Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, 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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 6 of 138
Found at i:1384230 original size:28 final size:28
Alignment explanation
Indices: 1384197--1384250 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
1384187 ATCACAGGCT
*
1384197 TTTCTTTTTTTTTTTA-TTTGATTTTTTG
1 TTTCTTTATTTTTTTACTTTG-TTTTTTG
1384225 TTTCTTTATTTTTTTACTTTGTTTTT
1 TTTCTTTATTTTTTTACTTTGTTTTT
1384251 ATTCTCTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.07, C:0.06, G:0.06, T:0.81
Consensus pattern (28 bp):
TTTCTTTATTTTTTTACTTTGTTTTTTG
Found at i:1384249 original size:27 final size:26
Alignment explanation
Indices: 1384196--1384278 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 26
1384186 GATCACAGGC
*
1384196 TTTTCTTTTTTTTTTTATTTGATTTTT
1 TTTTCTTTATTTTTTTATTTGA-TTTT
1384223 TGTTTCTTTATTTTTTTACTTTG-TTTT
1 T-TTTCTTTATTTTTTTA-TTTGATTTT
* * *
1384250 TATTCTCTTATTTTTCGTATTTAATTTT
1 TTTTCT-TTATTTTT-TTATTTGATTTT
1384278 T
1 T
1384279 GCATGATATA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
26 4 0.09
27 17 0.36
28 22 0.47
29 4 0.09
ACGTcount: A:0.11, C:0.07, G:0.05, T:0.77
Consensus pattern (26 bp):
TTTTCTTTATTTTTTTATTTGATTTT
Found at i:1384423 original size:21 final size:21
Alignment explanation
Indices: 1384399--1384478 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
1384389 ATAAATTTGT
*
1384399 ATGATATTTTATCTTAATTAC
1 ATGATATTTTATATTAATTAC
* *
1384420 ATGATAATTTATATTAATTGC
1 ATGATATTTTATATTAATTAC
** *
1384441 ATGATATCATATTATT-ATTGC
1 ATGATATTTTA-TATTAATTAC
*
1384462 ATGATATTATATTATTA
1 ATGATATTTTA-TATTA
1384479 TTTGCATAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
21 46 0.92
22 4 0.08
ACGTcount: A:0.36, C:0.06, G:0.07, T:0.50
Consensus pattern (21 bp):
ATGATATTTTATATTAATTAC
Found at i:1384479 original size:21 final size:21
Alignment explanation
Indices: 1384419--1384485 Score: 84
Period size: 21 Copynumber: 3.1 Consensus size: 21
1384409 ATCTTAATTA
1384419 CATGATAATT-TA-TATTAATTG
1 CATGAT-ATTATATTATT-ATTG
*
1384440 CATGATATCATATTATTATTG
1 CATGATATTATATTATTATTG
1384461 CATGATATTATATTATTATTTG
1 CATGATATTATATTATTA-TTG
1384483 CAT
1 CAT
1384486 AATTTTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
20 2 0.05
21 29 0.71
22 10 0.24
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.49
Consensus pattern (21 bp):
CATGATATTATATTATTATTG
Found at i:1386435 original size:9 final size:9
Alignment explanation
Indices: 1386421--1386460 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
1386411 GTCGATTTTC
1386421 ATTACTATT
1 ATTACTATT
1386430 ATTACTATT
1 ATTACTATT
** *
1386439 ATTGTTTTT
1 ATTACTATT
1386448 ATTACTATT
1 ATTACTATT
1386457 ATTA
1 ATTA
1386461 ATATAGTATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (9 bp):
ATTACTATT
Found at i:1386537 original size:5 final size:5
Alignment explanation
Indices: 1386529--1386590 Score: 63
Period size: 5 Copynumber: 11.8 Consensus size: 5
1386519 TATAGTATAG
* *
1386529 TATTA TATTA TATTA TATCA TCATTA TTATTA T-TATG TATTA TTATTA
1 TATTA TATTA TATTA TATTA T-ATTA -TATTA TAT-TA TATTA -TATTA
1386577 TATTA TATTA TATT
1 TATTA TATTA TATT
1386591 GTTGTTGTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
4 1 0.02
5 33 0.69
6 13 0.27
7 1 0.02
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:1386557 original size:3 final size:3
Alignment explanation
Indices: 1386529--1386635 Score: 118
Period size: 3 Copynumber: 37.3 Consensus size: 3
1386519 TATAGTATAG
* *
1386529 TAT TA- TAT TA- TAT TA- TAT CAT CAT TAT TAT TAT TAT GTAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
* * *
1386572 TAT TA- TAT TA- TAT TA- TAT TGT TGT TGT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1386617 TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
1386636 CTTTTCTTTT
Statistics
Matches: 93, Mismatches: 4, Indels: 14
0.84 0.04 0.13
Matches are distributed among these distances:
2 12 0.13
3 78 0.84
4 3 0.03
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1386576 original size:43 final size:42
Alignment explanation
Indices: 1386529--1386631 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 42
1386519 TATAGTATAG
1386529 TATTATATTATATTATATCATCATTATTATTATTATGTATTAT
1 TATTATATTATATTATATCATCATTATTATTATTAT-TATTAT
** ** *
1386572 TATTATATTATATTATATTGTTGTTGTTATTATTATTATTAT
1 TATTATATTATATTATATCATCATTATTATTATTATTATTAT
1386614 TATTATTATTATTATTAT
1 TATTA-TATTA-TATTAT
1386632 TATTCTTTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
42 11 0.21
43 36 0.68
44 6 0.11
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (42 bp):
TATTATATTATATTATATCATCATTATTATTATTATTATTAT
Found at i:1387547 original size:18 final size:19
Alignment explanation
Indices: 1387512--1387588 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
1387502 CAGGTTTTCT
* *
1387512 TTTTTTCATTTTATTTTTA
1 TTTTTTAATTGTATTTTTA
1387531 TTTTTTAATTGTA-TTTTA
1 TTTTTTAATTGTATTTTTA
*
1387549 -TTTTTAGTT-T-TTTATTA
1 TTTTTTAATTGTATTT-TTA
* *
1387566 TTTTACTAATTTTATTTTTA
1 TTTT-TTAATTGTATTTTTA
1387586 TTT
1 TTT
1387589 GAAAATTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.06
17 11 0.23
18 8 0.17
19 15 0.32
20 7 0.15
21 3 0.06
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTTTTAATTGTATTTTTA
Found at i:1387689 original size:14 final size:14
Alignment explanation
Indices: 1387669--1387702 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1387659 TTTTTTAAAA
*
1387669 AATAAAAAA-AGAG
1 AATAAAAAAGAAAG
1387682 AATAAAAAAGAAAG
1 AATAAAAAAGAAAG
1387696 AATAAAA
1 AATAAAA
1387703 TTTAAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (14 bp):
AATAAAAAAGAAAG
Found at i:1391953 original size:9 final size:9
Alignment explanation
Indices: 1391935--1391969 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1391925 GGGGAAAGAG
1391935 AAATGAAAA
1 AAATGAAAA
1391944 AAATTGAAAA
1 AAA-TGAAAA
*
1391954 AAAAGAAAA
1 AAATGAAAA
1391963 AAATGAA
1 AAATGAA
1391970 GTGAAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
AAATGAAAA
Found at i:1393054 original size:115 final size:115
Alignment explanation
Indices: 1392837--1393055 Score: 242
Period size: 115 Copynumber: 1.9 Consensus size: 115
1392827 CTCAATTTGA
* *
1392837 ATCATTTTTCTAACTCGTGGCATCATCTCAGTCATTTATCTTCGATCTTGACTCGATCTTAATCA
1 ATCATTTTCCTAACTCGTGGCATCATCCCAGTCATTTATCTTCGATCTTGACTCGATCTTAATCA
* ** * * *
1392902 TTTTTAGACTCATGACATCGTCTTAATCATCCGATCTCAGCTCGATCAAG
66 CTTTTAGACTCACAACATCATCCTAATCATCCAATCTCAGCTCGATCAAG
* * * **
1392952 ATCATTTTCCTAACTCGTGGCATCATCCCAGTCATTTATGTTTGAT-TTCGACTTGATCTTGGTC
1 ATCATTTTCCTAACTCGTGGCATCATCCCAGTCATTTATCTTCGATCTT-GACTCGATCTTAATC
* * * * * * *
1393016 GCTTTTAGACTTACAATATTATCCTAGTTATTCAATCTCA
65 ACTTTTAGACTCACAACATCATCCTAATCATCCAATCTCA
1393056 ATTCAGTTCA
Statistics
Matches: 83, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
114 2 0.02
115 81 0.98
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (115 bp):
ATCATTTTCCTAACTCGTGGCATCATCCCAGTCATTTATCTTCGATCTTGACTCGATCTTAATCA
CTTTTAGACTCACAACATCATCCTAATCATCCAATCTCAGCTCGATCAAG
Found at i:1393525 original size:3 final size:3
Alignment explanation
Indices: 1393517--1393678 Score: 157
Period size: 3 Copynumber: 57.7 Consensus size: 3
1393507 TATCTTATAC
1393517 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * * *
1393565 ATT ATT ATT ATT ATT ATT A-T AGG A-T AGT -TT A-T AGT A-T AGT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
1393608 A-T ATT A-T ATC ATC ATT ATT ATT TTT GTT ATT A-T ATT A-T ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1393651 ATT A-T ATT ATT GTT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1393679 ATTTTTTTAT
Statistics
Matches: 137, Mismatches: 11, Indels: 22
0.81 0.06 0.13
Matches are distributed among these distances:
2 20 0.15
3 117 0.85
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:1393612 original size:5 final size:5
Alignment explanation
Indices: 1393604--1393681 Score: 61
Period size: 5 Copynumber: 14.8 Consensus size: 5
1393594 TATAGTATAG
* *
1393604 TATTA TATTA TATCA TCATTA TTATT- T-TTGT TATTA TATTA TATTA
1 TATTA TATTA TATTA T-ATTA -TATTA TATT-A TATTA TATTA TATTA
*
1393650 TATTA TATTA TTGTTA TTATTA TTATTA TATT
1 TATTA TATTA -TATTA -TATTA -TATTA TATT
1393682 TTTTTATTCT
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
3 2 0.03
4 1 0.02
5 35 0.56
6 23 0.37
7 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (5 bp):
TATTA
Found at i:1394554 original size:5 final size:5
Alignment explanation
Indices: 1394544--1394591 Score: 53
Period size: 5 Copynumber: 9.2 Consensus size: 5
1394534 TAGGTTCTTC
*
1394544 TTATT TTATT TTCAATT TTATT TTATT TTA-T TGATT TTATTT TTATT
1 TTATT TTATT TT--ATT TTATT TTATT TTATT TTATT TTA-TT TTATT
1394591 T
1 T
1394592 GAAATTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
4 3 0.08
5 24 0.65
6 5 0.14
7 5 0.14
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (5 bp):
TTATT
Found at i:1394563 original size:12 final size:10
Alignment explanation
Indices: 1394544--1394591 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 10
1394534 TAGGTTCTTC
1394544 TTATTTTATT
1 TTATTTTATT
1394554 TTCAATTTTATT
1 TT--ATTTTATT
1394566 TTATTTTA-T
1 TTATTTTATT
*
1394575 TGATTTTATTT
1 TTATTTTA-TT
1394586 TTATTT
1 TTATTT
1394592 GAAATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 8 0.25
10 8 0.25
11 6 0.19
12 10 0.31
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (10 bp):
TTATTTTATT
Found at i:1394706 original size:20 final size:21
Alignment explanation
Indices: 1394683--1394730 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
1394673 TAAAAAAAGG
*
1394683 AAAATAAAAGAGAAA-GAATA
1 AAAATAAAAGAGAAACAAATA
*
1394703 AAAA-AAAAGGGAAACAAATA
1 AAAATAAAAGAGAAACAAATA
1394723 AAAATAAA
1 AAAATAAA
1394731 TAAATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.08
Consensus pattern (21 bp):
AAAATAAAAGAGAAACAAATA
Found at i:1403425 original size:22 final size:25
Alignment explanation
Indices: 1403385--1403435 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
1403375 TATATATTTA
*
1403385 ATAAATATATTTTTATTAAA-TAAT
1 ATAAATATATTATTATTAAATTAAT
1403409 ATAAAT-TATTATT-TTAAATTAAT
1 ATAAATATATTATTATTAAATTAAT
1403432 -TAAA
1 ATAAA
1403436 ATCAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 9 0.36
23 10 0.40
24 6 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATAAATATATTATTATTAAATTAAT
Found at i:1403479 original size:51 final size:51
Alignment explanation
Indices: 1403388--1403486 Score: 119
Period size: 51 Copynumber: 1.9 Consensus size: 51
1403378 ATATTTAATA
* * ***
1403388 AATATATTTTTATTAAATAATATAAATTATTATTTTAAATTAATTAAAATC
1 AATATATTTTTATTAAAAAATATAAATTAATATAAAAAATTAATTAAAATC
* *
1403439 AATATATTTTTATTGAAAAAATATATATTAATA-AAAAAATTAGTTAAA
1 AATATATTTTTATT-AAAAAATATAAATTAATATAAAAAATTAATTAAA
1403487 TATACAAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 25 0.62
52 15 0.38
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (51 bp):
AATATATTTTTATTAAAAAATATAAATTAATATAAAAAATTAATTAAAATC
Found at i:1404782 original size:2 final size:2
Alignment explanation
Indices: 1404777--1404808 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1404767 GAATGGAAAC
1404777 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1404809 GTTTCCGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1407358 original size:71 final size:71
Alignment explanation
Indices: 1407265--1407403 Score: 206
Period size: 71 Copynumber: 2.0 Consensus size: 71
1407255 CTCCATATTC
* * * * *
1407265 ACTTGTGAGTTCTGATCAAGTTTCACCTCTCACCTCGGCTCTCTCGTGTGAGTAAGTCTTATAAA
1 ACTTATGAGTTATGATCAAGTTTCACCTCTCACATCGGCTCTCCCGTGTGAGTAAGTCCTATAAA
1407330 CACTTT
66 CACTTT
* * *
1407336 ACTTATGAGTTATGGTCAAGTTTCACCTCTCACATTGGCTCTCCCGTGTGAGTAAGTCCTATCAA
1 ACTTATGAGTTATGATCAAGTTTCACCTCTCACATCGGCTCTCCCGTGTGAGTAAGTCCTATAAA
1407401 CAC
66 CAC
1407404 CTCATTTGGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (71 bp):
ACTTATGAGTTATGATCAAGTTTCACCTCTCACATCGGCTCTCCCGTGTGAGTAAGTCCTATAAA
CACTTT
Found at i:1410696 original size:2 final size:2
Alignment explanation
Indices: 1410689--1410725 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1410679 GAAATCCTTT
* *
1410689 TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1410726 TTGGTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1421402 original size:52 final size:50
Alignment explanation
Indices: 1421339--1421498 Score: 178
Period size: 52 Copynumber: 3.1 Consensus size: 50
1421329 TGAACAAGAA
* *
1421339 GACTTGTAAAAGAAAAATTCTAAGAGAACGAAG-ATTCTTAATAGGCAAGTTT
1 GACTTGCAAAAGAATAATT-TAAGAGAA--AAGAATTCTTAATAGGCAAGTTT
*
1421391 GACTTGCAAAAGAATAATTATAAGAGGAAATGAATTCTTAATAGGCAAGTTT
1 GACTTGCAAAAGAATAATT-TAAGA-GAAAAGAATTCTTAATAGGCAAGTTT
* * * * * *
1421443 AACTTACAGAAGAATAATTTAAAAGAAAATGAATTCTTAATAGGTAAATTT
1 GACTTGCAAAAGAATAATTTAAGAGAAAA-GAATTCTTAATAGGCAAGTTT
1421494 GACTT
1 GACTT
1421499 ATAGAATAAG
Statistics
Matches: 93, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
50 4 0.04
51 29 0.31
52 57 0.61
53 3 0.03
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (50 bp):
GACTTGCAAAAGAATAATTTAAGAGAAAAGAATTCTTAATAGGCAAGTTT
Found at i:1421499 original size:51 final size:52
Alignment explanation
Indices: 1421372--1421545 Score: 208
Period size: 52 Copynumber: 3.4 Consensus size: 52
1421362 GAGAACGAAG
* * *
1421372 ATTCTTAATAGGCAAGTTTGACTTGCAAAAGAATAATTATAAGAGGAAATGA
1 ATTCTTAATAGGCAAGTTTGACTTACAGAAGAATAATTATAAAAGGAAATGA
* *
1421424 ATTCTTAATAGGCAAGTTTAACTTACAGAAGAATAATT-TAAAAGAAAATGA
1 ATTCTTAATAGGCAAGTTTGACTTACAGAAGAATAATTATAAAAGGAAATGA
* * * * * *
1421475 ATTCTTAATAGGTAAATTTGACTTATAGAATAAGAATTCTAAAAGGAAAT-A
1 ATTCTTAATAGGCAAGTTTGACTTACAGAAGAATAATTATAAAAGGAAATGA
* *
1421526 GATTCTTTATAGGTAAGTTT
1 -ATTCTTAATAGGCAAGTTT
1421546 ATATGATTAT
Statistics
Matches: 106, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
51 44 0.42
52 62 0.58
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (52 bp):
ATTCTTAATAGGCAAGTTTGACTTACAGAAGAATAATTATAAAAGGAAATGA
Found at i:1425555 original size:290 final size:288
Alignment explanation
Indices: 1425037--1425610 Score: 995
Period size: 290 Copynumber: 2.0 Consensus size: 288
1425027 AAAGGGACTT
* *
1425037 GCTTTTCTTTGTTTTTGTGATTTCAGGTCCGCATGGCCTTCTCGAAGACGTTCTTTTCTGTATTT
1 GCTTTTCTTTGTTTTTGTGATTTCAGGTCCGCACGGCCTTCTCGAAGACGTTCTTTTCTATATTT
* *
1425102 GATGTTCCTGATTTGGCCCATATTACTCTGCTGTTGGATTGTTCTGTTTGTCCTCAAGATGAAGC
66 GATGTTCCTGATTTGGCCCATATCACTCTGCTATTGGATTGTTCTGTTTGTCCTCAAGATGAAGC
* *
1425167 GTCAGATAATGCAGATGATCAAGTATAAATACGTTCCCATCAGCATAGTGAAGCAGGTCAGAGCT
131 GTCAGATAATGCAGATGATCAAGTATAAATACGTTCCCATCAGCACAGTGAAACAGGTCAGAGCT
* * *
1425232 TGGAATTTGTTTAAATCACCGTATTTGATTCTGTTGTTTCTTCACACTTCCTCCTTTGAAATTTG
196 TGAAATTTGTTTAAATCACCGTATTTGATTCTGTTGTTTCCTCACACTCCCTCCTTTGAAATTTG
*
1425297 TGGTAAAACTTCTATCATTGGAATGCAC
261 TAGTAAAACTTCTATCATTGGAATGCAC
* * *
1425325 GCTTTTCTTTGTTTTTGTGATTTCAGGTCTGCACGGCCTTCTCGATGACTTTCTTTTCTATATTT
1 GCTTTTCTTTGTTTTTGTGATTTCAGGTCCGCACGGCCTTCTCGAAGACGTTCTTTTCTATATTT
*
1425390 GATTTTCCTGTATTTTGGCCCATATCACTCTGCTATTGGATTGTTCTGTTTGTCCTCAAGATGAA
66 GATGTTCCTG-A-TTTGGCCCATATCACTCTGCTATTGGATTGTTCTGTTTGTCCTCAAGATGAA
1425455 GCGTCAGATAATGCAGATGATCAAGTATAAATACGTTCCCATCAGCACAGTGAAACAGGTCAGAG
129 GCGTCAGATAATGCAGATGATCAAGTATAAATACGTTCCCATCAGCACAGTGAAACAGGTCAGAG
*
1425520 CTTGAAATTTGTTTTAATCACCGTATTTGATTCTGTTGTTTCCTCACACTCCCTCCTTTGAAATT
194 CTTGAAATTTGTTTAAATCACCGTATTTGATTCTGTTGTTTCCTCACACTCCCTCCTTTGAAATT
1425585 TGTAGTAAAACTTCTATCATTGGAAT
259 TGTAGTAAAACTTCTATCATTGGAAT
1425611 ATAATATTAA
Statistics
Matches: 269, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
288 69 0.26
289 1 0.00
290 199 0.74
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (288 bp):
GCTTTTCTTTGTTTTTGTGATTTCAGGTCCGCACGGCCTTCTCGAAGACGTTCTTTTCTATATTT
GATGTTCCTGATTTGGCCCATATCACTCTGCTATTGGATTGTTCTGTTTGTCCTCAAGATGAAGC
GTCAGATAATGCAGATGATCAAGTATAAATACGTTCCCATCAGCACAGTGAAACAGGTCAGAGCT
TGAAATTTGTTTAAATCACCGTATTTGATTCTGTTGTTTCCTCACACTCCCTCCTTTGAAATTTG
TAGTAAAACTTCTATCATTGGAATGCAC
Found at i:1441326 original size:21 final size:21
Alignment explanation
Indices: 1441300--1441344 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1441290 ATACTTACTT
1441300 AAAATTCAGTAATTAATTTAA
1 AAAATTCAGTAATTAATTTAA
* * * *
1441321 AAAATTTATTGATTATTTTAA
1 AAAATTCAGTAATTAATTTAA
1441342 AAA
1 AAA
1441345 CACAAATATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (21 bp):
AAAATTCAGTAATTAATTTAA
Found at i:1441765 original size:2 final size:2
Alignment explanation
Indices: 1441758--1441788 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1441748 CCCATTAGAT
1441758 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1441789 AATTGGAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1457859 original size:2 final size:2
Alignment explanation
Indices: 1457852--1457885 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1457842 AGTGAAATAA
1457852 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
1457886 TAGAAGTGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1459564 original size:24 final size:23
Alignment explanation
Indices: 1459531--1459586 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
1459521 AATTTAAAAG
*
1459531 ATAATTATTATTTTGT-ATATCAAA
1 ATAATAATTATTTT-TAAT-TCAAA
1459555 ATAATAATTATTTTTAATTCAAA
1 ATAATAATTATTTTTAATTCAAA
*
1459578 ATAAAAATT
1 ATAATAATT
1459587 TTAAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 14 0.48
24 15 0.52
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
ATAATAATTATTTTTAATTCAAA
Found at i:1459580 original size:23 final size:24
Alignment explanation
Indices: 1459531--1459586 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
1459521 AATTTAAAAG
*
1459531 ATAATTATTATTTTGTATATCAAA
1 ATAATAATTATTTTGTATATCAAA
1459555 ATAATAATTATTTT-TA-ATTCAAA
1 ATAATAATTATTTTGTATA-TCAAA
*
1459578 ATAAAAATT
1 ATAATAATT
1459587 TTAAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 1 0.03
23 15 0.52
24 13 0.45
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (24 bp):
ATAATAATTATTTTGTATATCAAA
Found at i:1462144 original size:10 final size:10
Alignment explanation
Indices: 1462131--1462174 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
1462121 GAAAGAGATG
1462131 AGCAAACAGC
1 AGCAAACAGC
1462141 AGCAAACAGC
1 AGCAAACAGC
*
1462151 AGCAAACAAC
1 AGCAAACAGC
* *
1462161 AGCTAACGGC
1 AGCAAACAGC
1462171 AGCA
1 AGCA
1462175 GGAACAGGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.48, C:0.30, G:0.20, T:0.02
Consensus pattern (10 bp):
AGCAAACAGC
Found at i:1473574 original size:36 final size:36
Alignment explanation
Indices: 1473518--1473587 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
1473508 GATTAGTGTA
*
1473518 TTTATATAAAATATTAAATTTGGTA-TTTATATTATT
1 TTTATATAAAATACTAAATTT-GTATTTTATATTATT
*
1473554 TTTATATAAAA-ACTATAATTTTTATTTTATATTA
1 TTTATATAAAATACTA-AATTTGTATTTTATATTA
1473588 ATATAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 5 0.17
36 25 0.83
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (36 bp):
TTTATATAAAATACTAAATTTGTATTTTATATTATT
Found at i:1473605 original size:31 final size:31
Alignment explanation
Indices: 1473543--1473605 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
1473533 AAATTTGGTA
* * *
1473543 TTTATATTATTTTTATATAAAAACTATAATT
1 TTTATATTATATTAATATAAAAACTACAATT
*
1473574 TTTATTTTATATTAATATAAAATA-TACAATT
1 TTTATATTATATTAATATAAAA-ACTACAATT
1473605 T
1 T
1473606 ATTTTTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (31 bp):
TTTATATTATATTAATATAAAAACTACAATT
Found at i:1493451 original size:16 final size:16
Alignment explanation
Indices: 1493430--1493461 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1493420 GACCTAACTC
1493430 TAAAGAATATAGATAG
1 TAAAGAATATAGATAG
1493446 TAAAGAATATAGATAG
1 TAAAGAATATAGATAG
1493462 GCATAGGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.25
Consensus pattern (16 bp):
TAAAGAATATAGATAG
Found at i:1494656 original size:1 final size:1
Alignment explanation
Indices: 1494650--1494679 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
1494640 ATCTATAGTT
1494650 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1494680 CTGAAAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1495339 original size:29 final size:26
Alignment explanation
Indices: 1495302--1495365 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 26
1495292 TAAATCGATA
*
1495302 AATTAATAAAAT-TTAATGTAAAAATTAAT
1 AATTTATAAAATATT-AT-TAAAAA--AAT
1495331 AATTTATAAAATATTATTAAAAAAAT
1 AATTTATAAAATATTATTAAAAAAAT
*
1495357 TATTTATAA
1 AATTTATAA
1495366 TTTAAATTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 11 0.34
28 6 0.19
29 13 0.41
30 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
AATTTATAAAATATTATTAAAAAAAT
Found at i:1510868 original size:23 final size:24
Alignment explanation
Indices: 1510834--1510881 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
1510824 ATTTATGTAT
*
1510834 TTATATTATATTT-TATATAAAAA
1 TTATATTATATTTCGATATAAAAA
1510857 TTATATCT-TATTTCGATATAAAAA
1 TTATAT-TATATTTCGATATAAAAA
1510881 T
1 T
1510882 ATAAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (24 bp):
TTATATTATATTTCGATATAAAAA
Found at i:1515944 original size:25 final size:25
Alignment explanation
Indices: 1515915--1515969 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1515905 ATTTTTTATT
* *
1515915 ATTTTTTAAATTATAATTATAATAA
1 ATTTTTTAAATCACAATTATAATAA
* * *
1515940 TTTTTTTTAATCACAATTATAGTAA
1 ATTTTTTAAATCACAATTATAATAA
1515965 ATTTT
1 ATTTT
1515970 ATTACTGTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (25 bp):
ATTTTTTAAATCACAATTATAATAA
Found at i:1519326 original size:34 final size:34
Alignment explanation
Indices: 1519287--1519358 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
1519277 ATCATAAGTG
* *
1519287 TTTTGTCATAATTTCATTTTATCTATTATTTATA
1 TTTTGTCATAATTTCATTTTACCCATTATTTATA
*
1519321 TTTTGTCATAATTTCATTTTACCCGTTATTTATA
1 TTTTGTCATAATTTCATTTTACCCATTATTTATA
1519355 TTTT
1 TTTT
1519359 ACTATACAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.04, T:0.61
Consensus pattern (34 bp):
TTTTGTCATAATTTCATTTTACCCATTATTTATA
Found at i:1519334 original size:17 final size:16
Alignment explanation
Indices: 1519287--1519340 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
1519277 ATCATAAGTG
1519287 TTTTGTCATAATTTCA
1 TTTTGTCATAATTTCA
* * *
1519303 TTTTATCTATTATTTATA
1 TTTTGTC-ATAATTT-CA
1519321 TTTTGTCATAATTTCA
1 TTTTGTCATAATTTCA
1519337 TTTT
1 TTTT
1519341 ACCCGTTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
16 11 0.37
17 12 0.40
18 7 0.23
ACGTcount: A:0.24, C:0.09, G:0.04, T:0.63
Consensus pattern (16 bp):
TTTTGTCATAATTTCA
Found at i:1519620 original size:41 final size:40
Alignment explanation
Indices: 1519575--1519667 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
1519565 AGAGTAAAGC
*
1519575 TTATATGAAATAATTATTTACAAATCAAAATTTATTAATAT
1 TTATATGAAATAATTATTTACAAAT-AAAAATTATTAATAT
* *
1519616 TTATATGAAAAAATTATTTATAAATAAAAATTATTAATAT
1 TTATATGAAATAATTATTTACAAATAAAAATTATTAATAT
* *
1519656 TTACATAAAATA
1 TTATATGAAATA
1519668 CTTTATTTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 23 0.50
41 23 0.50
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (40 bp):
TTATATGAAATAATTATTTACAAATAAAAATTATTAATAT
Found at i:1519635 original size:17 final size:18
Alignment explanation
Indices: 1519613--1519655 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1519603 AATTTATTAA
*
1519613 TATTTATATGA-AAAAAT
1 TATTTATATAATAAAAAT
1519630 TATTTATA-AATAAAAAT
1 TATTTATATAATAAAAAT
*
1519647 TATTAATAT
1 TATTTATAT
1519656 TTACATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 1 0.05
17 21 0.95
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TATTTATATAATAAAAAT
Found at i:1526832 original size:29 final size:28
Alignment explanation
Indices: 1526789--1526846 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
1526779 AACATTATAT
* *
1526789 ATTTTTAAATTTAATTTAAATTTGAATTG
1 ATTTTTAAATATAATTT-AATTTAAATTG
*
1526818 ATTTTTTAATATAATTTAATTTAAATTG
1 ATTTTTAAATATAATTTAATTTAAATTG
1526846 A
1 A
1526847 ATCGAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (28 bp):
ATTTTTAAATATAATTTAATTTAAATTG
Found at i:1526856 original size:34 final size:35
Alignment explanation
Indices: 1526796--1526870 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 35
1526786 TATATTTTTA
* *
1526796 AATTTAATTTAAATTTGAATTGATTTTTTA-ATAT
1 AATTTAATTTAAATTTGAATCGATTTTATAGATAT
*
1526830 AATTTAATTTAAA-TTGAATCGAATTTTATAGATTT
1 AATTTAATTTAAATTTGAATCG-ATTTTATAGATAT
1526865 AATTTA
1 AATTTA
1526871 TCTGTTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 7 0.19
34 20 0.56
35 9 0.25
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.52
Consensus pattern (35 bp):
AATTTAATTTAAATTTGAATCGATTTTATAGATAT
Found at i:1532084 original size:16 final size:17
Alignment explanation
Indices: 1532049--1532080 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1532039 AAGGAAGGTA
1532049 TCCATGGCAACAGCGCG
1 TCCATGGCAACAGCGCG
1532066 TCCAT-GCAAC-GCGCG
1 TCCATGGCAACAGCGCG
1532081 GTCCTGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.22, C:0.38, G:0.28, T:0.12
Consensus pattern (17 bp):
TCCATGGCAACAGCGCG
Found at i:1534545 original size:15 final size:16
Alignment explanation
Indices: 1534525--1534555 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1534515 GTTTGAATCC
1534525 AAGTTATG-TTTGCCT
1 AAGTTATGTTTTGCCT
1534540 AAGTTATGTTTTGCCT
1 AAGTTATGTTTTGCCT
1534556 TTCTCATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
AAGTTATGTTTTGCCT
Found at i:1536625 original size:27 final size:27
Alignment explanation
Indices: 1536583--1536643 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
1536573 ATAAATCATA
1536583 TTAACTGATACCGGTTACATAGATAAT
1 TTAACTGATACCGGTTACATAGATAAT
*
1536610 TTAACTGATACTGGTTACATAGATAAT
1 TTAACTGATACCGGTTACATAGATAAT
1536637 TTAACTG
1 TTAACTG
1536644 TTCCAGGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (27 bp):
TTAACTGATACCGGTTACATAGATAAT
Found at i:1536652 original size:27 final size:27
Alignment explanation
Indices: 1536583--1536652 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
1536573 ATAAATCATA
*
1536583 TTAACTGATACCGGTTACATAGATAAT
1 TTAACTGATACAGGTTACATAGATAAT
*
1536610 TTAACTGATACTGGTTACATAGATAAT
1 TTAACTGATACAGGTTACATAGATAAT
* *
1536637 TTAACTGTTCCAGGTT
1 TTAACTGATACAGGTT
1536653 TAAAATCATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (27 bp):
TTAACTGATACAGGTTACATAGATAAT
Found at i:1551597 original size:45 final size:45
Alignment explanation
Indices: 1551532--1551623 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
1551522 AGGGAACCTT
*
1551532 TTTAAGTTGAAATTGTAATGAAGGAATATACCTTATTAATTGCAA
1 TTTAAGTTGAAATTGCAATGAAGGAATATACCTTATTAATTGCAA
* *
1551577 TTTAAGTTGAAATTGCAATGAAGGGATATACCTTATTAGTTGCAA
1 TTTAAGTTGAAATTGCAATGAAGGAATATACCTTATTAATTGCAA
1551622 TT
1 TT
1551624 GCGGTCAATG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (45 bp):
TTTAAGTTGAAATTGCAATGAAGGAATATACCTTATTAATTGCAA
Found at i:1555094 original size:25 final size:26
Alignment explanation
Indices: 1555056--1555109 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
1555046 TAAAAAATAT
* *
1555056 TTTTTTACTGTTTATTTAATTTTATA
1 TTTTTTACTATTTATTTAACTTTATA
1555082 TTTTTTA-TATTTATTTAACTTTATA
1 TTTTTTACTATTTATTTAACTTTATA
1555107 TTT
1 TTT
1555110 ATATTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTTTTACTATTTATTTAACTTTATA
Found at i:1561849 original size:15 final size:15
Alignment explanation
Indices: 1561829--1561864 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
1561819 TACAAATTTA
1561829 TTTTTATTTTTTATT
1 TTTTTATTTTTTATT
1561844 TTTTTATTTTTTATT
1 TTTTTATTTTTTATT
1561859 TTTTTA
1 TTTTTA
1561865 GATTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTATTTTTTATT
Found at i:1561864 original size:8 final size:7
Alignment explanation
Indices: 1561825--1561862 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
1561815 TGTATACAAA
1561825 TTTA-TT
1 TTTATTT
1561831 TTTATTT
1 TTTATTT
1561838 TTTATTTT
1 TTTA-TTT
1561846 TTTATTT
1 TTTATTT
1561853 TTTATTT
1 TTTATTT
1561860 TTT
1 TTT
1561863 TAGATTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTATTT
Found at i:1572894 original size:9 final size:9
Alignment explanation
Indices: 1572880--1572905 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1572870 ATCATGACCA
1572880 TAAAATTTT
1 TAAAATTTT
1572889 TAAAATTTT
1 TAAAATTTT
1572898 TAAAATTT
1 TAAAATTT
1572906 ATTATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TAAAATTTT
Found at i:1573024 original size:14 final size:15
Alignment explanation
Indices: 1573007--1573049 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
1572997 ATTTAAGAAC
1573007 AAATATTTATA-ATA
1 AAATATTTATATATA
*
1573021 AAATATTTATATTTA
1 AAATATTTATATATA
*
1573036 AAA-ATTTATTTATA
1 AAATATTTATATATA
1573050 TGATAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATATTTATATATA
Found at i:1573205 original size:15 final size:15
Alignment explanation
Indices: 1573168--1573211 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1573158 TTATATTATA
1573168 CATAAATTAAATAAT
1 CATAAATTAAATAAT
* *
1573183 AAGT-AATTAAATATT
1 CA-TAAATTAAATAAT
1573198 CATAAATTAAATAA
1 CATAAATTAAATAA
1573212 AAATATTACT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
14 1 0.04
15 21 0.91
16 1 0.04
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (15 bp):
CATAAATTAAATAAT
Found at i:1588890 original size:31 final size:30
Alignment explanation
Indices: 1588833--1588891 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
1588823 TAAAATTTTT
*
1588833 AATTTATTCATTGATAAAATATTATCATCA
1 AATTTATTCATTAATAAAATATTATCATCA
*
1588863 AATTTATTTTATTAATAAAAT-TATATCAT
1 AATTTA-TTCATTAATAAAATAT-TATCAT
1588892 TCGATTTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (30 bp):
AATTTATTCATTAATAAAATATTATCATCA
Found at i:1589225 original size:18 final size:18
Alignment explanation
Indices: 1589204--1589243 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1589194 CATATGACTA
1589204 TGAACTTTTCTAGAAGTG
1 TGAACTTTTCTAGAAGTG
1589222 TGAACTTTTCTAGAAGTG
1 TGAACTTTTCTAGAAGTG
1589240 TGAA
1 TGAA
1589244 TGAAAGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.38
Consensus pattern (18 bp):
TGAACTTTTCTAGAAGTG
Found at i:1589916 original size:33 final size:33
Alignment explanation
Indices: 1589875--1589952 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 33
1589865 CTATGATTGG
1589875 TTTTTAAAAAAATGTT-TTATATTTAATTTATAT
1 TTTTTAAAAAAATGTTATTATATTTAATTT-TAT
* * *
1589908 TTTTT-AAAATA-GTTATTATTTTTTATTTTAT
1 TTTTTAAAAAAATGTTATTATATTTAATTTTAT
1589939 TTTTTATAAAAAAT
1 TTTTTA-AAAAAAT
1589953 ATATTTGATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
31 11 0.30
32 16 0.43
33 10 0.27
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (33 bp):
TTTTTAAAAAAATGTTATTATATTTAATTTTAT
Found at i:1589943 original size:31 final size:30
Alignment explanation
Indices: 1589883--1589944 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
1589873 GGTTTTTAAA
1589883 AAAATGTTTTATATTTAATTTATATTTTTT
1 AAAATGTTTTATATTTAATTTATATTTTTT
* *
1589913 AAAATAGTTATTATTTTTTATTT-TATTTTTT
1 AAAAT-GTT-TTATATTTAATTTATATTTTTT
1589944 A
1 A
1589945 TAAAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 5 0.18
31 12 0.43
32 11 0.39
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (30 bp):
AAAATGTTTTATATTTAATTTATATTTTTT
Found at i:1593663 original size:27 final size:28
Alignment explanation
Indices: 1593631--1593703 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
1593621 TAATATTAAA
1593631 AAATTAATTTTTAAAAATTGATAA-ATC
1 AAATTAATTTTTAAAAATTGATAATATC
* * *
1593658 AAATTAAATTTTT-ATAATTTATAATATT
1 AAATT-AATTTTTAAAAATTGATAATATC
*
1593686 AAATAAATATTTTAAAAA
1 AAATTAAT-TTTTAAAAA
1593704 ATTGTACCGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
27 17 0.46
28 17 0.46
29 3 0.08
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (28 bp):
AAATTAATTTTTAAAAATTGATAATATC
Found at i:1595519 original size:43 final size:44
Alignment explanation
Indices: 1595457--1595544 Score: 169
Period size: 43 Copynumber: 2.0 Consensus size: 44
1595447 GTTTTGCTAT
1595457 CAAATTTTTGGTATATGTTAAGTTTCAATTGCATAGTGTATGAG
1 CAAATTTTTGGTATATGTTAAGTTTCAATTGCATAGTGTATGAG
1595501 CAAA-TTTTGGTATATGTTAAGTTTCAATTGCATAGTGTATGAG
1 CAAATTTTTGGTATATGTTAAGTTTCAATTGCATAGTGTATGAG
1595544 C
1 C
1595545 TTGCATCCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 40 0.91
44 4 0.09
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (44 bp):
CAAATTTTTGGTATATGTTAAGTTTCAATTGCATAGTGTATGAG
Found at i:1598940 original size:19 final size:19
Alignment explanation
Indices: 1598918--1598957 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1598908 ATATAAATAA
1598918 TTAATTGTAA-AAATTAAAT
1 TTAATTG-AATAAATTAAAT
*
1598937 TTAATTGAATAAATTTAAT
1 TTAATTGAATAAATTAAAT
1598956 TT
1 TT
1598958 TTATTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
TTAATTGAATAAATTAAAT
Found at i:1603636 original size:17 final size:17
Alignment explanation
Indices: 1603614--1603650 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1603604 TAGGATTATA
1603614 AATCAAGACCGTAGATG
1 AATCAAGACCGTAGATG
*
1603631 AATCAAGACTGTAGATG
1 AATCAAGACCGTAGATG
1603648 AAT
1 AAT
1603651 TAGAATCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22
Consensus pattern (17 bp):
AATCAAGACCGTAGATG
Found at i:1608178 original size:26 final size:25
Alignment explanation
Indices: 1608149--1608211 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 25
1608139 ACTAATTAAC
1608149 TTAAATATTAATT-TTAATAAAATTAT
1 TTAAATATTAATTCTT-AT-AAATTAT
* *
1608175 TT-AATATAAAATTCTTATAAATTTT
1 TTAAATAT-TAATTCTTATAAATTAT
*
1608200 TTAAATAATAAT
1 TTAAATATTAAT
1608212 AATAATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
25 16 0.53
26 12 0.40
27 2 0.07
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
TTAAATATTAATTCTTATAAATTAT
Found at i:1608246 original size:3 final size:3
Alignment explanation
Indices: 1608203--1608229 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1608193 AAATTTTTTA
1608203 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1608230 TTTAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1610410 original size:2 final size:2
Alignment explanation
Indices: 1610403--1610428 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1610393 GGTAGGTGAC
1610403 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
1610429 TGTTCAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1617701 original size:2 final size:2
Alignment explanation
Indices: 1617694--1617718 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1617684 CGAGGAAGTA
1617694 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1617719 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1617723 original size:2 final size:2
Alignment explanation
Indices: 1617718--1617746 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1617708 TCTCTCTCTC
1617718 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1617747 TGCATTTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1625297 original size:41 final size:41
Alignment explanation
Indices: 1625252--1625335 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
1625242 ATAAAGAGAA
1625252 TGCACAGGATAATCAATTCATGCTGTTTTCAGACACCATTT
1 TGCACAGGATAATCAATTCATGCTGTTTTCAGACACCATTT
1625293 TGCACAGGATAATCAATTCATGCTGTTTTCAGACACCATTT
1 TGCACAGGATAATCAATTCATGCTGTTTTCAGACACCATTT
1625334 TG
1 TG
1625336 ATTCTTTATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (41 bp):
TGCACAGGATAATCAATTCATGCTGTTTTCAGACACCATTT
Found at i:1626208 original size:2 final size:2
Alignment explanation
Indices: 1626201--1626228 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1626191 TAATAACCAA
1626201 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
1626229 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1627022 original size:29 final size:28
Alignment explanation
Indices: 1626975--1627029 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
1626965 TTTAAATTTT
*
1626975 TATTTTTTTAATTAATTAAAATTTTAAA
1 TATTTTTTTAATCAATTAAAATTTTAAA
* *
1627003 TATTTATTTTTATCAATTAAATTTTTA
1 TATTT-TTTTAATCAATTAAAATTTTA
1627030 TTAAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
TATTTTTTTAATCAATTAAAATTTTAAA
Found at i:1627194 original size:29 final size:29
Alignment explanation
Indices: 1627127--1627197 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
1627117 ATTTAAAATT
* *
1627127 TTAACTAATTTATAATAAAAATATCAAAAT
1 TTAAATAA-TTATAATAAAAATATCAAAAC
* * *
1627157 TTGATTAATTATAAT-AAAATATTATAAAC
1 TTAAATAATTATAATAAAAATATCA-AAAC
1627186 TTAAATAATTAT
1 TTAAATAATTAT
1627198 TAATTTTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 8 0.24
29 20 0.59
30 6 0.18
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (29 bp):
TTAAATAATTATAATAAAAATATCAAAAC
Found at i:1636195 original size:16 final size:17
Alignment explanation
Indices: 1636163--1636196 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1636153 AAAAATCAAC
1636163 TTTAATAAAATTTATTT
1 TTTAATAAAATTTATTT
*
1636180 TTTATTAAAA-TTATTT
1 TTTAATAAAATTTATTT
1636196 T
1 T
1636197 AAATTATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAATAAAATTTATTT
Found at i:1639116 original size:17 final size:17
Alignment explanation
Indices: 1639090--1639123 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1639080 GATTCTCTGA
1639090 TTTTCCTCTCTTTATTT
1 TTTTCCTCTCTTTATTT
*
1639107 TTTTCTTCTCTTTATTT
1 TTTTCCTCTCTTTATTT
1639124 ATTCATTTAT
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:0.06, C:0.21, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTCCTCTCTTTATTT
Found at i:1643544 original size:10 final size:10
Alignment explanation
Indices: 1643531--1643564 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1643521 TCAAATAAAA
1643531 TTTATATATT
1 TTTATATATT
1643541 TTTAT-TAATT
1 TTTATAT-ATT
1643551 TTTATATATT
1 TTTATATATT
1643561 TTTA
1 TTTA
1643565 AAAATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 1 0.05
10 20 0.91
11 1 0.05
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTATATATT
Found at i:1643570 original size:20 final size:20
Alignment explanation
Indices: 1643531--1643572 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1643521 TCAAATAAAA
**
1643531 TTTATATATTTTTATTAATT
1 TTTATATATTTTTAAAAATT
1643551 TTTATATATTTTTAAAAATT
1 TTTATATATTTTTAAAAATT
1643571 TT
1 TT
1643573 ATAATATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATATATTTTTAAAAATT
Found at i:1643579 original size:20 final size:20
Alignment explanation
Indices: 1643527--1643579 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
1643517 TTAATCAAAT
1643527 AAAA-TTTAT-ATATTTTTA
1 AAAATTTTATAATATTTTTA
**
1643545 TTAATTTT-TATATATTTTTA
1 AAAATTTTATA-ATATTTTTA
1643565 AAAATTTTATAATAT
1 AAAATTTTATAATAT
1643580 AAAATAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
18 3 0.11
19 3 0.11
20 19 0.70
21 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AAAATTTTATAATATTTTTA
Found at i:1643596 original size:16 final size:16
Alignment explanation
Indices: 1643577--1643638 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
1643567 AATTTTATAA
*
1643577 TATAAAATAATAATTT
1 TATATAATAATAATTT
*
1643593 TATATTATAATATATTT
1 TATATAATAATA-ATTT
* *
1643610 AATATATTAA-AATTT
1 TATATAATAATAATTT
1643625 TATATTAA-AATAAT
1 TATA-TAATAATAAT
1643639 ATATAAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
15 9 0.25
16 16 0.44
17 11 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATAATAATAATTT
Found at i:1643651 original size:32 final size:32
Alignment explanation
Indices: 1643576--1643654 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
1643566 AAATTTTATA
*
1643576 ATAT-AAAA-TAATAATTTTATATTATAATAT
1 ATATAAAAATTAATAATTTTATATTAAAATAT
* *
1643606 ATTTAATATATTAA-AATTTTATATTAAAATAAT
1 ATATAA-AAATTAATAATTTTATATTAAAAT-AT
1643639 ATATAAAAATTAATAA
1 ATATAAAAATTAATAA
1643655 ATTAAAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
30 3 0.08
31 1 0.03
32 23 0.59
33 12 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
ATATAAAAATTAATAATTTTATATTAAAATAT
Found at i:1643671 original size:14 final size:14
Alignment explanation
Indices: 1643608--1643667 Score: 79
Period size: 13 Copynumber: 4.4 Consensus size: 14
1643598 TATAATATAT
1643608 TTAATATATTAAAA
1 TTAATATATTAAAA
*
1643622 TT-TTATATTAAAA
1 TTAATATATTAAAA
*
1643635 -TAATATATAAAAA
1 TTAATATATTAAAA
*
1643648 TTAATAAATTAAAA
1 TTAATATATTAAAA
1643662 TTAATA
1 TTAATA
1643668 AATTGAATCG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
12 1 0.03
13 19 0.49
14 19 0.49
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAATATATTAAAA
Found at i:1645077 original size:17 final size:17
Alignment explanation
Indices: 1645055--1645089 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1645045 TTAATTTGTA
1645055 ATTTTTAT-TATTTATAT
1 ATTTTTATATATTT-TAT
1645072 ATTTTTATATATTTTAT
1 ATTTTTATATATTTTAT
1645089 A
1 A
1645090 AATATATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTATATATTTTAT
Found at i:1645101 original size:10 final size:10
Alignment explanation
Indices: 1645063--1645115 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
1645053 TAATTTTTAT
*
1645063 TATTTATATA
1 TATTTAAATA
* *
1645073 TTTTTATATA
1 TATTTAAATA
*
1645083 TTTTATAAATA
1 TATT-TAAATA
1645094 TATTTAAATA
1 TATTTAAATA
*
1645104 AATTTAAATA
1 TATTTAAATA
1645114 TA
1 TA
1645116 AAATAATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 29 0.78
11 8 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TATTTAAATA
Found at i:1647864 original size:3 final size:3
Alignment explanation
Indices: 1647856--1647886 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1647846 AAGGTCCATT
1647856 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1647887 GCTCATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:1649597 original size:13 final size:11
Alignment explanation
Indices: 1649578--1649638 Score: 59
Period size: 11 Copynumber: 5.2 Consensus size: 11
1649568 AAGTCATTTA
1649578 AAATATGATAT
1 AAATATGATAT
1649589 GATAATATGATAT
1 -A-AATATGATAT
1649602 AAATATGATATT
1 AAATATGATA-T
*
1649614 AAAATATAATAT
1 -AAATATGATAT
* *
1649626 AAAAATGACAT
1 AAATATGATAT
1649637 AA
1 AA
1649639 TTTAAAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
11 19 0.45
12 4 0.10
13 19 0.45
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.33
Consensus pattern (11 bp):
AAATATGATAT
Found at i:1649609 original size:24 final size:24
Alignment explanation
Indices: 1649578--1649633 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1649568 AAGTCATTTA
* *
1649578 AAATATGATATGATAATATGATAT
1 AAATATGATATGAAAATATAATAT
*
1649602 AAATATGATATTAAAATATAATAT
1 AAATATGATATGAAAATATAATAT
*
1649626 AAAAATGA
1 AAATATGA
1649634 CATAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (24 bp):
AAATATGATATGAAAATATAATAT
Found at i:1650539 original size:16 final size:15
Alignment explanation
Indices: 1650514--1650543 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1650504 TTCATGTAAG
1650514 AAATTAAACGTTGGC
1 AAATTAAACGTTGGC
1650529 AAATATAAACGTTGG
1 AAAT-TAAACGTTGG
1650544 AACTGAGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.27
Consensus pattern (15 bp):
AAATTAAACGTTGGC
Found at i:1652962 original size:13 final size:13
Alignment explanation
Indices: 1652944--1652968 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1652934 TCAAGTTTGG
1652944 ATATTAAATTTAT
1 ATATTAAATTTAT
1652957 ATATTAAATTTA
1 ATATTAAATTTA
1652969 GATCAAATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATTAAATTTAT
Found at i:1654295 original size:19 final size:19
Alignment explanation
Indices: 1654271--1654312 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1654261 GAAAAAAACA
1654271 CTCTGTTTTTATTT-TCTCT
1 CTCTGTTTTT-TTTATCTCT
*
1654290 CTCTGTTTTTTTTATCTTT
1 CTCTGTTTTTTTTATCTCT
1654309 CTCT
1 CTCT
1654313 CTCTAAACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.05, C:0.21, G:0.05, T:0.69
Consensus pattern (19 bp):
CTCTGTTTTTTTTATCTCT
Found at i:1658839 original size:22 final size:23
Alignment explanation
Indices: 1658796--1658864 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 23
1658786 TAAAAAAACC
* * *
1658796 AATAAAATAAAAAATTA-CAAAT
1 AATAATATTAAAAATTATTAAAT
* *
1658818 ATTAA-ATTTAAAATTATTAAAT
1 AATAATATTAAAAATTATTAAAT
* *
1658840 AATAATATTAAAAAATATTATAT
1 AATAATATTAAAAATTATTAAAT
1658863 AA
1 AA
1658865 ACGGTGTTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
21 9 0.24
22 12 0.32
23 16 0.43
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (23 bp):
AATAATATTAAAAATTATTAAAT
Found at i:1658858 original size:23 final size:22
Alignment explanation
Indices: 1658796--1658864 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
1658786 TAAAAAAACC
* *
1658796 AATAAAATAAAAAAT-TACAAAT
1 AATAAATTAAAAAATAT-TAAAT
* * *
1658818 ATTAAATTTAAAATTATTAAAT
1 AATAAATTAAAAAATATTAAAT
*
1658840 AATAATATTAAAAAATATTATAT
1 AATAA-ATTAAAAAATATTAAAT
1658863 AA
1 AA
1658865 ACGGTGTTTA
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
22 19 0.53
23 17 0.47
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (22 bp):
AATAAATTAAAAAATATTAAAT
Found at i:1660091 original size:15 final size:16
Alignment explanation
Indices: 1660073--1660105 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1660063 AAAATAATAC
1660073 AAATAA-ATGATATAA
1 AAATAATATGATATAA
*
1660088 AAATAATATGATTTAA
1 AAATAATATGATATAA
1660104 AA
1 AA
1660106 TTTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (16 bp):
AAATAATATGATATAA
Found at i:1679300 original size:15 final size:16
Alignment explanation
Indices: 1679272--1679306 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1679262 GTGTTTGTTA
1679272 ATTTATTAAATATTTT
1 ATTTATTAAATATTTT
*
1679288 ATTT-TTAATTATTTT
1 ATTTATTAAATATTTT
1679303 ATTT
1 ATTT
1679307 GGAAAATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTATTAAATATTTT
Found at i:1689230 original size:20 final size:18
Alignment explanation
Indices: 1689194--1689227 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1689184 ATATGAATAA
1689194 CAAAAAAATAAACAACAC
1 CAAAAAAATAAACAACAC
1689212 CAAAAAAATAAA-AACA
1 CAAAAAAATAAACAACA
1689228 ACATGAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.76, C:0.18, G:0.00, T:0.06
Consensus pattern (18 bp):
CAAAAAAATAAACAACAC
Found at i:1693507 original size:93 final size:93
Alignment explanation
Indices: 1693403--1693576 Score: 330
Period size: 93 Copynumber: 1.9 Consensus size: 93
1693393 CATTTCAAAT
* *
1693403 TCATAATTTTTAAATATCAATTTTAATAATATATAAATTAATTTAAAAAATAATCAATCAAAAAT
1 TCATAATTTTTAAATATCAATTTTAATAATATATAAATTAATCTAAAAAATAATCAATCAAAAAC
1693468 TTTATATTTTTATTATAAATTCTTAAAC
66 TTTATATTTTTATTATAAATTCTTAAAC
1693496 TCATAATTTTTAAATATCAATTTTAATAATATATAAATTAATCTAAAAAATAATCAATCAAAAAC
1 TCATAATTTTTAAATATCAATTTTAATAATATATAAATTAATCTAAAAAATAATCAATCAAAAAC
1693561 TTTATATTTTTATTAT
66 TTTATATTTTTATTAT
1693577 CTCAAATTAC
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 79 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (93 bp):
TCATAATTTTTAAATATCAATTTTAATAATATATAAATTAATCTAAAAAATAATCAATCAAAAAC
TTTATATTTTTATTATAAATTCTTAAAC
Found at i:1695499 original size:17 final size:16
Alignment explanation
Indices: 1695479--1695513 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1695469 AAAATCTACT
1695479 AATACAAATTTTATAAG
1 AATA-AAATTTTATAAG
*
1695496 AATAAATTTTTATAAG
1 AATAAAATTTTATAAG
1695512 AA
1 AA
1695514 ATATCACACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (16 bp):
AATAAAATTTTATAAG
Found at i:1697177 original size:27 final size:27
Alignment explanation
Indices: 1697142--1697200 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
1697132 TCGAATTCAT
*
1697142 ATCACGGTGGTCATGCTCATGGATTTC
1 ATCATGGTGGTCATGCTCATGGATTTC
1697169 ATCATGGTGGTCATGCTCATGGATTTC
1 ATCATGGTGGTCATGCTCATGGATTTC
1697196 ATCAT
1 ATCAT
1697201 CACCATCACC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (27 bp):
ATCATGGTGGTCATGCTCATGGATTTC
Found at i:1708379 original size:287 final size:287
Alignment explanation
Indices: 1707850--1708412 Score: 887
Period size: 287 Copynumber: 2.0 Consensus size: 287
1707840 AAGTTTGGTT
* *
1707850 AGTCTTGTGTGAAGTTAGAAGATGAAATGAAAAAGATTACTTAGTCGTCGGAGAAAATATTGACC
1 AGTCTTGTGTGAAGCTAGAAGATGAAATGAAAAAGATTACTTAGTCGTCAGAGAAAATATTGACC
*
1707915 AATGAGATCTTAAGAGATAGTTTTGTATTTTATATGGTTTGTATTTGCATATATAATGATGTATT
66 AATGAGATCTTAAGAGATAGTTTTGTATTTTATATGGTTTGTATTTGCATATATAAAGATGTATT
* * * * *
1707980 ATCAGTTTGATTAAATATATGAATTTTACTTGGTAGATTATTTTATTGAAGAATTTTAGAATGAT
131 ATCAGTTGGATTAAAGATATAAATTTTACTTGATAAATTATTTTATTGAAGAATTTTAGAATGAT
* * * * *
1708045 TAAGAAAGAAGGCTTCGTATTACTTCGAGATTTTCTTTAAGGTAATACGACCGTGTTACGTCTTG
196 TAAAAAAGAAGACTTCATATTACTTCGAGATTTTCTTTAAAGTAATACGACCGTGTTACATCTTG
*
1708110 ATCTCGGGGTGTGACAAAAGTGGTATC
261 ATCTCGGGGCGTGACAAAAGTGGTATC
* * * *
1708137 AGTCTTGTGTGAAGCTAGAAGATGAAATGGAAAATATTACTTAGTTGTCAGAGAAAATGTTGACC
1 AGTCTTGTGTGAAGCTAGAAGATGAAATGAAAAAGATTACTTAGTCGTCAGAGAAAATATTGACC
1708202 AATGAGATCTTAAGAGATAGTTTTGTATTTTATATGGTTTGTATTTGCATATATAAAGATGTATT
66 AATGAGATCTTAAGAGATAGTTTTGTATTTTATATGGTTTGTATTTGCATATATAAAGATGTATT
1708267 ATCAGTTGGATTAAAGATATAAATTTTACTTGATAAATTATTTTATTGAAGAATTTTAGAATGAT
131 ATCAGTTGGATTAAAGATATAAATTTTACTTGATAAATTATTTTATTGAAGAATTTTAGAATGAT
* * * **
1708332 TAAAAAAGAATATTTCATATTACTTTG-GAGTTTT-TTTCAAAGTAATACGACCGTGTTGTATCT
196 TAAAAAAGAAGACTTCATATTACTTCGAGA-TTTTCTTT-AAAGTAATACGACCGTGTTACATCT
1708395 TGATCTCGGGGCGTGACA
259 TGATCTCGGGGCGTGACA
1708413 TTTTTCATCT
Statistics
Matches: 251, Mismatches: 23, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
286 5 0.02
287 246 0.98
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.38
Consensus pattern (287 bp):
AGTCTTGTGTGAAGCTAGAAGATGAAATGAAAAAGATTACTTAGTCGTCAGAGAAAATATTGACC
AATGAGATCTTAAGAGATAGTTTTGTATTTTATATGGTTTGTATTTGCATATATAAAGATGTATT
ATCAGTTGGATTAAAGATATAAATTTTACTTGATAAATTATTTTATTGAAGAATTTTAGAATGAT
TAAAAAAGAAGACTTCATATTACTTCGAGATTTTCTTTAAAGTAATACGACCGTGTTACATCTTG
ATCTCGGGGCGTGACAAAAGTGGTATC
Found at i:1710498 original size:48 final size:48
Alignment explanation
Indices: 1710436--1710531 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
1710426 TGAACATGGT
1710436 AGTTTTCATGGAGATGGCTAGTATTTCAAAACCTACCAAATGGTTCTC
1 AGTTTTCATGGAGATGGCTAGTATTTCAAAACCTACCAAATGGTTCTC
*
1710484 AGTTTTCATGGAGATGGCTAGTATTTCAAAGCCTACCAAATGGTTCTC
1 AGTTTTCATGGAGATGGCTAGTATTTCAAAACCTACCAAATGGTTCTC
1710532 CAACAAGGGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (48 bp):
AGTTTTCATGGAGATGGCTAGTATTTCAAAACCTACCAAATGGTTCTC
Found at i:1721029 original size:14 final size:14
Alignment explanation
Indices: 1720995--1721021 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1720985 TTTTATTAAA
1720995 TGAATTTAAATAAG
1 TGAATTTAAATAAG
1721009 TGAATTTAAATAA
1 TGAATTTAAATAA
1721022 TTTAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (14 bp):
TGAATTTAAATAAG
Found at i:1723349 original size:25 final size:25
Alignment explanation
Indices: 1723315--1723365 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1723305 ACTTCTAATG
1723315 GAATATATTCGCATATGGTTGTATA
1 GAATATATTCGCATATGGTTGTATA
* **
1723340 GAATTTATTCGTTTATGGTTGTATA
1 GAATATATTCGCATATGGTTGTATA
1723365 G
1 G
1723366 TTGTGTTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.45
Consensus pattern (25 bp):
GAATATATTCGCATATGGTTGTATA
Found at i:1725910 original size:8 final size:7
Alignment explanation
Indices: 1725878--1725909 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1725868 CCTTTTTATC
*
1725878 AAAATAA
1 AAAATTA
1725885 AAAATTA
1 AAAATTA
1725892 AAAATTA
1 AAAATTA
1725899 AAAATTA
1 AAAATTA
1725906 AAAA
1 AAAA
1725910 AAGAGTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (7 bp):
AAAATTA
Found at i:1726024 original size:16 final size:16
Alignment explanation
Indices: 1726003--1726034 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1725993 AAAATAATTT
1726003 ATTATAATATTTTTTA
1 ATTATAATATTTTTTA
*
1726019 ATTATAATTTTTTTTA
1 ATTATAATATTTTTTA
1726035 TAAAGTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTATAATATTTTTTA
Found at i:1726368 original size:21 final size:19
Alignment explanation
Indices: 1726338--1726378 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
1726328 TAATAAAAAT
*
1726338 ATAAATATAATAATCTTTTTC
1 ATAAAAATAA-AAT-TTTTTC
1726359 ATAAAAATAAAATTTTTTC
1 ATAAAAATAAAATTTTTTC
1726378 A
1 A
1726379 AAATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 3 0.16
21 9 0.47
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAAAAATAAAATTTTTTC
Found at i:1726700 original size:17 final size:17
Alignment explanation
Indices: 1726678--1726712 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1726668 AAGCTCAAGT
1726678 TAATAGGCATTAGCTCC
1 TAATAGGCATTAGCTCC
1726695 TAATAGGCATTAGCTCC
1 TAATAGGCATTAGCTCC
1726712 T
1 T
1726713 GCGGTCCTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (17 bp):
TAATAGGCATTAGCTCC
Found at i:1735311 original size:5 final size:5
Alignment explanation
Indices: 1735301--1735330 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1735291 TCAATTACTG
1735301 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
1735331 ACATCACCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:1736832 original size:60 final size:60
Alignment explanation
Indices: 1736744--1736871 Score: 238
Period size: 60 Copynumber: 2.1 Consensus size: 60
1736734 CTGGTCCAAG
*
1736744 AAGTGCCAGGATGAATCAGAGACGGTTAATTGGATTGCAATCAACACAAAGCCTTGTCCA
1 AAGTGCCAGGATGAATCAGAGACGGTTAATTGGATTACAATCAACACAAAGCCTTGTCCA
1736804 AAGTGCCAGGATGAATCAGAGACGGTTAATTGGATTACAATCAACACAAAGCCTTGTCCA
1 AAGTGCCAGGATGAATCAGAGACGGTTAATTGGATTACAATCAACACAAAGCCTTGTCCA
*
1736864 AAATGCCA
1 AAGTGCCA
1736872 CAAGCCAGTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (60 bp):
AAGTGCCAGGATGAATCAGAGACGGTTAATTGGATTACAATCAACACAAAGCCTTGTCCA
Found at i:1745774 original size:6 final size:6
Alignment explanation
Indices: 1745763--1745792 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1745753 ATTATTCATG
*
1745763 CTCGAA CTCGAA CTCGAA CTCGGA CTCGAA
1 CTCGAA CTCGAA CTCGAA CTCGAA CTCGAA
1745793 ATATTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (6 bp):
CTCGAA
Found at i:1750902 original size:372 final size:370
Alignment explanation
Indices: 1749833--1751131 Score: 1739
Period size: 372 Copynumber: 3.5 Consensus size: 370
1749823 GCTAAGTCTC
* *
1749833 GTCACGGACCTAAGAAAGAGTCCTGAATCCCACATCAAACATAATAGGAGGATCACTGGGGTATA
1 GTCACGGACCTAAGAAAGAGTCATGAATCCCACATCAAACATAATAGGAGGGTCACTGGGGTATA
* *
1749898 TAAGGGTTCACACCACCTTCGCCTTGTGAGGTACCTTTTGTAAGATAAAATCATGAGGTCAAGGG
66 TAAGGGTTCACACCACCTTCGCCTTGTGAGGTACCTTTTGTAGGATAAAACCATGAGGTCAAGGG
* * * * *
1749963 GGCTAGAGCGGATAATACCTTACAAGGGTG-AAACCGTGGTAGGAA-GCTGATCTGAGACGTCGA
131 GGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGCAGGAAGGCTGATCTGAGACGTCGA
* * * *
1750026 AAGGGTGAATGCTCGGGTC-CCACAGTCGCACGGGTTCAGAGCTTAAGTCTCGATCCGTGACAAG
196 AAGGGTGAATGCTCGGGTCTCGA-AGTCACGCGGGTTCGGAGCTTAAGTCTCGATCCGTGACAAG
** * *
1750090 TGGTATCAGAGCCAGCTTTAAACCGTTTGATCCACGCCCAAGCACCTCGAGAGAGGTAGGCAGGG
260 TGGTATCAGAGCCAGCCCTAAACCGTTCGATCCACG-CCAAGCACCTCGAGGGAGGTAGGCAGGG
*
1750155 TGGCCAGCCTCCGTGACAGGGACGTCACGAGGTTGGGTGCGAGAGAAT
324 TGGCCAGCCTCCGTGAAAGGG-CGTCACGAGGTTGGGTGCGAGAGAAT
* * *
1750203 GTCACGGACCTAAGAAAGAGTCTTGAATCTCACATCGAACATAATAGGAGGGTCACTGGGGTATA
1 GTCACGGACCTAAGAAAGAGTCATGAATCCCACATCAAACATAATAGGAGGGTCACTGGGGTATA
* * **
1750268 TAAGGGTTCACACCACCTTCGCCTTATGAGGTACCTTTTATAGGATAAAACTGTGAGGTC-AGAG
66 TAAGGGTTCACACCACCTTCGCCTTGTGAGGTACCTTTTGTAGGATAAAACCATGAGGTCAAG-G
* * * * *
1750332 GGACCAGAGCGGATAATACCTCACAAGGGGGTGAACCGTGGCAAGAAGGCTGATCTGAGATGTCG
130 GGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGCAGGAAGGCTGATCTGAGACGTCG
* * *
1750397 AAAGGGTGAATGCTCGGGTCTCGGAGCCACGCGGGTTTGGAGCTTAAGTCTCGATCCGTGACAAG
195 AAAGGGTGAATGCTCGGGTCTCGAAGTCACGCGGGTTCGGAGCTTAAGTCTCGATCCGTGACAAG
* * * * *
1750462 TGGTATAAGAACCAGCCCTAAATCATTCGATCCACGTCAAGCACCTCGAGGGAGGTAGGCAGGGT
260 TGGTATCAGAGCCAGCCCTAAACCGTTCGATCCACGCCAAGCACCTCGAGGGAGGTAGGCAGGGT
* * * * *
1750527 GGCCAACCTCCGCGATAAGGGCATCACGATGTTGGGTACGAGAGAAT
325 GGCCAGCCTCCGTGA-AAGGGCGTCACGAGGTTGGGTGCGAGAGAAT
* * * * *
1750574 ATAACGGACCTAA-AGAGGAGTCATGAATCCTACATCAAACATAATATGAGGGTCACTGGGGTAT
1 GTCACGGACCTAAGA-AAGAGTCATGAATCCCACATCAAACATAATAGGAGGGTCACTGGGGTAT
* * * * *
1750638 ATAAGGGTTCACACCACTTTCGTCTTGTGAGGCACCTTTTGTAGGATAAAACCGTGAGGCCAGAG
65 ATAAGGGTTCACACCACCTTCGCCTTGTGAGGTACCTTTTGTAGGATAAAACCATGAGGTCA-AG
* * * * * * *
1750703 GGGGCCAGAACAGACAATACCTCACAAGGGTGTGAATCGTGGC-GGTCAGGCTGATTTGGGACGC
129 GGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGCAGG-AAGGCTGATCTGAGACGT
* * * * * *
1750767 CGAAAGGGTGAATGC-CTGAGTCTCGAAGTCACGCGAGTTCGGAGCTTGAGTCTCGACCCATGAG
193 CGAAAGGGTGAATGCTC-GGGTCTCGAAGTCACGCGGGTTCGGAGCTTAAGTCTCGATCCGTGAC
* * *
1750831 AAGTGGTATCAGAGCTAGCCCTAAACCGTTCGATCCATGCCAAGCACCTCGAGGGAGATAGGCAG
257 AAGTGGTATCAGAGCCAGCCCTAAACCGTTCGATCCACGCCAAGCACCTCGAGGGAGGTAGGCAG
*
1750896 GGTGGCCAGCCTCCGTGACGAGGGCGTCACGAGGTTGGGTGCGAGAGAAT
322 GGTGGCCAGCCTCCGTGA-AAGGGCGTCACGAGGTTGGGTGCGAGAGAAT
* * *
1750946 GTCACGGACTTAAGGAAGAGTCATGAATCCCACATCGAACATAATAGGAGGGTCACTGGGGTATA
1 GTCACGGACCTAAGAAAGAGTCATGAATCCCACATCAAACATAATAGGAGGGTCACTGGGGTATA
* * * ** *
1751011 TAAAGGTTCACACTACTTTCGCCTTGTGAGGTACCTTTTGTAGGATAAAATTATGAGGTCATGGG
66 TAAGGGTTCACACCACCTTCGCCTTGTGAGGTACCTTTTGTAGGATAAAACCATGAGGTCAAGGG
*
1751076 GGCCAGAGCGGACAATACCTCACAAGGGTGTGAATCGTGGCAGGAAGGCTGATCTG
131 GGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGCAGGAAGGCTGATCTG
1751132 GGAACGGACC
Statistics
Matches: 805, Mismatches: 112, Indels: 23
0.86 0.12 0.02
Matches are distributed among these distances:
369 2 0.00
370 144 0.18
371 237 0.29
372 419 0.52
373 3 0.00
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (370 bp):
GTCACGGACCTAAGAAAGAGTCATGAATCCCACATCAAACATAATAGGAGGGTCACTGGGGTATA
TAAGGGTTCACACCACCTTCGCCTTGTGAGGTACCTTTTGTAGGATAAAACCATGAGGTCAAGGG
GGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGCAGGAAGGCTGATCTGAGACGTCGA
AAGGGTGAATGCTCGGGTCTCGAAGTCACGCGGGTTCGGAGCTTAAGTCTCGATCCGTGACAAGT
GGTATCAGAGCCAGCCCTAAACCGTTCGATCCACGCCAAGCACCTCGAGGGAGGTAGGCAGGGTG
GCCAGCCTCCGTGAAAGGGCGTCACGAGGTTGGGTGCGAGAGAAT
Found at i:1751922 original size:213 final size:213
Alignment explanation
Indices: 1751549--1751976 Score: 587
Period size: 213 Copynumber: 2.0 Consensus size: 213
1751539 CGAACATAAT
* *
1751549 AGGAGGGTCACTGGGGTATAAAAGGGTTCACACCACCTTCGTCTTGTGAGACGCCTTTTGTAAGA
1 AGGAGGGTCACTGGGGTATAAAAGGGTTCACACCACCTTCGCCTTGTGAGACACCTTTTGTAAGA
*
1751614 TAAAACCGTGAGGCCAGAGGGGGCCAGAGAGGACAATACCTCACAAGAGTGTGAACCGTAATGAT
66 CAAAACCGTGAGGCCAGAGGGGGCCAGAGAGGACAATACCTCACAAGAGTGTGAACCGTAATGAT
* * * * * * * * *
1751679 CAGGCTGATTCGGGATGCCGGAAGGGTGAATGCCCTCGTCCCAGAGTCGCGTGAGTTCGGAGCTT
131 CAGACTGATTCGGCATGCAGAAAAGGTGAATGCCCGCGTCCCAGAGTCACGCGAATTCGGAGCTT
*
1751744 GAGTCTCGACCCATGACA
196 AAGTCTCGACCCATGACA
* * *
1751762 AGGAGGGTCACTGGGGTATATAAGGGTTCACACCACTTTCGCCTTGTGAGGCACCTTTTGTAAGA
1 AGGAGGGTCACTGGGGTATAAAAGGGTTCACACCACCTTCGCCTTGTGAGACACCTTTTGTAAGA
*
1751827 CAAAACCGTGAGGCCA-AGGGGGCCAGAGCA-GACAATACCTCACAAGGGTGTGAACCGTGACA-
66 CAAAACCGTGAGGCCAGAGGGGGCCAGAG-AGGACAATACCTCACAAGAGTGTGAACCGT-A-AT
* * *
1751889 G-TCAGATTGATTCGAGACAT-CAGAAAAGGTGAATGCCCGGGTCCCAGAGTCACGCGAATTTGG
128 GATCAGACTGATTCG-G-CATGCAGAAAAGGTGAATGCCCGCGTCCCAGAGTCACGCGAATTCGG
*
1751952 AGCTTAAGTCTCGACCCGTGACA
191 AGCTTAAGTCTCGACCCATGACA
1751975 AG
1 AG
1751977 TGGTATCAGA
Statistics
Matches: 189, Mismatches: 21, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
212 50 0.26
213 136 0.72
214 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (213 bp):
AGGAGGGTCACTGGGGTATAAAAGGGTTCACACCACCTTCGCCTTGTGAGACACCTTTTGTAAGA
CAAAACCGTGAGGCCAGAGGGGGCCAGAGAGGACAATACCTCACAAGAGTGTGAACCGTAATGAT
CAGACTGATTCGGCATGCAGAAAAGGTGAATGCCCGCGTCCCAGAGTCACGCGAATTCGGAGCTT
AAGTCTCGACCCATGACA
Found at i:1756615 original size:5 final size:5
Alignment explanation
Indices: 1756605--1756629 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1756595 TCAATTACTG
1756605 TTAAA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA
1756630 ACATCACCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:1769835 original size:15 final size:15
Alignment explanation
Indices: 1769815--1769855 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1769805 ATTTAGATAA
1769815 ATGATGAAATTGATT
1 ATGATGAAATTGATT
*
1769830 ATGATGATATTGATT
1 ATGATGAAATTGATT
*
1769845 ACGATGAAATT
1 ATGATGAAATT
1769856 AAAAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (15 bp):
ATGATGAAATTGATT
Found at i:1788641 original size:21 final size:22
Alignment explanation
Indices: 1788617--1788661 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1788607 CAGTTAAAAA
*
1788617 TTTTATAATTTTTCATA-AATT
1 TTTTATAACTTTTCATACAATT
*
1788638 TTTTATAACTTTTGATACAATT
1 TTTTATAACTTTTCATACAATT
1788660 TT
1 TT
1788662 AATAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTATAACTTTTCATACAATT
Found at i:1789571 original size:21 final size:23
Alignment explanation
Indices: 1789536--1789584 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
1789526 TTATTGTATG
*
1789536 TAAATTTATTTTAATTTTATAT-
1 TAAATTTATTTTAATTATATATA
1789558 TAAATTTA-TTTAATTATATATA
1 TAAATTTATTTTAATTATATATA
1789580 TAAAT
1 TAAAT
1789585 GTAAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TAAATTTATTTTAATTATATATA
Found at i:1801700 original size:25 final size:25
Alignment explanation
Indices: 1801663--1801716 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1801653 TGGTGGGATG
1801663 TTTTTTTGGGTTG-TCATCCACATCT
1 TTTTTTTGGGTTGCT-ATCCACATCT
* *
1801688 TTTTTTTGTGTTGCTGTCCACATCT
1 TTTTTTTGGGTTGCTATCCACATCT
1801713 TTTT
1 TTTT
1801717 ATTGCGTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.09, C:0.19, G:0.15, T:0.57
Consensus pattern (25 bp):
TTTTTTTGGGTTGCTATCCACATCT
Found at i:1803210 original size:51 final size:52
Alignment explanation
Indices: 1803113--1803213 Score: 150
Period size: 52 Copynumber: 2.0 Consensus size: 52
1803103 TATAATCACA
1803113 CAAACGTACTTATTAAGAATATTTTTCCTCTTAAAATTTTTTTTTTGTAAGT
1 CAAACGTACTTATTAAGAATATTTTTCCTCTTAAAATTTTTTTTTTGTAAGT
* * * * *
1803165 CAAACTTACTTATTAAGAATTTTTTTTCTTTTAGAA-TTTTTTTTTGTAA
1 CAAACGTACTTATTAAGAATATTTTTCCTCTTAAAATTTTTTTTTTGTAA
1803214 ATATTTTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 13 0.30
52 31 0.70
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (52 bp):
CAAACGTACTTATTAAGAATATTTTTCCTCTTAAAATTTTTTTTTTGTAAGT
Found at i:1814853 original size:26 final size:26
Alignment explanation
Indices: 1814820--1814876 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
1814810 AAATAATAAT
* * *
1814820 AAAAATTATTGTAGTTGTGATTCAAA
1 AAAAATTATTATAATTATGATTCAAA
*
1814846 AAAAATTATTATAATTATGATTGAAA
1 AAAAATTATTATAATTATGATTCAAA
1814872 AAAAA
1 AAAAA
1814877 ATTAAGTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.35
Consensus pattern (26 bp):
AAAAATTATTATAATTATGATTCAAA
Found at i:1825653 original size:52 final size:52
Alignment explanation
Indices: 1825497--1825653 Score: 185
Period size: 52 Copynumber: 3.0 Consensus size: 52
1825487 TATGACCATA
*
1825497 CAAACTTGCCCATTAAGAATCC-CTCTTCTCTTAGAATTCTTT-TCTTGTAAGT
1 CAAACTTGCCTATTAAGAATCCTCT-TTCTCTTAGAATT-TTTCTCTTGTAAGT
* * * * *
1825549 CAAACTTGCCTATTAAGAATCTTTTTTCCCTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCTCTTTCTCTTAGAATTTTTCTCTTGTAAGT
* * *
1825601 CAAACTTACCTATTAAGAATCCTCTTTCT-TTTGAAATTTTTCTTTTGTAAGT
1 CAAACTTGCCTATTAAGAATCCTCTTTCTCTTAG-AATTTTTCTCTTGTAAGT
1825653 C
1 C
1825654 TTCTTGTCCA
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
51 5 0.06
52 82 0.93
53 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.43
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCTCTTTCTCTTAGAATTTTTCTCTTGTAAGT
Found at i:1825709 original size:11 final size:11
Alignment explanation
Indices: 1825678--1825709 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1825668 GCAATATCTG
*
1825678 ACAAATCTCAA
1 ACAAATCTCTA
1825689 ACAAATCTCTA
1 ACAAATCTCTA
1825700 ACAAATCTCT
1 ACAAATCTCT
1825710 TATGGGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (11 bp):
ACAAATCTCTA
Found at i:1826025 original size:25 final size:25
Alignment explanation
Indices: 1825958--1826026 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
1825948 CACTTCCCAT
*
1825958 ATCTCGAACCGTCAACTC-TTCCAC
1 ATCTCGAACCTTCAACTCTTTCCAC
* **
1825982 GTCTCGAACCTTCGGCTCTTTCCAC
1 ATCTCGAACCTTCAACTCTTTCCAC
* *
1826007 ATCTTGAATCTTCAACTCTT
1 ATCTCGAACCTTCAACTCTT
1826027 CTTACGTTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 14 0.40
25 21 0.60
ACGTcount: A:0.20, C:0.36, G:0.10, T:0.33
Consensus pattern (25 bp):
ATCTCGAACCTTCAACTCTTTCCAC
Found at i:1826669 original size:52 final size:51
Alignment explanation
Indices: 1826583--1826739 Score: 206
Period size: 52 Copynumber: 3.0 Consensus size: 51
1826573 TATGACCATA
* * * *
1826583 CAAACTTGCCCATTAAGAATCCCTCTTCTCTTAGAATTCTTCTCTTGTAAGT
1 CAAACTTGCCTATTAAGAAT-CTTTTTCTTTTAGAATTCTTCTCTTGTAAGT
*
1826635 CAAACTTGCCTATTAAGAATCTTTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCTTTTT-CTTTTAGAATTCTTCTCTTGTAAGT
* * * *
1826687 CAAACTTACCTATTAAGAATCTTCTTTTTTTTGGAATTCTTCTTTTGTAAGT
1 CAAACTTGCCTATTAAGAATCTT-TTTCTTTTAGAATTCTTCTCTTGTAAGT
1826739 C
1 C
1826740 TTCTTGTCCA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 4 0.04
52 86 0.92
53 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.44
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCTTTTTCTTTTAGAATTCTTCTCTTGTAAGT
Done.