TTTTTTGAGAATTTTA
1 TGTTTTTTTGAGATTTTTA
1747170 ATAAGTTCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 1 0.03
29 33 0.85
30 5 0.13
ACGTcount: A:0.22, C:0.01, G:0.19, T:0.57
Consensus pattern (29 bp):
TGTTTTTTTGAGATTTTTAGAAATTTAGG
Found at i:1747869 original size:17 final size:16
Alignment explanation
Indices: 1747847--1747881 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
1747837 AAAGATTTAT
1747847 TTAAAATTAATCATTAA
1 TTAAAATTAATCA-TAA
1747864 TTAAAATTAATCATAA
1 TTAAAATTAATCATAA
1747880 TT
1 TT
1747882 TTAACTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAAATTAATCATAA
Found at i:1748202 original size:42 final size:42
Alignment explanation
Indices: 1748107--1748203 Score: 176
Period size: 42 Copynumber: 2.3 Consensus size: 42
1748097 TTTAAGTTAA
*
1748107 AATTAGGATTTATTTACATAATAAGTAATTTAAGTTGTTTAG
1 AATTAGGATTTTTTTACATAATAAGTAATTTAAGTTGTTTAG
*
1748149 AATTAGGATTTTTTTACATAATAAGTAATTTAATTTGTTTAG
1 AATTAGGATTTTTTTACATAATAAGTAATTTAAGTTGTTTAG
1748191 AATTAGGATTTTT
1 AATTAGGATTTTT
1748204 AAGTTAAATA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.48
Consensus pattern (42 bp):
AATTAGGATTTTTTTACATAATAAGTAATTTAAGTTGTTTAG
Found at i:1749789 original size:58 final size:58
Alignment explanation
Indices: 1749699--1749818 Score: 222
Period size: 58 Copynumber: 2.1 Consensus size: 58
1749689 GAAATGTATG
*
1749699 TATGCTTGATTATGTGAGTGGATATGTTTTTGTATGTGCTATGTGGCTTATATGAACA
1 TATGCTTGATTATATGAGTGGATATGTTTTTGTATGTGCTATGTGGCTTATATGAACA
*
1749757 TATGCTTGATTATATGAGTGGATATGTTTTTGTATGTGCTATGTGGCTTATGTGAACA
1 TATGCTTGATTATATGAGTGGATATGTTTTTGTATGTGCTATGTGGCTTATATGAACA
1749815 TATG
1 TATG
1749819 GTTATGAGAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.23, C:0.07, G:0.26, T:0.45
Consensus pattern (58 bp):
TATGCTTGATTATATGAGTGGATATGTTTTTGTATGTGCTATGTGGCTTATATGAACA
Found at i:1750566 original size:31 final size:31
Alignment explanation
Indices: 1750413--1750566 Score: 208
Period size: 31 Copynumber: 5.0 Consensus size: 31
1750403 AGTCGAGGGA
*
1750413 TTACCTATG-TCTTACGGGACATATGGACATGA
1 TTACCTATGTTCTT-CGGGACATATGGACA-GG
1750445 TTACC--TG-TCTTACGGGACATATGGACAGG
1 TTACCTATGTTCTT-CGGGACATATGGACAGG
* **
1750474 ATTACCTATGTTCTTAGGGACATATGGACAAT
1 -TTACCTATGTTCTTCGGGACATATGGACAGG
1750506 TTACCTATGTTCTTCGGGACATATGGACAGG
1 TTACCTATGTTCTTCGGGACATATGGACAGG
1750537 TTACCTATGTTCTTCGGGACATATGGACAG
1 TTACCTATGTTCTTCGGGACATATGGACAG
1750567 ATTATTATAC
Statistics
Matches: 111, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
29 1 0.01
30 27 0.24
31 58 0.52
32 21 0.19
33 4 0.04
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACAGG
Found at i:1751310 original size:21 final size:21
Alignment explanation
Indices: 1751284--1751338 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
1751274 AAAATTACTA
* *
1751284 TAGCAGGGTATTGGTACATTG
1 TAGCAGGGTATCGGTACACTG
1751305 TAGCAGGGTATCGGTACACTG
1 TAGCAGGGTATCGGTACACTG
*
1751326 TAGTAGGGTATCG
1 TAGCAGGGTATCG
1751339 ATACCCCTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.13, G:0.35, T:0.29
Consensus pattern (21 bp):
TAGCAGGGTATCGGTACACTG
Found at i:1760489 original size:30 final size:30
Alignment explanation
Indices: 1760455--1760561 Score: 96
Period size: 30 Copynumber: 3.6 Consensus size: 30
1760445 ATCATATTAG
*
1760455 ATTTAAATGACCAAAATAG-TACAAACAAGA
1 ATTTAAAGGACCAAAATAGATA-AAACAAGA
*
1760485 ATTTAAAGGTCCAAAATAGATAAAACATA-A
1 ATTTAAAGGACCAAAATAGATAAAACA-AGA
* * *
1760515 ACTTAAGGGACTAAAATAG-TAAAA-ATAGA
1 ATTTAAAGGACCAAAATAGATAAAACA-AGA
*
1760544 CATTTAAAGGACTAAAAT
1 -ATTTAAAGGACCAAAAT
1760562 GGTATTAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
28 3 0.05
29 6 0.09
30 53 0.82
31 3 0.05
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.22
Consensus pattern (30 bp):
ATTTAAAGGACCAAAATAGATAAAACAAGA
Found at i:1761783 original size:3 final size:3
Alignment explanation
Indices: 1761777--1761814 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
1761767 ATTAAAAAAA
1761777 AAT AAT AAT AAT AAT AAT AAT -AT AAT AGATT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT A
1761815 TTTTTTTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 26 0.81
4 2 0.06
5 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1762533 original size:67 final size:65
Alignment explanation
Indices: 1762424--1762664 Score: 274
Period size: 67 Copynumber: 3.7 Consensus size: 65
1762414 AGGGATACTA
* * * *
1762424 TCTCAAGAGAGACAAAATTAGTTT-CAAGGGAAACAATCTCAAAGATGTTTGTTCT-AAAAAAAA
1 TCTCAAGAGAGACAAAATTTGTTTCCAA-AGAAACAA-CTCAAAGAT-TTTTTTCTCAAAAGAAA
1762487 TTG
63 TTG
1762490 TCTCAAGAGAGACAAAACTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTCTCAAAAGAAAT
1 TCTCAAGAGAGACAAAA-TTTGTTTCCAAAGAAACA-ACTCAAAGATTTTTTTCTCAAAAGAAAT
1762555 TG
64 TG
* * * * * * *
1762557 TTTCAAGATAGATAAAACTTTGTTTCTAGAGAAACAGACTCAAAGATTTTTTTTTCAAAAGATAT
1 TCTCAAGAGAGACAAAA-TTTGTTTCCAAAGAAACA-ACTCAAAGATTTTTTTCTCAAAAGAAAT
1762622 TG
64 TG
* *
1762624 TCTC-A-AGAGACAAAATTTGTTTCTAGAGAAACAACTCAAAG
1 TCTCAAGAGAGACAAAATTTGTTTCCAAAGAAACAACTCAAAG
1762665 CATACTGATA
Statistics
Matches: 157, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
63 8 0.05
64 18 0.11
65 8 0.05
66 25 0.16
67 94 0.60
68 4 0.03
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.30
Consensus pattern (65 bp):
TCTCAAGAGAGACAAAATTTGTTTCCAAAGAAACAACTCAAAGATTTTTTTCTCAAAAGAAATTG
Found at i:1762782 original size:32 final size:33
Alignment explanation
Indices: 1762734--1762804 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 33
1762724 TTCACATCAG
* * *
1762734 GATGTTGCATCCCCAAAGATG-CTCCAATATTC
1 GATGTTGAATCCCCAAAGATGCCCCCAACATTC
*
1762766 GATGTTGAATCTCCAAAGATGCCCCCAACATTC
1 GATGTTGAATCCCCAAAGATGCCCCCAACATTC
1762799 GATGTT
1 GATGTT
1762805 TCTTGCTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 19 0.56
33 15 0.44
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (33 bp):
GATGTTGAATCCCCAAAGATGCCCCCAACATTC
Found at i:1763867 original size:14 final size:14
Alignment explanation
Indices: 1763850--1763892 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1763840 TTTGCTCTTT
1763850 TTTTTCTTTATTTC
1 TTTTTCTTTATTTC
**
1763864 TTTTTCTTTGCTTC
1 TTTTTCTTTATTTC
* *
1763878 TTTTTGTTTTTTTC
1 TTTTTCTTTATTTC
1763892 T
1 T
1763893 CTTTGCTCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (14 bp):
TTTTTCTTTATTTC
Found at i:1763879 original size:22 final size:21
Alignment explanation
Indices: 1763853--1763925 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
1763843 GCTCTTTTTT
1763853 TTCTTTATTTCTTTTTCTTTGC
1 TTCTTTATTT-TTTTTCTTTGC
*
1763875 TTCTTTTTGTTTTTTTCTCTTTGC
1 TTC--TTTATTTTTTT-TCTTTGC
* *
1763899 -TCTTTGTTTTTTCTCTTTTGC
1 TTCTTTATTTTTTTTC-TTTGC
1763920 TTCTTT
1 TTCTTT
1763926 TCTTTTGTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
20 2 0.05
21 15 0.34
22 8 0.18
23 6 0.14
24 13 0.30
ACGTcount: A:0.01, C:0.18, G:0.07, T:0.74
Consensus pattern (21 bp):
TTCTTTATTTTTTTTCTTTGC
Found at i:1763896 original size:30 final size:29
Alignment explanation
Indices: 1763831--1763896 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
1763821 ATGCTTCTTG
*
1763831 TCTCCTTTTTTTGCTCTTTTTTTTCTTTA
1 TCTCTTTTTTTTGCTCTTTTTTTTCTTTA
*
1763860 TTTCTTTTTCTTTGCTTCTTTTTGTTT-TTT-
1 TCTCTTTTT-TTTGC-TCTTTTT-TTTCTTTA
1763890 TCTCTTT
1 TCTCTTT
1763897 GCTCTTTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 7 0.23
30 11 0.35
31 10 0.32
32 3 0.10
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.76
Consensus pattern (29 bp):
TCTCTTTTTTTTGCTCTTTTTTTTCTTTA
Found at i:1769043 original size:22 final size:21
Alignment explanation
Indices: 1769007--1769048 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1768997 ACGACGACAA
1769007 AGAGAAAGAAGAGAGGTTTTG
1 AGAGAAAGAAGAGAGGTTTTG
*
1769028 AGAGAGAGAGAGAGAGGTTTT
1 AGAGAAAGA-AGAGAGGTTTT
1769049 CTGGGCATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.19
Consensus pattern (21 bp):
AGAGAAAGAAGAGAGGTTTTG
Found at i:1777178 original size:30 final size:30
Alignment explanation
Indices: 1777046--1777181 Score: 109
Period size: 30 Copynumber: 4.5 Consensus size: 30
1777036 ATCATATTAG
* *
1777046 ATTTAAAGGACCAAACTAGTACAAACAAG-A
1 ATTTAAAGGACTAAAATAGTACAAA-AAGAA
* *
1777076 ATTTAAAGGTCCAAAATAG-ACAAAACA-AA
1 ATTTAAAGGACTAAAATAGTACAAAA-AGAA
* * *
1777105 ATTTTAAGGGACTAAAATAGAAAAAAAAAGAA
1 A-TTTAAAGGACTAAAATAG-TACAAAAAGAA
* * *
1777137 ACTTAAGGGACTAAAATAGTA-AAAATAGAC
1 ATTTAAAGGACTAAAATAGTACAAAA-AGAA
1777167 ATTTAAAGGACTAAA
1 ATTTAAAGGACTAAA
1777182 GTGGTAATAA
Statistics
Matches: 88, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
28 1 0.01
29 12 0.14
30 49 0.56
31 18 0.20
32 8 0.09
ACGTcount: A:0.57, C:0.10, G:0.14, T:0.19
Consensus pattern (30 bp):
ATTTAAAGGACTAAAATAGTACAAAAAGAA
Found at i:1777507 original size:38 final size:38
Alignment explanation
Indices: 1777451--1777531 Score: 144
Period size: 38 Copynumber: 2.1 Consensus size: 38
1777441 CGACTTAGAT
* *
1777451 GTAAATGTGGAAAGATAAAGGCTCAGAATAAAACAAAC
1 GTAAATGTGGAAAAATAAAGGCTCAGAACAAAACAAAC
1777489 GTAAATGTGGAAAAATAAAGGCTCAGAACAAAACAAAC
1 GTAAATGTGGAAAAATAAAGGCTCAGAACAAAACAAAC
1777527 GTAAA
1 GTAAA
1777532 CTTCATTCCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.54, C:0.11, G:0.20, T:0.15
Consensus pattern (38 bp):
GTAAATGTGGAAAAATAAAGGCTCAGAACAAAACAAAC
Found at i:1779436 original size:18 final size:18
Alignment explanation
Indices: 1779413--1779466 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
1779403 ACAGAATATT
1779413 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1779431 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1779449 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
1779467 ATAATCCCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1780049 original size:24 final size:24
Alignment explanation
Indices: 1780022--1780076 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
1780012 TCTACAGTGT
1780022 ATCGATGCATTCTTTAACGTGTGC
1 ATCGATGCATTCTTTAACGTGTGC
1780046 ATCGATGCATTCTTTAACGTGTGC
1 ATCGATGCATTCTTTAACGTGTGC
1780070 ATCGATG
1 ATCGATG
1780077 TTTGTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (24 bp):
ATCGATGCATTCTTTAACGTGTGC
Found at i:1786254 original size:18 final size:18
Alignment explanation
Indices: 1786231--1786265 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1786221 ACTGAATATT
1786231 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1786249 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1786266 GATAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1787199 original size:22 final size:23
Alignment explanation
Indices: 1787156--1787204 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
1787146 ATCTCACTCA
*
1787156 AATTCTAACAAGTTCTAAATC-T
1 AATTCTAACAACTTCTAAATCTT
*
1787178 AATTCTAAC-ACTTCGTATATCTT
1 AATTCTAACAACTTC-TAAATCTT
1787201 AATT
1 AATT
1787205 AAGTCGATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 4 0.17
22 14 0.61
23 5 0.22
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.41
Consensus pattern (23 bp):
AATTCTAACAACTTCTAAATCTT
Found at i:1788314 original size:27 final size:27
Alignment explanation
Indices: 1788284--1788350 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
1788274 TTTTTTTATT
*
1788284 TATTCCTTCAATTTTGCATGATTGTTG
1 TATTTCTTCAATTTTGCATGATTGTTG
1788311 TATTTCTTCAATTTTGCATGATTGTTG
1 TATTTCTTCAATTTTGCATGATTGTTG
1788338 TATTTCTTCAATT
1 TATTTCTTCAATT
1788351 CACCATTCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.19, C:0.13, G:0.12, T:0.55
Consensus pattern (27 bp):
TATTTCTTCAATTTTGCATGATTGTTG
Found at i:1788493 original size:30 final size:30
Alignment explanation
Indices: 1788457--1788525 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
1788447 ACATTTTTTT
*
1788457 AATTTAGTCCTTTAACTTTACATTTTACTC
1 AATTTAGTACTTTAACTTTACATTTTACTC
*
1788487 AATTTAGTACTTTAACTTTACATTTTACTT
1 AATTTAGTACTTTAACTTTACATTTTACTC
1788517 AATTTAGTA
1 AATTTAGTA
1788526 TATTTATCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.51
Consensus pattern (30 bp):
AATTTAGTACTTTAACTTTACATTTTACTC
Found at i:1790102 original size:17 final size:17
Alignment explanation
Indices: 1790082--1790116 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1790072 AAACATAAGC
1790082 ATAAAAAGAAAAAAATA
1 ATAAAAAGAAAAAAATA
* *
1790099 ATAAAAATAAATAAATA
1 ATAAAAAGAAAAAAATA
1790116 A
1 A
1790117 ATTATAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (17 bp):
ATAAAAAGAAAAAAATA
Found at i:1790102 original size:23 final size:23
Alignment explanation
Indices: 1790059--1790102 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1790049 AAAGCGTTAG
* *
1790059 ATAAAAATAAATAAAACATAAGC
1 ATAAAAAGAAATAAAAAATAAGC
1790082 ATAAAAAGAAA-AAAATAATAA
1 ATAAAAAGAAATAAAA-AATAA
1790103 AAATAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (23 bp):
ATAAAAAGAAATAAAAAATAAGC
Found at i:1790808 original size:14 final size:14
Alignment explanation
Indices: 1790789--1790826 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
1790779 GGTTGATTTT
*
1790789 TGCTTCGCTCGAAA
1 TGCTTCCCTCGAAA
1790803 TGCTTCCCTCGAAA
1 TGCTTCCCTCGAAA
1790817 TGCTTCCCTC
1 TGCTTCCCTC
1790827 TTGCTTTTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.16, C:0.37, G:0.16, T:0.32
Consensus pattern (14 bp):
TGCTTCCCTCGAAA
Found at i:1791670 original size:21 final size:21
Alignment explanation
Indices: 1791644--1791685 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1791634 ATACCTTGAG
1791644 CTGAATGAAATCGAACTCGAA
1 CTGAATGAAATCGAACTCGAA
1791665 CTGAATGAAATCGAACTCGAA
1 CTGAATGAAATCGAACTCGAA
1791686 AGGTCTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (21 bp):
CTGAATGAAATCGAACTCGAA
Found at i:1792019 original size:84 final size:85
Alignment explanation
Indices: 1791842--1792028 Score: 227
Period size: 84 Copynumber: 2.2 Consensus size: 85
1791832 AGCAGAATGG
* *
1791842 AATCGAACTCGACAAGTTTTATGGTGGCAGATAGCCCTTCTCGATTTAAGCTATACTGCAAATGA
1 AATCGAACTCGACAAGTTTTATGGTGGCAGATAGCCCTTCTAGACTTAAGCTATACTGCAAATGA
* * * *
1791907 TGTGCTTTTGAGCTGAGTGT
66 TGTGCCTTGGAGCTAAGCGT
* * * * *
1791927 AATTGAACTCGA-AGGTCTTT-TGGTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATG
1 AATCGAACTCGACAAGT-TTTATGGTGGCAGATAGCCCTTCTAGACTTAAGCTATACTGCAAATG
1791990 ATGTGCCTTGGAGCTAAGCGT
65 ATGTGCCTTGGAGCTAAGCGT
* *
1792011 AGTCGAACTC-AAAAGTTT
1 AATCGAACTCGACAAGTTT
1792029 GGTGTTTCAA
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
83 3 0.03
84 69 0.80
85 14 0.16
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (85 bp):
AATCGAACTCGACAAGTTTTATGGTGGCAGATAGCCCTTCTAGACTTAAGCTATACTGCAAATGA
TGTGCCTTGGAGCTAAGCGT
Found at i:1792115 original size:37 final size:37
Alignment explanation
Indices: 1792065--1792171 Score: 178
Period size: 37 Copynumber: 2.9 Consensus size: 37
1792055 GGTTTTTTTC
1792065 TCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTT
1 TCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTT
* * *
1792102 TCAAGGGAAACTGTCTCAAGAGAGACAAGATTTTGTT
1 TCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTT
*
1792139 TCAAGTGAAACTGTCTCAAGAGAGACAAAACTT
1 TCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1792172 GTAAACTGTC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (37 bp):
TCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTT
Found at i:1792856 original size:106 final size:106
Alignment explanation
Indices: 1792563--1793749 Score: 1734
Period size: 106 Copynumber: 11.3 Consensus size: 106
1792553 GTATTGTTCC
* * * * * * * * * *
1792563 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTATTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* * * * * * * *
1792628 TCAGCCGCCCCTTTG-CTGTGAAGTTGAGCTTGTGCTGTCTA
66 CCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
1792669 GAGTCTAATATCCTTTTGTTGTGAAGTTGAAATTGACTCTG-AA-T-A-AA-AT-TTTGTTGACA
1 GAGTCCAATATCC-TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACA
* * * * *
1792728 ATCAGCCGCCCCTTCGTCGTGAAGTTGATCTTGTGTTGTCTTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * *
1792771 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1792835 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1792876 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* *
1792941 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1792982 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
1793047 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1793088 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTTTAAAATTGAGAAATTGTTTATTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
1793153 CCAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1793194 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTTTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1793259 CCAGCGGT-CC--CGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1793297 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-AGGAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAGTTGTTTATTGACA
1793361 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1793403 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1793468 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1793509 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
1793574 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1793615 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-AGGAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAGTTGTTTATTGACA
*
1793679 ACCAGCGGTCCCTTCGTCGTGAAGTTGAAATTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1793721 GAGTCCAATATCCTTCGTTGTGAAGTTGA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGA
1793750 GCCTTGACTT
Statistics
Matches: 995, Mismatches: 70, Indels: 32
0.91 0.06 0.03
Matches are distributed among these distances:
100 23 0.02
101 55 0.06
102 6 0.01
103 96 0.10
104 4 0.00
105 8 0.01
106 782 0.79
107 21 0.02
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1793740 original size:527 final size:522
Alignment explanation
Indices: 1792563--1793749 Score: 1808
Period size: 527 Copynumber: 2.3 Consensus size: 522
1792553 GTATTGTTCC
* * * * * * *
1792563 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTATTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAATTGGAAATTGTTTATTGACAG
* * * * * * * * * *
1792628 TCAGCCGCCCCTTTG-CTGTGAAGTTGAGCTTGTGCTGTCTAGAGTCTAATATCCTTTTGTTGTG
65 CCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC-TTCGTTGTG
* * *
1792692 AAGTTGAAATTGACTCTGAATAAAATTTTGTTGACAATCAGCCGCCCCTTCGTCGTGAAGTTGAT
128 AAGTTGAAATTGACTATGAATAAAATTTTGTTGACAACCAGCCGCCCC-TCGTCGTGAAGTTGAA
*
1792757 CTTGTGTTGTCTTGGGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
192 CTTGCGTTGTCTTGGGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
*
1792822 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
257 TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
1792887 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGTGGTCCC
322 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCC
* *
1792952 TTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
387 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGG
* *
1793017 CTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
452 CTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGT
*
1793082 TGTCTT
517 TGTCTG
* * *
1793088 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTTTAAAATTGAGAAATTGTTTATTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAATTGTTTATTGACAG
* *
1793153 CCAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * **
1793218 GTTGAAATTGGCTATGAAATTGAGAAGTTTTTTGTTGACAACCAG-CGGTCC-CGTCGTGAAGTT
130 GTTGAAATTGACTATG-AA-T-A-AA--ATTTTGTTGACAACCAGCCGCCCCTCGTCGTGAAGTT
* *
1793281 GAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-AG
189 GAACTTGCGTTGTCTTGG-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGA-
1793344 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
252 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1793409 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCG
317 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCG
*
1793474 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAA
382 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTAAA
*
1793539 ATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACT
447 ATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACT
1793604 TGCGTTGTCTG
512 TGCGTTGTCTG
* *
1793615 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTATTGACAG
*
1793680 CCAGCGGTCCCTTCGTCGTGAAGTTGAAATTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
1793745 GTTGA
130 GTTGA
1793750 GCCTTGACTT
Statistics
Matches: 601, Mismatches: 50, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
524 28 0.05
525 93 0.15
526 6 0.01
527 452 0.75
528 3 0.00
529 4 0.01
530 15 0.02
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (522 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAATTGTTTATTGACAGC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
TTGAAATTGACTATGAATAAAATTTTGTTGACAACCAGCCGCCCCTCGTCGTGAAGTTGAACTTG
CGTTGTCTTGGGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTT
TATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTT
CGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCG
TCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCT
GAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTC
TG
Found at i:1795214 original size:12 final size:12
Alignment explanation
Indices: 1795199--1795241 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
1795189 TTTTTGGTCT
1795199 TTCTTTTTTTTC
1 TTCTTTTTTTTC
*
1795211 TTC-TTTTTTGC
1 TTCTTTTTTTTC
1795222 TTCTTTTCTTTT-
1 TTCTTTT-TTTTC
1795234 TTCTTTTT
1 TTCTTTTT
1795242 GCCCTTTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 11 0.41
12 13 0.48
13 3 0.11
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.81
Consensus pattern (12 bp):
TTCTTTTTTTTC
Found at i:1795219 original size:11 final size:11
Alignment explanation
Indices: 1795203--1795241 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1795193 TGGTCTTTCT
1795203 TTTTTTTCTTC
1 TTTTTTTCTTC
*
1795214 TTTTTTGCTTC
1 TTTTTTTCTTC
*
1795225 TTTTCTTTTTTC
1 TTTT-TTTCTTC
1795237 TTTTT
1 TTTTT
1795242 GCCCTTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (11 bp):
TTTTTTTCTTC
Found at i:1798897 original size:14 final size:14
Alignment explanation
Indices: 1798878--1798915 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
1798868 GGTTGATTTT
*
1798878 TGCTTCGCTCGAAA
1 TGCTTCCCTCGAAA
1798892 TGCTTCCCTCGAAA
1 TGCTTCCCTCGAAA
1798906 TGCTTCCCTC
1 TGCTTCCCTC
1798916 TTGCTTTTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.16, C:0.37, G:0.16, T:0.32
Consensus pattern (14 bp):
TGCTTCCCTCGAAA
Found at i:1799377 original size:2 final size:2
Alignment explanation
Indices: 1799334--1799366 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1799324 TAATGAAATA
1799334 AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1799367 CAAATTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1799991 original size:45 final size:45
Alignment explanation
Indices: 1799828--1800092 Score: 235
Period size: 45 Copynumber: 6.0 Consensus size: 45
1799818 TCTCCTCCAC
* * *
1799828 CACCACCCAAGCACCCTCACAAGAACAAGTCTCCACCACCACTAT
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCACCAT
* *
1799873 CACCACCTAAGCACCCTTACAAGTACAAGTCTCTACCACCACCAT
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCACCAT
* *
1799918 CACCACCCAAGCACCCTTACAAGGACAAGTCTCCACCTCCACCAT
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCACCAT
* * ** * *
1799963 CACCGCCCAAGCACCATTGTAAATACAAGTC-CC-CGC-CC-CCAC
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCAC-CACCACCAT
* * *
1800005 CACCA-CC-AG----TTTACAAATATAAGTCTCCTCCACCACCCCTACCAT
1 CACCACCCAAGCACCCTTACAAGTACAAG--T-CTCCACCA--CC-ACCAT
* *
1800050 CACCACCCAAGCATCCTTACAAGTACAAGTCTCCACCCCCACC
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCACC
1800093 TCCTCCGGTT
Statistics
Matches: 177, Mismatches: 26, Indels: 34
0.75 0.11 0.14
Matches are distributed among these distances:
36 10 0.06
38 1 0.01
39 1 0.01
40 5 0.03
41 3 0.02
42 7 0.04
43 5 0.03
44 3 0.02
45 117 0.66
46 4 0.02
47 2 0.01
48 7 0.04
49 1 0.01
51 11 0.06
ACGTcount: A:0.32, C:0.46, G:0.08, T:0.15
Consensus pattern (45 bp):
CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCACCAT
Found at i:1801436 original size:20 final size:20
Alignment explanation
Indices: 1801411--1801451 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1801401 ATGTTGGAGG
* *
1801411 AAATATTATATTTTACGTTT
1 AAATATTATATATTAAGTTT
1801431 AAATATTATATATTAAGTTT
1 AAATATTATATATTAAGTTT
1801451 A
1 A
1801452 TTACATCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (20 bp):
AAATATTATATATTAAGTTT
Found at i:1804328 original size:16 final size:19
Alignment explanation
Indices: 1804307--1804345 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
1804297 ATTCAAAGTT
1804307 TTCA-TTCCTTTG-A-TCC
1 TTCATTTCCTTTGTACTCC
1804323 TTCATTTCCTTTGTACTCC
1 TTCATTTCCTTTGTACTCC
1804342 TTCA
1 TTCA
1804346 AGGATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 8 0.40
18 1 0.05
19 7 0.35
ACGTcount: A:0.13, C:0.31, G:0.05, T:0.51
Consensus pattern (19 bp):
TTCATTTCCTTTGTACTCC
Found at i:1807475 original size:16 final size:16
Alignment explanation
Indices: 1807456--1807487 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1807446 ATTAACATGT
1807456 TTTAAAATTAAATTAA
1 TTTAAAATTAAATTAA
*
1807472 TTTAAATTTAAATTAA
1 TTTAAAATTAAATTAA
1807488 ATTTTTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAAATTAAATTAA
Found at i:1813770 original size:19 final size:20
Alignment explanation
Indices: 1813732--1813776 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1813722 ATTTGTTTTT
1813732 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATGAA
* *
1813752 ATTAAATTTTTAT-TTTGAA
1 AATAAATTTTTATCTATGAA
1813771 AATAAA
1 AATAAA
1813777 ATATTAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTATGAA
Found at i:1819000 original size:10 final size:10
Alignment explanation
Indices: 1818985--1819027 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
1818975 TTCATCACAC
1818985 CAAATCCTCT
1 CAAATCCTCT
1818995 CAAATCCTCT
1 CAAATCCTCT
* *
1819005 CAACTTCTCT
1 CAAATCCTCT
*
1819015 TAAATCCTCT
1 CAAATCCTCT
1819025 CAA
1 CAA
1819028 CTTAAGGTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (10 bp):
CAAATCCTCT
Found at i:1819019 original size:20 final size:20
Alignment explanation
Indices: 1818991--1819030 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1818981 ACACCAAATC
1818991 CTCTCAAATCCTCTCAACTT
1 CTCTCAAATCCTCTCAACTT
*
1819011 CTCTTAAATCCTCTCAACTT
1 CTCTCAAATCCTCTCAACTT
1819031 AAGGTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (20 bp):
CTCTCAAATCCTCTCAACTT
Found at i:1819053 original size:12 final size:12
Alignment explanation
Indices: 1819036--1819090 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
1819026 AACTTAAGGT
1819036 ATATTTTATTTA
1 ATATTTTATTTA
1819048 ATATTTTA-TTA
1 ATATTTTATTTA
*
1819059 GTA-TTTATTT-
1 ATATTTTATTTA
*
1819069 A-ATTAT-TTTA
1 ATATTTTATTTA
1819079 ATATTTTATTTA
1 ATATTTTATTTA
1819091 TTAATTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
9 4 0.12
10 7 0.21
11 11 0.32
12 12 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (12 bp):
ATATTTTATTTA
Found at i:1819065 original size:18 final size:17
Alignment explanation
Indices: 1819037--1819092 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 17
1819027 ACTTAAGGTA
*
1819037 TATTTTATTTAATATTT
1 TATTATATTTAATATTT
1819054 TATTAGTA-TT--TATTT
1 TATTA-TATTTAATATTT
*
1819069 AATTAT-TTTAATATTT
1 TATTATATTTAATATTT
1819085 TATT-TATT
1 TATTATATT
1819093 AATTTTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 11
0.69 0.07 0.24
Matches are distributed among these distances:
14 3 0.10
15 10 0.32
16 10 0.32
17 6 0.19
18 2 0.06
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
TATTATATTTAATATTT
Found at i:1819066 original size:22 final size:21
Alignment explanation
Indices: 1819036--1819098 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
1819026 AACTTAAGGT
1819036 ATATTTTATTTAA-TATTTTA
1 ATATTTTATTTAATTATTTTA
*
1819056 TTAGTATTTATTTAATTATTTTA
1 ATA-T-TTTATTTAATTATTTTA
1819079 ATATTTTATTT-ATTAATTTT
1 ATATTTTATTTAATT-ATTTT
1819099 TTTGCATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
20 5 0.14
21 13 0.35
22 10 0.27
23 9 0.24
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
ATATTTTATTTAATTATTTTA
Found at i:1824617 original size:14 final size:14
Alignment explanation
Indices: 1824594--1824626 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1824584 GAATAAAGAT
*
1824594 TAAATTTAAAAAAA
1 TAAATATAAAAAAA
1824608 TAAATATAAAAAAA
1 TAAATATAAAAAAA
1824622 TAAAT
1 TAAAT
1824627 TTATTAAATT
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAATATAAAAAAA
Found at i:1825215 original size:10 final size:10
Alignment explanation
Indices: 1825200--1825253 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
1825190 GCTTAATTTT
1825200 GAAA-TTTATA
1 GAAATTTTA-A
1825210 GAAATTTTAA
1 GAAATTTTAA
1825220 GAAATTTTCAA
1 GAAATTTT-AA
*
1825231 AAAATTTTAA
1 GAAATTTTAA
1825241 -AAATTTTAA
1 GAAATTTTAA
1825250 -AAAT
1 GAAAT
1825254 GCTTAATTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
9 13 0.32
10 15 0.37
11 13 0.32
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.39
Consensus pattern (10 bp):
GAAATTTTAA
Found at i:1825244 original size:9 final size:9
Alignment explanation
Indices: 1825201--1825253 Score: 61
Period size: 9 Copynumber: 5.4 Consensus size: 9
1825191 CTTAATTTTG
*
1825201 AAATTTATAG
1 AAATTT-TAA
1825211 AAATTTTAA
1 AAATTTTAA
1825220 GAAATTTTCAAA
1 -AAATTTT--AA
1825232 AAATTTTAA
1 AAATTTTAA
1825241 AAATTTTAA
1 AAATTTTAA
1825250 AAAT
1 AAAT
1825254 GCTTAATTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
9 17 0.44
10 13 0.33
11 7 0.18
12 2 0.05
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (9 bp):
AAATTTTAA
Found at i:1826209 original size:191 final size:191
Alignment explanation
Indices: 1825650--1826724 Score: 1774
Period size: 191 Copynumber: 5.6 Consensus size: 191
1825640 TAAGATAATT
* * *
1825650 AAATATAACATCATGTCAAAATTTAATTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
1 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
* * * *
1825715 ACATAAAAAATAGGAACACAATATGTATATTTACCAATAACCAGTTAGTCTAGTAGGATGATGCG
66 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAACCAGTTAGTCTAGTGGGATGAGGTG
* * *
1825780 TTAGATCCCTTAAGAAATGTTAGAAGTTCGAATCATGGTGTTTACAAATGGAGGAAACTAG
131 TTAGATCCCTTAAGAAAGGTTAGAAGTTCGAATCCTGGTGTTTACGAATGGAGGAAACTAG
*
1825841 AAATATAAAATCATGACAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
1 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
*
1825906 ACAT-AAAAATAGGAACACAATATGTATATCTACCAATAATCAGTTAGTCTAGTGGGATGAGGTG
66 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAACCAGTTAGTCTAGTGGGATGAGGTG
* * **
1825970 TTAGATCCCTTAAGAAATGTTAGAAGTTCGAATTCTACTGTTTACGAATGGAGGAAACTAG
131 TTAGATCCCTTAAGAAAGGTTAGAAGTTCGAATCCTGGTGTTTACGAATGGAGGAAACTAG
*
1826031 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAGGC
1 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
* * ****
1826096 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAACCAGTTAGTCTAGTGTGATAAAACA
66 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAACCAGTTAGTCTAGTGGGATGAGGTG
*
1826161 TTAGATCCCTTAAGAAAGGTTAGAAGTTTGAATCCTGGTGTTTACGAATGGAGGAAACTAG
131 TTAGATCCCTTAAGAAAGGTTAGAAGTTCGAATCCTGGTGTTTACGAATGGAGGAAACTAG
1826222 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
1 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
*
1826287 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAATCAGTTAGTCTAGTGGGATGAGGTG
66 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAACCAGTTAGTCTAGTGGGATGAGGTG
* * * *
1826352 TTAGATCCTTTAAGAAAGGTTAAAAGTTTGAATCCTGCTGTTTACGAATGGAGGAAACTAG
131 TTAGATCCCTTAAGAAAGGTTAGAAGTTCGAATCCTGGTGTTTACGAATGGAGGAAACTAG
1826413 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
1 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
* *
1826478 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAATCAGTTAGTCTAGTGGGATAAGGTG
66 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAACCAGTTAGTCTAGTGGGATGAGGTG
* * *
1826543 TTAGATCCATTAAAAAAGGTTAGAAGTTCGAATCCTGGTGTTTACGAATGGAAGAAACTAG
131 TTAGATCCCTTAAGAAAGGTTAGAAGTTCGAATCCTGGTGTTTACGAATGGAGGAAACTAG
*
1826604 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATCAGTAGAAATTAATATTTAAGC
1 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
* * * * * *
1826669 ACATAAAAAATAGGAACACAATATGGATATATACCAACAACTAGTTGGTCCAGTGG
66 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAACCAGTTAGTCTAGTGG
1826725 TCCAGTGAAA
Statistics
Matches: 830, Mismatches: 53, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
190 178 0.21
191 652 0.79
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (191 bp):
AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
ACATAAAAAATAGGAACACAATATGTATATCTACCAATAACCAGTTAGTCTAGTGGGATGAGGTG
TTAGATCCCTTAAGAAAGGTTAGAAGTTCGAATCCTGGTGTTTACGAATGGAGGAAACTAG
Found at i:1829114 original size:21 final size:23
Alignment explanation
Indices: 1829079--1829165 Score: 108
Period size: 23 Copynumber: 3.9 Consensus size: 23
1829069 CAACGAAGTG
* *
1829079 CCACATA-AAATGTCCCGAATGA
1 CCACATAGAATTGTCCCGAAGGA
1829101 CCACATAG-A-TGTCCCGAAGGA
1 CCACATAGAATTGTCCCGAAGGA
*
1829122 CCACGTAGAATTGTCCCGAAGGA
1 CCACATAGAATTGTCCCGAAGGA
* *
1829145 CCGCGTAGAATTGTCCCGAAG
1 CCACATAGAATTGTCCCGAAG
1829166 AACCGCGCAG
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
21 18 0.31
22 9 0.15
23 32 0.54
ACGTcount: A:0.32, C:0.28, G:0.23, T:0.17
Consensus pattern (23 bp):
CCACATAGAATTGTCCCGAAGGA
Found at i:1829140 original size:23 final size:23
Alignment explanation
Indices: 1829089--1829165 Score: 113
Period size: 23 Copynumber: 3.4 Consensus size: 23
1829079 CCACATAAAA
* *
1829089 TGTCCCGAATGACCACATAG-A-
1 TGTCCCGAAGGACCACGTAGAAT
1829110 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
*
1829133 TGTCCCGAAGGACCGCGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
1829156 TGTCCCGAAG
1 TGTCCCGAAG
1829166 AACCGCGCAG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
21 18 0.35
22 1 0.02
23 32 0.63
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:1829170 original size:23 final size:23
Alignment explanation
Indices: 1829089--1829177 Score: 110
Period size: 23 Copynumber: 4.0 Consensus size: 23
1829079 CCACATAAAA
* * *
1829089 TGTCCCGAATGACCACATAG-A-
1 TGTCCCGAAGGACCGCGTAGAAT
*
1829110 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCGCGTAGAAT
1829133 TGTCCCGAAGGACCGCGTAGAAT
1 TGTCCCGAAGGACCGCGTAGAAT
* *
1829156 TGTCCCGAAGAACCGCGCAGAA
1 TGTCCCGAAGGACCGCGTAGAA
1829178 CCCTCAACTC
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
21 18 0.30
22 1 0.02
23 42 0.69
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (23 bp):
TGTCCCGAAGGACCGCGTAGAAT
Found at i:1831712 original size:23 final size:23
Alignment explanation
Indices: 1831681--1831724 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1831671 TAAAAATAAT
1831681 TCTGCCTTTATGACACATTTTTC
1 TCTGCCTTTATGACACATTTTTC
* *
1831704 TCTGTCTTTATGACACGTTTT
1 TCTGCCTTTATGACACATTTT
1831725 CGATCGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.23, G:0.11, T:0.50
Consensus pattern (23 bp):
TCTGCCTTTATGACACATTTTTC
Found at i:1832163 original size:2 final size:2
Alignment explanation
Indices: 1832156--1832186 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1832146 TCTTTTTCAA
1832156 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1832187 TAATTAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1834088 original size:14 final size:13
Alignment explanation
Indices: 1834056--1834096 Score: 66
Period size: 14 Copynumber: 3.2 Consensus size: 13
1834046 CTATCGCAAA
1834056 TTCGCGTTGC-AT
1 TTCGCGTTGCGAT
1834068 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
1834081 TATCGCGTTGCGAT
1 T-TCGCGTTGCGAT
1834095 TT
1 TT
1834097 TCCATTTCGC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.37
13 4 0.15
14 13 0.48
ACGTcount: A:0.10, C:0.22, G:0.27, T:0.41
Consensus pattern (13 bp):
TTCGCGTTGCGAT
Found at i:1834139 original size:41 final size:41
Alignment explanation
Indices: 1834090--1834240 Score: 284
Period size: 41 Copynumber: 3.7 Consensus size: 41
1834080 TTATCGCGTT
*
1834090 GCGATTTTCCATTTCGCGTTGCGGTAGTTGAAAATCGCAAC
1 GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAAC
*
1834131 GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGTAAC
1 GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAAC
1834172 GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAAC
1 GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAAC
1834213 GCGATTTTCCATTTCGCGTTGCGATAGT
1 GCGATTTTCCATTTCGCGTTGCGATAGT
1834241 CTACAGTTGT
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 107 1.00
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (41 bp):
GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAAC
Found at i:1834256 original size:22 final size:22
Alignment explanation
Indices: 1834229--1834281 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1834219 TTCCATTTCG
1834229 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
1834251 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1834273 CGTTGCGAT
1 CGTTGCGAT
1834282 TTTCCAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:1834912 original size:6 final size:6
Alignment explanation
Indices: 1834883--1834926 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
1834873 GTCCTGTCTC
1834883 GTCG-G GTCG-G GTCGGTG TGTCGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTC-GTG -GTCGTG GTCGTG GTCGTG GTCGTG GT
1834927 AATACGTGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 8 0.22
6 21 0.58
7 4 0.11
8 3 0.08
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GTCGTG
Found at i:1835054 original size:22 final size:22
Alignment explanation
Indices: 1835026--1835078 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1835016 AATTTGGAAA
1835026 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
1835048 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
1835070 ATCGCAACG
1 ATCGCAACG
1835079 CGATTTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:1835131 original size:19 final size:20
Alignment explanation
Indices: 1835091--1835142 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
1835081 ATTTTCAACT
*
1835091 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
1835111 ATCGCAACGCGAAAT-GAAA
1 ATCGCAACGCGAAATGGAAA
*
1835130 ATTGCAACGCGAA
1 ATCGCAACGCGAA
1835143 TGCAACGCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1844372 original size:2 final size:2
Alignment explanation
Indices: 1844365--1844391 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1844355 CATGCACGCA
1844365 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1844392 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1847159 original size:26 final size:25
Alignment explanation
Indices: 1847130--1847185 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
1847120 TCATTGTTAA
*
1847130 GGGTGAGAGTAGGAGAGTATGATTTG
1 GGGTGAGAAT-GGAGAGTATGATTTG
* **
1847156 GGGTTTAGAATTTAGAGTATGATTTG
1 GGG-TGAGAATGGAGAGTATGATTTG
1847182 GGGT
1 GGGT
1847186 TTAAATTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
25 1 0.04
26 19 0.76
27 5 0.20
ACGTcount: A:0.25, C:0.00, G:0.41, T:0.34
Consensus pattern (25 bp):
GGGTGAGAATGGAGAGTATGATTTG
Found at i:1847186 original size:26 final size:25
Alignment explanation
Indices: 1847143--1847193 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 25
1847133 TGAGAGTAGG
1847143 AGAGTATGATTTGGGGTTTAGAATTT
1 AGAGTATGATTTGGGGTTTA-AATTT
1847169 AGAGTATGATTTGGGGTTTAAATTT
1 AGAGTATGATTTGGGGTTTAAATTT
1847194 TGTTTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.43
Consensus pattern (25 bp):
AGAGTATGATTTGGGGTTTAAATTT
Found at i:1847854 original size:21 final size:21
Alignment explanation
Indices: 1847838--1847884 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1847828 GCGTTGCATT
1847838 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
1847859 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
1847880 TCGCG
1 TCGCG
1847885 ATTTTGCGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:1847936 original size:19 final size:19
Alignment explanation
Indices: 1847912--1847959 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
1847902 TCTACAGTTG
*
1847912 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTCCAAAT
1847931 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
1847950 TCGTTGCGAT
1 TCGTTGCGAT
1847960 AGTCTACAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:1847995 original size:43 final size:41
Alignment explanation
Indices: 1847931--1848042 Score: 179
Period size: 43 Copynumber: 2.7 Consensus size: 41
1847921 TTTTTCAAAT
1847931 TCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTG
* *
1847972 TTGTTGCGATAGTTTACAAATTCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGAT--TTTCCAAATTCGTTGCGATAGTCTACAGTTG
*
1848015 TCGTTGCGATTTTCCAAATTCTTTGCGA
1 TCGTTGCGATTTTCCAAATTCGTTGCGA
1848043 AAATTCATTG
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
41 25 0.39
43 39 0.61
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (41 bp):
TCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTG
Found at i:1848426 original size:20 final size:20
Alignment explanation
Indices: 1848397--1848440 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1848387 AAAATCTTTT
* *
1848397 ATTTTTAACTATCATAACGA
1 ATTTTCAACTATCACAACGA
1848417 ATTTTCAACTATCACAACGA
1 ATTTTCAACTATCACAACGA
1848437 ATTT
1 ATTT
1848441 AGAAAATCGT
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:0.39, C:0.18, G:0.05, T:0.39
Consensus pattern (20 bp):
ATTTTCAACTATCACAACGA
Found at i:1848528 original size:21 final size:21
Alignment explanation
Indices: 1848467--1848528 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
1848457 AACTGTAGAT
*
1848467 TATCGCAACGCGAAATG-AAA
1 TATCGCAACGCGAAATGCAAC
* ** *
1848487 AATCGCAACGCGATTTTCAAC
1 TATCGCAACGCGAAATGCAAC
*
1848508 TATCGCAACACGAAATGCAAC
1 TATCGCAACGCGAAATGCAAC
1848529 GCGAATTTAT
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.18
Consensus pattern (21 bp):
TATCGCAACGCGAAATGCAAC
Found at i:1848848 original size:42 final size:42
Alignment explanation
Indices: 1848784--1848903 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
1848774 TTTCCCCGAA
* *
1848784 TTCCAGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
*
1848826 TTCCCGTGTTTGTTTAACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1848868 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1848904 TGTAATTCAT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:1849119 original size:21 final size:22
Alignment explanation
Indices: 1849093--1849135 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1849083 TAATTATTAA
1849093 AATATTTAAAATATATT-TATT
1 AATATTTAAAATATATTATATT
*
1849114 AATATTTATAATATATTATATT
1 AATATTTAAAATATATTATATT
1849136 TTTTTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATATTTAAAATATATTATATT
Found at i:1849208 original size:31 final size:30
Alignment explanation
Indices: 1849163--1849268 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 30
1849153 AATAATCAAT
*
1849163 TATATTATAATAATATAAGATATTTATTTTA
1 TATATTTTAATAATATAA-ATATTTATTTTA
* *
1849194 TTTATTTTAATAATATATAATAAATT-TTTTA
1 TATATTTTAATAATATA-AAT-ATTTATTTTA
*
1849225 TATA-TTTAATAATAAATAATA-TTA-TTTA
1 TATATTTTAATAATATA-AATATTTATTTTA
*
1849253 TATATTTCAATAATAT
1 TATATTTTAATAATAT
1849269 TTTAATAAAG
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
28 10 0.16
29 10 0.16
30 15 0.23
31 25 0.39
32 4 0.06
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (30 bp):
TATATTTTAATAATATAAATATTTATTTTA
Found at i:1849226 original size:60 final size:60
Alignment explanation
Indices: 1849123--1849277 Score: 140
Period size: 60 Copynumber: 2.6 Consensus size: 60
1849113 TAATATTTAT
* * *
1849123 AATA-TATTATATTTTTTTTAATATTATATAA-ATAATCAATTATAT-TATAATAATATAAG
1 AATATTATTTTATTTATTTTAATAATATATAATA-AATCAATTATATATATAATAATA-AAG
*** * *
1849182 -ATATTTATTTTATTTATTTTAATAATATATAATAAATTTTTTATATATTTAATAATAAAT
1 AATA-TTATTTTATTTATTTTAATAATATATAATAAATCAATTATATATATAATAATAAAG
* * *
1849242 AATATTA-TTTATATATTTCAATAATATTTTAATAAA
1 AATATTATTTTATTTATTTTAATAATA-TATAATAAA
1849278 GATATTTAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
58 3 0.04
59 17 0.22
60 46 0.58
61 13 0.16
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (60 bp):
AATATTATTTTATTTATTTTAATAATATATAATAAATCAATTATATATATAATAATAAAG
Found at i:1849264 original size:26 final size:26
Alignment explanation
Indices: 1849212--1849265 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
1849202 AATAATATAT
* *
1849212 AATAAATTTTTTATATATTTAATAATA
1 AATAAATTATTTATATATTT-ACAATA
1849239 AATAATATTATTTATATATTT-CAATA
1 AATAA-ATTATTTATATATTTACAATA
1849265 A
1 A
1849266 TATTTTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.21
27 5 0.21
28 14 0.58
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
AATAAATTATTTATATATTTACAATA
Found at i:1849297 original size:23 final size:23
Alignment explanation
Indices: 1849271--1849315 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1849261 AATAATATTT
1849271 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1849294 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1849316 ATATAGCATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1849521 original size:20 final size:20
Alignment explanation
Indices: 1849463--1849512 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1849453 TTTTCCGATG
1849463 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1849483 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1849503 TTTTCCAGAA
1 TTTTCCAGAA
1849513 TTCAAATTCC
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:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:1849531 original size:15 final size:15
Alignment explanation
Indices: 1849495--1849576 Score: 94
Period size: 15 Copynumber: 5.5 Consensus size: 15
1849485 TTCCAGAAAT
**
1849495 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
1849510 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
** *
1849524 GTAATTCATTTTTCA
1 GTAATTCAAATTCCA
1849539 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
* *
1849554 GTAATTCAAACTCTA
1 GTAATTCAAATTCCA
1849569 GTAATTCA
1 GTAATTCA
1849577 TTTTCTGAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
14 12 0.21
15 44 0.79
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:1849545 original size:30 final size:29
Alignment explanation
Indices: 1849495--1849561 Score: 116
Period size: 30 Copynumber: 2.3 Consensus size: 29
1849485 TTCCAGAAAT
1849495 GTAATTCATTTTCCAGAATTCAAATTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
*
1849524 GTAATTCATTTTTCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAG-AATTCAAATTCCA
1849554 GTAATTCA
1 GTAATTCA
1849562 AACTCTAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 15 0.42
30 21 0.58
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.40
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAAATTCCA
Found at i:1849573 original size:45 final size:44
Alignment explanation
Indices: 1849495--1849580 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 44
1849485 TTCCAGAAAT
** *
1849495 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTTCA
1 GTAATTCAAATTCCAGAATTCAAACTCCAGTAATTCATTTTTCA
*
1849539 GTAATTCAAATTCCAGTAATTCAAACTCTAGTAATTCATTTT
1 GTAATTCAAATTCCAG-AATTCAAACTCCAGTAATTCATTTT
1849581 CTGAAAAACC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 14 0.38
45 23 0.62
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAACTCCAGTAATTCATTTTTCA
Found at i:1857270 original size:25 final size:25
Alignment explanation
Indices: 1857238--1857287 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1857228 ATATATTTTA
1857238 TTTAGAATATATTAATATTTAAATT
1 TTTAGAATATATTAATATTTAAATT
1857263 TTTAGAATATATTAATATTTAAATT
1 TTTAGAATATATTAATATTTAAATT
1857288 AATATTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (25 bp):
TTTAGAATATATTAATATTTAAATT
Found at i:1858571 original size:11 final size:12
Alignment explanation
Indices: 1858555--1858596 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1858545 CCTGAGTGAT
1858555 ATTTATT-TTTA
1 ATTTATTATTTA
1858566 ATTTATTATTTA
1 ATTTATTATTTA
1858578 ATTTAGTTGATTTA
1 ATTTA-TT-ATTTA
*
1858592 TTTTA
1 ATTTA
1858597 GCCATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 7 0.26
12 9 0.33
13 2 0.07
14 9 0.33
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (12 bp):
ATTTATTATTTA
Found at i:1859847 original size:24 final size:24
Alignment explanation
Indices: 1859820--1859939 Score: 103
Period size: 24 Copynumber: 5.3 Consensus size: 24
1859810 AAACGGAGAT
1859820 ATCAGAAATCAAAACATAATTCAA
1 ATCAGAAATCAAAACATAATTCAA
* * *
1859844 ATCAG------AAA-AGAATCCAT
1 ATCAGAAATCAAAACATAATTCAA
* * *
1859861 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAAAACATAATTCAA
*
1859885 ATAAGAAATCAAAACATAATTCAA
1 ATCAGAAATCAAAACATAATTCAA
* *
1859909 ATCGGAAATCAGAACATAATTCAA
1 ATCAGAAATCAAAACATAATTCAA
1859933 ATC-GAAA
1 ATCAGAAA
1859940 ATCAGATAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 15
0.73 0.12 0.14
Matches are distributed among these distances:
17 11 0.14
18 3 0.04
23 6 0.08
24 56 0.74
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAACATAATTCAA
Found at i:1874241 original size:21 final size:21
Alignment explanation
Indices: 1874159--1874235 Score: 154
Period size: 21 Copynumber: 3.7 Consensus size: 21
1874149 TATGGGCTAG
1874159 GGGAATCGGTACCCATTCAAT
1 GGGAATCGGTACCCATTCAAT
1874180 GGGAATCGGTACCCATTCAAT
1 GGGAATCGGTACCCATTCAAT
1874201 GGGAATCGGTACCCATTCAAT
1 GGGAATCGGTACCCATTCAAT
1874222 GGGAATCGGTACCC
1 GGGAATCGGTACCC
1874236 CCTCAACCGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (21 bp):
GGGAATCGGTACCCATTCAAT
Found at i:1879311 original size:21 final size:21
Alignment explanation
Indices: 1879287--1879335 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1879277 TAGGGGAATT
1879287 GGTACCCATTCAATGGAAATC
1 GGTACCCATTCAATGGAAATC
*
1879308 GGTACCCATTCAATGGGAATC
1 GGTACCCATTCAATGGAAATC
*
1879329 GATACCC
1 GGTACCC
1879336 CCTCAACCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (21 bp):
GGTACCCATTCAATGGAAATC
Found at i:1879341 original size:21 final size:21
Alignment explanation
Indices: 1879289--1879341 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1879279 GGGGAATTGG
* *
1879289 TACCCATTCAATGGAAATCGG
1 TACCCACTCAATGGAAATCGA
* *
1879310 TACCCATTCAATGGGAATCGA
1 TACCCACTCAATGGAAATCGA
*
1879331 TACCCCCTCAA
1 TACCCACTCAA
1879342 CCGAACCAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
TACCCACTCAATGGAAATCGA
Found at i:1880012 original size:2 final size:2
Alignment explanation
Indices: 1880005--1880034 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1879995 AGATTAATAG
1880005 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
1880035 TAGGAGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1881098 original size:23 final size:23
Alignment explanation
Indices: 1881072--1881119 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1881062 TTCGGTATAT
1881072 TTCTACACGGCACTACAGTGCAA
1 TTCTACACGGCACTACAGTGCAA
** * *
1881095 TTCTACGTGGCACTTCGGTGCAA
1 TTCTACACGGCACTACAGTGCAA
1881118 TT
1 TT
1881120 TATATGAGCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (23 bp):
TTCTACACGGCACTACAGTGCAA
Found at i:1885889 original size:22 final size:22
Alignment explanation
Indices: 1885863--1885920 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
1885853 TCACTCTCTA
*
1885863 CGGCGACATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
* * *
1885885 TGGCGAAATCCATCCCTATCTC
1 CGGCGAAATCCGTCCCCATCTC
*
1885907 CAGCGAAATCCGTC
1 CGGCGAAATCCGTC
1885921 TATCTCCGTC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.41, G:0.17, T:0.21
Consensus pattern (22 bp):
CGGCGAAATCCGTCCCCATCTC
Found at i:1886009 original size:12 final size:12
Alignment explanation
Indices: 1885992--1886026 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1885982 CCGAGGGTTA
1885992 GTTTTTTTTTTT
1 GTTTTTTTTTTT
1886004 GTTTTTTTTTTT
1 GTTTTTTTTTTT
1886016 GAATTTTTTTT
1 G--TTTTTTTT
1886027 CTTATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 13 0.62
14 8 0.38
ACGTcount: A:0.06, C:0.00, G:0.09, T:0.86
Consensus pattern (12 bp):
GTTTTTTTTTTT
Found at i:1886327 original size:19 final size:20
Alignment explanation
Indices: 1886305--1886344 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1886295 AAATCGCAAC
1886305 GCGA-TTTTAGTTTCGCGTT
1 GCGATTTTTAGTTTCGCGTT
*
1886324 GCGATTTTTATTTTCGCGTT
1 GCGATTTTTAGTTTCGCGTT
1886344 G
1 G
1886345 TGAATTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.10, C:0.15, G:0.25, T:0.50
Consensus pattern (20 bp):
GCGATTTTTAGTTTCGCGTT
Found at i:1887737 original size:42 final size:41
Alignment explanation
Indices: 1887677--1887772 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 41
1887667 CCCCCACTTC
* * * * *
1887677 GAGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACACCT
1 GAGAGCCATCA-CTGATCGAACCGATTATACACCTCCACA-AT
1887720 -AGAGCCATCACTGGATCGAACCGATTATACACCTCCACAAT
1 GAGAGCCATCACT-GATCGAACCGATTATACACCTCCACAAT
1887761 GAGAGCCATCAC
1 GAGAGCCATCAC
1887773 CTATTCCATC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
41 3 0.07
42 43 0.93
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.18
Consensus pattern (41 bp):
GAGAGCCATCACTGATCGAACCGATTATACACCTCCACAAT
Found at i:1888177 original size:4 final size:4
Alignment explanation
Indices: 1888161--1888202 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
1888151 TTTTTCGACA
* * *
1888161 TTAT TTAT ATAT TTAT TTAT TTAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1888203 TTAGCGGCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:1888398 original size:42 final size:41
Alignment explanation
Indices: 1888346--1888463 Score: 173
Period size: 42 Copynumber: 2.9 Consensus size: 41
1888336 GATTCACCTG
* *
1888346 TCATCATTCAAGAGGCCCCTCCTATCGTTCAAGAGGCCACTC
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC-CTC
* *
1888388 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCTG
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCTC
* *
1888429 TCATCATTCAAGAGGTCTCTCCCACCGTTCAAGAG
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAG
1888464 CCCGATTCAC
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 34 0.49
42 35 0.51
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.23
Consensus pattern (41 bp):
TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCTC
Done.