Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008138.1 Hibiscus syriacus cultivar Beakdansim tig00110694_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: 3838456
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 18
Found at i:3098109 original size:46 final size:46
Alignment explanation
Indices: 3098030--3098117 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
3098020 GGATTCACAA
*
3098030 AAATAAAAAAATTTATAACTAACACGAAAAAAATATTAATTTAAAC
1 AAATAAAAAAATTTATAACTAACACGAAAAAAATAATAATTTAAAC
* *
3098076 AAATAAGATAAATTTATAACTAACAC-CAAAAAATAATAATTT
1 AAATAA-AAAAATTTATAACTAACACGAAAAAAATAATAATTT
3098118 CATAACAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
46 20 0.53
47 18 0.47
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.27
Consensus pattern (46 bp):
AAATAAAAAAATTTATAACTAACACGAAAAAAATAATAATTTAAAC
Found at i:3098998 original size:2 final size:2
Alignment explanation
Indices: 3098991--3099057 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
3098981 ATTACTAATG
3098991 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
*
3099033 AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3099058 GATTAAATGA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3099589 original size:23 final size:23
Alignment explanation
Indices: 3099563--3099649 Score: 61
Period size: 26 Copynumber: 3.5 Consensus size: 23
3099553 TTTTCTTCAT
3099563 TTTTTCTTTTTCTTTTTCTTTTC
1 TTTTTCTTTTTCTTTTTCTTTTC
*
3099586 TTTTAT-TTTCTTCATTTTTTCTTTTT
1 TTTT-TCTTT-TTC--TTTTTCTTTTC
*
3099612 TATTTTCTTCATT-TTTTTCATTTTC
1 T-TTTTCTT-TTTCTTTTTC-TTTTC
3099637 ATTTTTCATTTTT
1 -TTTTTC-TTTTT
3099650 TGTTTCCTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
23 7 0.14
24 10 0.20
25 11 0.22
26 15 0.30
27 7 0.14
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTCTTTTTCTTTTTCTTTTC
Found at i:3099610 original size:32 final size:32
Alignment explanation
Indices: 3099552--3099635 Score: 104
Period size: 32 Copynumber: 2.7 Consensus size: 32
3099542 TCTCCTTTCA
3099552 ATTTTCTTCATTTT-TTC--TTTTTC-TTTTT
1 ATTTTCTTCATTTTCTTCATTTTTTCTTTTTT
* *
3099580 CTTTTCTTTTATTTTCTTCATTTTTTCTTTTTT
1 ATTTTC-TTCATTTTCTTCATTTTTTCTTTTTT
*
3099613 ATTTTCTTCATTTTTTTCATTTT
1 ATTTTCTTCATTTTCTTCATTTT
3099636 CATTTTTCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
28 5 0.11
29 7 0.15
30 3 0.07
32 21 0.46
33 10 0.22
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.77
Consensus pattern (32 bp):
ATTTTCTTCATTTTCTTCATTTTTTCTTTTTT
Found at i:3099650 original size:23 final size:23
Alignment explanation
Indices: 3099576--3099650 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
3099566 TTCTTTTTCT
3099576 TTTTCTTTTCTTTTATTTTCTTCA
1 TTTT-TTTTCTTTTATTTTCTTCA
3099600 TTTTTTCTT-TTTTATTTTCTTCA
1 TTTTTT-TTCTTTTATTTTCTTCA
3099623 -TTTTTTTCATTTTCA-TTT-TTCA
1 TTTTTTTTC-TTTT-ATTTTCTTCA
3099645 TTTTTT
1 TTTTTT
3099651 GTTTCCTCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
21 2 0.04
22 9 0.20
23 28 0.61
24 7 0.15
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTTTTCTTTTATTTTCTTCA
Found at i:3106239 original size:22 final size:22
Alignment explanation
Indices: 3106211--3106253 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3106201 ATTAGTATTC
3106211 ATAATACTACATGTATTTTACT
1 ATAATACTACATGTATTTTACT
*
3106233 ATAATACTATATGTATTTTAC
1 ATAATACTACATGTATTTTAC
3106254 CTTTTCACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.47
Consensus pattern (22 bp):
ATAATACTACATGTATTTTACT
Found at i:3109721 original size:21 final size:21
Alignment explanation
Indices: 3109695--3109744 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
3109685 CAAGTGGTGG
*
3109695 TGGTGGTGGTGATGATGATTA
1 TGGTGGTGGTGATGATGATCA
*
3109716 TGGTGGTGGTGGTGATGATCA
1 TGGTGGTGGTGATGATGATCA
*
3109737 TGATGGTG
1 TGGTGGTG
3109745 ATAATGAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.16, C:0.02, G:0.46, T:0.36
Consensus pattern (21 bp):
TGGTGGTGGTGATGATGATCA
Found at i:3109724 original size:24 final size:24
Alignment explanation
Indices: 3109692--3109744 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
3109682 CGTCAAGTGG
* *
3109692 TGGTGGTGGTGGTGATGATGATTA
1 TGGTGGTGGTGGTGATGATCATGA
3109716 TGGTGGTGGTGGTGATGATCATGA
1 TGGTGGTGGTGGTGATGATCATGA
3109740 TGGTG
1 TGGTG
3109745 ATAATGAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.15, C:0.02, G:0.47, T:0.36
Consensus pattern (24 bp):
TGGTGGTGGTGGTGATGATCATGA
Found at i:3109727 original size:27 final size:27
Alignment explanation
Indices: 3109689--3109740 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
3109679 CATCGTCAAG
* *
3109689 TGGTGGTGGTGGTGGTGATGATGATTA
1 TGGTGGTGGTGGTGATGATCATGATTA
3109716 TGGTGGTGGTGGTGATGATCATGAT
1 TGGTGGTGGTGGTGATGATCATGAT
3109741 GGTGATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.02, G:0.46, T:0.37
Consensus pattern (27 bp):
TGGTGGTGGTGGTGATGATCATGATTA
Found at i:3114642 original size:8 final size:8
Alignment explanation
Indices: 3114629--3114671 Score: 59
Period size: 8 Copynumber: 5.0 Consensus size: 8
3114619 TATTTTTTTT
3114629 CAAAAAAA
1 CAAAAAAA
3114637 CAAAAAAAA
1 C-AAAAAAA
3114646 CAAAAAAA
1 CAAAAAAA
3114654 GGCAAAAAAA
1 --CAAAAAAA
3114664 CAAAAAAA
1 CAAAAAAA
3114672 AGGCCAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 16 0.50
9 8 0.25
10 8 0.25
ACGTcount: A:0.84, C:0.12, G:0.05, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:3114644 original size:9 final size:9
Alignment explanation
Indices: 3114630--3114672 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
3114620 ATTTTTTTTC
3114630 AAAAAAACA
1 AAAAAAACA
3114639 AAAAAAACA
1 AAAAAAACA
*
3114648 AAAAAAGGC-
1 AAAAAA-ACA
3114657 AAAAAAACA
1 AAAAAAACA
3114666 AAAAAAA
1 AAAAAAA
3114673 GGCCAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 1 0.03
9 28 0.93
10 1 0.03
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:3114672 original size:19 final size:19
Alignment explanation
Indices: 3114639--3114680 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
3114629 CAAAAAAACA
3114639 AAAAAAACAAAAAAAGG-C
1 AAAAAAACAAAAAAAGGCC
3114657 AAAAAAACAAAAAAAAGGCC
1 AAAAAAAC-AAAAAAAGGCC
3114677 AAAA
1 AAAA
3114681 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 8 0.36
19 9 0.41
20 5 0.23
ACGTcount: A:0.79, C:0.12, G:0.10, T:0.00
Consensus pattern (19 bp):
AAAAAAACAAAAAAAGGCC
Found at i:3129115 original size:25 final size:25
Alignment explanation
Indices: 3129082--3129131 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3129072 ATTTTATTAT
*
3129082 ACATTAATAAAGTGTACAATTAAGA
1 ACATCAATAAAGTGTACAATTAAGA
3129107 ACATCAATAAAGTGTACAATTAAGA
1 ACATCAATAAAGTGTACAATTAAGA
3129132 TTAATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.26
Consensus pattern (25 bp):
ACATCAATAAAGTGTACAATTAAGA
Found at i:3135988 original size:36 final size:36
Alignment explanation
Indices: 3135935--3136073 Score: 215
Period size: 36 Copynumber: 3.9 Consensus size: 36
3135925 ACGGTGTTGG
* *
3135935 ACATTGATACACAAATGTACCGAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
3135971 AGATTGATACATGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
3136007 ACATTGATACACGAATGTATCAAAGTTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
3136043 ACATTGATACACGAATGTATCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
3136074 ATTGATAAAT
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 94 1.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:3141208 original size:3 final size:3
Alignment explanation
Indices: 3141195--3141224 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
3141185 AATGGTACTA
3141195 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AA
3141225 GTATACTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3141278 original size:13 final size:14
Alignment explanation
Indices: 3141262--3141362 Score: 68
Period size: 14 Copynumber: 7.2 Consensus size: 14
3141252 TATTTATTAT
3141262 ATAATAT-TATATA
1 ATAATATATATATA
3141275 ATAATATACTATATA
1 ATAATATA-TATATA
*
3141290 A-AA-ATATA-AAA
1 ATAATATATATATA
*
3141301 ATTATATATATAATA
1 ATAATATATAT-ATA
* * *
3141316 TATAATAAAAATACA
1 -ATAATATATATATA
*
3141331 ATAATACACTATATA
1 ATAATATA-TATATA
3141346 AT-ATATAATATATA
1 ATAATAT-ATATATA
3141360 ATA
1 ATA
3141363 TAAATGTTAT
Statistics
Matches: 67, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
11 3 0.04
12 3 0.04
13 15 0.22
14 20 0.30
15 18 0.27
16 8 0.12
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAATATATATATA
Found at i:3141296 original size:23 final size:22
Alignment explanation
Indices: 3141257--3141323 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
3141247 CTAGATATTT
**
3141257 ATTATATA-ATATTATATAATA
1 ATTATATATATAAAATATAATA
*
3141278 A-TATACTATATAAAAATATAAAA
1 ATTATA-TATAT-AAAATATAATA
*
3141301 ATTATATATATAATATATAATA
1 ATTATATATATAAAATATAATA
3141323 A
1 A
3141324 AAATACAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 4 0.11
21 3 0.08
22 12 0.32
23 14 0.38
24 4 0.11
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTATATATATAAAATATAATA
Found at i:3141298 original size:33 final size:33
Alignment explanation
Indices: 3141259--3141421 Score: 125
Period size: 35 Copynumber: 4.7 Consensus size: 33
3141249 AGATATTTAT
3141259 TATATAATATTATATA-ATAATATACTATATAAAAA
1 TATA-AATATTATATATATAATATA-TA-ATAAAAA
*
3141294 TATAAAAATTATATATATAATATATAATAAAAA
1 TATAAATATTATATATATAATATATAATAAAAA
* * * *
3141327 TA-CAATAATACACTATATAATATATAATATATAA
1 TATAAATATTATA-TATATAATATATAATA-AAAA
* * *
3141361 TATAAATGTTATATAAAATAAAATA-AAGTATAAATA
1 TATAAATATTATAT-ATATAATATATAA-TA-AAA-A
3141397 TATAAATATTGTATACTATATAATA
1 TATAAATA-T-TATA-TATATAATA
3141422 CTAAACCAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 17
0.76 0.12 0.13
Matches are distributed among these distances:
32 6 0.06
33 25 0.25
34 20 0.20
35 31 0.30
36 8 0.08
37 1 0.01
38 10 0.10
39 1 0.01
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (33 bp):
TATAAATATTATATATATAATATATAATAAAAA
Found at i:3141373 original size:14 final size:14
Alignment explanation
Indices: 3141195--3141364 Score: 71
Period size: 15 Copynumber: 12.4 Consensus size: 14
3141185 AATGGTACTA
3141195 AATATATAATA-AT
1 AATATATAATATAT
3141208 AATA-ATAATA-AT
1 AATATATAATATAT
*
3141220 AATAAGTATACTAT-T
1 AAT-A-TATAATATAT
* *
3141235 AATATGTGCATACTA-
1 AATATAT-AATA-TAT
* * *
3141250 GATATTTATTATAT
1 AATATATAATATAT
3141264 AATAT-T-ATATAAT
1 AATATATAATAT-AT
3141277 AATATACT-ATATA-
1 AATATA-TAATATAT
* *
3141290 AAAATATAA-AAATT
1 AATATATAATATA-T
3141304 ATATATATAATATAT
1 A-ATATATAATATAT
*
3141319 AATA-A-AA-ATAC
1 AATATATAATATAT
3141330 AATA-ATACACTATAT
1 AATATATA-A-TATAT
3141345 AATATATAATATAT
1 AATATATAATATAT
3141359 AATATA
1 AATATA
3141365 AATGTTATAT
Statistics
Matches: 120, Mismatches: 16, Indels: 41
0.68 0.09 0.23
Matches are distributed among these distances:
11 8 0.07
12 20 0.17
13 25 0.21
14 25 0.21
15 37 0.31
16 5 0.04
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (14 bp):
AATATATAATATAT
Found at i:3141374 original size:56 final size:57
Alignment explanation
Indices: 3141274--3141385 Score: 129
Period size: 56 Copynumber: 2.0 Consensus size: 57
3141264 AATATTATAT
* * * *
3141274 AATAATATACTATATAAAAATATAAAAATTATATATATAATATATAATA-AAAATAC
1 AATAATACACTATATAAAAATATAAAAATAATATAAATAATATATAAAATAAAATAC
* * **
3141330 AATAATACACTATAT-AATATATAATATATAATATAAATGTTATATAAAATAAAATA
1 AATAATACACTATATAAAAATATAA-AAATAATATAAATAATATATAAAATAAAATA
3141386 AAGTATAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
55 8 0.17
56 32 0.70
57 6 0.13
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.35
Consensus pattern (57 bp):
AATAATACACTATATAAAAATATAAAAATAATATAAATAATATATAAAATAAAATAC
Found at i:3150181 original size:15 final size:15
Alignment explanation
Indices: 3150161--3150194 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
3150151 GATTTAGGAA
3150161 ATCCTGGATGATTGC
1 ATCCTGGATGATTGC
3150176 ATCCTGGATGATTGC
1 ATCCTGGATGATTGC
3150191 ATCC
1 ATCC
3150195 CTTTCCTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (15 bp):
ATCCTGGATGATTGC
Found at i:3151919 original size:81 final size:81
Alignment explanation
Indices: 3151783--3152356 Score: 815
Period size: 81 Copynumber: 7.1 Consensus size: 81
3151773 TTGTTCTAAA
* * * * *
3151783 TAAAATATTAATGACCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAT
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
3151848 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
3151864 TAAAAGATTAATGGCTTAGCTGTGCATTTGACATAAAGGTGTCAATTATGTCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
3151929 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
3151945 TAAAAGATTAATGGCCTAGCTATGCATTTGACAAAAATGTGTCAATTATCCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
3152010 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
3152026 TAAAAGATTAATGGCCTAGTTGTGAATTTGACAGAAAGGTATCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
3152091 GTTAAATACCTTTGAA
66 GTTAAATACCTTTGAG
* * * * *
3152107 TAAAAGATTATTGTCCTAGCTATGCATTTGACAGAAATGTGTCAATTATGTCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
3152172 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
3152188 TAAACGATTATTGGCCTAGCTGTGCATTTGACAGAAAGTTTTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
3152253 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * ** * * * *
3152269 TAAAAGATTATTTGCCTAGCTGTGCAACTGGCAAAAAGGTGTCAATCATGCAAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
** * *
3152334 GCAAAATTCCTTTGGG
66 GTTAAATACCTTTGAG
3152350 TAAAAGA
1 TAAAAGA
3152357 CTAAATGCTT
Statistics
Matches: 441, Mismatches: 52, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 441 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:3156398 original size:22 final size:21
Alignment explanation
Indices: 3156355--3156395 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3156345 TGCACTAATT
3156355 ATATTTTATTTTAGTCCTTTG
1 ATATTTTATTTTAGTCCTTTG
*
3156376 ATATTTTGTTCTTAG-CCTTT
1 ATATTTTATT-TTAGTCCTTT
3156396 TGAATTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.61
Consensus pattern (21 bp):
ATATTTTATTTTAGTCCTTTG
Found at i:3160882 original size:3 final size:3
Alignment explanation
Indices: 3160874--3160910 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
3160864 AAGTTAATAA
* *
3160874 ATT ATT ATT ATT ATT ATT ATT ATC ATC ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3160911 ATATAGATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:3162429 original size:99 final size:101
Alignment explanation
Indices: 3162303--3162492 Score: 262
Period size: 101 Copynumber: 1.9 Consensus size: 101
3162293 ATCAATTTTG
* * * * *
3162303 TCTTGTTTGAGACAATTTCCTTCG-AA-ACAAATTTTGAAATTGTTTCACTCGAAA-AAATATTA
1 TCTTGCTTGAGACAATTTCCTTCGAAACACAAATTTTAAAATTATTTAACTCGAAACAAAAATT-
* *
3162365 TCTCACTTGAGATGGTTTCTCTTAAAAACAAATTGCA
65 TATCACTTGAGATAGTTTCTCTTAAAAACAAATTGCA
3162402 TCTTGCTTGAGACAATTTCCCTT-GAAACACAAATTTTAAAATTATTTAACTCGAAACAAAAATT
1 TCTTGCTTGAGACAATTT-CCTTCGAAACACAAATTTTAAAATTATTTAACTCGAAACAAAAATT
*
3162466 TATCACTTGAGATAGTTTTTCTTAAAA
65 TATCACTTGAGATAGTTTCTCTTAAAA
3162493 TCAATTTTGC
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
99 18 0.23
100 6 0.08
101 49 0.62
102 6 0.08
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (101 bp):
TCTTGCTTGAGACAATTTCCTTCGAAACACAAATTTTAAAATTATTTAACTCGAAACAAAAATTT
ATCACTTGAGATAGTTTCTCTTAAAAACAAATTGCA
Found at i:3162559 original size:95 final size:97
Alignment explanation
Indices: 3162303--3162564 Score: 250
Period size: 95 Copynumber: 2.7 Consensus size: 97
3162293 ATCAATTTTG
* *
3162303 TCTTGTTTGAGACAATT-TCCTTCG-AA-ACAAATTTTGAAATTGTTTCACTCGAAAAAATATTA
1 TCTTGCTTGAGACAATTCCCCTT-GAAACACAAATTTTGAAATTGTTTCACTCGAAAAAA-ATT-
* *
3162365 TCTCACTTGAGATGGTTTCTCTTAAAAACAAATTGCA
63 TATCACTTGAGATAGTTTCTCTTAAAAACAAATT--A
* * * *
3162402 TCTTGCTTGAGACAATTTCCCTTGAAACACAAATTTTAAAATTATTTAACTCGAAACAAAAATTT
1 TCTTGCTTGAGACAATTCCCCTTGAAACACAAATTTTGAAATTGTTTCACTCG-AA-AAAAATTT
* *
3162467 ATCACTTGAGATAGTTTTTCTTAAAATC-AA-T-
64 ATCACTTGAGATAGTTTCTCTTAAAAACAAATTA
* * * * * *
3162498 T-TTGCTTGAGATAGTTCCCCTTGGAACACAGATTTTGGAATTGTTTCACTTGAAATGAAAATTT
1 TCTTGCTTGAGACAATTCCCCTTGAAACACAAATTTTGAAATTGTTTCACTCGAAA--AAAATTT
3162562 ATC
64 ATC
3162565 TCTTCTCAAA
Statistics
Matches: 137, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
93 1 0.01
94 2 0.01
95 51 0.37
96 1 0.01
99 18 0.13
100 8 0.06
101 47 0.34
102 5 0.04
103 4 0.03
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (97 bp):
TCTTGCTTGAGACAATTCCCCTTGAAACACAAATTTTGAAATTGTTTCACTCGAAAAAAATTTAT
CACTTGAGATAGTTTCTCTTAAAAACAAATTA
Found at i:3163841 original size:22 final size:21
Alignment explanation
Indices: 3163804--3163857 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 21
3163794 ATTGATACTG
*
3163804 GTAGGGTGTATGGATACCATA
1 GTAGGGTGTATCGATACCATA
3163825 GTAGGGTAGTATCGATACCATA
1 GTAGGGT-GTATCGATACCATA
3163847 GTAGGG-GTATC
1 GTAGGGTGTATC
3163858 AATATTGAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 5 0.16
21 7 0.23
22 19 0.61
ACGTcount: A:0.28, C:0.11, G:0.33, T:0.28
Consensus pattern (21 bp):
GTAGGGTGTATCGATACCATA
Found at i:3164344 original size:45 final size:45
Alignment explanation
Indices: 3164292--3164503 Score: 264
Period size: 45 Copynumber: 4.7 Consensus size: 45
3164282 AAAAGATGCC
* *
3164292 ATAGTTGAACTGTATATGGGTCCATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATACT
* * * * * * * *
3164337 ATGGTTGAAATGTATATAGGTGCTTTATAAACGGAAGAGCATGCT
1 ATAGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATACT
*
3164382 AAAGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATACT
* * * *
3164427 AGTA-TTGAAATGTATATGGGTACATTGTCAATAGAAAAGTATACA
1 A-TAGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATACT
*
3164472 ATAGTTGAAGTGTATATGGGTGCATTATCAAC
1 ATAGTTGAAATGTATATGGGTGCATTATCAAC
3164504 CAAAAAGATG
Statistics
Matches: 137, Mismatches: 28, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
44 2 0.01
45 134 0.98
46 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATACT
Found at i:3164528 original size:45 final size:45
Alignment explanation
Indices: 3164292--3164549 Score: 225
Period size: 45 Copynumber: 5.7 Consensus size: 45
3164282 AAAAGATGCC
* * *
3164292 ATAGTTGAACTGTATATGGGTCCATTATCAACAGAAAAGTATACT
1 ATAGTTTAAATGTATATGGGTGCATTATCAACAGAAAAGTATACT
* * * * * * * * *
3164337 ATGGTTGAAATGTATATAGGTGCTTTATAAACGGAAGAGCATGCT
1 ATAGTTTAAATGTATATGGGTGCATTATCAACAGAAAAGTATACT
* *
3164382 AAAGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATACT
1 ATAGTTTAAATGTATATGGGTGCATTATCAACAGAAAAGTATACT
* * * * *
3164427 AGTA-TTGAAATGTATATGGGTACATTGTCAATAGAAAAGTATACA
1 A-TAGTTTAAATGTATATGGGTGCATTATCAACAGAAAAGTATACT
* * **
3164472 ATAGTTGAAGTGTATATGGGTGCATTATCAACCA-AAAAG-ATGTT
1 ATAGTTTAAATGTATATGGGTGCATTATCAA-CAGAAAAGTATACT
* * * *
3164516 ATAGTTTAAAGTGCATATTGGTGTATTATAAACA
1 ATAGTTTAAA-TGTATATGGGTGCATTATCAACA
3164550 TAAATGGAGG
Statistics
Matches: 172, Mismatches: 37, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
44 14 0.08
45 156 0.91
46 2 0.01
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (45 bp):
ATAGTTTAAATGTATATGGGTGCATTATCAACAGAAAAGTATACT
Found at i:3164544 original size:135 final size:135
Alignment explanation
Indices: 3164296--3164549 Score: 312
Period size: 135 Copynumber: 1.9 Consensus size: 135
3164286 GATGCCATAG
* * * * *
3164296 TTGAACTGTATATGGGTCCATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATAGGTGCT
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACAATAGTTGAAATGTATATAGGTGCA
** * * *
3164361 TTATAAACGGAAGAGCATGCTAAAGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATAC
66 TTATAAACCAAAAAGCATGCTAAAGTTGAAATGCATATGGGTGCATTATAAACAGAAAAGTATAC
3164426 TAGTA
131 TAGTA
* * * *
3164431 TTGAAATGTATATGGGTACATTGTCAATAGAAAAGTATACAATAGTTGAAGTGTATATGGGTGCA
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACAATAGTTGAAATGTATATAGGTGCA
* * * * * *
3164496 TTATCAACCAAAAAG-ATGTTATAGTTTAAAGTGCATATTGGTGTATTATAAACA
66 TTATAAACCAAAAAGCATGCTAAAGTTGAAA-TGCATATGGGTGCATTATAAACA
3164550 TAAATGGAGG
Statistics
Matches: 98, Mismatches: 20, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
134 12 0.12
135 86 0.88
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (135 bp):
TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACAATAGTTGAAATGTATATAGGTGCA
TTATAAACCAAAAAGCATGCTAAAGTTGAAATGCATATGGGTGCATTATAAACAGAAAAGTATAC
TAGTA
Found at i:3165316 original size:2 final size:2
Alignment explanation
Indices: 3165309--3165336 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3165299 TGAAGGGATG
3165309 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
3165337 TGTACAACAA
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):
AT
Found at i:3167793 original size:45 final size:46
Alignment explanation
Indices: 3167690--3167805 Score: 173
Period size: 45 Copynumber: 2.5 Consensus size: 46
3167680 GCACCATTGT
* *
3167690 GAATGCATTTTATGCATCAATGCACTAAGGTTTTTATGAAAACATC
1 GAATGCATTTTATGCATCGATGCACTAAGGTTGTTATGAAAACATC
* *
3167736 GAATGCATTTTATGCATTGATGCACTCAGGCTTGTT-TG-AAACATC
1 GAATGCATTTTATGCATCGATGCACTAAGG-TTGTTATGAAAACATC
3167781 GAATGCATTTTATGCATCGATGCAC
1 GAATGCATTTTATGCATCGATGCAC
3167806 CCTTAGTGCA
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
45 31 0.48
46 29 0.45
47 4 0.06
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (46 bp):
GAATGCATTTTATGCATCGATGCACTAAGGTTGTTATGAAAACATC
Found at i:3169732 original size:10 final size:10
Alignment explanation
Indices: 3169717--3169741 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3169707 AAAGGAAGGG
3169717 TTAAATCGAA
1 TTAAATCGAA
3169727 TTAAATCGAA
1 TTAAATCGAA
3169737 TTAAA
1 TTAAA
3169742 ATGGGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (10 bp):
TTAAATCGAA
Found at i:3169894 original size:45 final size:45
Alignment explanation
Indices: 3169830--3170041 Score: 253
Period size: 45 Copynumber: 4.7 Consensus size: 45
3169820 CGAAAGATTA
*
3169830 AAATGCATATGGGTGCATTATCAACAGAAATGTATACTAGAGTTG
1 AAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTG
* * * * **
3169875 AAATGCATATGGATGCATTATCAACACAAGAGCATGTTAGAGTTG
1 AAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTG
* * **
3169920 AAATGTATATGGGTACATTATCAACAGAAAAGTATACTATTGTTG
1 AAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTG
* * * **
3169965 AAATGTATATGGGTACATTGTCAACAGAAAAGTATACTATTGTTG
1 AAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTG
* * *
3170010 AAGTGCATATGGGTGAATTATCAACCGAAAAG
1 AAATGCATATGGGTGCATTATCAACAGAAAAG
3170042 ATGTTATAGT
Statistics
Matches: 143, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 143 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (45 bp):
AAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTG
Found at i:3170059 original size:45 final size:45
Alignment explanation
Indices: 3169830--3170080 Score: 231
Period size: 45 Copynumber: 5.6 Consensus size: 45
3169820 CGAAAGATTA
* * *
3169830 AAATGCATATGGGTGCATTATCAACAGAAATGTATACTAGAGTTG
1 AAATGCATATGGGTGAATTATCAACAGAAAAGTATACTATAGTTG
* * * * * ** *
3169875 AAATGCATATGGATGCATTATCAACACAAGAGCATGTTAGAGTTG
1 AAATGCATATGGGTGAATTATCAACAGAAAAGTATACTATAGTTG
* *
3169920 AAATGTATATGGGT-ACATTATCAACAGAAAAGTATACTATTGTTG
1 AAATGCATATGGGTGA-ATTATCAACAGAAAAGTATACTATAGTTG
* * *
3169965 AAATGTATATGGGT-ACATTGTCAACAGAAAAGTATACTATTGTTG
1 AAATGCATATGGGTGA-ATTATCAACAGAAAAGTATACTATAGTTG
* * ** *
3170010 AAGTGCATATGGGTGAATTATCAACCGAAAAG-ATGTTATAGTTT
1 AAATGCATATGGGTGAATTATCAACAGAAAAGTATACTATAGTTG
* *
3170054 AAAGTGCATACT-GGTGTATTATAAACA
1 AAA-TGCATA-TGGGTGAATTATCAACA
3170081 TAAATAGAGG
Statistics
Matches: 172, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
44 10 0.06
45 160 0.93
46 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (45 bp):
AAATGCATATGGGTGAATTATCAACAGAAAAGTATACTATAGTTG
Found at i:3170075 original size:135 final size:134
Alignment explanation
Indices: 3169830--3170080 Score: 310
Period size: 135 Copynumber: 1.9 Consensus size: 134
3169820 CGAAAGATTA
* * *
3169830 AAATGCATATGGGTGCATTATCAACAGAAATGTATACTAGAGTTGAAATGCATATGGATGCATTA
1 AAATGCATATGGGTACATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGATGAATTA
* * *
3169895 TCAACACAAGAGCATGTTAGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAT
66 TCAACACAAAAGCATGTTAGAGTTGAAATGCATATGGGTA-ATTATAAACAGAAAAGTATACTAT
3169960 TGTTG
130 TGTTG
* * ** * *
3169965 AAATGTATATGGGTACATTGTCAACAGAAAAGTATACTATTGTTGAAGTGCATATGGGTGAATTA
1 AAATGCATATGGGTACATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGATGAATTA
* *
3170030 TCAAC-CGAAAAG-ATGTTATAGTTTAAAGTGCATACTGGTGT-ATTATAAACA
66 TCAACAC-AAAAGCATGTTAGAGTTGAAA-TGCATA-TGG-GTAATTATAAACA
3170081 TAAATAGAGG
Statistics
Matches: 98, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
134 14 0.14
135 79 0.81
136 3 0.03
137 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (134 bp):
AAATGCATATGGGTACATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGATGAATTA
TCAACACAAAAGCATGTTAGAGTTGAAATGCATATGGGTAATTATAAACAGAAAAGTATACTATT
GTTG
Found at i:3170706 original size:68 final size:68
Alignment explanation
Indices: 3170578--3170706 Score: 150
Period size: 68 Copynumber: 1.9 Consensus size: 68
3170568 GAGGCCTAAC
* * * * * ** *
3170578 TGTGCATATGATAGAAATGTGTCATTTATGTCAGTTAGATGAAAGACTAAGTGTCTTTGAGGACT
1 TGTGCATATGACAAAAAGGTGTCAGTTATGCCAGTTAGATGAAAGACTAAGTACCGTTGAGGACT
3170643 AGT
66 AGT
* * **
3170646 TGTGCATTTGACAAAAAGGTGTCAGTTATGCCAGTTAGATGAATGGTTAAGTACCGTTGAG
1 TGTGCATATGACAAAAAGGTGTCAGTTATGCCAGTTAGATGAAAGACTAAGTACCGTTGAG
3170707 TAAAATAATA
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
68 49 1.00
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.33
Consensus pattern (68 bp):
TGTGCATATGACAAAAAGGTGTCAGTTATGCCAGTTAGATGAAAGACTAAGTACCGTTGAGGACT
AGT
Found at i:3171733 original size:139 final size:139
Alignment explanation
Indices: 3171483--3171877 Score: 583
Period size: 139 Copynumber: 2.8 Consensus size: 139
3171473 GATAAACCAG
* * * *
3171483 TCAACATTTCAAGTGGAGAGTTCATAATGAGAATAACTCATCTGATGAGGGAGAAGAACTTCATA
1 TCAACATTTCAAGTGGAGAGATCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
3171548 ATGAGAATAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCA
66 ATGAGAATAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCA
3171613 CTCGAGGGA
131 CTCGAGGGA
* * * *
3171622 TCAACATTTCCAGTGAAGAGATCATAATGAGAAGAACTCGTCCGATGAGGGAAAAGAAGTTCATA
1 TCAACATTTCAAGTGGAGAGATCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
* * *
3171687 ATTAGAATAACTTGTTCAACCTTAACTCGATTCATCACATATGGAGTTGAGTCAGCAACACCTCA
66 ATGAGAATAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCA
*
3171752 CTTGAGGGA
131 CTCGAGGGA
* * * * *
3171761 TCAACGTTTCTAGTGGAGAGCTCATAATGAGAAGAACTCATCCGATAAGTGAGAAGAAGTTCATA
1 TCAACATTTCAAGTGGAGAGATCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
* * * * *
3171826 ATGAGAAGAACTTGTTCAACCTTAGCTTGTTTCCATCGCATAAGGAGTTGAA
66 ATGAGAATAACTTGTTCAACCTTAGCTCGATT-CATCACATATGGAGTTGAA
3171878 ATATCATCGA
Statistics
Matches: 227, Mismatches: 28, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
139 211 0.93
140 16 0.07
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (139 bp):
TCAACATTTCAAGTGGAGAGATCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
ATGAGAATAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCA
CTCGAGGGA
Found at i:3171902 original size:41 final size:42
Alignment explanation
Indices: 3171857--3171958 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
3171847 TTAGCTTGTT
* * *
3171857 TCCATCGCATAAGGAGTTGAA--A-TATCATCGACTTTTGCTCG
1 TCCATCACATAAGGAGTTGAATGAGCATCATC-A-TTTCGCTCG
*
3171898 TCCATCACATAAGGAGTTGGATGAGCATCATCATTTCGCTCG
1 TCCATCACATAAGGAGTTGAATGAGCATCATCATTTCGCTCG
3171940 TCCATCACATAAGGAGTTG
1 TCCATCACATAAGGAGTTG
3171959 GATCATCATC
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
41 19 0.35
42 27 0.50
43 2 0.04
44 6 0.11
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (42 bp):
TCCATCACATAAGGAGTTGAATGAGCATCATCATTTCGCTCG
Found at i:3173554 original size:29 final size:29
Alignment explanation
Indices: 3173521--3173579 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
3173511 GAATTTCTTG
*
3173521 TATTTATATTTCAACA-TCTTTACTTTATT
1 TATTTACATTTCAACACTCTTTA-TTTATT
3173550 TATTTACATTTCAACACCTCTTTATTTATT
1 TATTTACATTTCAACA-CTCTTTATTTATT
3173580 GTCATGTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 15 0.56
30 6 0.22
31 6 0.22
ACGTcount: A:0.27, C:0.17, G:0.00, T:0.56
Consensus pattern (29 bp):
TATTTACATTTCAACACTCTTTATTTATT
Found at i:3175274 original size:12 final size:12
Alignment explanation
Indices: 3175257--3175281 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3175247 TTTTTATATG
3175257 ACGCCGCGTATA
1 ACGCCGCGTATA
3175269 ACGCCGCGTATA
1 ACGCCGCGTATA
3175281 A
1 A
3175282 TGTAACGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.32, G:0.24, T:0.16
Consensus pattern (12 bp):
ACGCCGCGTATA
Found at i:3177233 original size:28 final size:28
Alignment explanation
Indices: 3177191--3177310 Score: 199
Period size: 28 Copynumber: 4.3 Consensus size: 28
3177181 AAGTAGTGAT
3177191 TGTAAAAATAT-AGGTTGTTATTGTAATA
1 TGTAAAAATATGA-GTTGTTATTGTAATA
3177219 TGTAAAAATA-GAGGTTGTTATTGTAATA
1 TGTAAAAATATGA-GTTGTTATTGTAATA
3177247 TGTAAAAATATGAGTTGTTATTGTAATA
1 TGTAAAAATATGAGTTGTTATTGTAATA
*
3177275 TGTAAAAATATGAGTTGTTATTGTAATT
1 TGTAAAAATATGAGTTGTTATTGTAATA
3177303 TGTAAAAA
1 TGTAAAAA
3177311 GTATATGTCA
Statistics
Matches: 89, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
28 87 0.98
29 2 0.02
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (28 bp):
TGTAAAAATATGAGTTGTTATTGTAATA
Found at i:3177277 original size:56 final size:56
Alignment explanation
Indices: 3177191--3177339 Score: 203
Period size: 56 Copynumber: 2.6 Consensus size: 56
3177181 AAGTAGTGAT
3177191 TGTAAAAATATAGGTTGTTATTGTAATATGTAAAAATA-GAGGTTGTTATTGTAATA
1 TGTAAAAATATAGGTTGTTATTGTAATATGTAAAAATATGA-GTTGTTATTGTAATA
*
3177247 TGTAAAAATAT-GAGTTGTTATTGTAATATGTAAAAATATGAGTTGTTATTGTAATT
1 TGTAAAAATATAG-GTTGTTATTGTAATATGTAAAAATATGAGTTGTTATTGTAATA
* ** * *
3177303 TGTAAAAAGTATATGTCATTATTGTAATTTATAAAAA
1 TGTAAAAA-TATAGGTTGTTATTGTAATATGTAAAAA
3177340 GATTTGTTCT
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
55 1 0.01
56 58 0.70
57 24 0.29
ACGTcount: A:0.40, C:0.01, G:0.17, T:0.42
Consensus pattern (56 bp):
TGTAAAAATATAGGTTGTTATTGTAATATGTAAAAATATGAGTTGTTATTGTAATA
Found at i:3177354 original size:29 final size:29
Alignment explanation
Indices: 3177293--3177455 Score: 165
Period size: 29 Copynumber: 5.6 Consensus size: 29
3177283 TATGAGTTGT
* *
3177293 TATTGTAATTTGTAAAAAGTATATG-TCAT-
1 TATTGTAATTTATAAAAAG-ATTTGTTC-TC
3177322 TATTGTAATTTATAAAAAGATTTGTTCTC
1 TATTGTAATTTATAAAAAGATTTGTTCTC
* * *
3177351 TATTTTAAATTATAAAAAGATTTGTTCTT
1 TATTGTAATTTATAAAAAGATTTGTTCTC
* *
3177380 TATTGTAATTTATAAGAAGATTT-ATCTTC
1 TATTGTAATTTATAAAAAGATTTGTTC-TC
*
3177409 TATTATAATTTATAAAAAGATTT-TTC-C
1 TATTGTAATTTATAAAAAGATTTGTTCTC
*
3177436 ATTATTGTAGTTTATAAAAA
1 --TATTGTAATTTATAAAAA
3177456 TCTTTGTCCT
Statistics
Matches: 114, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.01
28 7 0.06
29 106 0.93
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (29 bp):
TATTGTAATTTATAAAAAGATTTGTTCTC
Found at i:3177387 original size:58 final size:58
Alignment explanation
Indices: 3177319--3177455 Score: 188
Period size: 58 Copynumber: 2.4 Consensus size: 58
3177309 AAGTATATGT
* *
3177319 CATTATTGTAATTTATAAAAAGATTTGT-TCTCTATTTTAAATTATAAAAAGATTTGTT-
1 CATTATTGTAATTTATAAAAAGATTTATCT-TCTATTATAAATTATAAAAAGATTT-TTC
* * *
3177377 CTTTATTGTAATTTATAAGAAGATTTATCTTCTATTATAATTTATAAAAAGATTTTTC
1 CATTATTGTAATTTATAAAAAGATTTATCTTCTATTATAAATTATAAAAAGATTTTTC
*
3177435 CATTATTGTAGTTTATAAAAA
1 CATTATTGTAATTTATAAAAA
3177456 TCTTTGTCCT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
57 2 0.03
58 66 0.96
59 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (58 bp):
CATTATTGTAATTTATAAAAAGATTTATCTTCTATTATAAATTATAAAAAGATTTTTC
Found at i:3179452 original size:11 final size:11
Alignment explanation
Indices: 3179434--3179537 Score: 51
Period size: 11 Copynumber: 9.5 Consensus size: 11
3179424 TGTACTAAAT
3179434 ATATAATAAT-
1 ATATAATAATA
3179444 ATAATAATAATAA
1 AT-ATAATAAT-A
*
3179457 ATATATTAATA
1 ATATAATAATA
*
3179468 ATAT-GTAAATA
1 ATATAAT-AATA
* *
3179479 CTATATATATATT
1 ATATA-ATA-ATA
*
3179492 ATATAATACTA
1 ATATAATAATA
3179503 TATATAAT-ATA
1 -ATATAATAATA
3179514 A-A-AATAA-A
1 ATATAATAATA
3179522 ATATAA-AATA
1 ATATAATAATA
3179532 TATATA
1 -ATATA
3179538 TACTATATAT
Statistics
Matches: 72, Mismatches: 9, Indels: 25
0.68 0.08 0.24
Matches are distributed among these distances:
8 5 0.07
9 5 0.07
10 7 0.10
11 28 0.39
12 18 0.25
13 9 0.12
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (11 bp):
ATATAATAATA
Found at i:3179459 original size:15 final size:15
Alignment explanation
Indices: 3179431--3179470 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3179421 AATTGTACTA
3179431 AATATATAAT-AATAT
1 AATA-ATAATAAATAT
3179446 AATAATAATAAATAT
1 AATAATAATAAATAT
*
3179461 ATTAATAATA
1 AATAATAATA
3179471 TGTAAATACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAATAATAAATAT
Found at i:3179478 original size:26 final size:27
Alignment explanation
Indices: 3179429--3179499 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 27
3179419 ATAATTGTAC
3179429 TAAATATA-TAATAATATAATAATA-A
1 TAAATATATTAATAATATAATAATACA
*
3179454 TAAATATATTAATAATAT-GTAAATACTA
1 TAAATATATTAATAATATAAT-AATAC-A
*
3179482 TATATATATTATATAATA
1 TAAATATATTA-ATAATA
3179500 CTATATATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
25 9 0.23
26 13 0.33
28 11 0.28
29 6 0.15
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (27 bp):
TAAATATATTAATAATATAATAATACA
Found at i:3179512 original size:7 final size:7
Alignment explanation
Indices: 3179431--3179617 Score: 82
Period size: 7 Copynumber: 25.7 Consensus size: 7
3179421 AATTGTACTA
3179431 AATATAT
1 AATATAT
3179438 AATAATAT
1 AAT-ATAT
3179446 AATA-AT
1 AATATAT
*
3179452 AATAAAT
1 AATATAT
3179459 -ATATTAAT
1 AATA-T-AT
*
3179467 AATATGT
1 AATATAT
3179474 AA-ATACT
1 AATATA-T
3179481 ATATATAT
1 A-ATATAT
*
3179489 ATTATAT
1 AATATAT
*
3179496 AATA-CT
1 AATATAT
3179502 -ATATAT
1 AATATAT
3179508 AATATA-
1 AATATAT
* *
3179514 AAAATAA
1 AATATAT
*
3179521 AATATAA
1 AATATAT
3179528 AATATAT
1 AATATAT
3179535 ATATACTAT
1 A-ATA-TAT
3179544 ATATACTAT
1 A-ATA-TAT
*
3179553 ATTATAT
1 AATATAT
* *
3179560 AAAATAA
1 AATATAT
3179567 AATATAT
1 AATATAT
3179574 AAATACTATTT
1 -AATA-TA--T
*
3179585 ACTATAT
1 AATATAT
*
3179592 AAAATAT
1 AATATAT
3179599 AATATACT
1 AATATA-T
*
3179607 TATATA-
1 AATATAT
3179613 AATAT
1 AATAT
3179618 TATGTGTGTA
Statistics
Matches: 140, Mismatches: 22, Indels: 37
0.70 0.11 0.19
Matches are distributed among these distances:
5 3 0.02
6 22 0.16
7 60 0.43
8 28 0.20
9 23 0.16
10 3 0.02
11 1 0.01
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.40
Consensus pattern (7 bp):
AATATAT
Found at i:3179536 original size:52 final size:52
Alignment explanation
Indices: 3179426--3179582 Score: 159
Period size: 50 Copynumber: 3.1 Consensus size: 52
3179416 TTAATAATTG
* * * ** * *
3179426 TACTAAATATATAATAATATAATAATA-ATA-AATATATTAATAATATGTAAA
1 TACTATATATATACT-ATATAATACTATATATAATATAAAAATAAAATATAAA
*
3179477 TACTATATATATATTATATAATACTATATATAATATAAAAATAAAATATAAA
1 TACTATATATATACTATATAATACTATATATAATATAAAAATAAAATATAAA
3179529 -A-TATATATATACTATAT-ATACTATAT-T-ATAT-AAAATAAAATATATAAA
1 TACTATATATATACTATATAATACTATATATAATATAAAAAT-AAA-ATATAAA
3179577 TACTAT
1 TACTAT
3179583 TTACTATATA
Statistics
Matches: 92, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
46 5 0.05
47 7 0.08
48 8 0.09
49 10 0.11
50 28 0.30
51 17 0.18
52 17 0.18
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.39
Consensus pattern (52 bp):
TACTATATATATACTATATAATACTATATATAATATAAAAATAAAATATAAA
Found at i:3179567 original size:39 final size:40
Alignment explanation
Indices: 3179505--3179604 Score: 111
Period size: 39 Copynumber: 2.6 Consensus size: 40
3179495 TAATACTATA
*
3179505 TATAATATA-AAAATAAAATATAAAATATATATATACTATA
1 TATACTATATAAAATAAAATATAAAATATATA-ATACTATA
* *
3179545 TATACTATATTATAT-AAA-ATAAAATATATAAATACTAT-
1 TATACTATATAAAATAAAATATAAAATATAT-AATACTATA
*
3179583 T-TACTATATAAAATATAATATA
1 TATACTATATAAAATAAAATATA
3179605 CTTATATAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
37 11 0.22
38 3 0.06
39 21 0.42
40 12 0.24
41 3 0.06
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (40 bp):
TATACTATATAAAATAAAATATAAAATATATAATACTATA
Found at i:3179574 original size:2 final size:2
Alignment explanation
Indices: 3179432--3179560 Score: 61
Period size: 2 Copynumber: 69.5 Consensus size: 2
3179422 ATTGTACTAA
*
3179432 AT AT AT A- AT A- AT AT A- AT A- AT A- AT AA AT AT AT -T A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
3179467 A- AT AT GT AA AT ACT AT AT AT AT AT -T AT AT A- AT ACT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * *
3179508 A- AT AT AA AA AT A- AA AT AT A- AA AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
3179548 ACT AT AT -T AT AT A
1 A-T AT AT AT AT AT A
3179561 AAATAAAATA
Statistics
Matches: 99, Mismatches: 10, Indels: 36
0.68 0.07 0.25
Matches are distributed among these distances:
1 14 0.14
2 77 0.78
3 8 0.08
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (2 bp):
AT
Found at i:3179615 original size:19 final size:17
Alignment explanation
Indices: 3179441--3179617 Score: 77
Period size: 19 Copynumber: 10.3 Consensus size: 17
3179431 AATATATAAT
*
3179441 AATATA-ATAATA-ATA
1 AATATATATACTATATA
* *
3179456 AATATATTAATAATATGTA
1 AATATA-T-ATACTATATA
3179475 AATACTATATA-TATAT-
1 AATA-TATATACTATATA
*
3179491 TATATA-ATACTATATA
1 AATATATATACTATATA
* **
3179507 TAATATAAAAATAAAATATA
1 -AATAT--ATATACTATATA
3179527 AA-ATATATA-TATACTA
1 AATATATATACTATA-TA
* *
3179543 TATATACTATATTATATA
1 AATATA-TATACTATATA
*
3179561 AA-ATA-A-AATATATA
1 AATATATATACTATATA
*
3179575 AATACTATTTACTATATAA
1 AATA-TATATACTATAT-A
3179594 AATATAATATACTTATATA
1 AATAT-ATATAC-TATATA
3179613 AATAT
1 AATAT
3179618 TATGTGTGTA
Statistics
Matches: 126, Mismatches: 14, Indels: 40
0.70 0.08 0.22
Matches are distributed among these distances:
14 12 0.10
15 18 0.14
16 12 0.10
17 14 0.11
18 25 0.20
19 30 0.24
20 15 0.12
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.40
Consensus pattern (17 bp):
AATATATATACTATATA
Found at i:3181294 original size:2 final size:2
Alignment explanation
Indices: 3181287--3181317 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3181277 ATAAATGGTT
3181287 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3181318 TTACTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3185104 original size:20 final size:21
Alignment explanation
Indices: 3185079--3185171 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
3185069 TTTTCCCAAT
*
3185079 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3185099 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
3185120 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3185140 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3185161 TCGCAATGCGA
1 TCGCAATGCGA
3185172 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3185124 original size:41 final size:41
Alignment explanation
Indices: 3185079--3185171 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
3185069 TTTTCCCAAT
3185079 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
3185120 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
3185161 TCGCAATGCGA
1 TCGCAATGCGA
3185172 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:3185184 original size:41 final size:41
Alignment explanation
Indices: 3185098--3185232 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
3185088 GAATAAGTAA
** *
3185098 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
3185139 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
3185180 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
3185221 TTCGCAACGCGA
1 ATCGCAACGCGA
3185233 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:3185185 original size:20 final size:20
Alignment explanation
Indices: 3185160--3185253 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
3185150 AATTGGGAAA
*
3185160 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
3185180 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
3185201 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
3185221 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
3185241 TTCGCAACGCGAT
1 ATCGCAACGCGAT
3185254 TTACATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:3185469 original size:22 final size:22
Alignment explanation
Indices: 3185441--3185484 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3185431 CACTCTCTCA
3185441 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
3185463 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
3185485 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:3187041 original size:18 final size:18
Alignment explanation
Indices: 3187020--3187064 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3187010 TCCACTTCGG
* *
3187020 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
3187038 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
3187056 GAGCCATCA
1 GAGCCATCA
3187065 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:3187590 original size:20 final size:20
Alignment explanation
Indices: 3187537--3187590 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
3187527 TAGTTTACTT
3187537 TCGCAAC-ACGAAATGACTA
1 TCGCAACGACGAAATGACTA
*
3187556 TCGCAACG-CGGAAATGGCTA
1 TCGCAACGAC-GAAATGACTA
*
3187576 TCGCAACGACAAAAT
1 TCGCAACGACGAAAT
3187591 CGCAACGCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 8 0.27
20 21 0.70
21 1 0.03
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACGACGAAATGACTA
Found at i:3187594 original size:14 final size:14
Alignment explanation
Indices: 3187575--3187629 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
3187565 GGAAATGGCT
3187575 ATCGCAACGACAAA
1 ATCGCAACGACAAA
*
3187589 ATCGCAACGCGAAATGAA
1 ATCGCAA--CGACA--AA
3187607 ATCGCAACGACAAA
1 ATCGCAACGACAAA
3187621 ATCGCAACG
1 ATCGCAACG
3187630 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 18 0.51
16 8 0.23
18 9 0.26
ACGTcount: A:0.45, C:0.27, G:0.18, T:0.09
Consensus pattern (14 bp):
ATCGCAACGACAAA
Found at i:3187616 original size:32 final size:32
Alignment explanation
Indices: 3187555--3187646 Score: 139
Period size: 32 Copynumber: 2.8 Consensus size: 32
3187545 CGAAATGACT
**
3187555 ATCGCAACGCGGAAATGGCTATCGCAACGACAAA
1 ATCGCAACGC-GAAAT-GAAATCGCAACGACAAA
3187589 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
3187621 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATG-AAATCGCAA
3187647 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 31 0.56
33 14 0.25
34 10 0.18
ACGTcount: A:0.43, C:0.25, G:0.21, T:0.11
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:3187640 original size:19 final size:19
Alignment explanation
Indices: 3187586--3187651 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
3187576 TCGCAACGAC
3187586 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
3187605 -AAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAATG
3187618 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
3187637 AAAATCGCAATGCGA
1 AAAATCGCAACGCGA
3187652 TTTGTGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
14 10 0.26
16 4 0.11
18 10 0.26
19 14 0.37
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:3187682 original size:14 final size:14
Alignment explanation
Indices: 3187663--3187720 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3187653 TTGTGTTTCG
3187663 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3187677 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
3187693 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
3187709 CGTTGCGATTTT
1 CGTTGCGATTTT
3187721 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3187697 original size:32 final size:33
Alignment explanation
Indices: 3187658--3187736 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
3187648 GCGATTTGTG
3187658 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
3187690 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
3187723 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
3187737 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:3187735 original size:19 final size:19
Alignment explanation
Indices: 3187677--3187794 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
3187667 GCGATTTTGT
3187677 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3187695 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
3187709 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
3187728 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
3187748 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3187767 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
3187787 TGTTGCGA
1 CGTTGCGA
3187795 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:3189788 original size:19 final size:19
Alignment explanation
Indices: 3189764--3189917 Score: 220
Period size: 19 Copynumber: 8.6 Consensus size: 19
3189754 AAAACAGACT
* *
3189764 ATCGCAACGCGAAATGGAA
1 ATCGCAATGCGAAATGAAA
3189783 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3189802 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3189821 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3189840 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
3189854 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3189873 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3189892 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
3189906 ATCGCAATGCGA
1 ATCGCAATGCGA
3189918 TTTTCATTTC
Statistics
Matches: 125, Mismatches: 2, Indels: 18
0.86 0.01 0.12
Matches are distributed among these distances:
14 22 0.18
15 2 0.02
16 4 0.03
17 4 0.03
18 1 0.01
19 92 0.74
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3189936 original size:52 final size:52
Alignment explanation
Indices: 3189764--3189917 Score: 245
Period size: 52 Copynumber: 2.9 Consensus size: 52
3189754 AAAACAGACT
* *
3189764 ATCGCAACGCGAAATGGAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAA
3189821 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
3189873 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGA
3189918 TTTTCATTTC
Statistics
Matches: 95, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
52 68 0.72
53 1 0.01
55 2 0.02
57 24 0.25
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
Found at i:3189936 original size:71 final size:69
Alignment explanation
Indices: 3189781--3189912 Score: 225
Period size: 71 Copynumber: 1.9 Consensus size: 69
3189771 CGCGAAATGG
3189781 AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCA
3189846 ACGAGA
64 ACGAGA
3189852 AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAAAATCGCAA
1 AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAA
3189913 TGCGATTTTC
Statistics
Matches: 61, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
66 11 0.18
67 1 0.02
69 2 0.03
71 47 0.77
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.14
Consensus pattern (69 bp):
AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAAC
GAGA
Found at i:3191036 original size:24 final size:24
Alignment explanation
Indices: 3191009--3191062 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3190999 GTATTCGAAA
* *
3191009 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
3191033 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
3191057 TTTGAT
1 TTTGAT
3191063 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:3191254 original size:12 final size:12
Alignment explanation
Indices: 3191237--3191261 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3191227 ATATAATCCT
3191237 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3191249 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3191261 G
1 G
3191262 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3193605 original size:19 final size:19
Alignment explanation
Indices: 3193550--3193679 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
3193540 GGAAATTACT
3193550 ATCGCAATGCGAAAT-AAA
1 ATCGCAATGCGAAATGAAA
*
3193568 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3193582 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
3193601 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
3193615 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
3193634 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
3193648 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3193667 ATCGCAACGCGAA
1 ATCGCAATGCGAA
3193680 TTTAATTTTG
Statistics
Matches: 83, Mismatches: 13, Indels: 31
0.65 0.10 0.24
Matches are distributed among these distances:
14 27 0.33
15 2 0.02
16 8 0.10
17 4 0.05
18 10 0.12
19 32 0.39
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3193607 original size:33 final size:33
Alignment explanation
Indices: 3193550--3193675 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
3193540 GGAAATTACT
3193550 ATCGCAATGCGAAAT-AAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
3193582 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
3193614 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3193648 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
3193676 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
32 16 0.19
33 67 0.80
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3193644 original size:66 final size:65
Alignment explanation
Indices: 3193551--3193682 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 65
3193541 GAAATTACTA
*
3193551 TCGCAATGCGAAATAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATT
*
3193616 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAAT-AAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
3193681 T
65 T
3193682 T
1 T
3193683 AATTTTGCGT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 14 0.22
66 50 0.78
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (65 bp):
TCGCAATGCGAAATAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATT
Found at i:3193878 original size:14 final size:14
Alignment explanation
Indices: 3193859--3193895 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3193849 CATCAATTAA
3193859 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3193873 ACAAATCACCTTTT
1 ACAAATCAACTTTT
3193887 ACAAATCAA
1 ACAAATCAA
3193896 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3195318 original size:21 final size:21
Alignment explanation
Indices: 3195252--3195318 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3195242 GTGAATCGGG
*
3195252 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
3195272 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
3195294 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
3195315 CTCT
1 CTCT
3195319 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:3195337 original size:42 final size:41
Alignment explanation
Indices: 3195252--3195374 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
3195242 GTGAATCGGG
* * * * *
3195252 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
3195294 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
3195336 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
3195375 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:3197461 original size:19 final size:19
Alignment explanation
Indices: 3197378--3197470 Score: 70
Period size: 19 Copynumber: 5.1 Consensus size: 19
3197368 TCTTTTGGTT
*
3197378 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
3197397 GATAATGAGAATCGCAATGC
1 GA-AATGAAAATCGCAACGC
** *
3197417 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
3197435 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3197450 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
3197469 GA
1 GA
3197471 TTTTGGTTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
14 10 0.18
15 2 0.04
18 2 0.04
19 27 0.47
20 16 0.28
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3198134 original size:20 final size:20
Alignment explanation
Indices: 3198041--3198134 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
3198031 CGCTATGTAA
* *
3198041 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
3198061 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* * *
3198081 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTAAGT
*
3198102 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
3198122 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
3198135 TTTCCCAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 45 0.73
21 12 0.19
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:3198152 original size:21 final size:21
Alignment explanation
Indices: 3198123--3198215 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
3198113 ATAGTAAGTA
3198123 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
3198144 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
3198164 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
3198185 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
3198205 TCGCATTGCGA
1 TCGCATTGCGA
3198216 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:3198153 original size:41 final size:41
Alignment explanation
Indices: 3198062--3198196 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
3198052 AAAGTCAGTA
* * * ** *
3198062 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
3198102 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
3198144 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
3198185 TCGCGTTGCGAT
1 TCGCGTTGCGAT
3198197 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:3198197 original size:41 final size:41
Alignment explanation
Indices: 3198123--3198215 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
3198113 ATAGTAAGTA
3198123 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
3198164 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
3198205 TCGCATTGCGA
1 TCGCATTGCGA
3198216 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:3203423 original size:11 final size:11
Alignment explanation
Indices: 3203407--3203433 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3203397 ATCTCCCAAT
3203407 TTTTCTTTTTA
1 TTTTCTTTTTA
3203418 TTTTCTTTTTA
1 TTTTCTTTTTA
3203429 TTTTC
1 TTTTC
3203434 CCACTCCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTCTTTTTA
Found at i:3203528 original size:12 final size:12
Alignment explanation
Indices: 3203511--3203538 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3203501 TTTGTTCACC
3203511 CCCTAGGTTTTT
1 CCCTAGGTTTTT
3203523 CCCTAGGTTTTT
1 CCCTAGGTTTTT
3203535 CCCT
1 CCCT
3203539 TGTATCCCCA
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:0.07, C:0.32, G:0.14, T:0.46
Consensus pattern (12 bp):
CCCTAGGTTTTT
Found at i:3204154 original size:20 final size:20
Alignment explanation
Indices: 3204117--3204156 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3204107 ATAAAACTAT
*
3204117 TTTTTATTATATTATATTTG
1 TTTTTATTATATGATATTTG
3204137 TTTTTA-TATATGATTATTTG
1 TTTTTATTATATGA-TATTTG
3204157 AAAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (20 bp):
TTTTTATTATATGATATTTG
Found at i:3205138 original size:60 final size:60
Alignment explanation
Indices: 3205045--3205164 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 60
3205035 CATTTGACAC
* * * * *
3205045 GATGCCTTCAAGTTTCAATAGGAGGCATTCAACTGCGAGCTTCTTCGACCTCAATGTCAA
1 GATGCCTTCAAGTTTCAAGAGGAGGCATGCAACTACCAGCTTCTTCGACCTAAATGTCAA
* *
3205105 GATGCCTTCAAG-TTCAAGGGGAAGGCATGCAACTACCAGCTTGTTCGACCTAAATGTCAA
1 GATGCCTTCAAGTTTCAAGAGG-AGGCATGCAACTACCAGCTTCTTCGACCTAAATGTCAA
3205165 CATCGTAGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
59 7 0.13
60 45 0.87
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (60 bp):
GATGCCTTCAAGTTTCAAGAGGAGGCATGCAACTACCAGCTTCTTCGACCTAAATGTCAA
Found at i:3207552 original size:28 final size:26
Alignment explanation
Indices: 3207500--3207560 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
3207490 TAAAAAGAAC
* *
3207500 TAAATAATAAAAACAATTTGAACAAT
1 TAAATAATAAAAACAATTAGAACAAA
3207526 TAAATAATAATAAA-AATTAAGAAACAAA
1 TAAATAATAA-AAACAATT-AG-AACAAA
3207554 TAAATAA
1 TAAATAA
3207561 AAAGTACATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 14 0.47
27 4 0.13
28 12 0.40
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (26 bp):
TAAATAATAAAAACAATTAGAACAAA
Found at i:3211474 original size:22 final size:22
Alignment explanation
Indices: 3211449--3211497 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3211439 AATAAAATAA
* * *
3211449 AAACAGTAACCAAATTATAATT
1 AAACAGTAACAAAAATATAATC
*
3211471 AAACAGTGACAAAAATATAATC
1 AAACAGTAACAAAAATATAATC
3211493 AAACA
1 AAACA
3211498 AAAACAACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.59, C:0.14, G:0.06, T:0.20
Consensus pattern (22 bp):
AAACAGTAACAAAAATATAATC
Found at i:3215367 original size:16 final size:16
Alignment explanation
Indices: 3215343--3215384 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3215333 CTTTTTTTAA
*
3215343 TTTAGTTATAATATTC
1 TTTATTTATAATATTC
*
3215359 TTTATTTAT-TTATTC
1 TTTATTTATAATATTC
3215374 TTTATATTATA
1 TTTAT-TTATA
3215385 GATTAGATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (16 bp):
TTTATTTATAATATTC
Found at i:3215374 original size:15 final size:16
Alignment explanation
Indices: 3215354--3215383 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3215344 TTAGTTATAA
3215354 TATTCTTTAT-TTATT
1 TATTCTTTATATTATT
3215369 TATTCTTTATATTAT
1 TATTCTTTATATTAT
3215384 AGATTAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTCTTTATATTATT
Found at i:3215597 original size:16 final size:17
Alignment explanation
Indices: 3215569--3215604 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
3215559 GATATAAGAA
3215569 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
3215586 AAATTC-ATTTAATTTT
1 AAATTCAATTTAAATTT
3215602 AAA
1 AAA
3215605 ATAACATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:3215606 original size:17 final size:18
Alignment explanation
Indices: 3215568--3215606 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
3215558 AGATATAAGA
3215568 AAAATTCAATTTAAATTT
1 AAAATTCAATTTAAATTT
*
3215586 -AAATTC-ATTTAATTTT
1 AAAATTCAATTTAAATTT
3215602 AAAAT
1 AAAAT
3215607 AACATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATTCAATTTAAATTT
Found at i:3215787 original size:30 final size:30
Alignment explanation
Indices: 3215751--3215807 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
3215741 ATATTTCAGA
*
3215751 TAATTTAAAGTTTGTTGAGGTGTTACGGTG
1 TAATTTAAAGCTTGTTGAGGTGTTACGGTG
* *
3215781 TAATTTATAGCTTGTTGCGGTGTTACG
1 TAATTTAAAGCTTGTTGAGGTGTTACG
3215808 TAATAGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.21, C:0.07, G:0.28, T:0.44
Consensus pattern (30 bp):
TAATTTAAAGCTTGTTGAGGTGTTACGGTG
Found at i:3222416 original size:16 final size:17
Alignment explanation
Indices: 3222385--3222419 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3222375 CGTATCGCCG
*
3222385 ACAAAATTTTACTATTC
1 ACAAAATTTCACTATTC
3222402 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
3222418 AC
1 AC
3222420 TATTTACCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:3222930 original size:34 final size:34
Alignment explanation
Indices: 3222850--3222949 Score: 119
Period size: 34 Copynumber: 2.9 Consensus size: 34
3222840 ATTTTTCAAC
* * * *
3222850 AAACATCTACCAAACTTTGAAAAACTATTTTTTAAAG
1 AAACATTTACCAAACTTTG-AAAACCA--TTTAAAAA
*
3222887 AAACATTTACCAAAATTTGAAAACCATTTAAAAA
1 AAACATTTACCAAACTTTGAAAACCATTTAAAAA
*
3222921 AAACATTTACCAAACTTTGAAAATCATTT
1 AAACATTTACCAAACTTTGAAAACCATTT
3222950 TTTCAAAGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
34 33 0.59
36 6 0.11
37 17 0.30
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (34 bp):
AAACATTTACCAAACTTTGAAAACCATTTAAAAA
Found at i:3224542 original size:6 final size:6
Alignment explanation
Indices: 3224531--3224561 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3224521 TTGTATTCCT
3224531 CACCAA CACCAA CACCAA CACCAA CACCAA C
1 CACCAA CACCAA CACCAA CACCAA CACCAA C
3224562 TTGCGGATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (6 bp):
CACCAA
Found at i:3231973 original size:31 final size:31
Alignment explanation
Indices: 3231938--3231997 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
3231928 GCTTTGGGAC
* *
3231938 AAATCGAACGGATCGAGAACATTAGGGATTA
1 AAATCGAACGAATCAAGAACATTAGGGATTA
* * *
3231969 AAATCGGACGAATCAATAACGTTAGGGAT
1 AAATCGAACGAATCAAGAACATTAGGGAT
3231998 CATTTCCCCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.20
Consensus pattern (31 bp):
AAATCGAACGAATCAAGAACATTAGGGATTA
Found at i:3232852 original size:32 final size:32
Alignment explanation
Indices: 3232798--3232858 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
3232788 TGCATTTTCT
* * *
3232798 GTATTGAAGGTTGATGAAGATTTATGAATTGA
1 GTATTGAAGCTAGAAGAAGATTTATGAATTGA
*
3232830 GTATTGAAGCTAGAAGATGATTTATGAAT
1 GTATTGAAGCTAGAAGAAGATTTATGAAT
3232859 GGATCTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (32 bp):
GTATTGAAGCTAGAAGAAGATTTATGAATTGA
Found at i:3234839 original size:29 final size:29
Alignment explanation
Indices: 3234778--3234839 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
3234768 TTAGATCAAC
* **
3234778 TTTTTTCTTTTGTTTAAAATTTTCTCTC-
1 TTTTTTCTTTTGTTGAAAATTTTCAATCA
*
3234806 TTTTTTTTTGTTGTTGAAAATTTTCAATCA
1 TTTTTTCTT-TTGTTGAAAATTTTCAATCA
3234836 TTTT
1 TTTT
3234840 CGAGATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 8 0.29
29 16 0.57
30 4 0.14
ACGTcount: A:0.18, C:0.10, G:0.06, T:0.66
Consensus pattern (29 bp):
TTTTTTCTTTTGTTGAAAATTTTCAATCA
Found at i:3237242 original size:25 final size:26
Alignment explanation
Indices: 3237210--3237275 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 26
3237200 AGGAAAAAGG
*
3237210 AAAG-AAAAAATAAAATAGAT-GAAA
1 AAAGAAAAAAATAAAATAAATAGAAA
* * * *
3237234 AAGGAAAAATATTAAATAAATATAAA
1 AAAGAAAAAAATAAAATAAATAGAAA
*
3237260 AAAGAATAAAATAAAA
1 AAAGAAAAAAATAAAA
3237276 ATATTAATAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
24 3 0.10
25 13 0.42
26 15 0.48
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (26 bp):
AAAGAAAAAAATAAAATAAATAGAAA
Found at i:3237284 original size:17 final size:18
Alignment explanation
Indices: 3237238--3237284 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 18
3237228 ATGAAAAAGG
3237238 AAAAATATTAAATAAATAT
1 AAAAATATT-AATAAATAT
*
3237257 AAAAA-A-GAATAAA-AT
1 AAAAATATTAATAAATAT
3237272 AAAAATATTAATA
1 AAAAATATTAATA
3237285 TAACAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 7 0.29
16 7 0.29
17 4 0.17
18 1 0.04
19 5 0.21
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAAATATTAATAAATAT
Found at i:3237364 original size:17 final size:17
Alignment explanation
Indices: 3237258--3237364 Score: 51
Period size: 17 Copynumber: 6.2 Consensus size: 17
3237248 AATAAATATA
*
3237258 AAAAAGAATAAAATAA-
1 AAAAATAATAAAATAAT
* * *
3237274 AAATATTAATATAACAAT
1 AAA-AATAATAAAATAAT
* *
3237292 AATAATAATATATATAAT
1 AAAAATAATA-AAATAAT
*
3237310 AAATAACAA-AGAAA-AAT
1 AAA-AATAATA-AAATAAT
* * *
3237327 AAAAGTTTATAAAA-AAG
1 AAAA-ATAATAAAATAAT
3237344 AAAAATAATAAAATAAT
1 AAAAATAATAAAATAAT
3237361 AAAA
1 AAAA
3237365 TAAAAGAATA
Statistics
Matches: 64, Mismatches: 20, Indels: 13
0.66 0.21 0.13
Matches are distributed among these distances:
16 11 0.17
17 37 0.58
18 12 0.19
19 4 0.06
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (17 bp):
AAAAATAATAAAATAAT
Found at i:3237364 original size:23 final size:22
Alignment explanation
Indices: 3237311--3237378 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 22
3237301 ATATATAATA
**
3237311 AATAACAAAGAAAAATAAAAGTT
1 AATAA-AAAGAAAAATAAAAAAT
*
3237334 TATAAAAAAGAAAAATAATAAAAT
1 AAT-AAAAAGAAAAATAA-AAAAT
3237358 AATAAAATA-AAAGAATAAAAA
1 AATAAAA-AGAAA-AATAAAAA
3237379 TAAAAGTGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
23 24 0.65
24 13 0.35
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (22 bp):
AATAAAAAGAAAAATAAAAAAT
Found at i:3238831 original size:33 final size:34
Alignment explanation
Indices: 3238756--3238841 Score: 149
Period size: 34 Copynumber: 2.6 Consensus size: 34
3238746 TTTGTTTTTG
3238756 TTTTTGTGTTTCAAGAGAAACGATTTCAAAGGTT
1 TTTTTGTGTTTCAAGAGAAACGATTTCAAAGGTT
*
3238790 TTTTTGTGTTTTAAGAGAAACGATTTCAAAGG-T
1 TTTTTGTGTTTCAAGAGAAACGATTTCAAAGGTT
3238823 TTTTTGTGTTTCAAG-GAAA
1 TTTTTGTGTTTCAAGAGAAA
3238842 ACTGTCTCAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 4 0.08
33 15 0.30
34 31 0.62
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (34 bp):
TTTTTGTGTTTCAAGAGAAACGATTTCAAAGGTT
Found at i:3238881 original size:37 final size:37
Alignment explanation
Indices: 3238829--3239022 Score: 352
Period size: 37 Copynumber: 5.2 Consensus size: 37
3238819 AGGTTTTTTG
*
3238829 TGTTTCAAGGAAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
*
3238866 TGTTTCAAGGGAAACTGTCTCAAGAGATACAAGATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
3238903 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
*
3238940 TGTTTCAAGGGAATCTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
*
3238977 TGTTTCAAGGGAAACTGTCCCAAGAGAGACAAGATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
3239014 TGTTTCAAG
1 TGTTTCAAG
3239023 TTGGGTCAAT
Statistics
Matches: 151, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 151 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
Found at i:3239591 original size:110 final size:110
Alignment explanation
Indices: 3239448--3239651 Score: 309
Period size: 110 Copynumber: 1.9 Consensus size: 110
3239438 TGGGAAATTG
* * *
3239448 TTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTATCTTGAGTCTAATATCC
1 TTTGTTGACAATCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTATCTTGAGTCCAATATCC
*
3239513 TTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTA
66 TTCGCTGTAAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTA
* * * * * *
3239558 TTTGTTGGCAATCAGCCGCCCTTTTATTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCC
1 TTTGTTGACAATCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTATCTTGAGTCCAATATCC
*
3239623 TTCGCTGTAAAGTTGAAATTGGCTCTGAA
66 TTCGCTGTAAAGTTGAAATTGACTCTGAA
3239652 ATTGGGAAGC
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
110 83 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.36
Consensus pattern (110 bp):
TTTGTTGACAATCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTATCTTGAGTCCAATATCC
TTCGCTGTAAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTA
Found at i:3241071 original size:83 final size:85
Alignment explanation
Indices: 3240962--3241188 Score: 219
Period size: 95 Copynumber: 2.6 Consensus size: 85
3240952 GGCTAGCTGG
* * * *
3240962 ATCCATAAAGTCGGGGTGTTTTACCAATTGCTCTATAGGGACAACTCAATAT-GTA-AAT-ACCT
1 ATCCATAAAGCCGGGAT-TTTAACCAATTGCTCTAGAGGGACAACTCAATATAGTATAATCACCT
* *
3241024 TTATCAGGTTAGCTGAATCTT
65 TTATCAGGCTAGCTGAATATT
*
3241045 ATCCATAAAGCCGAGGATTTTAACCAATTGC-CTTAGAGGGACATCTCAAGCTTTATTATATAGT
1 ATCCATAAAGCCG-GGATTTTAACCAATTGCTC-TAGAGGG--A---CAA-C-TCA--ATATAGT
3241109 ATAATCACCTTTATCAGGCTAGCTGAATATT
55 ATAATCACCTTTATCAGGCTAGCTGAATATT
* **
3241140 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA
1 ATCCATAAAGC-CGGGATTTTAACCAATTGCTCTAGAGGGACAACTCAA
3241189 GCTTTATTAT
Statistics
Matches: 117, Mismatches: 11, Indels: 29
0.75 0.07 0.18
Matches are distributed among these distances:
82 1 0.01
83 30 0.26
84 3 0.03
85 1 0.01
86 1 0.01
88 5 0.04
89 2 0.02
90 5 0.04
92 4 0.03
93 4 0.03
94 3 0.03
95 56 0.48
96 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (85 bp):
ATCCATAAAGCCGGGATTTTAACCAATTGCTCTAGAGGGACAACTCAATATAGTATAATCACCTT
TATCAGGCTAGCTGAATATT
Found at i:3241188 original size:95 final size:95
Alignment explanation
Indices: 3241020--3241201 Score: 285
Period size: 95 Copynumber: 1.9 Consensus size: 95
3241010 ATATGTAAAT
* * *
3241020 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCCGAGGATTTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGAGTTTAACCAATTGCCTTAGAGGG
*
3241085 ACATCTCAAGCTTTATTATATAGTATAATC
66 ACAACTCAAGCTTTATTATATAGTATAATC
* * *
3241115 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCTGGGGCGTTTAACCAATTG-CTCTAGAGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGAGTTTAACCAATTGCCT-TAGAGG
3241179 GACAACTCAAGCTTTATTATATA
65 GACAACTCAAGCTTTATTATATA
3241202 TAAATAATAT
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
94 2 0.03
95 77 0.97
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGAGTTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTATATAGTATAATC
Found at i:3243349 original size:45 final size:46
Alignment explanation
Indices: 3243264--3243351 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
3243254 AAATAGCCTG
* *
3243264 AGTGCATAGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTA
1 AGTGCATAGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
*
3243310 AGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCATAGATGCATGGTCATGTGCATCGATGCATAAAATGCA
3243352 TTTGATGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 22 0.56
46 17 0.44
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (46 bp):
AGTGCATAGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
Found at i:3249824 original size:15 final size:15
Alignment explanation
Indices: 3249804--3249841 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
3249794 ACTCTTCTAG
3249804 TTTGATTTGTAAATC
1 TTTGATTTGTAAATC
3249819 TTTGATTTGTAAATC
1 TTTGATTTGTAAATC
3249834 TTTGATTT
1 TTTGATTT
3249842 TACTTTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.24, C:0.05, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTGATTTGTAAATC
Found at i:3251941 original size:20 final size:20
Alignment explanation
Indices: 3251916--3251985 Score: 140
Period size: 20 Copynumber: 3.5 Consensus size: 20
3251906 GCCTGAGTGA
3251916 ATCGATGCATGGTCTTGTGC
1 ATCGATGCATGGTCTTGTGC
3251936 ATCGATGCATGGTCTTGTGC
1 ATCGATGCATGGTCTTGTGC
3251956 ATCGATGCATGGTCTTGTGC
1 ATCGATGCATGGTCTTGTGC
3251976 ATCGATGCAT
1 ATCGATGCAT
3251986 CAAATGTACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.17, C:0.20, G:0.29, T:0.34
Consensus pattern (20 bp):
ATCGATGCATGGTCTTGTGC
Found at i:3254792 original size:30 final size:27
Alignment explanation
Indices: 3254758--3254812 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 27
3254748 CAAAGGACAA
3254758 AAAGATAATAAAATAAATAAATAATAAATC
1 AAAGA-AA-AAAATAAA-AAATAATAAATC
*
3254788 AAAGAAAATAATAAAAAATAATAAA
1 AAAGAAAAAAATAAAAAATAATAAA
3254813 GAGGATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 10 0.42
28 7 0.29
29 2 0.08
30 5 0.21
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (27 bp):
AAAGAAAAAAATAAAAAATAATAAATC
Found at i:3254811 original size:34 final size:36
Alignment explanation
Indices: 3254725--3254812 Score: 112
Period size: 38 Copynumber: 2.5 Consensus size: 36
3254715 AAAAGATGTT
3254725 AGAT-AAAAATAATAAATAAAAATCAAAGGACAAAA
1 AGATAAAAAATAATAAATAAAAATCAAAGGACAAAA
*
3254760 AGATAATAAAATAAATAAATAATAAATCAAA-GA-AAAT
1 AGATAA-AAAAT-AATAAATAA-AAATCAAAGGACAAAA
3254797 A-ATAAAAAATAATAAA
1 AGATAAAAAATAATAAA
3254813 GAGGATTTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
34 6 0.12
35 9 0.19
36 5 0.10
37 9 0.19
38 11 0.23
39 8 0.17
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (36 bp):
AGATAAAAAATAATAAATAAAAATCAAAGGACAAAA
Found at i:3254845 original size:6 final size:6
Alignment explanation
Indices: 3254836--3254998 Score: 55
Period size: 6 Copynumber: 25.3 Consensus size: 6
3254826 AATCAAAAGG
*
3254836 AAAAAT AAAAGA- AAAAAT AAAAAT AAAATAGAT GAAAAAGG AAAAAT
1 AAAAAT AAAA-AT AAAAAT AAAAAT -AAA-A-AT -AAAAA-T AAAAAT
* * * * *
3254883 ATTAAAT AAATAT AAAAAAT AATAAAAT AAAAAAT AATAAT -ATAAT AATAAT
1 A-AAAAT AAAAAT -AAAAAT -A-AAAAT -AAAAAT AAAAAT AAAAAT AAAAAT
* * * * **
3254935 AATATAT ATATAT AATAAAT AATAAAG AAAAAT AAAAAT --TTAT AAAAAT
1 AA-AAAT AAAAAT AA-AAAT AA-AAAT AAAAAT AAAAAT AAAAAT AAAAAT
3254984 AAAAAAT AAAAAT AA
1 -AAAAAT AAAAAT AA
3254999 CCAAAATGAA
Statistics
Matches: 123, Mismatches: 19, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
4 2 0.02
5 6 0.05
6 54 0.44
7 47 0.38
8 9 0.07
9 5 0.04
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (6 bp):
AAAAAT
Found at i:3254872 original size:23 final size:23
Alignment explanation
Indices: 3254837--3254914 Score: 61
Period size: 23 Copynumber: 3.4 Consensus size: 23
3254827 ATCAAAAGGA
*
3254837 AAAATAAAAGAAAAAATAAAAAT
1 AAAATAAAAGAAAAAAGAAAAAT
* * *
3254860 AAAATAGATGAAAAAGGAAAAAT
1 AAAATAAAAGAAAAAAGAAAAAT
* * *
3254883 ATTAAAT-AAATATAAAA-AATAAT
1 A--AAATAAAAGAAAAAAGAAAAAT
3254906 AAAATAAAA
1 AAAATAAAA
3254915 AATAATAATA
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
21 4 0.10
22 3 0.07
23 26 0.62
24 5 0.12
25 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (23 bp):
AAAATAAAAGAAAAAAGAAAAAT
Found at i:3254921 original size:3 final size:3
Alignment explanation
Indices: 3254900--3254959 Score: 58
Period size: 3 Copynumber: 20.7 Consensus size: 3
3254890 AAATATAAAA
3254900 AAT AAT AA- AAT AA- AA- AAT AAT AAT -AT AAT AAT AAT AAT -AT ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
3254944 ATAT AAT AAAT AAT AA
1 A-AT AAT -AAT AAT AA
3254960 AGAAAAATAA
Statistics
Matches: 51, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
2 10 0.20
3 31 0.61
4 10 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3254927 original size:20 final size:19
Alignment explanation
Indices: 3254877--3254998 Score: 73
Period size: 17 Copynumber: 6.8 Consensus size: 19
3254867 ATGAAAAAGG
*
3254877 AAAAATATTAAAT-AAATA
1 AAAAATAATAAATAAAATA
*
3254895 TAAAA-AAT-AATAAAATA
1 AAAAATAATAAATAAAATA
*
3254912 AAAAATAAT-AATATAAT-
1 AAAAATAATAAATAAAATA
* * *
3254929 AATAATAATATATATATATA
1 AAAAATAATAAATA-AAATA
* *
3254949 ATAAATAATAAAGAAAA-A
1 AAAAATAATAAATAAAATA
* *
3254967 TAAAAAT-TTATA-AAAATA
1 -AAAAATAATAAATAAAATA
3254985 AAAAATAA-AAATAA
1 AAAAATAATAAATAA
3254999 CCAAAATGAA
Statistics
Matches: 77, Mismatches: 18, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
16 3 0.04
17 31 0.40
18 24 0.31
19 9 0.12
20 10 0.13
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.27
Consensus pattern (19 bp):
AAAAATAATAAATAAAATA
Found at i:3256102 original size:38 final size:37
Alignment explanation
Indices: 3256060--3256180 Score: 109
Period size: 38 Copynumber: 3.5 Consensus size: 37
3256050 ACAATCCTTT
*
3256060 CAAAACAATAAACTAGTAATACCAAATAAGTATATTT-
1 CAAAACAATAAA-TAGTAATACCAAATAAGCATATTTA
* *
3256097 ----GC-A-AAATAGTAA-A-C-AATAAACATATTTA
1 CAAAACAATAAATAGTAATACCAAATAAGCATATTTA
* *
3256125 CAAAATAGTAAACTAGTAATACCAAATAAGCATATTTA
1 CAAAACAATAAA-TAGTAATACCAAATAAGCATATTTA
3256163 CAAAACAATAAATAGTAA
1 CAAAACAATAAATAGTAA
3256181 GCATATTTAC
Statistics
Matches: 64, Mismatches: 9, Indels: 22
0.67 0.09 0.23
Matches are distributed among these distances:
27 11 0.17
28 1 0.02
29 1 0.02
30 6 0.09
31 3 0.05
32 1 0.02
33 1 0.02
34 3 0.05
35 6 0.09
36 1 0.02
37 7 0.11
38 23 0.36
ACGTcount: A:0.56, C:0.12, G:0.07, T:0.25
Consensus pattern (37 bp):
CAAAACAATAAATAGTAATACCAAATAAGCATATTTA
Found at i:3256148 original size:65 final size:65
Alignment explanation
Indices: 3256021--3256200 Score: 218
Period size: 65 Copynumber: 2.7 Consensus size: 65
3256011 TTAAAAACTG
*
3256021 GCATATTTACAAAATAATAAACAATTAACACA-ATCCTTTCAAAACAATAAACTAGTAATACCAA
1 GCATATTTACAAAATAATAAACAA-TAA-ACATAT--TTACAAAACAATAAACTAGTAATACCAA
3256085 ATAA
62 ATAA
* * * * *
3256089 GTATATTTGCAAAATAGTAAACAATAAACATATTTACAAAATAGTAAACTAGTAATACCAAATAA
1 GCATATTTACAAAATAATAAACAATAAACATATTTACAAAACAATAAACTAGTAATACCAAATAA
* * * * *
3256154 GCATATTTACAAAACAATAAATAGTAAGCATATTTACGAAACAATAA
1 GCATATTTACAAAATAATAAACAATAAACATATTTACAAAACAATAA
3256201 GCATAATAAG
Statistics
Matches: 95, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
65 66 0.69
66 3 0.03
67 5 0.05
68 21 0.22
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (65 bp):
GCATATTTACAAAATAATAAACAATAAACATATTTACAAAACAATAAACTAGTAATACCAAATAA
Done.