Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold213
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: 483536
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
File 3 of 4
Found at i:311713 original size:19 final size:18
Alignment explanation
Indices: 311689--311751 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
311679 AATGTATAAC
311689 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
311708 TGTATCGATAC--AA--T
1 TGTATCGATACATAAGTT
311722 T-TATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
311740 TGTATCGATACA
1 TGTATCGATACA
311752 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.24
14 2 0.05
15 2 0.05
17 2 0.05
18 2 0.05
19 21 0.55
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:311732 original size:32 final size:32
Alignment explanation
Indices: 311689--311759 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
311679 AATGTATAAC
311689 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
311721 TTTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
311753 TGTATCG
1 TGTATCG
311760 CTACGAAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:316311 original size:13 final size:13
Alignment explanation
Indices: 316293--316318 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
316283 CATTTTGGGA
316293 TGTATCGATACAT
1 TGTATCGATACAT
316306 TGTATCGATACAT
1 TGTATCGATACAT
316319 CTTGTGTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:316315 original size:33 final size:32
Alignment explanation
Indices: 316273--316336 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
316263 TACAAGCCAA
*
316273 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
316306 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
316337 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:316573 original size:22 final size:24
Alignment explanation
Indices: 316547--316592 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
316537 TGTCCATCTT
316547 TTTAATAGAATC-T-ATATATATA
1 TTTAATAGAATCTTAATATATATA
*
316569 TTTAATATAATCTTAATATATATA
1 TTTAATAGAATCTTAATATATATA
316593 AGACATCCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.52
23 1 0.05
24 9 0.43
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTAATAGAATCTTAATATATATA
Found at i:318989 original size:20 final size:20
Alignment explanation
Indices: 318964--319008 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
318954 CCCATGATCC
318964 TGAAGGTGTATCGATACATT
1 TGAAGGTGTATCGATACATT
318984 TGAAGGTGTATCGATACATT
1 TGAAGGTGTATCGATACATT
319004 T-AAGG
1 TGAAGG
319009 GTTTTGACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.31, C:0.09, G:0.27, T:0.33
Consensus pattern (20 bp):
TGAAGGTGTATCGATACATT
Found at i:321446 original size:13 final size:13
Alignment explanation
Indices: 321428--321518 Score: 56
Period size: 13 Copynumber: 5.9 Consensus size: 13
321418 ATAAACCCTT
321428 TGTATCGATACAA
1 TGTATCGATACAA
321441 TGTATCGATACAGAGAA
1 TGTATCGATAC----AA
321458 TGCTGTATCGATACAA
1 ---TGTATCGATACAA
321474 TGTATCGATACAGAGAA
1 TGTATCGATAC----AA
321491 TGCTGTATCGATACAA
1 ---TGTATCGATACAA
321507 TGTATCGATACA
1 TGTATCGATACA
321519 GAGAATGCTG
Statistics
Matches: 64, Mismatches: 0, Indels: 28
0.70 0.00 0.30
Matches are distributed among these distances:
13 34 0.53
16 4 0.06
17 4 0.06
20 22 0.34
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:321466 original size:20 final size:20
Alignment explanation
Indices: 321441--321538 Score: 98
Period size: 20 Copynumber: 5.6 Consensus size: 20
321431 ATCGATACAA
321441 TGTATCGATACAGAGAATGC
1 TGTATCGATACAGAGAATGC
321461 TGTATCGATAC----AA---
1 TGTATCGATACAGAGAATGC
321474 TGTATCGATACAGAGAATGC
1 TGTATCGATACAGAGAATGC
321494 TGTATCGATAC----AA---
1 TGTATCGATACAGAGAATGC
321507 TGTATCGATACAGAGAATGC
1 TGTATCGATACAGAGAATGC
321527 TGTATCGATACA
1 TGTATCGATACA
321539 TCTGAGTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 28
0.70 0.00 0.30
Matches are distributed among these distances:
13 22 0.34
16 4 0.06
17 4 0.06
20 34 0.53
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (20 bp):
TGTATCGATACAGAGAATGC
Found at i:321470 original size:33 final size:33
Alignment explanation
Indices: 321428--321538 Score: 222
Period size: 33 Copynumber: 3.4 Consensus size: 33
321418 ATAAACCCTT
321428 TGTATCGATACAATGTATCGATACAGAGAATGC
1 TGTATCGATACAATGTATCGATACAGAGAATGC
321461 TGTATCGATACAATGTATCGATACAGAGAATGC
1 TGTATCGATACAATGTATCGATACAGAGAATGC
321494 TGTATCGATACAATGTATCGATACAGAGAATGC
1 TGTATCGATACAATGTATCGATACAGAGAATGC
321527 TGTATCGATACA
1 TGTATCGATACA
321539 TCTGAGTTTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (33 bp):
TGTATCGATACAATGTATCGATACAGAGAATGC
Found at i:326062 original size:3 final size:3
Alignment explanation
Indices: 326054--326084 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
326044 TCTGAGTCAC
*
326054 CAT CAT CAT CAT CAT CAT CAT CAT CTT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
326085 GTCCTTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:327707 original size:13 final size:13
Alignment explanation
Indices: 327689--327714 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
327679 CATTTTGGGA
327689 TGTATCGATACAT
1 TGTATCGATACAT
327702 TGTATCGATACAT
1 TGTATCGATACAT
327715 CTTGTGTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:327832 original size:13 final size:13
Alignment explanation
Indices: 327814--327838 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
327804 ATATTTGGTC
327814 ATGTATCAATACA
1 ATGTATCAATACA
327827 ATGTATCAATAC
1 ATGTATCAATAC
327839 TATACATTAT
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:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:327871 original size:20 final size:19
Alignment explanation
Indices: 327848--327886 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
327838 CTATACATTA
327848 TGTATCGATACATTTGAAGG
1 TGTATCGATACATTT-AAGG
327868 TGTATCGATACATTTAAGG
1 TGTATCGATACATTTAAGG
327887 GTTTTGACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATTTAAGG
Found at i:334302 original size:13 final size:13
Alignment explanation
Indices: 334284--334309 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
334274 TACACCAAGT
334284 ATGTATCGATACA
1 ATGTATCGATACA
334297 ATGTATCGATACA
1 ATGTATCGATACA
334310 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:334307 original size:32 final size:33
Alignment explanation
Indices: 334266--334329 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
334256 TAGCCAAACT
* **
334266 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
334298 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
334330 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:336565 original size:21 final size:21
Alignment explanation
Indices: 336532--336576 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
336522 TTGCAAGTTG
*
336532 AAATAAGGAAGTTGGCTAATGA
1 AAATAAGGAAGTTAGCTAA-GA
*
336554 AAATAATG-AGTTAGCTAAGA
1 AAATAAGGAAGTTAGCTAAGA
336574 AAA
1 AAA
336577 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.22
Consensus pattern (21 bp):
AAATAAGGAAGTTAGCTAAGA
Found at i:338398 original size:15 final size:15
Alignment explanation
Indices: 338378--338408 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
338368 TAAAAATGTC
*
338378 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
338393 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
338408 C
1 C
338409 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:340498 original size:13 final size:13
Alignment explanation
Indices: 340480--340516 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
340470 ATTTTTCCTT
340480 GTATCGATACAAA
1 GTATCGATACAAA
**
340493 GTATCGATACACT
1 GTATCGATACAAA
340506 GTATCGATACA
1 GTATCGATACA
340517 GGGGGATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (13 bp):
GTATCGATACAAA
Found at i:342171 original size:22 final size:19
Alignment explanation
Indices: 342133--342172 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
342123 AGTGTTTAAT
342133 GTTTTTTGCTTGACTTTGC
1 GTTTTTTGCTTGACTTTGC
342152 GTTTATTTGCATTGTACTTTG
1 GTTT-TTTGC-TTG-ACTTTG
342173 AATTTTAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 3 0.17
22 6 0.33
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.57
Consensus pattern (19 bp):
GTTTTTTGCTTGACTTTGC
Found at i:343071 original size:13 final size:13
Alignment explanation
Indices: 343053--343078 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
343043 TACACCAAGT
343053 ATGTATCGATACA
1 ATGTATCGATACA
343066 ATGTATCGATACA
1 ATGTATCGATACA
343079 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:343076 original size:32 final size:33
Alignment explanation
Indices: 343035--343098 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
343025 TAGCCAAACT
* **
343035 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
343067 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
343099 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:347349 original size:9 final size:9
Alignment explanation
Indices: 347335--347362 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
347325 ATTCATGGGC
347335 TTTTAGGCA
1 TTTTAGGCA
347344 TTTTAGGCA
1 TTTTAGGCA
347353 TTTTAGGCA
1 TTTTAGGCA
347362 T
1 T
347363 ACAAGTGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.46
Consensus pattern (9 bp):
TTTTAGGCA
Found at i:348247 original size:52 final size:51
Alignment explanation
Indices: 348162--348285 Score: 187
Period size: 52 Copynumber: 2.4 Consensus size: 51
348152 ATATGAAAAG
* *
348162 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGACAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGACAAA
* *
348213 TTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATGCATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACA-TTTAATAATGTATCGATACATCTGGACAAA
348265 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
348286 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
51 21 0.31
52 41 0.61
53 5 0.07
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGACAAA
Found at i:348298 original size:51 final size:50
Alignment explanation
Indices: 348162--348305 Score: 159
Period size: 52 Copynumber: 2.8 Consensus size: 50
348152 ATATGAAAAG
* *
348162 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGACAAAT
1 TTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGACAAAT
* *
348214 TTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATGCATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGGACAAAT
348265 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
348306 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 32 0.40
52 40 0.49
53 1 0.01
54 4 0.05
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (50 bp):
TTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGACAAAT
Found at i:348312 original size:13 final size:13
Alignment explanation
Indices: 348294--348318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
348284 CAAAGATCAG
348294 TGTATCGATACAA
1 TGTATCGATACAA
348307 TGTATCGATACA
1 TGTATCGATACA
348319 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:348396 original size:33 final size:33
Alignment explanation
Indices: 348359--348425 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
348349 AGTAGCTTAA
348359 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
348392 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
348425 A
1 A
348426 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:348399 original size:13 final size:13
Alignment explanation
Indices: 348381--348405 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
348371 CAAAAAAATA
348381 TGTATCGATACAT
1 TGTATCGATACAT
348394 TGTATCGATACA
1 TGTATCGATACA
348406 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:354781 original size:59 final size:59
Alignment explanation
Indices: 354676--354792 Score: 155
Period size: 59 Copynumber: 2.0 Consensus size: 59
354666 AATTTCTGTG
* *** * *
354676 CATTTTAAGGTCATTTAAGATATTTTACATAATCTAAGGGTGATTTAGCCATTTCCATT
1 CATTTTAAGGTCATTTAAGATATTTTACATAAGCTAAGGACCATTTAGCAATTCCCATT
*
354735 CATTTTAAGGTCATTTAAGTTA-TTTACCATAAGCTAAGGACCATTTAGCAATTCCCAT
1 CATTTTAAGGTCATTTAAGATATTTTA-CATAAGCTAAGGACCATTTAGCAATTCCCAT
354793 CATGTCAAGG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 4 0.08
59 46 0.92
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (59 bp):
CATTTTAAGGTCATTTAAGATATTTTACATAAGCTAAGGACCATTTAGCAATTCCCATT
Found at i:357017 original size:24 final size:22
Alignment explanation
Indices: 356971--357017 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
356961 AAATCCAAGC
**
356971 TTTCTCTTCTTTTTTTTCTTTT
1 TTTCTCTTCTTTTTTTTAATTT
356993 TTTCTCTCTCTCTTTTTTTAATTT
1 TTTCTCT-TCT-TTTTTTTAATTT
357017 T
1 T
357018 GGAATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 3 0.14
24 11 0.52
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTCTCTTCTTTTTTTTAATTT
Found at i:357714 original size:18 final size:18
Alignment explanation
Indices: 357671--357715 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
357661 GTCTTTGACT
*
357671 TTTGATTTTCAAGTTAAC
1 TTTGACTTTCAAGTTAAC
* *
357689 TATTGACTTTCAGGTTTAC
1 T-TTGACTTTCAAGTTAAC
357708 TTTGACTT
1 TTTGACTT
357716 CCCTAAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.51
Consensus pattern (18 bp):
TTTGACTTTCAAGTTAAC
Found at i:363196 original size:17 final size:17
Alignment explanation
Indices: 363174--363247 Score: 51
Period size: 17 Copynumber: 4.4 Consensus size: 17
363164 ACTAATTCCT
363174 TATTAAAAAATATTTAA
1 TATTAAAAAATATTTAA
*** * *
363191 TATTAAACTTTAATTAT
1 TATTAAAAAATATTTAA
* * *
363208 TTTTTAAAAAT-TATAA
1 TATTAAAAAATATTTAA
* *
363224 AATTAAAAAATATTTTA
1 TATTAAAAAATATTTAA
363241 TATTAAA
1 TATTAAA
363248 TCTTGAATTA
Statistics
Matches: 37, Mismatches: 19, Indels: 2
0.64 0.33 0.03
Matches are distributed among these distances:
16 10 0.27
17 27 0.73
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTAAAAAATATTTAA
Found at i:363288 original size:53 final size:52
Alignment explanation
Indices: 363179--363968 Score: 663
Period size: 53 Copynumber: 15.2 Consensus size: 52
363169 TTCCTTATTA
* ** * * * *
363179 AAAAATATTTAATATTAAA-CTTTAATTATTTTTTAAAAATTAT-AAAATTA
1 AAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAATTT
**
363229 AAAAATATTTTATATTAAATCTTGAATTACTATTTAAAAAATAATAAAAATTT
1 AAAAATATTTTATATTAAATCTCAAATTACTATTT-AAAAATAATAAAAATTT
** * * *
363282 AAAAATATTTTATATCGAACCTTAAATTACTATTTAAAAAATAATAAAAATTAA
1 AAAAATATTTTATATTAAATCTCAAATTACTATTT-AAAAATAATAAAAATT-T
* ** *
363336 AAAATATATTTTATATTAAATTTTGAATTACTAGTTAAAAATAATAAAAA--T
1 AAAA-ATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAATTT
* * * *
363387 -----TA-TTTCTATTAAAT-TCTGAATTACTGTTT--AAA-AATAAAAATTA
1 AAAAATATTTTATATTAAATCTC-AAATTACTATTTAAAAATAATAAAAATTT
* * * * *
363430 AATAAATAGTTTATAGTAAATCTCAAATTAGTATTTAAAAATAACAAAATTTTTT
1 AA-AAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAA--ATTT
* * * *
363485 AAAAATATTCTATATTAAATCACGAATTACTATTTAAAAATAATAAAAAAATT
1 AAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAAT-AAAAATTT
* * * *
363538 AAAAAGAATATAT-TTAAAATCTCAAATTACTATTT-AAAATAATAAAAAATT
1 AAAAATATTTTATATT-AAATCTCAAATTACTATTTAAAAATAATAAAAATTT
* *
363589 AAAAATATGTTTTATATAAAATCTCAAACTACTATTTAAAAA-AATAAAAAATTT
1 AAAAATA--TTTTATATTAAATCTCAAATTACTATTTAAAAATAAT-AAAAATTT
* * * * * **
363643 AAAAGT-CTTT-TATTATATCCCAAATTACTATTTGAAAATAATAAAAAAAT
1 AAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAATTT
** *** * * *
363693 AAAAATATTTTGA-GGTAAATCTTGGATTACTTTTTAAACATAATAAATAATTG
1 AAAAATATTTT-ATATTAAATCTCAAATTACTATTTAAAAATAATAAA-AATTT
*
363746 AAAAA-ATTTTATATTAAATCTTC-AATTACTATTTAAAAATAATAAATATTT
1 AAAAATATTTTATATTAAATC-TCAAATTACTATTTAAAAATAATAAAAATTT
* *
363797 AAAAATATTATATATTAAATCTCAAATTACTATTTAAAAAATAATAAAAAATTA
1 AAAAATATTTTATATTAAATCTCAAATTACTATTT-AAAAATAAT-AAAAATTT
* * * *
363851 AAAACATATTTTATATTAAATCTAAAATTATTATTTAAAAATAATTAAAATTA
1 AAAA-ATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAATTT
* * *
363904 ATAAAATATTTTAGGA-TAAATATCAAATTACTATTTAAAAATAATAAAAAATTA
1 A-AAAATATTTTA-TATTAAATCTCAAATTACTATTTAAAAATAAT-AAAAATTT
363958 AAAAATATTTT
1 AAAAATATTTT
363969 TTATGTCTTA
Statistics
Matches: 602, Mismatches: 95, Indels: 83
0.77 0.12 0.11
Matches are distributed among these distances:
41 8 0.01
42 3 0.00
43 1 0.00
44 21 0.03
45 2 0.00
49 2 0.00
50 71 0.12
51 48 0.08
52 101 0.17
53 183 0.30
54 101 0.17
55 61 0.10
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (52 bp):
AAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAATTT
Found at i:363318 original size:104 final size:102
Alignment explanation
Indices: 363179--363968 Score: 637
Period size: 104 Copynumber: 7.6 Consensus size: 102
363169 TTCCTTATTA
* ** * * *
363179 AAAAATATTTAATATTAAA-CTTTAATTATTTTTTAAAAATTATAAAATTAAAAAATATTTTATA
1 AAAAATATTTTATA-TAAATCTCAAATTACTATTTAAAAATTAAAAAATTAAAAAATATTTTATA
**
363243 TTAAATCTTGAATTACTATTTAAAAAATAATAAAAATTT
65 TTAAATCTCAAATTACTATTT-AAAAATAATAAAAATTT
* * * *
363282 AAAAATATTTTATATCGAACCTTAAATTACTATTTAAAAAATAATAAAAATTAAAAAATATATTT
1 AAAAATATTTTATAT-AAATCTCAAATTACTATTT-AAAAATTA-AAAAATT-AAAAA-ATATTT
* ** *
363347 TATATTAAATTTTGAATTACTAGTTAAAAATAATAAAAA-TT
61 TATATTAAATCTCAAATTACTATTTAAAAATAATAAAAATTT
* * * *
363388 ----AT-TTCTAT-TAAAT-TCTGAATTACTGTTTAAAAA-T-AAAAATTAAATAAATAGTTTAT
1 AAAAATATTTTATATAAATCTC-AAATTACTATTTAAAAATTAAAAAATTAAA-AAATATTTTAT
* * * *
363444 AGTAAATCTCAAATTAGTATTTAAAAATAACAAAATTTTTT
64 ATTAAATCTCAAATTACTATTTAAAAATAATAAAA--ATTT
* * * *
363485 AAAAATATTCTATATTAAATCACGAATTACTATTTAAAAATAATAAAAAAATTAAAAAGA-A-TA
1 AAAAATATTTTATA-TAAATCTCAAATTACTATTTAAAAAT--T-AAAAAATTAAAAA-ATATTT
*
363548 TAT-TTAAAATCTCAAATTACTATTT-AAAATAATAAAAAATT
61 TATATT-AAATCTCAAATTACTATTTAAAAATAATAAAAATTT
* * * * *
363589 AAAAATATGTTTTATATAAAATCTCAAACTACTATTTAAAAAAATAAAAAATTTAAAAGT-CTTT
1 AAAAATA--TTTTATAT-AAATCTCAAATTACTATTT-AAAAATTAAAAAATTAAAAAATATTTT
* * * **
363653 -TATTATATCCCAAATTACTATTTGAAAATAATAAAAAAAT
62 ATATTAAATCTCAAATTACTATTTAAAAATAATAAAAATTT
** *** * * * *
363693 AAAAATATTTTGAGGTAAATCTTGGATTACTTTTTAAACATAATAAATAATTGAAAAA-ATTTTA
1 AAAAATATTTT-ATATAAATCTCAAATTACTATTTAAA-A-ATTAAAAAATTAAAAAATATTTTA
*
363757 TATTAAATCTTC-AATTACTATTTAAAAATAATAAATATTT
63 TATTAAATC-TCAAATTACTATTTAAAAATAATAAAAATTT
*
363797 AAAAATATTATATATTAAATCTCAAATTACTATTTAAAAAATAATAAAAAATTAAAAACATATTT
1 AAAAATATTTTATA-TAAATCTCAAATTACTATTT-AAAAAT--TAAAAAATTAAAAA-ATATTT
* * * *
363862 TATATTAAATCTAAAATTATTATTTAAAAATAATTAAAATTA
61 TATATTAAATCTCAAATTACTATTTAAAAATAATAAAAATTT
* *
363904 ATAAAATATTTTAGGATAAATATCAAATTACTATTTAAAAATAATAAAAAATTAAAAAATATTTT
1 A-AAAATATTTTA-TATAAATCTCAAATTACTATTTAAAAAT--TAAAAAATTAAAAAATATTTT
363969 TTATGTCTTA
Statistics
Matches: 559, Mismatches: 79, Indels: 95
0.76 0.11 0.13
Matches are distributed among these distances:
94 39 0.07
95 9 0.02
97 2 0.00
98 6 0.01
99 12 0.02
100 1 0.00
101 10 0.02
102 28 0.05
103 54 0.10
104 139 0.25
105 26 0.05
106 51 0.09
107 109 0.19
108 61 0.11
109 12 0.02
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (102 bp):
AAAAATATTTTATATAAATCTCAAATTACTATTTAAAAATTAAAAAATTAAAAAATATTTTATAT
TAAATCTCAAATTACTATTTAAAAATAATAAAAATTT
Found at i:363399 original size:44 final size:45
Alignment explanation
Indices: 363326--363426 Score: 136
Period size: 44 Copynumber: 2.3 Consensus size: 45
363316 TAAAAAATAA
* *
363326 TAAAAATTAAAAAATATATTTTATATTAAATTTTGAATTACTAG-T
1 TAAAAATAAAAAAATATATTTTATATTAAATTCTGAATTACT-GTT
*
363371 TAAAAATAATAAAAAT-TA-TTTCTATTAAATTCTGAATTACTGTT
1 TAAAAATAA-AAAAATATATTTTATATTAAATTCTGAATTACTGTT
363415 TAAAAATAAAAA
1 TAAAAATAAAAA
363427 TTAAATAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
43 4 0.08
44 31 0.61
45 10 0.20
46 6 0.12
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (45 bp):
TAAAAATAAAAAAATATATTTTATATTAAATTCTGAATTACTGTT
Found at i:363503 original size:148 final size:151
Alignment explanation
Indices: 363227--363965 Score: 428
Period size: 160 Copynumber: 4.8 Consensus size: 151
363217 ATTATAAAAT
* *
363227 TAAAAAATATTTTATATTAAATCTTGAATTACTATTTAAAAAATAATAAAAATTTAAAAATATTT
1 TAAAAAATATTTTATATTAAATCTTGAATTACTATTT--AAAATAATAAAAATTAAAAAATAGTT
* * * *
363292 TATATCGAACCTTAAATTACTATTTAAAAAATAATAAAAATTAAAAAATATATTTTATATTAAAT
64 TATATCAAACCTCAAATTACTATTTAAAAAATAACAAAAATTAAAAAATATATTCTATATTAAAT
***
363357 TTTGAATTACTAGTTAAAAATAA
129 CACGAATTACTAGTTAAAAATAA
* * *
363380 TAAAAATTA-TTTCTATTAAAT-TCTGAATTACTGTTT-AAA-AATAAAAATTAAATAAATAGTT
1 TAAAAAATATTTTATATTAAATCT-TGAATTACTATTTAAAATAATAAAAATTAAA-AAATAGTT
* * * **
363441 TATAGT-AAATCTCAAATTAGTATTT-AAAAATAACAAAATTTTTTAAAA-ATATTCTATATTAA
64 TATA-TCAAACCTCAAATTACTATTTAAAAAATAACAAAA-ATTAAAAAATATATTCTATATTAA
*
363503 ATCACGAATTACTATTTAAAAATAA
127 ATCACGAATTACTAGTTAAAAATAA
* **
363528 TAAAAAA-ATTAAAAAGAATATATTTAAAATCTCAAATTACTATTTAAAATAATAAAAAATT-AA
1 TAAAAAATATT-------TTATA-TT-AAATCTTGAATTACTATTTAAAATAAT-AAAAATTAAA
* * * * * *
363591 AAATATGTTTTATATAAAATCTCAAACTACTATTTAAAAAA-ATA-AAAAATT-TAAAA-GTCTT
56 AAATA-G-TTTATATCAAACCTCAAATTACTATTTAAAAAATA-ACAAAAATTAAAAAATATATT
* * * * *
363652 -T-TATTATATCCCAAATTACTATTTGAAAATAA
118 CTATATTAAATCACGAATTACTAGTTAAAAATAA
* * *
363684 TAAAAAAATAAAAATATTT-TGAGGTAAATCTTGGATTACTTTTTAAACATAATAAATAATTGAA
1 T-AAAAAAT----AT-TTTAT-A-TTAAATCTTGAATTACTATTTAAA-ATAATAAA-AATT-AA
* * * * * *
363748 AAAAT--TTTATATTAAATCTTC-AATTACTATTT-AAAAATAATAAATATT-TAAAA-ATATTA
55 AAAATAGTTTATATCAAA-CCTCAAATTACTATTTAAAAAATAACAAAAATTAAAAAATATATTC
* * *
363807 TATATTAAATCTCAAATTACTATTTAAAAAATAATAAAAAA
119 TATATTAAATCACGAATTACTAGTT---AAA-AAT----AA
** * * *
363848 TTAAAAACATATTTTATATTAAATCTAAAATTATTATTTAAAAATAATTAAAATTAATAAAATAT
1 -TAAAAA-ATATTTTATATTAAATCTTGAATTACTATTT-AAAATAATAAAAATTAA-AAAATAG
* ** *
363913 TTTAGGAT-AAATATCAAATTACTATTT-AAAAATAATAAAAAATTAAAAAATAT
62 TTTA-TATCAAACCTCAAATTACTATTTAAAAAATAA-CAAAAATTAAAAAATAT
363966 TTTTTATGTC
Statistics
Matches: 463, Mismatches: 63, Indels: 110
0.73 0.10 0.17
Matches are distributed among these distances:
147 1 0.00
148 65 0.14
149 35 0.08
150 1 0.00
151 1 0.00
152 23 0.05
153 14 0.03
154 35 0.08
155 28 0.06
156 63 0.14
157 23 0.05
158 32 0.07
159 35 0.08
160 71 0.15
161 17 0.04
162 6 0.01
163 3 0.01
164 7 0.02
165 3 0.01
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (151 bp):
TAAAAAATATTTTATATTAAATCTTGAATTACTATTTAAAATAATAAAAATTAAAAAATAGTTTA
TATCAAACCTCAAATTACTATTTAAAAAATAACAAAAATTAAAAAATATATTCTATATTAAATCA
CGAATTACTAGTTAAAAATAA
Found at i:364561 original size:22 final size:22
Alignment explanation
Indices: 364533--364575 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
364523 TATGTACATG
364533 TTATAATCT-TATGTACATATTA
1 TTATAAT-TGTATGTACATATTA
364555 TTATAATTGTATGTACATATT
1 TTATAATTGTATGTACATATT
364576 TTTTTATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (22 bp):
TTATAATTGTATGTACATATTA
Found at i:364713 original size:22 final size:23
Alignment explanation
Indices: 364688--364741 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 23
364678 TTTTTTTACT
364688 ATATGTACATTTA-ATTA-AAGTC
1 ATATGTACATTTACATTATAA-TC
364710 ATATGT--ATTTACTATTATAATC
1 ATATGTACATTTAC-ATTATAATC
364732 ATATGTACAT
1 ATATGTACAT
364742 ATTCTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
20 5 0.19
22 18 0.67
23 2 0.07
24 2 0.07
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.44
Consensus pattern (23 bp):
ATATGTACATTTACATTATAATC
Found at i:364939 original size:22 final size:22
Alignment explanation
Indices: 364889--364940 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
364879 TATGCACAAA
* *
364889 TAATTATACTATATGTACATAT
1 TAATTTTACTAAATGTACATAT
** *
364911 TGTTTTTACTAAATGTATATAT
1 TAATTTTACTAAATGTACATAT
364933 TAATTTTA
1 TAATTTTA
364941 TTATACATAC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.52
Consensus pattern (22 bp):
TAATTTTACTAAATGTACATAT
Found at i:365063 original size:22 final size:22
Alignment explanation
Indices: 365027--365081 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
365017 AGCTTGAAGG
*
365027 GTCAATTCTTT-CCTTTTGAGA
1 GTCAATTGTTTCCCTTTTGAGA
365048 GTCAATTGTTTCCCTTTTGAGA
1 GTCAATTGTTTCCCTTTTGAGA
365070 GTCAATTGTTTC
1 GTCAATTGTTTC
365082 TTTTAGGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 10 0.31
22 22 0.69
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.47
Consensus pattern (22 bp):
GTCAATTGTTTCCCTTTTGAGA
Found at i:366985 original size:22 final size:21
Alignment explanation
Indices: 366971--367025 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
366961 AATTGTATTT
366971 TTTCATCCAAAAAATGCATTC
1 TTTCATCCAAAAAATGCATTC
** *
366992 TTTCATCCAACCAATGCATTA
1 TTTCATCCAAAAAATGCATTC
*
367013 TTTCATCTAAAAA
1 TTTCATCCAAAAA
367026 TACCTTTTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.35
Consensus pattern (21 bp):
TTTCATCCAAAAAATGCATTC
Found at i:371241 original size:27 final size:27
Alignment explanation
Indices: 371210--371268 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
371200 TAATAATTAT
371210 ATATTTT-TTATTATATTAATATTTAAA
1 ATATTTTATTATTATATTAATA-TTAAA
* *
371237 ATATTTTATTTTTATATTAATATTAAT
1 ATATTTTATTATTATATTAATATTAAA
371264 ATATT
1 ATATT
371269 AATAATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
ATATTTTATTATTATATTAATATTAAA
Found at i:371309 original size:28 final size:29
Alignment explanation
Indices: 371209--371310 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 29
371199 GTAATAATTA
*
371209 TATATTTTTTATTATATTAATATTTAAAATAT
1 TATA-TTTATATTATA-TAAT-TTTAAAATAT
* * * *
371241 TTTATTTTTA-TAT-TAATATTAATATAT
1 TATATTTATATTATATAATTTTAAAATAT
371268 TAATAATTTATATTATATAATTTTAAAATA-
1 T-AT-ATTTATATTATATAATTTTAAAATAT
371298 TATATTTATATTA
1 TATATTTATATTA
371311 AATTATAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
27 9 0.15
28 15 0.25
29 8 0.14
30 7 0.12
31 17 0.29
32 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TATATTTATATTATATAATTTTAAAATAT
Found at i:371327 original size:28 final size:27
Alignment explanation
Indices: 371220--371342 Score: 101
Period size: 28 Copynumber: 4.4 Consensus size: 27
371210 ATATTTTTTA
*
371220 TTATATTAATATTTAAAATATTT-TATTT
1 TTATATTAATATTTAAAA-ATTTATA-AT
* *
371248 TTATATTAATA-TTAATATATTAATAAT
1 TTATATTAATATTTAA-AAATTTATAAT
* *
371275 TTATATTATATAATTTTAAAATATAT-AT
1 TTATATTA-AT-ATTTAAAAATTTATAAT
371303 TTATATTAA-ATTATAAAAATTTATAAT
1 TTATATTAATATT-TAAAAATTTATAAT
*
371330 ATTATATTTATAT
1 -TTATATTAATAT
371343 AATTATATTT
Statistics
Matches: 76, Mismatches: 10, Indels: 17
0.74 0.10 0.17
Matches are distributed among these distances:
25 3 0.04
26 9 0.12
27 19 0.25
28 34 0.45
29 8 0.11
30 3 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTATATTAATATTTAAAAATTTATAAT
Found at i:371336 original size:34 final size:31
Alignment explanation
Indices: 371279--371349 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 31
371269 AATAATTTAT
* *
371279 ATTATATAATTTTAAAATATATATTTATATTAA
1 ATTATAAAAATTTAAAATATATATTTATA-T-A
*
371312 ATTATAAAAATTTATAATATTATATTTATATA
1 ATTATAAAAATTTAAAATA-TATATTTATATA
371344 ATTATA
1 ATTATA
371350 TTTAAAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 7 0.21
33 17 0.50
34 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
ATTATAAAAATTTAAAATATATATTTATATA
Found at i:371360 original size:12 final size:14
Alignment explanation
Indices: 371321--371353 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
371311 AATTATAAAA
371321 ATTTATA-ATATTAT
1 ATTTATATA-ATTAT
371335 ATTTATATAATTAT
1 ATTTATATAATTAT
371349 ATTTA
1 ATTTA
371354 AAATTATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.94
15 1 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTTATATAATTAT
Found at i:371423 original size:14 final size:14
Alignment explanation
Indices: 371404--371433 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
371394 GAGAATAGAT
371404 ATTTAATCCCGCAC
1 ATTTAATCCCGCAC
371418 ATTTAATCCCGCAC
1 ATTTAATCCCGCAC
371432 AT
1 AT
371434 GCCAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.30
Consensus pattern (14 bp):
ATTTAATCCCGCAC
Found at i:371686 original size:10 final size:10
Alignment explanation
Indices: 371671--371702 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
371661 AATATTAATA
371671 TTATTTATAT
1 TTATTTATAT
*
371681 TTATTTAAAT
1 TTATTTATAT
371691 TTATTTATAT
1 TTATTTATAT
371701 TT
1 TT
371703 TTAATGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTATTTATAT
Found at i:372319 original size:6 final size:6
Alignment explanation
Indices: 372286--372323 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
372276 GATTTATAGT
372286 TTTATA TTTAATA TTT-TA TTTCATA TTTATA TTTATA T
1 TTTATA TTT-ATA TTTATA TTT-ATA TTTATA TTTATA T
372324 AAAAATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.17
6 13 0.45
7 11 0.38
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTATA
Found at i:372393 original size:16 final size:16
Alignment explanation
Indices: 372355--372394 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
372345 TAATTTTTTG
* *
372355 AAATAATATAAAATAT
1 AAATAAAATAAAATAA
*
372371 AATTAAAATAAAATAA
1 AAATAAAATAAAATAA
372387 AAATAAAA
1 AAATAAAA
372395 ATTTTAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AAATAAAATAAAATAA
Found at i:373178 original size:15 final size:14
Alignment explanation
Indices: 373148--373218 Score: 54
Period size: 15 Copynumber: 4.9 Consensus size: 14
373138 ATCCAATTTA
*
373148 AAAAAATT-ATATT
1 AAAAAATTAAAATT
373161 AAAAAATTAAAATAT
1 AAAAAATTAAAAT-T
***
373176 AAAAAATTATTTTT
1 AAAAAATTAAAATT
*
373190 AATAAAAATTTTAAATT
1 -A-AAAAA-TTAAAATT
373207 AAAAAATTAAAA
1 AAAAAATTAAAA
373219 AAATAAGAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
13 8 0.18
14 9 0.20
15 17 0.39
16 6 0.14
17 4 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAAAATTAAAATT
Found at i:373474 original size:28 final size:29
Alignment explanation
Indices: 373422--373476 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
373412 GTTTTTTAAA
*
373422 GTATAATTTATTTTTAATTTTTAAAATAG
1 GTATAATTTATTTTTAATTTATAAAATAG
*
373451 GTATGATTTATTTTT-ATTTATAAAAT
1 GTATAATTTATTTTTAATTTATAAAAT
373477 TAATTTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.56
Consensus pattern (29 bp):
GTATAATTTATTTTTAATTTATAAAATAG
Found at i:373699 original size:74 final size:69
Alignment explanation
Indices: 373488--373707 Score: 199
Period size: 74 Copynumber: 3.0 Consensus size: 69
373478 AATTTGATTA
* * * *
373488 AAGGTATTATTTATTTTTATTTATAAAAGTTTAAATTTGTTTTTATTTAATTATACGCATTTAAA
1 AAGGTATAATTTATTTTTATTTATAAAA-TTTAAATTTTTTTTTGTTTAATTATACGAATTTAAA
373553 TTTTT
65 TTTTT
** * * ** *
373558 AAGGTATAATTTATTTCGATTTGTAAAAATTTAAATGTGTTTTTTTATGTATAATTATGTGAGTT
1 AAGGTATAATTTATTTTTATTTAT-AAAATTTAAA--T-TTTTTTT-TGTTTAATTATACGAATT
373623 TAAATTTTT
61 TAAATTTTT
* * *
373632 GATA-GTGTACTTTATTTTTATTTATAGAAATTTAAAATTTATTTTTTGGTTTAATTATACAAAT
1 -A-AGGTATAATTTATTTTTATTTATA-AAATTT-AAATTT-TTTTTT-GTTTAATTATACGAAT
373696 TTAAATTTTT
60 TTAAATTTTT
373706 AA
1 AA
373708 ACATGGTGGC
Statistics
Matches: 118, Mismatches: 21, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
70 26 0.22
71 4 0.03
72 2 0.02
73 10 0.08
74 49 0.42
75 23 0.19
76 4 0.03
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.55
Consensus pattern (69 bp):
AAGGTATAATTTATTTTTATTTATAAAATTTAAATTTTTTTTTGTTTAATTATACGAATTTAAAT
TTTT
Found at i:374731 original size:25 final size:25
Alignment explanation
Indices: 374697--374746 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
374687 AATCACAAAA
374697 AATTTCTTTTGAACTACAAAGTCCT
1 AATTTCTTTTGAACTACAAAGTCCT
374722 AATTTCTTTTGAACTACAAAGTCCT
1 AATTTCTTTTGAACTACAAAGTCCT
374747 TTAATCATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (25 bp):
AATTTCTTTTGAACTACAAAGTCCT
Found at i:376850 original size:40 final size:40
Alignment explanation
Indices: 376745--376857 Score: 102
Period size: 40 Copynumber: 2.8 Consensus size: 40
376735 CAAACTTTGC
* *
376745 GCATTCAATGCTATCCACATAAAAAATAATAATTAAAATATA
1 GCATTAAATGCTATCCA-A-AATAAATAATAATTAAAATATA
* * * * * *
376787 -AAATAAAAGAATATACAATATAAATAATAATTAAAATATA
1 GCATTAAATG-CTATCCAAAATAAATAATAATTAAAATATA
* *
376827 GCATTTAATGCTATCCAAAATAAAAAATAAT
1 GCATTAAATGCTATCCAAAATAAATAATAAT
376858 AATTTTGAAT
Statistics
Matches: 53, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
40 37 0.70
41 11 0.21
42 5 0.09
ACGTcount: A:0.58, C:0.10, G:0.04, T:0.28
Consensus pattern (40 bp):
GCATTAAATGCTATCCAAAATAAATAATAATTAAAATATA
Found at i:380976 original size:91 final size:91
Alignment explanation
Indices: 380783--380981 Score: 233
Period size: 91 Copynumber: 2.2 Consensus size: 91
380773 ATTCTTCAAC
*
380783 TTTGACATTTACAATCAATCAACTTTTCCCATTTTCTATAAAAAAGAATCTAATTTCGAAATATA
1 TTTGACATTTACAATCAATCAACTTTTCCCATTTTCTACAAAAAAGAATCTAATTTCG-AATATA
*
380848 ATCCATTCATTAGTCTAATCCTTATAG
65 ATCCATGCATTAGTCTAATCCTTATAG
* ** * * *
380875 TTTAACATTTACAATCAATCAACTTTT-CTTTCTTTCTACCAAAACA-AATCTGATTCTTG-ATA
1 TTTGACATTTACAATCAATCAACTTTTCCCAT-TTTCTA-CAAAAAAGAATCTAATT-TCGAATA
* * *
380937 TAATTCATGCATTAGTTTAATCCTTGTAG
63 TAATCCATGCATTAGTCTAATCCTTATAG
*
380966 TTTGACATTTATAATC
1 TTTGACATTTACAATC
380982 CATACATTAG
Statistics
Matches: 91, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
91 44 0.48
92 40 0.44
93 7 0.08
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (91 bp):
TTTGACATTTACAATCAATCAACTTTTCCCATTTTCTACAAAAAAGAATCTAATTTCGAATATAA
TCCATGCATTAGTCTAATCCTTATAG
Found at i:383843 original size:158 final size:157
Alignment explanation
Indices: 383418--383843 Score: 581
Period size: 155 Copynumber: 2.7 Consensus size: 157
383408 TAATATTAAA
* *
383418 CATAAAAAAATTAATAATATTAAAAATCTCAAACAATATTAAGAGGTATCTAAACGAA-CATTTT
1 CATAAAAAAATTAATAATA-TAAAAATCTCAAACAATATTAAGAGGCATCTAAAC-AAGCATTTC
* * * * * *
383482 TTATTAATTAAAAAATATAACCTAAAACTACGTTAAACTAAGATTTTTTATTTTTGATATCTTAA
64 ATATTAATTAAAAAATATAACCTAAAACCACATTAAACTAAGTTTTTTTATTTTTGACATATTAA
383547 ACATATTTTGACAGATTAAACAAGCATGC
129 ACATATTTTGACAGATTAAACAAGCATGC
*
383576 CAT---AAAATTAATAATATAAAAACTCTCAAACAATATCAAGAGGCATCTAAACAAGCATTTCA
1 CATAAAAAAATTAATAATATAAAAA-TCTCAAACAATATTAAGAGGCATCTAAACAAGCATTTCA
* * *
383638 TATTAATTAAAAAATATAACCCAAAACCACATTAAATTAAGTCTTTTTATTTTTGACATATTAAA
65 TATTAATTAAAAAATATAACCTAAAACCACATTAAACTAAGTTTTTTTATTTTTGACATATTAAA
* *
383703 CATATTTTGACATATTAAACAAGCATGT
130 CATATTTTGACAGATTAAACAAGCATGC
* * * * * * *
383731 CATAAAAAAATTAATAATATCAGAAATCTCAAACAAAATTAAAAGACATTTAAATAAGTATTTCA
1 CATAAAAAAATTAATAATAT-AAAAATCTCAAACAATATTAAGAGGCATCTAAACAAGCATTTCA
* *
383796 TATTAATTAAAAAATATAACCTAAAACCATATTAAACTAATTTTTTTT
65 TATTAATTAAAAAATATAACCTAAAACCACATTAAACTAAGTTTTTTT
383844 TTACTTAATT
Statistics
Matches: 235, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
154 8 0.03
155 131 0.56
158 92 0.39
159 4 0.02
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (157 bp):
CATAAAAAAATTAATAATATAAAAATCTCAAACAATATTAAGAGGCATCTAAACAAGCATTTCAT
ATTAATTAAAAAATATAACCTAAAACCACATTAAACTAAGTTTTTTTATTTTTGACATATTAAAC
ATATTTTGACAGATTAAACAAGCATGC
Found at i:384038 original size:28 final size:30
Alignment explanation
Indices: 383982--384055 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
383972 AGTTATTAAC
*
383982 TTTTTTTTTCTTTC-TTTCTTTTATCTCCT
1 TTTTTTTTTCTTTCATTTCTGTTATCTCCT
384011 TTTTTTTTTCTTTTCATTT-TGTT-T-TCCT
1 TTTTTTTTTC-TTTCATTTCTGTTATCTCCT
* *
384039 TTCTTTCTTCCTTTCAT
1 TT-TTTTTTTCTTTCAT
384056 ATAATATGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 12 0.31
29 17 0.44
30 7 0.18
31 3 0.08
ACGTcount: A:0.04, C:0.20, G:0.01, T:0.74
Consensus pattern (30 bp):
TTTTTTTTTCTTTCATTTCTGTTATCTCCT
Found at i:384621 original size:15 final size:16
Alignment explanation
Indices: 384603--384646 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
384593 TATTATGATC
384603 TTTATTTTTAAAA-TT
1 TTTATTTTTAAAATTT
*
384618 TTTA-ATTTAAAATTT
1 TTTATTTTTAAAATTT
384633 TTTATTTTATAAAA
1 TTTATTTT-TAAAA
384647 AAATTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 7 0.29
15 10 0.42
16 2 0.08
17 5 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATTTTTAAAATTT
Found at i:384628 original size:14 final size:14
Alignment explanation
Indices: 384609--384639 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
384599 GATCTTTATT
384609 TTTAAAATTTTTAA
1 TTTAAAATTTTTAA
*
384623 TTTAAAATTTTTTA
1 TTTAAAATTTTTAA
384637 TTT
1 TTT
384640 TATAAAAAAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTAAAATTTTTAA
Found at i:384708 original size:22 final size:22
Alignment explanation
Indices: 384683--384724 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
384673 TTTTAATACA
384683 AAATTTTTTATTTAATTAAATT
1 AAATTTTTTATTTAATTAAATT
*
384705 AAATTTTTTATTTTATTAAA
1 AAATTTTTTATTTAATTAAA
384725 ATTTAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AAATTTTTTATTTAATTAAATT
Found at i:384726 original size:23 final size:23
Alignment explanation
Indices: 384656--384727 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 23
384646 AAAATTAATT
* * *
384656 ATTAATTTTTTTAGTTTTTTTAAT
1 ATTAAATTTTTTA-TTTTATTAAA
** *
384680 ACAAAATTTTTTATTTAATT-AA
1 ATTAAATTTTTTATTTTATTAAA
384702 ATTAAATTTTTTATTTTATTAAA
1 ATTAAATTTTTTATTTTATTAAA
384725 ATT
1 ATT
384728 TAATAATTAA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
22 18 0.47
23 10 0.26
24 10 0.26
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (23 bp):
ATTAAATTTTTTATTTTATTAAA
Found at i:389573 original size:22 final size:22
Alignment explanation
Indices: 389538--389579 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
389528 ATATTAAAAA
*
389538 TTATATTTTTAAATA-ATTTTT
1 TTATATTTTAAAATATATTTTT
389559 TTATAATTTTAAAATATATTT
1 TTAT-ATTTTAAAATATATTT
389580 AATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATATTTTAAAATATATTTTT
Found at i:389593 original size:11 final size:12
Alignment explanation
Indices: 389573--389607 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
389563 AATTTTAAAA
389573 TATATTTAATAT
1 TATATTTAATAT
389585 T-TATTTAATAT
1 TATATTTAATAT
*
389596 TAAATTTAATAT
1 TATATTTAATAT
389608 CAACTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TATATTTAATAT
Found at i:396402 original size:66 final size:65
Alignment explanation
Indices: 396313--396485 Score: 213
Period size: 65 Copynumber: 2.6 Consensus size: 65
396303 AAATCCACAT
* *
396313 AAAATCTTGTGGCACCAAGTCACCTTTATCAAAATAAAACCTCAAAGGTCCAATCACAAC-AATG
1 AAAATCTTGTGACGCCAAGTCACCTTTATCAAAATAAAACCT-AAAGGTCCAATCAC-ACTAATG
*
396377 GC
64 AC
* * * ** * *
396379 AAAATCTTGTGACGCTAGGTCACCTTTATCAAAATAAGACCTAAAGGTCTGATCGCCCTAATGAC
1 AAAATCTTGTGACGCCAAGTCACCTTTATCAAAATAAAACCTAAAGGTCCAATCACACTAATGAC
* *
396444 AAAATCTTATGATGCCAAGTCACCTTTATCAAAATAAAACCT
1 AAAATCTTGTGACGCCAAGTCACCTTTATCAAAATAAAACCT
396486 TAAAAGTCTA
Statistics
Matches: 91, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 1 0.01
65 53 0.58
66 37 0.41
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.25
Consensus pattern (65 bp):
AAAATCTTGTGACGCCAAGTCACCTTTATCAAAATAAAACCTAAAGGTCCAATCACACTAATGAC
Found at i:400177 original size:29 final size:29
Alignment explanation
Indices: 400116--400177 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
400106 ATGCGTTATG
* * **
400116 GAAGACTGATAAACACCAGATAACTAATG
1 GAAGACTGATAAACACCAGACAACAAACA
*
400145 GAAGACTGATATACACCAGACAACAAACA
1 GAAGACTGATAAACACCAGACAACAAACA
400174 GAAG
1 GAAG
400178 CCTAAAATCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.50, C:0.19, G:0.18, T:0.13
Consensus pattern (29 bp):
GAAGACTGATAAACACCAGACAACAAACA
Found at i:401052 original size:2 final size:2
Alignment explanation
Indices: 401045--401071 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
401035 ATGTTTATTT
401045 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 T
401072 TCTTTTTTCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:402076 original size:17 final size:17
Alignment explanation
Indices: 402056--402102 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
402046 TTTTAAAATA
*
402056 TTTATATATTTATATTT
1 TTTATATATTTATATAT
*
402073 TTTATATCA-TAATATAT
1 TTTATAT-ATTTATATAT
*
402090 TTTAAATATTTAT
1 TTTATATATTTAT
402103 TTCATAACGA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 1 0.04
17 22 0.92
18 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATATATTTATATAT
Found at i:403466 original size:2 final size:2
Alignment explanation
Indices: 403459--403510 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
403449 TATCATATTC
*
403459 AT AT AT AT AG 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
*
403501 AT AG AT AT AT
1 AT AT AT AT AT
403511 GAGCCCTATC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:405024 original size:10 final size:11
Alignment explanation
Indices: 404998--405039 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
404988 AATTTATGAA
404998 AAAATAATATG
1 AAAATAATATG
405009 AAAATAATAT-
1 AAAATAATATG
405019 AAAATAAATATG
1 AAAAT-AATATG
405031 TAAAA-AATA
1 -AAAATAATA
405040 ATTGTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 5 0.18
11 19 0.68
13 4 0.14
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (11 bp):
AAAATAATATG
Found at i:405028 original size:22 final size:21
Alignment explanation
Indices: 404998--405039 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
404988 AATTTATGAA
404998 AAAATAATATG-AAAATAATAT
1 AAAATAATATGTAAAA-AATAT
405019 AAAATAAATATGTAAAAAATA
1 AAAAT-AATATGTAAAAAATA
405040 ATTGTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 10 0.53
23 4 0.21
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (21 bp):
AAAATAATATGTAAAAAATAT
Found at i:405071 original size:52 final size:52
Alignment explanation
Indices: 405009--405108 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 52
404999 AAATAATATG
* *
405009 AAAATAATATAAA-A-TAAATATGTAAAAAATAATTGTTAAAATATTATAGTGT
1 AAAAAAATATAAATACTAAATAAGTAAAAAATAATT-TTAAAAT-TTATAGTGT
* * *
405061 AAAAAAATATAAATACTACATAAGTAAATAATTATTTTAAAATTTATA
1 AAAAAAATATAAATACTAAATAAGTAAAAAATAATTTTAAAATTTATA
405109 TAATACAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
52 17 0.41
53 8 0.20
54 16 0.39
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (52 bp):
AAAAAAATATAAATACTAAATAAGTAAAAAATAATTTTAAAATTTATAGTGT
Found at i:405147 original size:18 final size:18
Alignment explanation
Indices: 405099--405152 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
405089 TAATTATTTT
405099 AAAATTTATAT-AATA-C
1 AAAATTTATATAAATATC
405115 -AAA-TTAT-TAACATATC
1 AAAATTTATATAA-ATATC
405131 AAAATTTATATAAATAT-
1 AAAATTTATATAAATATC
405148 AAAAT
1 AAAAT
405153 ATCTTAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 6 0.19
16 1 0.03
17 8 0.25
18 8 0.25
19 3 0.09
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATTTATATAAATATC
Found at i:405219 original size:12 final size:12
Alignment explanation
Indices: 405202--405239 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
405192 ATTATCGTAA
405202 TAATTTATTAAT
1 TAATTTATTAAT
*
405214 TAATTT-TTATT
1 TAATTTATTAAT
405225 ATAATTTATTAAT
1 -TAATTTATTAAT
405238 TA
1 TA
405240 CTATAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 4 0.18
12 14 0.64
13 4 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TAATTTATTAAT
Found at i:405280 original size:18 final size:19
Alignment explanation
Indices: 405259--405301 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
405249 TACCAACGTA
405259 TATATAAAATTGT-TTAAT
1 TATATAAAATTGTATTAAT
*
405277 TATATAAAATTTTATTAAT
1 TATATAAAATTGTATTAAT
*
405296 AATATA
1 TATATA
405302 TAAGATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TATATAAAATTGTATTAAT
Found at i:408889 original size:17 final size:16
Alignment explanation
Indices: 408848--408904 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 16
408838 TTAAACTAGC
408848 TAAAATAT--TATATT
1 TAAAATATCATATATT
* *
408862 TAAATTTTCATCATATT
1 TAAAATATCAT-ATATT
408879 TAAAATATCATATATT
1 TAAAATATCATATATT
408895 ATATAAATAT
1 -TA-AAATAT
408905 TGACATATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 6 0.18
16 6 0.18
17 16 0.47
18 6 0.18
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAAATATCATATATT
Found at i:413317 original size:20 final size:20
Alignment explanation
Indices: 413243--413314 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
413233 AAAAAGACAT
* *
413243 AATGTATCGATACATTGTAG
1 AATGTATCGATACATTGAAA
* * *
413263 AATATATCGATACATTCATA
1 AATGTATCGATACATTGAAA
* *
413283 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGAAA
413303 AATGTATCGATA
1 AATGTATCGATA
413315 TATCAAGGTA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:413882 original size:18 final size:17
Alignment explanation
Indices: 413859--413899 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
413849 AAATAATTTT
413859 TAAAATAAGATACAAATA
1 TAAAATAA-ATACAAATA
*
413877 TAAAAT-AATATAAATA
1 TAAAATAAATACAAATA
413893 TAAAATA
1 TAAAATA
413900 TATAAATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 14 0.67
17 1 0.05
18 6 0.29
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAAATAAATACAAATA
Found at i:413904 original size:15 final size:16
Alignment explanation
Indices: 413872--413907 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
413862 AATAAGATAC
413872 AAATATAAAATAATAT
1 AAATATAAAATAATAT
413888 AAATATAAAAT-ATAT
1 AAATATAAAATAATAT
413903 AAATA
1 AAATA
413908 CAATATGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATATAAAATAATAT
Found at i:414722 original size:21 final size:22
Alignment explanation
Indices: 414671--414724 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
414661 TTTAAAAGCC
*
414671 TTAATATAAAACAATAGTTTCT
1 TTAATATAAAACAATAGTTTAT
* * *
414693 TTAAAATAAAA-ATTATTTTAT
1 TTAATATAAAACAATAGTTTAT
414714 TTAATATAAAA
1 TTAATATAAAA
414725 TATAACCTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (22 bp):
TTAATATAAAACAATAGTTTAT
Found at i:414768 original size:22 final size:22
Alignment explanation
Indices: 414716--414775 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
414706 TATTTTATTT
*
414716 AATATAAAATATAACCTAAAAA
1 AATATAAAATATAACATAAAAA
* *
414738 AATTTTAAAA-ATAATATAAATAA
1 AA-TATAAAATATAACATAAA-AA
414761 AATATAAATATATAA
1 AATATAAA-ATATAA
414776 ATATGTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
22 15 0.50
23 11 0.37
24 4 0.13
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (22 bp):
AATATAAAATATAACATAAAAA
Found at i:414861 original size:20 final size:21
Alignment explanation
Indices: 414836--414874 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
414826 TTACATAATA
*
414836 ATATAATAT-TTCAAATATTT
1 ATATAATATGTTAAAATATTT
414856 ATATAATATGTTAAAATAT
1 ATATAATATGTTAAAATAT
414875 ATAAACAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (21 bp):
ATATAATATGTTAAAATATTT
Found at i:415036 original size:20 final size:19
Alignment explanation
Indices: 415008--415052 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
414998 TTTTTTATAT
415008 TTAAAATTAATTATAAAATA
1 TTAAAATTAA-TATAAAATA
*
415028 TTAATATTAATATAAAA-A
1 TTAAAATTAATATAAAATA
415046 -TAAAATT
1 TTAAAATT
415053 TTAACATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 6 0.26
18 1 0.04
19 7 0.30
20 9 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAAATTAATATAAAATA
Found at i:415049 original size:25 final size:24
Alignment explanation
Indices: 415020--415076 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
415010 AAAATTAATT
*
415020 ATAAAATATTAATATTAATATAAAA
1 ATAAAATATTAACATT-ATATAAAA
* * *
415045 ATAAAATTTTAACATTATTTAAAT
1 ATAAAATATTAACATTATATAAAA
415069 ATAAAATA
1 ATAAAATA
415077 ATTATTAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
ATAAAATATTAACATTATATAAAA
Found at i:415609 original size:16 final size:15
Alignment explanation
Indices: 415588--415638 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
415578 TAAATTCGAG
415588 TTAAATTTTAAATAAT
1 TTAAA-TTTAAATAAT
*
415604 TTAAA--TAAAAAAT
1 TTAAATTTAAATAAT
*
415617 TTTAATTTAAATTAAT
1 TTAAATTTAAA-TAAT
415633 TTAAAT
1 TTAAAT
415639 AATTAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 11 0.39
15 4 0.14
16 13 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAATTTAAATAAT
Found at i:415646 original size:29 final size:29
Alignment explanation
Indices: 415594--415653 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
415584 CGAGTTAAAT
415594 TTTAAATAATTTAAATAAAAAATTT-TAA
1 TTTAAATAATTTAAATAAAAAATTTATAA
**
415622 TTTAAATTAATTTAAATAATTAATTTATAA
1 TTTAAA-TAATTTAAATAAAAAATTTATAA
415652 TT
1 TT
415654 AACTCATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 6 0.21
29 17 0.61
30 5 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTAAATAATTTAAATAAAAAATTTATAA
Found at i:415664 original size:24 final size:23
Alignment explanation
Indices: 415618--415664 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
415608 ATAAAAAATT
* *
415618 TTAATTTAAATTAATTTAAATAA
1 TTAATTTAAATTAACTCAAATAA
*
415641 TTAATTTATAATTAACTCATATAA
1 TTAATTTA-AATTAACTCAAATAA
415665 AATTGATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAATTTAAATTAACTCAAATAA
Found at i:416813 original size:19 final size:18
Alignment explanation
Indices: 416789--416888 Score: 57
Period size: 18 Copynumber: 5.4 Consensus size: 18
416779 TACTATAAAA
416789 TTTCAAATGATTGTTATAT
1 TTTCAAATGA-TGTTATAT
* *
416808 TTTC-AAT-ATGTATAAAAA
1 TTTCAAATGATGT-T-ATAT
416826 TTTCAAATGACTGTTATAT
1 TTTCAAATGA-TGTTATAT
* *
416845 TTT-TAAT-ATGTATAAAAT
1 TTTCAAATGATGT-T-ATAT
416863 TTT-AAATGACTGTTATAT
1 TTTCAAATGA-TGTTATAT
*
416881 TTTTAAAT
1 TTTCAAAT
416889 TATTATTATA
Statistics
Matches: 63, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
16 6 0.10
17 4 0.06
18 27 0.43
19 18 0.29
20 5 0.08
21 3 0.05
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (18 bp):
TTTCAAATGATGTTATAT
Found at i:416846 original size:18 final size:18
Alignment explanation
Indices: 416825--416888 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
416815 ATGTATAAAA
*
416825 ATTTCAAATGACTGTTAT
1 ATTTTAAATGACTGTTAT
* *
416843 ATTTTTAAT-A-TGTATAAA
1 ATTTTAAATGACTGT-T-AT
416861 ATTTTAAATGACTGTTAT
1 ATTTTAAATGACTGTTAT
416879 ATTTTTAAAT
1 A-TTTTAAAT
416889 TATTATTATA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
16 3 0.08
17 2 0.06
18 18 0.50
19 10 0.28
20 3 0.08
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.50
Consensus pattern (18 bp):
ATTTTAAATGACTGTTAT
Found at i:416884 original size:36 final size:36
Alignment explanation
Indices: 416782--416886 Score: 174
Period size: 37 Copynumber: 2.9 Consensus size: 36
416772 AAATTACTAC
* *
416782 TATAAAATTTCAAATGATTGTTATATTTTCAATATG
1 TATAAAATTTCAAATGACTGTTATATTTTTAATATG
416818 TATAAAAATTTCAAATGACTGTTATATTTTTAATATG
1 TAT-AAAATTTCAAATGACTGTTATATTTTTAATATG
*
416855 TATAAAATTTTAAATGACTGTTATATTTTTAA
1 TATAAAATTTCAAATGACTGTTATATTTTTAA
416887 ATTATTATTA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
36 31 0.48
37 34 0.52
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.48
Consensus pattern (36 bp):
TATAAAATTTCAAATGACTGTTATATTTTTAATATG
Found at i:416920 original size:41 final size:37
Alignment explanation
Indices: 416785--416925 Score: 167
Period size: 37 Copynumber: 3.7 Consensus size: 37
416775 TTACTACTAT
* * *
416785 AAAATTTCAAATGATTGTTATATTTTCAATATGTATA
1 AAAATTTTAAATGACTGTTATATTTTTAATATGTATA
*
416822 AAAATTTCAAATGACTGTTATATTTTTAATATGTAT-
1 AAAATTTTAAATGACTGTTATATTTTTAATATGTATA
*
416858 AAAATTTTAAATGACTGTTATATTTTTAAATTATTATTATA
1 AAAATTTTAAATGACTGTTATATTTTT-AA-TA-T-GTATA
* * *
416899 AAAATTTTAAATTACTATTATAATTTT
1 AAAATTTTAAATGACTGTTATATTTTT
416926 GAATCGATTC
Statistics
Matches: 92, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
36 26 0.28
37 36 0.39
38 2 0.02
39 1 0.01
40 3 0.03
41 24 0.26
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (37 bp):
AAAATTTTAAATGACTGTTATATTTTTAATATGTATA
Found at i:416923 original size:19 final size:19
Alignment explanation
Indices: 416860--416925 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
416850 ATATGTATAA
* *
416860 AATTTTAAATGACTGTTAT
1 AATTTTAAATTACTATTAT
* *
416879 ATTTTTAAATTATTATTAT
1 AATTTTAAATTACTATTAT
416898 AAAAATTTTAAATTACTATTAT
1 ---AATTTTAAATTACTATTAT
416920 AATTTT
1 AATTTT
416926 GAATCGATTC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 21 0.55
22 17 0.45
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (19 bp):
AATTTTAAATTACTATTAT
Found at i:417574 original size:11 final size:11
Alignment explanation
Indices: 417558--417582 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
417548 TTTATAAATA
417558 TAAATAGAATT
1 TAAATAGAATT
417569 TAAATAGAATT
1 TAAATAGAATT
417580 TAA
1 TAA
417583 GATTTATGTT
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:0.08, T:0.36
Consensus pattern (11 bp):
TAAATAGAATT
Found at i:417978 original size:28 final size:28
Alignment explanation
Indices: 417946--417999 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
417936 AGAATAAGTC
417946 TAAATATATTAAATAATAATTATTTAGT
1 TAAATATATTAAATAATAATTATTTAGT
* ** *
417974 TAAATATTTTTCATAGTAATTATTTA
1 TAAATATATTAAATAATAATTATTTA
418000 ATTTTTTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (28 bp):
TAAATATATTAAATAATAATTATTTAGT
Found at i:418297 original size:22 final size:23
Alignment explanation
Indices: 418258--418303 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
418248 CATAGAAATT
*
418258 TTATTTATTTACTCAAT-AATAA
1 TTATTTATTTAATCAATAAATAA
418280 TTATTTATTATAAT-AATAAATAA
1 TTATTTATT-TAATCAATAAATAA
418303 T
1 T
418304 AATAAATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
TTATTTATTTAATCAATAAATAA
Found at i:418589 original size:21 final size:23
Alignment explanation
Indices: 418551--418592 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
418541 TCAAATCTAA
418551 AATATGATATTAAAAAATATATT
1 AATATGATATTAAAAAATATATT
418574 AATATGATA-T-AAAAATATA
1 AATATGATATTAAAAAATATA
418593 AACACATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 1 0.05
23 9 0.47
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (23 bp):
AATATGATATTAAAAAATATATT
Found at i:419264 original size:13 final size:13
Alignment explanation
Indices: 419246--419279 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
419236 TTATATATAA
419246 AATATATTTACCT
1 AATATATTTACCT
419259 AATATATTTACCT
1 AATATATTTACCT
419272 AATATATT
1 AATATATT
419280 AAAAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTTACCT
Found at i:419643 original size:13 final size:13
Alignment explanation
Indices: 419620--419653 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
419610 TATATATATG
419620 ATAATATATTAAAT
1 ATAA-ATATTAAAT
419634 ATAAATATTAAAT
1 ATAAATATTAAAT
419647 ATAAATA
1 ATAAATA
419654 CTTTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAAATATTAAAT
Found at i:419850 original size:13 final size:13
Alignment explanation
Indices: 419832--419857 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
419822 ACAATACATC
419832 AAATATAAATATT
1 AAATATAAATATT
419845 AAATATAAATATT
1 AAATATAAATATT
419858 TTTAAAAAAT
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATATAAATATT
Found at i:420171 original size:18 final size:17
Alignment explanation
Indices: 420148--420190 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
420138 AAATAATTTT
420148 TAAAATAAGATATAAATA
1 TAAAATAA-ATATAAATA
*
420166 TAAAAT-AATATAATTA
1 TAAAATAAATATAAATA
420182 TAAAATAAA
1 TAAAATAAA
420191 ACAAATACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 14 0.61
17 3 0.13
18 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
TAAAATAAATATAAATA
Found at i:422943 original size:45 final size:46
Alignment explanation
Indices: 422878--422968 Score: 112
Period size: 48 Copynumber: 2.0 Consensus size: 46
422868 CGAAGCTGCT
* * *
422878 GGAATAGATGCTGGAAACTG-CTTTGATCGTGGATGGGAGGCTGTC
1 GGAATAGAAGCTGGAAACTGTCTTTGATCGTGAATCGGAGGCTGTC
* *
422923 GGAATGGAAGCTGGAGACTGCTTCTTTGATCGTGAATCGGAGGCTG
1 GGAATAGAAGCTGGAAACTG--TCTTTGATCGTGAATCGGAGGCTG
422969 CTATAATGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
45 17 0.45
48 21 0.55
ACGTcount: A:0.22, C:0.14, G:0.37, T:0.26
Consensus pattern (46 bp):
GGAATAGAAGCTGGAAACTGTCTTTGATCGTGAATCGGAGGCTGTC
Found at i:423151 original size:31 final size:31
Alignment explanation
Indices: 423102--423162 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
423092 TGTCGCCGTC
* *
423102 GCTGCTGGAAGTTGCTGTAGGAGCTGTGGGA
1 GCTGCTGGAAATTACTGTAGGAGCTGTGGGA
*
423133 GCTGTTGGAAATTACTGTAGGAGCTGTGGG
1 GCTGCTGGAAATTACTGTAGGAGCTGTGGG
423163 GGGCTTCTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.18, C:0.11, G:0.43, T:0.28
Consensus pattern (31 bp):
GCTGCTGGAAATTACTGTAGGAGCTGTGGGA
Found at i:423441 original size:22 final size:22
Alignment explanation
Indices: 423407--423449 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
423397 GTTCGTGGAT
*
423407 TGGAGGCTGCCGTGGGAGCTGC
1 TGGAGGCTGCCGTGGAAGCTGC
423429 TGGA-GCTGTCCGTGGAAGCTG
1 TGGAGGCTG-CCGTGGAAGCTG
423450 GAAGAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.12, C:0.21, G:0.47, T:0.21
Consensus pattern (22 bp):
TGGAGGCTGCCGTGGAAGCTGC
Found at i:423901 original size:13 final size:14
Alignment explanation
Indices: 423883--424134 Score: 100
Period size: 14 Copynumber: 19.2 Consensus size: 14
423873 TGAAATGTTT
*
423883 ATGAAATG-CATGC
1 ATGAAATGAAATGC
423896 ATGAAATGAAATGC
1 ATGAAATGAAATGC
* *
423910 ATAAAATGAAAATTAC
1 ATGAAATG-AAA-TGC
* *
423926 GTGAAATG-TATGC
1 ATGAAATGAAATGC
423939 ATGAAATGAAAATGC
1 ATGAAATG-AAATGC
*
423954 ATG-CATG-AA-GC
1 ATGAAATGAAATGC
* **
423965 TTGAAATG---TTT
1 ATGAAATGAAATGC
* *
423976 ATGACATG-CATGC
1 ATGAAATGAAATGC
423989 ATGAAATGAAATGC
1 ATGAAATGAAATGC
*
424003 ATGAAATGAAAAT-T
1 ATGAAATG-AAATGC
*
424017 ATG---TGAAATGT
1 ATGAAATGAAATGC
424028 ATGAAATGAAAATGC
1 ATGAAATG-AAATGC
*
424043 ATG-CATG-AA-GC
1 ATGAAATGAAATGC
* **
424054 TTGAAATG---TTT
1 ATGAAATGAAATGC
*
424065 ATGAAATG-CATGC
1 ATGAAATGAAATGC
424078 ATGAAATGAAATGC
1 ATGAAATGAAATGC
424092 ATGAAATGAAA---
1 ATGAAATGAAATGC
* **
424103 ATTATCTGAAATGC
1 ATGAAATGAAATGC
424117 ATGAAATGAAAATGC
1 ATGAAATG-AAATGC
424132 ATG
1 ATG
424135 CATAAAATGT
Statistics
Matches: 177, Mismatches: 37, Indels: 48
0.68 0.14 0.18
Matches are distributed among these distances:
10 4 0.02
11 35 0.20
12 10 0.06
13 34 0.19
14 55 0.31
15 31 0.18
16 8 0.05
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.27
Consensus pattern (14 bp):
ATGAAATGAAATGC
Found at i:423904 original size:89 final size:88
Alignment explanation
Indices: 423803--424137 Score: 376
Period size: 89 Copynumber: 3.7 Consensus size: 88
423793 TTGCATATGA
* * * *
423803 ATGCATGGAATGAAA-GCAAATGCAATGAAATGCATGTATGCATGAAATGAAAAATTACATGCAT
1 ATGCATGAAATGAAATGCAAATGAAATGAAATGAATGTATGCATGAAATG-AAAA-TGCATGCAT
*
423867 GAAGCATGAAATGTTTATGAAATGC
64 GAAGCTTGAAATGTTTATGAAATGC
* **
423892 ATGCATGAAATGAAATGCATAAAATGAAAATTACGTGAAATGTATGCATGAAATGAAAATGCATG
1 ATGCATGAAATGAAATGC---AAATG-AAATGAAATG-AATGTATGCATGAAATGAAAATGCATG
*
423957 CATGAAGCTTGAAATGTTTATGACATGC
61 CATGAAGCTTGAAATGTTTATGAAATGC
* *
423985 ATGCATGAAATGAAATGC--ATGAAATGAAAAT-TATGTGAAATGTATGAAATGAAAATGCATGC
1 ATGCATGAAATGAAATGCAAATGAAATG-AAATGAATGT---ATGCATGAAATGAAAATGCATGC
424047 ATGAAGCTTGAAATGTTTATGAAATGC
62 ATGAAGCTTGAAATGTTTATGAAATGC
* * *
424074 ATGCATGAAATGAAATGC--ATGAAATGAAAATTATCTGAAATGCATGAAATGAAAATGCATGCA
1 ATGCATGAAATGAAATGCAAATGAAATG-AAATGA-ATG-TATGCATGAAATGAAAATGCATGCA
424137 T
63 T
424138 AAAATGTTAC
Statistics
Matches: 214, Mismatches: 19, Indels: 26
0.83 0.07 0.10
Matches are distributed among these distances:
86 4 0.02
87 4 0.02
88 5 0.02
89 117 0.55
90 2 0.01
91 2 0.01
93 54 0.25
94 10 0.05
95 16 0.07
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (88 bp):
ATGCATGAAATGAAATGCAAATGAAATGAAATGAATGTATGCATGAAATGAAAATGCATGCATGA
AGCTTGAAATGTTTATGAAATGC
Found at i:423973 original size:93 final size:92
Alignment explanation
Indices: 423840--424137 Score: 466
Period size: 89 Copynumber: 3.3 Consensus size: 92
423830 AAATGCATGT
* *
423840 ATGCATGAAATGAAAAATTACATGCATGAAGCATGAAATGTTTATGAAATGCATGCATGAAATGA
1 ATGCATGAAATG-AAAA-TGCATGCATGAAGCTTGAAATGTTTATGAAATGCATGCATGAAATGA
*
423905 AATGCATAAAATGAAAATTACGTGAAATG
64 AATGCATGAAATGAAAATTACGTGAAATG
*
423934 TATGCATGAAATGAAAATGCATGCATGAAGCTTGAAATGTTTATGACATGCATGCATGAAATGAA
1 -ATGCATGAAATGAAAATGCATGCATGAAGCTTGAAATGTTTATGAAATGCATGCATGAAATGAA
*
423999 ATGCATGAAATGAAAATTATGTGAAATG
65 ATGCATGAAATGAAAATTACGTGAAATG
424027 -T--ATGAAATGAAAATGCATGCATGAAGCTTGAAATGTTTATGAAATGCATGCATGAAATGAAA
1 ATGCATGAAATGAAAATGCATGCATGAAGCTTGAAATGTTTATGAAATGCATGCATGAAATGAAA
424089 TGCATGAAATGAAAATTATC-TG-AA--
66 TGCATGAAATGAAAATTA-CGTGAAATG
424113 ATGCATGAAATGAAAATGCATGCAT
1 ATGCATGAAATGAAAATGCATGCAT
424138 AAAATGTTAC
Statistics
Matches: 192, Mismatches: 7, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
87 1 0.01
88 2 0.01
89 101 0.53
91 1 0.01
93 71 0.37
94 4 0.02
95 12 0.06
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (92 bp):
ATGCATGAAATGAAAATGCATGCATGAAGCTTGAAATGTTTATGAAATGCATGCATGAAATGAAA
TGCATGAAATGAAAATTACGTGAAATG
Found at i:424095 original size:27 final size:29
Alignment explanation
Indices: 423860--424099 Score: 86
Period size: 31 Copynumber: 8.0 Consensus size: 29
423850 TGAAAAATTA
*
423860 CATGCATGAAGCATGAAATGTTTATGAAATG
1 CATGCATGAA-CATGAAATG-TCATGAAATG
*
423891 CATGCATGAA-ATGAAATG-CATAAAATG
1 CATGCATGAACATGAAATGTCATGAAATG
* * * * **
423918 AAAATTACGTGAA-ATGTATGCATGAAATGAAAATG
1 --CA-TGCATGAACATG-A--AATGTCATG-AAATG
* * *
423953 CATGCATGAAGCTTGAAATGTTTATGACATG
1 CATGCATGAA-CATGAAATG-TCATGAAATG
423984 CATGCATGAA-ATGAAATG-CATGAAATG
1 CATGCATGAACATGAAATGTCATGAAATG
* * * **
424011 AAAAT-TATGTGAA-ATG-TATGAAATGAAAATG
1 --CATGCA--TGAACATGAAATGTCATG-AAATG
* *
424042 CATGCATGAAGCTTGAAATGTTTATGAAATG
1 CATGCATGAA-CATGAAATG-TCATGAAATG
424073 CATGCATGAA-ATGAAATG-CATGAAATG
1 CATGCATGAACATGAAATGTCATGAAATG
424100 AAAATTATCT
Statistics
Matches: 156, Mismatches: 31, Indels: 48
0.66 0.13 0.20
Matches are distributed among these distances:
27 22 0.14
28 5 0.03
29 30 0.19
30 22 0.14
31 51 0.33
32 12 0.08
33 5 0.03
34 4 0.03
35 5 0.03
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (29 bp):
CATGCATGAACATGAAATGTCATGAAATG
Found at i:424155 original size:40 final size:39
Alignment explanation
Indices: 423985--424134 Score: 122
Period size: 39 Copynumber: 3.5 Consensus size: 39
423975 TATGACATGC
* *
423985 ATGCATGAAATGAAATGCATGAAATGAAAATTATGTGAA
1 ATGCATGAAATGAAATGCATGAAATGAAAATTATCTAAA
* * *
424024 ATGTATGAAATGAAAATGCATGCATGAAGCTTGAAATGTTTAT-GAAA
1 ATGCATGAAATG-AAATGCATG-A--AA---TGAAA--ATTATCTAAA
*
424071 TGCATGCATGAAATGAAATGCATGAAATGAAAATTATCTGAA
1 ---ATGCATGAAATGAAATGCATGAAATGAAAATTATCTAAA
424113 ATGCATGAAATGAAAATGCATG
1 ATGCATGAAATG-AAATGCATG
424135 CATAAAATGT
Statistics
Matches: 89, Mismatches: 8, Indels: 27
0.72 0.06 0.22
Matches are distributed among these distances:
39 23 0.26
40 18 0.20
41 5 0.06
42 2 0.02
43 7 0.08
46 7 0.08
47 2 0.02
48 5 0.06
49 9 0.10
50 11 0.12
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.27
Consensus pattern (39 bp):
ATGCATGAAATGAAATGCATGAAATGAAAATTATCTAAA
Found at i:424214 original size:6 final size:6
Alignment explanation
Indices: 424203--424264 Score: 58
Period size: 6 Copynumber: 10.8 Consensus size: 6
424193 ATGCAATGCA
* * *
424203 TTTTAT TTTTAT TATTAT TATTAT TTTTAT TTTT-T TATT-T TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* *
424249 TTAT-T TTTTAT GTTTA
1 TTTTAT TTTTAT TTTTA
424265 ATAAATTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
5 12 0.26
6 35 0.74
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:424223 original size:9 final size:9
Alignment explanation
Indices: 424205--424256 Score: 72
Period size: 9 Copynumber: 5.9 Consensus size: 9
424195 GCAATGCATT
424205 TTATTTTTA
1 TTATTTTTA
*
424214 TTATTATTA
1 TTATTTTTA
424223 TTATTTTTA
1 TTATTTTTA
424232 TT-TTTTTA
1 TTATTTTTA
424240 TT-TTTTTA
1 TTATTTTTA
424248 TTTATTTTT
1 -TTATTTTT
424257 TATGTTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
8 14 0.36
9 20 0.51
10 5 0.13
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTATTTTTA
Found at i:424871 original size:21 final size:22
Alignment explanation
Indices: 424820--424873 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
424810 TTTAAAAACC
*
424820 TTAATATAAAACAATAGTTTCT
1 TTAATATAAAACAATAGTTTAT
* * *
424842 TTAAAATAAAAC-TTATTTTAT
1 TTAATATAAAACAATAGTTTAT
424863 TTAATATAAAA
1 TTAATATAAAA
424874 TATAACCTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (22 bp):
TTAATATAAAACAATAGTTTAT
Found at i:425092 original size:13 final size:13
Alignment explanation
Indices: 425074--425099 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
425064 AGGGCTAAAC
425074 TTTAAATAATATT
1 TTTAAATAATATT
425087 TTTAAATAATATT
1 TTTAAATAATATT
425100 AATTCGATCT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTAAATAATATT
Found at i:425190 original size:19 final size:20
Alignment explanation
Indices: 425148--425188 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
425138 TTTTTATATT
425148 TAAA-ATTAATTATAAAATA
1 TAAATATTAATTATAAAATA
425167 TAAATATTAA-TATAAAA-A
1 TAAATATTAATTATAAAATA
425185 TAAA
1 TAAA
425189 ATTTTAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 11 0.52
20 5 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAATATTAATTATAAAATA
Found at i:432848 original size:2 final size:2
Alignment explanation
Indices: 432835--432869 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
432825 GTGAAATTAA
*
432835 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
432870 ATGTTCATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:434505 original size:21 final size:22
Alignment explanation
Indices: 434462--434505 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
434452 GTTTTTAACC
* **
434462 TATTGATTTTTTAAATACTATT
1 TATTGATTTTTTAAAAAAAATT
434484 TATTG-TTTTTTAAAAAAAATT
1 TATTGATTTTTTAAAAAAAATT
434505 T
1 T
434506 CACTTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (22 bp):
TATTGATTTTTTAAAAAAAATT
Found at i:434727 original size:19 final size:20
Alignment explanation
Indices: 434683--434728 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
434673 TTTGGGCTTT
*
434683 TAATTTAAAAATTTTCATAA
1 TAATTTAAAAATTGTCATAA
434703 TAATTTAAAAA-TGT-ATAA
1 TAATTTAAAAATTGTCATAA
434721 TATATTTA
1 TA-ATTTA
434729 TATTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 7 0.29
20 11 0.46
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (20 bp):
TAATTTAAAAATTGTCATAA
Found at i:434761 original size:39 final size:41
Alignment explanation
Indices: 434708--434790 Score: 116
Period size: 39 Copynumber: 2.1 Consensus size: 41
434698 CATAATAATT
* *
434708 TAAAAATGTATAATATATTTATATTATTTTTTAT-TA-TAA
1 TAAAAATGTATAATATATTTATATAAATTTTTATATATTAA
* *
434747 TAAATATGTTTAATATATTTATATAAATTTTTATATATTAA
1 TAAAAATGTATAATATATTTATATAAATTTTTATATATTAA
434788 TAA
1 TAA
434791 TTTAATTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 30 0.79
40 2 0.05
41 6 0.16
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (41 bp):
TAAAAATGTATAATATATTTATATAAATTTTTATATATTAA
Found at i:434781 original size:18 final size:18
Alignment explanation
Indices: 434760--434822 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
434750 ATATGTTTAA
434760 TATATTTATATAAATTTT
1 TATATTTATATAAATTTT
434778 TATATATTA-AT-AA--TT
1 TATAT-TTATATAAATTTT
434793 TA-ATTTATATAAAATTTT
1 TATATTTATAT-AAATTTT
*
434811 AAATATTTATAT
1 -TATATTTATAT
434823 TTGTATATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
13 3 0.08
14 4 0.11
15 4 0.11
16 2 0.06
17 2 0.06
18 9 0.25
19 4 0.11
20 8 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATTTATATAAATTTT
Found at i:435395 original size:2 final size:2
Alignment explanation
Indices: 435388--435426 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
435378 ACCACTCAAG
435388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
435427 ATTTCAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:436600 original size:20 final size:20
Alignment explanation
Indices: 436561--436600 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
436551 TTTTTTTTAT
*
436561 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
436581 ATATTATATATT-TATATAAA
1 ATATTATA-ATTATATATAAA
436601 TTTTGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:438146 original size:30 final size:30
Alignment explanation
Indices: 438112--438170 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
438102 AAAATTATTT
*
438112 TATTTATTAATATTTATAATTA-AATTTAAA
1 TATTTATTAATATTTA-AATAATAATTTAAA
* *
438142 TATTTTTTATTATTTAAATAATAATTTAA
1 TATTTATTAATATTTAAATAATAATTTAA
438171 TTAAATGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TATTTATTAATATTTAAATAATAATTTAAA
Done.