Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, 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: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 10 of 131
Found at i:2485111 original size:25 final size:23
Alignment explanation
Indices: 2485053--2485112 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
2485043 TATTATTAAA
* *
2485053 ATTTTAAAATATATTATTTTTAT
1 ATTTTAAATTATATTATTTTCAT
**
2485076 ATTTTTTATTATATTATTATATCAT
1 ATTTTAAATTATATTATT-T-TCAT
2485101 ATTTTAAATTAT
1 ATTTTAAATTAT
2485113 TGAAGGAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 15 0.52
24 1 0.03
25 13 0.45
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTTAAATTATATTATTTTCAT
Found at i:2490513 original size:21 final size:21
Alignment explanation
Indices: 2490489--2490539 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
2490479 CCCGAAATTA
2490489 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
2490510 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
2490531 AT-AAATATT
1 ATAAAATATT
2490540 TAAAAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 7 0.23
21 23 0.77
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATAAAATATTATTTTTTAAAT
Found at i:2490548 original size:30 final size:30
Alignment explanation
Indices: 2490512--2490572 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2490502 TTTTAAATAT
* * *
2490512 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATTATTATATAAATATAAATAATTA
*
2490542 AAAATATTATTATATAAATATATATAATTA
1 AAAATATTATTATATAAATATAAATAATTA
2490572 A
1 A
2490573 TTAATTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
AAAATATTATTATATAAATATAAATAATTA
Found at i:2491291 original size:41 final size:42
Alignment explanation
Indices: 2491214--2491317 Score: 178
Period size: 42 Copynumber: 2.5 Consensus size: 42
2491204 AAAAATTATA
*
2491214 TAAATATAT-AATATAAAAATT-AAAATAAATTTTTA-TTTT
1 TAAATTTATAAATATAAAAATTAAAAATAAATTTTTATTTTT
2491253 TAAATTTATAAATATAAAAATTAAAAATAAATTTTTATTTTT
1 TAAATTTATAAATATAAAAATTAAAAATAAATTTTTATTTTT
2491295 TAAATTTATAAATATAAAAATTA
1 TAAATTTATAAATATAAAAATTA
2491318 TTTATACTCA
Statistics
Matches: 61, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
39 8 0.13
40 12 0.20
41 14 0.23
42 27 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (42 bp):
TAAATTTATAAATATAAAAATTAAAAATAAATTTTTATTTTT
Found at i:2493500 original size:15 final size:15
Alignment explanation
Indices: 2493480--2493513 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2493470 TTATATAAAC
2493480 TTTAAAAAAAATAAT
1 TTTAAAAAAAATAAT
* *
2493495 TTTAAAATAAATTAT
1 TTTAAAAAAAATAAT
2493510 TTTA
1 TTTA
2493514 TCATAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTAAAAAAAATAAT
Found at i:2497382 original size:13 final size:13
Alignment explanation
Indices: 2497364--2497390 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2497354 ACAACAGTAT
2497364 CAATGGCTTGAAC
1 CAATGGCTTGAAC
2497377 CAATGGCTTGAAC
1 CAATGGCTTGAAC
2497390 C
1 C
2497391 GTTGAACCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (13 bp):
CAATGGCTTGAAC
Found at i:2501816 original size:2 final size:2
Alignment explanation
Indices: 2501809--2501833 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2501799 CAGTGAAACC
2501809 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 A
2501834 AATAAACACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2502817 original size:21 final size:20
Alignment explanation
Indices: 2502775--2502818 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2502765 CTAATGTTTT
*
2502775 TTAGATCCCCTTACATTTAC
1 TTAGATCCCCTTACATTCAC
* *
2502795 TTAGATGCCCTTCTCATTCAC
1 TTAGATCCCCTT-ACATTCAC
2502816 TTA
1 TTA
2502819 TATTTACTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.41
Consensus pattern (20 bp):
TTAGATCCCCTTACATTCAC
Found at i:2508809 original size:10 final size:9
Alignment explanation
Indices: 2508784--2508813 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2508774 TCCATCTGTC
2508784 AAAGGGGAA
1 AAAGGGGAA
2508793 AAAGGGGAA
1 AAAGGGGAA
2508802 AAAGGGGGAA
1 AAA-GGGGAA
2508812 AA
1 AA
2508814 CATTAACACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (9 bp):
AAAGGGGAA
Found at i:2522811 original size:18 final size:18
Alignment explanation
Indices: 2522781--2522826 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
2522771 TCATTATAAA
2522781 ATTTATT-ATTTTTAAG-T
1 ATTTATTAATTTTT-AGCT
2522798 ATTTATTAATTTTTAGCT
1 ATTTATTAATTTTTAGCT
2522816 ATTTATTAATT
1 ATTTATTAATT
2522827 AGTTTATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.63
Consensus pattern (18 bp):
ATTTATTAATTTTTAGCT
Found at i:2523471 original size:16 final size:17
Alignment explanation
Indices: 2523450--2523482 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2523440 TCTAATCGAA
2523450 TTTTTA-TATTTAAATT
1 TTTTTATTATTTAAATT
*
2523466 TTTTTATTATTTTAATT
1 TTTTTATTATTTAAATT
2523483 AATAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTATTATTTAAATT
Found at i:2530529 original size:2 final size:2
Alignment explanation
Indices: 2530522--2530546 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2530512 CGGGACTTAT
2530522 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 T
2530547 TAAGGATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2532788 original size:12 final size:12
Alignment explanation
Indices: 2532771--2532795 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2532761 TATCAAATAA
2532771 ATTTATTTAATT
1 ATTTATTTAATT
2532783 ATTTATTTAATT
1 ATTTATTTAATT
2532795 A
1 A
2532796 AAAAATATTT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTATTTAATT
Found at i:2533364 original size:20 final size:18
Alignment explanation
Indices: 2533325--2533358 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2533315 TATAAATTGA
2533325 TAAATATTATTATAAAAT
1 TAAATATTATTATAAAAT
2533343 TAAATA-TATTATAAAA
1 TAAATATTATTATAAAA
2533359 ATATTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATATTATTATAAAAT
Found at i:2551392 original size:32 final size:32
Alignment explanation
Indices: 2551355--2551425 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
2551345 AACACTTGGT
*
2551355 CTACTCTATTGTAATACAAAACTATGTATGTG
1 CTACTCTATTGTAATACAAAACTATATATGTG
2551387 CTACTCTATTGTAATACAAAACTATATATGTG
1 CTACTCTATTGTAATACAAAACTATATATGTG
2551419 CTACTCT
1 CTACTCT
2551426 TGAAAGTAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (32 bp):
CTACTCTATTGTAATACAAAACTATATATGTG
Found at i:2565268 original size:15 final size:15
Alignment explanation
Indices: 2565246--2565282 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
2565236 ATCAAAATTA
2565246 AATTGTTGATTATAG
1 AATTGTTGATTATAG
* *
2565261 AGTTGTTGATTCTAG
1 AATTGTTGATTATAG
2565276 AATTGTT
1 AATTGTT
2565283 TCATTAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.27, C:0.03, G:0.22, T:0.49
Consensus pattern (15 bp):
AATTGTTGATTATAG
Found at i:2571146 original size:15 final size:16
Alignment explanation
Indices: 2571126--2571155 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2571116 CCCTGACTGG
2571126 ACCACC-TTCTTTTTC
1 ACCACCGTTCTTTTTC
2571141 ACCACCGTTCTTTTT
1 ACCACCGTTCTTTTT
2571156 ATCTTTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.37, G:0.03, T:0.47
Consensus pattern (16 bp):
ACCACCGTTCTTTTTC
Found at i:2576719 original size:2 final size:2
Alignment explanation
Indices: 2576712--2576742 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2576702 GTACAGTAGT
2576712 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2576743 ATTGGGGTGA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2586533 original size:11 final size:11
Alignment explanation
Indices: 2586517--2586555 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
2586507 TGATACAGTG
2586517 ATATAAAAATA
1 ATATAAAAATA
*
2586528 ATATAAATAAAAA
1 ATAT-AA-AAATA
2586541 ATATAAAAATA
1 ATATAAAAATA
2586552 ATAT
1 ATAT
2586556 GATTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 12 0.50
12 4 0.17
13 8 0.33
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:2586605 original size:21 final size:22
Alignment explanation
Indices: 2586566--2586611 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2586556 GATTTAAAAT
* *
2586566 TTTAATAAAAATCATAAATAAA
1 TTTAATAAAAATAAAAAATAAA
*
2586588 TTTAAT-AAAATAAAAAATATA
1 TTTAATAAAAATAAAAAATAAA
2586609 TTT
1 TTT
2586612 TATATTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAATAAAAATAAAAAATAAA
Found at i:2586613 original size:22 final size:22
Alignment explanation
Indices: 2586563--2586613 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
2586553 TATGATTTAA
* *
2586563 AATTTTAATAAAAATCATAAAT
1 AATTTTAATAAAAATAAAAAAT
*
2586585 AAATTTAAT-AAAATAAAAAAT
1 AATTTTAATAAAAATAAAAAAT
2586606 ATATTTTA
1 A-ATTTTA
2586614 TATTTTTGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
AATTTTAATAAAAATAAAAAAT
Found at i:2588679 original size:17 final size:17
Alignment explanation
Indices: 2588659--2588693 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2588649 ATAAATATTC
* *
2588659 TTAATCAATAAGAGTTT
1 TTAATAAATAAGAATTT
2588676 TTAATAAATAAGAATTT
1 TTAATAAATAAGAATTT
2588693 T
1 T
2588694 GGTGATCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (17 bp):
TTAATAAATAAGAATTT
Found at i:2589212 original size:15 final size:15
Alignment explanation
Indices: 2589192--2589221 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2589182 AAAAATGTTT
*
2589192 TATGAAATTTTCCTA
1 TATGAAAATTTCCTA
2589207 TATGAAAATTTCCTA
1 TATGAAAATTTCCTA
2589222 CTCTTTTGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (15 bp):
TATGAAAATTTCCTA
Found at i:2589533 original size:7 final size:7
Alignment explanation
Indices: 2589523--2589562 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
2589513 AAAATAAAAA
*
2589523 AAAATGT
1 AAAAGGT
2589530 AAAAGGT
1 AAAAGGT
2589537 AAAAGGT
1 AAAAGGT
2589544 AAAAGGT
1 AAAAGGT
2589551 AAAAGGT
1 AAAAGGT
2589558 AAAAG
1 AAAAG
2589563 AAAACTCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.60, C:0.00, G:0.25, T:0.15
Consensus pattern (7 bp):
AAAAGGT
Found at i:2592454 original size:13 final size:13
Alignment explanation
Indices: 2592436--2592461 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2592426 GCCAACCTCC
2592436 CTTTTTTTTTTTT
1 CTTTTTTTTTTTT
2592449 CTTTTTTTTTTTT
1 CTTTTTTTTTTTT
2592462 TCTAGAAACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
CTTTTTTTTTTTT
Found at i:2592456 original size:14 final size:14
Alignment explanation
Indices: 2592437--2592464 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2592427 CCAACCTCCC
2592437 TTTTTTTTTTTTCT
1 TTTTTTTTTTTTCT
2592451 TTTTTTTTTTTTCT
1 TTTTTTTTTTTTCT
2592465 AGAAACGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTTTTTTTTTTTCT
Found at i:2595273 original size:2 final size:2
Alignment explanation
Indices: 2595268--2595305 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2595258 ATATATATAT
2595268 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2595306 GGGCATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2598062 original size:4 final size:4
Alignment explanation
Indices: 2598038--2598097 Score: 77
Period size: 4 Copynumber: 15.2 Consensus size: 4
2598028 GATTCTGTTA
* * * *
2598038 ACAT ACAT AAAT ACAT GCAT ACAT ACAT ATAT ACAT ACAC ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2598086 ACAT A-AT ACAT A
1 ACAT ACAT ACAT A
2598098 TATATATATA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
3 3 0.06
4 44 0.94
ACGTcount: A:0.52, C:0.22, G:0.02, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:2605366 original size:15 final size:15
Alignment explanation
Indices: 2605348--2605377 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2605338 TTAATTTATT
*
2605348 TTATATTTTAAATAA
1 TTATATTTAAAATAA
2605363 TTATATTTAAAATAA
1 TTATATTTAAAATAA
2605378 AAATAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATATTTAAAATAA
Found at i:2605399 original size:24 final size:22
Alignment explanation
Indices: 2605357--2605434 Score: 63
Period size: 24 Copynumber: 3.5 Consensus size: 22
2605347 TTTATATTTT
*
2605357 AAATAATTA-TATTTA-AAATAA
1 AAATAATTATTATATATAAAT-A
2605378 AAATAATTATTATATGATAAATGA
1 AAATAATTATTATAT-ATAAAT-A
** *
2605402 TTATAATTATTTAAATATAAATA
1 AAATAATTA-TTATATATAAATA
2605425 AAAT-ATTATT
1 AAATAATTATT
2605435 CATAAATATT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
21 11 0.24
22 8 0.17
23 4 0.09
24 18 0.39
25 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (22 bp):
AAATAATTATTATATATAAATA
Found at i:2605432 original size:43 final size:42
Alignment explanation
Indices: 2605366--2605466 Score: 129
Period size: 41 Copynumber: 2.4 Consensus size: 42
2605356 TAAATAATTA
*
2605366 TATTTAAAATAAA-AATAATTATTATATGATAAATGATTATAAT
1 TATTTAAAATAAATAATAATTATTAT-TCATAAAT-ATTATAAT
2605409 TATTTAAATATAAATAA-AA-TATTATTCATAAATATTATAAT
1 TATTTAAA-ATAAATAATAATTATTATTCATAAATATTATAAT
*
2605450 TATATAAAA-AAATAATA
1 TATTTAAAATAAATAATA
2605467 TTCATTTGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
39 6 0.11
40 2 0.04
41 15 0.28
42 7 0.13
43 14 0.26
44 7 0.13
45 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (42 bp):
TATTTAAAATAAATAATAATTATTATTCATAAATATTATAAT
Found at i:2605439 original size:18 final size:18
Alignment explanation
Indices: 2605418--2605471 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
2605408 TTATTTAAAT
2605418 ATAAATAAAATATTATTC
1 ATAAATAAAATATTATTC
**
2605436 ATAAATATTATAATTA-T-
1 ATAAATAAAAT-ATTATTC
*
2605453 ATAAA-AAAATAATATTC
1 ATAAATAAAATATTATTC
2605470 AT
1 AT
2605472 TTGAATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 7
0.70 0.12 0.17
Matches are distributed among these distances:
15 3 0.11
16 4 0.14
17 7 0.25
18 10 0.36
19 4 0.14
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAATAAAATATTATTC
Found at i:2607411 original size:16 final size:16
Alignment explanation
Indices: 2607368--2607417 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
2607358 AGTAAATTTG
* *
2607368 ATAATTTAAAATATAAT
1 ATAATTTAATATA-AAA
2607385 ATAATTATAATATAAAA
1 ATAATT-TAATATAAAA
*
2607402 ATAATTTAATTTAAAA
1 ATAATTTAATATAAAA
2607418 TTTTAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 9 0.31
17 14 0.48
18 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAATTTAATATAAAA
Found at i:2607455 original size:39 final size:37
Alignment explanation
Indices: 2607360--2607474 Score: 101
Period size: 39 Copynumber: 3.0 Consensus size: 37
2607350 ATCTTACGAG
*
2607360 TAAATTTGATAATTTAAAATATAATATAATTATAATA
1 TAAATTTAATAATTTAAAATATAATATAATTATAATA
** *
2607397 TAAAAATAATTTAATTTAAAATTTTAATAATAATTAT-ATA
1 TAAATTTAA--TAATTTAAAA-TATAAT-ATAATTATAATA
* *
2607437 TAAATTTAATAAAATTAAAA-ATACATAT-TTTATAATA
1 TAAATTTAAT-AATTTAAAATATA-ATATAATTATAATA
2607474 T
1 T
2607475 TTTATCTATA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
36 4 0.06
37 14 0.23
38 3 0.05
39 18 0.29
40 15 0.24
41 8 0.13
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (37 bp):
TAAATTTAATAATTTAAAATATAATATAATTATAATA
Found at i:2607458 original size:40 final size:40
Alignment explanation
Indices: 2607381--2607458 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
2607371 ATTTAAAATA
** *
2607381 TAATATAATTATAATATAAAAATAATTTAATTTAAAATTT
1 TAATATAATTATAATATAAAAATAATAAAATTAAAAATTT
**
2607421 TAATAATAATTAT-ATATAAATTTAATAAAATTAAAAAT
1 TAAT-ATAATTATAATATAAAAATAATAAAATTAAAAAT
2607459 ACATATTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 24 0.75
41 8 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (40 bp):
TAATATAATTATAATATAAAAATAATAAAATTAAAAATTT
Found at i:2607628 original size:24 final size:24
Alignment explanation
Indices: 2607596--2607646 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2607586 AAATAGAAAT
* **
2607596 AAAATTTATTATAATTGTAATTAA
1 AAAAATTATTATAAACGTAATTAA
2607620 AAAAATTATTATAAACGTAATTAA
1 AAAAATTATTATAAACGTAATTAA
2607644 AAA
1 AAA
2607647 TTTATATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (24 bp):
AAAAATTATTATAAACGTAATTAA
Found at i:2607662 original size:22 final size:23
Alignment explanation
Indices: 2607596--2607662 Score: 57
Period size: 24 Copynumber: 2.9 Consensus size: 23
2607586 AAATAGAAAT
2607596 AAAATTTAT-TATAATTGTAATTAA
1 AAAATTTATAT-TAATT-TAATTAA
* * **
2607620 AAAAATTATTATAAACGTAATT-A
1 AAAATTTA-TATTAATTTAATTAA
2607643 AAAATTTATATTAATTTAAT
1 AAAATTTATATTAATTTAAT
2607663 CTTATTAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
22 9 0.27
23 8 0.24
24 12 0.36
25 3 0.09
26 1 0.03
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (23 bp):
AAAATTTATATTAATTTAATTAA
Found at i:2608894 original size:29 final size:29
Alignment explanation
Indices: 2608841--2608919 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
2608831 TTTTGAATTA
* **
2608841 TTTTATTTTTTTCAAATAAGTTTTTATAT
1 TTTTATTTTATTCAAATAAAATTTTATAT
*
2608870 TTTTATTTTATTCAAATAAAATTTTATCT
1 TTTTATTTTATTCAAATAAAATTTTATAT
* * *
2608899 CTTGATTTATATTTAAATAAA
1 TTTTATTT-TATTCAAATAAA
2608920 TTCCTATTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 31 0.74
30 11 0.26
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (29 bp):
TTTTATTTTATTCAAATAAAATTTTATAT
Found at i:2609060 original size:23 final size:23
Alignment explanation
Indices: 2609034--2609077 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2609024 TTAAGGGCGA
2609034 TAAAAAAAAT-ATAAAAATTTATC
1 TAAAAAAAATGAT-AAAATTTATC
*
2609057 TAAATAAAATGATAAAATTTA
1 TAAAAAAAATGATAAAATTTA
2609078 AATTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
TAAAAAAAATGATAAAATTTATC
Found at i:2615011 original size:180 final size:181
Alignment explanation
Indices: 2614705--2615051 Score: 599
Period size: 180 Copynumber: 1.9 Consensus size: 181
2614695 GCCATCTTTA
2614705 AGATCAACCAGAAAATCACATAGATTCAAGCTTTTCTAATTCTTGACAAGGCCAAATTAATATCC
1 AGATCAACCAGAAAATCACATAGATTCAAGCTTTTCTAATTCTTGACAAGGCCAAATTAATATCC
* *
2614770 ATTCATTCAATTCCAAAAGTAAGCATGAAAACCCAAGAACCCGCTGACATCAAATCAGAAAATCA
66 ATTCATTCAATTCCAAAAGTAAGCATGAAAACCCAAGAAACCGCTGACATCAAAGCAGAAAATCA
* *
2614835 AAACAGC-AAATCTTTGAGTTCAGGCTGCAAAAGCTCACACGGCCCTGTTT
131 AAACAGCAAAATCTTTAAATTCAGGCTGCAAAAGCTCACACGGCCCTGTTT
* *
2614885 AGATCAACCAGACAATCACATAGATTCAAGCTTTTCCT-ATTCTTGACAAGGCGAAATTAATATC
1 AGATCAACCAGAAAATCACATAGATTCAAGCTTTT-CTAATTCTTGACAAGGCCAAATTAATATC
* *
2614949 CATTCATTCAATTCTAAAAGTAAGCATGAAAACCCAAGAAACTGCTGACATCAAAGCAGAAAATC
65 CATTCATTCAATTCCAAAAGTAAGCATGAAAACCCAAGAAACCGCTGACATCAAAGCAGAAAATC
2615014 AAAACAGCAAAATCTTTAAATTCAGGCTGCAAAAGCTC
130 AAAACAGCAAAATCTTTAAATTCAGGCTGCAAAAGCTC
2615052 CATGTGAATT
Statistics
Matches: 157, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
180 128 0.82
181 29 0.18
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.23
Consensus pattern (181 bp):
AGATCAACCAGAAAATCACATAGATTCAAGCTTTTCTAATTCTTGACAAGGCCAAATTAATATCC
ATTCATTCAATTCCAAAAGTAAGCATGAAAACCCAAGAAACCGCTGACATCAAAGCAGAAAATCA
AAACAGCAAAATCTTTAAATTCAGGCTGCAAAAGCTCACACGGCCCTGTTT
Found at i:2615595 original size:41 final size:39
Alignment explanation
Indices: 2615505--2615598 Score: 95
Period size: 41 Copynumber: 2.4 Consensus size: 39
2615495 ATTAATATCA
*
2615505 TATTTATTTATATTAAATATAATATAAAAATTATATAAT
1 TATTTATTTATATAAAATATAATATAAAAATTATATAAT
* *
2615544 TA-TAATTTTATATCAAAATATTAAATATAAAATATT-T-TATT
1 TATTTA-TTTATAT-AAAATA-T-AATATAAAA-ATTATATAAT
2615585 TATTTATTTATATA
1 TATTTATTTATATA
2615599 TAATTTTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
38 2 0.04
39 9 0.20
40 6 0.13
41 13 0.29
42 12 0.27
43 3 0.07
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (39 bp):
TATTTATTTATATAAAATATAATATAAAAATTATATAAT
Found at i:2622767 original size:6 final size:6
Alignment explanation
Indices: 2622756--2622791 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
2622746 CACACTCCAT
* *
2622756 ATATAA ATATAA ATATGA ATATAA ATGTAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
2622792 CTTATTTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (6 bp):
ATATAA
Found at i:2623095 original size:24 final size:25
Alignment explanation
Indices: 2623068--2623116 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2623058 AAAATTTCAT
*
2623068 AATTTTTAAT-GTCAAAAAAATAAA
1 AATTTTAAATAGTCAAAAAAATAAA
*
2623092 AATTTTAAATATTCAAAAAAATAAA
1 AATTTTAAATAGTCAAAAAAATAAA
2623117 TAAGACATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (25 bp):
AATTTTAAATAGTCAAAAAAATAAA
Found at i:2624251 original size:93 final size:93
Alignment explanation
Indices: 2624104--2624280 Score: 336
Period size: 93 Copynumber: 1.9 Consensus size: 93
2624094 TGAGAATTGA
**
2624104 TGATTATTGATTAGTTTCGTTTGATTGCGGTGTGAATTTTGATCCCAAAATGCCAATCCTGAAAC
1 TGATTATTGATTAGTTTCGTGAGATTGCGGTGTGAATTTTGATCCCAAAATGCCAATCCTGAAAC
2624169 AGAAATACAATGTATGATTGATGATTAT
66 AGAAATACAATGTATGATTGATGATTAT
2624197 TGATTATTGATTAGTTTCGTGAGATTGCGGTGTGAATTTTGATCCCAAAATGCCAATCCTGAAAC
1 TGATTATTGATTAGTTTCGTGAGATTGCGGTGTGAATTTTGATCCCAAAATGCCAATCCTGAAAC
2624262 AGAAATACAATGTATGATT
66 AGAAATACAATGTATGATT
2624281 TCACTTTAAA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 82 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (93 bp):
TGATTATTGATTAGTTTCGTGAGATTGCGGTGTGAATTTTGATCCCAAAATGCCAATCCTGAAAC
AGAAATACAATGTATGATTGATGATTAT
Found at i:2629841 original size:24 final size:24
Alignment explanation
Indices: 2629814--2629861 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2629804 ATCATTCAAT
*
2629814 TAATTCATATCATGACATGTAAAA
1 TAATCCATATCATGACATGTAAAA
* *
2629838 TAATCCATGTCATGACATTTAAAA
1 TAATCCATATCATGACATGTAAAA
2629862 ATTCAAATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (24 bp):
TAATCCATATCATGACATGTAAAA
Found at i:2636301 original size:1 final size:1
Alignment explanation
Indices: 2636295--2636320 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2636285 AGGAAAATTG
2636295 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
2636321 CCCATCACGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2638406 original size:23 final size:23
Alignment explanation
Indices: 2638354--2638398 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2638344 ACTTAGTTCA
2638354 AATAAAAAAATAAAAATTATTTC
1 AATAAAAAAATAAAAATTATTTC
* *
2638377 AATAAAAATATGAAAATTATTT
1 AATAAAAAAATAAAAATTATTT
2638399 TAGTAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AATAAAAAAATAAAAATTATTTC
Found at i:2645710 original size:13 final size:14
Alignment explanation
Indices: 2645676--2645707 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2645666 TTTTACAGAT
2645676 AATAATTTTTGAAA
1 AATAATTTTTGAAA
2645690 AATAATTTTTGAAA
1 AATAATTTTTGAAA
2645704 AATA
1 AATA
2645708 TTTATATTTT
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:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (14 bp):
AATAATTTTTGAAA
Found at i:2645735 original size:25 final size:25
Alignment explanation
Indices: 2645701--2645749 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
2645691 ATAATTTTTG
*
2645701 AAAAATA-TTTATATTTTTTGAATT
1 AAAAATATTTTATATTATTTGAATT
*
2645725 AAAAGATATTTTTTATTATTTGAAT
1 AAAA-ATATTTTATATTATTTGAAT
2645750 GAGTTAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 3 0.14
26 14 0.67
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (25 bp):
AAAAATATTTTATATTATTTGAATT
Found at i:2645836 original size:25 final size:24
Alignment explanation
Indices: 2645806--2645878 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 24
2645796 TATTAATATA
2645806 ATTATTAAAATATTAAAATTTATTT
1 ATTATTAAAATATTAAAA-TTATTT
*
2645831 ATTATTAAAATATATTGAAATTATTT
1 ATTATT-AAA-ATATTAAAATTATTT
*
2645857 ATTATTAAAATTATTAATATTA
1 ATTATTAAAA-TATTAAAATTA
2645879 AAAAATAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 15 0.36
27 8 0.19
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (24 bp):
ATTATTAAAATATTAAAATTATTT
Found at i:2645842 original size:48 final size:51
Alignment explanation
Indices: 2645772--2645873 Score: 115
Period size: 47 Copynumber: 2.0 Consensus size: 51
2645762 TGTTTTTTTG
* *
2645772 AAAATTTTATTTTTTTTCAAATAATATT-AA-TA-TAATTATTAAAA-TATT
1 AAAATTTTATTTTTATTAAAAT-ATATTAAATTATTAATTATTAAAATTATT
*
2645820 AAAA-TTTATTTATTATTAAAATATATTGAAATTATTTATTATTAAAATTATT
1 AAAATTTTATTT-TTATTAAAATATATT-AAATTATTAATTATTAAAATTATT
2645872 AA
1 AA
2645874 TATTAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
47 12 0.27
48 12 0.27
49 2 0.04
50 2 0.04
51 11 0.24
52 6 0.13
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (51 bp):
AAAATTTTATTTTTATTAAAATATATTAAATTATTAATTATTAAAATTATT
Found at i:2645846 original size:10 final size:9
Alignment explanation
Indices: 2645805--2645878 Score: 59
Period size: 9 Copynumber: 8.6 Consensus size: 9
2645795 ATATTAATAT
2645805 AATTATTAA
1 AATTATTAA
2645814 AA-TATTAA
1 AATTATTAA
2645822 AATTTATT--
1 AA-TTATTAA
*
2645830 TATTATTAA
1 AATTATTAA
*
2645839 AATATATTGA
1 AAT-TATTAA
2645849 AATTATT--
1 AATTATTAA
*
2645856 TATTATTAA
1 AATTATTAA
2645865 AATTATTAA
1 AATTATTAA
*
2645874 TATTA
1 AATTA
2645879 AAAAATAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
7 11 0.21
8 9 0.17
9 20 0.38
10 12 0.23
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (9 bp):
AATTATTAA
Found at i:2645879 original size:15 final size:16
Alignment explanation
Indices: 2645842--2645937 Score: 68
Period size: 16 Copynumber: 5.6 Consensus size: 16
2645832 TTATTAAAAT
*
2645842 ATATTGAAATTATTTA
1 ATATTAAAATTATTTA
*
2645858 TTATTAAAATTA-TTA
1 ATATTAAAATTATTTA
* *
2645873 ATATTAAAAAATAATTA
1 ATATT-AAAATTATTTA
*
2645890 TATTTTAATAATACTATTTA
1 -ATATTAA-AAT--TATTTA
2645910 ATATTAAAATATTATGTTA
1 ATATT-AAA-ATTAT-TTA
2645929 ATATTAAAA
1 ATATTAAAA
2645938 ATGCTTAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
15 7 0.11
16 16 0.25
17 6 0.10
18 12 0.19
19 13 0.21
20 9 0.14
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (16 bp):
ATATTAAAATTATTTA
Found at i:2645882 original size:16 final size:17
Alignment explanation
Indices: 2645848--2645939 Score: 80
Period size: 19 Copynumber: 5.2 Consensus size: 17
2645838 AAATATATTG
*
2645848 AAATTATTTATTATT-A
1 AAATTATTTAATATTAA
2645864 AAATTA-TTAATATTAA
1 AAATTATTTAATATTAA
* * *
2645880 AAAATAATTATATTTTAA
1 AAATTATTTA-ATATTAA
*
2645898 TAATACTATTTAATATTAA
1 -AA-ATTATTTAATATTAA
2645917 AATATTATGTTAATATTAA
1 AA-ATTAT-TTAATATTAA
2645936 AAAT
1 AAAT
2645940 GCTTAAAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
15 7 0.11
16 12 0.19
17 3 0.05
18 15 0.24
19 20 0.32
20 6 0.10
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (17 bp):
AAATTATTTAATATTAA
Found at i:2646018 original size:18 final size:17
Alignment explanation
Indices: 2645995--2646054 Score: 75
Period size: 18 Copynumber: 3.4 Consensus size: 17
2645985 TATTATAATT
2645995 TTATTTATTAATAGTATA
1 TTATTTATTAATA-TATA
*
2646013 TTATTTATTAATATAAA
1 TTATTTATTAATATATA
2646030 TTTATTTATTAATATTATA
1 -TTATTTATTAATA-TATA
*
2646049 ATATTT
1 TTATTT
2646055 GTCATAACGT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 3 0.08
18 31 0.84
19 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TTATTTATTAATATATA
Found at i:2646018 original size:23 final size:23
Alignment explanation
Indices: 2645967--2646018 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
2645957 TTATTATTCT
*
2645967 TTATATTATTTATTAATATATTA
1 TTATTTTATTTATTAATATATTA
*
2645990 TAATTTTATTTATTAATAGTA-TA
1 TTATTTTATTTATTAATA-TATTA
2646013 TTATTT
1 TTATTT
2646019 ATTAATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TTATTTTATTTATTAATATATTA
Found at i:2646034 original size:36 final size:41
Alignment explanation
Indices: 2645968--2646054 Score: 121
Period size: 36 Copynumber: 2.2 Consensus size: 41
2645958 TATTATTCTT
2645968 TATATTATTTATTAATATATTATAATTTTATTTATTAATAG
1 TATATTATTTATTAATATATTATAATTTTATTTATTAATAG
*
2646009 TATATTATTTATT-A-ATA-TA-AA-TTTATTTATTAATAT
1 TATATTATTTATTAATATATTATAATTTTATTTATTAATAG
*
2646045 TATAATATTT
1 TATATTATTT
2646055 GTCATAACGT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
36 23 0.52
37 2 0.05
38 2 0.05
39 3 0.07
40 1 0.02
41 13 0.30
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (41 bp):
TATATTATTTATTAATATATTATAATTTTATTTATTAATAG
Found at i:2646668 original size:58 final size:57
Alignment explanation
Indices: 2646516--2646726 Score: 293
Period size: 57 Copynumber: 3.7 Consensus size: 57
2646506 TTTTGTGCAG
* * * *
2646516 GAAAAATTGATA-TTTCAACTTTTTCTC-AAAATATTTTTGGAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAATTTATTTTCAA
* * *
2646571 GGAAAATTGATACTTTCAAC-TTTTCTTCAAAAATTTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTTC-TCAAAAATATTTTTTGAAAATTTATTTTCAA
*
2646628 GAAAAATTAATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAAGTTTATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAA-TTTATTTTCAA
* *
2646686 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTT
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTT
2646727 TTGGATTTTA
Statistics
Matches: 137, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
55 16 0.12
56 9 0.07
57 59 0.43
58 53 0.39
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.45
Consensus pattern (57 bp):
GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAATTTATTTTCAA
Found at i:2646747 original size:115 final size:112
Alignment explanation
Indices: 2646516--2646727 Score: 309
Period size: 115 Copynumber: 1.9 Consensus size: 112
2646506 TTTTGTGCAG
* * *
2646516 GAAAAATTGATATTTCAACTTTTTCTCAAAATATTTTTGGAAACTTTAATTTCGAGGAAAATTGA
1 GAAAAATTAATATTTCAACTTTTTCTCAAAATATTTTTGAAAACTTTAATTTCAAGGAAAATTGA
* *
2646581 TACTTTCAACTTTTCTTCAAAAATTTTTTTTGAAAATTTATTTTTAA
66 TACTTTCAACTTTTCTCCAAAAATTTTTTTTGAAAATTTATTTTAAA
* *
2646628 GAAAAATTAATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAAGTTTATTTTCAAGGAAAAT
1 GAAAAATTAATA-TTTCAACTTTTTCTC-AAAATA-TTTTTGAAAACTTTAATTTCAAGGAAAAT
2646693 TGATACTTTCAACTTTT-TCCCAAAAATATTTTTTT
63 TGATACTTTCAACTTTTCT-CCAAAAAT-TTTTTTT
2646728 TGGATTTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
112 11 0.12
113 15 0.17
114 7 0.08
115 49 0.55
116 7 0.08
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (112 bp):
GAAAAATTAATATTTCAACTTTTTCTCAAAATATTTTTGAAAACTTTAATTTCAAGGAAAATTGA
TACTTTCAACTTTTCTCCAAAAATTTTTTTTGAAAATTTATTTTAAA
Found at i:2646752 original size:5 final size:5
Alignment explanation
Indices: 2646744--2646836 Score: 84
Period size: 5 Copynumber: 17.6 Consensus size: 5
2646734 TTATTTAAAG
2646744 AAAAT AAAAT --AAT AAAAT AAAAT AAAAGT GAAAAT AAAAAT AAAGA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT -AAAAT AAA-AT
*
2646790 AAAGT AAAAT AAAAT AAAAAT AAAAAT AAAAT AAAGAT AAAAAT AAA
1 AAAAT AAAAT AAAAT -AAAAT -AAAAT AAAAT AAA-AT -AAAAT AAA
2646837 TAATATTAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 18
0.78 0.03 0.19
Matches are distributed among these distances:
3 3 0.04
5 43 0.57
6 23 0.30
7 7 0.09
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:2646777 original size:17 final size:16
Alignment explanation
Indices: 2646740--2646836 Score: 75
Period size: 17 Copynumber: 6.1 Consensus size: 16
2646730 GATTTTATTT
2646740 AAAG-AAAATAAAAT-
1 AAAGTAAAATAAAATA
2646754 -AA-TAAAATAAAATA
1 AAAGTAAAATAAAATA
2646768 AAAGTGAAAATAAAA-A
1 AAAGT-AAAATAAAATA
2646784 TAAAG-AAAAGTAAAATA
1 -AAAGTAAAA-TAAAATA
2646801 AAA-TAAAAATAAAAATA
1 AAAGT-AAAAT-AAAATA
2646818 AAA-TAAAGATAAAAATA
1 AAAGTAAA-AT-AAAATA
2646835 AA
1 AA
2646837 TAATATTAAA
Statistics
Matches: 71, Mismatches: 0, Indels: 21
0.77 0.00 0.23
Matches are distributed among these distances:
13 12 0.17
15 6 0.08
16 14 0.20
17 39 0.55
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.16
Consensus pattern (16 bp):
AAAGTAAAATAAAATA
Found at i:2646785 original size:6 final size:6
Alignment explanation
Indices: 2646744--2646841 Score: 78
Period size: 6 Copynumber: 16.0 Consensus size: 6
2646734 TTATTTAAAG
* * *
2646744 AAAAT- AAAATA ATAAA-A TAAAATA AAAGTG AAAATA AAAATA AAGAAAA
1 AAAATA AAAATA A-AAATA -AAAATA AAAATA AAAATA AAAATA AA-AATA
*
2646793 GTAAAAT- AAAATA AAAATA AAAAT- AAAATA AAGATA AAAATA AATAATA
1 --AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA-AATA
2646842 TTAAACAAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
5 15 0.20
6 44 0.59
7 12 0.16
8 2 0.03
9 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:2647254 original size:4 final size:4
Alignment explanation
Indices: 2647198--2647317 Score: 54
Period size: 4 Copynumber: 30.2 Consensus size: 4
2647188 AAATTAATCA
* * * * *
2647198 AAAT AAA- AAGAT AAAT ATAT TAAT AGAT AACAC AAA- AAA- AAAT AATT
1 AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT
* * * * *
2647245 AGAT AAAT AAAAG AAAT AGAT AAAT AAAA AAAGT AGAT AAAT -AAT AAA-
1 AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT
*
2647293 AATAT TAAT AAA- AAAT AAAT AAAT A
1 AA-AT AAAT AAAT AAAT AAAT AAAT A
2647318 TATATTAAGT
Statistics
Matches: 85, Mismatches: 21, Indels: 20
0.67 0.17 0.16
Matches are distributed among these distances:
3 16 0.19
4 58 0.68
5 11 0.13
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2647264 original size:17 final size:17
Alignment explanation
Indices: 2647244--2647294 Score: 77
Period size: 17 Copynumber: 2.9 Consensus size: 17
2647234 AAAAAATAAT
2647244 TAGATAAATAAAAGAAA-
1 TAGATAAATAAAA-AAAG
2647261 TAGATAAATAAAAAAAG
1 TAGATAAATAAAAAAAG
2647278 TAGATAAATAATAAAAA
1 TAGATAAATAA-AAAAA
2647295 TATTAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 3 0.09
17 24 0.75
18 5 0.16
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.20
Consensus pattern (17 bp):
TAGATAAATAAAAAAAG
Found at i:2647557 original size:16 final size:16
Alignment explanation
Indices: 2647536--2647567 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2647526 AACTTGACAC
2647536 TTTTTTTTTGTTTTTG
1 TTTTTTTTTGTTTTTG
2647552 TTTTTTTTTGTTTTTG
1 TTTTTTTTTGTTTTTG
2647568 CTTGTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (16 bp):
TTTTTTTTTGTTTTTG
Found at i:2647762 original size:42 final size:42
Alignment explanation
Indices: 2647652--2647800 Score: 221
Period size: 41 Copynumber: 3.6 Consensus size: 42
2647642 TCAGAGGCTT
* *
2647652 AACTTTTGGAAAGTAAATTGCTCCTCTAAATAGAGGCACCAT
1 AACTTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGCACCAC
* * *
2647694 AAC-TTTGAAAAGTAAATTGCTTCTCTAAACAGAGGCACCCC
1 AACTTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGCACCAC
*
2647735 AACTTTTGGAAAGTAAATTGCTCCTCTAAATAGAGGCACCAC
1 AACTTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGCACCAC
*
2647777 AA-TTTTGAAAAATAAATTGCTCCT
1 AACTTTTGAAAAGTAAATTGCTCCT
2647801 TGACAATCAT
Statistics
Matches: 95, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
41 56 0.59
42 39 0.41
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (42 bp):
AACTTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGCACCAC
Found at i:2649677 original size:18 final size:18
Alignment explanation
Indices: 2649656--2649700 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2649646 ATTTGAATCT
2649656 TTTTTTTTCATTT-TCTCA
1 TTTTTTTTC-TTTCTCTCA
* *
2649674 TTTTTTTTCTTTCTTTCT
1 TTTTTTTTCTTTCTCTCA
2649692 TTTTTTTTC
1 TTTTTTTTC
2649701 CTCTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTTTCTTTCTCTCA
Found at i:2649716 original size:35 final size:35
Alignment explanation
Indices: 2649666--2649745 Score: 89
Period size: 35 Copynumber: 2.4 Consensus size: 35
2649656 TTTTTTTTCA
*
2649666 TTTTCTCA--TTT-TTTTTCTTTC-T-TTCTTTTT
1 TTTTCTCATTTTTATTTTTCTTTCATCATCTTTTT
*
2649696 TTTTCCTCTATTTTTATTTTTTTTTCATCATCTTTTT
1 TTTT-CTC-ATTTTTATTTTTCTTTCATCATCTTTTT
2649733 TTTTCTCATTTTT
1 TTTTCTCATTTTT
2649746 CATCTATTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
30 4 0.10
31 3 0.07
32 1 0.02
34 3 0.07
35 15 0.37
36 4 0.10
37 11 0.27
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.76
Consensus pattern (35 bp):
TTTTCTCATTTTTATTTTTCTTTCATCATCTTTTT
Found at i:2649731 original size:21 final size:20
Alignment explanation
Indices: 2649691--2649736 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2649681 TCTTTCTTTC
*
2649691 TTTTTTTTTCCTCTATTTTT
1 TTTTTTTTTCATCTATTTTT
2649711 ATTTTTTTTTCATC-ATCTTTT
1 -TTTTTTTTTCATCTAT-TTTT
2649732 TTTTT
1 TTTTT
2649737 CTCATTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTTTTTCATCTATTTTT
Found at i:2649741 original size:15 final size:15
Alignment explanation
Indices: 2649712--2649745 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
2649702 TCTATTTTTA
2649712 TTTTTTTTTCATCAT
1 TTTTTTTTTCATCAT
2649727 CTTTTTTTTTC-TCAT
1 -TTTTTTTTTCATCAT
2649742 TTTT
1 TTTT
2649746 CATCTATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 4 0.22
16 10 0.56
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTTTTCATCAT
Found at i:2653823 original size:58 final size:58
Alignment explanation
Indices: 2653639--2653852 Score: 265
Period size: 57 Copynumber: 3.7 Consensus size: 58
2653629 TTTTGTGAAA
* *
2653639 AAAAATTGATACTTTCAACTTTTCCTCAAAAACT-TTTTTTG-AAAATTTAGTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAA-TATTTTTTGAAAAACTTAATTTTAAG
* * ***
2653696 AAAAATTGATACTTTGAACTTTTCCTCAAAAATATTTTTT-AGAAAGCTTTAATTGCGAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGA-AAAAC-TTAATTTTAAG
* *
2653755 AAAAATTGATACTTTCAACTTTTTCCT-GAAAATATTTTTTGAAAAACTTATTTTTAAG
1 AAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTGAAAAACTTAATTTTAAG
* *
2653813 AAAAATTGATACTTTTAACTTTTTCTCAAAAATATTTTTT
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
2653853 TTTGGATTTT
Statistics
Matches: 133, Mismatches: 17, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
56 1 0.01
57 43 0.32
58 40 0.30
59 41 0.31
60 8 0.06
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44
Consensus pattern (58 bp):
AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAAACTTAATTTTAAG
Found at i:2653844 original size:117 final size:115
Alignment explanation
Indices: 2653639--2653852 Score: 340
Period size: 117 Copynumber: 1.8 Consensus size: 115
2653629 TTTTGTGAAA
*
2653639 AAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTAGTTTTAAGAAAAATTG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAAC-TTTTTTGAAAACTTAGTTTTAAGAAAAATTG
2653704 ATACTTTGAACTTTTCCTCAAAAATATTTTTTAGAAAGCTTTAATTGCGAG
65 ATACTTTGAACTTTTCCTCAAAAATATTTTTTAGAAAGCTTTAATTGCGAG
* *
2653755 AAAAATTGATACTTTCAACTTTTTCCTGAAAATA-TTTTTTGAAAAACTTATTTTTAAGAAAAAT
1 AAAAATTGATACTTTCAAC-TTTTCCTCAAAA-ACTTTTTTG-AAAACTTAGTTTTAAGAAAAAT
* *
2653819 TGATACTTTTAACTTTTTCTCAAAAATATTTTTT
63 TGATACTTTGAACTTTTCCTCAAAAATATTTTTT
2653853 TTTGGATTTT
Statistics
Matches: 90, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
116 26 0.29
117 63 0.70
118 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44
Consensus pattern (115 bp):
AAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTGAAAACTTAGTTTTAAGAAAAATTGA
TACTTTGAACTTTTCCTCAAAAATATTTTTTAGAAAGCTTTAATTGCGAG
Found at i:2653879 original size:5 final size:5
Alignment explanation
Indices: 2653871--2653951 Score: 66
Period size: 5 Copynumber: 16.6 Consensus size: 5
2653861 TTATTTAAAG
*
2653871 AAAAT AAAAT --AAT AAAAT AAAAT AAAAGT GAAAAT AAAAT AAAAA AGTAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAAT A--AAAT
*
2653923 -AAA- AAAAT AAAAT -AAAT -AACT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
2653952 GAATATTAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
3 3 0.05
4 13 0.21
5 38 0.60
6 2 0.03
7 7 0.11
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:2653889 original size:13 final size:13
Alignment explanation
Indices: 2653871--2653951 Score: 68
Period size: 13 Copynumber: 6.6 Consensus size: 13
2653861 TTATTTAAAG
2653871 AAAATAAAATAAT
1 AAAATAAAATAAT
2653884 AAAATAAAAT-A-
1 AAAATAAAATAAT
* *
2653895 AAAGT-GAA-AAT
1 AAAATAAAATAAT
2653906 AAAATAAAA-AAGT
1 AAAATAAAATAA-T
*
2653919 -AAATAAAAAAAT
1 AAAATAAAATAAT
2653931 AAAAT-AAATAACT
1 AAAATAAAATAA-T
2653944 AAAATAAA
1 AAAATAAA
2653952 GAATATTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
10 3 0.05
11 8 0.15
12 19 0.35
13 23 0.42
14 2 0.04
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.19
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:2653904 original size:25 final size:23
Alignment explanation
Indices: 2653867--2653950 Score: 70
Period size: 22 Copynumber: 3.7 Consensus size: 23
2653857 GATTTTATTT
*
2653867 AAAGAAAATAAAATAATAAAATA
1 AAAGTAAATAAAATAATAAAATA
2653890 AAA-TAAAAGTGAAAATAA-AATAA-A
1 AAAGT-AAA-T-AAAATAATAA-AATA
*
2653914 AAAGTAAATAAAAAAATAAAAT-
1 AAAGTAAATAAAATAATAAAATA
*
2653936 AAA-TAACTAAAATAA
1 AAAGTAAATAAAATAA
2653951 AGAATATTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
21 10 0.20
22 11 0.22
23 9 0.18
24 10 0.20
25 10 0.20
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (23 bp):
AAAGTAAATAAAATAATAAAATA
Found at i:2653906 original size:12 final size:10
Alignment explanation
Indices: 2653871--2653951 Score: 66
Period size: 8 Copynumber: 8.3 Consensus size: 10
2653861 TTATTTAAAG
2653871 AAAATAAAAT
1 AAAATAAAAT
2653881 --AATAAAAT
1 AAAATAAAAT
2653889 AAAATAAAAGT
1 AAAATAAAA-T
2653900 GAAAATAAAAT
1 -AAAATAAAAT
*
2653911 AAAAAAGTAAAT
1 AAAATA--AAAT
2653923 -AAA-AAAAT
1 AAAATAAAAT
2653931 AAAAT-AAAT
1 AAAATAAAAT
*
2653940 -AACTAAAAT
1 AAAATAAAAT
2653949 AAA
1 AAA
2653952 GAATATTAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 20
0.73 0.02 0.25
Matches are distributed among these distances:
8 15 0.25
9 11 0.19
10 15 0.25
11 5 0.08
12 13 0.22
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.19
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:2653922 original size:17 final size:17
Alignment explanation
Indices: 2653866--2653941 Score: 66
Period size: 17 Copynumber: 4.4 Consensus size: 17
2653856 GGATTTTATT
*
2653866 TAAAGAAAATAAAATAA-
1 TAAATAAAATAAAA-AAG
**
2653883 TAAAATAAAATAAAAGTG
1 T-AAATAAAATAAAAAAG
*
2653901 AAAATAAAATAAAAAAG
1 TAAATAAAATAAAAAAG
*
2653918 TAAATAAAA-AAATAAAA
1 TAAATAAAATAAA-AAAG
2653935 TAAATAA
1 TAAATAA
2653942 CTAAAATAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
16 3 0.06
17 33 0.69
18 12 0.25
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (17 bp):
TAAATAAAATAAAAAAG
Found at i:2654378 original size:24 final size:25
Alignment explanation
Indices: 2654351--2654406 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
2654341 AATATATTAA
2654351 TAGATAACACAAAA-AAATA-ATAAT
1 TAGATAA-ACAAAAGAAATAGATAAT
* *
2654375 TAGATAAATAAAAGAAATAGATAAA
1 TAGATAAACAAAAGAAATAGATAAT
2654400 TA-ATAAA
1 TAGATAAA
2654407 AATATTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 5 0.18
24 17 0.61
25 6 0.21
ACGTcount: A:0.68, C:0.04, G:0.07, T:0.21
Consensus pattern (25 bp):
TAGATAAACAAAAGAAATAGATAAT
Found at i:2654397 original size:17 final size:15
Alignment explanation
Indices: 2654378--2654435 Score: 64
Period size: 17 Copynumber: 3.7 Consensus size: 15
2654368 TAATAATTAG
2654378 ATAAATAAAAGAAATA
1 ATAAATAAAA-AAATA
2654394 GATAAATAATAAAAATA
1 -ATAAATAA-AAAAATA
* *
2654411 TTAAATGAAAAAATA
1 ATAAATAAAAAAATA
2654426 A-AAATAAAAA
1 ATAAATAAAAA
2654436 TATTTATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 8 0.22
15 7 0.19
16 6 0.17
17 13 0.36
18 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (15 bp):
ATAAATAAAAAAATA
Found at i:2654435 original size:28 final size:28
Alignment explanation
Indices: 2654395--2654462 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
2654385 AAAGAAATAG
2654395 ATAAATAATAAAAATA-TTAAATGAAAAA
1 ATAAA-AATAAAAATATTTAAATGAAAAA
* * *
2654423 ATAAAAATAAAAATATTTATATTAAATA
1 ATAAAAATAAAAATATTTAAATGAAAAA
2654451 ATAAAAATAAAA
1 ATAAAAATAAAA
2654463 TAAAAGCTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 10 0.28
28 26 0.72
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (28 bp):
ATAAAAATAAAAATATTTAAATGAAAAA
Found at i:2654607 original size:15 final size:15
Alignment explanation
Indices: 2654587--2654635 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
2654577 CAATATTTAT
2654587 TTATAATAATATGTA
1 TTATAATAATATGTA
* *
2654602 TTATAATATTATTTA
1 TTATAATAATATGTA
*
2654617 TT-TATTAATATAGTA
1 TTATAATAATAT-GTA
2654632 TTAT
1 TTAT
2654636 TTATAAGTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 7 0.26
15 19 0.70
16 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (15 bp):
TTATAATAATATGTA
Found at i:2654792 original size:22 final size:22
Alignment explanation
Indices: 2654752--2654797 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2654742 AAAAATGATC
* *
2654752 TTATTTTTTATTAATCAATAAA
1 TTATTTTTCATTAACCAATAAA
* *
2654774 TTATTTTTCATTGACCAATCAA
1 TTATTTTTCATTAACCAATAAA
2654796 TT
1 TT
2654798 TTCTGTCAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (22 bp):
TTATTTTTCATTAACCAATAAA
Found at i:2655254 original size:26 final size:23
Alignment explanation
Indices: 2655224--2655282 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 23
2655214 TATCTCAAAC
2655224 TCAAGTTTGAGCTCGAATATAAATAA
1 TCAAGTTT-AG-TCGAATATAAA-AA
*
2655250 TCAAGCTTTTGTCGAATATAAAAA
1 TCAAG-TTTAGTCGAATATAAAAA
*
2655274 TCGAGTTTA
1 TCAAGTTTA
2655283 TTTTTATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 3 0.10
24 6 0.21
25 11 0.38
26 6 0.21
27 3 0.10
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (23 bp):
TCAAGTTTAGTCGAATATAAAAA
Found at i:2657093 original size:14 final size:14
Alignment explanation
Indices: 2657058--2657308 Score: 142
Period size: 14 Copynumber: 17.8 Consensus size: 14
2657048 GTTTTAAGGG
2657058 TTTTAGGGTTT-GA
1 TTTTAGGGTTTGGA
*
2657071 CTTTAAGGGTTTGGA
1 -TTTTAGGGTTTGGA
* *
2657086 TTTTAGGGCTTGAA
1 TTTTAGGGTTTGGA
**
2657100 TTTTAGGGAATGGA
1 TTTTAGGGTTTGGA
*
2657114 TGGTTTAGGGTTTTGA
1 T--TTTAGGGTTTGGA
*
2657130 TTTTAAGGTTTAGAGA
1 TTTTAGGGTTT-G-GA
2657146 TTTTAGGGTTTTGG-
1 TTTTAGGG-TTTGGA
** *
2657160 TTTTAAAGTTTGAGG
1 TTTTAGGGTTTG-GA
* * *
2657175 TTTGA-AGTTTTGA
1 TTTTAGGGTTTGGA
***
2657188 TTTT---G-AAAG-
1 TTTTAGGGTTTGGA
*
2657197 TTTTGGGGTTTGGA
1 TTTTAGGGTTTGGA
*
2657211 TTTTAGGGTTTTGAA
1 TTTTAGGG-TTTGGA
* *
2657226 TTTAAGGGTTTGAA
1 TTTTAGGGTTTGGA
*
2657240 TTCTAGGGTTTTGGA
1 TTTTAGGG-TTTGGA
*
2657255 TTATAGGGGTTTGGA
1 TTTTA-GGGTTTGGA
2657270 TTTTAGGGTTTGGA
1 TTTTAGGGTTTGGA
2657284 TTTTAGGGTTTTGGA
1 TTTTAGGG-TTTGGA
2657299 -TTTAGGGTTT
1 TTTTAGGGTTT
2657309 CAATTTAGGG
Statistics
Matches: 187, Mismatches: 33, Indels: 35
0.73 0.13 0.14
Matches are distributed among these distances:
9 4 0.02
10 1 0.01
11 1 0.01
12 1 0.01
13 12 0.06
14 97 0.52
15 44 0.24
16 24 0.13
17 3 0.02
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.48
Consensus pattern (14 bp):
TTTTAGGGTTTGGA
Found at i:2657186 original size:15 final size:16
Alignment explanation
Indices: 2657158--2657208 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
2657148 TTAGGGTTTT
*
2657158 GGTTTTAAAG-TTTGA
1 GGTTTGAAAGTTTTGA
2657173 GGTTTG-AAGTTTTGA
1 GGTTTGAAAGTTTTGA
* *
2657188 -TTTTGAAAGTTTTGG
1 GGTTTGAAAGTTTTGA
2657203 GGTTTG
1 GGTTTG
2657209 GATTTTAGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 7 0.24
15 18 0.62
16 4 0.14
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (16 bp):
GGTTTGAAAGTTTTGA
Found at i:2657228 original size:15 final size:15
Alignment explanation
Indices: 2657205--2657340 Score: 113
Period size: 15 Copynumber: 9.3 Consensus size: 15
2657195 AGTTTTGGGG
*
2657205 TTTGGATTTTAGGGT
1 TTTGAATTTTAGGGT
*
2657220 TTTGAATTTAAGGG-
1 TTTGAATTTTAGGGT
*
2657234 TTTGAATTCTAGGGT
1 TTTGAATTTTAGGGT
* * *
2657249 TTTGGATTATAGGGG
1 TTTGAATTTTAGGGT
*
2657264 TTTGGATTTTAGGG-
1 TTTGAATTTTAGGGT
*
2657278 TTTGGATTTTAGGGT
1 TTTGAATTTTAGGGT
*
2657293 TTTGGA-TTTAGGG-
1 TTTGAATTTTAGGGT
*
2657306 TTTCAA-TTTAGGGAT
1 TTTGAATTTTAGGG-T
*
2657321 TTTAAAATTTTA-GGT
1 TTT-GAATTTTAGGGT
2657336 TTTGA
1 TTTGA
2657341 TTTAATTATA
Statistics
Matches: 103, Mismatches: 12, Indels: 13
0.80 0.09 0.10
Matches are distributed among these distances:
13 11 0.11
14 34 0.33
15 50 0.49
16 4 0.04
17 4 0.04
ACGTcount: A:0.21, C:0.01, G:0.29, T:0.49
Consensus pattern (15 bp):
TTTGAATTTTAGGGT
Found at i:2657234 original size:29 final size:29
Alignment explanation
Indices: 2657202--2657308 Score: 137
Period size: 29 Copynumber: 3.7 Consensus size: 29
2657192 GAAAGTTTTG
*
2657202 GGGTTTGGATTTTAGGGTTTTGAATTTAA
1 GGGTTTGGATTTTAGGGTTTTGGATTTAA
* * *
2657231 GGGTTTGAATTCTAGGGTTTTGGATTATAG
1 GGGTTTGGATTTTAGGGTTTTGGATT-TAA
*
2657261 GGGTTTGGATTTTAGGG-TTTGGATTTTA
1 GGGTTTGGATTTTAGGGTTTTGGATTTAA
2657289 GGGTTTTGGA-TTTAGGGTTT
1 GGG-TTTGGATTTTAGGGTTT
2657309 CAATTTAGGG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.16
29 39 0.58
30 17 0.25
ACGTcount: A:0.17, C:0.01, G:0.35, T:0.48
Consensus pattern (29 bp):
GGGTTTGGATTTTAGGGTTTTGGATTTAA
Found at i:2657255 original size:44 final size:44
Alignment explanation
Indices: 2657205--2657308 Score: 147
Period size: 44 Copynumber: 2.4 Consensus size: 44
2657195 AGTTTTGGGG
2657205 TTTGGATTTTAGGGTTTTGAATTTAAGGGTTTGAATTCTAGGGT
1 TTTGGATTTTAGGGTTTTGAATTTAAGGGTTTGAATTCTAGGGT
* * * * * *
2657249 TTTGGATTATAGGGGTTTGGATTTTAGGGTTTGGATTTTAGGGT
1 TTTGGATTTTAGGGTTTTGAATTTAAGGGTTTGAATTCTAGGGT
2657293 TTTGGA-TTTAGGGTTT
1 TTTGGATTTTAGGGTTT
2657309 CAATTTAGGG
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 8 0.15
44 44 0.85
ACGTcount: A:0.17, C:0.01, G:0.33, T:0.49
Consensus pattern (44 bp):
TTTGGATTTTAGGGTTTTGAATTTAAGGGTTTGAATTCTAGGGT
Found at i:2658877 original size:78 final size:78
Alignment explanation
Indices: 2658788--2658941 Score: 299
Period size: 78 Copynumber: 2.0 Consensus size: 78
2658778 AAGGTTTGCA
2658788 GGGTATAGTCAGGGCTACAAGGGAGTTGGTGGTTAGTGGGGTGGAATGGCCTGTAGGGTGGGTGG
1 GGGTATAGTCAGGGCTACAAGGGAGTTGGTGGTTAGTGGGGTGGAATGGCCTGTAGGGTGGGTGG
2658853 CCAGTGGTGCCAT
66 CCAGTGGTGCCAT
*
2658866 GGGTATGGTCAGGGCTACAAGGGAGTTGGTGGTTAGTGGGGTGGAATGGCCTGTAGGGTGGGTGG
1 GGGTATAGTCAGGGCTACAAGGGAGTTGGTGGTTAGTGGGGTGGAATGGCCTGTAGGGTGGGTGG
2658931 CCAGTGGTGCC
66 CCAGTGGTGCC
2658942 GTGCAAGGCA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.16, C:0.12, G:0.49, T:0.24
Consensus pattern (78 bp):
GGGTATAGTCAGGGCTACAAGGGAGTTGGTGGTTAGTGGGGTGGAATGGCCTGTAGGGTGGGTGG
CCAGTGGTGCCAT
Found at i:2659261 original size:90 final size:91
Alignment explanation
Indices: 2659150--2659320 Score: 308
Period size: 90 Copynumber: 1.9 Consensus size: 91
2659140 TGATATGTAC
2659150 AATTAAGATATGATAGTTTTATTTATTGATCAATTTTTTTT-AAATTTATATAATTTAAATTATT
1 AATTAAGATATGATAGTTTTATTTATTGATCAATTTTTTTTAAAATTTATATAATTTAAATTATT
2659214 AATATAATTTTTAAAAATATATTAAT
66 AATATAATTTTTAAAAATATATTAAT
*
2659240 AATTTAGATATGATAGTTTTATTTATTGATCAATTTTTTTTCAAAATTTATATAATTTAAATTAT
1 AATTAAGATATGATAGTTTTATTTATTGATCAATTTTTTTT-AAAATTTATATAATTTAAATTAT
*
2659305 TACTATAATTTTTAAA
65 TAATATAATTTTTAAA
2659321 GACATAATAT
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
90 40 0.52
92 37 0.48
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (91 bp):
AATTAAGATATGATAGTTTTATTTATTGATCAATTTTTTTTAAAATTTATATAATTTAAATTATT
AATATAATTTTTAAAAATATATTAAT
Found at i:2659351 original size:90 final size:90
Alignment explanation
Indices: 2659150--2659329 Score: 279
Period size: 92 Copynumber: 2.0 Consensus size: 90
2659140 TGATATGTAC
* *
2659150 AATTAAGATATGATAGTTTTATTTATTGATCAATTTTTTTTAAATTTATATAATTTAAATTATTA
1 AATTTAGATATGATAATTTTATTTATTGATCAATTTTTTTTAAATTTATATAATTTAAATTATTA
* *
2659215 ATATAATTTTTAAAAATATATTAAT
66 ATATAATTTTTAAAAACATAATAAT
*
2659240 AATTTAGATATGATAGTTTTATTTATTGATCAATTTTTTTTCAAAATTTATATAATTTAAATTAT
1 AATTTAGATATGATAATTTTATTTATTGATCAATTTTTTTT--AAATTTATATAATTTAAATTAT
* *
2659305 TACTATAATTTTTAAAGACATAATA
64 TAATATAATTTTTAAAAACATAATA
2659330 TGACATTTAA
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
90 40 0.48
92 43 0.52
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (90 bp):
AATTTAGATATGATAATTTTATTTATTGATCAATTTTTTTTAAATTTATATAATTTAAATTATTA
ATATAATTTTTAAAAACATAATAAT
Found at i:2659369 original size:92 final size:90
Alignment explanation
Indices: 2659181--2659370 Score: 208
Period size: 92 Copynumber: 2.1 Consensus size: 90
2659171 TTTATTGATC
* *
2659181 AATTTTTTTTAAATTTATATAATTTAAATTATTAATATAATTTTTAAAAATATATTAATAATTTA
1 AATTTTTTTTAAATTTATATAATTTAAATTATTAATATAATTTTTAAAAACATAATAATAATTTA
* ** * **
2659246 GATATGATAGTTTTATTTATTGATC
66 GATATGATAATTTTATAAATTAAAA
* *
2659271 AATTTTTTTTCAAAATTTATATAATTTAAATTATTACTATAATTTTTAAAGACATAAT-ATGACA
1 AATTTTTTTT--AAATTTATATAATTTAAATTATTAATATAATTTTTAAAAACATAATAAT-A-A
*
2659335 TTTA-A-AT-TTAATTTTATAAATTAAAA
62 TTTAGATATGATAATTTTATAAATTAAAA
2659361 ATATTTTTTT
1 A-ATTTTTTT
2659371 CATTTAAAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
90 23 0.27
91 12 0.14
92 44 0.52
93 5 0.06
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (90 bp):
AATTTTTTTTAAATTTATATAATTTAAATTATTAATATAATTTTTAAAAACATAATAATAATTTA
GATATGATAATTTTATAAATTAAAA
Found at i:2660007 original size:17 final size:17
Alignment explanation
Indices: 2659977--2660016 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2659967 TAGGGTCAAT
*
2659977 TTTATGTATATAAATTA
1 TTTATATATATAAATTA
*
2659994 TTTATATATCTAAATTA
1 TTTATATATATAAATTA
*
2660011 TATATA
1 TTTATA
2660017 AAGTAAGTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTATATATATAAATTA
Found at i:2660217 original size:19 final size:19
Alignment explanation
Indices: 2660193--2660233 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2660183 TATATAAATT
2660193 AAATTTAATGATGAATTTA
1 AAATTTAATGATGAATTTA
* * *
2660212 AAATTTATTTATTAATTTA
1 AAATTTAATGATGAATTTA
2660231 AAA
1 AAA
2660234 CGAATTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
AAATTTAATGATGAATTTA
Found at i:2662414 original size:2 final size:2
Alignment explanation
Indices: 2662397--2662433 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2662387 GCTACGTACT
* *
2662397 TA TA TG TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2662434 TGTCTACATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2683124 original size:2 final size:2
Alignment explanation
Indices: 2683117--2683149 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2683107 TGCCTTCTTT
2683117 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2683150 TTCAGTATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2693364 original size:23 final size:23
Alignment explanation
Indices: 2693338--2693384 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2693328 CTTAACTAAA
*
2693338 ATTTAATAATTATTTAAATTTTT
1 ATTTAATAATTAATTAAATTTTT
**
2693361 ATTTTTTAATTAATTAAATTTTT
1 ATTTAATAATTAATTAAATTTTT
2693384 A
1 A
2693385 AATATTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTAATAATTAATTAAATTTTT
Found at i:2693404 original size:29 final size:31
Alignment explanation
Indices: 2693345--2693412 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 31
2693335 AAAATTTAAT
* *
2693345 AATTATTTAAATTTTTATTTTTTAATTAATTA
1 AATT-TTTAAATATTTATTTTTTAATCAATTA
*
2693377 AATTTTTAAATATTTA--TTTTCATCAATTA
1 AATTTTTAAATATTTATTTTTTAATCAATTA
2693406 AATTTTT
1 AATTTTT
2693413 GTTAGAGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 18 0.55
31 11 0.33
32 4 0.12
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (31 bp):
AATTTTTAAATATTTATTTTTTAATCAATTA
Found at i:2693489 original size:30 final size:29
Alignment explanation
Indices: 2693444--2693533 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 29
2693434 TATTTTTATC
* *
2693444 TAATCAAATATTTAATTGAGTAAAAATAAA
1 TAATTAAAAATTTAATTGA-TAAAAATAAA
* * *
2693474 TAATTAAAGATTTAATTTGATGAAAATAGA
1 TAATTAAAAATTTAA-TTGATAAAAATAAA
* *
2693504 TATTTAAAAATTTAATTGATCCAAAATAAA
1 TAATTAAAAATTTAATTGAT-AAAAATAAA
2693534 AGATGTACGA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
29 5 0.10
30 41 0.82
31 4 0.08
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (29 bp):
TAATTAAAAATTTAATTGATAAAAATAAA
Found at i:2695676 original size:76 final size:76
Alignment explanation
Indices: 2695550--2695704 Score: 256
Period size: 76 Copynumber: 2.0 Consensus size: 76
2695540 AACAAATAAA
* * * *
2695550 TAAACTGAATAGTGCAGCTTTCGAGTCTTATTTTAAACATGAAGACATTTCAAGCTCCAAGCCTC
1 TAAACTGAATAGTGCAACCTTCAAGTCTTATTTTAAACACGAAGACATTTCAAGCTCCAAGCCTC
2695615 CAACTAAAGAT
66 CAACTAAAGAT
*
2695626 TAAACTGAATGGTGCAACCTTCAAGTCTTATTTTAAACACGAAGACATTTCAAGCTCCAAGCCTC
1 TAAACTGAATAGTGCAACCTTCAAGTCTTATTTTAAACACGAAGACATTTCAAGCTCCAAGCCTC
*
2695691 CATCTAAAGAT
66 CAACTAAAGAT
2695702 TAA
1 TAA
2695705 GACAACAATG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (76 bp):
TAAACTGAATAGTGCAACCTTCAAGTCTTATTTTAAACACGAAGACATTTCAAGCTCCAAGCCTC
CAACTAAAGAT
Found at i:2706358 original size:33 final size:34
Alignment explanation
Indices: 2706269--2706365 Score: 117
Period size: 34 Copynumber: 2.9 Consensus size: 34
2706259 TACATTCCGG
* *
2706269 AAAGCATTACAATTATTTAAAACTTAATTTTCAA
1 AAAGCATTATAATTATTTAAAAATTAATTTTCAA
* *
2706303 AAAGTATTGTAATTATTTAAAAA-TATATTTTCAA
1 AAAGCATTATAATTATTTAAAAATTA-ATTTTCAA
* *
2706337 AAA-CATTATAATTATTCAAAAATTCATTT
1 AAAGCATTATAATTATTTAAAAATTAATTT
2706366 CCGTAAGTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
33 22 0.42
34 31 0.58
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (34 bp):
AAAGCATTATAATTATTTAAAAATTAATTTTCAA
Found at i:2710607 original size:12 final size:12
Alignment explanation
Indices: 2710590--2710615 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2710580 TTGTTCTCTT
2710590 GGTATGAATATG
1 GGTATGAATATG
2710602 GGTATGAATATG
1 GGTATGAATATG
2710614 GG
1 GG
2710616 GAATCTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (12 bp):
GGTATGAATATG
Found at i:2712258 original size:2 final size:2
Alignment explanation
Indices: 2712253--2712278 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2712243 CTCTCTCTCC
2712253 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
2712279 GAGACGGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2713987 original size:21 final size:20
Alignment explanation
Indices: 2713963--2714022 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 20
2713953 AACTACTATT
2713963 ATTAATTCTAGTTTTTAATTA
1 ATTAATTC-AGTTTTTAATTA
*
2713984 ATT-ATTAAGTTTTT--TTA
1 ATTAATTCAGTTTTTAATTA
*
2714001 ATTAA-TCAATTTTTAAATTA
1 ATTAATTCAGTTTTT-AATTA
2714021 AT
1 AT
2714023 AAATAAAGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
17 13 0.41
18 1 0.03
19 7 0.22
20 8 0.25
21 3 0.09
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (20 bp):
ATTAATTCAGTTTTTAATTA
Found at i:2714046 original size:2 final size:2
Alignment explanation
Indices: 2714039--2714078 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2714029 AGCTTAAAGT
2714039 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2714079 AACTTTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2714287 original size:22 final size:23
Alignment explanation
Indices: 2714245--2714288 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2714235 TTTTTGATAA
*
2714245 AAAATTTAAATAGATAGATTAAG
1 AAAATTTAAATAGATAAATTAAG
2714268 AAAATTTAATATA-A-AAATTAA
1 AAAATTTAA-ATAGATAAATTAA
2714289 TAATGTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 10 0.53
24 3 0.16
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (23 bp):
AAAATTTAAATAGATAAATTAAG
Found at i:2718541 original size:14 final size:14
Alignment explanation
Indices: 2718522--2718561 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2718512 GCCAAAACTG
*
2718522 ACACACACACATGC
1 ACACACACACATCC
*
2718536 ACACACACACACCC
1 ACACACACACATCC
*
2718550 ACACCCACACAT
1 ACACACACACAT
2718562 TTATACATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.50, G:0.03, T:0.05
Consensus pattern (14 bp):
ACACACACACATCC
Found at i:2718609 original size:18 final size:18
Alignment explanation
Indices: 2718597--2718634 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2718587 GATATATGTT
2718597 TATGTACATATATATATA
1 TATGTACATATATATATA
* *
2718615 TATGTAGATATACATATA
1 TATGTACATATATATATA
2718633 TA
1 TA
2718635 GGATTTAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (18 bp):
TATGTACATATATATATA
Found at i:2718646 original size:24 final size:24
Alignment explanation
Indices: 2718584--2718635 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2718574 ATACATAAAC
** *
2718584 ATAGATATATGTTTATGTACATAT
1 ATAGATATATGTAGATATACATAT
*
2718608 ATATATATATGTAGATATACATAT
1 ATAGATATATGTAGATATACATAT
2718632 ATAG
1 ATAG
2718636 GATTTAGTAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (24 bp):
ATAGATATATGTAGATATACATAT
Found at i:2721819 original size:29 final size:29
Alignment explanation
Indices: 2721777--2721842 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
2721767 CAAATATATT
* *
2721777 TTTAATTATATATTTCATTTAGGTCTCTC
1 TTTAAATATATATTTCATTTAGGTCTATC
2721806 TTTAAATATATATTTCATTTAGGTCTATC
1 TTTAAATATATATTTCATTTAGGTCTATC
*
2721835 TTTTAATA
1 TTTAAATA
2721843 CCCACAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.55
Consensus pattern (29 bp):
TTTAAATATATATTTCATTTAGGTCTATC
Found at i:2733781 original size:2 final size:2
Alignment explanation
Indices: 2733774--2733814 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2733764 CATTTCGAGC
*
2733774 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2733815 TGATTGATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2735505 original size:2 final size:2
Alignment explanation
Indices: 2735498--2735533 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2735488 GACAGAAAGA
2735498 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
2735534 TTATGCAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2738978 original size:23 final size:24
Alignment explanation
Indices: 2738942--2738995 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
2738932 ATAGGTACAA
*
2738942 TAAAA-TATTAAAATATATTAATT
1 TAAAATTATTAAAATATAATAATT
**
2738965 TAAAATTATT-AAATATAATGTTT
1 TAAAATTATTAAAATATAATAATT
2738988 TAAAATTA
1 TAAAATTA
2738996 ATTATTCGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TAAAATTATTAAAATATAATAATT
Found at i:2742013 original size:33 final size:33
Alignment explanation
Indices: 2741975--2742066 Score: 96
Period size: 33 Copynumber: 2.7 Consensus size: 33
2741965 GTGTAATAAA
* *
2741975 ATATAAAAAAAAATTTTGT-TTTAATTTATATAT
1 ATATAAAAAAAAATTTT-TATATAATTTACATAT
** *
2742008 ATATAAAAATTAATTTTTATATATTTTACATAT
1 ATATAAAAAAAAATTTTTATATAATTTACATAT
2742041 ATATAAAAATTAAAATTTTATATATA
1 ATATAAAAA--AAAATTTT-TATATA
2742067 TATATGTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
32 1 0.02
33 35 0.73
35 6 0.12
36 6 0.12
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (33 bp):
ATATAAAAAAAAATTTTTATATAATTTACATAT
Found at i:2747466 original size:11 final size:11
Alignment explanation
Indices: 2747450--2747489 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
2747440 AATCTCATAA
2747450 GAGATTTGTTT
1 GAGATTTGTTT
*
2747461 GAGATTTGTTA
1 GAGATTTGTTT
2747472 GAGATTTGTTT
1 GAGATTTGTTT
*
2747483 GGGATTT
1 GAGATTT
2747490 ATCAGATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:2762561 original size:16 final size:16
Alignment explanation
Indices: 2762540--2762579 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
2762530 TATATTAACA
2762540 TAATAAAAAATATATT
1 TAATAAAAAATATATT
*
2762556 TAAT-AAAAATATTTT
1 TAATAAAAAATATATT
*
2762571 TAAGAAAAA
1 TAATAAAAA
2762580 GTTAAAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
TAATAAAAAATATATT
Found at i:2762612 original size:33 final size:32
Alignment explanation
Indices: 2762575--2762647 Score: 76
Period size: 33 Copynumber: 2.2 Consensus size: 32
2762565 TATTTTTAAG
* *
2762575 AAAAAGTTAAAAGTATTAATTTTT-TAAAAAAAT
1 AAAAAGTTAAAAATATT--TTTTTAAAAAAAAAT
*
2762608 AAAAATTTTAAAAATATTTTTTTAAAAAAAAAT
1 AAAAA-GTTAAAAATATTTTTTTAAAAAAAAAT
*
2762641 TAAAAGT
1 AAAAAGT
2762648 ATCAATTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
32 6 0.18
33 17 0.52
34 10 0.30
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (32 bp):
AAAAAGTTAAAAATATTTTTTTAAAAAAAAAT
Found at i:2762618 original size:25 final size:27
Alignment explanation
Indices: 2762567--2762618 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 27
2762557 AATAAAAATA
*
2762567 TTTTTAAGAAAAAGTTAAAAGTATTAAT
1 TTTTTAAGAAAAAG-TAAAAATATTAAT
*
2762595 TTTTTAA-AAAAA-TAAAAATTTTAA
1 TTTTTAAGAAAAAGTAAAAATATTAA
2762619 AAATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 10 0.45
27 5 0.23
28 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (27 bp):
TTTTTAAGAAAAAGTAAAAATATTAAT
Found at i:2762629 original size:30 final size:29
Alignment explanation
Indices: 2762593--2762703 Score: 77
Period size: 30 Copynumber: 3.7 Consensus size: 29
2762583 AAAAGTATTA
2762593 ATTTTTTAAAAAAATAAAAATTTTAAAAAT
1 ATTTTTT-AAAAAATAAAAATTTTAAAAAT
*
2762623 ATTTTTT-TAAAA-AAAAA--TTAAAAGTAT
1 ATTTTTTAAAAAATAAAAATTTTAAAA--AT
* * *
2762650 CAATTTTTCTTAAAAATTAAATTTTTAAAAAT
1 --ATTTTT-TAAAAAATAAAAATTTTAAAAAT
*
2762682 ATTTTTAAAAAAAATTAAAAAT
1 ATTTTT-TAAAAAA-TAAAAAT
2762704 ATCAATTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
25 6 0.10
27 7 0.11
28 4 0.06
29 6 0.10
30 19 0.31
31 9 0.15
32 5 0.08
34 6 0.10
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (29 bp):
ATTTTTTAAAAAATAAAAATTTTAAAAAT
Found at i:2762716 original size:59 final size:56
Alignment explanation
Indices: 2762559--2762714 Score: 206
Period size: 59 Copynumber: 2.7 Consensus size: 56
2762549 ATATATTTAA
* *
2762559 TAAAAATATTTTTAAGAAAAAGTTAAAAGTATTAATTTTTTAAAAAAATAAAAATTT
1 TAAAAATATTTTTAA-AAAAAATTAAAAGTATCAATTTTTTAAAAAAATAAAAATTT
* * *
2762616 TAAAAATATTTTTTTAAAAAAAAATTAAAAGTATCAATTTTTCT-TAAAAATTAAATTTT
1 TAAAAATA--TTTTT-AAAAAAAATTAAAAGTATCAATTTTT-TAAAAAAATAAAAATTT
*
2762675 TAAAAATATTTTTAAAAAAAATTAAAAATATCAATTTTTT
1 TAAAAATATTTTTAAAAAAAATTAAAAGTATCAATTTTTT
2762715 TTGTATTAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
55 1 0.01
56 25 0.28
57 13 0.15
59 47 0.53
60 3 0.03
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.42
Consensus pattern (56 bp):
TAAAAATATTTTTAAAAAAAATTAAAAGTATCAATTTTTTAAAAAAATAAAAATTT
Done.