Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009461.1 Hibiscus syriacus cultivar Beakdansim tig00113724_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: 2346588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 12
Found at i:1749996 original size:19 final size:19
Alignment explanation
Indices: 1749925--1749990 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
1749915 TTATATATAT
1749925 TTATTTTTATAATATTTTA
1 TTATTTTTATAATATTTTA
*
1749944 TTA-TTTT-TAATATATATA
1 TTATTTTTATAATAT-TTTA
1749962 TTTATTTTTATAATATTTTA
1 -TTATTTTTATAATATTTTA
1749982 TTATTTTTA
1 TTATTTTTA
1749991 ATATATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 6 0.15
18 7 0.17
19 15 0.37
20 7 0.17
21 6 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTTTTATAATATTTTA
Found at i:1750067 original size:41 final size:40
Alignment explanation
Indices: 1749917--1750070 Score: 129
Period size: 41 Copynumber: 3.8 Consensus size: 40
1749907 ATAATCTATT
* * *
1749917 ATATATATTTATTTTTATAATATTTTATTATTTT--T-AAT
1 ATATATATTTATTTTTA-AATATTTAATAATTTTAATAAAA
* * * *
1749955 ATATATATTTATTTTTATAATATTTTATTATTTTTAATATAT
1 ATATATATTTATTTTTA-AATA-TTTAATAATTTTAATAAAA
*
1749997 ATATATATATAATTTTT-AATAATTTAATAATTTTAA-AAAA
1 ATATATAT-TTATTTTTAAAT-ATTTAATAATTTTAATAAAA
*
1750037 ATTTATATTTATTTTTTAAATATTTAAATAATTT
1 ATATATATTTA-TTTTTAAATATTT-AATAATTT
1750071 ATATTTATAA
Statistics
Matches: 95, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
38 22 0.23
39 10 0.11
40 18 0.19
41 27 0.28
42 11 0.12
43 7 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (40 bp):
ATATATATTTATTTTTAAATATTTAATAATTTTAATAAAA
Found at i:1750260 original size:22 final size:22
Alignment explanation
Indices: 1750226--1750267 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1750216 GTCAACACCA
*
1750226 TGAAATGTCATGTTAGCATTTG
1 TGAAATGTCATGTCAGCATTTG
* *
1750248 TGAACTGTTATGTCAGCATT
1 TGAAATGTCATGTCAGCATT
1750268 ATAACTGTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.40
Consensus pattern (22 bp):
TGAAATGTCATGTCAGCATTTG
Found at i:1760103 original size:19 final size:20
Alignment explanation
Indices: 1760075--1760156 Score: 78
Period size: 19 Copynumber: 4.0 Consensus size: 20
1760065 TGACATATAA
* *
1760075 ATATATATATATACATGCAT
1 ATATACATATATACATACAT
1760095 -TATACATATAT-CATACAT
1 ATATACATATATACATACAT
* *
1760113 ATGTACATATATACATATACTT
1 ATATACATATATAC--ATACAT
1760135 ATATACACTTATATACATACAT
1 ATATACA--TATATACATACAT
1760157 CATTGATCAT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
18 6 0.12
19 20 0.40
20 1 0.02
22 16 0.32
24 7 0.14
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.39
Consensus pattern (20 bp):
ATATACATATATACATACAT
Found at i:1760121 original size:8 final size:8
Alignment explanation
Indices: 1760102--1760253 Score: 66
Period size: 8 Copynumber: 18.9 Consensus size: 8
1760092 CATTATACAT
1760102 ATATCATAC
1 ATAT-ATAC
*
1760111 ATATGTAC
1 ATATATAC
1760119 ATATATAC
1 ATATATAC
1760127 --ATATAC
1 ATATATAC
*
1760133 TTATATAC
1 ATATATAC
1760141 ACTTATATAC
1 A--TATATAC
*
1760151 ATACAT-C
1 ATATATAC
1760158 ATTGATCATAC
1 A-T-AT-ATAC
1760169 ATA-ATTAC
1 ATATA-TAC
1760177 ATATATAC
1 ATATATAC
*
1760185 TTA-ATTAC
1 ATATA-TAC
*
1760193 TTATATAC
1 ATATATAC
* *
1760201 --ACACAC
1 ATATATAC
* *
1760207 ATTTATAT
1 ATATATAC
*
1760215 ATATATAT
1 ATATATAC
*
1760223 ATATATAT
1 ATATATAC
*
1760231 ATATATAT
1 ATATATAC
*
1760239 ATATATAT
1 ATATATAC
1760247 ATATATA
1 ATATATA
1760254 TATAAAAGTT
Statistics
Matches: 116, Mismatches: 13, Indels: 29
0.73 0.08 0.18
Matches are distributed among these distances:
6 10 0.09
7 4 0.03
8 81 0.70
9 8 0.07
10 11 0.09
11 2 0.02
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.41
Consensus pattern (8 bp):
ATATATAC
Found at i:1760215 original size:2 final size:2
Alignment explanation
Indices: 1760210--1760257 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1760200 CACACACATT
1760210 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
1760252 TA TA TA
1 TA TA TA
1760258 AAAGTTGTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1760349 original size:28 final size:29
Alignment explanation
Indices: 1760313--1760368 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1760303 TTAATTCTGA
* *
1760313 GGACTAAAATGAA-TTTTAATTAAATTCG
1 GGACCAAAATAAACTTTTAATTAAATTCG
*
1760341 GGACCAAAATAAACTTTTAATTTAATTC
1 GGACCAAAATAAACTTTTAATTAAATTC
1760369 AAATCCAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (29 bp):
GGACCAAAATAAACTTTTAATTAAATTCG
Found at i:1767272 original size:29 final size:31
Alignment explanation
Indices: 1767233--1767297 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
1767223 TCTTAATATT
*
1767233 AATTCTAAGGAATAAAAT-AAATTTTAATTA
1 AATTCTAAGGAACAAAATAAAATTTTAATTA
* *
1767263 AATTCT-AGGACCAAAATAAAATTTTAATTT
1 AATTCTAAGGAACAAAATAAAATTTTAATTA
1767293 AATTC
1 AATTC
1767298 AAATCCAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (31 bp):
AATTCTAAGGAACAAAATAAAATTTTAATTA
Found at i:1772811 original size:2 final size:2
Alignment explanation
Indices: 1772804--1772849 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1772794 CATCCTGCCA
1772804 AT AT AT AT 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 AT AT AT AT
1772846 AT AT
1 AT AT
1772850 TGTAATGCAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1773789 original size:16 final size:17
Alignment explanation
Indices: 1773768--1773830 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 17
1773758 TAAATAAATA
*
1773768 ATAATTA-ATTAATTTT
1 ATAATTATAATAATTTT
1773784 ATAATTATAATAATTTTCT
1 ATAATTATAATAA-TTT-T
**
1773803 ATAATTGA-AAT-ATAAT
1 ATAATT-ATAATAATTTT
1773819 ATAATTATAATA
1 ATAATTATAATA
1773831 GCAATGTTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
15 1 0.03
16 17 0.45
17 5 0.13
18 4 0.11
19 10 0.26
20 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
ATAATTATAATAATTTT
Found at i:1774301 original size:32 final size:33
Alignment explanation
Indices: 1774247--1774312 Score: 125
Period size: 32 Copynumber: 2.0 Consensus size: 33
1774237 GTTTGCATGG
1774247 TATGAGTAGCCATAGAACAGTTGAAATTGCCAT
1 TATGAGTAGCCATAGAACAGTTGAAATTGCCAT
1774280 TATGAGTAGCCA-AGAACAGTTGAAATTGCCAT
1 TATGAGTAGCCATAGAACAGTTGAAATTGCCAT
1774312 T
1 T
1774313 CTCTGGCCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 21 0.64
33 12 0.36
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (33 bp):
TATGAGTAGCCATAGAACAGTTGAAATTGCCAT
Found at i:1782124 original size:18 final size:18
Alignment explanation
Indices: 1782103--1782143 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1782093 CTATCATAGC
* *
1782103 CACGTTTACGATCACGGT
1 CACGTTCACGATCACGAT
*
1782121 CACGGTCACGATCACGAT
1 CACGTTCACGATCACGAT
1782139 CACGT
1 CACGT
1782144 CCATTATCAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (18 bp):
CACGTTCACGATCACGAT
Found at i:1786735 original size:21 final size:22
Alignment explanation
Indices: 1786711--1786754 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
1786701 TATTAGATTT
1786711 AAGTTGAAACA-TTTCAGATCA
1 AAGTTGAAACATTTTCAGATCA
1786732 AAGTTGAAACATTTTCAGATCA
1 AAGTTGAAACATTTTCAGATCA
1786754 A
1 A
1786755 TTTACTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (22 bp):
AAGTTGAAACATTTTCAGATCA
Found at i:1793681 original size:25 final size:24
Alignment explanation
Indices: 1793620--1793681 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
1793610 CGGATGAATA
*
1793620 AAAATAAATAATTGAAATTAATTAT
1 AAAAT-AATAAATGAAATTAATTAT
* *
1793645 AAAA-AATAAAATGATATTTATTGAT
1 AAAATAAT-AAATGAAATTAATT-AT
1793670 AAAATAATAAAT
1 AAAATAATAAAT
1793682 TAATCTCACC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 3 0.10
24 11 0.35
25 14 0.45
26 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (24 bp):
AAAATAATAAATGAAATTAATTAT
Found at i:1793716 original size:31 final size:31
Alignment explanation
Indices: 1793678--1793741 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
1793668 ATAAAATAAT
1793678 AAATTAATCTCACCCATCACCTTTTAGTAGA
1 AAATTAATCTCACCCATCACCTTTTAGTAGA
1793709 AAATTAATCTCACCCATCACCTTTTAGTAGA
1 AAATTAATCTCACCCATCACCTTTTAGTAGA
1793740 AA
1 AA
1793742 TTCCAATCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (31 bp):
AAATTAATCTCACCCATCACCTTTTAGTAGA
Found at i:1804230 original size:13 final size:13
Alignment explanation
Indices: 1804214--1804247 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
1804204 TCATATCCAT
1804214 TTTTCTTTCTTTA
1 TTTTCTTTCTTTA
1804227 TTTTCTTTCTTTA
1 TTTTCTTTCTTTA
1804240 TTTTCTTT
1 TTTTCTTT
1804248 TCACAATGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTCTTTCTTTA
Found at i:1813585 original size:20 final size:18
Alignment explanation
Indices: 1813538--1813610 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
1813528 ACTGAATATT
*
1813538 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1813556 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
1813575 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
1813594 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1813611 GATTATCCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 31 0.65
19 2 0.04
20 15 0.31
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1820454 original size:18 final size:18
Alignment explanation
Indices: 1820427--1820499 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
1820417 ACTGAATATT
1820427 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1820445 TGTCCTGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
1820464 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
1820483 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1820500 GATTATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 31 0.66
19 2 0.04
20 14 0.30
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1820474 original size:38 final size:38
Alignment explanation
Indices: 1820426--1820508 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
1820416 CACTGAATAT
* *
1820426 TTGTCCCGAAGGACCACTATGTCCTGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
*
1820464 TTGTTCCGAAGAACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
*
1820502 TTATCCC
1 TTGTCCC
1820509 TCGACTCTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
Found at i:1821664 original size:9 final size:9
Alignment explanation
Indices: 1821650--1821680 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1821640 TTCACATGTG
1821650 GAGAAAGAA
1 GAGAAAGAA
1821659 GAGAAAGAA
1 GAGAAAGAA
1821668 GAG-AAGAA
1 GAGAAAGAA
1821676 GAGAA
1 GAGAA
1821681 CTCTGGAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (9 bp):
GAGAAAGAA
Found at i:1822469 original size:22 final size:21
Alignment explanation
Indices: 1822437--1822477 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1822427 TCATCTCTAT
1822437 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
1822458 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
1822478 TTTACGCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.37, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:1822807 original size:11 final size:11
Alignment explanation
Indices: 1822791--1822862 Score: 67
Period size: 11 Copynumber: 6.4 Consensus size: 11
1822781 ATTGGAGTGC
1822791 AAAAAGAAAAG
1 AAAAAGAAAAG
1822802 AAAAAGACAAA-
1 AAAAAGA-AAAG
*
1822813 AAGAAAAAAAAG
1 AA-AAAGAAAAG
1822825 AAAAAAGAAGAA-
1 -AAAAAGAA-AAG
1822837 AAAAAGAAAAG
1 AAAAAGAAAAG
**
1822848 AAAATCAAAAG
1 AAAAAGAAAAG
1822859 AAAA
1 AAAA
1822863 TCAAAATGAG
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
10 2 0.04
11 33 0.65
12 12 0.24
13 4 0.08
ACGTcount: A:0.82, C:0.03, G:0.14, T:0.01
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:1822812 original size:19 final size:18
Alignment explanation
Indices: 1822790--1822843 Score: 76
Period size: 18 Copynumber: 3.0 Consensus size: 18
1822780 AATTGGAGTG
1822790 CAAAAAGAAAAGAAAAAGA
1 CAAAAAGAAAA-AAAAAGA
1822809 CAAAAAG-AAAAAAAAGA
1 CAAAAAGAAAAAAAAAGA
1822826 -AAAAAGAAGAAAAAAAGA
1 CAAAAAGAA-AAAAAAAGA
1822844 AAAGAAAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.18
17 8 0.24
18 12 0.36
19 7 0.21
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (18 bp):
CAAAAAGAAAAAAAAAGA
Found at i:1822827 original size:23 final size:22
Alignment explanation
Indices: 1822791--1822851 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
1822781 ATTGGAGTGC
*
1822791 AAAAAGAAAAGAAAAAGACA-AA
1 AAAAAAAAAAGAAAAAGA-AGAA
1822813 AAGAAAAAAAAGAAAAAAGAAGAA
1 AA-AAAAAAAAG-AAAAAGAAGAA
*
1822837 AAAAAGAAAAGAAAA
1 AAAAAAAAAAGAAAA
1822852 TCAAAAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 6 0.18
23 17 0.50
24 11 0.32
ACGTcount: A:0.84, C:0.02, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAGAAAAAGAAGAA
Found at i:1822829 original size:16 final size:16
Alignment explanation
Indices: 1822791--1822862 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 16
1822781 ATTGGAGTGC
1822791 AAAAAGAAAAGAAAAAGA
1 AAAAAG-AAA-AAAAAGA
1822809 CAAAAAGAAAAAAAAGA
1 -AAAAAGAAAAAAAAGA
1822826 AAAAAGAAGAAAAAA-A
1 AAAAAGAA-AAAAAAGA
*
1822842 GAAAAGAAAATCAAAAGA
1 AAAAAGAAAA--AAAAGA
1822860 AAA
1 AAA
1822863 TCAAAATGAG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.04
16 16 0.34
17 17 0.36
18 6 0.13
19 6 0.13
ACGTcount: A:0.82, C:0.03, G:0.14, T:0.01
Consensus pattern (16 bp):
AAAAAGAAAAAAAAGA
Found at i:1822835 original size:27 final size:28
Alignment explanation
Indices: 1822791--1822862 Score: 92
Period size: 27 Copynumber: 2.5 Consensus size: 28
1822781 ATTGGAGTGC
*
1822791 AAAAAGAAAAGAAAAAGACAAAAAGAAA
1 AAAAAGAAAAGAAAAAGAAAAAAAGAAA
*
1822819 AAAAAGAAAA-AAGAAGAAAAAAAGAAA
1 AAAAAGAAAAGAAAAAGAAAAAAAGAAA
*
1822846 AGAAAATCAAAAGAAAA
1 A-AAAA-GAAAAGAAAA
1822863 TCAAAATGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 16 0.43
28 14 0.38
29 4 0.11
30 3 0.08
ACGTcount: A:0.82, C:0.03, G:0.14, T:0.01
Consensus pattern (28 bp):
AAAAAGAAAAGAAAAAGAAAAAAAGAAA
Found at i:1822863 original size:11 final size:11
Alignment explanation
Indices: 1822843--1822868 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1822833 AGAAAAAAAG
1822843 AAAAGAAAATC
1 AAAAGAAAATC
1822854 AAAAGAAAATC
1 AAAAGAAAATC
1822865 AAAA
1 AAAA
1822869 TGAGAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAGAAAATC
Found at i:1829599 original size:24 final size:24
Alignment explanation
Indices: 1829508--1829599 Score: 82
Period size: 24 Copynumber: 3.7 Consensus size: 24
1829498 GAGTATTTTA
1829508 TTATTAT-TTTATTTAGGAATTAG
1 TTATTATATTTATTTAGGAATTAG
* *
1829531 TTATTTTTATTTATTTA-GAACTTCTTG
1 TTA-TTATATTTATTTAGGAA--T-TAG
1829558 TTTGATTA-ATTTATTTAGGAATTAG
1 -TT-ATTATATTTATTTAGGAATTAG
*
1829583 TTATTATATTTACTTAG
1 TTATTATATTTATTTAG
1829600 AACTCTCGGG
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
23 7 0.13
24 17 0.31
25 10 0.18
26 2 0.04
27 11 0.20
28 7 0.13
29 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.11, T:0.58
Consensus pattern (24 bp):
TTATTATATTTATTTAGGAATTAG
Found at i:1831583 original size:30 final size:30
Alignment explanation
Indices: 1831547--1831607 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
1831537 TTCTAAATTA
1831547 AAGCTTCTAATTTTAGTTTAATTTGATTTT
1 AAGCTTCTAATTTTAGTTTAATTTGATTTT
*
1831577 AAGCTTCTAATTTTAGTTTATTTTGATTTT
1 AAGCTTCTAATTTTAGTTTAATTTGATTTT
1831607 A
1 A
1831608 CTCTCATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.07, G:0.10, T:0.57
Consensus pattern (30 bp):
AAGCTTCTAATTTTAGTTTAATTTGATTTT
Found at i:1834384 original size:108 final size:108
Alignment explanation
Indices: 1834195--1834398 Score: 275
Period size: 108 Copynumber: 1.9 Consensus size: 108
1834185 ATGAATATGG
* ** * * *
1834195 TGAGGTGATTTTATCTGAGTTTAATTCTTTCTCTTAGTCTTGGTCGAGAGATTTTATAATGAGTC
1 TGAGGTGATTTTATCTGAGTTTAATTCTTTCTCTTAGTATCAGTAGAGAGATTTTATAATAACTC
*
1834260 GTAGATATGATAACAAACATATGATCATTATAGCTACATGTAC
66 GTAAATATGATAACAAACATATGATCATTATAGCTACATGTAC
* *
1834303 TGAGGTGATTTTATCTGAGTTTTATTCTTTCTCTTAGTATCAGTAGAGAGATTTTATAGTAACTC
1 TGAGGTGATTTTATCTGAGTTTAATTCTTTCTCTTAGTATCAGTAGAGAGATTTTATAATAACTC
* * * *
1834368 TTAAA-ATTGGTGACAAACATATGATTATTAT
66 GTAAATA-TGATAACAAACATATGATCATTAT
1834399 GACTATCCGT
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
107 1 0.01
108 81 0.99
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.42
Consensus pattern (108 bp):
TGAGGTGATTTTATCTGAGTTTAATTCTTTCTCTTAGTATCAGTAGAGAGATTTTATAATAACTC
GTAAATATGATAACAAACATATGATCATTATAGCTACATGTAC
Found at i:1836578 original size:21 final size:22
Alignment explanation
Indices: 1836560--1836600 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1836550 TGACCTTTGG
1836560 TACGTT-TTTGGTC-TTCTTTA
1 TACGTTGTTTGGTCATTCTTTA
*
1836580 TAGGTTGTTTGGTCATTCTTT
1 TACGTTGTTTGGTCATTCTTT
1836601 TCATTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.59
Consensus pattern (22 bp):
TACGTTGTTTGGTCATTCTTTA
Found at i:1836852 original size:179 final size:181
Alignment explanation
Indices: 1836507--1836863 Score: 495
Period size: 179 Copynumber: 2.0 Consensus size: 181
1836497 TGGTCGCTTC
* * * *
1836507 TGTTTTTGTCACTTCACCATTAGATCGCATATGGTGTGATGAATGACCTTTGGTACGTTTTTGGT
1 TGTTTTTGTCAATTCACCATTAGATCACAAATGGTGTGATGAATGACCTTTGGTACGTTTTCGGT
* * *
1836572 CTTCTTTATAGGTTGTTTGGTCATTCTTTTCATTTATATTTTTTTTATCAAAGTTAGATTTAACA
66 CTTCTTTATAGGTCGTTTGGTCATGCTTTTCATTTATATTCTTTTTATCAAAGTTAGATTTAACA
* * * *
1836637 TCGTCTCGATTGATCAAAATAACACTTATTCATTATCCTGTTGATCTTCTA
131 TCGTCTCGACTAATCAAAATAACACATATACATTATCCTGTTGATCTTCTA
* *
1836688 TGTTTTTGTCAATTCACCATTAGATCACAAATGGTGTGGTGAATGATCTTTTGGTACGTTTTCGG
1 TGTTTTTGTCAATTCACCATTAGATCACAAATGGTGTGATGAATGA-CCTTTGGTACGTTTTCGG
* ** *
1836753 TCTTCTTTATTGGTCGTTTGGTTGTGCTTTTCA-TT-TA-TCTTTTTATCAAAGTTAGATTTGAC
65 TCTTCTTTATAGGTCGTTTGGTCATGCTTTTCATTTATATTCTTTTTATCAAAGTTAGATTTAAC
* * * *
1836815 GTTGTCTCGACTAATCAAAATAACACATATACATTATCTTGTTTATCTT
130 ATCGTCTCGACTAATCAAAATAACACATATACATTATCCTGTTGATCTT
1836864 TCCTGTTTTG
Statistics
Matches: 154, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
179 64 0.42
180 2 0.01
181 44 0.29
182 44 0.29
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.46
Consensus pattern (181 bp):
TGTTTTTGTCAATTCACCATTAGATCACAAATGGTGTGATGAATGACCTTTGGTACGTTTTCGGT
CTTCTTTATAGGTCGTTTGGTCATGCTTTTCATTTATATTCTTTTTATCAAAGTTAGATTTAACA
TCGTCTCGACTAATCAAAATAACACATATACATTATCCTGTTGATCTTCTA
Found at i:1837864 original size:16 final size:18
Alignment explanation
Indices: 1837832--1837866 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1837822 ATATAAAAAC
1837832 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
1837850 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
1837866 A
1 A
1837867 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:1837907 original size:24 final size:23
Alignment explanation
Indices: 1837876--1837934 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
1837866 AAATGAGTAA
*
1837876 AATATATAAAAAAGTAAAAGCAT
1 AATATATAAAAAAGTAAAAGAAT
* * *
1837899 ATATATATATATAAGTAAAATAAT
1 A-ATATATAAAAAAGTAAAAGAAT
1837923 AATA-ATAAAAAA
1 AATATATAAAAAA
1837935 AAGAAAATCA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 6 0.21
23 4 0.14
24 19 0.66
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (23 bp):
AATATATAAAAAAGTAAAAGAAT
Found at i:1838463 original size:37 final size:37
Alignment explanation
Indices: 1838413--1838501 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 37
1838403 GTGCTTGTGG
* * * *
1838413 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACT-CT
1 ATCCTATTTTTAGGAATTTAAATCCTAGCA-AAATGCT
* * *
1838450 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAATTTAAATCCTAGCAAAATGCT
1838487 ATCCTATTTTTAGGA
1 ATCCTATTTTTAGGA
1838502 GTCTGAATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
36 3 0.07
37 41 0.93
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAATTTAAATCCTAGCAAAATGCT
Found at i:1839467 original size:109 final size:102
Alignment explanation
Indices: 1839060--1840030 Score: 850
Period size: 109 Copynumber: 9.3 Consensus size: 102
1839050 GCATTGTTCC
* ** *
1839060 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATCGGCTCT-GAA--TTGAAATT-GTTGTTGACAA
*
1839125 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
62 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
* * * * *
1839166 GAGTCCAATATCCTTCG-CTGTGAAGTTAAAATTGACTCTGAA-TGAAATT-TTGTTGACAAGCA
1 GAGTCCAATATCCTCCGTC-GTGAAGTTGAAATCGGCTCTGAATTGAAATTGTTGTTGACAACCA
* * * *
1839228 GCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
65 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
* * * *
1839266 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATCGGCTCTG-AATTGA-AA-TTGTTGTTGACAAC
* * *
1839331 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
63 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
* * ** *
1839371 GAGTGGCACGATATCCTCCGTCGTGGAGTTGAAATC-GCGGATGAAACTGAAAAGTTGTTCGTTG
1 GAGT--C-CAATATCCTCCGTCGTGAAGTTGAAATCGGC-TCTG-AATTG-AAA-TTGTT-GTTG
1839435 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
58 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT-G
* *
1839481 G-GTAGCACGATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGTTGA
1 GAGT--C-CAATATCCTCCGTCGTGAAGTTGAAATCGGCTCT-GAATT--GAAATTG-TTGTTGA
* *
1839545 CAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTC
59 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
* * * * * **
1839589 GAGTCCAATATCCTTCG-CTGTGAAGTTGAGATTGGCTC-----CGAAATTGCTTGTCGACAGTC
1 GAGTCCAATATCCTCCGTC-GTGAAGTTGAAATCGGCTCTGAATTGAAATTG-TTGTTGACAACC
1839648 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT-G
* * *
1839688 G-GTAGCACGATATCCTCCGTCGTGGAGTTAAAATCGGCTCTGGAATTGGGAAATTGTTTGTTGA
1 GAGT--C-CAATATCCTCCGTCGTGAAGTTGAAATCGGCTCT-GAATT--GAAATTG-TTGTTGA
* *
1839752 CAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTC
59 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
* * * * * * * **
1839796 GAGTCCAATATCCTTCG-CTGTGAAGTCGAGATTGACTC-----CGAAATTGTTTGTCGACAGTC
1 GAGTCCAATATCCTCCGTC-GTGAAGTTGAAATCGGCTCTGAATTGAAATTG-TTGTTGACAACC
* * * *
1839855 AGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTG
64 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC-TG
* * * * *
1839895 G-GTCCAATATCCTTCG-CTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATTTTTGTTGACAA
1 GAGTCCAATATCCTCCGTC-GTGAAGTTGAAATCGGCTCTG-AA-T-TGAAATTGTTGTTGACAA
*
1839958 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
62 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
* *
1839999 GAGTCCAATATCCTTCG-CTGTGAAGTCGAAAT
1 GAGTCCAATATCCTCCGTC-GTGAAGTTGAAAT
1840031 TGACTTTAGC
Statistics
Matches: 731, Mismatches: 88, Indels: 93
0.80 0.10 0.10
Matches are distributed among these distances:
98 138 0.19
99 3 0.00
100 82 0.11
101 27 0.04
102 10 0.01
103 2 0.00
104 4 0.01
105 131 0.18
106 89 0.12
107 5 0.01
108 40 0.05
109 189 0.26
110 10 0.01
111 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (102 bp):
GAGTCCAATATCCTCCGTCGTGAAGTTGAAATCGGCTCTGAATTGAAATTGTTGTTGACAACCAG
CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
Found at i:1839669 original size:207 final size:205
Alignment explanation
Indices: 1839064--1840035 Score: 1176
Period size: 207 Copynumber: 4.7 Consensus size: 205
1839054 TGTTCCGAGT
** *
1839064 CCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACAACCAG
1 CCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAACCAG
* *
1839129 CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTA
66 CCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTG
* * * * *
1839194 AAATTGACTCTGAATGAAATT-TTGTTGACAAG-CAGCGGTCCCTTCGTCGTGGAGTTGAACTTG
131 AAATTGACTC----CGAAATTGTTGTCGAC-AGTCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
*
1839257 CGTTGTCT--GG-AG
191 TGTTGTCTCGGGTAG
* * * * * *
1839269 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAGCA
1 -CCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAACCA
* * * * *
1839333 GCGGTCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCTGGAGTGGCACGATATCCTCCG-TCGTG
65 GCCGTCCCTTCGCT-GTGAAGTTGAACTTGTGTTGTCTCGAGT--C-CAATATCCTTCGCT-GTG
* ** * * **
1839396 GAGTTGAAATCGCGGATGAAACTGAAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAA
125 AAGTTGAAAT------TGACTCCG-AAA-TTGTT-GTCGACAGTCAGCCGTCCCTTCGTTGTGAA
1839461 GTTGAACTTGTGTTGTCTCGGGTAG
181 GTTGAACTTGTGTTGTCTCGGGTAG
* * *
1839486 CACGATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGTTGACAACCA
1 C-CAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAACCA
1839551 GCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTT
65 GCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTT
* *
1839616 GAGATTGGCTCCGAAATTGCTTGTCGACAGTCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGT
130 GAAATTGACTCCGAAATTG-TTGTCGACAGTCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGT
1839681 TGTCTCGGGTAG
194 TGTCTCGGGTAG
* * * *
1839693 CACGATATCCTCCGTCGTGGAGTTAAAATCGGCTCTGGAATTGGGAAATTGTTTGTTGACAACCA
1 C-CAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAACCA
*
1839758 GCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTC
65 GCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTT
* * * * *
1839823 GAGATTGACTCCGAAATTGTTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGC
130 GAAATTGACTCCGAAATTG-TTGTCGACAGTCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGT
*
1839888 TGTCTTGGGT--
194 TGTCTCGGGTAG
* * * *
1839898 CCAATATCCTTCG-CTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATT-TTTGTTGACAACCA
1 CCAATATCCTCCGTC-GTGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAACCA
* *
1839961 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTC
65 GCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTT
1840026 GAAATTGACT
130 GAAATTGACT
1840036 TTAGCTAAAA
Statistics
Matches: 676, Mismatches: 65, Indels: 53
0.85 0.08 0.07
Matches are distributed among these distances:
203 88 0.13
204 39 0.06
205 50 0.07
206 42 0.06
207 253 0.37
208 26 0.04
209 4 0.01
210 2 0.00
211 3 0.00
212 2 0.00
213 3 0.00
214 45 0.07
215 21 0.03
216 5 0.01
217 43 0.06
218 49 0.07
219 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (205 bp):
CCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAACCAG
CCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTG
AAATTGACTCCGAAATTGTTGTCGACAGTCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
TCTCGGGTAG
Found at i:1840905 original size:72 final size:75
Alignment explanation
Indices: 1840768--1840938 Score: 199
Period size: 72 Copynumber: 2.3 Consensus size: 75
1840758 TAAAATCTTC
* * *
1840768 TTAAAAAAAACAACCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGATCTCAAGCGAGA
1 TTAAGAAAAACAACCTTGAGTGAAATGAAAT-CATTCTTTCGAGTAAAAACGATCTCAAGCGAGA
*
1840833 CAAA-TCTTGTT
65 CAAAGT-ATGTT
* * *
1840844 TTAAGAAAAACAATCTTGGGTGAAAT-AAAT-ATTCTTTCGAG-AAAAAC-AGTCTCAAGTGAGA
1 TTAAGAAAAACAACCTTGAGTGAAATGAAATCATTCTTTCGAGTAAAAACGA-TCTCAAGCGAGA
1840905 CAAAGTATGTT
65 CAAAGTATGTT
**
1840916 TTAAGAAAAACAAATTTGAGTGA
1 TTAAGAAAAACAACCTTGAGTGA
1840939 GATAATCATA
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
71 1 0.01
72 44 0.53
73 11 0.13
75 4 0.05
76 23 0.28
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.27
Consensus pattern (75 bp):
TTAAGAAAAACAACCTTGAGTGAAATGAAATCATTCTTTCGAGTAAAAACGATCTCAAGCGAGAC
AAAGTATGTT
Found at i:1841748 original size:22 final size:22
Alignment explanation
Indices: 1841722--1841798 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
1841712 TTGTGTTTGG
1841722 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1841744 TCAAAGGTTTGGCATTTGATAC
1 TCAAAGGTTTGGCATTTGATGC
*
1841766 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1841788 TCAAAGGTTTG
1 TCAAAGGTTTG
1841799 ATGGGGTACT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1842461 original size:16 final size:15
Alignment explanation
Indices: 1842442--1842521 Score: 51
Period size: 16 Copynumber: 5.1 Consensus size: 15
1842432 TCTTTTTGAT
1842442 TTTTGCTCTTTTTTTC
1 TTTT-CTCTTTTTTTC
* *
1842458 TTTTGTTCTTGTTTCTC
1 TTTT-CTCTT-TTTTTC
1842475 TTTT-TCTTTGTTTT-
1 TTTTCTCTTT-TTTTC
1842489 TTTTCT-TTTTTGCTTC
1 TTTTCTCTTTTT--TTC
1842505 TTTTCT-TTTTTGTTC
1 TTTTCTCTTTTT-TTC
1842520 TT
1 TT
1842522 GATTGGATCT
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
13 2 0.04
14 8 0.15
15 15 0.28
16 20 0.37
17 9 0.17
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (15 bp):
TTTTCTCTTTTTTTC
Found at i:1842497 original size:8 final size:8
Alignment explanation
Indices: 1842448--1842515 Score: 55
Period size: 8 Copynumber: 8.0 Consensus size: 8
1842438 TGATTTTTGC
1842448 TCTTTTTT
1 TCTTTTTT
*
1842456 TCTTTTGT
1 TCTTTTTT
*
1842464 TCTTGTTTC
1 TCTT-TTTT
1842473 TCTTTTTCTT
1 TC-TTTT-TT
*
1842483 TGTTTTTTT
1 T-CTTTTTT
1842492 TCTTTTTT
1 TCTTTTTT
* *
1842500 GCTTCTTT
1 TCTTTTTT
1842508 TCTTTTTT
1 TCTTTTTT
1842516 GTTCTTGATT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
8 29 0.63
9 9 0.20
10 8 0.17
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (8 bp):
TCTTTTTT
Found at i:1843685 original size:8 final size:8
Alignment explanation
Indices: 1843669--1843707 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1843659 AATGTAGATG
1843669 AAAATGCA
1 AAAATGCA
*
1843677 AAAAGGCA
1 AAAATGCA
1843685 AAAATGC-
1 AAAATGCA
1843692 AAAATGCA
1 AAAATGCA
*
1843700 AGAATGCA
1 AAAATGCA
1843708 CGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:1843695 original size:15 final size:15
Alignment explanation
Indices: 1843669--1843707 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1843659 AATGTAGATG
1843669 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
1843685 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
1843700 AGAATGCA
1 AAAATGCA
1843708 CGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:1844252 original size:18 final size:18
Alignment explanation
Indices: 1844229--1844268 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1844219 ATTAGTCTTT
*
1844229 CAGAAGTGGATGTGAATC
1 CAGAAGTGGATGTGAAGC
1844247 CAGAAGTGGATGTGAAGC
1 CAGAAGTGGATGTGAAGC
1844265 CAGA
1 CAGA
1844269 CTTGAAGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.17
Consensus pattern (18 bp):
CAGAAGTGGATGTGAAGC
Found at i:1846408 original size:17 final size:16
Alignment explanation
Indices: 1846382--1846415 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1846372 ATATAAAAAC
*
1846382 ATAAATATAGGATAAAT
1 ATAAAAATA-GATAAAT
1846399 ATAAAAATAGATAAAT
1 ATAAAAATAGATAAAT
1846415 A
1 A
1846416 AATGAGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (16 bp):
ATAAAAATAGATAAAT
Found at i:1846456 original size:24 final size:23
Alignment explanation
Indices: 1846425--1846483 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
1846415 AAATGAGTAA
*
1846425 AATATATAAAAAAGTAAAAGCAT
1 AATATATAAAAAAGTAAAAGAAT
* * *
1846448 ATATATATATATAAGTAAAATAAT
1 A-ATATATAAAAAAGTAAAAGAAT
1846472 AATA-ATAAAAAA
1 AATATATAAAAAA
1846484 AGAAAATCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 6 0.21
23 4 0.14
24 19 0.66
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (23 bp):
AATATATAAAAAAGTAAAAGAAT
Found at i:1847013 original size:37 final size:37
Alignment explanation
Indices: 1846963--1847049 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 37
1846953 GTGCTTGTGG
* * * *
1846963 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAATTTAAATCCTAGCAAAACTCT
* * * *
1847000 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAATTTAAATCCTAGCAAAACTCT
1847037 ATCCTATTTTTAG
1 ATCCTATTTTTAG
1847050 AGTCTGAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (37 bp):
ATCCTATTTTTAGGAATTTAAATCCTAGCAAAACTCT
Found at i:1849501 original size:20 final size:20
Alignment explanation
Indices: 1849472--1849649 Score: 132
Period size: 20 Copynumber: 8.8 Consensus size: 20
1849462 TCGCATTGCA
* *
1849472 ATTTTCCAAATTCGCAACGCT
1 ATTTT-CAAATTCGCAACTCG
*
1849493 ATTTTCAAATTCGCAACGCG
1 ATTTTCAAATTCGCAACTCG
* *
1849513 AATCTGT-AAA-TCGCAACACTG
1 -AT-TTTCAAATTCGCAACTC-G
1849534 A-TTTCAAATTCGCAACTCG
1 ATTTTCAAATTCGCAACTCG
*
1849553 A-TTTCTTAATTCGCAACTCG
1 ATTTTC-AAATTCGCAACTCG
* *
1849573 ATTTTCGATTTCGCAACTCG
1 ATTTTCAAATTCGCAACTCG
* *
1849593 ATTTTCGATTTCGCAACTCG
1 ATTTTCAAATTCGCAACTCG
** * *
1849613 ATTTTTGATTTCGCAACACG
1 ATTTTCAAATTCGCAACTCG
*
1849633 AATTTT-AATTTCGCAAC
1 -ATTTTCAAATTCGCAAC
1849650 AGGTTTAATT
Statistics
Matches: 138, Mismatches: 11, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.01
19 9 0.07
20 105 0.76
21 20 0.14
22 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.35
Consensus pattern (20 bp):
ATTTTCAAATTCGCAACTCG
Found at i:1849587 original size:60 final size:60
Alignment explanation
Indices: 1849472--1849650 Score: 168
Period size: 60 Copynumber: 3.0 Consensus size: 60
1849462 TCGCATTGCA
* * ** * * *
1849472 ATTTTCCAAATTCGCAACGCTATTTTCAAATTCGCAACGCGAATCTGTAA-ATCGCAACACTG
1 ATTTT-CAAATTCGCAACTCGATTTTTGAATTCGCAACACGAAT-TTTAATTTCGCAACAC-G
* * *
1849534 A-TTTCAAATTCGCAACTCGATTTCTT-AATTCGCAACTCG-ATTTTCGATTTCGCAACTCG
1 ATTTTCAAATTCGCAACTCGATTT-TTGAATTCGCAACACGAATTTT-AATTTCGCAACACG
* * *
1849593 ATTTTCGATTTCGCAACTCGATTTTTGATTTCGCAACACGAATTTTAATTTCGCAACA
1 ATTTTCAAATTCGCAACTCGATTTTTGAATTCGCAACACGAATTTTAATTTCGCAACA
1849651 GGTTTAATTT
Statistics
Matches: 97, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
58 2 0.02
59 7 0.07
60 78 0.80
61 9 0.09
62 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.35
Consensus pattern (60 bp):
ATTTTCAAATTCGCAACTCGATTTTTGAATTCGCAACACGAATTTTAATTTCGCAACACG
Found at i:1849606 original size:40 final size:40
Alignment explanation
Indices: 1849542--1849649 Score: 148
Period size: 40 Copynumber: 2.7 Consensus size: 40
1849532 TGATTTCAAA
*
1849542 TTCGCAACTCGATTTCTTAA-TTCGCAACTCGATTTTCGAT
1 TTCGCAACTCGATTT-TCAATTTCGCAACTCGATTTTCGAT
* *
1849582 TTCGCAACTCGATTTTCGATTTCGCAACTCGATTTTTGAT
1 TTCGCAACTCGATTTTCAATTTCGCAACTCGATTTTCGAT
*
1849622 TTCGCAACACGAATTTT-AATTTCGCAAC
1 TTCGCAACTCG-ATTTTCAATTTCGCAAC
1849650 AGGTTTAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
39 2 0.03
40 54 0.89
41 5 0.08
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (40 bp):
TTCGCAACTCGATTTTCAATTTCGCAACTCGATTTTCGAT
Found at i:1849840 original size:16 final size:15
Alignment explanation
Indices: 1849805--1849843 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1849795 TCCCCATCTC
*
1849805 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
1849820 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1849836 TAATTTTT
1 TAATTTTT
1849844 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1850796 original size:3 final size:3
Alignment explanation
Indices: 1850788--1850812 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1850778 ATATAACCCT
1850788 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
1850813 TCCCTGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1854253 original size:20 final size:20
Alignment explanation
Indices: 1854228--1854321 Score: 109
Period size: 20 Copynumber: 4.8 Consensus size: 20
1854218 AGTAGTTTCT
*
1854228 GAAAATTAAATTCGCAACGC
1 GAAAATTAAAATCGCAACGC
1854248 GAAAATTAAAATCGCAACGC
1 GAAAATTAAAATCGCAACGC
* * * *
1854268 AAAAATGAAAATCCCAACGA
1 GAAAATTAAAATCGCAACGC
* *
1854288 GAAAATGAAAATCACAACGC
1 GAAAATTAAAATCGCAACGC
*
1854308 -AAAACTAAAATCGC
1 GAAAATTAAAATCGC
1854322 GTTGCGATTT
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
19 11 0.17
20 52 0.83
ACGTcount: A:0.53, C:0.20, G:0.13, T:0.14
Consensus pattern (20 bp):
GAAAATTAAAATCGCAACGC
Found at i:1854393 original size:20 final size:20
Alignment explanation
Indices: 1854354--1854393 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1854344 TGCAATTTTG
* * *
1854354 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGAATTTAAGTTTC
1854374 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCGAATTTAAGTTTC
1854394 AAAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGAATTTAAGTTTC
Found at i:1854751 original size:19 final size:20
Alignment explanation
Indices: 1854727--1854774 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 20
1854717 GATTGAGATA
1854727 GACGGATT-TCGGAGATGGG
1 GACGGATTCTCGGAGATGGG
1854746 GACGGATTTCGTCGGAGATGGG
1 GACGGA-TTC-TCGGAGATGGG
1854768 GACGGAT
1 GACGGAT
1854775 GTCGCCGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.23
20 2 0.08
21 1 0.04
22 17 0.65
ACGTcount: A:0.21, C:0.12, G:0.46, T:0.21
Consensus pattern (20 bp):
GACGGATTCTCGGAGATGGG
Found at i:1854954 original size:20 final size:20
Alignment explanation
Indices: 1854929--1854999 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
1854919 TAAACGCGCT
*
1854929 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGAG
1854949 TTGCGAATTTGACTTCTGAG
1 TTGCGAATTTGACTTCTGAG
* * *
1854969 TTGCGACATTGGAGTTC-GCG
1 TTGCGA-ATTTGACTTCTGAG
1854989 TTGCGAATTTG
1 TTGCGAATTTG
1855000 TTGATCATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.09
20 33 0.73
21 8 0.18
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.39
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGAG
Found at i:1864577 original size:17 final size:18
Alignment explanation
Indices: 1864536--1864574 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1864526 ATTATATAAG
1864536 TAAAATA-TTAAATAAAT
1 TAAAATACTTAAATAAAT
1864553 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAT
1864571 TAAA
1 TAAA
1864575 TACAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:1865132 original size:20 final size:20
Alignment explanation
Indices: 1865107--1865149 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1865097 AATCACAACC
1865107 CATACATCCCAATTTGGAAA
1 CATACATCCCAATTTGGAAA
1865127 CATACATCCCAATTTGGAAA
1 CATACATCCCAATTTGGAAA
1865147 CAT
1 CAT
1865150 TTATTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.26
Consensus pattern (20 bp):
CATACATCCCAATTTGGAAA
Found at i:1865488 original size:14 final size:14
Alignment explanation
Indices: 1865469--1865500 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1865459 TACATCCATT
1865469 TTATTTTTATAATA
1 TTATTTTTATAATA
1865483 TTATTTTTATAATA
1 TTATTTTTATAATA
1865497 TTAT
1 TTAT
1865501 ATATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTATTTTTATAATA
Found at i:1866331 original size:131 final size:129
Alignment explanation
Indices: 1866162--1866499 Score: 444
Period size: 131 Copynumber: 2.6 Consensus size: 129
1866152 TTCGGTCGGA
* * * *
1866162 GTAATAAATGATTGCTTTAATGCATGAAAGTGTATTTATTTTCGATTGGAAATAATTTGATATTG
1 GTAATAAATGATTGTTTTAATGC-TGAAAG-GTATTTATTCTCGATTGGAAATAATTAGATATTA
* * * *
1866227 TTGTTTTC-TTTCGAATTAATACTGATTTTTATGACGAAATAGTAATATATCTTTATTTCAATTG
64 TTGTTTTCACTT-GAATCAATACTGAATTTTAAGACGAAATAGTAATATATCTTTATTTCAATTG
1866291 GG
128 GG
*
1866293 GTAATAAATGATTGTTTTAATGCTGGAAAGGTAATTTATTCTCGATTAGAAATAATTAGATATTA
1 GTAATAAATGATTGTTTTAATGCT-GAAAGGT-ATTTATTCTCGATTGGAAATAATTAGATATTA
* * * * * * *
1866358 TCGTTTTCACTTGAATCGATATTGAATTTTAAGATGAAATAGTAATATTTTTTTATTTCGATTGG
64 TTGTTTTCACTTGAATCAATACTGAATTTTAAGACGAAATAGTAATATATCTTTATTTCAATTGG
1866423 G
129 G
* *
1866424 GTAATAAATGATTGTTTTAATGCACGAAAGGTCATTTATTCTCGATTGAAAATAATTAGATATTA
1 GTAATAAATGATTGTTTTAATGC-TGAAAGGT-ATTTATTCTCGATTGGAAATAATTAGATATTA
1866489 TTGTTTTCACT
64 TTGTTTTCACT
1866500 CTTAAAATTA
Statistics
Matches: 182, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
130 3 0.02
131 177 0.97
132 2 0.01
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (129 bp):
GTAATAAATGATTGTTTTAATGCTGAAAGGTATTTATTCTCGATTGGAAATAATTAGATATTATT
GTTTTCACTTGAATCAATACTGAATTTTAAGACGAAATAGTAATATATCTTTATTTCAATTGGG
Found at i:1869005 original size:3 final size:3
Alignment explanation
Indices: 1868997--1869066 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
1868987 CCGAGTTTTA
* * * *
1868997 TAT TAT TAT TAT TAT T-T AAC TAT TAT TGT TAT TATT TAT TTT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT T-AT
* *
1869043 TAT TTT TA- TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1869067 TATTTATGTA
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
2 3 0.06
3 43 0.84
4 5 0.10
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:1869022 original size:20 final size:18
Alignment explanation
Indices: 1868993--1869073 Score: 89
Period size: 17 Copynumber: 4.6 Consensus size: 18
1868983 TTGTCCGAGT
1868993 TTTATATTATTATTATTA
1 TTTATATTATTATTATTA
*
1869011 TTTAACTATTATTGTTATTA
1 TTT-A-TATTATTATTATTA
1869031 TTTAT-TT-TTAATTATT-
1 TTTATATTATT-ATTATTA
*
1869047 TTTATATTATTTTTATTA
1 TTTATATTATTATTATTA
1869065 TTTAT-TTAT
1 TTTATATTAT
1869074 GTAGGCCTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
16 7 0.13
17 18 0.33
18 11 0.20
19 2 0.04
20 16 0.30
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (18 bp):
TTTATATTATTATTATTA
Found at i:1875221 original size:21 final size:21
Alignment explanation
Indices: 1875197--1875236 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1875187 CCCCCTTTGA
*
1875197 AGGGGAACCGATCCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1875218 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1875237 TGGGGTTCTG
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:0.25, C:0.42, G:0.25, T:0.07
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1877681 original size:2 final size:2
Alignment explanation
Indices: 1877674--1877728 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1877664 TGTTTATTTC
1877674 AT AT AT AT 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 AT AT AT AT
1877716 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1877729 ATTTTATATG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1877795 original size:2 final size:2
Alignment explanation
Indices: 1877788--1877857 Score: 90
Period size: 2 Copynumber: 35.5 Consensus size: 2
1877778 ATATGCGCAT
* *
1877788 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TG T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1877829 TA T- TA TA TG TCA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA T
1877858 GTGTGTGTGT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
1 2 0.03
2 57 0.95
3 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1877898 original size:2 final size:2
Alignment explanation
Indices: 1877857--1877883 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1877847 TATATATATA
1877857 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1877884 ATTTTTTTTT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1879899 original size:38 final size:38
Alignment explanation
Indices: 1879857--1880058 Score: 111
Period size: 38 Copynumber: 5.4 Consensus size: 38
1879847 TCATTTCATT
* *
1879857 ATATATATATATATATATTAAT-ATTTTTGAAAA-ATATA
1 ATATATA-ATATATAGA-AAATGATTTTTGAAAATATATA
* *
1879895 ATATATAATTTTTAGAAAATGATTTTTGAAAATATATA
1 ATATATAATATATAGAAAATGATTTTTGAAAATATATA
* * * **
1879933 ATATAT--TGTTTA-AAAATCG-GTTTAAAAAATATATA
1 ATATATAATATATAGAAAAT-GATTTTTGAAAATATATA
* * * * *
1879968 TTATACAGT-TTTTG-AAATGATTTTTGAAAAAATATATA
1 ATATATAATATATAGAAAATGATTTTTG--AAAATATATA
* *
1880006 TTATATAAT-T-T-GCAAATGATTTTTGAAAAAATATATA
1 ATATATAATATATAGAAAATGATTTTTG--AAAATATATA
1880043 TATATATAATATATAG
1 -ATATATAATATATAG
1880059 TTTTGAAAAC
Statistics
Matches: 133, Mismatches: 17, Indels: 25
0.76 0.10 0.14
Matches are distributed among these distances:
35 23 0.17
36 20 0.15
37 43 0.32
38 44 0.33
39 1 0.01
40 1 0.01
41 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (38 bp):
ATATATAATATATAGAAAATGATTTTTGAAAATATATA
Found at i:1879914 original size:23 final size:27
Alignment explanation
Indices: 1879863--1879913 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 27
1879853 CATTATATAT
*
1879863 ATATATATATATTAATATTTTTGAAAA
1 ATATATATATATTAATATTTTAGAAAA
1879890 ATATA-ATATA-TAAT-TTTTAGAAAA
1 ATATATATATATTAATATTTTAGAAAA
1879914 TGATTTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 9 0.39
25 4 0.17
26 5 0.22
27 5 0.22
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (27 bp):
ATATATATATATTAATATTTTAGAAAA
Found at i:1879922 original size:37 final size:36
Alignment explanation
Indices: 1879879--1880048 Score: 140
Period size: 37 Copynumber: 4.6 Consensus size: 36
1879869 ATATATTAAT
1879879 ATTTTTGAAAAATATAATATATAATTTTTAGAAAATG
1 ATTTTTGAAAAATATAATATATAATTTTT-GAAAATG
* *
1879916 ATTTTTGAAAATATATAATATAT--TGTTTAAAAATCG
1 ATTTTTGAAAA-ATATAATATATAATTTTTGAAAAT-G
* *
1879952 --GTTTAAAAAATAT-ATATTATACAGTTTTTG-AAATG
1 ATTTTTGAAAAATATAATA-TATA-A-TTTTTGAAAATG
*
1879987 ATTTTTGAAAAAATATATATTATATAA--TTTGCAAATG
1 ATTTTTG-AAAAATATA-A-TATATAATTTTTGAAAATG
1880024 ATTTTTGAAAAAATATATATATATA
1 ATTTTTG-AAAAATATA-ATATATA
1880049 TAATATATAG
Statistics
Matches: 111, Mismatches: 8, Indels: 29
0.75 0.05 0.20
Matches are distributed among these distances:
32 3 0.03
33 7 0.06
34 7 0.06
35 6 0.05
36 19 0.17
37 42 0.38
38 19 0.17
39 1 0.01
40 5 0.05
41 2 0.02
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (36 bp):
ATTTTTGAAAAATATAATATATAATTTTTGAAAATG
Found at i:1880049 original size:45 final size:43
Alignment explanation
Indices: 1879998--1880154 Score: 120
Period size: 40 Copynumber: 3.8 Consensus size: 43
1879988 TTTTTGAAAA
* **
1879998 AATATATATTATATA-ATTTGCAAATGATTTTTGAAAAAATATAT
1 AATATATAATATATAGATTTG-AAAACA-TTTTGAAAAAATATAT
*
1880042 ATATATATAATATATAGTTTTGAAAACATTTTG----AA-A-AT
1 A-ATATATAATATATAGATTTGAAAACATTTTGAAAAAATATAT
* * ***
1880080 -ATATATAATATATAGTTTTGAAAATATTTT-TTGAAA-ATAT
1 AATATATAATATATAGATTTGAAAACATTTTGAAAAAATATAT
*
1880120 -ATATATAATATATAGTTTTGAAAACATTTTGAAAA
1 AATATATAATATATAGATTTGAAAACATTTTGAAAA
1880155 TATTTTTTGA
Statistics
Matches: 96, Mismatches: 9, Indels: 19
0.77 0.07 0.15
Matches are distributed among these distances:
36 29 0.30
38 2 0.02
39 4 0.04
40 33 0.34
41 1 0.01
44 6 0.06
45 17 0.18
46 4 0.04
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (43 bp):
AATATATAATATATAGATTTGAAAACATTTTGAAAAAATATAT
Found at i:1880082 original size:38 final size:38
Alignment explanation
Indices: 1880040--1880157 Score: 195
Period size: 36 Copynumber: 3.1 Consensus size: 38
1880030 GAAAAAATAT
1880040 ATATATATATAATATATAGTTTTGAAAACATTTTG-AA
1 ATATATATATAATATATAGTTTTGAAAACATTTTGAAA
*
1880077 A-ATATATATAATATATAGTTTTGAAAATATTTTTTGAAA
1 ATATATATATAATATATAGTTTTGAAAACA--TTTTGAAA
1880116 ATATATATATAATATATAGTTTTGAAAACATTTTGAAA
1 ATATATATATAATATATAGTTTTGAAAACATTTTGAAA
1880154 ATAT
1 ATAT
1880158 TTTTTGAAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 7
0.89 0.02 0.08
Matches are distributed among these distances:
36 27 0.36
37 1 0.01
38 17 0.23
39 3 0.04
40 27 0.36
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (38 bp):
ATATATATATAATATATAGTTTTGAAAACATTTTGAAA
Found at i:1880109 original size:11 final size:11
Alignment explanation
Indices: 1880059--1880160 Score: 55
Period size: 11 Copynumber: 8.4 Consensus size: 11
1880049 TAATATATAG
*
1880059 TTTTGAAAACA
1 TTTTGAAAATA
1880070 TTTTGAAAATA
1 TTTTGAAAATA
*
1880081 TATAT-AATATATA
1 T-TTTGAA-A-ATA
1880094 GTTTTGAAAATA
1 -TTTTGAAAATA
1880106 TTTTTTGAAAATA
1 --TTTTGAAAATA
1880119 TATATAT-AATATATA
1 T-T-T-TGAA-A-ATA
*
1880134 GTTTTGAAAACA
1 -TTTTGAAAATA
1880146 TTTTGAAAATA
1 TTTTGAAAATA
1880157 TTTT
1 TTTT
1880161 TTGAAAAATA
Statistics
Matches: 72, Mismatches: 6, Indels: 26
0.69 0.06 0.25
Matches are distributed among these distances:
11 28 0.39
12 9 0.12
13 22 0.31
14 8 0.11
15 4 0.06
16 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (11 bp):
TTTTGAAAATA
Found at i:1880155 original size:51 final size:49
Alignment explanation
Indices: 1880095--1880203 Score: 157
Period size: 48 Copynumber: 2.2 Consensus size: 49
1880085 TAATATATAG
1880095 TTTTGAAAATATTTTTTGAAAATATATATATAATATATAGTTT-TGAAAACA
1 TTTTGAAAATATTTTTTG-AAA-A-ATATATAATATATAGTTTATGAAAACA
* *
1880146 TTTTGAAAATATTTTTTGAAAAATATATAATATATAGTTTATTAAAATA
1 TTTTGAAAATATTTTTTGAAAAATATATAATATATAGTTTATGAAAACA
*
1880195 TTTTTAAAA
1 TTTTGAAAA
1880204 AGTATATATA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
48 18 0.33
49 15 0.28
50 3 0.06
51 18 0.33
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (49 bp):
TTTTGAAAATATTTTTTGAAAAATATATAATATATAGTTTATGAAAACA
Found at i:1880171 original size:14 final size:13
Alignment explanation
Indices: 1880095--1880167 Score: 62
Period size: 13 Copynumber: 5.7 Consensus size: 13
1880085 TAATATATAG
1880095 TTTTGAAAATATT
1 TTTTGAAAATATT
1880108 TTTTGAAAATATAT
1 TTTTGAAAATAT-T
* * * *
1880122 ATAT-AATATATAG
1 TTTTGAAAATAT-T
*
1880135 TTTTGAAAACA--
1 TTTTGAAAATATT
1880146 TTTTGAAAATATT
1 TTTTGAAAATATT
1880159 TTTTGAAAA
1 TTTTGAAAA
1880168 ATATATAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
11 10 0.21
13 30 0.64
14 7 0.15
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (13 bp):
TTTTGAAAATATT
Found at i:1880210 original size:37 final size:35
Alignment explanation
Indices: 1880146--1880271 Score: 137
Period size: 37 Copynumber: 3.4 Consensus size: 35
1880136 TTTGAAAACA
*
1880146 TTTTGAAAATATTTTTTGAAAAATATATAATATATAG
1 TTTTTAAAATA-TTTTT-AAAAATATATAATATATAG
1880183 TTTATTAAAATATTTTTAAAAAGTATAT-ATAATATAG
1 TTT-TTAAAATATTTTTAAAAA-TATATAAT-ATATAG
* * * *
1880220 TTTTTGAAATTTTTTTTTGAAAACATATAATATATAG
1 TTTTT-AAA-ATATTTTTAAAAATATATAATATATAG
1880257 TTTTTAAAATATTTT
1 TTTTTAAAATATTTT
1880272 ATTTTCGAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 14
0.78 0.07 0.14
Matches are distributed among these distances:
35 5 0.07
36 12 0.16
37 40 0.53
38 19 0.25
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (35 bp):
TTTTTAAAATATTTTTAAAAATATATAATATATAG
Found at i:1880303 original size:41 final size:39
Alignment explanation
Indices: 1880157--1880290 Score: 119
Period size: 37 Copynumber: 3.6 Consensus size: 39
1880147 TTTGAAAATA
*
1880157 TTTTTT-GAAAAATATATAATATATAGTTTATTAAAATA--
1 TTTTTTCG-AAAACATATAATATATAGTTT-TTAAAATATT
*
1880195 -TTTTT--AAAA-AGTATATATAATATAGTTTTTGAAAT-TT
1 TTTTTTCGAAAACA-TATA-AT-ATATAGTTTTTAAAATATT
1880232 TTTTTT-GAAAACATATAATATATAGTTTTTAAAATATT
1 TTTTTTCGAAAACATATAATATATAGTTTTTAAAATATT
1880270 TTATTTTCG-AAA-ATATAATAT
1 TT-TTTTCGAAAACATATAATAT
1880291 TATATATATT
Statistics
Matches: 83, Mismatches: 2, Indels: 22
0.78 0.02 0.21
Matches are distributed among these distances:
34 1 0.01
35 8 0.10
36 8 0.10
37 29 0.35
38 20 0.24
39 15 0.18
40 2 0.02
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.49
Consensus pattern (39 bp):
TTTTTTCGAAAACATATAATATATAGTTTTTAAAATATT
Found at i:1881322 original size:18 final size:17
Alignment explanation
Indices: 1881301--1881481 Score: 65
Period size: 18 Copynumber: 10.4 Consensus size: 17
1881291 AAAGGTAATG
1881301 AAAATATAAAATAAAGAA
1 AAAATATAAAATAAA-AA
**
1881319 AAAA-ATGGAATAAATAA
1 AAAATATAAAATAAA-AA
*
1881336 AATAAGATAAGAA-AAAAA
1 AA-AATATAA-AATAAAAA
* **
1881354 GATAAGGTAAAGATAAAAA
1 -AAAATATAAA-ATAAAAA
1881373 AAGTAA-ATAAAATAAATAA
1 AA--AATATAAAATAAA-AA
*
1881392 AATAA-ATAAAA-ATAAA
1 AA-AATATAAAATAAAAA
* *
1881408 AAAATA-AACAGAATAAA
1 AAAATATAAAATAA-AAA
*
1881425 AAAATA-AACATAAAGAA
1 AAAATATAAAATAAA-AA
*
1881442 ATAAATA-AAGATAAAGAA
1 A-AAATATAAAATAAA-AA
*
1881460 AAAATA-AAAATAAAAG
1 AAAATATAAAATAAAAA
1881476 AAAATA
1 AAAATA
1881482 AATAAAGAAA
Statistics
Matches: 133, Mismatches: 16, Indels: 30
0.74 0.09 0.17
Matches are distributed among these distances:
15 5 0.04
16 14 0.11
17 45 0.34
18 46 0.35
19 19 0.14
20 4 0.03
ACGTcount: A:0.75, C:0.01, G:0.08, T:0.15
Consensus pattern (17 bp):
AAAATATAAAATAAAAA
Found at i:1881340 original size:5 final size:5
Alignment explanation
Indices: 1881330--1881674 Score: 89
Period size: 5 Copynumber: 67.6 Consensus size: 5
1881320 AAAATGGAAT
* * * ** *
1881330 AAATA AAATA AGATA AGA-A AAA-A AGATA AGGTA AAGATA AAA-A AAGT-
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AA-ATA AAATA AAATA
* *
1881377 AAATA AAAT- AAATA AAAT- AAATA AAA-A TAAA-A AAATA AACAGA ATAAAA
1 AAATA AAATA AAATA AAATA AAATA AAATA -AAATA AAATA AA-ATA A-AATA
* * *
1881426 AAATA AACATA AAGAAA TAAATA AAGATA AAGAAA AAATAA AAATA AAAGA
1 AAATA AA-ATA AA-ATA -AAATA AA-ATA AA-ATA AAAT-A AAATA AAATA
* * *
1881477 AAAT- AAAT- AAAGA AAATA ACAA-A CGAAA-A ATAATA AAGT- CAATGA
1 AAATA AAATA AAATA AAATA A-AATA --AAATA A-AATA AAATA AAAT-A
*** *
1881522 AAATA ATAA-A AAA-A AATATGA TGGTA AAATA AATTA AAATA AAATA
1 AAATA A-AATA AAATA AA-AT-A AAATA AAATA AAATA AAATA AAATA
* * * *
1881568 AAATA ACA-A AAA-A AAATAA AAATA AAACA AAAAA AAAGTA ATGAAAA
1 AAATA AAATA AAATA AAAT-A AAATA AAATA AAATA AAA-TA A--AATA
* * * *
1881615 AAACA GAAACA CAAATA AAATG AAA-A GAA-A AAATA AAATA AAATA AAAGTA
1 AAATA -AAATA -AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA-TA
1881666 AGAATA AAA
1 A-AATA AAA
1881675 ATAATATATA
Statistics
Matches: 260, Mismatches: 45, Indels: 70
0.69 0.12 0.19
Matches are distributed among these distances:
4 51 0.20
5 129 0.50
6 69 0.27
7 9 0.03
8 2 0.01
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (5 bp):
AAATA
Found at i:1881345 original size:14 final size:13
Alignment explanation
Indices: 1881306--1881487 Score: 81
Period size: 14 Copynumber: 13.4 Consensus size: 13
1881296 TAATGAAAAT
*
1881306 ATAAAATAAAGAA
1 ATAAAATAAATAA
*
1881319 A-AAAATGGAATAA
1 ATAAAAT-AAATAA
1881332 ATAAAATAAGATAA
1 ATAAAATAA-ATAA
1881346 GA-AAAA-AAGATAA
1 -ATAAAATAA-ATAA
* *
1881359 GGTAAAGATAAAAAA
1 -ATAAA-ATAAATAA
1881374 AGT-AAATAAAATAA
1 A-TAAAAT-AAATAA
1881388 ATAAAATAAATAAAA
1 ATAAAATAAAT--AA
1881403 ATAAAA-AAATAA
1 ATAAAATAAATAA
* * *
1881415 ACAGAATAAAAAA
1 ATAAAATAAATAA
*
1881428 ATAAACATAAAGAA
1 ATAAA-ATAAATAA
1881442 AT-AAATAAAGATAA
1 ATAAAAT-AA-ATAA
* *
1881456 AGAAAA-AATAAAA
1 ATAAAATAA-ATAA
*
1881469 ATAAAAGAAAATAA
1 ATAAAA-TAAATAA
1881483 ATAAA
1 ATAAA
1881488 GAAAATAACA
Statistics
Matches: 131, Mismatches: 19, Indels: 37
0.70 0.10 0.20
Matches are distributed among these distances:
12 13 0.10
13 44 0.34
14 53 0.40
15 19 0.15
16 2 0.02
ACGTcount: A:0.75, C:0.01, G:0.08, T:0.15
Consensus pattern (13 bp):
ATAAAATAAATAA
Found at i:1881456 original size:41 final size:38
Alignment explanation
Indices: 1881378--1881489 Score: 99
Period size: 37 Copynumber: 2.9 Consensus size: 38
1881368 AAAAAAAGTA
*
1881378 AATAAAATAAATAAAATAAATAAAAATAAA-AAA-ATAAACAG
1 AATAAAA-AAATAAAAT-AA-AGAAATAAATAAAGAT-AA-AG
1881419 AATAAAAAAATAAACATAAAGAAATAAATAAAGATAAAG
1 AATAAAAAAATAAA-ATAAAGAAATAAATAAAGATAAAG
*
1881458 -A-AAAAATA-AAAATAAAAGAAAATAAATAAAGA
1 AATAAAAAAATAAAAT-AAAG-AAATAAATAAAGA
1881490 AAATAACAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 14
0.80 0.03 0.17
Matches are distributed among these distances:
35 2 0.03
36 7 0.11
37 19 0.30
38 1 0.02
39 10 0.16
40 14 0.22
41 11 0.17
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (38 bp):
AATAAAAAAATAAAATAAAGAAATAAATAAAGATAAAG
Found at i:1881472 original size:49 final size:45
Alignment explanation
Indices: 1881377--1881492 Score: 85
Period size: 49 Copynumber: 2.4 Consensus size: 45
1881367 TAAAAAAAGT
*
1881377 AAAT-AAAATAAATAAAATAAATAAAAATAAAAAAATAA-ACAGAATAAAA
1 AAATAAAAATAAA-GAAA-AAAT-AAAATAAAAAAA-AATA-A-AATAAAA
*
1881426 AAATAAACATAAAGAAATAAATAAAGATAAAGAAAAAATAAAAATAAAA
1 AAATAAAAATAAAGAAA-AAATAAA-ATAAA-AAAAAAT-AAAATAAAA
*
1881475 GAAA-ATAAATAAAGAAAA
1 -AAATAAAAATAAAGAAAA
1881493 TAACAAACGA
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
48 4 0.07
49 37 0.65
50 15 0.26
51 1 0.02
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (45 bp):
AAATAAAAATAAAGAAAAAATAAAATAAAAAAAAATAAAATAAAA
Found at i:1881492 original size:18 final size:18
Alignment explanation
Indices: 1881334--1881492 Score: 79
Period size: 18 Copynumber: 8.9 Consensus size: 18
1881324 TGGAATAAAT
1881334 AAAATAAGAT-AAGAAAA-
1 AAAATAA-ATAAAGAAAAG
*
1881351 AAAGATAAGGTAAAGATAAA-
1 AAA-ATAA-ATAAAGA-AAAG
*
1881371 AAAAGTAAATAAA-ATAAAT
1 AAAA-TAAATAAAGA-AAAG
*
1881390 AAAATAAAT--A-AAAAT
1 AAAATAAATAAAGAAAAG
* * *
1881405 AAAA-AAATAAACAGAAT
1 AAAATAAATAAAGAAAAG
*
1881422 AAAA-AAATAAACATAAAG
1 AAAATAAATAAAGA-AAAG
1881440 -AAATAAATAAAGATAAAG
1 AAAATAAATAAAGA-AAAG
* *
1881458 AAAA-AATAAAAATAAAAG
1 AAAATAA-ATAAAGAAAAG
1881476 AAAATAAATAAAGAAAA
1 AAAATAAATAAAGAAAA
1881493 TAACAAACGA
Statistics
Matches: 119, Mismatches: 10, Indels: 25
0.77 0.06 0.16
Matches are distributed among these distances:
14 4 0.03
15 8 0.07
16 3 0.03
17 23 0.19
18 49 0.41
19 23 0.19
20 9 0.08
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.14
Consensus pattern (18 bp):
AAAATAAATAAAGAAAAG
Found at i:1881492 original size:23 final size:23
Alignment explanation
Indices: 1881361--1881495 Score: 69
Period size: 23 Copynumber: 5.5 Consensus size: 23
1881351 AAAGATAAGG
*
1881361 TAAAGATAAA-AAAAGTAAATAAAA
1 TAAAGA-AAATAAAAGAAAAT-AAA
*
1881385 TAAATAAAATAAATA-AAAATAAA
1 TAAAGAAAATAAA-AGAAAATAAA
* * * *
1881408 AAAATAAACAGAATAAAAAAATAAACA
1 TAAAGAAA-ATAA-AAGAAAAT-AA-A
* *
1881435 TAAAGAAATAAATAAAGATAAAGAAA
1 TAAAGAAA-ATA-AAAGA-AAATAAA
*
1881461 -AAATAAAAATAAAAGAAAATAAA
1 TAAA-GAAAATAAAAGAAAATAAA
1881484 TAAAGAAAATAA
1 TAAAGAAAATAA
1881496 CAAACGAAAA
Statistics
Matches: 86, Mismatches: 14, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
23 26 0.30
24 24 0.28
25 12 0.14
26 6 0.07
27 14 0.16
28 4 0.05
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.16
Consensus pattern (23 bp):
TAAAGAAAATAAAAGAAAATAAA
Found at i:1881505 original size:13 final size:13
Alignment explanation
Indices: 1881308--1881495 Score: 88
Period size: 13 Copynumber: 14.5 Consensus size: 13
1881298 ATGAAAATAT
*
1881308 AAAATAAAGAAA-
1 AAAATAAATAAAG
* *
1881320 AAAATGGAATAAAT
1 AAAAT-AAATAAAG
1881334 AAAATAAGAT-AAG
1 AAAATAA-ATAAAG
* *
1881347 AAAAAAAGATAAGG
1 AAAATAA-ATAAAG
*
1881361 TAAAGATAAAAAAAG
1 -AAA-ATAAATAAAG
* *
1881376 TAAATAAAATAAAT
1 AAAAT-AAATAAAG
*
1881390 AAAATAAATAAAA
1 AAAATAAATAAAG
* *
1881403 ATAAAAAAATAAAC
1 A-AAATAAATAAAG
*
1881417 AGAATAAA-AAA-
1 AAAATAAATAAAG
* *
1881428 ATAA-ACATAAAG
1 AAAATAAATAAAG
1881440 -AAATAAATAAAG
1 AAAATAAATAAAG
* *
1881452 ATAAAGAAA-AAAT
1 A-AAATAAATAAAG
*
1881465 AAAA-ATA-AAAG
1 AAAATAAATAAAG
1881476 AAAATAAATAAAG
1 AAAATAAATAAAG
1881489 AAAATAA
1 AAAATAA
1881496 CAAACGAAAA
Statistics
Matches: 134, Mismatches: 27, Indels: 29
0.71 0.14 0.15
Matches are distributed among these distances:
10 2 0.01
11 17 0.13
12 20 0.15
13 47 0.35
14 38 0.28
15 7 0.05
16 3 0.02
ACGTcount: A:0.76, C:0.01, G:0.09, T:0.15
Consensus pattern (13 bp):
AAAATAAATAAAG
Found at i:1881506 original size:37 final size:36
Alignment explanation
Indices: 1881423--1881509 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 36
1881413 AAACAGAATA
* *
1881423 AAAAAATAAACAT-AAAGAAATAAATAAAGATAAAG
1 AAAAAAGAAAAATAAAAGAAATAAATAAAGATAAAG
* *
1881458 AAAAAATAAAAATAAAAGAAAATAAATAAAGA-AAAT
1 AAAAAAGAAAAATAAAAG-AAATAAATAAAGATAAAG
*
1881494 AACAAACGAAAAATAA
1 AA-AAAAGAAAAATAA
1881510 TAAAGTCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
35 12 0.27
36 9 0.20
37 24 0.53
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (36 bp):
AAAAAAGAAAAATAAAAGAAATAAATAAAGATAAAG
Found at i:1881583 original size:23 final size:23
Alignment explanation
Indices: 1881557--1881680 Score: 87
Period size: 23 Copynumber: 5.3 Consensus size: 23
1881547 AAAATAAATT
1881557 AAAATAAAATAAAATAACAAAAA
1 AAAATAAAATAAAATAACAAAAA
*
1881580 AAAATAAAA-ATAA-AACAAAAA
1 AAAATAAAATAAAATAACAAAAA
*
1881601 AAAAGT--AATGAAAAAAACAGAAACA
1 AAAA-TAAAAT-AAAATAACA-AAA-A
* * *
1881626 CAAATAAAATGAAAAGAA-AAAAT
1 AAAATAAAAT-AAAATAACAAAAA
*
1881649 AAAATAAAATAAAAGTAAGAATAAA
1 AAAATAAAATAAAA-TAACAA-AAA
1881674 AATAATA
1 AA-AATA
1881681 TATATAATTG
Statistics
Matches: 81, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
20 2 0.02
21 12 0.15
22 11 0.14
23 24 0.30
24 9 0.11
25 9 0.11
26 14 0.17
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.13
Consensus pattern (23 bp):
AAAATAAAATAAAATAACAAAAA
Found at i:1881594 original size:24 final size:22
Alignment explanation
Indices: 1881557--1881662 Score: 97
Period size: 23 Copynumber: 4.6 Consensus size: 22
1881547 AAAATAAATT
*
1881557 AAAATAAAATAAAATAACAAAAA
1 AAAATAAAATAAAACAA-AAAAA
1881580 AAAATAAAAATAAAACAAAAAAA
1 AAAAT-AAAATAAAACAAAAAAA
* * *
1881603 AAGTAATGAAA-AAAACAGAAACA
1 AA--AATAAAATAAAACAAAAAAA
* * *
1881626 CAAATAAAATGAAAAGAAAAAAT
1 AAAATAAAAT-AAAACAAAAAAA
1881649 AAAATAAAATAAAA
1 AAAATAAAATAAAA
1881663 GTAAGAATAA
Statistics
Matches: 67, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
21 6 0.09
22 4 0.06
23 40 0.60
24 14 0.21
25 3 0.04
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.11
Consensus pattern (22 bp):
AAAATAAAATAAAACAAAAAAA
Found at i:1881648 original size:18 final size:17
Alignment explanation
Indices: 1881556--1881662 Score: 58
Period size: 17 Copynumber: 5.9 Consensus size: 17
1881546 TAAAATAAAT
*
1881556 TAAAATAAAATAAAATAA
1 TAAAATAAAAGAAAA-AA
*
1881574 CAAAA-AAAA-ATAAAAA
1 TAAAATAAAAGA-AAAAA
* *
1881590 TAAAACAAAAAAAAAGTAA
1 TAAAATAAAAGAAAA--AA
1881609 TGAAAA-AAACAGAAACACAAA
1 T-AAAATAAA-AG-AA-A-AAA
1881630 TAAAATGAAAAGAAAAAA
1 TAAAAT-AAAAGAAAAAA
*
1881648 TAAAATAAAATAAAA
1 TAAAATAAAAGAAAA
1881663 GTAAGAATAA
Statistics
Matches: 73, Mismatches: 4, Indels: 25
0.72 0.04 0.25
Matches are distributed among these distances:
16 7 0.10
17 22 0.30
18 14 0.19
19 7 0.10
20 11 0.15
21 7 0.10
22 4 0.05
23 1 0.01
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.12
Consensus pattern (17 bp):
TAAAATAAAAGAAAAAA
Found at i:1881671 original size:22 final size:23
Alignment explanation
Indices: 1881627--1881674 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
1881617 ACAGAAACAC
1881627 AAATAAAATGAAAAGAAAAAATA
1 AAATAAAATGAAAAGAAAAAATA
* *
1881650 AAATAAAAT-AAAAGTAAGAATA
1 AAATAAAATGAAAAGAAAAAATA
1881672 AAA
1 AAA
1881675 ATAATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (23 bp):
AAATAAAATGAAAAGAAAAAATA
Found at i:1881711 original size:15 final size:15
Alignment explanation
Indices: 1881693--1881732 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 15
1881683 TATAATTGTA
1881693 ATAATAATAATGATG
1 ATAATAATAATGATG
1881708 ATAATAA-AA--ATG
1 ATAATAATAATGATG
*
1881720 AAAATAATAATGA
1 ATAATAATAATGA
1881733 AACGAACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
12 9 0.43
13 2 0.10
14 2 0.10
15 8 0.38
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (15 bp):
ATAATAATAATGATG
Found at i:1881791 original size:25 final size:25
Alignment explanation
Indices: 1881763--1881833 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
1881753 AATGGTAAAA
1881763 ATAAAAAATAAATAAATAAATATAT
1 ATAAAAAATAAATAAATAAATATAT
* * *
1881788 AT-AAAAAGAAGTAAA-AAAAATAT
1 ATAAAAAATAAATAAATAAATATAT
*
1881811 ATATAATAATAAATAAACTAAAT
1 ATA-AAAAATAAATAAA-TAAAT
1881834 TGAAGGAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
23 9 0.26
24 11 0.31
25 12 0.34
27 3 0.09
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (25 bp):
ATAAAAAATAAATAAATAAATATAT
Found at i:1883336 original size:85 final size:85
Alignment explanation
Indices: 1883193--1884699 Score: 1767
Period size: 85 Copynumber: 17.8 Consensus size: 85
1883183 GTCATCAAGA
* * * * ** * * *
1883193 TGAATGGAATCGAACTCGATA-ATTTTTGCTGACAGATAGCTTTTCTCGACTTAAGCTATGTTGT
1 TGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
* * * *
1883257 GAATTTGACATGCCCTTCAGC
65 AAATTTGATATGCCTTTGAGC
* * *
1883278 TGAATGTAATCGAGCTCGAAGGTATTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
*
1883343 AATTTAATATGCCTTTGAGC
66 AATTTGATATGCCTTTGAGC
* * * * * * * * *
1883363 TGAATGTAATCAAACTTGGAGGTCTTTGCTGACAGATAACCCTTCTTGCCTTAAGTTATGTTGTA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
*
1883428 AATTGGATATGCCTTTGAGC
66 AATTTGATATGCCTTTGAGC
* * * * *
1883448 TGAATGTAATCGAAATCAGAA-GTCTTTATTGACAAATAGTCATTCTCGCCTTGAGCTATGCTGT
1 TGAATGTAATCGAACTC-GAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
* *
1883512 AAATTTGATGTGTCTTTGAGC
65 AAATTTGATATGCCTTTGAGC
* * * * * * * *
1883533 TGAATGTAATCGAACTCAAAGGTCTTGGTTGACATATAACCATTCTCACCTTGAGTTATGTTGTA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
* * * *
1883598 GATTTGATGTGCCTTTTAGT
66 AATTTGATATGCCTTTGAGC
* * * * * *
1883618 TGAGTGTAATCGAACTCGAAGATCTTGGTTGACAGATAGTCCTTCTCGCCTTGAGCTAAGCTGCA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
* *
1883683 AATTTGATGTGCATTTGAGC
66 AATTTGATATGCCTTTGAGC
* * * * **
1883703 TGAGTGTAATCAAACTCGAAGGACTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTACA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
*
1883768 AATTTGATGTGCCTTTGAGC
66 AATTTGATATGCCTTTGAGC
* * * * *
1883788 TGAGTGTAATCGAACTCGAAGGTCTTGGTTGATAGATAGCCCTTATCGCCTTGAGCTATGCTATA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
* *
1883853 AATTTAATGTGCCTTTGAGC
66 AATTTGATATGCCTTTGAGC
* * * * * * **
1883873 TGAGTGTAATCGAACTCGAAGGACTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGTTGCG
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
1883938 AATTTGATATGCCTTTGAGC
66 AATTTGATATGCCTTTGAGC
* * *
1883958 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATACTGT
1 TGAATGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
*
1884023 AAATTTGATTTGCCTTTGAGC
65 AAATTTGATATGCCTTTGAGC
* * *
1884044 TGAATGTAATCGAAATCGAAGGTCTTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTATA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
**
1884109 AATTTGATATGTTTTTGAGC
66 AATTTGATATGCCTTTGAGC
* * *
1884129 TGAATGTAATCGAACTCAAAGGT-TTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGT
1 TGAATGTAATCGAACTCGAAGGTCTTT-GTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
*
1884193 AAATTTGATAGGCCTTTGAGC
65 AAATTTGATATGCCTTTGAGC
* * *
1884214 T-AAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCATTTTCGCCTTGAGTTATGCTGT
1 TGAA-TGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
**
1884278 AAGGTTGATATGCCTTTGAGC
65 AAATTTGATATGCCTTTGAGC
** *
1884299 TGAGCGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
1884364 AA--T-ATA--CCTTTGAGC
66 AATTTGATATGCCTTTGAGC
* * *
1884379 TGAATGTAATCGAACTCGAAGGTCTTTTGTTGACATATAACCCTTCTCACCTTGAGCTATGCTGT
1 TGAATGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
* *
1884444 AAATTTGATGTGCCTTTGAGT
65 AAATTTGATATGCCTTTGAGC
* * * * * * **
1884465 TGAGTGT-ATCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTCACCTTGAGTTATGCTGGG
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
1884529 AATTTGATATGCCTTTGAGC
66 AATTTGATATGCCTTTGAGC
* * *
1884549 T-AAGTGTAATCGAACTCGAAAGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGACCTATGCTA
1 TGAA-TGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTG
*
1884613 TAAATTTGATGTGCCTTTGAGC
64 TAAATTTGATATGCCTTTGAGC
* * * * * * * *
1884635 TTAATATAATCAAAATTGAATGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGGTGTA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
1884700 CTAGGTTTGT
Statistics
Matches: 1225, Mismatches: 179, Indels: 36
0.85 0.12 0.03
Matches are distributed among these distances:
80 31 0.03
81 39 0.03
82 3 0.00
83 3 0.00
84 67 0.05
85 917 0.75
86 163 0.13
87 2 0.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (85 bp):
TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
AATTTGATATGCCTTTGAGC
Found at i:1885865 original size:94 final size:95
Alignment explanation
Indices: 1885694--1885876 Score: 269
Period size: 94 Copynumber: 1.9 Consensus size: 95
1885684 AATATATAAA
* * *
1885694 CACCTTTATCAGGTTAGCTAAATATTATCCATAAAGTTAGTGCGTTTAACCAATTGCCTTAAAGG
1 CACCTTTATCAGGCTAGCCAAATATTATCCATAAAGTTAGGGCGTTTAACCAATTGCCTTAAAGG
*
1885759 GACAACTCAAGCTTTATTGTATATTATTAT
66 GACAACTAAAGCTTTATTGTATATTATTAT
* * * * * *
1885789 CACCTTTATCAGGCTAGCCGAATCTTATCCATAAAG-TCGGGCGTTTAACTAATTGCTTTAGAGG
1 CACCTTTATCAGGCTAGCCAAATATTATCCATAAAGTTAGGGCGTTTAACCAATTGCCTTAAAGG
1885853 GACAACTAAAGCTTTATTGTATAT
66 GACAACTAAAGCTTTATTGTATAT
1885877 ATATAATATT
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
94 46 0.59
95 32 0.41
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (95 bp):
CACCTTTATCAGGCTAGCCAAATATTATCCATAAAGTTAGGGCGTTTAACCAATTGCCTTAAAGG
GACAACTAAAGCTTTATTGTATATTATTAT
Found at i:1889909 original size:38 final size:38
Alignment explanation
Indices: 1889855--1889980 Score: 114
Period size: 39 Copynumber: 3.2 Consensus size: 38
1889845 ATAAGAAAAA
*
1889855 AAAATATAAGGTAAAGATAAAAAAGTAAATAAAACAAAT
1 AAAATA-AAGATAAAGATAAAAAAGTAAATAAAACAAAT
*
1889894 AAAATAAAGATAAAGA-AAAATAAATAAAT-AAACAGAAT
1 AAAATAAAGATAAAGATAAAA-AAGTAAATAAAACA-AAT
* *
1889932 AAAAATAAACATAAAGAAATAAATAAAGATAAAGAAAA-AAAT
1 -AAAATAAAGATAAAG--ATAAA-AAAG-TAAATAAAACAAAT
1889974 ACAAATA
1 A-AAATA
1889981 CAAATACAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
37 9 0.12
38 19 0.26
39 20 0.28
41 2 0.03
42 13 0.18
43 6 0.08
44 3 0.04
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (38 bp):
AAAATAAAGATAAAGATAAAAAAGTAAATAAAACAAAT
Found at i:1889940 original size:33 final size:33
Alignment explanation
Indices: 1889896--1889958 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1889886 AAACAAATAA
* * *
1889896 AATAAAGATAAAGAAAAATAAATAAATAAACAG
1 AATAAAAATAAACAAAAAGAAATAAATAAACAG
*
1889929 AATAAAAATAAACATAAAGAAATAAATAAA
1 AATAAAAATAAACAAAAAGAAATAAATAAA
1889959 GATAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (33 bp):
AATAAAAATAAACAAAAAGAAATAAATAAACAG
Found at i:1889965 original size:18 final size:18
Alignment explanation
Indices: 1889890--1889974 Score: 82
Period size: 18 Copynumber: 4.5 Consensus size: 18
1889880 TAAATAAAAC
1889890 AAATAAAATAAAGATAAAG
1 AAAT-AAATAAAGATAAAG
*
1889909 AAAAATAAATAAATA-AACAG
1 --AAATAAATAAAGATAA-AG
* *
1889929 AATAAAAATAAACATAAAG
1 AA-ATAAATAAAGATAAAG
1889948 AAATAAATAAAGATAAAG
1 AAATAAATAAAGATAAAG
*
1889966 AAAAAAATA
1 AAATAAATA
1889975 CAAATACAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
18 24 0.44
19 15 0.27
20 12 0.22
21 4 0.07
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.15
Consensus pattern (18 bp):
AAATAAATAAAGATAAAG
Found at i:1889979 original size:6 final size:6
Alignment explanation
Indices: 1889970--1890368 Score: 532
Period size: 6 Copynumber: 65.8 Consensus size: 6
1889960 ATAAAGAAAA
** ** **
1889970 AAATAC AAATAC AAATAC AAATAC AAATAC AAACGC AAACGC AAACGC
1 AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC
** ** ** ** ** **
1890018 AAACGC AAACGC AAACGC AAACGC AAACGC AAACGC AAATAC AAATAC
1 AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC
1890066 AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC
1 AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC
*
1890114 AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATGC AAATAC
1 AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC
1890162 AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC
1 AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC
1890210 AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC
1 AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC
*
1890258 AAATAT AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC
1 AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC
* *
1890306 AAATAC AAATAC AACAAAAC AAA-AC GAAAATAAC AAA-AG AAATAAC
1 AAATAC AAATAC -A-AATAC AAATAC --AAAT-AC AAATAC AAAT-AC
1890352 AAATAC AAATAC AAATA
1 AAATAC AAATAC AAATA
1890369 AAAAAATATG
Statistics
Matches: 374, Mismatches: 11, Indels: 16
0.93 0.03 0.04
Matches are distributed among these distances:
5 6 0.02
6 349 0.93
7 13 0.03
8 4 0.01
9 2 0.01
ACGTcount: A:0.65, C:0.18, G:0.03, T:0.14
Consensus pattern (6 bp):
AAATAC
Found at i:1890428 original size:6 final size:6
Alignment explanation
Indices: 1890417--1890562 Score: 71
Period size: 5 Copynumber: 25.3 Consensus size: 6
1890407 ATAACAAAAG
** * * * *
1890417 AAATAA AAATAA AAGCAA AAA-AG TAATGA AAA-AA AAACAA AAAT-A
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
1890462 AAAT-A AAATGAA AAGA-AA AAAT-A AAAT-A AAAT-A AAAT-A AAAT-A
1 AAATAA AAAT-AA AA-ATAA AAATAA AAATAA AAATAA AAATAA AAATAA
* * * *
1890505 AAAT-A AAATAA AAATAA TATATATA TAATAA TAATAA TAAATGA AAATAA
1 AAATAA AAATAA AAATAA -AAATA-A AAATAA AAATAA -AAATAA AAATAA
*
1890555 TAATAA AA
1 AAATAA AA
1890563 GGAACCCAAA
Statistics
Matches: 112, Mismatches: 18, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
5 48 0.43
6 48 0.43
7 14 0.12
8 2 0.02
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:1890458 original size:10 final size:10
Alignment explanation
Indices: 1890384--1890521 Score: 80
Period size: 10 Copynumber: 12.7 Consensus size: 10
1890374 ATATGATGGT
*
1890384 AAAATAAATA
1 AAAATAAAAA
* *
1890394 AAAACAAAAC
1 AAAATAAAAA
*
1890404 GAAATAACAAA
1 AAAATAA-AAA
1890415 AGAAATAAAAA
1 A-AAATAAAAA
*
1890426 TAAAAGCAAAAA
1 -AAAA-TAAAAA
*
1890438 AGTAATGAAAAA
1 A-AAAT-AAAAA
*
1890450 AAAACAAAAA
1 AAAATAAAAA
1890460 TAAAATAAAATGA
1 -AAAATAAAA--A
1890473 AAAGA-AAAAA
1 AAA-ATAAAAA
*
1890483 TAAAATAAAAT
1 -AAAATAAAAA
*
1890494 AAAATAAAAT
1 AAAATAAAAA
1890504 AAAATAAAATA
1 AAAATAAAA-A
1890515 AAAATAA
1 AAAATAA
1890522 TATATATATA
Statistics
Matches: 100, Mismatches: 15, Indels: 25
0.71 0.11 0.18
Matches are distributed among these distances:
10 38 0.38
11 33 0.33
12 27 0.27
13 2 0.02
ACGTcount: A:0.78, C:0.04, G:0.05, T:0.13
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:1892209 original size:12 final size:13
Alignment explanation
Indices: 1892188--1892221 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
1892178 TAATCTTAGC
1892188 ATTC-TTTTTATT
1 ATTCATTTTTATT
1892200 ATT-ATTTTTATT
1 ATTCATTTTTATT
1892212 ATTCATTTTT
1 ATTCATTTTT
1892222 TCTTCTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTCATTTTTATT
Found at i:1892261 original size:5 final size:5
Alignment explanation
Indices: 1892251--1892480 Score: 104
Period size: 5 Copynumber: 44.6 Consensus size: 5
1892241 TGTTTTCAAG
* *
1892251 TTTAT TTTAT TTTAT TTTAT TATTAT TTTCA- TTTGT TTTAT GTT-T TTTACT
1 TTTAT TTTAT TTTAT TTTAT T-TTAT TTT-AT TTTAT TTTAT TTTAT TTTA-T
* * *
1892302 TCTTAT TAT-T TTTAT TTT-T TTTACT TTTAAAGT TTAACAT TTTTT TTTAT
1 T-TTAT TTTAT TTTAT TTTAT TTTA-T TTT--A-T TT--TAT TTTAT TTTAT
* * * *
1892352 TTTTT CCTTTGA- TTTAT TTAAT ATT-T TTTAT TTTATT TTTAT GTTAT
1 TTTAT --TTT-AT TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT
*
1892399 TTTAT TTTAT TTTAT TATT-T TTTAT TTTAT TTT-T CTTTGAT TGT-T
1 TTTAT TTTAT TTTAT T-TTAT TTTAT TTTAT TTTAT -TTT-AT TTTAT
* * *
1892444 TTTAT TTTTT TGTTAT TTT-T ATT-T TTTAA TTTAT TTT
1 TTTAT TTTAT T-TTAT TTTAT TTTAT TTTAT TTTAT TTT
1892481 TTCCTTTGAT
Statistics
Matches: 171, Mismatches: 27, Indels: 54
0.68 0.11 0.21
Matches are distributed among these distances:
4 26 0.15
5 103 0.60
6 27 0.16
7 10 0.06
8 5 0.03
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:1892266 original size:52 final size:51
Alignment explanation
Indices: 1892153--1892258 Score: 119
Period size: 52 Copynumber: 2.1 Consensus size: 51
1892143 TCCTTTGAAA
** *
1892153 TTTTAGTTATTCATTTTTTTCTTTTTAATCTTAGCATTCTTTTTATTATTAT
1 TTTTA-TTATTCATTTTTTTCTTTTTAATCTTAGCATTCTTTCAAGTATTAT
*
1892205 TTTTATTATTCA-TTTTTTCTTCTTTTAATTTTAGCATGT-TTTCAAGT-TTAT
1 TTTTATTATTCATTTTTTTC-T-TTTTAATCTTAGCAT-TCTTTCAAGTATTAT
1892256 TTT
1 TTT
1892259 ATTTTATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
50 7 0.15
51 15 0.32
52 24 0.51
53 1 0.02
ACGTcount: A:0.19, C:0.09, G:0.05, T:0.67
Consensus pattern (51 bp):
TTTTATTATTCATTTTTTTCTTTTTAATCTTAGCATTCTTTCAAGTATTAT
Found at i:1892386 original size:36 final size:35
Alignment explanation
Indices: 1892341--1892470 Score: 111
Period size: 41 Copynumber: 3.5 Consensus size: 35
1892331 AAGTTTAACA
*
1892341 TTTTT-TTTTATTTTTTCCTTTGATTTATTTAATAT
1 TTTTTATTTTATTTTTT-CTTTGATTTATTTATTAT
* *
1892376 TTTTTATTTTATTTTTATGTTATTTTATTTTATTTTATTAT
1 TTTTTATTTTA--TTT-T-TTCTTTGA-TTTA-TTTATTAT
* *
1892417 TTTTTATTTTA-TTTTTCTTTGATTGTTTTTATTTT
1 TTTTTATTTTATTTTTTCTTTGATT-TATTTATTAT
1892452 TTTGTTATTTTTATTTTTT
1 TTT-TTA-TTTTATTTTTT
1892471 AATTTATTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
35 17 0.22
36 15 0.19
37 6 0.08
38 10 0.13
39 5 0.06
40 6 0.08
41 18 0.23
ACGTcount: A:0.15, C:0.02, G:0.04, T:0.78
Consensus pattern (35 bp):
TTTTTATTTTATTTTTTCTTTGATTTATTTATTAT
Found at i:1895687 original size:2 final size:2
Alignment explanation
Indices: 1895680--1895714 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1895670 GATAATTACA
1895680 AT AT AT AT 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 AT AT AT AT A
1895715 GTAACAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1897610 original size:12 final size:11
Alignment explanation
Indices: 1897582--1897622 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
1897572 TAACAAAATA
* *
1897582 AATAATATAAA
1 AATAATACAAG
1897593 AATAATACAAG
1 AATAATACAAG
1897604 TAATAATACAAG
1 -AATAATACAAG
1897616 AATAATA
1 AATAATA
1897623 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:1897727 original size:12 final size:12
Alignment explanation
Indices: 1897705--1897749 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
1897695 GAATAAAAGG
1897705 AAAATATAATAGT
1 AAAA-ATAATAGT
*
1897718 AAAAATAATAAT
1 AAAAATAATAGT
*
1897730 AAATATAATAGT
1 AAAAATAATAGT
*
1897742 AATAATAA
1 AAAAATAA
1897750 AAATACAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:1897733 original size:24 final size:24
Alignment explanation
Indices: 1897706--1897754 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1897696 AATAAAAGGA
*
1897706 AAATATAATAGTAAAAATAATAAT
1 AAATATAATAGTAAAAATAAAAAT
*
1897730 AAATATAATAGTAATAATAAAAAT
1 AAATATAATAGTAAAAATAAAAAT
1897754 A
1 A
1897755 CAAAGAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (24 bp):
AAATATAATAGTAAAAATAAAAAT
Found at i:1898368 original size:37 final size:37
Alignment explanation
Indices: 1898327--1898418 Score: 139
Period size: 37 Copynumber: 2.5 Consensus size: 37
1898317 GTGCTTGTGG
* * *
1898327 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCATAGCAAAACTCT
* *
1898364 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCATAGCAAAACTCT
1898401 ATCCTATTTTTAGGAGTT
1 ATCCTATTTTTAGGAGTT
1898419 GGATATCCTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCATAGCAAAACTCT
Found at i:1898956 original size:106 final size:106
Alignment explanation
Indices: 1898638--1900119 Score: 2181
Period size: 106 Copynumber: 14.0 Consensus size: 106
1898628 AAATTGTTCT
* * * ** * *
1898638 GAGTCCAGTATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* * *
1898702 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTT-CTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC-GTTGTCTG
* * * *
1898744 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * * * *
1898803 TCAGCCGCCCCTTCGTCTTGAAGTTGAGCTTGTGTTATCT-
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1898843 TAGGTCCAAGATCATTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 GA-GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* *
1898908 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1898950 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1899015 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** *
1899056 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTTAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
1899121 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1899162 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
1899227 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1899268 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGCAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1899333 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1899374 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1899439 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1899480 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
1899545 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCCTTTTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1899586 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGACATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
1899651 CCAGTGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1899692 GAGTCCAATATCCTTCACTGTAAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGAAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
1899757 CCAGCGGTCCCTTCGTCGTGAAGCTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1899798 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1899863 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1899904 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1899969 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1900010 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
1900075 CCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1900116 GAGT
1 GAGT
1900120 GGCACGATAT
Statistics
Matches: 1250, Mismatches: 116, Indels: 20
0.90 0.08 0.01
Matches are distributed among these distances:
99 1 0.00
100 78 0.06
101 3 0.00
102 4 0.00
104 3 0.00
105 3 0.00
106 1156 0.92
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1901087 original size:21 final size:22
Alignment explanation
Indices: 1901028--1901103 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
1901018 TTGTGTTTGG
*
1901028 TCAAAGGTTTGGCATTTGACGC
1 TCAAAGGTTTGGCATTTGATGC
*
1901050 TCAAAGGTTTAGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1901072 TCAAAGG-TTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1901093 TCAAAGGTTTG
1 TCAAAGGTTTG
1901104 ATGGGGTAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
21 20 0.40
22 30 0.60
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.34
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1901741 original size:7 final size:7
Alignment explanation
Indices: 1901709--1901783 Score: 55
Period size: 7 Copynumber: 10.7 Consensus size: 7
1901699 TTTTTGTCCC
1901709 TTTTTC-
1 TTTTTCT
**
1901715 TTTTTGA
1 TTTTTCT
*
1901722 TTTTTGT
1 TTTTTCT
*
1901729 TCTTTCT
1 TTTTTCT
1901736 TTTTTCT
1 TTTTTCT
*
1901743 TTTGT-T
1 TTTTTCT
*
1901749 TTCTTCT
1 TTTTTCT
1901756 TTTTTGCT
1 TTTTT-CT
1901764 TCTTTTCT
1 T-TTTTCT
*
1901772 TTTTTGT
1 TTTTTCT
1901779 TTTTT
1 TTTTT
1901784 TTCTTTCTGT
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
6 9 0.16
7 36 0.65
8 6 0.11
9 4 0.07
ACGTcount: A:0.01, C:0.12, G:0.07, T:0.80
Consensus pattern (7 bp):
TTTTTCT
Found at i:1901745 original size:20 final size:20
Alignment explanation
Indices: 1901711--1901785 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
1901701 TTTGTCCCTT
**
1901711 TTTCTTTTTGATTTTTGTTC
1 TTTCTTTTTTCTTTTTGTTC
*
1901731 TTTCTTTTTTC-TTTTGTTT
1 TTTCTTTTTTCTTTTTGTTC
*
1901750 TCTTCTTTTTTGCTTCTT-TTC
1 T-TTCTTTTTT-CTTTTTGTTC
1901771 TTT-TTTGTTT-TTTTT
1 TTTCTTT-TTTCTTTTT
1901786 CTTTCTGTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
18 4 0.09
19 11 0.24
20 23 0.51
21 4 0.09
22 3 0.07
ACGTcount: A:0.01, C:0.12, G:0.07, T:0.80
Consensus pattern (20 bp):
TTTCTTTTTTCTTTTTGTTC
Found at i:1901773 original size:16 final size:15
Alignment explanation
Indices: 1901732--1901789 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 15
1901722 TTTTTGTTCT
1901732 TTCTTTT-TTCTTTTG
1 TTCTTTTCTT-TTTTG
1901747 TT-TTCTTCTTTTTTG
1 TTCTT-TTCTTTTTTG
1901762 CTTCTTTTCTTTTTTG
1 -TTCTTTTCTTTTTTG
*
1901778 TTTTTTTTCTTT
1 -TTCTTTTCTTT
1901790 CTGTTCTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
14 2 0.05
15 9 0.24
16 24 0.65
17 2 0.05
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (15 bp):
TTCTTTTCTTTTTTG
Found at i:1901775 original size:35 final size:34
Alignment explanation
Indices: 1901722--1901788 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 34
1901712 TTCTTTTTGA
1901722 TTTTTGTTCTTTCTTTTTTCT-TTTGTTTTCTTCT
1 TTTTTGTTCTTTCTTTTTT-TGTTTGTTTTCTTCT
*
1901756 TTTTTGCTTCTTT-TCTTTTTTGTTTTTTTTCTT
1 TTTTTG-TTCTTTCT-TTTTTTGTTTGTTTTCTT
1901789 TCTGTTCTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 8 0.28
35 21 0.72
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (34 bp):
TTTTTGTTCTTTCTTTTTTTGTTTGTTTTCTTCT
Found at i:1906418 original size:12 final size:12
Alignment explanation
Indices: 1906401--1906428 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1906391 TATATATATA
1906401 AAAAAGAAAAAG
1 AAAAAGAAAAAG
1906413 AAAAAGAAAAAG
1 AAAAAGAAAAAG
1906425 AAAA
1 AAAA
1906429 TAAATAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:1906972 original size:2 final size:2
Alignment explanation
Indices: 1906965--1906992 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1906955 AGAACATACG
1906965 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
1906993 ACAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1907073 original size:24 final size:27
Alignment explanation
Indices: 1907046--1907099 Score: 78
Period size: 24 Copynumber: 2.1 Consensus size: 27
1907036 AAAGAGAAAG
1907046 TAAAAAAATATA-ATA-ATAA-AAAAA
1 TAAAAAAATATACATATATAATAAAAA
*
1907070 TAAAAAAATATACATATATAATATAAA
1 TAAAAAAATATACATATATAATAAAAA
1907097 TAA
1 TAA
1907100 GTAGAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 12 0.46
25 3 0.12
26 4 0.15
27 7 0.27
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (27 bp):
TAAAAAAATATACATATATAATAAAAA
Found at i:1907079 original size:16 final size:16
Alignment explanation
Indices: 1906990--1907079 Score: 56
Period size: 16 Copynumber: 5.2 Consensus size: 16
1906980 ATATATATAT
* *
1906990 ATAACAAAAT-AAATA
1 ATAAAAAAATAAAAAA
1907005 ATATAAAAAATAATACAAGA
1 ATA-AAAAAATAA-A-AA-A
*
1907025 ATAATAAAAAGAAAGAGAA
1 ATAA-AAAAATAAA-A-AA
* *
1907044 AGTAAAAAAATATAATA
1 A-TAAAAAAATAAAAAA
1907061 ATAAAAAAATAAAAAA
1 ATAAAAAAATAAAAAA
1907077 ATA
1 ATA
1907080 TACATATATA
Statistics
Matches: 58, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
15 3 0.05
16 22 0.38
17 3 0.05
18 2 0.03
19 13 0.22
20 15 0.26
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (16 bp):
ATAAAAAAATAAAAAA
Found at i:1915672 original size:30 final size:30
Alignment explanation
Indices: 1915523--1915655 Score: 248
Period size: 30 Copynumber: 4.4 Consensus size: 30
1915513 TCCGAAGGAC
1915523 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1915553 CTATCCAGAGGTCATAAAGATCTTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1915583 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1915613 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1915643 CTATCCATAGGTC
1 CTATCCAGAGGTC
1915656 CCGAAGAACC
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 100 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1915672 original size:60 final size:60
Alignment explanation
Indices: 1915523--1915680 Score: 235
Period size: 60 Copynumber: 2.6 Consensus size: 60
1915513 TCCGAAGGAC
* *
1915523 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCTTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1915583 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
* * * * *
1915643 CTATCCATAGGTCCCGAAGAACCTAGGTAAACTATCCA
1 CTATCCAGAGGTCACAAAGATCCTCGGT-AACTATCCA
1915681 TATATTCCTT
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
60 81 0.90
61 9 0.10
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (60 bp):
CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
Done.