Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold65
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: 3097370
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.31
Warning! 315397 characters in sequence are not A, C, G, or T
File 12 of 17
Found at i:2308822 original size:6 final size:6
Alignment explanation
Indices: 2308801--2308839 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
2308791 ATCAAAATTT
*
2308801 ATATAA ATATATA ATATAA ATATAA TTAT-A ATATAA ATA
1 ATATAA ATATA-A ATATAA ATATAA ATATAA ATATAA ATA
2308840 AGTAGCTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.14
6 19 0.66
7 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
ATATAA
Found at i:2308825 original size:11 final size:12
Alignment explanation
Indices: 2308801--2308839 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
2308791 ATCAAAATTT
2308801 ATATAAATATATA
1 ATATAAATATA-A
2308814 ATATAAATATAA
1 ATATAAATATAA
*
2308826 TTAT-AATATAA
1 ATATAAATATAA
2308837 ATA
1 ATA
2308840 AGTAGCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 9 0.38
12 4 0.17
13 11 0.46
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATAAATATAA
Found at i:2311613 original size:32 final size:31
Alignment explanation
Indices: 2311570--2311631 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
2311560 TATGTAAAAT
*
2311570 TAAAATATT-AAATACTTTTTATTTTAAAATTC
1 TAAAATATTAAAATA-TTTTTA-ATTAAAATTC
*
2311602 TAAAATTTTAAAATATTTTTAATTAAAATT
1 TAAAATATTAAAATATTTTTAATTAAAATT
2311632 AAATAAGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 8 0.30
32 14 0.52
33 5 0.19
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (31 bp):
TAAAATATTAAAATATTTTTAATTAAAATTC
Found at i:2312204 original size:18 final size:17
Alignment explanation
Indices: 2312172--2312205 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2312162 TACACTTTTT
*
2312172 AATATTTGTATTAATAA
1 AATATTTGTACTAATAA
2312189 AATATATTGTACTAATA
1 AATAT-TTGTACTAATA
2312206 TTATTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (17 bp):
AATATTTGTACTAATAA
Found at i:2313128 original size:26 final size:25
Alignment explanation
Indices: 2313098--2313170 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 25
2313088 GATTATATTG
*
2313098 TATAAAAATTATAATATAATGTAATA
1 TATAAAAA-TATAATATAATATAATA
*
2313124 TATAAATATATTAATAT-ATATAATA
1 TATAAAAATA-TAATATAATATAATA
*
2313149 TTTAATAAATATAA-AT-ATATAA
1 TATAA-AAATATAATATAATATAA
2313171 ATTATTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 8 0.20
25 16 0.39
26 17 0.41
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (25 bp):
TATAAAAATATAATATAATATAATA
Found at i:2313133 original size:18 final size:17
Alignment explanation
Indices: 2313107--2313168 Score: 74
Period size: 16 Copynumber: 3.6 Consensus size: 17
2313097 GTATAAAAAT
2313107 TATAATATAATGTAATATA
1 TATAATAT-AT-TAATATA
2313126 TA-AATATATTAATATA
1 TATAATATATTAATATA
*
2313142 TATAATAT-TTAATAAA
1 TATAATATATTAATATA
2313158 TATAAATATAT
1 TAT-AATATAT
2313169 AAATTATTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
16 19 0.49
17 12 0.31
18 6 0.15
19 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TATAATATATTAATATA
Found at i:2313154 original size:7 final size:8
Alignment explanation
Indices: 2313109--2313179 Score: 56
Period size: 8 Copynumber: 8.5 Consensus size: 8
2313099 ATAAAAATTA
2313109 TAATATAAT
1 TAATAT-AT
2313118 GTAATATAT
1 -TAATATAT
*
2313127 AAATATAT
1 TAATATAT
2313135 TAATATAT
1 TAATATAT
2313143 ATAATAT-T
1 -TAATATAT
2313151 TAATAAATAT
1 TAAT--ATAT
*
2313161 AAATATAT
1 TAATATAT
*
2313169 AAAT-TAT
1 TAATATAT
2313176 TAAT
1 TAAT
2313180 TTTTAAGCGA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
7 10 0.19
8 23 0.43
9 10 0.19
10 10 0.19
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (8 bp):
TAATATAT
Found at i:2313185 original size:32 final size:34
Alignment explanation
Indices: 2313123--2313185 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
2313113 ATAATGTAAT
*
2313123 ATATAAATATATTAATATATATAATATTTAATAA
1 ATATAAATATATAAATATATATAATATTTAATAA
*
2313157 ATATAAATATATAAAT-TAT-TAATTTTTAA
1 ATATAAATATATAAATATATATAATATTTAA
2313186 GCGAAGCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 9 0.33
33 3 0.11
34 15 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (34 bp):
ATATAAATATATAAATATATATAATATTTAATAA
Found at i:2313643 original size:2 final size:2
Alignment explanation
Indices: 2313638--2313662 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2313628 TTTGTGTGTG
2313638 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
2313663 TTGCCTAAAA
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:2314247 original size:2 final size:2
Alignment explanation
Indices: 2314240--2314277 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2314230 TTCATTTGAT
2314240 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2314278 AAGAGGATTT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2314425 original size:2 final size:2
Alignment explanation
Indices: 2314413--2314456 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2314403 ATTTTCGTAC
*
2314413 AT AT GT 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
2314455 AT
1 AT
2314457 CAACTATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2314767 original size:12 final size:11
Alignment explanation
Indices: 2314741--2314765 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2314731 ACTTTTATGG
2314741 TTTAAAAAATA
1 TTTAAAAAATA
2314752 TTTAAAAAATA
1 TTTAAAAAATA
2314763 TTT
1 TTT
2314766 TATATTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TTTAAAAAATA
Found at i:2314786 original size:21 final size:21
Alignment explanation
Indices: 2314760--2314800 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2314750 TATTTAAAAA
* *
2314760 ATATTTTATATTAATATTTAT
1 ATATTTTATAATAAAATTTAT
2314781 ATATTTTATAATAAAATTTA
1 ATATTTTATAATAAAATTTA
2314801 ATAAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATTTTATAATAAAATTTAT
Found at i:2317421 original size:24 final size:25
Alignment explanation
Indices: 2317394--2317447 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
2317384 AATATTTTAC
* *
2317394 AAATTATTATTTTGAATAA-TATTA
1 AAATAATTAATTTGAATAACTATTA
*
2317418 AAATAATTAATTTGTATAACTATTA
1 AAATAATTAATTTGAATAACTATTA
*
2317443 CAATA
1 AAATA
2317448 TGTGCAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (25 bp):
AAATAATTAATTTGAATAACTATTA
Found at i:2318745 original size:3 final size:3
Alignment explanation
Indices: 2318737--2318762 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2318727 CTCTTCACTA
2318737 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
2318763 ATCTAATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:2318815 original size:2 final size:2
Alignment explanation
Indices: 2318810--2318836 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2318800 ATATTATTGG
2318810 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2318837 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2323021 original size:2 final size:2
Alignment explanation
Indices: 2323016--2323058 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2323006 AAATTTCACG
2323016 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2323058 T
1 T
2323059 CCTTTTTGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2327551 original size:7 final size:7
Alignment explanation
Indices: 2327488--2327570 Score: 50
Period size: 7 Copynumber: 12.3 Consensus size: 7
2327478 TATAATACGA
2327488 AATATAT
1 AATATAT
2327495 AA-AT-T
1 AATATAT
2327500 AATATAT
1 AATATAT
2327507 AAGT-TAT
1 AA-TATAT
**
2327514 TGTATAT
1 AATATAT
2327521 AAATATAT
1 -AATATAT
* *
2327529 GATTTAT
1 AATATAT
2327536 AAT-TAT
1 AATATAT
2327542 AATATAT
1 AATATAT
2327549 AAT-TAT
1 AATATAT
* *
2327555 TATTTAT
1 AATATAT
*
2327562 AATAAAT
1 AATATAT
2327569 AA
1 AA
2327571 AAAATTAATT
Statistics
Matches: 58, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
5 3 0.05
6 16 0.28
7 33 0.57
8 6 0.10
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (7 bp):
AATATAT
Found at i:2327561 original size:20 final size:20
Alignment explanation
Indices: 2327499--2327570 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
2327489 ATATATAAAT
* *
2327499 TAATATATAAGTTATTGTATA
1 TAATATATAA-TTATTATTTA
* *
2327520 TAAATATATGATT-TATAATTA
1 T-AATATATAATTAT-TATTTA
2327541 TAATATATAATTATTATTTA
1 TAATATATAATTATTATTTA
*
2327561 TAATAAATAA
1 TAATATATAA
2327571 AAAATTAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
20 25 0.61
21 8 0.20
22 8 0.20
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (20 bp):
TAATATATAATTATTATTTA
Found at i:2332403 original size:66 final size:66
Alignment explanation
Indices: 2332297--2332430 Score: 250
Period size: 66 Copynumber: 2.0 Consensus size: 66
2332287 AAATAATTAC
2332297 TCAATTGGTGATGCAAAGGACTTGAACAAGGAAAAGAGAGATAGATAAGGCTTGATGATAAAATT
1 TCAATTGGTGATGCAAAGGACTTGAACAAGGAAAAGAGAGATAGATAAGGCTTGATGATAAAATT
2332362 T
66 T
* *
2332363 TCAATTGGTGATGCAAAGGACTTGAACAAGGAAAAGAGAGATAGATAAGGTTTGGTGATAAAATT
1 TCAATTGGTGATGCAAAGGACTTGAACAAGGAAAAGAGAGATAGATAAGGCTTGATGATAAAATT
2332428 T
66 T
2332429 TC
1 TC
2332431 TTTTTCCTTG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.41, C:0.07, G:0.26, T:0.25
Consensus pattern (66 bp):
TCAATTGGTGATGCAAAGGACTTGAACAAGGAAAAGAGAGATAGATAAGGCTTGATGATAAAATT
T
Found at i:2334403 original size:21 final size:21
Alignment explanation
Indices: 2334369--2334436 Score: 84
Period size: 23 Copynumber: 3.1 Consensus size: 21
2334359 GATTTAACTT
*
2334369 ATTTTTAATTATATATAT-TA
1 ATTTTTATTTATATATATATA
2334389 ATTTTGTATTTATATATTATATA
1 ATTTT-TATTTATATA-TATATA
2334412 ATTTTTATTATATAATATATATA
1 ATTTTTATT-TAT-ATATATATA
2334435 AT
1 AT
2334437 ATATTATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
20 5 0.12
21 9 0.21
22 7 0.17
23 18 0.43
24 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (21 bp):
ATTTTTATTTATATATATATA
Found at i:2334506 original size:14 final size:14
Alignment explanation
Indices: 2334489--2334522 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2334479 ATTCTAAAAT
2334489 TTAATTAAAAATTA
1 TTAATTAAAAATTA
**
2334503 TTAATTATTAATTA
1 TTAATTAAAAATTA
2334517 TTAATT
1 TTAATT
2334523 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTAATTAAAAATTA
Found at i:2334508 original size:7 final size:7
Alignment explanation
Indices: 2334498--2334522 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2334488 TTTAATTAAA
2334498 AATTATT
1 AATTATT
2334505 AATTATT
1 AATTATT
2334512 AATTATT
1 AATTATT
2334519 AATT
1 AATT
2334523 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTATT
Found at i:2341419 original size:24 final size:23
Alignment explanation
Indices: 2341388--2341433 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2341378 AATATTTAAA
*
2341388 TTTTAAATATATTAAAT-ATTATT
1 TTTTAAATA-AATAAATAATTATT
2341411 TTTTAAAATAAATAAATAATTAT
1 TTTT-AAATAAATAAATAATTAT
2341434 ATAAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTAAATAAATAAATAATTATT
Found at i:2341765 original size:31 final size:32
Alignment explanation
Indices: 2341708--2341767 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
2341698 ATCAAAATAA
* *
2341708 AAATATTTATATAATATTTTTATTAAATACAT
1 AAATATTTATATAATAATATTATTAAATACAT
*
2341740 AAATATTT-TATATTAATATTATTAAATA
1 AAATATTTATATAATAATATTATTAAATA
2341768 AATATTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (32 bp):
AAATATTTATATAATAATATTATTAAATACAT
Found at i:2342350 original size:20 final size:20
Alignment explanation
Indices: 2342325--2342367 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
2342315 CATAAATGCA
2342325 TTTGGATGCATGATACGAGT
1 TTTGGATGCATGATACGAGT
*
2342345 TTTGGATGCGTGATACGAGT
1 TTTGGATGCATGATACGAGT
2342365 TTT
1 TTT
2342368 TTTTTTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.09, G:0.30, T:0.40
Consensus pattern (20 bp):
TTTGGATGCATGATACGAGT
Found at i:2344958 original size:19 final size:19
Alignment explanation
Indices: 2344921--2344960 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2344911 AATACAAATA
* **
2344921 TATTTTTTTAAAATTTTTT
1 TATTTATTTAAAAAATTTT
2344940 TATTTATTTAAAAAATTTT
1 TATTTATTTAAAAAATTTT
2344959 TA
1 TA
2344961 AAAGATTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTATTTAAAAAATTTT
Found at i:2346516 original size:18 final size:18
Alignment explanation
Indices: 2346493--2346528 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2346483 GAGCTTTTTC
*
2346493 AAATCATCAAAGAAAATA
1 AAATCATAAAAGAAAATA
*
2346511 AAATCATAAAATAAAATA
1 AAATCATAAAAGAAAATA
2346529 TTTTTGTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.08, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCATAAAAGAAAATA
Found at i:2348343 original size:6 final size:6
Alignment explanation
Indices: 2348322--2348374 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
2348312 TTGTGTCTCA
2348322 ATTTA- ATTTA- ATTTAT ATTTAT -TTT-T -TTTAT ATTTAT ATTATAT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATT-TAT
*
2348366 AATTAT ATT
1 ATTTAT ATT
2348375 ATGTAAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
4 4 0.10
5 14 0.33
6 19 0.45
7 5 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTAT
Found at i:2348416 original size:13 final size:13
Alignment explanation
Indices: 2348398--2348422 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2348388 TTATTCAAAG
2348398 ATAAATTTATTTA
1 ATAAATTTATTTA
2348411 ATAAATTTATTT
1 ATAAATTTATTT
2348423 GTGTGAGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATAAATTTATTTA
Found at i:2348548 original size:19 final size:19
Alignment explanation
Indices: 2348517--2348565 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
2348507 ATTAATATCT
*
2348517 ATAAATATTAAT-ATAAAA
1 ATAAATTTTAATAATAAAA
*
2348535 ATAATATTTTAATAATATAA
1 ATAA-ATTTTAATAATAAAA
2348555 ATAAATTTTAA
1 ATAAATTTTAA
2348566 GAAAAGTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 4 0.15
19 14 0.52
20 9 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAAATTTTAATAATAAAA
Found at i:2351795 original size:32 final size:31
Alignment explanation
Indices: 2351759--2351858 Score: 80
Period size: 31 Copynumber: 3.2 Consensus size: 31
2351749 ATTTTAATTA
2351759 TTAATTATTAATAAAATTATTTTTATTTAAAT
1 TTAATTATTAATAAAA-TATTTTTATTTAAAT
* * *
2351791 TTAATTATAAAATAAAA-AATATTATTTAATAT
1 TTAATTAT-TAATAAAATATTTTTATTTAA-AT
* * *
2351823 TTTA-TAATAATAATATGATTTTT-TTTAAAAT
1 TTAATTATTAATAAAAT-ATTTTTATTT-AAAT
2351854 TTAAT
1 TTAAT
2351859 CTAATTTAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
30 6 0.12
31 20 0.38
32 19 0.37
33 7 0.13
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (31 bp):
TTAATTATTAATAAAATATTTTTATTTAAAT
Found at i:2351991 original size:3 final size:3
Alignment explanation
Indices: 2351983--2352010 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2351973 GACAGATCAG
2351983 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2352011 TTTTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2352680 original size:21 final size:20
Alignment explanation
Indices: 2352631--2352682 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
2352621 TTTAATTTCA
2352631 AACTCAAATTTAAATTTGTT
1 AACTCAAATTTAAATTTGTT
** *
2352651 ATTTAAAATTTAAAATTT-TGT
1 AACTCAAATTT-AAATTTGT-T
2352672 AACTCAAATTT
1 AACTCAAATTT
2352683 GATTTGAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (20 bp):
AACTCAAATTTAAATTTGTT
Found at i:2352918 original size:32 final size:30
Alignment explanation
Indices: 2352867--2352925 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 30
2352857 AACAACTAAA
2352867 ATTACATATTAAAATATTTAAACTTAATTC
1 ATTACATATTAAAATATTTAAACTTAATTC
2352897 ATTACATAACTTAAACA-ATTTAAACTTAA
1 ATTACAT-A-TTAAA-ATATTTAAACTTAA
2352926 ACTCAACTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 7 0.27
31 1 0.04
32 17 0.65
33 1 0.04
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (30 bp):
ATTACATATTAAAATATTTAAACTTAATTC
Found at i:2353802 original size:27 final size:27
Alignment explanation
Indices: 2353772--2353825 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
2353762 TCAAATAATA
*
2353772 AAAATACATATACGAAGCCAAAAGACT
1 AAAATACATATACAAAGCCAAAAGACT
*
2353799 AAAATACATATATAAAGCCAAAAGACT
1 AAAATACATATACAAAGCCAAAAGACT
2353826 CTTGCCTGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.57, C:0.17, G:0.09, T:0.17
Consensus pattern (27 bp):
AAAATACATATACAAAGCCAAAAGACT
Found at i:2354841 original size:23 final size:21
Alignment explanation
Indices: 2354812--2354864 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
2354802 TTATCATTAA
2354812 ATAAAAATAT-AAAAAATAATGTT
1 ATAAAAATATGAAAAAAT-A--TT
*
2354835 ATAAAAATATGAATAAATATT
1 ATAAAAATATGAAAAAATATT
2354856 ATAAAAATA
1 ATAAAAATA
2354865 AAATCTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 11 0.39
23 11 0.39
24 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (21 bp):
ATAAAAATATGAAAAAATATT
Found at i:2356894 original size:20 final size:20
Alignment explanation
Indices: 2356850--2356895 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
2356840 CATTATTAAA
2356850 AAATTAACTATTTTAAAAAT
1 AAATTAACTATTTTAAAAAT
* *
2356870 TAATTAA-TATTTTAGATAAT
1 AAATTAACTATTTTA-AAAAT
2356890 AAATTA
1 AAATTA
2356896 TAATTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
AAATTAACTATTTTAAAAAT
Found at i:2357539 original size:14 final size:14
Alignment explanation
Indices: 2357520--2357550 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2357510 ATATTCAATT
*
2357520 TTAAATTAAATTAA
1 TTAAATTAAATGAA
2357534 TTAAATTAAATGAA
1 TTAAATTAAATGAA
2357548 TTA
1 TTA
2357551 GGGACAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
TTAAATTAAATGAA
Found at i:2358839 original size:17 final size:17
Alignment explanation
Indices: 2358804--2358839 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2358794 AATAAAACAC
*
2358804 AATAATAACATTATAAA
1 AATAATAACAATATAAA
2358821 AATAATAACAATACTAAA
1 AATAATAACAATA-TAAA
2358839 A
1 A
2358840 GTCTTGGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (17 bp):
AATAATAACAATATAAA
Found at i:2359487 original size:20 final size:20
Alignment explanation
Indices: 2359459--2359499 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2359449 TTTTAATTTT
* *
2359459 AAATTAAATTAAAACTTTAA
1 AAATAAAATTAAAACCTTAA
*
2359479 AAATAAAATTTAAACCTTAA
1 AAATAAAATTAAAACCTTAA
2359499 A
1 A
2359500 TCGGACTGGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAAAATTAAAACCTTAA
Found at i:2359723 original size:2 final size:2
Alignment explanation
Indices: 2359716--2359743 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2359706 GAAAGTTTAC
2359716 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
2359744 TACAAAAAAT
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:2359844 original size:35 final size:33
Alignment explanation
Indices: 2359774--2359851 Score: 93
Period size: 35 Copynumber: 2.3 Consensus size: 33
2359764 ATTTTATTTT
* * *
2359774 AAATTAAATAATTATAATACATTTAACTCATTA
1 AAATAAAATAATTATAATAAATTTAACTCAATA
* *
2359807 AAATAAAATAATTATAATAATAATTTAATTTAATA
1 AAATAAAATAATTATAAT-A-AATTTAACTCAATA
2359842 AAATAAAATA
1 AAATAAAATA
2359852 TAAAATGCGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
33 17 0.45
34 1 0.03
35 20 0.53
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (33 bp):
AAATAAAATAATTATAATAAATTTAACTCAATA
Found at i:2360290 original size:13 final size:14
Alignment explanation
Indices: 2360267--2360295 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2360257 GATTGATTTT
2360267 TTATATTAAAAAAA
1 TTATATTAAAAAAA
2360281 TTAT-TTAAAAAAA
1 TTATATTAAAAAAA
2360294 TT
1 TT
2360296 TAAATTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTATATTAAAAAAA
Found at i:2360331 original size:26 final size:26
Alignment explanation
Indices: 2360274--2360331 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
2360264 TTTTTATATT
* *
2360274 AAAA-AAATTATTTAAAAAAATTTAA
1 AAAATAAATAATTCAAAAAAATTTAA
** *
2360299 ATTATAAATAATTCAAATAAATTTAA
1 AAAATAAATAATTCAAAAAAATTTAA
2360325 AAAATAA
1 AAAATAA
2360332 TATTTAATTA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAATAAATAATTCAAAAAAATTTAA
Found at i:2360394 original size:2 final size:2
Alignment explanation
Indices: 2360389--2360418 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2360379 ATAGCAAATA
2360389 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
2360419 TCGACTGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2360803 original size:26 final size:25
Alignment explanation
Indices: 2360770--2360831 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
2360760 TATTATTATG
2360770 ATAAAATTATA-AAAAATAATATAAAA
1 ATAAAATTATATAAAAAT-ATAT-AAA
* *
2360796 ATAAAATTATATTAAAATTTATAAA
1 ATAAAATTATATAAAAATATATAAA
2360821 ATATAAATTAT
1 ATA-AAATTAT
2360832 TAATATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 6 0.19
26 21 0.66
27 5 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
ATAAAATTATATAAAAATATATAAA
Found at i:2360857 original size:18 final size:18
Alignment explanation
Indices: 2360804--2360857 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
2360794 AAATAAAATT
2360804 ATATTAAAATTTATA-AA
1 ATATTAAAATTTATATAA
2360821 ATA-T-AAA-TTAT-TAA
1 ATATTAAAATTTATATAA
2360835 TATATTAAAATTTATATAA
1 -ATATTAAAATTTATATAA
2360854 ATAT
1 ATAT
2360858 ATAATATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
14 6 0.19
15 6 0.19
16 2 0.06
17 6 0.19
18 8 0.26
19 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATTAAAATTTATATAA
Found at i:2362478 original size:90 final size:90
Alignment explanation
Indices: 2362322--2362502 Score: 310
Period size: 90 Copynumber: 2.0 Consensus size: 90
2362312 GTTTTGCACT
2362322 CAACTCTAATAATGCATTCATTCTCTCGATCTACCCATCTTGCATCAACACTCTTTTACTAACAA
1 CAACTCTAATAATGCATTCATTCTCTCGATCTACCCATCTTGCATCAACACTCTTTTACTAACAA
2362387 AGTTTGATACATCAATATCATCTAC
66 AGTTTGATACATCAATATCATCTAC
* * * *
2362412 CAACTCTGATAATGCATTTC-TTCTCTCGATCTGCCCATCTTGCATCAATACTCTTTTACTAGCA
1 CAACTCTAATAATGCA-TTCATTCTCTCGATCTACCCATCTTGCATCAACACTCTTTTACTAACA
2362476 AAGTTTGATACATCAATATCATCTAC
65 AAGTTTGATACATCAATATCATCTAC
2362502 C
1 C
2362503 TCTCTCTTAG
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
90 83 0.97
91 3 0.03
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (90 bp):
CAACTCTAATAATGCATTCATTCTCTCGATCTACCCATCTTGCATCAACACTCTTTTACTAACAA
AGTTTGATACATCAATATCATCTAC
Found at i:2364491 original size:267 final size:266
Alignment explanation
Indices: 2364017--2364547 Score: 850
Period size: 267 Copynumber: 2.0 Consensus size: 266
2364007 AGAGCACCTT
*
2364017 GCATCTCCTCCTTGAGCCCCTACTCCGTGGAGTCTAGCTCTTCGATACGGCTCTCCACTATCTCA
1 GCATCTCCTCCTTGAGCCCATACTCCGTGGAGTCTAGCTCTTCGATACGGCTCTCCACTATCTCA
* * *
2364082 AGGTTTTCTCGCATATCTCCAACGGTCACCTCGAGCTTGGCCACCCTACCATCCATGGCCGATAG
66 AGGTTTTCCCACATATCTCCAACGGTCACCTCGAGCTTGGCCAACCTACCATCCATGGCCGATAG
* * * *
2364147 AACATCCCTTGAGCTACTGGCCTTCTTTCTTCTCCCACGAGTCTCCAGGACCTCTTGTGTCTGGT
131 AACATCCCTCGAACTACTAGCCTTCTTTCCTCTCCCACGAGTCTCCAGGACCTCTTGTGTCTGGT
** *
2364212 TTTCTGCTTGAGA-TGCTATCTCTATGATCAGTAGATTCACAAAACTCGAGCTTTGATACCAACT
196 TTTCTGCTTGAGACT-CTATCTCTACAATCAGTACATTCACAAAACTCGAGCTTTGATACCAACT
2364276 GTCACAG
260 GTCACAG
*
2364283 GCATCTCCTCCTTGAGCCCATACTCCGTGGAGTCTAGCTCTTCGATGCGGCTCTCCACTATCTCT
1 GCATCTCCTCCTTGAGCCCATACTCCGTGGAGTCTAGCTCTTCGATACGGCTCTCCACTATCTC-
* *
2364348 AAGGTTTTCCCACATATCTCCAACGGTCACCTCGAGCTTGGTCAACCTGCCATCCATGGCCGATA
65 AAGGTTTTCCCACATATCTCCAACGGTCACCTCGAGCTTGGCCAACCTACCATCCATGGCCGATA
* * *
2364413 GAACATCCCTCGAACTGCTAGCCTTCTTTCCTCTCCCACGAGTCTCTAGGACCTTTTGTGTCTGG
130 GAACATCCCTCGAACTACTAGCCTTCTTTCCTCTCCCACGAGTCTCCAGGACCTCTTGTGTCTGG
* *
2364478 CTTTT-TGCTTGAGACTCTATCTCTACAATTAGTACTTTCACAAAACTCGAGCTTTGATACCAAC
195 -TTTTCTGCTTGAGACTCTATCTCTACAATCAGTACATTCACAAAACTCGAGCTTTGATACCAAC
2364542 TGTCAC
259 TGTCAC
2364548 GGGCCTGGAC
Statistics
Matches: 243, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
266 62 0.26
267 176 0.72
268 5 0.02
ACGTcount: A:0.20, C:0.32, G:0.17, T:0.31
Consensus pattern (266 bp):
GCATCTCCTCCTTGAGCCCATACTCCGTGGAGTCTAGCTCTTCGATACGGCTCTCCACTATCTCA
AGGTTTTCCCACATATCTCCAACGGTCACCTCGAGCTTGGCCAACCTACCATCCATGGCCGATAG
AACATCCCTCGAACTACTAGCCTTCTTTCCTCTCCCACGAGTCTCCAGGACCTCTTGTGTCTGGT
TTTCTGCTTGAGACTCTATCTCTACAATCAGTACATTCACAAAACTCGAGCTTTGATACCAACTG
TCACAG
Found at i:2364793 original size:205 final size:206
Alignment explanation
Indices: 2364433--2364832 Score: 660
Period size: 205 Copynumber: 1.9 Consensus size: 206
2364423 CGAACTGCTA
*
2364433 GCCTTCTTTCCTCTCCCACGAGTCTCTAGGACCTTTTGTGTCTGGCTTTTTGCTTGAGACTCTAT
1 GCCTTCTTTCCTCTCCCACGAGTCTCCAGGACCTTTTGTGTCTGGCTTTTTGCTTGAGACTCTAT
* * *
2364498 CTCTACAATTAGTACTTTCACAAAACTCGAGCTTTGATACCAACTGTCACGGGCCTGGACTTTAG
66 CTCTACAATCAGTACCTTCACAAAACTCGAGCTTTGATACCAACTGTCACGGGCCTAGACTTTAG
* * * *
2364563 CCTAGCAAGCCACGTGGCCTTAGGCTGGAAAATCACTTTCTTGTATGCCTAAGTCAGTTTTTAAA
131 CCTAGCAAGCCACGCGACCTTAGGCTCGAAAATCACTTTCTTGTATGCCTAAGTCAGCTTTTAAA
2364628 CACTTAAAAAT
196 CACTTAAAAAT
* *
2364639 GCCTTCTTTCCTCTCCCACGAGTCTCCAGGACCTTTTGTGTCTGGTTTTTTGCTTGAGAGT-TAT
1 GCCTTCTTTCCTCTCCCACGAGTCTCCAGGACCTTTTGTGTCTGGCTTTTTGCTTGAGACTCTAT
* *
2364703 CTCTACGATCAGTACCTTCACAAAACTCGAGCTTTGATACCAACTGTCACGGGCTTAGACTTTAG
66 CTCTACAATCAGTACCTTCACAAAACTCGAGCTTTGATACCAACTGTCACGGGCCTAGACTTTAG
*
2364768 CCTAGCAAAG-CACGCGACTTTAGGCTCGAAAATCACTTTCTTGTATGCCTAAGTCAGCTTTTAA
131 CCTAGC-AAGCCACGCGACCTTAGGCTCGAAAATCACTTTCTTGTATGCCTAAGTCAGCTTTTAA
2364832 A
195 A
2364833 GGGAAACTCT
Statistics
Matches: 180, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
205 119 0.66
206 61 0.34
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (206 bp):
GCCTTCTTTCCTCTCCCACGAGTCTCCAGGACCTTTTGTGTCTGGCTTTTTGCTTGAGACTCTAT
CTCTACAATCAGTACCTTCACAAAACTCGAGCTTTGATACCAACTGTCACGGGCCTAGACTTTAG
CCTAGCAAGCCACGCGACCTTAGGCTCGAAAATCACTTTCTTGTATGCCTAAGTCAGCTTTTAAA
CACTTAAAAAT
Found at i:2367142 original size:18 final size:19
Alignment explanation
Indices: 2367117--2367162 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
2367107 TTTATAATTA
*
2367117 AATTTAATTAA-AAATATT
1 AATTTAATTAATAAATAAT
*
2367135 ATTTTAATTAATAAATAAT
1 AATTTAATTAATAAATAAT
2367154 AATTTAATT
1 AATTTAATT
2367163 TAATTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATTTAATTAATAAATAAT
Found at i:2368148 original size:28 final size:29
Alignment explanation
Indices: 2368102--2368158 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
2368092 ATGAGGATTC
*
2368102 TATTTATATATACTTTATCAAAAAATTTA
1 TATTTATATATACTCTATCAAAAAATTTA
*
2368131 TATTTAT-TATACTCTATCAAGAAATTTA
1 TATTTATATATACTCTATCAAAAAATTTA
2368159 CGCTGTGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (29 bp):
TATTTATATATACTCTATCAAAAAATTTA
Found at i:2371789 original size:38 final size:40
Alignment explanation
Indices: 2371724--2371805 Score: 114
Period size: 38 Copynumber: 2.1 Consensus size: 40
2371714 AAATCTTTAA
*
2371724 TTTTTATCTGAAACTTTTAAATACAAAAATGACAAAAAGC
1 TTTTTATCTGAAACTTTCAAATACAAAAATGACAAAAAGC
* * *
2371764 TTTTT-TCTGCAAC-TTCAAATGCAAAAATGGCAAAAAGC
1 TTTTTATCTGAAACTTTCAAATACAAAAATGACAAAAAGC
2371802 TTTT
1 TTTT
2371806 GATGGAAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 26 0.68
39 7 0.18
40 5 0.13
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (40 bp):
TTTTTATCTGAAACTTTCAAATACAAAAATGACAAAAAGC
Found at i:2372239 original size:20 final size:21
Alignment explanation
Indices: 2372202--2372241 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2372192 GTTAATTTTT
*
2372202 TTAATTTATATGAATTTTAAG
1 TTAATTTAAATGAATTTTAAG
2372223 TTAATTTAAAT-AATTTTAA
1 TTAATTTAAATGAATTTTAA
2372242 ATTTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TTAATTTAAATGAATTTTAAG
Found at i:2372770 original size:15 final size:16
Alignment explanation
Indices: 2372751--2372792 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2372741 GATGAATTAA
2372751 ATTAAATTATAATTTT
1 ATTAAATTATAATTTT
* *
2372767 -TTAATTTTTAATTTT
1 ATTAAATTATAATTTT
2372782 AATTAAATTAT
1 -ATTAAATTAT
2372793 TTAAAATAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
15 13 0.65
17 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTAAATTATAATTTT
Found at i:2378812 original size:2 final size:2
Alignment explanation
Indices: 2378805--2378840 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2378795 TTAATGGGGA
2378805 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
2378841 TCTTCCTTTA
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:2379135 original size:25 final size:25
Alignment explanation
Indices: 2379107--2379159 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
2379097 ACCCATAAAT
*
2379107 TAATATATTATATAAATATAAAAAA
1 TAATATATTATATAAATAAAAAAAA
* **
2379132 TAATATATTTTATAGTTAAAAAAAA
1 TAATATATTATATAAATAAAAAAAA
2379157 TAA
1 TAA
2379160 ACCATAGCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
TAATATATTATATAAATAAAAAAAA
Found at i:2379748 original size:36 final size:37
Alignment explanation
Indices: 2379705--2379807 Score: 101
Period size: 36 Copynumber: 2.9 Consensus size: 37
2379695 TTGCTGTTAT
2379705 ATTTATATAAT-TTTTATATTATAATTATATTTAA-A
1 ATTTATATAATATTTTATATTATAATTATATTTAATA
* * *
2379740 ATATTATATATTTATTTTAAATTTTAA-TATA-TTAATA
1 AT-TTATATA-ATATTTTATATTATAATTATATTTAATA
* *
2379777 ATTTAT-TAATATTTTTTATTAT-TTTATATTT
1 ATTTATATAATATTTTATATTATAATTATATTT
2379808 TTACTCATGT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
34 14 0.26
35 6 0.11
36 15 0.28
37 8 0.15
38 11 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (37 bp):
ATTTATATAATATTTTATATTATAATTATATTTAATA
Found at i:2379769 original size:21 final size:20
Alignment explanation
Indices: 2379720--2379772 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
2379710 TATAATTTTT
2379720 ATATTATA-ATTATATTTAAA
1 ATATTATATATT-TATTTAAA
*
2379740 ATATTATATATTTATTTTAA
1 ATATTATATATTTATTTAAA
*
2379760 ATTTTAATATATT
1 ATATT-ATATATT
2379773 AATAATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTATATATTTATTTAAA
Found at i:2384806 original size:24 final size:23
Alignment explanation
Indices: 2384766--2384810 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
2384756 TGTTATGTTG
2384766 CTCCTAACCATAGCTTAAACTGC
1 CTCCTAACCATAGCTTAAACTGC
*
2384789 CTCCTAAGCACTAGCTTAAACT
1 CTCCTAACCA-TAGCTTAAACT
2384811 CCCTTTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.31, C:0.33, G:0.09, T:0.27
Consensus pattern (23 bp):
CTCCTAACCATAGCTTAAACTGC
Found at i:2385945 original size:34 final size:35
Alignment explanation
Indices: 2385897--2385980 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 35
2385887 AAATCCAAGC
* * *
2385897 AAATTTCAAAATCAAGCGTCT-AAGACC-CTGAAGT
1 AAATTTCAAGATCAAG-GTCTCAAAACCTCTGAAGA
*
2385931 AAATTTCAAGATCAA-GTCTCAAAACCTTTGAAGA
1 AAATTTCAAGATCAAGGTCTCAAAACCTCTGAAGA
2385965 AAATTTCAAGATCAAG
1 AAATTTCAAGATCAAG
2385981 TCATCCAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
32 4 0.09
33 5 0.12
34 34 0.79
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (35 bp):
AAATTTCAAGATCAAGGTCTCAAAACCTCTGAAGA
Found at i:2389522 original size:3 final size:3
Alignment explanation
Indices: 2389514--2389544 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2389504 TAAAAAGATT
2389514 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2389545 ACATGAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2389870 original size:2 final size:2
Alignment explanation
Indices: 2389863--2389887 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2389853 CCAAAACCTA
2389863 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
2389888 ATTACAGTTA
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:2390016 original size:22 final size:22
Alignment explanation
Indices: 2389991--2390041 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2389981 TAATTATAAA
* *
2389991 ATTTTCTAATATGTTATTAATC
1 ATTTACTAATATCTTATTAATC
* *
2390013 ATTTACTATTATCTTATTCATC
1 ATTTACTAATATCTTATTAATC
*
2390035 AATTACT
1 ATTTACT
2390042 GTCTTTCTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.31, C:0.14, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTACTAATATCTTATTAATC
Found at i:2404239 original size:15 final size:15
Alignment explanation
Indices: 2404208--2404244 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2404198 AATAAAAATT
2404208 TAAAACA-TTTAAAA
1 TAAAACATTTTAAAA
*
2404222 TAAAACATTTTAACA
1 TAAAACATTTTAAAA
2404237 T-AAACATT
1 TAAAACATT
2404245 AACTTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAACATTTTAAAA
Found at i:2407618 original size:16 final size:16
Alignment explanation
Indices: 2407594--2407631 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2407584 TATTTTTTCT
*
2407594 AATTCATTTTTTTAAAA
1 AATT-ATTTTTTAAAAA
2407611 AATTATTTTTTAAAAA
1 AATTATTTTTTAAAAA
2407627 AATTA
1 AATTA
2407632 ATCTTTAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTATTTTTTAAAAA
Found at i:2407772 original size:20 final size:21
Alignment explanation
Indices: 2407734--2407773 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2407724 ATATTTTTTA
*
2407734 TATAATAAAATATACTTAATT
1 TATAATAAAATAAACTTAATT
*
2407755 TATAA-AAAATAAATTTAAT
1 TATAATAAAATAAACTTAAT
2407774 ATATTATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
TATAATAAAATAAACTTAATT
Found at i:2408273 original size:20 final size:20
Alignment explanation
Indices: 2408248--2408286 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2408238 AATAATAATA
2408248 ATATTTAAATTTTTTAAATG
1 ATATTTAAATTTTTTAAATG
*
2408268 ATATTTTAATTTTTTAAAT
1 ATATTTAAATTTTTTAAAT
2408287 TTGTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
ATATTTAAATTTTTTAAATG
Found at i:2408596 original size:20 final size:19
Alignment explanation
Indices: 2408557--2408596 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2408547 AGTTATGTTT
* *
2408557 ATTATTTTTATTAAATTTG
1 ATTATTGTTATTAAAATTG
2408576 ATTATTGTTATTTAAAATTG
1 ATTATTGTTA-TTAAAATTG
2408596 A
1 A
2408597 ATTCAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (19 bp):
ATTATTGTTATTAAAATTG
Found at i:2410292 original size:19 final size:19
Alignment explanation
Indices: 2410270--2410311 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2410260 ACCCAACTTA
2410270 TTTTTTAA-ATAAATTTAAT
1 TTTTTTAATATAAATTT-AT
*
2410289 TTTTTTAATTTAAATTTAT
1 TTTTTTAATATAAATTTAT
2410308 TTTT
1 TTTT
2410312 AACTTAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTAATATAAATTTAT
Found at i:2410646 original size:17 final size:18
Alignment explanation
Indices: 2410624--2410663 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
2410614 ATGTATTATT
2410624 ATAATAT-TTTTTAAATA
1 ATAATATATTTTTAAATA
2410641 ATAATATAAATTTTTAAATA
1 ATAATAT--ATTTTTAAATA
2410661 ATA
1 ATA
2410664 TGACAGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
20 13 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAATATATTTTTAAATA
Found at i:2411304 original size:14 final size:14
Alignment explanation
Indices: 2411280--2411367 Score: 60
Period size: 14 Copynumber: 6.4 Consensus size: 14
2411270 AATGATACAG
2411280 TTTAAATAATTAATA
1 TTTAAA-AATTAATA
2411295 TTTAAAAATTAATA
1 TTTAAAAATTAATA
**
2411309 TAAAAAAATTAA-A
1 TTTAAAAATTAATA
*
2411322 ATTATAAAA-TAATA
1 TTTA-AAAATTAATA
* *
2411336 TTCATAATATT-ATA
1 TTTA-AAAATTAATA
*
2411350 -TT-AAAATTACTA
1 TTTAAAAATTAATA
2411362 TTTAAA
1 TTTAAA
2411368 TTTCTAATTA
Statistics
Matches: 56, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
11 5 0.09
12 2 0.04
13 8 0.14
14 34 0.61
15 7 0.12
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTAAAAATTAATA
Found at i:2414011 original size:13 final size:12
Alignment explanation
Indices: 2413998--2414035 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
2413988 AAAGAAAAAT
2413998 TTTAAAATATAA
1 TTTAAAATATAA
2414010 TTTAAAAGTATAA
1 TTTAAAA-TATAA
*
2414023 ATTAAAATA-AA
1 TTTAAAATATAA
2414034 TT
1 TT
2414036 AATAATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 3 0.13
12 9 0.39
13 11 0.48
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (12 bp):
TTTAAAATATAA
Found at i:2414693 original size:6 final size:6
Alignment explanation
Indices: 2414674--2414725 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
2414664 ATGTTATATT
* * *
2414674 AATAAA AATGAA AATAAA AATAAA AATAATA AA-AATA TATAAA AATATA
1 AATAAA AATAAA AATAAA AATAAA AATAA-A AATAA-A AATAAA AATAAA
2414723 AAT
1 AAT
2414726 TATTAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
6 34 0.87
7 5 0.13
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (6 bp):
AATAAA
Found at i:2414703 original size:27 final size:25
Alignment explanation
Indices: 2414673--2414725 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
2414663 AATGTTATAT
2414673 TAATAAAAATGAAAATAAAAATAAAAA
1 TAATAAAAAT--AAATAAAAATAAAAA
* *
2414700 TAATAAAAATATATAAAAATATAAA
1 TAATAAAAATAAATAAAAATAAAAA
2414725 T
1 T
2414726 TATTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 14 0.58
27 10 0.42
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (25 bp):
TAATAAAAATAAATAAAAATAAAAA
Found at i:2414715 original size:10 final size:10
Alignment explanation
Indices: 2414693--2414722 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2414683 GAAAATAAAA
2414693 ATAAAAATA-
1 ATAAAAATAT
2414702 ATAAAAATAT
1 ATAAAAATAT
2414712 ATAAAAATAT
1 ATAAAAATAT
2414722 A
1 A
2414723 AATTATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:2415187 original size:5 final size:5
Alignment explanation
Indices: 2415177--2415217 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
2415167 TATTATTAAA
* *
2415177 AAATT AAATT AAATT AACTT AAATT -AATT -AATT AAAAT AAA
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAA
2415218 AATTAATAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
4 8 0.25
5 24 0.75
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (5 bp):
AAATT
Found at i:2415455 original size:13 final size:12
Alignment explanation
Indices: 2415439--2415507 Score: 51
Period size: 13 Copynumber: 6.0 Consensus size: 12
2415429 AATTTAATAT
2415439 TTAAATATAAAAA
1 TTAAAT-TAAAAA
2415452 TTAAATT---AA
1 TTAAATTAAAAA
*
2415461 TTAATTTAAATAA
1 TTAAATTAAA-AA
2415474 TTAAATT---AA
1 TTAAATTAAAAA
2415483 TTAAATTAAAAA
1 TTAAATTAAAAA
*
2415495 TAAAAATTAAAAA
1 T-TAAATTAAAAA
2415508 ATTTTAACAT
Statistics
Matches: 45, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
9 17 0.38
12 4 0.09
13 24 0.53
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTAAATTAAAAA
Found at i:2415459 original size:5 final size:5
Alignment explanation
Indices: 2415449--2415492 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
2415439 TTAAATATAA
*
2415449 AAATT AAATT -AATT AATTT AAA-T -AATT AAATT -AATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAA
2415493 AATAAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
3 2 0.06
4 10 0.30
5 21 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
AAATT
Found at i:2415464 original size:9 final size:9
Alignment explanation
Indices: 2415449--2415491 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
2415439 TTAAATATAA
2415449 AAATTAAATT
1 AAATT-AATT
2415459 -AATTAATTT
1 AAATTAA-TT
2415468 AAA-TAATT
1 AAATTAATT
2415476 AAATTAATT
1 AAATTAATT
2415485 AAATTAA
1 AAATTAA
2415492 AAATAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 7 0.23
9 21 0.70
10 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AAATTAATT
Found at i:2415475 original size:22 final size:21
Alignment explanation
Indices: 2415439--2415504 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 21
2415429 AATTTAATAT
2415439 TTAAATATAAAAATTAAATTAA
1 TTAAAT-TAAAAATTAAATTAA
*
2415461 TTAATTTAAATAATTAAATTAA
1 TTAAATTAAA-AATTAAATTAA
*
2415483 TTAAATTAAAAATAAAAATTAA
1 TTAAATTAAAAAT-TAAATTAA
2415505 AAAATTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
21 7 0.18
22 32 0.82
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAAATTAAAAATTAAATTAA
Found at i:2417605 original size:20 final size:22
Alignment explanation
Indices: 2417577--2417629 Score: 74
Period size: 20 Copynumber: 2.5 Consensus size: 22
2417567 TTTTAATATT
*
2417577 TAAATTAATAAAA-AATAAA-A
1 TAAAATAATAAAATAATAAATA
2417597 TAAAATAATAAAATAATAAATA
1 TAAAATAATAAAATAATAAATA
*
2417619 TATAATAATAA
1 TAAAATAATAA
2417630 TAATTAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.41
21 6 0.21
22 11 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
TAAAATAATAAAATAATAAATA
Found at i:2417614 original size:3 final size:3
Alignment explanation
Indices: 2417582--2417633 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
2417572 ATATTTAAAT
2417582 TAA TAA -AA -AA TAA -AA TAA -AA TAA TAA -AA TAA TAAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TA-A TAA
2417624 TAA TAA TAA T
1 TAA TAA TAA T
2417634 TAAACTTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
2 10 0.23
3 27 0.63
4 6 0.14
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:2417617 original size:25 final size:28
Alignment explanation
Indices: 2417583--2417633 Score: 72
Period size: 25 Copynumber: 1.9 Consensus size: 28
2417573 TATTTAAATT
2417583 AATAAAAAATA-A-AATAA-AATAATAA
1 AATAAAAAATATATAATAATAATAATAA
*
2417608 AATAATAAATATATAATAATAATAAT
1 AATAAAAAATATATAATAATAATAAT
2417634 TAAACTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 10 0.45
26 1 0.05
27 5 0.23
28 6 0.27
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (28 bp):
AATAAAAAATATATAATAATAATAATAA
Found at i:2418095 original size:16 final size:16
Alignment explanation
Indices: 2418074--2418124 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
2418064 GGTCAAATTT
2418074 TTAATTTTTAATATAA
1 TTAATTTTTAATATAA
*
2418090 TTAATTTTT--TATAT
1 TTAATTTTTAATATAA
* * *
2418104 TTAATATTAAATATTA
1 TTAATTTTTAATATAA
2418120 TTAAT
1 TTAAT
2418125 AATAAATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 11 0.39
16 17 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAATTTTTAATATAA
Found at i:2425510 original size:1 final size:1
Alignment explanation
Indices: 2425506--2425530 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2425496 TTTTTTTTTT
2425506 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
2425531 CGGTTCTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:2426600 original size:24 final size:24
Alignment explanation
Indices: 2426568--2426615 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2426558 TGAATGGTGC
2426568 ATTCCGAATCAGCCCACAGATTTT
1 ATTCCGAATCAGCCCACAGATTTT
*
2426592 ATTCCGAATCAGCTCACAGATTTT
1 ATTCCGAATCAGCCCACAGATTTT
2426616 CTTTTCCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (24 bp):
ATTCCGAATCAGCCCACAGATTTT
Found at i:2427510 original size:13 final size:14
Alignment explanation
Indices: 2427492--2427520 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2427482 CATTTTTAGT
2427492 AATTATA-TTTTAA
1 AATTATATTTTTAA
2427505 AATTATATTTTTAA
1 AATTATATTTTTAA
2427519 AA
1 AA
2427521 AGATTTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AATTATATTTTTAA
Found at i:2428382 original size:19 final size:20
Alignment explanation
Indices: 2428360--2428414 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
2428350 TGGTATATTT
2428360 AATAAATATAA-AAATATAA
1 AATAAATATAATAAATATAA
* *
2428379 AATAAATATAATATATATAT
1 AATAAATATAATAAATATAA
2428399 AA-AAATATAATTAAAT
1 AATAAATATAA-TAAAT
2428415 TTTAATATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAAATATAATAAATATAA
Found at i:2428421 original size:30 final size:29
Alignment explanation
Indices: 2428356--2428422 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
2428346 GACATGGTAT
2428356 ATTTAATA-AATATAAAAATATAAAATAA
1 ATTTAATATAATATAAAAATATAAAATAA
* *
2428384 ATATAATATATATATAAAAATAT-AATTAA
1 ATTTAATATA-ATATAAAAATATAAAATAA
2428413 ATTTTAATAT
1 A-TTTAATAT
2428423 TTTATGTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 7 0.21
29 7 0.21
30 19 0.58
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
ATTTAATATAATATAAAAATATAAAATAA
Found at i:2429082 original size:16 final size:17
Alignment explanation
Indices: 2429053--2429090 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
2429043 TGAATGTATT
2429053 AAATTTTAATAATAA-A
1 AAATTTTAATAATAACA
2429069 AAATATTTAA-AATAACA
1 AAAT-TTTAATAATAACA
2429086 AAATT
1 AAATT
2429091 GGTAATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATTTTAATAATAACA
Found at i:2429173 original size:22 final size:21
Alignment explanation
Indices: 2429129--2429185 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
2429119 TTTCATACGT
2429129 ATATTTTATATATATATATAA
1 ATATTTTATATATATATATAA
* *
2429150 ATATTTTA-ATATATGTATTCA
1 ATATTTTATATATATATA-TAA
2429171 A-ATTTTAT-TATATAT
1 ATATTTTATATATATAT
2429186 TATATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
ATATTTTATATATATATATAA
Found at i:2431359 original size:2 final size:2
Alignment explanation
Indices: 2431352--2431393 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
2431342 CTCTGTCCAT
2431352 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
2431394 TCGAGATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2432245 original size:23 final size:23
Alignment explanation
Indices: 2432215--2432268 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
2432205 TTTAATATGT
*
2432215 TAAATATAAATATAAT-TATTTAA
1 TAAATATAAA-ATAATATATTAAA
2432238 TAAATATAAAATAATATATTAAA
1 TAAATATAAAATAATATATTAAA
2432261 TATAATAT
1 TA-AATAT
2432269 GATATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 5 0.18
23 18 0.64
24 5 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAATATAAAATAATATATTAAA
Found at i:2432262 original size:19 final size:20
Alignment explanation
Indices: 2432207--2432265 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 20
2432197 TAAAAATTTT
*
2432207 TAATATGTTAAATATAAATA
1 TAATATATTAAATATAAATA
*
2432227 TAATTATTTAATAAATATAAA-A
1 TAA-TA--TATTAAATATAAATA
2432249 TAATATATTAAATATAA
1 TAATATATTAAATATAA
2432266 TATGATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 11 0.33
20 3 0.09
21 4 0.12
22 4 0.12
23 11 0.33
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TAATATATTAAATATAAATA
Found at i:2432273 original size:19 final size:19
Alignment explanation
Indices: 2432207--2432273 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
2432197 TAAAAATTTT
* *
2432207 TAATATGTTAAATATAAATA
1 TAATATGATATAT-TAAATA
* *
2432227 TAAT-T-ATTTAATAAATA
1 TAATATGATATATTAAATA
* *
2432244 TAAAATAATATATTAAATA
1 TAATATGATATATTAAATA
2432263 TAATATGATAT
1 TAATATGATAT
2432274 TTTTTAATAA
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
17 9 0.25
18 3 0.08
19 20 0.56
20 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAATATGATATATTAAATA
Found at i:2432297 original size:43 final size:43
Alignment explanation
Indices: 2432207--2432323 Score: 120
Period size: 43 Copynumber: 2.8 Consensus size: 43
2432197 TAAAAATTTT
* *
2432207 TAATATGTTAAATATAA-ATATAATTATTTAAT-AAATATAAAA
1 TAATATATTAAATATAATATAT-ATTTTTTAATAAAATATAAAA
*
2432249 TAATATATTAAATATAATATGATATTTTTTAATAAAAT-TAATGA
1 TAATATATTAAATATAATAT-ATATTTTTTAATAAAATATAA-AA
*
2432293 -AATATATTTAATAT-ATATCATA-TTTTTAATA
1 TAATATATTAAATATAATAT-ATATTTTTTAATA
2432324 TATTTAATAA
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
41 9 0.14
42 23 0.35
43 27 0.41
44 7 0.11
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (43 bp):
TAATATATTAAATATAATATATATTTTTTAATAAAATATAAAA
Found at i:2432305 original size:9 final size:9
Alignment explanation
Indices: 2432293--2432337 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
2432283 AAATTAATGA
2432293 AATATATTT
1 AATATATTT
*
2432302 AATATATAT
1 AATATATTT
* *
2432311 CATATTTTT
1 AATATATTT
2432320 AATATATTT
1 AATATATTT
2432329 AATA-ATTT
1 AATATATTT
2432337 A
1 A
2432338 TATTTATAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
8 5 0.17
9 25 0.83
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (9 bp):
AATATATTT
Found at i:2432417 original size:2 final size:2
Alignment explanation
Indices: 2432410--2432447 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2432400 ACATACATAC
2432410 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
2432448 TGCCTTACCC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2433440 original size:16 final size:17
Alignment explanation
Indices: 2433419--2433466 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 17
2433409 TATTTTAATG
2433419 TATAATTTTTAAAATA-
1 TATAATTTTTAAAATAT
2433435 TATAA-TTTT-AAATAT
1 TATAATTTTTAAAATAT
*
2433450 TTTATATTTTTAAAATA
1 TATA-ATTTTTAAAATA
2433467 ATTTTTTCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 5 0.19
15 7 0.26
16 6 0.22
17 4 0.15
18 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATAATTTTTAAAATAT
Found at i:2433460 original size:17 final size:15
Alignment explanation
Indices: 2433419--2433466 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 15
2433409 TATTTTAATG
2433419 TATA-ATTTTTAAAA
1 TATATATTTTTAAAA
*
2433433 TATATAATTTTAAATA
1 TATATATTTTTAAA-A
*
2433449 TTTTATATTTTTAAAA
1 -TATATATTTTTAAAA
2433465 TA
1 TA
2433467 ATTTTTTCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 4 0.15
15 9 0.33
16 2 0.07
17 12 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATATTTTTAAAA
Found at i:2433753 original size:20 final size:20
Alignment explanation
Indices: 2433728--2433765 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2433718 ATATTTTTAT
2433728 TAAAAT-TTAATTATAAAATA
1 TAAAATATTAA-TATAAAATA
2433748 TAAAATATTAATATAAAA
1 TAAAATATTAATATAAAA
2433766 ATTATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAATATTAATATAAAATA
Found at i:2436698 original size:15 final size:16
Alignment explanation
Indices: 2436678--2436740 Score: 60
Period size: 15 Copynumber: 4.0 Consensus size: 16
2436668 ATATAAATAT
2436678 AATATAAAAT-TATTA
1 AATATAAAATATATTA
*
2436693 AATATATAAATATTTTA
1 AATATA-AAATATATTA
*
2436710 AATAT-AAATATAAT-
1 AATATAAAATATATTA
*
2436724 AATATTTAAATATATTA
1 AATA-TAAAATATATTA
2436741 TATCATATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 4 0.10
15 14 0.36
16 12 0.31
17 9 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATAAAATATATTA
Found at i:2436717 original size:23 final size:22
Alignment explanation
Indices: 2436665--2436737 Score: 75
Period size: 23 Copynumber: 3.4 Consensus size: 22
2436655 GTCGATCGTA
2436665 TAAATATAAATATAAT-ATA--
1 TAAATATAAATATAATAATATT
2436684 -AAATTATTAAATAT-ATAAATATTT
1 TAAA-TA-TAAATATAAT-AATA-TT
2436708 TAAATATAAATATAATAATATT
1 TAAATATAAATATAATAATATT
2436730 TAAATATA
1 TAAATATA
2436738 TTATATCATA
Statistics
Matches: 45, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
18 3 0.07
19 4 0.09
20 7 0.16
21 3 0.07
22 10 0.22
23 11 0.24
24 4 0.09
25 3 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAATATAAATATAATAATATT
Found at i:2436754 original size:23 final size:22
Alignment explanation
Indices: 2436691--2436737 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2436681 ATAAAATTAT
2436691 TAAATAT-ATAAATATTTTAAATA
1 TAAATATAAT-AAT-TTTTAAATA
*
2436714 TAAATATAATAATATTTAAATA
1 TAAATATAATAATTTTTAAATA
2436736 TA
1 TA
2436738 TTATATCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 10 0.45
24 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATATAATAATTTTTAAATA
Found at i:2437970 original size:16 final size:16
Alignment explanation
Indices: 2437951--2437983 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2437941 ATTTTGATGG
2437951 TTTTCTTTTTTCTTTT
1 TTTTCTTTTTTCTTTT
*
2437967 TTTTTTTTTTTCTTTT
1 TTTTCTTTTTTCTTTT
2437983 T
1 T
2437984 CTTGAGTAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (16 bp):
TTTTCTTTTTTCTTTT
Found at i:2442441 original size:32 final size:33
Alignment explanation
Indices: 2442400--2442470 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
2442390 CAAAATTAGC
2442400 TTTTAATATATTAATAATT-TATTTT-ATATAAT
1 TTTTAATATATTAAT-ATTATATTTTCATATAAT
* *
2442432 TTTTGATATATTAATATTATATTTTCATATGAT
1 TTTTAATATATTAATATTATATTTTCATATAAT
2442465 ATTTTA
1 -TTTTA
2442471 TTTTTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 3 0.09
32 20 0.61
33 6 0.18
34 4 0.12
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (33 bp):
TTTTAATATATTAATATTATATTTTCATATAAT
Found at i:2442501 original size:13 final size:13
Alignment explanation
Indices: 2442483--2442508 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2442473 TTTTAAAAAA
2442483 TTATATTTATATT
1 TTATATTTATATT
2442496 TTATATTTATATT
1 TTATATTTATATT
2442509 ATGTTTAAAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATATTTATATT
Found at i:2442808 original size:16 final size:17
Alignment explanation
Indices: 2442787--2442823 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
2442777 TTCATTCCAC
2442787 GAATTTCTATTTA-TTT
1 GAATTTCTATTTATTTT
*
2442803 GAATTTTTATTTATTTT
1 GAATTTCTATTTATTTT
2442820 GAAT
1 GAAT
2442824 GGAGAGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.62
Consensus pattern (17 bp):
GAATTTCTATTTATTTT
Found at i:2443007 original size:17 final size:17
Alignment explanation
Indices: 2442978--2443048 Score: 63
Period size: 17 Copynumber: 4.0 Consensus size: 17
2442968 TTTTTAATAT
*
2442978 ATATTAGATATATATTA
1 ATATTATATATATATTA
*
2442995 A-AGTTGTATATATATTA
1 ATA-TTATATATATATTA
2443012 ATATTATATATATAATTATA
1 ATATTATATATAT-A-T-TA
* *
2443032 ATTTTATACATATATTA
1 ATATTATATATATATTA
2443049 TACATATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.02
17 25 0.57
18 3 0.07
19 2 0.05
20 13 0.30
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (17 bp):
ATATTATATATATATTA
Found at i:2443038 original size:20 final size:19
Alignment explanation
Indices: 2443010--2443057 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
2443000 GTATATATAT
*
2443010 TAATATTATATATATAATTA
1 TAATATTATACATAT-ATTA
*
2443030 TAATTTTATACATATATTA
1 TAATATTATACATATATTA
2443049 TACATATTA
1 TA-ATATTA
2443058 AATAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATATTATACATATATTA
Found at i:2443050 original size:31 final size:30
Alignment explanation
Indices: 2443012--2443069 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
2443002 ATATATATTA
*
2443012 ATATTATATATA-TAATTATAATTTTATACAT
1 ATATTATACATATTAA--ATAATTTTATACAT
2443043 ATATTATACATATTAAATAATTTTATA
1 ATATTATACATATTAAATAATTTTATA
2443070 ATTTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 11 0.44
31 11 0.44
32 3 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (30 bp):
ATATTATACATATTAAATAATTTTATACAT
Found at i:2445731 original size:13 final size:13
Alignment explanation
Indices: 2445715--2445781 Score: 53
Period size: 13 Copynumber: 4.9 Consensus size: 13
2445705 ATAAAAATTA
2445715 TTAAATTATTTTT
1 TTAAATTATTTTT
2445728 TTAAATTATTTTT
1 TTAAATTATTTTT
* * * *
2445741 ATTTATTTATATTA
1 -TTAAATTATTTTT
2445755 TTAAATTAATTTATT
1 TTAAATT-ATTT-TT
**
2445770 TTTTATTATTTT
1 TTAAATTATTTT
2445782 AATAATTTAA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
13 19 0.46
14 16 0.39
15 6 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTAAATTATTTTT
Found at i:2445744 original size:19 final size:19
Alignment explanation
Indices: 2445720--2445756 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2445710 AATTATTAAA
*
2445720 TTATTTTTTTAAATTATTT
1 TTATTTATTTAAATTATTT
*
2445739 TTATTTATTTATATTATT
1 TTATTTATTTAAATTATT
2445757 AAATTAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTATTTATTTAAATTATTT
Found at i:2445744 original size:40 final size:42
Alignment explanation
Indices: 2445700--2445781 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 42
2445690 GTGGGGTTTG
2445700 TATTTATAAAAATTATTAAATT-ATTT-TTTTAAATTATTTT
1 TATTTATAAAAATTATTAAATTAATTTATTTTAAATTATTTT
** * **
2445740 TATTTATTTATATTATTAAATTAATTTATTTTTTATTATTTT
1 TATTTATAAAAATTATTAAATTAATTTATTTTAAATTATTTT
2445782 AATAATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 19 0.54
41 4 0.11
42 12 0.34
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (42 bp):
TATTTATAAAAATTATTAAATTAATTTATTTTAAATTATTTT
Found at i:2445787 original size:23 final size:26
Alignment explanation
Indices: 2445728--2445790 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
2445718 AATTATTTTT
*
2445728 TTAAATTATTTTTATTTATTTATATTA
1 TTAAATTA-ATTTATTTATTTATATTA
2445755 TTAAATTAATTTATTT-TTTATTATT-
1 TTAAATTAATTTATTTATTTA-TATTA
2445780 TT-AA-TAATTTA
1 TTAAATTAATTTA
2445791 ATTAATATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
23 7 0.21
24 2 0.06
25 6 0.18
26 11 0.32
27 8 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TTAAATTAATTTATTTATTTATATTA
Found at i:2445794 original size:32 final size:32
Alignment explanation
Indices: 2445728--2445796 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
2445718 AATTATTTTT
* *
2445728 TTAAATTATTTTTATTTATTTATATTATTAAA
1 TTAATTTATTTTTATTTATTTATATAATTAAA
*
2445760 TTAATTTATTTTT-TATTATTT-TAATAATTTAA
1 TTAATTTATTTTTAT-TTATTTAT-ATAATTAAA
2445792 TTAAT
1 TTAAT
2445797 ATTCAATCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 2 0.06
32 30 0.94
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (32 bp):
TTAATTTATTTTTATTTATTTATATAATTAAA
Found at i:2447737 original size:31 final size:31
Alignment explanation
Indices: 2447697--2447760 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
2447687 GCAAAGAAAG
*
2447697 AAAACTTTTCAGCAAGAAATCTGCTAGTCAT
1 AAAAATTTTCAGCAAGAAATCTGCTAGTCAT
2447728 AAAAATTTTCAGCAAGAAATCTGCTAGTCAT
1 AAAAATTTTCAGCAAGAAATCTGCTAGTCAT
2447759 AA
1 AA
2447761 CTTTATTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (31 bp):
AAAAATTTTCAGCAAGAAATCTGCTAGTCAT
Found at i:2451651 original size:15 final size:15
Alignment explanation
Indices: 2451622--2451657 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
2451612 ATAATGAATC
2451622 AATTCAATTTAAATTA
1 AATT-AATTTAAATTA
*
2451638 AATTAATTTGAATTA
1 AATTAATTTAAATTA
2451653 AATTA
1 AATTA
2451658 TTTTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (15 bp):
AATTAATTTAAATTA
Done.