Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007068.1 Hibiscus syriacus cultivar Beakdansim tig00018390_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: 617230
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:563664 original size:23 final size:23
Alignment explanation
Indices: 563609--563664 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
563599 CGAAACCTCG
563609 ATCAGGAAAATAAAGTTAAAAAA
1 ATCAGGAAAATAAAGTTAAAAAA
* * * *
563632 ATCTGCAAAATAACGTTCAAAAA
1 ATCAGGAAAATAAAGTTAAAAAA
*
563655 ATGAGGAAAA
1 ATCAGGAAAA
563665 GGAATACCAC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.18
Consensus pattern (23 bp):
ATCAGGAAAATAAAGTTAAAAAA
Found at i:564017 original size:2 final size:2
Alignment explanation
Indices: 564010--564045 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
564000 ATATGCATGC
564010 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
564046 TGATTTAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:564242 original size:29 final size:29
Alignment explanation
Indices: 564209--564285 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 29
564199 ATTTTTAATC
* *
564209 TAAGTAATTAAAGTATTTTTTTATCAAAA
1 TAAGTACTTAAAGTATTTTTTGATCAAAA
*
564238 TAAGTACTTAAAGTTATCATTTTGATCAAAA
1 TAAGTACTTAAAG-TAT-TTTTTGATCAAAA
564269 T-AGATACTTAAAGTATT
1 TAAG-TACTTAAAGTATT
564286 AAATCTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 12 0.29
30 8 0.20
31 21 0.51
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (29 bp):
TAAGTACTTAAAGTATTTTTTGATCAAAA
Found at i:565568 original size:48 final size:49
Alignment explanation
Indices: 565495--565592 Score: 180
Period size: 48 Copynumber: 2.0 Consensus size: 49
565485 TGATAATTAA
*
565495 TTTCAGTGTTGAATTGAATAACATTAATGAGTAATGGATAACATGTGGG
1 TTTCAGTGTTGAATTAAATAACATTAATGAGTAATGGATAACATGTGGG
565544 TTTCAGTGTT-AATTAAATAACATTAATGAGTAATGGATAACATGTGGG
1 TTTCAGTGTTGAATTAAATAACATTAATGAGTAATGGATAACATGTGGG
565592 T
1 T
565593 CTTCGTCGGT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 38 0.79
49 10 0.21
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (49 bp):
TTTCAGTGTTGAATTAAATAACATTAATGAGTAATGGATAACATGTGGG
Found at i:566628 original size:19 final size:20
Alignment explanation
Indices: 566589--566629 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
566579 CGGTTATACT
* *
566589 ATCCGGTTTTAAAATATCCG
1 ATCCGGTTTTAAAAAAACCG
566609 ATCCGG-TTTAAAAAAACCG
1 ATCCGGTTTTAAAAAAACCG
566628 AT
1 AT
566630 TTTCCCCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Consensus pattern (20 bp):
ATCCGGTTTTAAAAAAACCG
Found at i:568522 original size:25 final size:22
Alignment explanation
Indices: 568490--568542 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
568480 AGACATCGAC
*
568490 AAATAATTGATCTTAAATAATATAA
1 AAATAATT--TCTTAAAAAAT-TAA
*
568515 TAATAATTTCTTAAAAAATTAA
1 AAATAATTTCTTAAAAAATTAA
568537 AAATAA
1 AAATAA
568543 CATTAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 8 0.32
23 10 0.40
25 7 0.28
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
AAATAATTTCTTAAAAAATTAA
Found at i:568597 original size:14 final size:15
Alignment explanation
Indices: 568572--568600 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
568562 TACATATTTT
568572 TTTTATTAAATTCTC
1 TTTTATTAAATTCTC
568587 TTTTA-TAAATTCTC
1 TTTTATTAAATTCTC
568601 ATCAAATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.14, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTATTAAATTCTC
Found at i:572781 original size:56 final size:56
Alignment explanation
Indices: 572720--572918 Score: 283
Period size: 56 Copynumber: 3.6 Consensus size: 56
572710 CAGGGCCCCA
* *
572720 AAAAATAGGGGCCCCGAAATCGAATATATCTATCAGTTGTTGCCATTAATAAGCAT
1 AAAAATAAGGGCCCCGAAATCGAATATATCTATCAGTTGTTGCCATTAAAAAGCAT
* * * * *
572776 AAAAATAAGGTCCCCGAAATCGAGTATATCTATCCGTTATTGCCATTAAGAAGCAT
1 AAAAATAAGGGCCCCGAAATCGAATATATCTATCAGTTGTTGCCATTAAAAAGCAT
* * *
572832 AAAAATAGGGGCCCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAAAAACAT
1 AAAAATAAGGGCCCCGAAATCGAATATATCTATCAGTTGTTGCCATTAAAAAGCAT
* *
572888 AAAAATAAGGGTCCAG-AATCGAATATATCTA
1 AAAAATAAGGGCCCCGAAATCGAATATATCTA
572919 AAAAAATAGG
Statistics
Matches: 127, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
55 14 0.11
56 113 0.89
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.26
Consensus pattern (56 bp):
AAAAATAAGGGCCCCGAAATCGAATATATCTATCAGTTGTTGCCATTAAAAAGCAT
Found at i:573491 original size:16 final size:16
Alignment explanation
Indices: 573470--573725 Score: 113
Period size: 16 Copynumber: 16.0 Consensus size: 16
573460 AACAAGTGTG
*
573470 AGGTCATTCGATCATT
1 AGGTCATTCGGTCATT
* *
573486 AGGTCACTCGATCATT
1 AGGTCATTCGGTCATT
* *
573502 AAGTCATTTGGTCATT
1 AGGTCATTCGGTCATT
* * **
573518 TGGACATTTAGTCATTT
1 AGGTCATTCGGTCA-TT
* * *
573535 A-GACATCCGGTCTTT
1 AGGTCATTCGGTCATT
** ***
573550 AAATCATTCAACCATT
1 AGGTCATTCGGTCATT
* * *
573566 CA-GTCGTTAGGTCATC
1 -AGGTCATTCGGTCATT
*
573582 AGGTCATTCGATCATT
1 AGGTCATTCGGTCATT
* *
573598 -GAGTCATTTGGTCACT
1 AG-GTCATTCGGTCATT
* ** *
573614 CGACCATTAGGTCATT
1 AGGTCATTCGGTCATT
* * **
573630 CGATCATTCAATCATT
1 AGGTCATTCGGTCATT
* *
573646 AAGTCATTCGATCATT
1 AGGTCATTCGGTCATT
*
573662 AGGTCATTAGGTCATT
1 AGGTCATTCGGTCATT
* *
573678 AAGTCATTAGGTCATT
1 AGGTCATTCGGTCATT
*
573694 AGATCATTCGGTCATT
1 AGGTCATTCGGTCATT
* *
573710 AGATCATTTGGTCATT
1 AGGTCATTCGGTCATT
573726 CAGTCATTTT
Statistics
Matches: 179, Mismatches: 55, Indels: 12
0.73 0.22 0.05
Matches are distributed among these distances:
15 5 0.03
16 170 0.95
17 4 0.02
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (16 bp):
AGGTCATTCGGTCATT
Found at i:573604 original size:8 final size:9
Alignment explanation
Indices: 573584--573733 Score: 57
Period size: 8 Copynumber: 18.7 Consensus size: 9
573574 AGGTCATCAG
573584 GTCATTCGA
1 GTCATTCGA
573593 -TCATT-GA
1 GTCATTCGA
*
573600 GTCATTTG-
1 GTCATTCGA
*
573608 GTCACTCGA
1 GTCATTCGA
* *
573617 -CCATTAG-
1 GTCATTCGA
573624 GTCATTCGA
1 GTCATTCGA
573633 -TCATTC-A
1 GTCATTCGA
* *
573640 ATCATT-AA
1 GTCATTCGA
573648 GTCATTCGA
1 GTCATTCGA
*
573657 -TCATTAG-
1 GTCATTCGA
*
573664 GTCATTAG-
1 GTCATTCGA
*
573672 GTCATT-AA
1 GTCATTCGA
*
573680 GTCATTAG-
1 GTCATTCGA
*
573688 GTCATTAGA
1 GTCATTCGA
573697 -TCATTCG-
1 GTCATTCGA
*
573704 GTCATTAGA
1 GTCATTCGA
*
573713 -TCATTTG-
1 GTCATTCGA
573720 GTCATTC-A
1 GTCATTCGA
573728 GTCATT
1 GTCATT
573734 TTTCCATTCC
Statistics
Matches: 109, Mismatches: 16, Indels: 33
0.69 0.10 0.21
Matches are distributed among these distances:
7 3 0.03
8 104 0.95
9 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (9 bp):
GTCATTCGA
Found at i:573626 original size:40 final size:40
Alignment explanation
Indices: 573577--573733 Score: 165
Period size: 40 Copynumber: 3.9 Consensus size: 40
573567 AGTCGTTAGG
* * * *
573577 TCATCAGGTCATTCGATCATTGAGTCATTTGGTCACTCGA
1 TCATTAGGTCATTAGATCATTGAGTCATTAGGTCATTCGA
* * * * *
573617 CCATTAGGTCATTCGATCATTCAATCATTAAGTCATTCGA
1 TCATTAGGTCATTAGATCATTGAGTCATTAGGTCATTCGA
* * *
573657 TCATTAGGTCATTAGGTCATTAAGTCATTAGGTCATTAGA
1 TCATTAGGTCATTAGATCATTGAGTCATTAGGTCATTCGA
*
573697 TCATTCGGTCATTAGATCATTTG-GTCATTCA-GTCATT
1 TCATTAGGTCATTAGATCA-TTGAGTCATT-AGGTCATT
573734 TTTCCATTCC
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
40 95 0.97
41 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (40 bp):
TCATTAGGTCATTAGATCATTGAGTCATTAGGTCATTCGA
Found at i:573724 original size:24 final size:24
Alignment explanation
Indices: 573572--573733 Score: 141
Period size: 24 Copynumber: 6.8 Consensus size: 24
573562 CATTCAGTCG
*
573572 TTAGGTCA-TCAGGTCATTCGATCA
1 TTAGGTCATTC-GGTCATTAGATCA
* * * *
573596 TT-GAGTCATTTGGTCACTCGACCA
1 TTAG-GTCATTCGGTCATTAGATCA
*
573620 TTAGGTCATTCGATCATTCA-ATCA
1 TTAGGTCATTCGGTCATT-AGATCA
* * *
573644 TTAAGTCATTCGATCATTAGGTCA
1 TTAGGTCATTCGGTCATTAGATCA
** *
573668 TTAGGTCATTAAGTCATTAGGTCA
1 TTAGGTCATTCGGTCATTAGATCA
*
573692 TTAGATCATTCGGTCATTAGATCA
1 TTAGGTCATTCGGTCATTAGATCA
* *
573716 TTTGGTCATTCAGTCATT
1 TTAGGTCATTCGGTCATT
573734 TTTCCATTCC
Statistics
Matches: 112, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.02
24 108 0.96
25 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (24 bp):
TTAGGTCATTCGGTCATTAGATCA
Found at i:573765 original size:24 final size:24
Alignment explanation
Indices: 573641--573765 Score: 103
Period size: 24 Copynumber: 5.2 Consensus size: 24
573631 GATCATTCAA
573641 TCATTA-AGTCATTCGA-TCATTAGG
1 TCATTAGA-TCATTC-AGTCATTAGG
* *
573665 TCATTAGGTCATTAAGTCATTAGG
1 TCATTAGATCATTCAGTCATTAGG
* *
573689 TCATTAGATCATTCGGTCATTAGA
1 TCATTAGATCATTCAGTCATTAGG
* * **
573713 TCATTTGGTCATTCAGTCATT-TT
1 TCATTAGATCATTCAGTCATTAGG
** *
573736 TCCATTCCATCATTCAGCCATTAGG
1 T-CATTAGATCATTCAGTCATTAGG
573761 TCATT
1 TCATT
573766 TTATATCCCA
Statistics
Matches: 80, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
23 2 0.03
24 77 0.96
25 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (24 bp):
TCATTAGATCATTCAGTCATTAGG
Found at i:577439 original size:49 final size:49
Alignment explanation
Indices: 577367--577467 Score: 193
Period size: 49 Copynumber: 2.1 Consensus size: 49
577357 GAAAGATAAT
577367 TGGAGAATCGTGGCGGTGCAAGGAAGCCGCCATGAAAGAGGGTTCTATG
1 TGGAGAATCGTGGCGGTGCAAGGAAGCCGCCATGAAAGAGGGTTCTATG
*
577416 TGGAGAATCGTGGCGGTGCAAGGAAGCCGCCATGAAAGAGGGTTTTATG
1 TGGAGAATCGTGGCGGTGCAAGGAAGCCGCCATGAAAGAGGGTTCTATG
577465 TGG
1 TGG
577468 GAAGCGGTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.26, C:0.15, G:0.40, T:0.20
Consensus pattern (49 bp):
TGGAGAATCGTGGCGGTGCAAGGAAGCCGCCATGAAAGAGGGTTCTATG
Found at i:578563 original size:20 final size:20
Alignment explanation
Indices: 578538--578578 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
578528 TTTAAAATAC
578538 TAAAATAATT-TATTTATAAT
1 TAAAAT-ATTATATTTATAAT
*
578558 TAAAATATTATTTTTATAAT
1 TAAAATATTATATTTATAAT
578578 T
1 T
578579 TTATTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAAAATATTATATTTATAAT
Found at i:578570 original size:22 final size:21
Alignment explanation
Indices: 578493--578572 Score: 56
Period size: 22 Copynumber: 3.6 Consensus size: 21
578483 AACAATAAAT
*
578493 AATATTATTTATCATAAAACTTAA
1 AATATTATTT-T-TTAAAA-TTAA
*
578517 TATTATTATTTTTTAAAATACTAA
1 -AATATTATTTTTTAAAAT--TAA
*
578541 AATA--ATTTATTTATAATTAA
1 AATATTATTT-TTTAAAATTAA
578561 AATATTATTTTT
1 AATATTATTTTT
578573 ATAATTTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
20 7 0.15
21 6 0.13
22 12 0.26
23 8 0.17
24 4 0.09
25 9 0.20
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTATTTTTTAAAATTAA
Found at i:578720 original size:23 final size:23
Alignment explanation
Indices: 578671--578735 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
578661 GTGTTATATT
* **
578671 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
578694 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
*
578717 ATATTATTAGATATTATTA
1 ATATT-TTAAATA-TATTA
578736 GTTTTGAATG
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
23 23 0.72
24 6 0.19
25 3 0.09
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:579440 original size:20 final size:20
Alignment explanation
Indices: 579415--579455 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
579405 TTTAAAATAC
579415 TAAAATAATT-TATTTATAAT
1 TAAAAT-ATTATATTTATAAT
*
579435 TAAAATATTATTTTTATAAT
1 TAAAATATTATATTTATAAT
579455 T
1 T
579456 TTATTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAAAATATTATATTTATAAT
Found at i:579447 original size:22 final size:21
Alignment explanation
Indices: 579370--579449 Score: 56
Period size: 22 Copynumber: 3.6 Consensus size: 21
579360 AACAATAAAT
*
579370 AATATTATTTATCATAAAACTTAA
1 AATATTATTT-T-TTAAAA-TTAA
*
579394 TATTATTATTTTTTAAAATACTAA
1 -AATATTATTTTTTAAAAT--TAA
*
579418 AATA--ATTTATTTATAATTAA
1 AATATTATTT-TTTAAAATTAA
579438 AATATTATTTTT
1 AATATTATTTTT
579450 ATAATTTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
20 7 0.15
21 6 0.13
22 12 0.26
23 8 0.17
24 4 0.09
25 9 0.20
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTATTTTTTAAAATTAA
Found at i:579597 original size:23 final size:23
Alignment explanation
Indices: 579548--579612 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
579538 GTGTTATATT
* **
579548 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
579571 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
*
579594 ATATTATTAGATATTATTA
1 ATATT-TTAAATA-TATTA
579613 GTTTTGAATG
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
23 23 0.72
24 6 0.19
25 3 0.09
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:579803 original size:877 final size:877
Alignment explanation
Indices: 577983--580484 Score: 4912
Period size: 877 Copynumber: 2.9 Consensus size: 877
577973 ATGGTGGACA
577983 AAAATTTTAAAAATGAAGGGTAAAATATGTATTTAGTCACCCAATAATTTTTATAATTTTTTGGT
1 AAAATTTTAAAAATGAAGGGTAAAATATGTATTTAGTCACCCAATAATTTTTATAATTTTTTGGT
578048 CATCATACTTTTTCCCCTCAAAATCATACTTAAATTTACGTTTCAGTTATCCATGGTTAAAAATA
66 CATCATACTTTTTCCCCTCAAAATCATACTTAAATTTACGTTTCAGTTATCCATGGTTAAAAATA
578113 ATAATTGTTGATATAACAATTTTTTTAATGATAATATGAGATTATCTTATAGTCGCACATTATCA
131 ATAATTGTTGATATAACAATTTTTTTAATGATAATATGAGATTATCTTATAGTCGCACATTATCA
578178 TTATCGTTAAATTTTTAACGATAATTAACCAAAACGTAACTTGAGGTATGATTTTGAAAAAATAA
196 TTATCGTTAAATTTTTAACGATAATTAACCAAAACGTAACTTGAGGTATGATTTTGAAAAAATAA
578243 TTAAATGACCTAAACGGAACCACAAGAATAGTTGGATGATTAAATACTCAGATTACCCAAAAATC
261 TTAAATGACCTAAACGGAACCACAAGAATAGTTGGATGATTAAATACTCAGATTACCCAAAAATC
578308 AATGTGGGAGGGAATCTTATTTGGATTACATTCCAATTTACAAAGTAAAAGGATGAAATAGTATT
326 AATGTGGGAGGGAATCTTATTTGGATTACATTCCAATTTACAAAGTAAAAGGATGAAATAGTATT
578373 TTCTGAAAAAATATATTTTGGAAAACGTTTTATGATATTTGAAAGATGTTTAAATCTTTTTTCTA
391 TTCTGAAAAAATATATTTTGGAAAACGTTTTATGATATTTGAAAGATGTTTAAATCTTTTTTCTA
578438 CTAGTTGATTA-TTTTTAT-AAAAAATTATTTATTATAAATATTAAAAACAATAAATAATATTAT
456 CTAGTTGATTATTTTTTATAAAAAAATTATTTATTATAAATATTAAAAACAATAAATAATATTAT
578501 TTATCATAAAACTTAATATTATTATTTTTTAAAATACTAAAATAATTTATTTATAATTAAAATAT
521 TTATCATAAAACTTAATATTATTATTTTTTAAAATACTAAAATAATTTATTTATAATTAAAATAT
578566 TATTTTTATAATTTTATTATTAAAAATATTAATATTGATATATTTTATTGAAATAAAAATATTAT
586 TATTTTTATAATTTTATTATTAAAAATATTAATATTGATATATTTTATTGAAATAAAAATATTAT
578631 CAATTATATTAATTATTTATTAAAGTAACAGTGTTATATTATATTTTAAAAATATTAATTAGTAT
651 CAATTATATTAATTATTTATTAAAGTAACAGTGTTATATTATATTTTAAAAATATTAATTAGTAT
578696 ATTTTAAATATCTTTATTAAAATATTATTAGATATTATTAGTTTTGAATGAAAAAACCATTTAAT
716 ATTTTAAATATCTTTATTAAAATATTATTAGATATTATTAGTTTTGAATGAAAAAACCATTTAAT
578761 AAATATATATGACTTGAACCTAAAATAATCAAATTCAAATGAACTTGAAGTGATATTAATTTAGT
781 AAATATATATGACTTGAACCTAAAATAATCAAATTCAAATGAACTTGAAGTGATATTAATTTAGT
578826 CAATCCATTTAATATTATTGTATATACTTACT
846 CAATCCATTTAATATTATTGTATATACTTACT
578858 AAAATTTTAAAAATGAAGGGTAAAATATGTATTTAGTCACCCAATAATTTTTATAATTTTTTGGT
1 AAAATTTTAAAAATGAAGGGTAAAATATGTATTTAGTCACCCAATAATTTTTATAATTTTTTGGT
578923 CATCATACTTTTTCCCCTCAAAATCATACTTAAATTTACGTTTCAGTTATCCATGGTTAAAAATA
66 CATCATACTTTTTCCCCTCAAAATCATACTTAAATTTACGTTTCAGTTATCCATGGTTAAAAATA
578988 ATAATTGTTGATATAACAATTTTTTTAATGATAATATGAGATTATCTTATAGTCGCACATTATCA
131 ATAATTGTTGATATAACAATTTTTTTAATGATAATATGAGATTATCTTATAGTCGCACATTATCA
579053 TTATCGTTAAATTTTTAACGATAATTAACCAAAACGTAACTTGAGGTATGATTTTGAAAAAATAA
196 TTATCGTTAAATTTTTAACGATAATTAACCAAAACGTAACTTGAGGTATGATTTTGAAAAAATAA
579118 TTAAATGACCTAAACGGAACCACAAGAATAGTTGGATGATTAAATACTCAGATTACCCAAAAATC
261 TTAAATGACCTAAACGGAACCACAAGAATAGTTGGATGATTAAATACTCAGATTACCCAAAAATC
579183 AATGTGGGAGGGAATCTTATTTGGATTACATTCCAATTTACAAAGTAAAAGGATGAAATAGTATT
326 AATGTGGGAGGGAATCTTATTTGGATTACATTCCAATTTACAAAGTAAAAGGATGAAATAGTATT
579248 TTCTGAAAAAATATATTTTGGAAAACGTTTTATGATATTTGAAAGATGTTTAAATCTTTTTTCTA
391 TTCTGAAAAAATATATTTTGGAAAACGTTTTATGATATTTGAAAGATGTTTAAATCTTTTTTCTA
579313 CTAGTTGATTATTTTTTATAAAAAAATTATTTATTATAAATATTAAAAACAATAAATAATATTAT
456 CTAGTTGATTATTTTTTATAAAAAAATTATTTATTATAAATATTAAAAACAATAAATAATATTAT
579378 TTATCATAAAACTTAATATTATTATTTTTTAAAATACTAAAATAATTTATTTATAATTAAAATAT
521 TTATCATAAAACTTAATATTATTATTTTTTAAAATACTAAAATAATTTATTTATAATTAAAATAT
579443 TATTTTTATAATTTTATTATTAAAAATATTAATATTGATATATTTTATTGAAATAAAAATATTAT
586 TATTTTTATAATTTTATTATTAAAAATATTAATATTGATATATTTTATTGAAATAAAAATATTAT
579508 CAATTATATTAATTATTTATTAAAGTAACAGTGTTATATTATATTTTAAAAATATTAATTAGTAT
651 CAATTATATTAATTATTTATTAAAGTAACAGTGTTATATTATATTTTAAAAATATTAATTAGTAT
579573 ATTTTAAATATCTTTATTAAAATATTATTAGATATTATTAGTTTTGAATGAAAAAACCATTTAAT
716 ATTTTAAATATCTTTATTAAAATATTATTAGATATTATTAGTTTTGAATGAAAAAACCATTTAAT
579638 AAATATATATGACTTGAACCTAAAATAATCAAATTCAAATGAACTTGAAGTGATATTAATTTAGT
781 AAATATATATGACTTGAACCTAAAATAATCAAATTCAAATGAACTTGAAGTGATATTAATTTAGT
579703 CAATCCATTTAATATTATTGTATATACTTACT
846 CAATCCATTTAATATTATTGTATATACTTACT
579735 AAAATTTTAAAAATGAAGGGTAAAATATGTATTTAGTCACCCAATAATTTTTATAATTTTTTGGT
1 AAAATTTTAAAAATGAAGGGTAAAATATGTATTTAGTCACCCAATAATTTTTATAATTTTTTGGT
579800 CATCATACTTTTTCCCCTCAAAATCATACTTAAATTTACGTTTCAGTTATCCATGGTTAAAAATA
66 CATCATACTTTTTCCCCTCAAAATCATACTTAAATTTACGTTTCAGTTATCCATGGTTAAAAATA
579865 ATAATTGTTGATATAACAATTTTTTTAATGATAATATGAGATTATCTTATAGTCGCACATTATCA
131 ATAATTGTTGATATAACAATTTTTTTAATGATAATATGAGATTATCTTATAGTCGCACATTATCA
579930 TTATCGTTAAATTTTTAACGATAATTAACCAAAACGTAACTTGAGGTATGATTTTGAAAAAATAA
196 TTATCGTTAAATTTTTAACGATAATTAACCAAAACGTAACTTGAGGTATGATTTTGAAAAAATAA
579995 TTAAATGACCTAAACGGAACCACAAGAATAGTTGGATGATTAAATA---AGATTACCCAAAAATC
261 TTAAATGACCTAAACGGAACCACAAGAATAGTTGGATGATTAAATACTCAGATTACCCAAAAATC
580057 AATGTGGGAGGGAATCTTATTTGGATTACATTCCAATTTACAAAGTAAAAGGATGAAATAGTATT
326 AATGTGGGAGGGAATCTTATTTGGATTACATTCCAATTTACAAAGTAAAAGGATGAAATAGTATT
*
580122 TTCTGAAAAAATATATTTTGGAAAACGTTTTATGATATTTGAAAGATGTTTAAATCTTTTTTCCA
391 TTCTGAAAAAATATATTTTGGAAAACGTTTTATGATATTTGAAAGATGTTTAAATCTTTTTTCTA
580187 CTAGTTGATTATTTTTT-TAAAAAAAATTATTTATTATAAATATTAAAAACAATAAATAATATTA
456 CTAGTTGATTATTTTTTAT-AAAAAAATTATTTATTATAAATATTAAAAACAATAAATAATATTA
* *
580251 TTTATCATAAAACTTAATATTATTATTTTTAAAAATACTAAAATAATTTATTTATTATTAAAATA
520 TTTATCATAAAACTTAATATTATTATTTTTTAAAATACTAAAATAATTTATTTATAATTAAAATA
580316 TTATTTTTATAATTTTATTATTAAAAATATTAATATTGATATATTTTATTGAAATAAAAATATTA
585 TTATTTTTATAATTTTATTATTAAAAATATTAATATTGATATATTTTATTGAAATAAAAATATTA
580381 TCAATTATATTAATTATTTATTAAAGTAACAGTGTTATATTATATTTTAAAAATATTAATTAGTA
650 TCAATTATATTAATTATTTATTAAAGTAACAGTGTTATATTATATTTTAAAAATATTAATTAGTA
580446 TATTTTAAATATCTTTATTAAAATATTATTAG-T-TTATTA
715 TATTTTAAATATCTTTATTAAAATATTATTAGATATTATTA
580485 TAATATTATT
Statistics
Matches: 1621, Mismatches: 3, Indels: 9
0.99 0.00 0.01
Matches are distributed among these distances:
872 6 0.00
873 2 0.00
874 432 0.27
875 466 0.29
876 7 0.00
877 708 0.44
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (877 bp):
AAAATTTTAAAAATGAAGGGTAAAATATGTATTTAGTCACCCAATAATTTTTATAATTTTTTGGT
CATCATACTTTTTCCCCTCAAAATCATACTTAAATTTACGTTTCAGTTATCCATGGTTAAAAATA
ATAATTGTTGATATAACAATTTTTTTAATGATAATATGAGATTATCTTATAGTCGCACATTATCA
TTATCGTTAAATTTTTAACGATAATTAACCAAAACGTAACTTGAGGTATGATTTTGAAAAAATAA
TTAAATGACCTAAACGGAACCACAAGAATAGTTGGATGATTAAATACTCAGATTACCCAAAAATC
AATGTGGGAGGGAATCTTATTTGGATTACATTCCAATTTACAAAGTAAAAGGATGAAATAGTATT
TTCTGAAAAAATATATTTTGGAAAACGTTTTATGATATTTGAAAGATGTTTAAATCTTTTTTCTA
CTAGTTGATTATTTTTTATAAAAAAATTATTTATTATAAATATTAAAAACAATAAATAATATTAT
TTATCATAAAACTTAATATTATTATTTTTTAAAATACTAAAATAATTTATTTATAATTAAAATAT
TATTTTTATAATTTTATTATTAAAAATATTAATATTGATATATTTTATTGAAATAAAAATATTAT
CAATTATATTAATTATTTATTAAAGTAACAGTGTTATATTATATTTTAAAAATATTAATTAGTAT
ATTTTAAATATCTTTATTAAAATATTATTAGATATTATTAGTTTTGAATGAAAAAACCATTTAAT
AAATATATATGACTTGAACCTAAAATAATCAAATTCAAATGAACTTGAAGTGATATTAATTTAGT
CAATCCATTTAATATTATTGTATATACTTACT
Found at i:580332 original size:28 final size:31
Alignment explanation
Indices: 580267--580380 Score: 94
Period size: 28 Copynumber: 3.7 Consensus size: 31
580257 ATAAAACTTA
* * * *
580267 ATATTATTATTTTTAAAAATACTAA-AATAAT
1 ATATT-TTATTATTAAAAATATTAATATTGAT
* * *
580298 TTA-TTTATTATT-AAAATATT-ATTTTTAT
1 ATATTTTATTATTAAAAATATTAATATTGAT
580326 A-ATTTTATTATTAAAAATATTAATATTGAT
1 ATATTTTATTATTAAAAATATTAATATTGAT
*
580356 ATATTTTATTGAAATAAAAATATTA
1 ATATTTTATT--ATTAAAAATATTA
580381 TCAATTATAT
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
27 2 0.03
28 19 0.29
29 15 0.23
30 8 0.12
31 10 0.15
33 12 0.18
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (31 bp):
ATATTTTATTATTAAAAATATTAATATTGAT
Found at i:580333 original size:14 final size:14
Alignment explanation
Indices: 580301--580341 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
580291 AAATAATTTA
580301 TTTATTATTAAAAT
1 TTTATTATTAAAAT
* * *
580315 ATTATTTTTATAAT
1 TTTATTATTAAAAT
580329 TTTATTATTAAAA
1 TTTATTATTAAAA
580342 ATATTAATAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATTATTAAAAT
Found at i:580337 original size:31 final size:30
Alignment explanation
Indices: 580301--580380 Score: 92
Period size: 33 Copynumber: 2.6 Consensus size: 30
580291 AAATAATTTA
* *
580301 TTTATTATT-AAAATATT-ATTTTTATAAT
1 TTTATTATTAAAAATATTAATATTGATAAT
580329 TTTATTATTAAAAATATTAATATTGATATAT
1 TTTATTATTAAAAATATTAATATTGATA-AT
*
580360 TTTATTGAAATAAAAATATTA
1 TTTATT--ATTAAAAATATTA
580381 TCAATTATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
28 9 0.20
29 8 0.18
30 7 0.16
31 8 0.18
33 12 0.27
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (30 bp):
TTTATTATTAAAAATATTAATATTGATAAT
Found at i:580471 original size:23 final size:23
Alignment explanation
Indices: 580422--580472 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
580412 GTGTTATATT
**
580422 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
580445 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
580468 ATATT
1 ATATT
580473 ATTAGTTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:580483 original size:19 final size:19
Alignment explanation
Indices: 580459--580495 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
580449 TTTAAATATC
580459 TTTATTAAAATATTATTAG
1 TTTATTAAAATATTATTAG
*
580478 TTTATTATAATATTATTA
1 TTTATTAAAATATTATTA
580496 AATATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTATTAAAATATTATTAG
Found at i:580528 original size:19 final size:18
Alignment explanation
Indices: 580460--580528 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 18
580450 TTAAATATCT
580460 TTATTAA-AATATTATTA
1 TTATTAATAATATTATTA
580477 GTTTATT-ATAATATTATTAAA
1 --TTATTAATAATATTATT--A
*
580498 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATT-A
580518 TTATTAATAAT
1 TTATTAATAAT
580529 TTAATAATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
18 1 0.02
19 24 0.57
20 5 0.12
21 12 0.29
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (18 bp):
TTATTAATAATATTATTA
Found at i:580699 original size:21 final size:22
Alignment explanation
Indices: 580652--580708 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
580642 TTTTATTATA
580652 ATATTAGAAATA-TAATATAAT
1 ATATTAGAAATATTAATATAAT
580673 ATTATTAGAAATATTAATA-AAT
1 A-TATTAGAAATATTAATATAAT
**
580695 ATATTTTAAATATT
1 ATATTAGAAATATT
580709 TTAATGATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 12 0.38
22 15 0.47
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (22 bp):
ATATTAGAAATATTAATATAAT
Found at i:581787 original size:24 final size:24
Alignment explanation
Indices: 581760--581838 Score: 131
Period size: 24 Copynumber: 3.3 Consensus size: 24
581750 ACAAGTGTGA
581760 GGTCATTCGATCATTAGGTTACTT
1 GGTCATTCGATCATTAGGTTACTT
581784 GGTCATTCGATCATTAGGTTACTT
1 GGTCATTCGATCATTAGGTTACTT
* * *
581808 GGTCATTCGATCATTAAGTCATTT
1 GGTCATTCGATCATTAGGTTACTT
581832 GGTCATT
1 GGTCATT
581839 TGGACATTCG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (24 bp):
GGTCATTCGATCATTAGGTTACTT
Found at i:581834 original size:48 final size:48
Alignment explanation
Indices: 581760--582094 Score: 225
Period size: 48 Copynumber: 7.0 Consensus size: 48
581750 ACAAGTGTGA
* * *
581760 GGTCATTCGATCATTAGGTTACTT-GGTCATTCGATCATTAGGTTACTT-
1 GGTCATTCGATCATTAAGTCA-TTCGGTCATTCGATCATTAGGTCA-TTC
* * *
581808 GGTCATTCGATCATTAAGTCATTTGGTCATTTGGA-CATTCGGTCATTC
1 GGTCATTCGATCATTAAGTCATTCGGTCA-TTCGATCATTAGGTCATTC
** * ** * *
581856 GGAAATCCGATCATTAAGTCATTCAATCATTCAATCGTTAGGTCA-TC
1 GGTCATTCGATCATTAAGTCATTCGGTCATTCGATCATTAGGTCATTC
* **
581903 AGGTCATTCGATCATTGAGTCATTCGGTCATTCGCCCATTAGGTCATTC
1 -GGTCATTCGATCATTAAGTCATTCGGTCATTCGATCATTAGGTCATTC
* * * ** * ** *
581952 GATCATTCAATCATTAAGTCATTCGATCATTAAATCATTCGACCATTA
1 GGTCATTCGATCATTAAGTCATTCGGTCATTCGATCATTAGGTCATTC
* * * * * * *
582000 GGAT-ATTAGGTCATTAAATCATTAGGTCTTTCGGTCATTAGATCATTC
1 GG-TCATTCGATCATTAAGTCATTCGGTCATTCGATCATTAGGTCATTC
** * **
582048 GGTCATTC-AGTCATT-TTTCCATTCGATCATTCGGCCATTAGGTCATT
1 GGTCATTCGA-TCATTAAGT-CATTCGGTCATTCGATCATTAGGTCATT
582095 ATGTCATTTT
Statistics
Matches: 217, Mismatches: 60, Indels: 20
0.73 0.20 0.07
Matches are distributed among these distances:
47 11 0.05
48 199 0.92
49 7 0.03
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (48 bp):
GGTCATTCGATCATTAAGTCATTCGGTCATTCGATCATTAGGTCATTC
Found at i:581855 original size:8 final size:8
Alignment explanation
Indices: 581760--582094 Score: 88
Period size: 8 Copynumber: 41.9 Consensus size: 8
581750 ACAAGTGTGA
581760 GGTCATTC
1 GGTCATTC
* *
581768 GATCATTA
1 GGTCATTC
*
581776 GGTTACTT-
1 GGTCA-TTC
581784 GGTCATTC
1 GGTCATTC
* *
581792 GATCATTA
1 GGTCATTC
*
581800 GGTTACTT-
1 GGTCA-TTC
581808 GGTCATTC
1 GGTCATTC
* *
581816 GATCATTA
1 GGTCATTC
* *
581824 AGTCATTT
1 GGTCATTC
*
581832 GGTCATTT
1 GGTCATTC
*
581840 GGACATTC
1 GGTCATTC
581848 GGTCATTC
1 GGTCATTC
** *
581856 GGAAATCC
1 GGTCATTC
* *
581864 GATCATTA
1 GGTCATTC
*
581872 AGTCATTC
1 GGTCATTC
**
581880 AATCATTC
1 GGTCATTC
** * *
581888 AATCGTTA
1 GGTCATTC
581896 GGTCA-TC
1 GGTCATTC
581903 AGGTCATTC
1 -GGTCATTC
*
581912 GATCATT-
1 GGTCATTC
581919 GAGTCATTC
1 G-GTCATTC
581928 GGTCATTC
1 GGTCATTC
** *
581936 GCCCATTA
1 GGTCATTC
581944 GGTCATTC
1 GGTCATTC
*
581952 GATCATTC
1 GGTCATTC
** *
581960 AATCATTA
1 GGTCATTC
*
581968 AGTCATTC
1 GGTCATTC
* *
581976 GATCATTA
1 GGTCATTC
**
581984 AATCATTC
1 GGTCATTC
** *
581992 GACCATTA
1 GGTCATTC
*
582000 GGAT-ATTA
1 GG-TCATTC
*
582008 GGTCATTA
1 GGTCATTC
** *
582016 AATCATTA
1 GGTCATTC
*
582024 GGTCTTTC
1 GGTCATTC
*
582032 GGTCATTA
1 GGTCATTC
*
582040 GATCATTC
1 GGTCATTC
582048 GGTCATTC
1 GGTCATTC
*
582056 AGTCATT-
1 GGTCATTC
**
582063 TTTCCATTC
1 GGT-CATTC
*
582072 GATCATTC
1 GGTCATTC
* *
582080 GGCCATTA
1 GGTCATTC
582088 GGTCATT
1 GGTCATT
582095 ATGTCATTTT
Statistics
Matches: 235, Mismatches: 80, Indels: 24
0.69 0.24 0.07
Matches are distributed among these distances:
7 8 0.03
8 219 0.93
9 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (8 bp):
GGTCATTC
Found at i:581900 original size:24 final size:24
Alignment explanation
Indices: 581865--581990 Score: 121
Period size: 24 Copynumber: 5.2 Consensus size: 24
581855 CGGAAATCCG
* *
581865 ATCATTAAGTCATTCAATCATTCA
1 ATCATTAGGTCATTCGATCATTCA
* * *
581889 ATCGTTAGGTCA-TCAGGTCATTCG
1 ATCATTAGGTCATTC-GATCATTCA
* *
581913 ATCATT-GAGTCATTCGGTCATTCG
1 ATCATTAG-GTCATTCGATCATTCA
**
581937 CCCATTAGGTCATTCGATCATTCA
1 ATCATTAGGTCATTCGATCATTCA
* *
581961 ATCATTAAGTCATTCGATCATTAA
1 ATCATTAGGTCATTCGATCATTCA
581985 ATCATT
1 ATCATT
581991 CGACCATTAG
Statistics
Matches: 84, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
23 3 0.04
24 78 0.93
25 3 0.04
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (24 bp):
ATCATTAGGTCATTCGATCATTCA
Found at i:584956 original size:189 final size:189
Alignment explanation
Indices: 584636--585017 Score: 719
Period size: 189 Copynumber: 2.0 Consensus size: 189
584626 GTAATATTTG
584636 TTCAAAATATTTTTTAGTCATTAATAAGATGTATATACCTTGCAAATATAAATACTCGAACCTGA
1 TTCAAAATATTTTTTAGTCATTAATAAGATGTATATACCTTGCAAATATAAATACTCGAACCTGA
*
584701 ATTCTGTAGAAAACGTAGCATTTTTTACCACTGAAATCATTTGAAGAATGAATTGCACTTTAAAT
66 ATTCTGTAGAAAACGTAGCATTTTTTACCACTGAAATCATTTGAAGAATGAATCGCACTTTAAAT
*
584766 TTCTAATTCTACCTTAATTAAGGGGAATAATTATTAATCCTTTAAAAAACAAATCTTCT
131 TTCTAATTCTACCTTAATTAAGGGGAATAATTATTAACCCTTTAAAAAACAAATCTTCT
* *
584825 TTCAAAATATTTTTTAGTCATTAATAAGATGTATATACCTTGCAAATATAACTACTCGAATCTGA
1 TTCAAAATATTTTTTAGTCATTAATAAGATGTATATACCTTGCAAATATAAATACTCGAACCTGA
*
584890 ATTCTGTAGAAAACGTAGCATTTTTTACCACTGAAATCATTTGAAGAATTAATCGCACTTTAAAT
66 ATTCTGTAGAAAACGTAGCATTTTTTACCACTGAAATCATTTGAAGAATGAATCGCACTTTAAAT
584955 TTCTAATTCTACCTTAATTAAGGGGAATAATTATTAACCCTTTAAAAAACAAATCTTCT
131 TTCTAATTCTACCTTAATTAAGGGGAATAATTATTAACCCTTTAAAAAACAAATCTTCT
585014 TTCA
1 TTCA
585018 TGAACCACAC
Statistics
Matches: 188, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
189 188 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (189 bp):
TTCAAAATATTTTTTAGTCATTAATAAGATGTATATACCTTGCAAATATAAATACTCGAACCTGA
ATTCTGTAGAAAACGTAGCATTTTTTACCACTGAAATCATTTGAAGAATGAATCGCACTTTAAAT
TTCTAATTCTACCTTAATTAAGGGGAATAATTATTAACCCTTTAAAAAACAAATCTTCT
Found at i:587266 original size:49 final size:49
Alignment explanation
Indices: 587194--587294 Score: 193
Period size: 49 Copynumber: 2.1 Consensus size: 49
587184 GAAAGATAAT
587194 TGGAGAATCGTGGCGGTGCAAGGAAGCCGCCATGAAAGAGGGTTCTATG
1 TGGAGAATCGTGGCGGTGCAAGGAAGCCGCCATGAAAGAGGGTTCTATG
*
587243 TGGAGAATCGTGGCGGTGCAAGGAAGCCGCCATGAAAGAGGGTTTTATG
1 TGGAGAATCGTGGCGGTGCAAGGAAGCCGCCATGAAAGAGGGTTCTATG
587292 TGG
1 TGG
587295 GAAGCGGTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.26, C:0.15, G:0.40, T:0.20
Consensus pattern (49 bp):
TGGAGAATCGTGGCGGTGCAAGGAAGCCGCCATGAAAGAGGGTTCTATG
Found at i:599078 original size:2 final size:2
Alignment explanation
Indices: 599073--599098 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
599063 CCCAAAAAAT
599073 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
599099 AGAAAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:599138 original size:18 final size:19
Alignment explanation
Indices: 599106--599143 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
599096 ATAAGAAAAG
*
599106 AAAAATAACACCCTTTTAA
1 AAAAATAACACCCTTCTAA
*
599125 AAAAATGACA-CCTTCTAA
1 AAAAATAACACCCTTCTAA
599143 A
1 A
599144 TAAGAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.53, C:0.21, G:0.03, T:0.24
Consensus pattern (19 bp):
AAAAATAACACCCTTCTAA
Found at i:608256 original size:5 final size:5
Alignment explanation
Indices: 608248--608277 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
608238 TAAAAGGGGT
608248 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
608278 AATATTGTTT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Done.