Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008909.1 Hibiscus syriacus cultivar Beakdansim tig00112206_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2327114
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:2018230 original size:12 final size:12
Alignment explanation
Indices: 2018215--2018252 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
2018205 ATTATCACCA
2018215 TCGTCATCGTCG
1 TCGTCATCGTCG
2018227 TCGTCATCGTCG
1 TCGTCATCGTCG
*
2018239 TCGTCGTCGTCG
1 TCGTCATCGTCG
2018251 TC
1 TC
2018253 CTGAGTAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.05, C:0.34, G:0.26, T:0.34
Consensus pattern (12 bp):
TCGTCATCGTCG
Found at i:2018439 original size:16 final size:16
Alignment explanation
Indices: 2018418--2018473 Score: 103
Period size: 16 Copynumber: 3.5 Consensus size: 16
2018408 TCCGTATCCG
*
2018418 ATCCGAAAAATCGGAT
1 ATCCGAAAATTCGGAT
2018434 ATCCGAAAATTCGGAT
1 ATCCGAAAATTCGGAT
2018450 ATCCGAAAATTCGGAT
1 ATCCGAAAATTCGGAT
2018466 ATCCGAAA
1 ATCCGAAA
2018474 TTTCATATCG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (16 bp):
ATCCGAAAATTCGGAT
Found at i:2021506 original size:9 final size:9
Alignment explanation
Indices: 2021492--2021527 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2021482 ATCTGCAAAA
2021492 AAATTAAAT
1 AAATTAAAT
2021501 AAATTAAAT
1 AAATTAAAT
*
2021510 -ACTTAAAT
1 AAATTAAAT
2021518 AAATTAAAT
1 AAATTAAAT
2021527 A
1 A
2021528 CAAAATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (9 bp):
AAATTAAAT
Found at i:2021517 original size:17 final size:17
Alignment explanation
Indices: 2021495--2021528 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2021485 TGCAAAAAAA
2021495 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
2021512 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
2021529 AAAATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:2021585 original size:10 final size:10
Alignment explanation
Indices: 2021572--2021607 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
2021562 AGAGATTATA
2021572 AGAGAAGTTG
1 AGAGAAGTTG
2021582 AGAGAAGTTG
1 AGAGAAGTTG
*
2021592 AGAGAAATTG
1 AGAGAAGTTG
2021602 AGAGAA
1 AGAGAA
2021608 TTTGGTGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.36, T:0.17
Consensus pattern (10 bp):
AGAGAAGTTG
Found at i:2028406 original size:20 final size:20
Alignment explanation
Indices: 2028383--2028434 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2028373 AACGCGATCC
2028383 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
2028403 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
2028423 CCAAAATCGCAA
1 CCAGAATCGCAA
2028435 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:2028515 original size:20 final size:20
Alignment explanation
Indices: 2028490--2028683 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
2028480 GATTTTCCAT
* *
2028490 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
2028510 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
2028530 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2028550 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
2028570 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
2028590 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2028610 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
2028630 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
2028651 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
2028671 AATCGCAACGCGA
1 AATCGCAACGCGA
2028684 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:2028535 original size:40 final size:39
Alignment explanation
Indices: 2028486--2028683 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
2028476 TTGCGATTTT
* ** *
2028486 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
2028524 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
2028565 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
2028605 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
2028644 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
2028684 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:2028573 original size:60 final size:60
Alignment explanation
Indices: 2028490--2028682 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
2028480 GATTTTCCAT
* ** * *
2028490 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
2028550 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
2028610 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
2028671 AATCGCAACGCG
1 AATCGCAACGCG
2028683 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:2029103 original size:33 final size:33
Alignment explanation
Indices: 2029064--2029134 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2029054 TTCACTTAGA
*
2029064 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2029097 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2029130 TTTCA
1 TTTCA
2029135 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2029291 original size:19 final size:19
Alignment explanation
Indices: 2029267--2029311 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2029257 GCAACGAGAG
**
2029267 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
2029286 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
2029305 AATCGCA
1 AATCGCA
2029312 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:2029329 original size:19 final size:19
Alignment explanation
Indices: 2029307--2029404 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
2029297 GAAACCAAAA
*
2029307 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2029326 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2029340 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2029359 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
2029373 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
2029392 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2029405 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2029348 original size:14 final size:14
Alignment explanation
Indices: 2029329--2029418 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
2029319 TTTCATTTCG
2029329 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2029343 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2029362 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2029376 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
2029393 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
2029409 CGTTGCGATT
1 CGTTGCGATT
2029419 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2029354 original size:33 final size:33
Alignment explanation
Indices: 2029312--2029426 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
2029302 CAAAATCGCA
2029312 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2029345 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
2029378 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2029411 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2029427 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2030705 original size:19 final size:19
Alignment explanation
Indices: 2030681--2030793 Score: 120
Period size: 19 Copynumber: 6.4 Consensus size: 19
2030671 GATTCTCTCG
2030681 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2030700 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2030719 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2030733 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2030753 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2030767 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2030786 TTGCGATT
1 TTGCGATT
2030794 GTATTTTCCG
Statistics
Matches: 79, Mismatches: 4, Indels: 22
0.75 0.04 0.21
Matches are distributed among these distances:
14 17 0.22
16 9 0.11
17 6 0.08
18 3 0.04
19 32 0.41
20 12 0.15
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2030758 original size:34 final size:33
Alignment explanation
Indices: 2030700--2030793 Score: 136
Period size: 34 Copynumber: 2.8 Consensus size: 33
2030690 TCATTTCGCA
2030700 TTGCGATTTTCATTTCGCATTGCGATTCTC-TCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCAT-G
*
2030733 TTGCGATTTTCATTTCCGCATTGCGATTTTCATG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCATG
* *
2030767 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
2030794 GTATTTTCCG
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
33 26 0.46
34 29 0.52
35 1 0.02
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCATG
Found at i:2033093 original size:12 final size:12
Alignment explanation
Indices: 2033076--2033100 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2033066 TCTTCGGGGA
2033076 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2033088 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2033100 C
1 C
2033101 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2033309 original size:24 final size:24
Alignment explanation
Indices: 2033275--2033321 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2033265 CTGAAACATC
2033275 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2033299 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2033322 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2034032 original size:20 final size:20
Alignment explanation
Indices: 2034004--2034372 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
2033994 AAATTTCAGT
* * * *
2034004 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2034024 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2034044 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2034064 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2034084 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2034104 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2034124 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2034144 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2034164 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2034184 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
2034204 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2034224 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2034244 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
2034264 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
2034284 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2034304 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2034324 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
2034344 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
2034364 GTTGCGATT
1 GTTGCGATT
2034373 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:2043269 original size:20 final size:20
Alignment explanation
Indices: 2043244--2043289 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
2043234 CTTACACACA
2043244 TCCTTTAGCTTGAATAAAGT
1 TCCTTTAGCTTGAATAAAGT
2043264 TCCTTTAGCTTGAATAAAGT
1 TCCTTTAGCTTGAATAAAGT
2043284 TCCTTT
1 TCCTTT
2043290 TATTTTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (20 bp):
TCCTTTAGCTTGAATAAAGT
Found at i:2047084 original size:14 final size:15
Alignment explanation
Indices: 2047065--2047097 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2047055 ACTCTCTCAA
*
2047065 TTCTCTC-TATTTTT
1 TTCTCTCGTATATTT
2047079 TTCTCTCGTATATTT
1 TTCTCTCGTATATTT
2047094 TTCT
1 TTCT
2047098 TTTTCTCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.09, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TTCTCTCGTATATTT
Found at i:2053529 original size:6 final size:6
Alignment explanation
Indices: 2053518--2053553 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
2053508 TAAATTAATT
2053518 GTGCCA GTGCCA GTGCCA GTGCCA GTGCCA GTGCCA
1 GTGCCA GTGCCA GTGCCA GTGCCA GTGCCA GTGCCA
2053554 AGGGGAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (6 bp):
GTGCCA
Found at i:2056189 original size:31 final size:31
Alignment explanation
Indices: 2056154--2056214 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2056144 AAAACATAAG
2056154 ATATGATCACTTTCA-TTTTCATTTAATTAAT
1 ATATGATCA-TTTCAGTTTTCATTTAATTAAT
* * *
2056185 ATATGGTCATTTTAGTTTTTATTTAATTAA
1 ATATGATCATTTCAGTTTTCATTTAATTAA
2056215 AATGTGGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.31, C:0.08, G:0.07, T:0.54
Consensus pattern (31 bp):
ATATGATCATTTCAGTTTTCATTTAATTAAT
Found at i:2056430 original size:25 final size:24
Alignment explanation
Indices: 2056394--2056464 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 24
2056384 TAAAATTAAG
2056394 TTAATA-ATAAAATATATTTAATAAC
1 TTAATATATAAAATAT-TTT-ATAAC
* *
2056419 TTAATATA-AAAATATTTTGTAAG
1 TTAATATATAAAATATTTTATAAC
*
2056442 TTAATATATATAAA-ATATTATAA
1 TTAATATATA-AAATATTTTATAA
2056465 ATTTAAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 11 0.28
24 11 0.28
25 16 0.41
26 1 0.03
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (24 bp):
TTAATATATAAAATATTTTATAAC
Found at i:2056445 original size:23 final size:24
Alignment explanation
Indices: 2056390--2056449 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
2056380 ATTTTAAAAT
2056390 TAAGTTAATAATAAAATATATTTAA
1 TAAGTTAAT-ATAAAATATATTTAA
* **
2056415 TAACTTAATATAAAA-ATATTTTG
1 TAAGTTAATATAAAATATATTTAA
2056438 TAAGTTAATATA
1 TAAGTTAATATA
2056450 TATAAAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 17 0.55
24 6 0.19
25 8 0.26
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (24 bp):
TAAGTTAATATAAAATATATTTAA
Found at i:2059709 original size:2 final size:2
Alignment explanation
Indices: 2059694--2059742 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
2059684 ACACACATAC
* *
2059694 AT AT AC AT AC 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
2059736 AT AT AT A
1 AT AT AT A
2059743 AGACATGATC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2068914 original size:16 final size:16
Alignment explanation
Indices: 2068893--2068926 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2068883 TTACTATTCA
*
2068893 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
2068909 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
2068925 CG
1 CG
2068927 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:2089282 original size:7 final size:7
Alignment explanation
Indices: 2089270--2089300 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2089260 GTCAAAGAAA
2089270 GTCAACG
1 GTCAACG
2089277 GTCAACG
1 GTCAACG
*
2089284 GTTAACG
1 GTCAACG
2089291 GTCAACG
1 GTCAACG
2089298 GTC
1 GTC
2089301 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:2089307 original size:5 final size:5
Alignment explanation
Indices: 2089297--2089393 Score: 86
Period size: 5 Copynumber: 17.8 Consensus size: 5
2089287 AACGGTCAAC
* *
2089297 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
* *
2089346 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
2089394 AGACCGGTCA
Statistics
Matches: 76, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
5 60 0.79
7 16 0.21
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:2089322 original size:17 final size:17
Alignment explanation
Indices: 2089302--2089394 Score: 101
Period size: 17 Copynumber: 5.9 Consensus size: 17
2089292 TCAACGGTCG
2089302 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
*
2089319 GGTCGGGTCGGGTC--G
1 GGTCGGGTCGGGTCAAC
** *
2089334 GGTC--AAC-GGTC--G
1 GGTCGGGTCGGGTCAAC
2089346 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
2089363 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
2089380 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
2089395 GACCGGTCAA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
12 9 0.14
13 1 0.02
14 1 0.02
15 8 0.12
17 46 0.71
ACGTcount: A:0.10, C:0.23, G:0.49, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:2089389 original size:22 final size:22
Alignment explanation
Indices: 2089290--2089376 Score: 174
Period size: 22 Copynumber: 4.0 Consensus size: 22
2089280 AACGGTTAAC
2089290 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
2089312 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
2089334 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
2089356 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
2089377 AACGGTCGGG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:2089414 original size:19 final size:19
Alignment explanation
Indices: 2089392--2089489 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
2089382 TCGGGTCGGG
2089392 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
2089411 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
2089430 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
2089449 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
2089469 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
2089489 T
1 T
2089490 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 39 0.57
20 17 0.25
21 9 0.13
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:2089420 original size:10 final size:9
Alignment explanation
Indices: 2089390--2089488 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
2089380 GGTCGGGTCG
*
2089390 GGTCAGACC
1 GGTCAAACC
2089399 GGTCAAACC
1 GGTCAAACC
*
2089408 GGTTCAGACC
1 GG-TCAAACC
2089418 GGTCAAACC
1 GGTCAAACC
*
2089427 GGTTCGAACC
1 GG-TCAAACC
*
2089437 GGTTGAAACC
1 GG-TCAAACC
2089447 GGTCAAACC
1 GGTCAAACC
2089456 GGTCAGAACC
1 GGTCA-AACC
*
2089466 GGTTGAAAACC
1 GG-T-CAAACC
*
2089477 GGTTAAACC
1 GGTCAAACC
2089486 GGT
1 GGT
2089489 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:2089447 original size:29 final size:28
Alignment explanation
Indices: 2089391--2089488 Score: 124
Period size: 29 Copynumber: 3.4 Consensus size: 28
2089381 GTCGGGTCGG
* * *
2089391 GTCAGACCGGTCAAACCGGTTCAGACCG
1 GTCAAACCGGTCAAACCGGTTGAAACCG
*
2089419 GTCAAACCGGTTCGAACCGGTTGAAACCG
1 GTCAAACCGG-TCAAACCGGTTGAAACCG
2089448 GTCAAACCGGTCAGAACCGGTTGAAAACCG
1 GTCAAACCGGTCA-AACCGGTTG-AAACCG
*
2089478 GTTAAACCGGT
1 GTCAAACCGGT
2089489 TTCCAGCAGC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 11 0.18
29 34 0.56
30 16 0.26
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTGAAACCG
Found at i:2096675 original size:5 final size:5
Alignment explanation
Indices: 2096665--2096739 Score: 69
Period size: 5 Copynumber: 13.8 Consensus size: 5
2096655 AACGGTCAAC
* *
2096665 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
2096714 GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTC--G GGTCG GGTCG GGTC
2096740 AGACCGGTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
5 46 0.79
7 12 0.21
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:2096690 original size:17 final size:17
Alignment explanation
Indices: 2096670--2096740 Score: 97
Period size: 17 Copynumber: 3.9 Consensus size: 17
2096660 TCAACGGTCG
2096670 GGTCGGGTCGGGTCAACGGTC
1 GGTCGGGTCGGGTCAA----C
2096691 GGGTCGGGTCGGGTCAAC
1 G-GTCGGGTCGGGTCAAC
2096709 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
2096726 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
2096741 GACCGGTCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 31 0.63
18 2 0.04
21 1 0.02
22 15 0.31
ACGTcount: A:0.10, C:0.23, G:0.49, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:2096735 original size:22 final size:22
Alignment explanation
Indices: 2096658--2096722 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
2096648 AACGGTCAAC
2096658 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
2096680 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
2096702 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
2096723 AACGGTCGGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:2096760 original size:19 final size:19
Alignment explanation
Indices: 2096738--2096835 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
2096728 TCGGGTCGGG
2096738 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
2096757 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
2096776 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
2096795 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
2096815 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
2096835 T
1 T
2096836 TCCAGAAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 39 0.57
20 17 0.25
21 9 0.13
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:2096766 original size:10 final size:9
Alignment explanation
Indices: 2096736--2096834 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
2096726 GGTCGGGTCG
*
2096736 GGTCAGACC
1 GGTCAAACC
2096745 GGTCAAACC
1 GGTCAAACC
*
2096754 GGTTCAGACC
1 GG-TCAAACC
2096764 GGTCAAACC
1 GGTCAAACC
*
2096773 GGTTCGAACC
1 GG-TCAAACC
*
2096783 GGTTGAAACC
1 GG-TCAAACC
2096793 GGTCAAACC
1 GGTCAAACC
2096802 GGTCAGAACC
1 GGTCA-AACC
*
2096812 GGTTGAAAACC
1 GG-T-CAAACC
*
2096823 GGTTAAACC
1 GGTCAAACC
2096832 GGT
1 GGT
2096835 TTCCAGAAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:2096793 original size:29 final size:28
Alignment explanation
Indices: 2096737--2096834 Score: 124
Period size: 29 Copynumber: 3.4 Consensus size: 28
2096727 GTCGGGTCGG
* * *
2096737 GTCAGACCGGTCAAACCGGTTCAGACCG
1 GTCAAACCGGTCAAACCGGTTGAAACCG
*
2096765 GTCAAACCGGTTCGAACCGGTTGAAACCG
1 GTCAAACCGG-TCAAACCGGTTGAAACCG
2096794 GTCAAACCGGTCAGAACCGGTTGAAAACCG
1 GTCAAACCGGTCA-AACCGGTTG-AAACCG
*
2096824 GTTAAACCGGT
1 GTCAAACCGGT
2096835 TTCCAGAAGC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 11 0.18
29 34 0.56
30 16 0.26
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTGAAACCG
Found at i:2104805 original size:148 final size:148
Alignment explanation
Indices: 2104537--2104823 Score: 479
Period size: 148 Copynumber: 1.9 Consensus size: 148
2104527 TGGAGGATTA
* *
2104537 TATCATGTACCTATGTCGAAATATAAATAAATAAAAGGCTGTAAGAAACAAAATAATATCTTCTC
1 TATCATGTACCTATGTCGAAATATAAATAAATAAAAGGCTGTAAGAAACAAAATAATACCGTCTC
**
2104602 AGGGTAAAGAAGGATATCATTTTGTATCGTATCCATTATATGAAAGCACCAATTCCA-TTGAACA
66 AGGGTAAAGAAGGATATCATTCCGTATCGTATCCATTATATGAAAGCACCAATTCCAGTT-AACA
*
2104666 ATATTAGTTGACTTTATTT
130 ATATAAGTTGACTTTATTT
*
2104685 TATCATGTACCTATGTCGAAATATAAATAAATAAAAGGCTGTAAGAAATAAAATAATACCGTCTC
1 TATCATGTACCTATGTCGAAATATAAATAAATAAAAGGCTGTAAGAAACAAAATAATACCGTCTC
*
2104750 AGGGTAAAGAAGGATATCATTCCGTATCGTATCCATTCTATCG-AAGCACCAATTCCAGTTAACA
66 AGGGTAAAGAAGGATATCATTCCGTATCGTATCCATTATAT-GAAAGCACCAATTCCAGTTAACA
2104814 ATATAAGTTG
130 ATATAAGTTG
2104824 TTCACTTTAA
Statistics
Matches: 130, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
148 127 0.98
149 3 0.02
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (148 bp):
TATCATGTACCTATGTCGAAATATAAATAAATAAAAGGCTGTAAGAAACAAAATAATACCGTCTC
AGGGTAAAGAAGGATATCATTCCGTATCGTATCCATTATATGAAAGCACCAATTCCAGTTAACAA
TATAAGTTGACTTTATTT
Found at i:2105340 original size:23 final size:23
Alignment explanation
Indices: 2105312--2105364 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
2105302 GCTTGACTGG
*
2105312 TTGACCGACCCGACCCATTGACT
1 TTGACCGACCCAACCCATTGACT
* *
2105335 TTGACCAACCCAACTCATTGACT
1 TTGACCGACCCAACCCATTGACT
2105358 TTGACCG
1 TTGACCG
2105365 TTGACCGTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.36, G:0.15, T:0.25
Consensus pattern (23 bp):
TTGACCGACCCAACCCATTGACT
Found at i:2106115 original size:29 final size:30
Alignment explanation
Indices: 2106049--2106220 Score: 149
Period size: 29 Copynumber: 5.9 Consensus size: 30
2106039 ATAATCCTCA
* *
2106049 TCATGATTCTGCATGAGACTATGTTCCTCAT-
1 TCATGATTCTGCATGAGATTAT-ATCCTC-TG
2106080 TC-TGATTCTGCATGAGATTATATCCTC-G
1 TCATGATTCTGCATGAGATTATATCCTCTG
*
2106108 TCATGATTCTACATGAGATTATATCC-CTG
1 TCATGATTCTGCATGAGATTATATCCTCTG
* * *
2106137 TCCTGATTCTCCACGAGATTATAT-CTCTG
1 TCATGATTCTGCATGAGATTATATCCTCTG
* * * * *
2106166 TCTTGTTTCTGCATGGGATTGTATCC-CCG
1 TCATGATTCTGCATGAGATTATATCCTCTG
* * * *
2106195 TCTTGTTTCTGCATGGGATTGTATCC
1 TCATGATTCTGCATGAGATTATATCC
2106221 CCTTCCTATT
Statistics
Matches: 123, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
28 4 0.03
29 98 0.80
30 19 0.15
31 2 0.02
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (30 bp):
TCATGATTCTGCATGAGATTATATCCTCTG
Found at i:2110962 original size:19 final size:19
Alignment explanation
Indices: 2110938--2110976 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2110928 ATGCTGCTAC
*
2110938 ACCACAATATGCATGCCAA
1 ACCACAACATGCATGCCAA
2110957 ACCACAACATGCATGCCAA
1 ACCACAACATGCATGCCAA
2110976 A
1 A
2110977 TGACCATTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.33, G:0.10, T:0.13
Consensus pattern (19 bp):
ACCACAACATGCATGCCAA
Found at i:2129518 original size:29 final size:29
Alignment explanation
Indices: 2129466--2129523 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
2129456 GTGTTGGCCG
**
2129466 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCAGCGACCTAC
* *
2129495 TAGGTCGCCATGTCTTCCCAGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCAGCGACCTAC
2129524 AAGAGATTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.36, G:0.26, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCAGCGACCTAC
Found at i:2129596 original size:14 final size:14
Alignment explanation
Indices: 2129560--2129602 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
2129550 CCAACACGCT
*
2129560 GGCCATCCAACCGA
1 GGCCATCCGACCGA
2129574 GGCCATCCGACCGA
1 GGCCATCCGACCGA
*
2129588 GGCCATCCGAACGA
1 GGCCATCCGACCGA
2129602 G
1 G
2129603 CTATGCGAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.26, C:0.40, G:0.28, T:0.07
Consensus pattern (14 bp):
GGCCATCCGACCGA
Found at i:2129665 original size:33 final size:33
Alignment explanation
Indices: 2129601--2129665 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2129591 CATCCGAACG
* *
2129601 AGCTATGCGAGGGCATCCGAGGGCAATCGAGCA
1 AGCTATGCGAGGGAATCCGAGGGCAACCGAGCA
2129634 AGCTATGCGAGGGAATCCGAGGG-AAGCCGAGC
1 AGCTATGCGAGGGAATCCGAGGGCAA-CCGAGC
2129666 GAGGGTAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.07
33 27 0.93
ACGTcount: A:0.28, C:0.23, G:0.38, T:0.11
Consensus pattern (33 bp):
AGCTATGCGAGGGAATCCGAGGGCAACCGAGCA
Found at i:2129705 original size:29 final size:29
Alignment explanation
Indices: 2129672--2129727 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
2129662 GAGCGAGGGT
* *
2129672 AGGTCGCTCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
2129701 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
2129728 TGTGTTGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.20, C:0.29, G:0.38, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:2129828 original size:29 final size:29
Alignment explanation
Indices: 2129786--2129871 Score: 172
Period size: 29 Copynumber: 3.0 Consensus size: 29
2129776 GAGCAAGGGT
2129786 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
2129815 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
2129844 AGGTCGCCCGGAGTGCATGGCGACCTAC
1 AGGTCGCCCGGAGTGCATGGCGACCTAC
2129872 GGCCAACACT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.20, C:0.31, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:2134088 original size:29 final size:29
Alignment explanation
Indices: 2134005--2134090 Score: 70
Period size: 30 Copynumber: 2.9 Consensus size: 29
2133995 GAATTTAATG
* * *
2134005 ATAATTTTATTATAATTTA-ATAAAATTTA
1 ATAATTATCTTATAATTTACA-AAATTTTA
2134034 ATAATTATCTTATAACAGTTT-C-AAATTTTA
1 ATAATTATCTTAT-A-A-TTTACAAAATTTTA
* *
2134064 ATGATTATTTTATAATTTACAAAATTT
1 ATAATTATCTTATAATTTACAAAATTT
2134091 CATTTATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
27 3 0.07
28 2 0.04
29 18 0.39
30 19 0.41
31 1 0.02
32 3 0.07
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (29 bp):
ATAATTATCTTATAATTTACAAAATTTTA
Found at i:2137753 original size:37 final size:36
Alignment explanation
Indices: 2137694--2137813 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
2137684 ATCCCATTAT
* *
2137694 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
2137730 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
2137766 CATTTTT-AAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
2137801 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
2137814 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 30 0.39
36 23 0.30
37 24 0.31
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:2137769 original size:21 final size:21
Alignment explanation
Indices: 2137745--2137805 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2137735 TTCAAAGAAA
2137745 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
**
2137766 CATTT-TTAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
2137780 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
2137801 CATTT
1 CATTT
2137806 TTTCAAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 14
0.62 0.09 0.30
Matches are distributed among these distances:
14 5 0.17
15 6 0.21
16 1 0.03
19 1 0.03
20 6 0.21
21 10 0.34
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.33
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:2137822 original size:35 final size:35
Alignment explanation
Indices: 2137712--2137840 Score: 138
Period size: 35 Copynumber: 3.7 Consensus size: 35
2137702 AACAAACATC
* * *
2137712 TACCAAACTTTGAAAAACTATTTTTCAAAGAAACATT
1 TACCAAACTTTG-AAAACCATTTTTTAAAG-AACAGT
*
2137749 TACCAAACTTTGAAAACCA-TTTTTAAAGAAACATT
1 TACCAAACTTTGAAAACCATTTTTTAAAG-AACAGT
***
2137784 TACCAAACTTTGAAAACCATTTTTTCAAAG-TTGGT
1 TACCAAACTTTGAAAACCATTTTTT-AAAGAACAGT
2137819 TACCAAAC-TTGAAAACCATTTT
1 TACCAAACTTTGAAAACCATTTT
2137841 AATACTTTCA
Statistics
Matches: 84, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
34 14 0.17
35 43 0.51
36 11 0.13
37 16 0.19
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (35 bp):
TACCAAACTTTGAAAACCATTTTTTAAAGAACAGT
Found at i:2141905 original size:16 final size:17
Alignment explanation
Indices: 2141880--2141911 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2141870 TCGCCGACCG
2141880 AATTTCACTATTCACGA
1 AATTTCACTATTCACGA
2141897 AATTT-ACTATTCACG
1 AATTTCACTATTCACG
2141912 TGAATAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (17 bp):
AATTTCACTATTCACGA
Found at i:2142379 original size:38 final size:37
Alignment explanation
Indices: 2142321--2142466 Score: 171
Period size: 35 Copynumber: 4.1 Consensus size: 37
2142311 CCCATTATCA
* * *
2142321 TTTTTC-AACAAACATCTACCAAACTTTGAAAAACTAT
1 TTTTTCAAAGAAACATTTACCAAACTTTG-AAAACCAT
2142358 TTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 TTTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
*
2142394 -TTTTCAAAGAAACATTTATCAAACTTTGAAAACCAT
1 TTTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
* *
2142430 TTTTTCAAA-ATTA-A-TTA-CAAAATTTGAAAACCAT
1 TTTTTCAAAGA-AACATTTACCAAACTTTGAAAACCAT
2142464 TTT
1 TTT
2142467 AATACTTTCA
Statistics
Matches: 99, Mismatches: 6, Indels: 11
0.85 0.05 0.09
Matches are distributed among these distances:
34 19 0.19
35 37 0.37
36 2 0.02
37 21 0.21
38 20 0.20
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.35
Consensus pattern (37 bp):
TTTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
Found at i:2142395 original size:21 final size:21
Alignment explanation
Indices: 2142371--2142431 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
2142361 TTCAAAGAAA
*
2142371 CATTTACCAAACTTTGAAAAC
1 CATTTATCAAACTTTGAAAAC
2142392 CATTT-TCAAA----G-AAA-
1 CATTTATCAAACTTTGAAAAC
2142406 CATTTATCAAACTTTGAAAAC
1 CATTTATCAAACTTTGAAAAC
2142427 CATTT
1 CATTT
2142432 TTTCAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 14
0.68 0.02 0.30
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 1 0.03
19 1 0.03
20 7 0.22
21 10 0.31
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.33
Consensus pattern (21 bp):
CATTTATCAAACTTTGAAAAC
Found at i:2148200 original size:27 final size:27
Alignment explanation
Indices: 2148162--2148216 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2148152 GCAAGAGCAT
2148162 GGGACCGAGACCACCCAAACCTCAGAA
1 GGGACCGAGACCACCCAAACCTCAGAA
2148189 GGGACCGAGACCACCCAAACCTCAGAA
1 GGGACCGAGACCACCCAAACCTCAGAA
2148216 G
1 G
2148217 AGCAACAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.36, G:0.24, T:0.04
Consensus pattern (27 bp):
GGGACCGAGACCACCCAAACCTCAGAA
Found at i:2150404 original size:11 final size:11
Alignment explanation
Indices: 2150388--2150419 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
2150378 ACCGATCAAG
2150388 TCTAAACTTTT
1 TCTAAACTTTT
2150399 TCTAAACTTTT
1 TCTAAACTTTT
2150410 TCTAAA-TTTT
1 TCTAAACTTTT
2150420 GATTTAGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (11 bp):
TCTAAACTTTT
Found at i:2163604 original size:37 final size:36
Alignment explanation
Indices: 2163556--2163830 Score: 235
Period size: 37 Copynumber: 7.6 Consensus size: 36
2163546 ATGATTTTCG
* * *
2163556 AAAATTTATATATTATATAGTTTTTGAAAATATTTTT
1 AAAATATATATAATATATAGTTTTT-AAAACATTTTT
* *
2163593 AAAATATATATAATATATAGTTTTGAAAACATTTTG
1 AAAATATATATAATATATAGTTTTTAAAACATTTTT
* *
2163629 AAAACGTTTATATATTATATAGTTTTTAAAACA-TTTT
1 AAAA--TATATATAATATATAGTTTTTAAAACATTTTT
* * *
2163666 GAAA-ATATATAGTATATAGTTTTAAAAACATTTTTGT
1 AAAATATATATAATATATAGTTTTTAAAACA-TTTT-T
* *
2163703 GAAAT-TATATAATATATAGTTTTAAAAACATTTTT
1 AAAATATATATAATATATAGTTTTTAAAACATTTTT
* * *
2163738 GAAAA-CT-TAT-ATA-ATA-TTTTTAAAACGTTTTG
1 -AAAATATATATAATATATAGTTTTTAAAACATTTTT
* *
2163770 AAAA-CTATGTAATATATAGTTTTCTAAAACGTATTTTT
1 AAAATATATATAATATATAGTTTT-TAAAAC--ATTTTT
* *
2163808 GAAATATATATATTATATAGTTT
1 AAAATATATATAATATATAGTTT
2163831 ATATCATATT
Statistics
Matches: 197, Mismatches: 25, Indels: 30
0.78 0.10 0.12
Matches are distributed among these distances:
31 6 0.03
32 15 0.08
33 6 0.03
34 29 0.15
35 8 0.04
36 30 0.15
37 57 0.29
38 31 0.16
39 15 0.08
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.46
Consensus pattern (36 bp):
AAAATATATATAATATATAGTTTTTAAAACATTTTT
Found at i:2163696 original size:72 final size:70
Alignment explanation
Indices: 2163495--2163830 Score: 299
Period size: 72 Copynumber: 4.6 Consensus size: 70
2163485 GTTTTTTTAT
* * *
2163495 TATAGTTTGTAAAA-ATGTTTTTGACAAA-ATATAATATATAATTTTCAGAAAATGATTTTCGAA
1 TATAGTTTTTAAAACA--TTTTTGA-AAATATATAATATATAGTTTT-A-AAAA-CATTTT-GAA
*
2163558 AATTTATATATTA
59 AA-TTATATAATA
* * *
2163571 TATAGTTTTTGAAAATATTTTTAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAACGT
1 TATAGTTTTT-AAAACATTTTTGAAA-ATATATAATATATAGTTTTAAAAACATTTTGAAAA---
*
2163636 TTATATATTA
61 TTATATAATA
* *
2163646 TATAGTTTTTAAAACA-TTTTGAAAATATATAGTATATAGTTTTAAAAACATTTTTGTGAAATTA
1 TATAGTTTTTAAAACATTTTTGAAAATATATAATATATAGTTTTAAAAACA-TTTTG-AAAATTA
2163710 TATAATA
64 TATAATA
* * * *
2163717 TATAGTTTTAAAAACATTTTTGAAAACT-TAT-ATA-ATA-TTTTTAAAACGTTTTGAAAACTAT
1 TATAGTTTTTAAAACATTTTTGAAAA-TATATAATATATAGTTTTAAAAACATTTTGAAAATTAT
*
2163778 GTAATA
65 ATAATA
*
2163784 TATAGTTTTCTAAAACGTATTTTTGAAATATATATATTATATAGTTT
1 TATAGTTTT-TAAAAC--ATTTTTGAAA-ATATATAATATATAGTTT
2163831 ATATCATATT
Statistics
Matches: 222, Mismatches: 20, Indels: 38
0.79 0.07 0.14
Matches are distributed among these distances:
67 20 0.09
68 10 0.05
69 9 0.04
70 14 0.06
71 30 0.14
72 38 0.17
73 21 0.09
74 16 0.07
75 27 0.12
76 16 0.07
77 20 0.09
78 1 0.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (70 bp):
TATAGTTTTTAAAACATTTTTGAAAATATATAATATATAGTTTTAAAAACATTTTGAAAATTATA
TAATA
Found at i:2163712 original size:109 final size:105
Alignment explanation
Indices: 2163562--2163830 Score: 332
Period size: 109 Copynumber: 2.5 Consensus size: 105
2163552 TTCGAAAATT
* * * *
2163562 TATATATTATATAGTTTTTGAAA-ATATTTTTAAAATATATATAATATATAGTTTTGAAAACA-T
1 TATATAATATATAGTTTTTAAAACATATTTTTGAAATATATATAATATATAGTTTTAAAAACATT
2163625 TTTGAAAACGTTTATATATTATATAGTTTTTAAAACATTTTGAAAA-
66 TTTGAAAAC---T-TATA-TA-ATA-TTTTTAAAACATTTTGAAAAC
* *
2163671 TATATAGTATATAGTTTTAAAAACAT-TTTTGTGAAAT-TATATAATATATAGTTTTAAAAACAT
1 TATATAATATATAGTTTTTAAAACATATTTT-TGAAATATATATAATATATAGTTTTAAAAACAT
*
2163734 TTTTGAAAACTTATATAATATTTTTAAAACGTTTTGAAAAC
65 TTTTGAAAACTTATATAATATTTTTAAAACATTTTGAAAAC
* * *
2163775 TATGTAATATATAGTTTTCTAAAACGTATTTTTGAAATATATATATTATATAGTTT
1 TATATAATATATAGTTTT-TAAAACATATTTTTGAAATATATATAATATATAGTTT
2163831 ATATCATATT
Statistics
Matches: 142, Mismatches: 11, Indels: 17
0.84 0.06 0.10
Matches are distributed among these distances:
103 19 0.13
104 19 0.13
105 14 0.10
106 24 0.17
107 1 0.01
109 48 0.34
110 17 0.12
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (105 bp):
TATATAATATATAGTTTTTAAAACATATTTTTGAAATATATATAATATATAGTTTTAAAAACATT
TTTGAAAACTTATATAATATTTTTAAAACATTTTGAAAAC
Found at i:2163909 original size:12 final size:12
Alignment explanation
Indices: 2163892--2163923 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2163882 TTTTTCTCCA
2163892 GGTCCAAAAACG
1 GGTCCAAAAACG
*
2163904 GGTCCAGAAACG
1 GGTCCAAAAACG
2163916 GGTCCAAA
1 GGTCCAAA
2163924 TCCAGTCAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.38, C:0.25, G:0.28, T:0.09
Consensus pattern (12 bp):
GGTCCAAAAACG
Found at i:2165204 original size:12 final size:12
Alignment explanation
Indices: 2165187--2165250 Score: 62
Period size: 12 Copynumber: 5.2 Consensus size: 12
2165177 AAACTTAACC
2165187 TTTTATTATTAT
1 TTTTATTATTAT
2165199 TTTTATTATTAT
1 TTTTATTATTAT
2165211 TTCTT-TCT-TTCAT
1 TT-TTAT-TATT-AT
*
2165224 TATTATTATTAT
1 TTTTATTATTAT
2165236 TTTT-TTATATAT
1 TTTTATTAT-TAT
2165248 TTT
1 TTT
2165251 ATTCATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
11 4 0.09
12 31 0.70
13 9 0.20
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:2165206 original size:9 final size:9
Alignment explanation
Indices: 2165192--2165260 Score: 50
Period size: 9 Copynumber: 7.2 Consensus size: 9
2165182 TAACCTTTTA
2165192 TTATTATTT
1 TTATTATTT
2165201 TTATTATTAT
1 TTATTATT-T
*
2165211 TTCTT-TCTT
1 TTATTAT-TT
* *
2165220 TCATTATTA
1 TTATTATTT
2165229 TTATTATTT
1 TTATTATTT
*
2165238 TTTTATATATT
1 TTAT-TAT-TT
2165249 TTATTCATTT
1 TTATT-ATTT
2165259 TT
1 TT
2165261 TATTTATTAG
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
9 24 0.52
10 15 0.33
11 7 0.15
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (9 bp):
TTATTATTT
Found at i:2173368 original size:36 final size:36
Alignment explanation
Indices: 2173326--2173401 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2173316 TATAGCTAAA
*
2173326 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2173362 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2173398 AAAA
1 AAAA
2173402 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:2177897 original size:15 final size:15
Alignment explanation
Indices: 2177879--2177908 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2177869 CCACGGTGCT
2177879 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
2177894 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
2177909 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:2178373 original size:36 final size:36
Alignment explanation
Indices: 2178331--2178406 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2178321 TATAGCTAAA
*
2178331 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2178367 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2178403 AAAA
1 AAAA
2178407 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:2186443 original size:4 final size:4
Alignment explanation
Indices: 2186381--2186425 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
2186371 GTTCTTTCCC
2186381 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
2186426 ATTGTTGGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
CTTT
Found at i:2188020 original size:134 final size:134
Alignment explanation
Indices: 2187775--2188222 Score: 594
Period size: 134 Copynumber: 3.4 Consensus size: 134
2187765 TGAATCCCTG
* * * *
2187775 CTGATAACTACTTATCATGCTTTCCGATATGTTCTATTACTGGATGGCTTTCTTTCTTTGGAAAT
1 CTGAAAACTACTTATCATGCTTTCCTATATGTTCTCTTACAGGATGGCTTTCTTTCTTTGGAAAT
* ** * *
2187840 GAATCTTCATTTCTATTTGTTTTTGAAATTATGTTGGATTCCCTGTGAATGTTTGCATTAATAGT
66 GAATCTTCATTTCTATTTGTTTCTGAAATTATGTTCTATTTCCTGTGAATGTTTGCATTTATAGT
2187905 CACA
131 CACA
* * * * *
2187909 CTGAAAACTACCTATCATGCTTTCCCATATGTTTTCTGACAGTATGGCTTTCTTTCTTTGGAAAT
1 CTGAAAACTACTTATCATGCTTTCCTATATGTTCTCTTACAGGATGGCTTTCTTTCTTTGGAAAT
**
2187974 GAATCTTCATTTCTATTTGTTTCTGAAATTATGTTCTATTTCCTGTGTGTGTTTGCATTTATAGT
66 GAATCTTCATTTCTATTTGTTTCTGAAATTATGTTCTATTTCCTGTGAATGTTTGCATTTATAGT
2188039 CACA
131 CACA
* * * * ** * *
2188043 ATG-AAACTACTTATCATGCTTTCCTGTATGCTCTCTTACCGGATGATTTTCTATCTTT-GATAG
1 CTGAAAACTACTTATCATGCTTTCCTATATGTTCTCTTACAGGATGGCTTTCTTTCTTTGGA-AA
* *
2188106 TGAATCTTCATTTCTATGTGTTTCTGAAATTATGTTCTATTTCCTGTGAATGTTTGCGTTTATAG
65 TGAATCTTCATTTCTATTTGTTTCTGAAATTATGTTCTATTTCCTGTGAATGTTTGCATTTATAG
2188171 TCACA
130 TCACA
* * * * *
2188176 TTGAAAACTACTTGTCATGCTTTCCTATGTGTTTTCTTACTGGATGG
1 CTGAAAACTACTTATCATGCTTTCCTATATGTTCTCTTACAGGATGG
2188223 TTTGAAATTT
Statistics
Matches: 272, Mismatches: 40, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
132 2 0.01
133 113 0.42
134 157 0.58
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (134 bp):
CTGAAAACTACTTATCATGCTTTCCTATATGTTCTCTTACAGGATGGCTTTCTTTCTTTGGAAAT
GAATCTTCATTTCTATTTGTTTCTGAAATTATGTTCTATTTCCTGTGAATGTTTGCATTTATAGT
CACA
Found at i:2195645 original size:12 final size:12
Alignment explanation
Indices: 2195628--2195653 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2195618 TGCCTTATTT
2195628 TCTGACCTATCA
1 TCTGACCTATCA
2195640 TCTGACCTATCA
1 TCTGACCTATCA
2195652 TC
1 TC
2195654 GATTAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.35, G:0.08, T:0.35
Consensus pattern (12 bp):
TCTGACCTATCA
Found at i:2199240 original size:30 final size:30
Alignment explanation
Indices: 2199205--2199351 Score: 132
Period size: 30 Copynumber: 5.1 Consensus size: 30
2199195 AAATTTTAAA
2199205 AAATATTTTTTATTTTTATCTTAACTTATT
1 AAATATTTTTTATTTTTATCTTAACTTATT
* * *
2199235 AAATATATTTTATTTTTTTCTTAACCTATT
1 AAATATTTTTTATTTTTATCTTAACTTATT
* *
2199265 AAATA---TTT-TTTTTATTTTAA-TGTAAAT
1 AAATATTTTTTATTTTTATCTTAACT-T-ATT
* *
2199292 ATATATTTTTTATTTTTATC-TCACTTA--
1 AAATATTTTTTATTTTTATCTTAACTTATT
*
2199319 AAATATATTTTTATTTTTATCTTAA-TTTTT
1 AAATAT-TTTTTATTTTTATCTTAACTTATT
2199349 AAA
1 AAA
2199352 AATATATTTT
Statistics
Matches: 93, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
26 11 0.12
27 14 0.15
28 16 0.17
29 3 0.03
30 41 0.44
31 8 0.09
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (30 bp):
AAATATTTTTTATTTTTATCTTAACTTATT
Found at i:2199362 original size:14 final size:13
Alignment explanation
Indices: 2199343--2199387 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 13
2199333 TTTTATCTTA
2199343 ATTTTTAAAAATAT
1 ATTTTT-AAAATAT
2199357 ATTTTTAAAATAT
1 ATTTTTAAAATAT
*
2199370 ATTAACTTAAAATAT
1 ATT--TTTAAAATAT
2199385 ATT
1 ATT
2199388 ATTATTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 10 0.36
14 6 0.21
15 12 0.43
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (13 bp):
ATTTTTAAAATAT
Found at i:2206586 original size:21 final size:21
Alignment explanation
Indices: 2206560--2206604 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2206550 GATTTCTGGG
* *
2206560 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2206581 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2206602 CAA
1 CAA
2206605 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2206674 original size:23 final size:22
Alignment explanation
Indices: 2206630--2206674 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2206620 AATGCCAGAG
*
2206630 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
* *
2206652 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
2206675 AAATATTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:2207311 original size:32 final size:32
Alignment explanation
Indices: 2207270--2207365 Score: 124
Period size: 32 Copynumber: 3.0 Consensus size: 32
2207260 GAGTCGAGGG
*
2207270 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTAAGGAACATATGGACAGT
***
2207302 TTTACCTATG-TCTTTTGAGACATATGGACAG-
1 TTTACCTATGTTCTAAGGA-ACATATGGACAGT
*
2207333 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTAAGGAACATATGGACAGT
2207365 T
1 T
2207366 ACCGAGGATC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
31 26 0.48
32 28 0.52
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTAAGGAACATATGGACAGT
Found at i:2207342 original size:31 final size:30
Alignment explanation
Indices: 2207271--2207368 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 30
2207261 AGTCGAGGGT
*
2207271 TTACCTATGTTCTACGGAACATATGGACAG
1 TTACCTATGTTCTAAGGAACATATGGACAG
***
2207301 TTTTACCTATG-TCTTTTGAGACATATGGACAG
1 --TTACCTATGTTCTAAGGA-ACATATGGACAG
2207333 TATACCTATGTTCTAAGGAACATATGGACAG
1 T-TACCTATGTTCTAAGGAACATATGGACAG
2207364 TTACC
1 TTACC
2207369 GAGGATCTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
30 5 0.09
31 26 0.46
32 26 0.46
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (30 bp):
TTACCTATGTTCTAAGGAACATATGGACAG
Found at i:2207393 original size:30 final size:30
Alignment explanation
Indices: 2207357--2207539 Score: 341
Period size: 30 Copynumber: 6.1 Consensus size: 30
2207347 AAGGAACATA
2207357 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
2207387 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
2207417 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
2207447 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
2207477 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* *
2207507 TGGACAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
2207536 TGGA
1 TGGA
2207540 TAGGTCCTTC
Statistics
Matches: 151, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
29 18 0.12
30 133 0.88
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:2210660 original size:13 final size:13
Alignment explanation
Indices: 2210642--2210672 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2210632 TTAATTTTAT
2210642 TAATTTTTATAGA
1 TAATTTTTATAGA
2210655 TAATTTTTATAGA
1 TAATTTTTATAGA
2210668 TAATT
1 TAATT
2210673 GTTAAGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (13 bp):
TAATTTTTATAGA
Found at i:2223593 original size:83 final size:83
Alignment explanation
Indices: 2223486--2223731 Score: 300
Period size: 83 Copynumber: 3.0 Consensus size: 83
2223476 GAAAGGTGTG
* * * ** *
2223486 TTCCAGGAGAACCGTTTTCAATTATTATTCA-ATGAATCTCTATCATGTCATAGTGTTTCATCCC
1 TTCCAGGAAAAACGTTTTCCATTATTATTCAGAT-AATCTCTGCCATGTCATAGTGTTTCATCTC
*
2223550 ATCCAAAATGAAATGCACG-
65 ATCCGAAATGAAATG-ACGA
* *
2223569 TTCTAGGAAAAACGTTTTCCATTATTATTTAGATAATCTCTGCCATGTCATAGTGTTTCATCTCA
1 TTCCAGGAAAAACGTTTTCCATTATTATTCAGATAATCTCTGCCATGTCATAGTGTTTCATCTCA
2223634 TCCGAAATGAAA-GACGCA
66 TCCGAAATGAAATGACG-A
** * * * * *
2223652 TTCCAGGGGAATCATTTTCCATTATTATTCATATAATCTCTGCCATGTCATAATGTTCCATCTCA
1 TTCCAGGAAAAACGTTTTCCATTATTATTCAGATAATCTCTGCCATGTCATAGTGTTTCATCTCA
2223717 TCCGAAATGAAATGA
66 TCCGAAATGAAATGA
2223732 GCATGTTTCA
Statistics
Matches: 141, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
81 3 0.02
82 1 0.01
83 133 0.94
84 4 0.03
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (83 bp):
TTCCAGGAAAAACGTTTTCCATTATTATTCAGATAATCTCTGCCATGTCATAGTGTTTCATCTCA
TCCGAAATGAAATGACGA
Found at i:2224851 original size:101 final size:101
Alignment explanation
Indices: 2224676--2224879 Score: 399
Period size: 101 Copynumber: 2.0 Consensus size: 101
2224666 AGTCACTGCA
2224676 ATTCAACATGGACTCTGATGATGATGCGGATGAAGTTCCTACAAATATGATACAATATGAACCTC
1 ATTCAACATGGACTCTGATGATGATGCGGATGAAGTTCCTACAAATATGATACAATATGAACCTC
2224741 TAGCACACATGTATGAAGCTGACTATGATGCGATAT
66 TAGCACACATGTATGAAGCTGACTATGATGCGATAT
2224777 ATTCAACATGGACTCTGATGATGATGCGGATGAAGTTCCTACAAATATGATACAATATGAACCTC
1 ATTCAACATGGACTCTGATGATGATGCGGATGAAGTTCCTACAAATATGATACAATATGAACCTC
*
2224842 TAGCACACATGTATGAAGCTGACTATGATGTGATAT
66 TAGCACACATGTATGAAGCTGACTATGATGCGATAT
2224878 AT
1 AT
2224880 GAGCCATAAT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (101 bp):
ATTCAACATGGACTCTGATGATGATGCGGATGAAGTTCCTACAAATATGATACAATATGAACCTC
TAGCACACATGTATGAAGCTGACTATGATGCGATAT
Found at i:2229160 original size:41 final size:40
Alignment explanation
Indices: 2229115--2229192 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 40
2229105 CCTAATTCAT
2229115 AGTAAACTAAAAATACTAA-TAATTAAATAATTAAAATCCTA
1 AGTAAAC-AAAAATACTAATTAATTAAATAA-TAAAATCCTA
* *
2229156 AGTAAACCAAAATCCTAATTAATTAAATAATAAAATC
1 AGTAAACAAAAATACTAATTAATTAAATAATAAAATC
2229193 TAGAATGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 16 0.47
41 18 0.53
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.28
Consensus pattern (40 bp):
AGTAAACAAAAATACTAATTAATTAAATAATAAAATCCTA
Found at i:2229986 original size:13 final size:13
Alignment explanation
Indices: 2229968--2230001 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
2229958 AAAATATATG
2229968 AGTTTCAAGCCAC
1 AGTTTCAAGCCAC
2229981 AGTTTCAAGCCAC
1 AGTTTCAAGCCAC
2229994 AGTTTCAA
1 AGTTTCAA
2230002 CAATGTAAAC
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:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (13 bp):
AGTTTCAAGCCAC
Found at i:2243340 original size:2 final size:2
Alignment explanation
Indices: 2243333--2243386 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
2243323 CTGGAAAGTA
2243333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2243375 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2243387 TTAAAAATAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2247000 original size:42 final size:42
Alignment explanation
Indices: 2246769--2247003 Score: 144
Period size: 42 Copynumber: 5.6 Consensus size: 42
2246759 AATTGAGACT
* **
2246769 TTAGCGGCGTTTTTTGTGAAAACGCTACAATAGAGT-ATAAA
1 TTAGCGGCGTTTTTTGTAAAAACGCCGCAATAGAGTGATAAA
* * *
2246810 TATAGCGGCG-TTTTTGTTAAAAACGCCGCCATATGA-TGGTATA
1 T-TAGCGGCGTTTTTTG-TAAAAACGCCGCAATA-GAGTGATAAA
* * * **
2246853 -TAGTGGCGTTTTTT-CAACAAACGCCGCAATTA-A-TAATAGTT
1 TTAGCGGCGTTTTTTGTAA-AAACGCCGCAA-TAGAGTGATA-AA
* * * * * * *
2246894 TTTGCGTCGTTTTTAG-ATAAACGCCGCAATATAGTGTTAAT
1 TTAGCGGCGTTTTTTGTAAAAACGCCGCAATAGAGTGATAAA
* *** *
2246935 TTAGCGGCGTTTATACCAAAAACGCCGCAATAGAGTGGTAAA
1 TTAGCGGCGTTTTTTGTAAAAACGCCGCAATAGAGTGATAAA
*
2246977 TTAGCGGCGTTTTTTGTATAAACGCCG
1 TTAGCGGCGTTTTTTGTAAAAACGCCG
2247004 TAAAAACATG
Statistics
Matches: 148, Mismatches: 33, Indels: 25
0.72 0.16 0.12
Matches are distributed among these distances:
40 8 0.05
41 50 0.34
42 85 0.57
43 5 0.03
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (42 bp):
TTAGCGGCGTTTTTTGTAAAAACGCCGCAATAGAGTGATAAA
Found at i:2248121 original size:52 final size:52
Alignment explanation
Indices: 2248056--2248214 Score: 300
Period size: 52 Copynumber: 3.1 Consensus size: 52
2248046 TACTGAATAA
2248056 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
*
2248108 TATGTTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
*
2248160 TATGGTGAAGACTGTTGATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
2248212 TAT
1 TAT
2248215 TTTGTTGTTA
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 104 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.43
Consensus pattern (52 bp):
TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
Found at i:2251834 original size:15 final size:15
Alignment explanation
Indices: 2251814--2251843 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2251804 AATGGCTAAC
2251814 TTGAAAGCGGAAAAT
1 TTGAAAGCGGAAAAT
2251829 TTGAAAGCGGAAAAT
1 TTGAAAGCGGAAAAT
2251844 GAAGCAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.27, T:0.20
Consensus pattern (15 bp):
TTGAAAGCGGAAAAT
Found at i:2251891 original size:21 final size:20
Alignment explanation
Indices: 2251844--2251892 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
2251834 AGCGGAAAAT
*
2251844 GAAGCAAGGGAAGCAGAGAGA
1 GAAGC-AGGGAAGCAGAGAAA
*
2251865 GCAGCAGTGGAAGCAGAGAAA
1 GAAGCAG-GGAAGCAGAGAAA
2251886 GAAGCAG
1 GAAGCAG
2251893 CGGCAACACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.45, C:0.12, G:0.41, T:0.02
Consensus pattern (20 bp):
GAAGCAGGGAAGCAGAGAAA
Found at i:2252300 original size:44 final size:44
Alignment explanation
Indices: 2252234--2252353 Score: 145
Period size: 44 Copynumber: 2.7 Consensus size: 44
2252224 ATCATGTGTT
* * *
2252234 ATTTAGCGGCGTTTGCAAACTAGAAATGCTGCAATATACTAAAC
1 ATTTAGCGGCGTTTGCAAACTAGAAACGCCGCAATATACCAAAC
* * **
2252278 ATTTAGCGGCGTTTGTATACTAGAAACGCCGCAATATACCATGC
1 ATTTAGCGGCGTTTGCAAACTAGAAACGCCGCAATATACCAAAC
2252322 ATTTAGCGGCGTTTTTGC--ACTAGAAACGCCGC
1 ATTTAGCGGCG--TTTGCAAACTAGAAACGCCGC
2252354 TAATTCTCAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
44 62 0.94
46 4 0.06
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.28
Consensus pattern (44 bp):
ATTTAGCGGCGTTTGCAAACTAGAAACGCCGCAATATACCAAAC
Found at i:2252564 original size:43 final size:43
Alignment explanation
Indices: 2252516--2252613 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 43
2252506 GTTTTTAGAA
* * * * *
2252516 AAAACGCCGTTAAACATCAACGCCTATTGCGGCGTTT-TTCTG
1 AAAACGCCGCTAAACAACAAAGCCTATTACGGCGTTTGTTCAG
* *
2252558 ACAAACGCCGCTAAATAACAAATCCTATTACGGCGTTTGTTCAG
1 A-AAACGCCGCTAAACAACAAAGCCTATTACGGCGTTTGTTCAG
2252602 AAAACGCCGCTA
1 AAAACGCCGCTA
2252614 TATGTTGTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
42 1 0.02
43 41 0.87
44 5 0.11
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (43 bp):
AAAACGCCGCTAAACAACAAAGCCTATTACGGCGTTTGTTCAG
Found at i:2252696 original size:12 final size:14
Alignment explanation
Indices: 2252660--2252696 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
2252650 CGTCGTTAAC
2252660 TTTAGCGGCGCTAT
1 TTTAGCGGCGCTAT
2252674 TTTCAGCGGCGCT-T
1 TTT-AGCGGCGCTAT
2252688 TTT-GCGGCG
1 TTTAGCGGCG
2252697 TTTGTCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.27
14 7 0.32
15 9 0.41
ACGTcount: A:0.08, C:0.24, G:0.32, T:0.35
Consensus pattern (14 bp):
TTTAGCGGCGCTAT
Found at i:2261132 original size:85 final size:85
Alignment explanation
Indices: 2260989--2261158 Score: 340
Period size: 85 Copynumber: 2.0 Consensus size: 85
2260979 CATCAAAGTC
2260989 TAACACCTTAAAGAGTAAGGTCTTCATGTTTGTTTGTAAATTGATATATTATGTTACCAATGTGT
1 TAACACCTTAAAGAGTAAGGTCTTCATGTTTGTTTGTAAATTGATATATTATGTTACCAATGTGT
2261054 GATTGATAAATCATGTATTT
66 GATTGATAAATCATGTATTT
2261074 TAACACCTTAAAGAGTAAGGTCTTCATGTTTGTTTGTAAATTGATATATTATGTTACCAATGTGT
1 TAACACCTTAAAGAGTAAGGTCTTCATGTTTGTTTGTAAATTGATATATTATGTTACCAATGTGT
2261139 GATTGATAAATCATGTATTT
66 GATTGATAAATCATGTATTT
2261159 GATTCTATGT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.42
Consensus pattern (85 bp):
TAACACCTTAAAGAGTAAGGTCTTCATGTTTGTTTGTAAATTGATATATTATGTTACCAATGTGT
GATTGATAAATCATGTATTT
Found at i:2261792 original size:15 final size:15
Alignment explanation
Indices: 2261774--2261805 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2261764 ACAATAATTC
2261774 TTTTAACACCGATTT
1 TTTTAACACCGATTT
2261789 TTTTAACACCGATTT
1 TTTTAACACCGATTT
2261804 TT
1 TT
2261806 CTATATTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (15 bp):
TTTTAACACCGATTT
Found at i:2265990 original size:15 final size:16
Alignment explanation
Indices: 2265970--2265999 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2265960 ATCTTAAATT
2265970 TAATCA-AAAACTCAA
1 TAATCAGAAAACTCAA
2265985 TAATCAGAAAACTCA
1 TAATCAGAAAACTCA
2266000 CCTTTGGCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.57, C:0.20, G:0.03, T:0.20
Consensus pattern (16 bp):
TAATCAGAAAACTCAA
Found at i:2273885 original size:17 final size:17
Alignment explanation
Indices: 2273844--2273877 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2273834 TGATTAAGCG
*
2273844 CTGAATGATTCAATGGC
1 CTGAATGATTCAAAGGC
2273861 CTGAATGATTCAAAGGC
1 CTGAATGATTCAAAGGC
2273878 TTGTATGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (17 bp):
CTGAATGATTCAAAGGC
Found at i:2277650 original size:14 final size:13
Alignment explanation
Indices: 2277615--2277650 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2277605 AATAAAGTTT
*
2277615 AAAATTTTAAAAA
1 AAAATTATAAAAA
2277628 AAAATTATAAAAA
1 AAAATTATAAAAA
2277641 AAAATGTATA
1 AAAAT-TATA
2277651 CCGCATAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (13 bp):
AAAATTATAAAAA
Found at i:2286198 original size:22 final size:22
Alignment explanation
Indices: 2286158--2286199 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2286148 CAAATTTATT
*
2286158 AAATTAAATCAAAATTATGATC
1 AAATTAAATAAAAATTATGATC
2286180 AAATTAAA-AAAAATATATGA
1 AAATTAAATAAAAAT-TATGA
2286200 CTATTGAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (22 bp):
AAATTAAATAAAAATTATGATC
Found at i:2289316 original size:23 final size:23
Alignment explanation
Indices: 2289290--2289337 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
2289280 ATAAAGTACA
* *
2289290 ATAACATACTGGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
2289313 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
2289336 AT
1 AT
2289338 TGACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:2289843 original size:23 final size:23
Alignment explanation
Indices: 2289817--2289888 Score: 108
Period size: 23 Copynumber: 3.1 Consensus size: 23
2289807 TATTTTACAT
*
2289817 TATAAGCACTACCTATTACATTA
1 TATAAGCGCTACCTATTACATTA
*
2289840 TATAAACGCTACCTATTACATTA
1 TATAAGCGCTACCTATTACATTA
* *
2289863 TATAAGCGTTACCTATTACATCA
1 TATAAGCGCTACCTATTACATTA
2289886 TAT
1 TAT
2289889 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.36
Consensus pattern (23 bp):
TATAAGCGCTACCTATTACATTA
Found at i:2290329 original size:21 final size:23
Alignment explanation
Indices: 2290304--2290376 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
2290294 ATACTTTACA
*
2290304 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
2290327 ATATAAACGCTAACTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2290350 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
2290373 ATAT
1 ATAT
2290377 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:2290400 original size:488 final size:490
Alignment explanation
Indices: 2289411--2291210 Score: 3313
Period size: 488 Copynumber: 3.7 Consensus size: 490
2289401 TTATAATATG
*
2289411 TTGAAAGTGTCTATACTTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCTATAC-TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
* *
2289476 TTCAATTTTTTTTTAATAGTGTTTCATGTTTTCCACCTGCAATATTAATTTAATAATATCATTTG
65 TTCAA-TTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTG
2289541 CACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAAT
129 CACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAAT
*
2289606 ATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTATTTTTAATTTAATAATAATAT
194 ATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATAT
2289671 ATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCA
259 ATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCA
*
2289736 CTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTAAAAAAAGTATGGACACTTTTATAAAAAG
324 CTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAG
* * *
2289801 AATAGATATTTTACATTATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATAT
389 GATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATAT
*
2289866 AAGCGTTACCTATTACATCATATTTTTACCTATTATA
454 AAGCGCTACCTATTACATCATATTTTTACCTATTATA
*
2289903 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACATTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
2289968 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAACAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
* *
2290033 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAATAATAC
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
2290098 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
* * *
2290163 -T-TTAATGTAAAAAATAAATCATTAGACACCTATAATTACTAAATTAATATCTTAAAACTCACT
261 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
2290226 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
326 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
* *
2290291 TAAATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTAACTATTACATTATATAA
391 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
2290356 GCGCTACCTATTACATCATATTTTTACCTATTATA
456 GCGCTACCTATTACATCATATTTTTACCTATTATA
2290391 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
2290456 TCAATATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
2290521 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAATAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
2290586 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
*
2290651 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAATTCACT
261 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
*
2290716 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAATATGGACACTTTTATAAAAAGGA
326 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
2290781 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
391 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
2290846 GCGCTACCTATTACATCATATTTTTACCTATTATA
456 GCGCTACCTATTACATCATATTTTTACCTATTATA
2290881 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
2290946 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
* *
2291010 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
*
2291075 TAACCAAAGATAATACTAAATATGTAATATATATGTTTATTG-TTTTAATTTAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
*
2291139 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC-TAAAACTCACT
261 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
2291203 CAAAAGAT
326 CAAAAGAT
2291211 GTACATACAT
Statistics
Matches: 1270, Mismatches: 36, Indels: 9
0.97 0.03 0.01
Matches are distributed among these distances:
487 18 0.01
488 547 0.43
489 164 0.13
490 474 0.37
491 51 0.04
492 16 0.01
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (490 bp):
TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
GCGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:2290829 original size:23 final size:23
Alignment explanation
Indices: 2290794--2290866 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
2290784 ATACTTTACA
*
2290794 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2290817 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2290840 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
2290863 ATAT
1 ATAT
2290867 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:2291285 original size:42 final size:42
Alignment explanation
Indices: 2291226--2291333 Score: 216
Period size: 42 Copynumber: 2.6 Consensus size: 42
2291216 TACATAAATA
2291226 TGTAGTTATTGTACATACCTAAATTTAATGATAATATATACT
1 TGTAGTTATTGTACATACCTAAATTTAATGATAATATATACT
2291268 TGTAGTTATTGTACATACCTAAATTTAATGATAATATATACT
1 TGTAGTTATTGTACATACCTAAATTTAATGATAATATATACT
2291310 TGTAGTTATTGTACATACCTAAAT
1 TGTAGTTATTGTACATACCTAAAT
2291334 ATGTACTGCG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (42 bp):
TGTAGTTATTGTACATACCTAAATTTAATGATAATATATACT
Found at i:2293512 original size:21 final size:21
Alignment explanation
Indices: 2293488--2293532 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2293478 AATCGGATCA
* *
2293488 GATCCGGATATTT-GGATATTC
1 GATCC-GAAATTTCGGATATCC
2293509 GATCCGAAATTTCGGATATCC
1 GATCCGAAATTTCGGATATCC
2293530 GAT
1 GAT
2293533 TTTTTCGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (21 bp):
GATCCGAAATTTCGGATATCC
Found at i:2303619 original size:35 final size:36
Alignment explanation
Indices: 2303558--2303652 Score: 104
Period size: 35 Copynumber: 2.7 Consensus size: 36
2303548 TCAATTTTGA
* * * **
2303558 AAAAATGATTTTTAAAATTTGATAAATATTTTTTTG
1 AAAAATGATTTTCAAAGTTTGGTAAATATTTCCTTG
* *
2303594 -AAAATGGTTTTCAAAGTTTGGTAAATGTTTCCTTG
1 AAAAATGATTTTCAAAGTTTGGTAAATATTTCCTTG
2303629 AAAAAT-ATTTTTCAAAGTTTGGTA
1 AAAAATGA-TTTTCAAAGTTTGGTA
2303653 GATGTTTTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
35 28 0.57
36 21 0.43
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (36 bp):
AAAAATGATTTTCAAAGTTTGGTAAATATTTCCTTG
Found at i:2303641 original size:36 final size:36
Alignment explanation
Indices: 2303558--2303659 Score: 109
Period size: 36 Copynumber: 2.9 Consensus size: 36
2303548 TCAATTTTGA
* * * **
2303558 AAAAATGATTTTT-AAAATTTGATAAATATTTTTTTG
1 AAAAAT-ATTTTTCAAAGTTTGGTAAATGTTTCCTTG
**
2303594 -AAAATGGTTTTCAAAGTTTGGTAAATGTTTCCTTG
1 AAAAATATTTTTCAAAGTTTGGTAAATGTTTCCTTG
*
2303629 AAAAATATTTTTCAAAGTTTGGTAGATGTTT
1 AAAAATATTTTTCAAAGTTTGGTAAATGTTT
2303660 TGAAAAATGA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
34 4 0.07
35 23 0.43
36 27 0.50
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (36 bp):
AAAAATATTTTTCAAAGTTTGGTAAATGTTTCCTTG
Found at i:2306753 original size:12 final size:12
Alignment explanation
Indices: 2306719--2306753 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2306709 TATCATGTTC
**
2306719 TCATATCACAGG
1 TCATATCACATA
2306731 TCATATCACATA
1 TCATATCACATA
2306743 TCATATCACAT
1 TCATATCACAT
2306754 GAACATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (12 bp):
TCATATCACATA
Found at i:2313416 original size:15 final size:15
Alignment explanation
Indices: 2313393--2313425 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2313383 CGTAGGACTC
2313393 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
2313408 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
2313423 CTA
1 CTA
2313426 TTATACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:2313587 original size:12 final size:12
Alignment explanation
Indices: 2313570--2313599 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2313560 TATCATGTTC
*
2313570 TCATATCACATG
1 TCATATCACATA
2313582 TCATATCACATA
1 TCATATCACATA
2313594 TCATAT
1 TCATAT
2313600 ATATGTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (12 bp):
TCATATCACATA
Found at i:2314003 original size:64 final size:64
Alignment explanation
Indices: 2313897--2314073 Score: 196
Period size: 64 Copynumber: 2.8 Consensus size: 64
2313887 TAATGAAGGT
* * * ** ** * **
2313897 ATGCATCGATGCACTACTGATTCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGTATTCGATGT-GTCACTATTAATGGG
* * *
2313961 ATGCATCGATGCACTCCTTATGCATCGATGCACCG-ATTGTATTCAATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGAATTGTATTCGATGTGTCACTATTAATGGG
*
2314025 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGTATTCGATGT
2314074 CTTTATTTTA
Statistics
Matches: 94, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
63 3 0.03
64 91 0.97
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGTATTCGATGTGTCACTATTAATGGG
Found at i:2314094 original size:64 final size:63
Alignment explanation
Indices: 2313960--2314121 Score: 184
Period size: 64 Copynumber: 2.5 Consensus size: 63
2313950 TTATTGCTGG
* * * *
2313960 GATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGTATTCAATGTTTCACTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCAATGTTTCACTATTAAAGA
* * *
2314024 GATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCAATGT-TTCACTATTAAAGA
** *
2314087 GAGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCAC
2314122 ATTCAAACAA
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 4 0.05
64 78 0.92
65 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (63 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCAATGTTTCACTATTAAAGA
Found at i:2318114 original size:31 final size:31
Alignment explanation
Indices: 2318079--2318182 Score: 84
Period size: 31 Copynumber: 3.2 Consensus size: 31
2318069 AAGTCGGTGT
2318079 TGAACCTATAAAAGGAATTACCAACAATGAC
1 TGAACCTATAAAAGGAATTACCAACAATGAC
* * **
2318110 TGAACCTGTAAGAGATAGGAATTACCAGTCGGTG-C
1 TGAACCTAT-A-A-A-AGGAATTACCA-ACAATGAC
* * * *
2318145 TGGACCTATACAAGGAATTACTAGCAATGAC
1 TGAACCTATAAAAGGAATTACCAACAATGAC
2318176 TGAACCT
1 TGAACCT
2318183 GCCAGAGTCT
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
30 3 0.05
31 25 0.45
32 2 0.04
33 1 0.02
34 2 0.04
35 19 0.35
36 3 0.05
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.22
Consensus pattern (31 bp):
TGAACCTATAAAAGGAATTACCAACAATGAC
Found at i:2318173 original size:66 final size:66
Alignment explanation
Indices: 2318060--2318183 Score: 194
Period size: 66 Copynumber: 1.9 Consensus size: 66
2318050 TAGGTCCATA
*
2318060 AGGAATTACAAGTCGGTGTTGAACCTATAAAAGGAATTACCAACAATGACTGAACCTGTAAGAGA
1 AGGAATTACAAGTCGGTGCTGAACCTATAAAAGGAATTACCAACAATGACTGAACCTGTAAGAGA
2318125 T
66 T
* * * * *
2318126 AGGAATTACCAGTCGGTGCTGGACCTATACAAGGAATTACTAGCAATGACTGAACCTG
1 AGGAATTACAAGTCGGTGCTGAACCTATAAAAGGAATTACCAACAATGACTGAACCTG
2318184 CCAGAGTCTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 52 1.00
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (66 bp):
AGGAATTACAAGTCGGTGCTGAACCTATAAAAGGAATTACCAACAATGACTGAACCTGTAAGAGA
T
Found at i:2319604 original size:25 final size:25
Alignment explanation
Indices: 2319571--2319659 Score: 160
Period size: 25 Copynumber: 3.6 Consensus size: 25
2319561 AATTACATCT
* *
2319571 CATGGACCAATTATATCTATTCATG
1 CATGAACCAATTATATCCATTCATG
2319596 CATGAACCAATTATATCCATTCATG
1 CATGAACCAATTATATCCATTCATG
2319621 CATGAACCAATTATATCCATTCATG
1 CATGAACCAATTATATCCATTCATG
2319646 CATGAACCAATTAT
1 CATGAACCAATTAT
2319660 CAATGGGTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 62 1.00
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (25 bp):
CATGAACCAATTATATCCATTCATG
Found at i:2319898 original size:26 final size:26
Alignment explanation
Indices: 2319857--2319918 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
2319847 GAAGGTAAAT
*
2319857 ATTTGAAAACGGCTTACCGGGTTCGA
1 ATTTGAAAACGACTTACCGGGTTCGA
*
2319883 ATTTGAAAATGACTTACCGGGTTCGA
1 ATTTGAAAACGACTTACCGGGTTCGA
2319909 ATTTGAAAAC
1 ATTTGAAAAC
2319919 ACGGACTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (26 bp):
ATTTGAAAACGACTTACCGGGTTCGA
Found at i:2320056 original size:18 final size:18
Alignment explanation
Indices: 2320033--2320070 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2320023 ACTCTGACCA
2320033 AAGTCAATA-GCTCGAGTC
1 AAGTCAA-AGGCTCGAGTC
*
2320051 AAGTCAAAGGGTCGAGTC
1 AAGTCAAAGGCTCGAGTC
2320069 AA
1 AA
2320071 AGAAGTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.18
Consensus pattern (18 bp):
AAGTCAAAGGCTCGAGTC
Found at i:2322093 original size:21 final size:21
Alignment explanation
Indices: 2322064--2322120 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
2322054 GGGTCTACGC
*
2322064 GGTCCTTCGGGACAATATAGT
1 GGTCCTTCGGGACAATATAAT
*
2322085 GGTCATTCGGGACAATATAAT
1 GGTCCTTCGGGACAATATAAT
*
2322106 AGTCCTTCGGGACAA
1 GGTCCTTCGGGACAA
2322121 ATTTCATATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (21 bp):
GGTCCTTCGGGACAATATAAT
Found at i:2322844 original size:22 final size:22
Alignment explanation
Indices: 2322816--2322857 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2322806 AACAGTACTG
* *
2322816 TAGCAGGGGTATTGGTTCCCTA
1 TAGCAGGGGAATCGGTTCCCTA
2322838 TAGCAGGGGAATCGGTTCCC
1 TAGCAGGGGAATCGGTTCCC
2322858 CTCTGACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.21, G:0.33, T:0.26
Consensus pattern (22 bp):
TAGCAGGGGAATCGGTTCCCTA
Found at i:2322940 original size:20 final size:22
Alignment explanation
Indices: 2322895--2322947 Score: 74
Period size: 20 Copynumber: 2.5 Consensus size: 22
2322885 TTAGGTATTG
*
2322895 TTCACGGTACTATTTATTATTA
1 TTCACGGTACTATTTATTACTA
*
2322917 TTCACAGTACT-TTT-TTACTA
1 TTCACGGTACTATTTATTACTA
2322937 TTCACGGTACT
1 TTCACGGTACT
2322948 GTTCATACCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 15 0.54
21 3 0.11
22 10 0.36
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (22 bp):
TTCACGGTACTATTTATTACTA
Found at i:2326934 original size:13 final size:13
Alignment explanation
Indices: 2326916--2326941 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2326906 GTAAAACTTG
2326916 GTAAGTGTAGTGT
1 GTAAGTGTAGTGT
2326929 GTAAGTGTAGTGT
1 GTAAGTGTAGTGT
2326942 AAATTATTAC
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:0.23, C:0.00, G:0.38, T:0.38
Consensus pattern (13 bp):
GTAAGTGTAGTGT
Done.