Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008752.1 Hibiscus syriacus cultivar Beakdansim tig00111843_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: 1143363
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:569219 original size:11 final size:11
Alignment explanation
Indices: 569203--569227 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
569193 CTAAAATGGA
569203 AAATAATAATT
1 AAATAATAATT
569214 AAATAATAATT
1 AAATAATAATT
569225 AAA
1 AAA
569228 GTACTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATAATAATT
Found at i:570402 original size:3 final size:3
Alignment explanation
Indices: 570394--570436 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
570384 ATAAAAATTT
570394 TAA TAA TAA TAA T-A TAA -ATA TAA TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
570437 ATAAAAAGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 5 0.14
3 30 0.83
4 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:570418 original size:14 final size:14
Alignment explanation
Indices: 570394--570440 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
570384 ATAAAAATTT
570394 TAATAATAATAATA
1 TAATAATAATAATA
570408 TAA-ATATAATAATA
1 TAATA-ATAATAATA
570422 TAATAATAATAATA
1 TAATAATAATAATA
570436 -AATAA
1 TAATAA
570441 AAAGGGGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.19
14 24 0.77
15 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:570795 original size:42 final size:43
Alignment explanation
Indices: 570748--570953 Score: 308
Period size: 42 Copynumber: 4.8 Consensus size: 43
570738 CTCCTTTGAA
* **
570748 AACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTT-
1 AACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTC
*
570790 AACATCTTGCACTGAAGGTCTTACAGATGATCCGAAGGCTTT-
1 AACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTC
* *
570832 AACATCTTGCACTGAAGATCTTACAGATGACCCGAAGGATTTC
1 AACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTC
* *
570875 AACATCTTGCACTGAAGGTCTTACAGATGACCTGAAGGGTTTC
1 AACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTC
* *
570918 AACATCTTGCACTAAAGGTCTTACAGATGGCCCGAA
1 AACATCTTGCACTGAAGGTCTTACAGATGACCCGAA
570954 TGACTCAAAT
Statistics
Matches: 150, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
42 77 0.51
43 73 0.49
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (43 bp):
AACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTC
Found at i:571654 original size:22 final size:22
Alignment explanation
Indices: 571629--571705 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
571619 AATAAAGCTT
*
571629 TCATCTTTGAAAAGAGAATATA
1 TCATATTTGAAAAGAGAATATA
571651 TCATATTTGAAAAGAGAATATA
1 TCATATTTGAAAAGAGAATATA
*
571673 TCATATTTGAAAAGAGAATCTA
1 TCATATTTGAAAAGAGAATATA
*
571695 TCATCTTTGAA
1 TCATATTTGAA
571706 GAATATAGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (22 bp):
TCATATTTGAAAAGAGAATATA
Found at i:572474 original size:40 final size:40
Alignment explanation
Indices: 572430--572516 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 40
572420 GATATGAATA
*
572430 TTCAAAATGCATTCAA-AATTGTTTCTTGTTGATGTGAGCC
1 TTCAAAATGC-TTCAACAATTGCTTCTTGTTGATGTGAGCC
* * * *
572470 TTCAAAATGCTTTAACATTTGCTTCTTGTTGATTTGAGCT
1 TTCAAAATGCTTCAACAATTGCTTCTTGTTGATGTGAGCC
572510 TTCAAAA
1 TTCAAAA
572517 ATGCCCAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
39 4 0.10
40 37 0.90
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (40 bp):
TTCAAAATGCTTCAACAATTGCTTCTTGTTGATGTGAGCC
Found at i:576786 original size:30 final size:29
Alignment explanation
Indices: 576718--576804 Score: 101
Period size: 30 Copynumber: 3.1 Consensus size: 29
576708 GCAATGATGC
576718 AAATGTAAAAATG--AAAATGAA-AATAC-
1 AAATGTAAAAATGCAAAAAT-AAGAATACA
**
576744 AAATGTAAAAATGCAAAAATGTGAATACA
1 AAATGTAAAAATGCAAAAATAAGAATACA
*
576773 AAGATGTATAAATGCAAAAATAAGAATACA
1 AA-ATGTAAAAATGCAAAAATAAGAATACA
576803 AA
1 AA
576805 TTGTGCAATG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
26 13 0.25
28 10 0.20
29 2 0.04
30 26 0.51
ACGTcount: A:0.62, C:0.06, G:0.13, T:0.20
Consensus pattern (29 bp):
AAATGTAAAAATGCAAAAATAAGAATACA
Found at i:577543 original size:10 final size:10
Alignment explanation
Indices: 577528--577557 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
577518 ATGTATATAC
577528 AAAATAGAAA
1 AAAATAGAAA
577538 AAAATAAGAAA
1 AAAAT-AGAAA
577549 AAAATAGAA
1 AAAATAGAA
577558 TAGTTAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAATAGAAA
Found at i:578776 original size:50 final size:50
Alignment explanation
Indices: 578714--578821 Score: 198
Period size: 50 Copynumber: 2.1 Consensus size: 50
578704 TTTTTATGGT
578714 TTTATAGAGTATTTAATTATTTAAAAATATCAGAAAATGATATCTAGATGC
1 TTTA-AGAGTATTTAATTATTTAAAAATATCAGAAAATGATATCTAGATGC
*
578765 TTTAAGAGTATTTATTTATTTAAAAATATCAGAAAATGATATCTAGATGC
1 TTTAAGAGTATTTAATTATTTAAAAATATCAGAAAATGATATCTAGATGC
578815 TTTAAGA
1 TTTAAGA
578822 CAACCCCTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
50 52 0.93
51 4 0.07
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.40
Consensus pattern (50 bp):
TTTAAGAGTATTTAATTATTTAAAAATATCAGAAAATGATATCTAGATGC
Found at i:578837 original size:50 final size:50
Alignment explanation
Indices: 578730--578837 Score: 153
Period size: 50 Copynumber: 2.2 Consensus size: 50
578720 GAGTATTTAA
** ***
578730 TTATTTAAAAATATCAGAAAATGATATCTAGATGCTTTAAGAGTATTTAT
1 TTATTTAAAAATATCAGAAAATGATATCTAGATGCTTTAAGACAACCCAT
*
578780 TTATTTAAAAATATCAGAAAATGATATCTAGATGCTTTAAGACAACCCCT
1 TTATTTAAAAATATCAGAAAATGATATCTAGATGCTTTAAGACAACCCAT
*
578830 TTCTTTAA
1 TTATTTAA
578838 TATTAAAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (50 bp):
TTATTTAAAAATATCAGAAAATGATATCTAGATGCTTTAAGACAACCCAT
Found at i:578999 original size:21 final size:18
Alignment explanation
Indices: 578958--578999 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
578948 TCCCTTTCTT
578958 AATATTAAAAAATAAATA
1 AATATTAAAAAATAAATA
578976 AATATTAATATAAATAAGATA
1 AATATTAA-A-AAATAA-ATA
578997 AAT
1 AAT
579000 TTTCCTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 1 0.05
20 6 0.29
21 6 0.29
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
AATATTAAAAAATAAATA
Found at i:580572 original size:3 final size:3
Alignment explanation
Indices: 580564--580619 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
580554 TAAAAATATT
* *
580564 TAA TAA TAA TAA -CA TAA -ATA TAA TAA TGA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
580608 TAA TAA TAA TAA
1 TAA TAA TAA TAA
580620 AAACCGAGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 43 0.93
4 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:583714 original size:136 final size:136
Alignment explanation
Indices: 583516--583765 Score: 324
Period size: 136 Copynumber: 1.8 Consensus size: 136
583506 CAAAGTAAGA
* * * *
583516 CTAGACGTCCTCAACACAAAGGAAAAATGTCATCCATCGGCCAGATCTCTTCAATATAAAGGAGT
1 CTAGACGTCCTCAACACAAAGGAAAAATGTCATCCATCGACCAGATATCCTCAAGATAAAGGAGT
* *
583581 AGTGTTATCCTTAGACAATCAGA-TTTCCTCAACACGAAGGAACCGTGTTGTCTCCAAATCTCCA
66 AGTGTTATCCTCAGACAATCAGACTTT-CTCAACACGAAGGAACCATGTTGTCTCCAAATCTCCA
583645 AATACGG
130 AATACGG
* ** ** * *
583652 CTAGATGTCCTCAACATGAAGGAAAAATGTTGTCCATTGACCAGATATCCTCAACGCT-AAGGAG
1 CTAGACGTCCTCAACACAAAGGAAAAATGTCATCCATCGACCAGATATCCTCAA-GATAAAGGAG
* * *
583716 TAGTGTTATCCTCAGACAATCAGACTTTTTTAACGCGAAGGAACCATGTT
65 TAGTGTTATCCTCAGACAATCAGACTTTCTCAACACGAAGGAACCATGTT
583766 ATCTTTAAAT
Statistics
Matches: 96, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
136 92 0.96
137 4 0.04
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (136 bp):
CTAGACGTCCTCAACACAAAGGAAAAATGTCATCCATCGACCAGATATCCTCAAGATAAAGGAGT
AGTGTTATCCTCAGACAATCAGACTTTCTCAACACGAAGGAACCATGTTGTCTCCAAATCTCCAA
ATACGG
Found at i:584383 original size:3 final size:3
Alignment explanation
Indices: 584375--584458 Score: 152
Period size: 3 Copynumber: 28.3 Consensus size: 3
584365 GTCTGAGTTG
*
584375 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
584423 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
584459 CAGGTTACAA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
2 2 0.03
3 76 0.97
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:584928 original size:22 final size:25
Alignment explanation
Indices: 584903--584953 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 25
584893 CGCTGTAATG
*
584903 AAATACGACCAAA-TAG-TAA-ACC
1 AAATACAACCAAATTAGTTAACACC
*
584925 AAATCCAACCAAATTAGTTAACACC
1 AAATACAACCAAATTAGTTAACACC
584950 AAAT
1 AAAT
584954 CAAATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.46
23 3 0.12
24 3 0.12
25 7 0.29
ACGTcount: A:0.53, C:0.24, G:0.06, T:0.18
Consensus pattern (25 bp):
AAATACAACCAAATTAGTTAACACC
Found at i:584953 original size:25 final size:22
Alignment explanation
Indices: 584910--584954 Score: 63
Period size: 25 Copynumber: 1.9 Consensus size: 22
584900 ATGAAATACG
584910 ACCAAATAGTAAACCAAATCCA
1 ACCAAATAGTAAACCAAATCCA
584932 ACCAAATTAGTTAACACCAAATC
1 ACCAAA-TAG-TAA-ACCAAATC
584955 AAATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 3 0.15
25 8 0.40
ACGTcount: A:0.51, C:0.27, G:0.04, T:0.18
Consensus pattern (22 bp):
ACCAAATAGTAAACCAAATCCA
Found at i:592814 original size:21 final size:21
Alignment explanation
Indices: 592790--592835 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
592780 TAATTTTTAA
592790 TTTAATATTT-AAAATTAATAT
1 TTTAATATTTCAAAATTAAT-T
* *
592811 TTTATTTTTTCAAAATTAATT
1 TTTAATATTTCAAAATTAATT
592832 TTTA
1 TTTA
592836 TCAATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTAATATTTCAAAATTAATT
Found at i:592861 original size:15 final size:16
Alignment explanation
Indices: 592841--592870 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
592831 TTTTATCAAT
592841 AATTTT-AAATAATTA
1 AATTTTAAAATAATTA
592856 AATTTTAAAATAATT
1 AATTTTAAAATAATT
592871 TTCTAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTTAAAATAATTA
Found at i:592884 original size:13 final size:11
Alignment explanation
Indices: 592858--592912 Score: 56
Period size: 11 Copynumber: 4.6 Consensus size: 11
592848 AATAATTAAA
592858 TTTTAAAATAAT
1 TTTTAAAAT-AT
592870 TTTCTAAAAATAT
1 TTT-T-AAAATAT
592883 TTTTAAAATAT
1 TTTTAAAATAT
* *
592894 TTTTACAACACT
1 TTTTAAAATA-T
592906 TTTTAAA
1 TTTTAAA
592913 TCACCTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
11 15 0.41
12 11 0.30
13 6 0.16
14 5 0.14
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:597061 original size:20 final size:21
Alignment explanation
Indices: 597018--597062 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
597008 TCTAGTGTAT
*
597018 GCCTAGAAGAAATTCTGAAGA
1 GCCTAGAAGAAATTCTGAAAA
597039 GCCTAGAAGAAATT-TGAAAA
1 GCCTAGAAGAAATTCTGAAAA
597059 GCCT
1 GCCT
597063 TTAGAACCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (21 bp):
GCCTAGAAGAAATTCTGAAAA
Found at i:599486 original size:18 final size:18
Alignment explanation
Indices: 599463--599497 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
599453 CTAGGAGATT
599463 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
599481 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
599498 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:600543 original size:149 final size:149
Alignment explanation
Indices: 600363--600656 Score: 579
Period size: 149 Copynumber: 2.0 Consensus size: 149
600353 GTCGAGGGTC
600363 TACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATAC
1 TACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATAC
*
600428 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTATA
66 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTATA
600493 TGGCACTACGGTGCACTTA
131 TGGCACTACGGTGCACTTA
600512 TACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATAC
1 TACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATAC
600577 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTATA
66 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTATA
600642 TGGCACTACGGTGCA
131 TGGCACTACGGTGCA
600657 ATTCTACGGG
Statistics
Matches: 144, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 144 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (149 bp):
TACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTATA
TGGCACTACGGTGCACTTA
Found at i:600687 original size:23 final size:23
Alignment explanation
Indices: 600643--600687 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
600633 ATCATTATAT
*
600643 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
600666 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
600688 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:608508 original size:16 final size:16
Alignment explanation
Indices: 608487--608519 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
608477 TAATAAATAA
608487 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
608503 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
608519 A
1 A
608520 ATTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:608630 original size:10 final size:10
Alignment explanation
Indices: 608584--608614 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
608574 CATTTAATAA
608584 ATAAACGAAC
1 ATAAACGAAC
608594 ATAAACGAAC
1 ATAAACGAAC
608604 ATAAACGAAC
1 ATAAACGAAC
608614 A
1 A
608615 CGAACATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.61, C:0.19, G:0.10, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:608651 original size:16 final size:16
Alignment explanation
Indices: 608601--608644 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
608591 AACATAAACG
* *
608601 AACATAAACGAACACG
1 AACATAAATGAACACA
608617 AACATAAATGAACACA
1 AACATAAATGAACACA
608633 AACATAAATGAA
1 AACATAAATGAA
608645 TATAAACGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.61, C:0.18, G:0.09, T:0.11
Consensus pattern (16 bp):
AACATAAATGAACACA
Found at i:616208 original size:6 final size:6
Alignment explanation
Indices: 616197--616229 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
616187 TATTATAAAA
*
616197 AATATT AATATT ATTATT AATATT AATATT AAT
1 AATATT AATATT AATATT AATATT AATATT AAT
616230 TTTTAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
AATATT
Found at i:616210 original size:18 final size:18
Alignment explanation
Indices: 616187--616227 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
616177 TGACATAGAT
616187 TATTATAAAAAATATTAA
1 TATTATAAAAAATATTAA
* **
616205 TATTATTATTAATATTAA
1 TATTATAAAAAATATTAA
616223 TATTA
1 TATTA
616228 ATTTTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTATAAAAAATATTAA
Found at i:616240 original size:18 final size:18
Alignment explanation
Indices: 616197--616240 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
616187 TATTATAAAA
616197 AATATTAATATTATTATT
1 AATATTAATATTATTATT
*
616215 AATATTAATATTAATTTTT
1 AATATTAATATT-ATTATT
616234 AAT-TTAA
1 AATATTAA
616241 ATTTGATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AATATTAATATTATTATT
Found at i:616240 original size:24 final size:23
Alignment explanation
Indices: 616197--616254 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 23
616187 TATTATAAAA
616197 AATATTAATATTATTATT-AATATT
1 AATATTAAT-TTATTATTAAAT-TT
616221 AATATTAATTT-TTAATTTAAATTT
1 AATATTAATTTATT-A-TTAAATTT
*
616245 GATATTAATT
1 AATATTAATT
616255 GTGATCATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.07
23 3 0.10
24 22 0.73
25 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
AATATTAATTTATTATTAAATTT
Found at i:617333 original size:34 final size:34
Alignment explanation
Indices: 617267--617333 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
617257 ACAAAAACTT
*
617267 AATTAATAATAACAATTAATATAAAATGATATTA
1 AATTAATAATAACAATTAATATAAAATAATATTA
*
617301 AATTAATGAATAA-AATTAAT-TATTAATAATATT
1 AATTAAT-AATAACAATTAATATA-AAATAATATT
617334 GTTAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 2 0.07
34 22 0.76
35 5 0.17
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (34 bp):
AATTAATAATAACAATTAATATAAAATAATATTA
Found at i:618513 original size:42 final size:42
Alignment explanation
Indices: 618447--618529 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
618437 AATGCGAACT
*
618447 CCAATTTCGCAACACAGTTTCTGCAATCGCAACGCGAATTTA
1 CCAAATTCGCAACACAGTTTCTGCAATCGCAACGCGAATTTA
* *
618489 CCAAATTCGTAACTCAGTTTCTGCAATCGCAACGCGAATTT
1 CCAAATTCGCAACACAGTTTCTGCAATCGCAACGCGAATTT
618530 CTTTCTCGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (42 bp):
CCAAATTCGCAACACAGTTTCTGCAATCGCAACGCGAATTTA
Found at i:618584 original size:61 final size:62
Alignment explanation
Indices: 618473--618590 Score: 150
Period size: 61 Copynumber: 1.9 Consensus size: 62
618463 GTTTCTGCAA
* * ** *
618473 TCGCAACGCGAATTTACCAAATTCGTAACTCAGTTTCTGCAATCGCAACGCGAATTTCTTTC
1 TCGCAACGCGAATTTACCAAATTCGCAACGCAGAATCTGAAATCGCAACGCGAATTTCTTTC
* *
618535 TCGCAACGCG-ATTTTCCAAATTCGCAACGC-GAATCTGTAAATCGTAACGCGAATTT
1 TCGCAACGCGAATTTACCAAATTCGCAACGCAGAATCTG-AAATCGCAACGCGAATTT
618591 GTAATTCGCA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
60 5 0.10
61 33 0.69
62 10 0.21
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (62 bp):
TCGCAACGCGAATTTACCAAATTCGCAACGCAGAATCTGAAATCGCAACGCGAATTTCTTTC
Found at i:618621 original size:20 final size:20
Alignment explanation
Indices: 618593--618661 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
618583 GCGAATTTGT
618593 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
*
618613 AATTTGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
*
618633 AATTTGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
618653 AATTCGCAA
1 AATTCGCAA
618662 AGCGCGTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.19
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:618833 original size:22 final size:22
Alignment explanation
Indices: 618808--618858 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
618798 TCACTCTCTA
*
618808 CGGCGACATCCGTCCCCATCTC
1 CGGCGACATCCGTCCCCATATC
618830 CGGCGACATCCGTCCCCATATC
1 CGGCGACATCCGTCCCCATATC
*
618852 CGACGAC
1 CGGCGAC
618859 CCCCCTCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.16
Consensus pattern (22 bp):
CGGCGACATCCGTCCCCATATC
Found at i:619216 original size:20 final size:20
Alignment explanation
Indices: 619193--619231 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
619183 TTTGAAACTT
*
619193 AAATTCGCAGCACGAAAATG
1 AAATTCGCAACACGAAAATG
619213 AAATTCGCAACACGAAAAT
1 AAATTCGCAACACGAAAAT
619232 CGTAACACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.21, G:0.15, T:0.15
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:619276 original size:20 final size:19
Alignment explanation
Indices: 619239--619325 Score: 93
Period size: 20 Copynumber: 4.4 Consensus size: 19
619229 AATCGTAACA
*
619239 CGATTTTAGTTTCGCGTTG
1 CGATTTTATTTTCGCGTTG
*
619258 CGATTTTCATTTTCACGTTG
1 CGATTTT-ATTTTCGCGTTG
* *
619278 CAAATTTTATTTTTGCGTTG
1 C-GATTTTATTTTCGCGTTG
*
619298 CGATTTTCATTTTCGTGTTG
1 CGATTTT-ATTTTCGCGTTG
*
619318 CGAATTTA
1 CGATTTTA
619326 AGTTTCAAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 13 0.23
20 38 0.68
21 5 0.09
ACGTcount: A:0.16, C:0.15, G:0.18, T:0.51
Consensus pattern (19 bp):
CGATTTTATTTTCGCGTTG
Found at i:619318 original size:40 final size:40
Alignment explanation
Indices: 619241--619331 Score: 128
Period size: 40 Copynumber: 2.3 Consensus size: 40
619231 TCGTAACACG
619241 ATTTTAGTTTCGCGTTGCGATTTTCATTTTCACGTTGCAA
1 ATTTTAGTTTCGCGTTGCGATTTTCATTTTCACGTTGCAA
* * ** *
619281 ATTTTATTTTTGCGTTGCGATTTTCATTTTCGTGTTGCGA
1 ATTTTAGTTTCGCGTTGCGATTTTCATTTTCACGTTGCAA
*
619321 ATTTAAGTTTC
1 ATTTTAGTTTC
619332 AAAAACTACT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (40 bp):
ATTTTAGTTTCGCGTTGCGATTTTCATTTTCACGTTGCAA
Found at i:620830 original size:42 final size:42
Alignment explanation
Indices: 620771--620867 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 42
620761 CCCCACTTCG
* * * *
620771 AGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACACCA
1 AGAGCCATCACCTGATCGAGCCAATTATACACCTCCACACCA
*
620813 AGAGCCATCACCTGATCGAGCCAATTATACACCTCCACACCG
1 AGAGCCATCACCTGATCGAGCCAATTATACACCTCCACACCA
620855 AGAGCCATCACCT
1 AGAGCCATCACCT
620868 ATTCCATCAC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.30, C:0.37, G:0.16, T:0.16
Consensus pattern (42 bp):
AGAGCCATCACCTGATCGAGCCAATTATACACCTCCACACCA
Found at i:621013 original size:21 final size:21
Alignment explanation
Indices: 620982--621031 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
620972 GTTAGGGGAG
* *
620982 TTACGTAATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
* *
621003 TTGCGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
621024 TTACGTGA
1 TTACGTGA
621032 CGACAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:621469 original size:21 final size:21
Alignment explanation
Indices: 621440--621515 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
621430 ATTCACCTCT
* *
621440 CATCGTTCAAGAGGCCTCTCC
1 CATCGTTCAAGAGGCCCCTTC
* *
621461 CATCATTCAAGAGGCCCCTTT
1 CATCGTTCAAGAGGCCCCTTC
621482 CATCGTTCAAGAGGCCCCTTC
1 CATCGTTCAAGAGGCCCCTTC
*
621503 CACCGTTCAAGAG
1 CATCGTTCAAGAG
621516 CTCGATTCAC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTTC
Found at i:623068 original size:20 final size:20
Alignment explanation
Indices: 623007--623061 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
622997 CCACCTTTAA
**
623007 GAAAATCAAATTTACAACGC
1 GAAAATCAAATTCGCAACGC
623027 GAAAATCAAATTCGCAACGC
1 GAAAATCAAATTCGCAACGC
*
623047 GAAAGTCAAATTCGC
1 GAAAATCAAATTCGC
623062 GTTGCGATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.45, C:0.22, G:0.15, T:0.18
Consensus pattern (20 bp):
GAAAATCAAATTCGCAACGC
Found at i:623080 original size:20 final size:20
Alignment explanation
Indices: 623057--623141 Score: 91
Period size: 20 Copynumber: 4.2 Consensus size: 20
623047 GAAAGTCAAA
* *
623057 TTCGCGTTGCGATTTTTATT
1 TTCGCGTTGCGAATTTGATT
*
623077 TTCGCG-TGTCGAATTCGATT
1 TTCGCGTTG-CGAATTTGATT
* *
623097 TTCGTGTTGCAAATTTGATT
1 TTCGCGTTGCGAATTTGATT
* *
623117 TTTGCGTTGCGAATTTGACT
1 TTCGCGTTGCGAATTTGATT
623137 TTCGC
1 TTCGC
623142 AATAATCGCA
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
19 2 0.04
20 48 0.92
21 2 0.04
ACGTcount: A:0.14, C:0.16, G:0.22, T:0.47
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTGATT
Found at i:623405 original size:18 final size:18
Alignment explanation
Indices: 623382--623417 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
623372 AAGCCGGTTG
623382 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
623400 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
623418 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:625672 original size:24 final size:24
Alignment explanation
Indices: 625638--625691 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
625628 CTGAAACATC
*
625638 ATCAAAATCC-GAGTATTGACCAAG
1 ATCAAAATCCGGA-TATTAACCAAG
*
625662 ATCAAAGTCCGGATATTAACCAAG
1 ATCAAAATCCGGATATTAACCAAG
625686 ATCAAA
1 ATCAAA
625692 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGGATATTAACCAAG
Found at i:625838 original size:12 final size:12
Alignment explanation
Indices: 625817--625850 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
625807 GGTTGTGGGT
*
625817 TTTGAGATTGTG
1 TTTGATATTGTG
625829 TTTGATATTGTG
1 TTTGATATTGTG
*
625841 TTTGGTATTG
1 TTTGATATTG
625851 AAAATATGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:626476 original size:14 final size:16
Alignment explanation
Indices: 626441--626477 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
626431 GAAATCATTG
626441 AAAATTATATAGAAAT
1 AAAATTATATAGAAAT
*
626457 AAAATTATGTA-AAA-
1 AAAATTATATAGAAAT
626471 AAAATTA
1 AAAATTA
626478 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAATTATATAGAAAT
Found at i:626705 original size:21 final size:21
Alignment explanation
Indices: 626628--626900 Score: 135
Period size: 20 Copynumber: 13.4 Consensus size: 21
626618 AAATAAAAGT
* *
626628 TGTTGCGAAATTA-AAATTCG
1 TGTTGCGAATTTAGAAAATCG
*
626648 TGTT-CGAA-TTCGAAAATCG
1 TGTTGCGAATTTAGAAAATCG
* * *
626667 AGTTGCGAA--AACAAAATCTG
1 TGTTGCGAATTTAGAAAATC-G
*
626687 TGTTGCG-ATTTAGAAAATCT
1 TGTTGCGAATTTAGAAAATCG
** **
626707 TGTTGCGAA-AAAGAATTTCG
1 TGTTGCGAATTTAGAAAATCG
* *
626727 CGTTGCGAATTCAG-AAATCG
1 TGTTGCGAATTTAGAAAATCG
* *
626747 AGTTGCGAATTTA-AAATTCCG
1 TGTTGCGAATTTAGAAAAT-CG
*
626768 TGTTGCGAATTT-GAAATTTCG
1 TGTTGCGAATTTAGAAA-ATCG
626789 TGTTGCGAATTTAGAAAATCG
1 TGTTGCGAATTTAGAAAATCG
* * *
626810 AGTTGCGAGA--AAGAAATTCG
1 TGTTGCGA-ATTTAGAAAATCG
* * * *
626830 TGATGTG-ATTGCAGAAACT-G
1 TGTTGCGAATT-TAGAAAATCG
* * *
626850 AGTTGCGAATTTGGGAAATTCG
1 TGTTGCGAATTT-AGAAAATCG
* *
626872 TGTTGCGAATTT-GGAAATTG
1 TGTTGCGAATTTAGAAAATCG
626892 TGTTGCGAA
1 TGTTGCGAA
626901 ATTGGAGTTC
Statistics
Matches: 191, Mismatches: 43, Indels: 38
0.70 0.16 0.14
Matches are distributed among these distances:
18 3 0.02
19 20 0.10
20 85 0.45
21 64 0.34
22 19 0.10
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (21 bp):
TGTTGCGAATTTAGAAAATCG
Found at i:626815 original size:103 final size:102
Alignment explanation
Indices: 626680--626900 Score: 272
Period size: 103 Copynumber: 2.1 Consensus size: 102
626670 TGCGAAAACA
** * *
626680 AAATCTGTGTTGCG-ATTTAGAAAATCTTGTTGCGAAAAAGAATTTCGCGTTGCGAATT-CAGAA
1 AAAT-TGTGTTGCGAATTTAGAAAATCGAGTTGCGAAAAAGAAATTCGCGATGCG-ATTGCAGAA
626743 A-TCGAGTTGCGAATTT-AAAATTCCGTGTTGCGAATTT-G
64 ACT-GAGTTGCGAATTTGAAAATT-CGTGTTGCGAATTTGG
* * *
626781 AAATTTCGTGTTGCGAATTTAGAAAATCGAGTTGCGAGAAAGAAATTCGTGATGTGATTGCAGAA
1 AAA-TT-GTGTTGCGAATTTAGAAAATCGAGTTGCGAAAAAGAAATTCGCGATGCGATTGCAGAA
*
626846 ACTGAGTTGCGAATTTGGGAAATTCGTGTTGCGAATTTGG
64 ACTGAGTTGCGAATTT-GAAAATTCGTGTTGCGAATTTGG
626886 AAATTGTGTTGCGAA
1 AAATTGTGTTGCGAA
626901 ATTGGAGTTC
Statistics
Matches: 104, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
101 4 0.04
102 12 0.12
103 62 0.60
104 17 0.16
105 9 0.09
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.33
Consensus pattern (102 bp):
AAATTGTGTTGCGAATTTAGAAAATCGAGTTGCGAAAAAGAAATTCGCGATGCGATTGCAGAAAC
TGAGTTGCGAATTTGAAAATTCGTGTTGCGAATTTGG
Found at i:626876 original size:22 final size:21
Alignment explanation
Indices: 626851--626924 Score: 98
Period size: 20 Copynumber: 3.6 Consensus size: 21
626841 CAGAAACTGA
626851 GTTGCGAATTTGGGAAATTCGT
1 GTTGCGAATTT-GGAAATTCGT
626873 GTTGCGAATTTGGAAATT-GT
1 GTTGCGAATTTGGAAATTCGT
* * *
626893 GTTGCGAAATTGG-AGTTCGC
1 GTTGCGAATTTGGAAATTCGT
626913 GTTGCGAATTTG
1 GTTGCGAATTTG
626925 TTAGTTATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 3 0.06
20 26 0.55
21 7 0.15
22 11 0.23
ACGTcount: A:0.22, C:0.09, G:0.32, T:0.36
Consensus pattern (21 bp):
GTTGCGAATTTGGAAATTCGT
Found at i:626905 original size:20 final size:21
Alignment explanation
Indices: 626723--626924 Score: 127
Period size: 21 Copynumber: 9.8 Consensus size: 21
626713 GAAAAAGAAT
* **
626723 TTCGCGTTGCGAATTCAGAAA
1 TTCGTGTTGCGAATTTGGAAA
* *
626744 -TCGAGTTGCGAATTT-AAAA
1 TTCGTGTTGCGAATTTGGAAA
626763 TTCCGTGTTGCGAATTT-GAAA
1 TT-CGTGTTGCGAATTTGGAAA
*
626784 TTTCGTGTTGCGAATTTAGAAA
1 -TTCGTGTTGCGAATTTGGAAA
* * **
626806 ATCGAGTTGCGAGA--AAGAAA
1 TTCGTGTTGCGA-ATTTGGAAA
* *
626826 TTCGTGATGTG-A-TTGCAGAAA
1 TTCGTGTTGCGAATTTG--GAAA
* *
626847 CT-GAGTTGCGAATTTGGGAAA
1 TTCGTGTTGCGAATTT-GGAAA
626868 TTCGTGTTGCGAATTTGGAAA
1 TTCGTGTTGCGAATTTGGAAA
* *
626889 TT-GTGTTGCGAAATTGG-AG
1 TTCGTGTTGCGAATTTGGAAA
*
626908 TTCGCGTTGCGAATTTG
1 TTCGTGTTGCGAATTTG
626925 TTAGTTATTT
Statistics
Matches: 144, Mismatches: 24, Indels: 27
0.74 0.12 0.14
Matches are distributed among these distances:
18 1 0.01
19 6 0.04
20 57 0.40
21 58 0.40
22 21 0.15
23 1 0.01
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (21 bp):
TTCGTGTTGCGAATTTGGAAA
Found at i:630239 original size:32 final size:31
Alignment explanation
Indices: 630163--630270 Score: 126
Period size: 32 Copynumber: 3.4 Consensus size: 31
630153 TAGAATGACA
*
630163 ACATTTTTTATTAATATTTTCCTATGACATG
1 ACATATTTTATTAATATTTTCCTATGACATG
* *
630194 ACTTTTTTTTATTAATATTTTCCTATGACATG
1 AC-ATATTTTATTAATATTTTCCTATGACATG
* * ** *
630226 AGCATATTCTATTAACATTTTATTATGACATA
1 A-CATATTTTATTAATATTTTCCTATGACATG
630258 ACATATTTTATTA
1 ACATATTTTATTA
630271 GTATATAATT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
31 13 0.20
32 52 0.79
33 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (31 bp):
ACATATTTTATTAATATTTTCCTATGACATG
Found at i:631485 original size:2 final size:2
Alignment explanation
Indices: 631478--631510 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
631468 AAATATTAGA
631478 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
631511 AAATAACGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:631541 original size:20 final size:19
Alignment explanation
Indices: 631502--631541 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
631492 ATATATATAT
*
631502 ATATATATAAAATAACGAA
1 ATATATATAAAAAAACGAA
*
631521 ATATAGTATAAAAAAATGAA
1 ATATA-TATAAAAAAACGAA
631541 A
1 A
631542 ATAATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (19 bp):
ATATATATAAAAAAACGAA
Found at i:633441 original size:106 final size:106
Alignment explanation
Indices: 633311--633663 Score: 519
Period size: 106 Copynumber: 3.3 Consensus size: 106
633301 GTATTGTTCC
* * * *
633311 GAGTCCAATAT-CATCTGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTATTGACA
1 GAGTCCAATATCCTTC-GTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* *
633375 ACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
* *
633417 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
633482 CCAGCGGTCCCTTCGTCTTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
*
633523 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
633588 CCAGCGGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
* * *
633629 GAGTGGCACGATATCCTCCGTTGTGGAGTTGAAAT
1 GAGT--C-CAATATCCTTCGTTGTGAAGTTGAAAT
633664 CACGGATGGC
Statistics
Matches: 224, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
106 197 0.88
107 3 0.01
108 1 0.00
109 23 0.10
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
Found at i:637101 original size:134 final size:134
Alignment explanation
Indices: 636865--637124 Score: 459
Period size: 134 Copynumber: 1.9 Consensus size: 134
636855 TAGGCGACTC
636865 TTTCATTCTTCCCAACCTCGTATGATGGCCCAAGACACACCCCATGGAGTTCTCGAATATAGAGA
1 TTTCATTCTTCCCAACCTCGTATGATGGCCCAAGACACACCCCATGGAGTTCTCGAATATAGAGA
*
636930 GATTCAGGAACAAAGGTTTGCCTGGGATAGGGGACATCAGGATAGGAGTATGAGACAAGTAACGG
66 GATACAGGAACAAAGGTTTGCCTGGGATAGGGGACATCAGGATAGGAGTATGAGACAAGTAACGG
636995 CTCT
131 CTCT
* * *
636999 TTTC-TTCTTCCCAGCCTCGTCATGCTGGCCCAGGACACACCCCATGGAGTTCTCGAATATAGAG
1 TTTCATTCTTCCCAACCTCGT-ATGATGGCCCAAGACACACCCCATGGAGTTCTCGAATATAGAG
*
637063 AGATACAGGAACAAAGGTTTTCCTGGGATAGGGGACATCAGGATAGGAGTATGAGACAAGTA
65 AGATACAGGAACAAAGGTTTGCCTGGGATAGGGGACATCAGGATAGGAGTATGAGACAAGTA
637125 CTCTTTTACT
Statistics
Matches: 120, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
133 15 0.12
134 105 0.88
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (134 bp):
TTTCATTCTTCCCAACCTCGTATGATGGCCCAAGACACACCCCATGGAGTTCTCGAATATAGAGA
GATACAGGAACAAAGGTTTGCCTGGGATAGGGGACATCAGGATAGGAGTATGAGACAAGTAACGG
CTCT
Found at i:645410 original size:2 final size:2
Alignment explanation
Indices: 645403--645434 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
645393 AGTAAAATAC
645403 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
645435 ACACATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:652324 original size:15 final size:15
Alignment explanation
Indices: 652304--652352 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
652294 ACGTGACATT
652304 TTATTATTTTATTAA
1 TTATTATTTTATTAA
652319 TTATTA-TTTA-T-A
1 TTATTATTTTATTAA
* *
652331 TTGTTATTTAATTAA
1 TTATTATTTTATTAA
652346 TT-TTATT
1 TTATTATT
652353 CAACTAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 6 0.21
13 4 0.14
14 10 0.34
15 9 0.31
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TTATTATTTTATTAA
Found at i:653000 original size:22 final size:21
Alignment explanation
Indices: 652975--653018 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
652965 AATGTTGGAG
*
652975 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGA-TACCCTGCTACA
*
652997 GGGAATCGATACCCTGCTACA
1 GGGAACCGATACCCTGCTACA
653018 G
1 G
653019 TACTGTTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.18
Consensus pattern (21 bp):
GGGAACCGATACCCTGCTACA
Found at i:653030 original size:11 final size:11
Alignment explanation
Indices: 653014--653055 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
653004 GATACCCTGC
653014 TACAGTACTGT
1 TACAGTACTGT
*
653025 TACAGTACAGT
1 TACAGTACTGT
*
653036 TACAGTACTGC
1 TACAGTACTGT
653047 TACAGTACT
1 TACAGTACT
653056 TCCGTAAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (11 bp):
TACAGTACTGT
Found at i:653815 original size:25 final size:25
Alignment explanation
Indices: 653778--653847 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
653768 CAGCTTGTAT
653778 AAATTTGCACCGAAGTGCCACGTAG
1 AAATTTGCACCGAAGTGCCACGTAG
* *
653803 AATTTTGTC-CCGAAG-GACCGCGTAG
1 AAATTTG-CACCGAAGTG-CCACGTAG
*
653828 AAATTTGCACCGTAGTGCCA
1 AAATTTGCACCGAAGTGCCA
653848 TATAATATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
24 2 0.06
25 32 0.89
26 2 0.06
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (25 bp):
AAATTTGCACCGAAGTGCCACGTAG
Found at i:658903 original size:21 final size:23
Alignment explanation
Indices: 658860--658905 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
658850 AGAATGTTGG
* *
658860 AGGGAAACCGATTCCCCTGCTAC
1 AGGGAAACCGATTACCCTACTAC
658883 AGGG-AACCGA-TACCCTACTAC
1 AGGGAAACCGATTACCCTACTAC
658904 AG
1 AG
658906 TACTGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 6 0.29
23 4 0.19
ACGTcount: A:0.30, C:0.33, G:0.22, T:0.15
Consensus pattern (23 bp):
AGGGAAACCGATTACCCTACTAC
Found at i:659606 original size:25 final size:25
Alignment explanation
Indices: 659578--659652 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
659568 CACCACAGCT
*
659578 CGTATAAATTTGCACCGAAGTGCCA
1 CGTAGAAATTTGCACCGAAGTGCCA
* *
659603 CGTAGAATTTTGTC-CCGAAG-GACCG
1 CGTAGAAATTTG-CACCGAAGTG-CCA
*
659628 CGTAGAAATTTGCACCGTAGTGCCA
1 CGTAGAAATTTGCACCGAAGTGCCA
659653 TATAAGATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
24 2 0.05
25 36 0.90
26 2 0.05
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (25 bp):
CGTAGAAATTTGCACCGAAGTGCCA
Found at i:659898 original size:19 final size:21
Alignment explanation
Indices: 659862--659901 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
659852 TATCGTATCA
659862 TATAACATGGTCATTATCATT
1 TATAACATGGTCATTATCATT
*
659883 TATAACA-GTTCA-TATCATT
1 TATAACATGGTCATTATCATT
659902 GTTCTTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.42
Consensus pattern (21 bp):
TATAACATGGTCATTATCATT
Found at i:661797 original size:14 final size:13
Alignment explanation
Indices: 661774--661803 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
661764 ATAACTATTT
661774 TATATATCCATTA
1 TATATATCCATTA
661787 TATATTATCCATTA
1 TATA-TATCCATTA
661801 TAT
1 TAT
661804 TTTTAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (13 bp):
TATATATCCATTA
Found at i:664208 original size:23 final size:23
Alignment explanation
Indices: 664182--664231 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
664172 CTTTACTTCT
* *
664182 TTTAAATT-AATTTATTTGTTTTC
1 TTTAAATTAAATCT-TTTATTTTC
*
664205 TTTATATTAAATCTTTTATTTTC
1 TTTAAATTAAATCTTTTATTTTC
664228 TTTA
1 TTTA
664232 CAAACTTCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTAAATTAAATCTTTTATTTTC
Found at i:668387 original size:25 final size:25
Alignment explanation
Indices: 668352--668413 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
668342 CCTAATAAGC
*
668352 AATGTTTGAAAATAATTTTGAAAAC
1 AATGTTTGAAAATAATTTTGAAAAA
* *
668377 CATGTTTGAAAATAATTTTTAAAAA
1 AATGTTTGAAAATAATTTTGAAAAA
668402 AATGTTTGAAAA
1 AATGTTTGAAAA
668414 ATTATGATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.48, C:0.03, G:0.11, T:0.37
Consensus pattern (25 bp):
AATGTTTGAAAATAATTTTGAAAAA
Found at i:668414 original size:12 final size:13
Alignment explanation
Indices: 668352--668413 Score: 74
Period size: 12 Copynumber: 4.9 Consensus size: 13
668342 CCTAATAAGC
668352 AATGTTTGAAAAT
1 AATGTTTGAAAAT
*
668365 AAT-TTTGAAAAC
1 AATGTTTGAAAAT
*
668377 CATGTTTGAAAAT
1 AATGTTTGAAAAT
* *
668390 AAT-TTTTAAAAA
1 AATGTTTGAAAAT
668402 AATGTTTGAAAA
1 AATGTTTGAAAA
668414 ATTATGATAC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
12 20 0.50
13 20 0.50
ACGTcount: A:0.48, C:0.03, G:0.11, T:0.37
Consensus pattern (13 bp):
AATGTTTGAAAAT
Found at i:668414 original size:13 final size:13
Alignment explanation
Indices: 668352--668414 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
668342 CCTAATAAGC
*
668352 AATGTTTGAAAAT
1 AATGTTTGAAAAA
*
668365 AAT-TTTGAAAAC
1 AATGTTTGAAAAA
* *
668377 CATGTTTGAAAAT
1 AATGTTTGAAAAA
*
668390 AAT-TTTTAAAAA
1 AATGTTTGAAAAA
668402 AATGTTTGAAAAA
1 AATGTTTGAAAAA
668415 TTATGATACA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
12 20 0.49
13 21 0.51
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (13 bp):
AATGTTTGAAAAA
Found at i:668480 original size:17 final size:19
Alignment explanation
Indices: 668438--668478 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
668428 AGTTTTCATG
668438 AAAACAACATAATTAAATCA
1 AAAACAACA-AATTAAATCA
668458 AAAACAAC-AATTAAATCA
1 AAAACAACAAATTAAATCA
668476 AAA
1 AAA
668479 CATTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 13 0.62
20 8 0.38
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAACAACAAATTAAATCA
Found at i:672771 original size:23 final size:22
Alignment explanation
Indices: 672707--672811 Score: 119
Period size: 22 Copynumber: 4.9 Consensus size: 22
672697 GTACGACGAC
* *
672707 TATGTCCCAAAAGACCACTGTA
1 TATGTCCCGAAGGACCACTGTA
* *
672729 TATATCCCGAAAGACCACTGTA
1 TATGTCCCGAAGGACCACTGTA
*
672751 TATGTCCCCTAAGGACCACTGTA
1 TATGT-CCCGAAGGACCACTGTA
*
672774 TATGTCTCGAAGGACCAC----
1 TATGTCCCGAAGGACCACTGTA
672792 TATGTCCCGAAGGACCACTG
1 TATGTCCCGAAGGACCACTG
672812 ATAATCCCTC
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
18 17 0.24
22 35 0.49
23 20 0.28
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (22 bp):
TATGTCCCGAAGGACCACTGTA
Found at i:672797 original size:18 final size:18
Alignment explanation
Indices: 672774--672810 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
672764 GACCACTGTA
*
672774 TATGTCTCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
672792 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
672810 T
1 T
672811 GATAATCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.22
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:675432 original size:19 final size:19
Alignment explanation
Indices: 675408--675460 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
675398 AGTTGATCTA
675408 GTGCATCGGTACACTTTGG
1 GTGCATCGGTACACTTTGG
675427 GTGCATCGGTACACTTTGG
1 GTGCATCGGTACACTTTGG
*
675446 GTACATCGGTACACT
1 GTGCATCGGTACACT
675461 AATTACATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (19 bp):
GTGCATCGGTACACTTTGG
Found at i:675516 original size:19 final size:19
Alignment explanation
Indices: 675492--675556 Score: 103
Period size: 19 Copynumber: 3.4 Consensus size: 19
675482 AGAGCCAGGA
*
675492 GTGCATCGATGCATGGTCG
1 GTGCATCGATGCATGGTTG
*
675511 GTGCATCGATGCATTGTTG
1 GTGCATCGATGCATGGTTG
*
675530 GTGCATCGATGCATGGTTT
1 GTGCATCGATGCATGGTTG
675549 GTGCATCG
1 GTGCATCG
675557 GTACATAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.15, C:0.18, G:0.34, T:0.32
Consensus pattern (19 bp):
GTGCATCGATGCATGGTTG
Found at i:680144 original size:20 final size:20
Alignment explanation
Indices: 680115--680282 Score: 138
Period size: 20 Copynumber: 7.7 Consensus size: 20
680105 TAAATAAAAT
680115 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
680135 GCACGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
680161 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
680181 GCATGAAAGGATGCCATAAATA
1 GCATGAAAGGATG-CATTAA-G
*
680203 ACATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
680223 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
680249 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
680269 GCATGAAAGAATGC
1 GCATGAAAGGATGC
680283 CATAAATAAA
Statistics
Matches: 119, Mismatches: 15, Indels: 28
0.73 0.09 0.17
Matches are distributed among these distances:
20 53 0.45
21 16 0.13
22 14 0.12
24 2 0.02
25 6 0.05
26 28 0.24
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.19
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:680169 original size:46 final size:46
Alignment explanation
Indices: 680053--680295 Score: 386
Period size: 46 Copynumber: 5.3 Consensus size: 46
680043 AAACCGAATA
*
680053 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGCCTAC
1 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG----C
*
680103 CATAAATAAAATGCATGAAAGGATGCATTAAGGCACGAAAGGATGC
1 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
680149 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
680195 CATAAAT--AA--CATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
680237 CATAAATAAAATGCATGAAATGATGCATTAAGGCATGAAAGAATGC
1 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
680283 CATAAATAAAATG
1 CATAAATAAAATG
680296 AAATTTAACG
Statistics
Matches: 184, Mismatches: 5, Indels: 12
0.92 0.02 0.06
Matches are distributed among these distances:
42 40 0.22
44 4 0.02
46 97 0.53
50 43 0.23
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.20
Consensus pattern (46 bp):
CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:680216 original size:88 final size:88
Alignment explanation
Indices: 680053--680298 Score: 384
Period size: 88 Copynumber: 2.7 Consensus size: 88
680043 AAACCGAATA
680053 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGCCTACCATAAATAAAATGCA
1 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATG----CCATAAAT--AA--CA
680118 TGAAAGGATGCATTAAGGCACGAAAGGATGC
58 TGAAAGGATGCATTAAGGCACGAAAGGATGC
*
680149 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAACATGAAAGGA
1 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGCCATAAATAACATGAAAGGA
*
680214 TGCATTAAGGCATGAAAGGATGC
66 TGCATTAAGGCACGAAAGGATGC
* *
680237 CATAAATAAAATGCATGAAATGATGCATTAAGGCATGAAAGAATGCCATAAATAAAATGAAA
1 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGCCATAAATAACATGAAA
680299 TTTAACGAAT
Statistics
Matches: 145, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
88 91 0.63
90 2 0.01
92 8 0.06
96 44 0.30
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.20
Consensus pattern (88 bp):
CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGCCATAAATAACATGAAAGGA
TGCATTAAGGCACGAAAGGATGC
Found at i:680261 original size:26 final size:26
Alignment explanation
Indices: 680053--680295 Score: 131
Period size: 20 Copynumber: 10.5 Consensus size: 26
680043 AAACCGAATA
680053 CATAAATAAAATGCATGAAAGGATG-
1 CATAAATAAAATGCATGAAAGGATGC
* *
680078 CAT---T--AAGGCATGAAAGAATGCCTAC
1 CATAAATAAAATGCATGAAAGGATG----C
680103 CATAAATAAAATGCATGAAAGGATG-
1 CATAAATAAAATGCATGAAAGGATGC
* *
680128 CAT---T--AAGGCACGAAAGGATGC
1 CATAAATAAAATGCATGAAAGGATGC
680149 CATAAATAAAATGCATGAAAGGATG-
1 CATAAATAAAATGCATGAAAGGATGC
*
680174 CAT---T--AAGGCATGAAAGGATGC
1 CATAAATAAAATGCATGAAAGGATGC
680195 CATAAAT--AA--CATGAAAGGATG-
1 CATAAATAAAATGCATGAAAGGATGC
*
680216 CAT---T--AAGGCATGAAAGGATGC
1 CATAAATAAAATGCATGAAAGGATGC
*
680237 CATAAATAAAATGCATGAAATGATG-
1 CATAAATAAAATGCATGAAAGGATGC
* *
680262 CAT---T--AAGGCATGAAAGAATGC
1 CATAAATAAAATGCATGAAAGGATGC
680283 CATAAATAAAATG
1 CATAAATAAAATG
680296 AAATTTAACG
Statistics
Matches: 169, Mismatches: 15, Indels: 67
0.67 0.06 0.27
Matches are distributed among these distances:
18 3 0.02
20 68 0.40
21 15 0.09
22 16 0.09
24 6 0.04
25 15 0.09
26 31 0.18
28 1 0.01
30 14 0.08
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.20
Consensus pattern (26 bp):
CATAAATAAAATGCATGAAAGGATGC
Found at i:683058 original size:30 final size:30
Alignment explanation
Indices: 683022--683078 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
683012 GTTTTTACGT
* *
683022 ATAAAATATTACACAATTATTTTAAAAATC
1 ATAAAATAATACACAATTATTCTAAAAATC
*
683052 ATAAAATAATACAGAATTATTCTAAAA
1 ATAAAATAATACACAATTATTCTAAAA
683079 TATTAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (30 bp):
ATAAAATAATACACAATTATTCTAAAAATC
Found at i:683079 original size:21 final size:20
Alignment explanation
Indices: 683053--683100 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
683043 TTAAAAATCA
*
683053 TAAAATAATACAGAATTATT
1 TAAAATAATAAAGAATTATT
* *
683073 CTAAAATATTAAATAATTATT
1 -TAAAATAATAAAGAATTATT
683094 TAAAATA
1 TAAAATA
683101 TTTAGAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (20 bp):
TAAAATAATAAAGAATTATT
Found at i:683137 original size:17 final size:17
Alignment explanation
Indices: 683117--683150 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
683107 AAACAATATG
683117 AAATATAAAATGTTAAA
1 AAATATAAAATGTTAAA
* *
683134 AAATATTAAATTTTAAA
1 AAATATAAAATGTTAAA
683151 GATTCGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
AAATATAAAATGTTAAA
Found at i:685676 original size:28 final size:28
Alignment explanation
Indices: 685581--685678 Score: 76
Period size: 28 Copynumber: 3.5 Consensus size: 28
685571 TGGATACTTT
* * *
685581 TTATTTTAATTTGTAAAAATTATTGGATA
1 TTATTGTAATTTATAAAAATTATAGG-TA
* * ** *
685610 TTATTGTAATTT-GAAAAATGTAGACCTT
1 TTATTGTAATTTATAAAAAT-TATAGGTA
685638 TTCA-TGT-ATTTATAAAAATTATAGGTA
1 TT-ATTGTAATTTATAAAAATTATAGGTA
685665 TTATTGTAATTTAT
1 TTATTGTAATTTAT
685679 GAGAAGTTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 11
0.69 0.16 0.15
Matches are distributed among these distances:
26 1 0.02
27 13 0.25
28 24 0.46
29 14 0.27
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (28 bp):
TTATTGTAATTTATAAAAATTATAGGTA
Found at i:685726 original size:27 final size:28
Alignment explanation
Indices: 685665--685730 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
685655 ATTATAGGTA
* *
685665 TTATTGTAATTTATGAGAAGTTTTTTCT
1 TTATTGTAATTTATGAAAAGTTTTTGCT
*
685693 TTGATTGTAATTTAT-AAATAG-TTTTGGT
1 TT-ATTGTAATTTATGAAA-AGTTTTTGCT
685721 TTATTGTAAT
1 TTATTGTAAT
685731 ATTAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
27 8 0.24
28 11 0.33
29 14 0.42
ACGTcount: A:0.27, C:0.02, G:0.15, T:0.56
Consensus pattern (28 bp):
TTATTGTAATTTATGAAAAGTTTTTGCT
Found at i:685807 original size:16 final size:16
Alignment explanation
Indices: 685786--685818 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
685776 TTTATTGTAA
685786 TTTATAAT-TTTCATTT
1 TTTATAATATTT-ATTT
685802 TTTATAATATTTATTT
1 TTTATAATATTTATTT
685818 T
1 T
685819 AGAAATTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATAATATTTATTT
Found at i:688446 original size:85 final size:85
Alignment explanation
Indices: 688297--688462 Score: 228
Period size: 85 Copynumber: 2.0 Consensus size: 85
688287 ATATAATAAC
* * * *
688297 GACACACGAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATAACATGCAATGTAATTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACAGGGGCTTCAATAACACGCAATGTAAGTCATA
688362 AATGCG-TATCATAAATTTAT
66 AATGCGCT-TCATAAATTTAT
* * * *
688382 GACACACAAATGTGTGTCATCTTCATTTATGTCAGGGGCTTCAATGACGCGCAATG-AGCGTCAT
1 GACACACAAATGTGTGTCATCTTCATTTATGACAGGGGCTTCAATAACACGCAATGTA-AGTCAT
688446 AAATGCGCTTCATAAAT
65 AAATGCGCTTCATAAAT
688463 GAGCACCATA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
84 1 0.01
85 69 0.97
86 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTCATTTATGACAGGGGCTTCAATAACACGCAATGTAAGTCATA
AATGCGCTTCATAAATTTAT
Found at i:688463 original size:26 final size:26
Alignment explanation
Indices: 688434--688498 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
688424 AATGACGCGC
688434 AATGAGCGTCATAAATGCGCT-TCATA
1 AATGAGCGTCATAAATGCG-TGTCATA
** *
688460 AATGAGCACCATAAATGTGTGTCATA
1 AATGAGCGTCATAAATGCGTGTCATA
*
688486 AATGTGCGTCATA
1 AATGAGCGTCATA
688499 GATTTATGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 1 0.03
26 31 0.97
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (26 bp):
AATGAGCGTCATAAATGCGTGTCATA
Found at i:688481 original size:85 final size:85
Alignment explanation
Indices: 688297--688484 Score: 224
Period size: 85 Copynumber: 2.2 Consensus size: 85
688287 ATATAATAAC
* * * *
688297 GACACACGAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATAACATGCAATGTAATTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACAGGGGCTTCAATAACACGCAATGTAAGTCATA
*
688362 AATGCGTATCATAAATTTAT
66 AATGCGTATCATAAATTGAT
* * * *
688382 GACACACAAATGTGTGTCATCTTCATTTATGTCAGGGGCTTCAATGACGCGCAATG-AGCGTCAT
1 GACACACAAATGTGTGTCATCTTCATTTATGACAGGGGCTTCAATAACACGCAATGTA-AGTCAT
688446 AAATGCGCT-TCATAAA-TGA-
65 AAATGCG-TATCATAAATTGAT
*
688465 G-CACCATAAATGTGTGTCAT
1 GACA-CACAAATGTGTGTCAT
688485 AAATGTGCGT
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
82 2 0.02
83 16 0.18
84 3 0.03
85 68 0.76
86 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTCATTTATGACAGGGGCTTCAATAACACGCAATGTAAGTCATA
AATGCGTATCATAAATTGAT
Found at i:688485 original size:13 final size:13
Alignment explanation
Indices: 688434--688498 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
688424 AATGACGCGC
*
688434 AATGAGCGTCATA
1 AATGTGCGTCATA
* *
688447 AATGCGCTTCATA
1 AATGTGCGTCATA
* **
688460 AATGAGCACCATA
1 AATGTGCGTCATA
*
688473 AATGTGTGTCATA
1 AATGTGCGTCATA
688486 AATGTGCGTCATA
1 AATGTGCGTCATA
688499 GATTTATGAT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (13 bp):
AATGTGCGTCATA
Found at i:693227 original size:20 final size:20
Alignment explanation
Indices: 693202--693377 Score: 120
Period size: 20 Copynumber: 8.0 Consensus size: 20
693192 AAATAAAATG
693202 CATGAAAGGATGCATTAAGA
1 CATGAAAGGATGCATTAAGA
*
693222 CATGAAAGGATGTCATAAATAAAA
1 CATGAAAGGATG-CAT---TAAGA
*
693246 TGCATGAAAGGATGCATTAAGG
1 --CATGAAAGGATGCATTAAGA
*
693268 CATGAAAGGATGTCATATATAAAA
1 CATGAAAGGATG-C--AT-TAAGA
* *
693292 TGCATGAAAGGATCCATAAATAAAA
1 --CATGAAAGGATGCAT---TAAGA
*
693317 TTCAT-AAATGGATGCATTAAGG
1 --CATGAAA-GGATGCATTAAGA
693339 CATGAAAGGATGCATTAAGA
1 CATGAAAGGATGCATTAAGA
*
693359 CATGAAATGATGCATTAAG
1 CATGAAAGGATGCATTAAG
693378 GTATGAAATG
Statistics
Matches: 128, Mismatches: 12, Indels: 32
0.74 0.07 0.19
Matches are distributed among these distances:
20 57 0.45
21 7 0.05
22 6 0.05
23 4 0.03
24 10 0.08
25 21 0.16
26 23 0.18
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.23
Consensus pattern (20 bp):
CATGAAAGGATGCATTAAGA
Found at i:693256 original size:46 final size:45
Alignment explanation
Indices: 693189--693843 Score: 405
Period size: 46 Copynumber: 14.3 Consensus size: 45
693179 AAACCAAATA
693189 CATAAATAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATG
1 CATAAATAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATG
*
693234 TCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 -CATAAATAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATG
* * *
693280 TCATATATAAAATGCATGAAAGGATCCATAAATAAAATTCAT-AAATGGATG
1 -CATAAATAAAATGCATGAAAGGATGCAT---TAAGA--CATGAAA-GGATG
* *
693331 CAT---T--AAGGCATGAAAGGATGCATTAAGACATGAAATGATG
1 CATAAATAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATG
* * * * * *
693371 CAT---T--AAGGTATGAAATGATACCATAAATAAAATGCATGAAATGATG
1 CATAAATAAAATGCATGAAAGGAT-GCAT---TAAGA--CATGAAAGGATG
* * * * *
693417 CAT---T--AAGGCATGAATGGATGCCACAAATAAAATGCATGAAAGAATG
1 CATAAATAAAATGCATGAAAGGATG---C-ATTAAGA--CATGAAAGGATG
* *
693463 CAT---T--AAGGCATGAAAGGATGCCATAAATTAA-ATGCATGAAAAGATG
1 CATAAATAAAATGCATGAAAGGATG-C----ATTAAGA--CATGAAAGGATG
* *
693509 CAT---T--AAGGCATGAAAGGATGCCATAAATTAA-ATGCATGAAAGGATAC
1 CATAAATAAAATGCATGAAAGGATG-C----ATTAAGA--CATGAAAGGAT-G
* * *
693556 CATAAATAAAATGCATGAAATGATACATTAAGGCATGAAAGGATG
1 CATAAATAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATG
* * *
693601 CCATAAATAAAATGCATGAAAGGATACATTAAGGCATAAAAGGATG
1 -CATAAATAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATG
* * *
693647 CAATAAATAAAATGCACGAAAGGATGAATTAAGGCATGAAAGGATG
1 C-ATAAATAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATG
*
693693 CCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 -CATAAATAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATG
* * * * *
693739 TCATAAATAAAATGCATGAAATGATGCATTATGGCATGGACGGATG
1 -CATAAATAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATG
*
693785 CCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAA-GATG
1 -CATAAATAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATG
693830 CCATAAATAAAATG
1 -CATAAATAAAATG
693844 AAATTTAACG
Statistics
Matches: 529, Mismatches: 50, Indels: 61
0.83 0.08 0.10
Matches are distributed among these distances:
40 24 0.05
41 6 0.01
42 4 0.01
44 5 0.01
45 36 0.07
46 405 0.77
47 15 0.03
48 1 0.00
49 4 0.01
50 7 0.01
51 9 0.02
52 13 0.02
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (45 bp):
CATAAATAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATG
Found at i:693329 original size:25 final size:25
Alignment explanation
Indices: 693189--693317 Score: 107
Period size: 20 Copynumber: 5.5 Consensus size: 25
693179 AAACCAAATA
*
693189 CATAAATAAAATGCATGAAAGGATG
1 CATAAATAAAATGCATGAAAGGATC
* *
693214 CAT---TAAGA--CATGAAAGGATGT
1 CATAAATAAAATGCATGAAAGGAT-C
*
693235 CATAAATAAAATGCATGAAAGGATG
1 CATAAATAAAATGCATGAAAGGATC
* *
693260 CAT---T--AAGGCATGAAAGGATGT
1 CATAAATAAAATGCATGAAAGGAT-C
*
693281 CATATATAAAATGCATGAAAGGATC
1 CATAAATAAAATGCATGAAAGGATC
693306 CATAAATAAAAT
1 CATAAATAAAAT
693318 TCATAAATGG
Statistics
Matches: 83, Mismatches: 9, Indels: 24
0.72 0.08 0.21
Matches are distributed among these distances:
20 25 0.30
21 6 0.07
22 5 0.06
24 5 0.06
25 17 0.20
26 25 0.30
ACGTcount: A:0.49, C:0.09, G:0.19, T:0.22
Consensus pattern (25 bp):
CATAAATAAAATGCATGAAAGGATC
Found at i:693383 original size:20 final size:20
Alignment explanation
Indices: 693322--693529 Score: 114
Period size: 20 Copynumber: 9.4 Consensus size: 20
693312 TAAAATTCAT
693322 AAATGGATGCATTAAGGCATG
1 AAAT-GATGCATTAAGGCATG
* *
693343 AAAGGATGCATTAAGACATG
1 AAATGATGCATTAAGGCATG
*
693363 AAATGATGCATTAAGGTATG
1 AAATGATGCATTAAGGCATG
* *
693383 AAATGATACCATAAATAAAATGCATG
1 AAATGAT-GCAT---T--AAGGCATG
693409 AAATGATGCATTAAGGCATG
1 AAATGATGCATTAAGGCATG
* *
693429 -AATGGATGCCACAAATAAAATGCATG
1 AAAT-GATG---C--AT-TAAGGCATG
693455 AAA-GAATGCATTAAGGCATG
1 AAATG-ATGCATTAAGGCATG
* *
693475 AAAGGATGCCATAAATTAAATGCATG
1 AAATGATG-C----ATT-AAGGCATG
*
693501 AAAAGATGCATTAAGGCATG
1 AAATGATGCATTAAGGCATG
*
693521 AAAGGATGC
1 AAATGATGC
693530 CATAAATTAA
Statistics
Matches: 147, Mismatches: 18, Indels: 45
0.70 0.09 0.21
Matches are distributed among these distances:
19 3 0.02
20 78 0.53
21 13 0.09
22 1 0.01
23 2 0.01
24 1 0.01
25 10 0.07
26 37 0.25
27 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.22
Consensus pattern (20 bp):
AAATGATGCATTAAGGCATG
Found at i:693546 original size:72 final size:72
Alignment explanation
Indices: 693470--693765 Score: 319
Period size: 72 Copynumber: 4.2 Consensus size: 72
693460 ATGCATTAAG
*
693470 GCATGAAAGGATGCCATAAATTAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCATAA
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCATAA
*
693535 ATTAAAT
66 ATAAAAT
* * *
693542 GCATGAAAGGATACCATAAATAAAATGCATGAAATGATACATTAAGGCATGAAAGGATGCCATAA
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCATAA
693607 ATAAAAT
66 ATAAAAT
* * * * *
693614 GCATGAAAGGAT-ACATTAAGGCATAAAA-GGATGCAATAA-AT--A-AAATGCACGAAAGGATG
1 GCATGAAAGGATGCCA-TAA---ATAAAATGCATG-AA-AAGATGCATTAAGGCATGAAAGGATG
* *
693673 -----AAT-TAAG
60 CCATAAATAAAAT
* *
693680 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAA
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCATAA
693745 ATAAAAT
66 ATAAAAT
*
693752 GCATGAAATGATGC
1 GCATGAAAGGATGC
693766 ATTATGGCAT
Statistics
Matches: 184, Mismatches: 22, Indels: 36
0.76 0.09 0.15
Matches are distributed among these distances:
62 1 0.01
63 10 0.05
64 4 0.02
65 1 0.01
66 31 0.17
67 5 0.03
71 5 0.03
72 111 0.60
73 1 0.01
74 4 0.02
75 10 0.05
76 1 0.01
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (72 bp):
GCATGAAAGGATGCCATAAATAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCATAA
ATAAAAT
Found at i:693585 original size:118 final size:118
Alignment explanation
Indices: 693424--693671 Score: 381
Period size: 118 Copynumber: 2.1 Consensus size: 118
693414 ATGCATTAAG
* * *
693424 GCATGAATGGATGCCACAAATAAAATGCATGAAAGAATGCATTAAGGCATGAAAGGATGCCATAA
1 GCATGAAAGGATACCACAAATAAAATGCATGAAAGAATACATTAAGGCATGAAAGGATGCCATAA
* * * * *
693489 ATTAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCATAAATTAAAT
66 ATAAAATGCATGAAAAGATACATTAAGGCATAAAAGGATGCAATAAATAAAAT
*
693542 GCATGAAAGGATACCATAAATAAAATGCATGAAATG-ATACATTAAGGCATGAAAGGATGCCATA
1 GCATGAAAGGATACCACAAATAAAATGCATGAAA-GAATACATTAAGGCATGAAAGGATGCCATA
*
693606 AATAAAATGCATGAAAGGATACATTAAGGCATAAAAGGATGCAATAAATAAAAT
65 AATAAAATGCATGAAAAGATACATTAAGGCATAAAAGGATGCAATAAATAAAAT
*
693660 GCACGAAAGGAT
1 GCATGAAAGGAT
693672 GAATTAAGGC
Statistics
Matches: 118, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
118 117 0.99
119 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.20
Consensus pattern (118 bp):
GCATGAAAGGATACCACAAATAAAATGCATGAAAGAATACATTAAGGCATGAAAGGATGCCATAA
ATAAAATGCATGAAAAGATACATTAAGGCATAAAAGGATGCAATAAATAAAAT
Found at i:693587 original size:164 final size:163
Alignment explanation
Indices: 693222--693717 Score: 611
Period size: 164 Copynumber: 3.1 Consensus size: 163
693212 TGCATTAAGA
** * * *
693222 CATGAAAGGATGTCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATATA
1 CATGAAAGGATACCATAAATAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAA
* ** *
693287 TAAAATGCATGAAAGGATCCATAAATAAAATTCATAAATGGATG-C----ATT-AAGGCATGAAA
66 TAAAATGCATGAAAGGATACAT---T--AAGGCATAAA-GGATGCCATAAATTAAATGCATGAAA
* * *
693346 GGATGCATTAAGACATGAAATGATG-C----ATT-AAGG
125 GGATGCATTAAGGCATGAAAGGATGCCATAAATTAAATG
* * * *
693379 TATGAAATGATACCATAAATAAAATGCATGAAATGATGCATTAAGGCATGAATGGATGCCACAAA
1 CATGAAAGGATACCATAAATAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAA
* * *
693444 TAAAATGCATGAAAGAATGCATTAAGGCATGAAAGGATGCCATAAATTAAATGCATGAAAAGATG
66 TAAAATGCATGAAAGGATACATTAAGGCAT-AAAGGATGCCATAAATTAAATGCATGAAAGGATG
693509 CATTAAGGCATGAAAGGATGCCATAAATTAAATG
130 CATTAAGGCATGAAAGGATGCCATAAATTAAATG
*
693543 CATGAAAGGATACCATAAATAAAATGCATGAAATGATACATTAAGGCATGAAAGGATGCCATAAA
1 CATGAAAGGATACCATAAATAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAA
* * *
693608 TAAAATGCATGAAAGGATACATTAAGGCATAAAAGGATGCAATAAATAAAATGCACGAAAGGATG
66 TAAAATGCATGAAAGGATACATTAAGGCAT-AAAGGATGCCATAAATTAAATGCATGAAAGGATG
* *
693673 AATTAAGGCATGAAAGGATGCCATAAATAAAATG
130 CATTAAGGCATGAAAGGATGCCATAAATTAAATG
693707 CATGAAAGGAT
1 CATGAAAGGAT
693718 GCATTAAGGC
Statistics
Matches: 294, Mismatches: 32, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
152 10 0.03
153 4 0.01
154 1 0.00
157 79 0.27
158 32 0.11
159 1 0.00
163 3 0.01
164 164 0.56
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (163 bp):
CATGAAAGGATACCATAAATAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAA
TAAAATGCATGAAAGGATACATTAAGGCATAAAGGATGCCATAAATTAAATGCATGAAAGGATGC
ATTAAGGCATGAAAGGATGCCATAAATTAAATG
Found at i:693657 original size:210 final size:202
Alignment explanation
Indices: 693189--693769 Score: 733
Period size: 210 Copynumber: 2.8 Consensus size: 202
693179 AAACCAAATA
*
693189 CATAAATAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATGTCATAAATAAAATGCATGAA
1 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG-CATAAATAAAATGCATGAA
* * * **
693254 AGGATGCATTAAGGCATGAAAGGATGTCATATATAAAATGCATGAAAGGATCCATAAATAAAATT
65 AGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCAT---T--AAGG
* * * *
693319 CAT-AAATGGATGC----ATT-AAGGCATGAAAGGATGCATTAAGACATGAAATGATGCATTAAG
125 CATGAAA-GGATGCATAAATTAAATGCATGAAAGGATCCATTAAAACATGAAATGATACATTAAG
* *
693378 GTATGAAATGATAC
189 GCATGAAAGGATAC
* * *
693392 CATAAATAAAATGCATGAAATGATGCATTAAGGCATGAATGGATGCCACAAATAAAATGCATGAA
1 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG-CATAAATAAAATGCATGAA
* * *
693457 AGAATGCATTAAGGCATGAAAGGATGCCATAAATTAAATGCATGAAAAGATGCATTAAGGCATGA
65 AGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGA
693522 AAGGATGCCATAAATTAAATGCATGAAAGGATACCATAAATAAAATGCATGAAATGATACATTAA
130 AAGGATG-CATAAATTAAATGCATGAAAGGAT-CCAT---TAAAA--CATGAAATGATACATTAA
*
693587 GGCATGAAAGGATGC
188 GGCATGAAAGGATAC
* * *
693602 CATAAATAAAATGCATGAAAGGATACATTAAGGCATAAAAGGATGCAATAAATAAAATGCACGAA
1 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC-ATAAATAAAATGCATGAA
*
693667 AGGATGAATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGA
65 AGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGA
* * *
693732 AAGGATGTCATAAATAAAATGCATGAAATGATGCATTA
130 AAGGATG-CATAAATTAAATGCATGAAAGGATCCATTA
693770 TGGCATGGAC
Statistics
Matches: 330, Mismatches: 34, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
198 10 0.03
199 4 0.01
200 1 0.00
203 112 0.34
204 14 0.04
205 3 0.01
206 2 0.01
208 4 0.01
209 4 0.01
210 176 0.53
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (202 bp):
CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCATAAATAAAATGCATGAAA
GGATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAA
AGGATGCATAAATTAAATGCATGAAAGGATCCATTAAAACATGAAATGATACATTAAGGCATGAA
AGGATAC
Found at i:693689 original size:20 final size:20
Alignment explanation
Indices: 693614--693738 Score: 72
Period size: 20 Copynumber: 5.7 Consensus size: 20
693604 TAAATAAAAT
693614 GCATGAAAGGAT-ACATTAAG
1 GCATGAAAGGATGA-ATTAAG
* *
693634 GCATAAAAGGATGCAATAAATAAAAT
1 GCATGAAAGGATG-AAT---T--AAG
*
693660 GCACGAAAGGATGAATTAAG
1 GCATGAAAGGATGAATTAAG
* *
693680 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATG-----AAT-TAAG
*
693706 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGAATTAAG
693726 GCATGAAAGGATG
1 GCATGAAAGGATG
693739 TCATAAATAA
Statistics
Matches: 81, Mismatches: 11, Indels: 26
0.69 0.09 0.22
Matches are distributed among these distances:
20 40 0.49
21 4 0.05
22 2 0.02
24 1 0.01
25 6 0.07
26 28 0.35
ACGTcount: A:0.47, C:0.10, G:0.25, T:0.18
Consensus pattern (20 bp):
GCATGAAAGGATGAATTAAG
Found at i:693715 original size:118 final size:114
Alignment explanation
Indices: 693467--693719 Score: 287
Period size: 118 Copynumber: 2.1 Consensus size: 114
693457 AGAATGCATT
* * * *
693467 AAGGCATGAAAGGATGCCATAAATTAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCA
1 AAGGCATGAAAGGATGCCATAAATAAAATGCATGAAAAGATACATTAAGGCATAAAAGGATGCAA
* * * * *
693532 TAAATTAAATGCATGAAAGGATACCATAAATAAAATGCATGAAATGATACATT
66 TAAATAAAATGCACGAAAGGATA-CAT--AT-AAAGGCATGAAATGATAAATA
*
693585 AAGGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATACATTAAGGCATAAAAGGATGCAA
1 AAGGCATGAAAGGATGCCATAAATAAAATGCATGAAAAGATACATTAAGGCATAAAAGGATGCAA
693650 TAAATAAAATGCACGAAAGGATGA-AT-T-AAGGCATGAAAGGATGCCATAAATAA
66 TAAATAAAATGCACGAAAGGAT-ACATATAAAGGCATG-AA--ATG--ATAAAT-A
*
693703 AATGCATGAAAGGATGC
1 AAGGCATGAAAGGATGC
693720 ATTAAGGCAT
Statistics
Matches: 117, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
112 7 0.06
113 2 0.02
114 1 0.01
115 3 0.03
117 7 0.06
118 96 0.82
119 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.20
Consensus pattern (114 bp):
AAGGCATGAAAGGATGCCATAAATAAAATGCATGAAAAGATACATTAAGGCATAAAAGGATGCAA
TAAATAAAATGCACGAAAGGATACATATAAAGGCATGAAATGATAAATA
Found at i:696867 original size:16 final size:16
Alignment explanation
Indices: 696823--696867 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
696813 TTTCCTGAAA
*
696823 TTTAATATTTTCTTCT
1 TTTAATATTTTTTTCT
* *
696839 TTTATTATATTTTTCT
1 TTTAATATTTTTTTCT
*
696855 TTTAACATTTTTT
1 TTTAATATTTTTT
696868 ATATATAACA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTAATATTTTTTTCT
Found at i:696881 original size:15 final size:15
Alignment explanation
Indices: 696857--696895 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
696847 ATTTTTCTTT
696857 TAACATTTTTTATATA
1 TAACATTTTTTA-ATA
*
696873 TAACATTTTTTAATT
1 TAACATTTTTTAATA
696888 TAACATTT
1 TAACATTT
696896 GCTTCTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (15 bp):
TAACATTTTTTAATA
Found at i:705984 original size:5 final size:5
Alignment explanation
Indices: 705974--706013 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
705964 TTTCGCAAAG
705974 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
706014 TGAAAAGCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:706476 original size:30 final size:31
Alignment explanation
Indices: 706436--706518 Score: 109
Period size: 29 Copynumber: 2.8 Consensus size: 31
706426 AAATAGAAAG
* *
706436 TAAAAGGACTAAAATAGTAATTACCAACATT
1 TAAAAGGACTAAAATAGTAATTACCAAAATC
* *
706467 TAAAA-GACT-AAATAGTAA-AAACAAAATC
1 TAAAAGGACTAAAATAGTAATTACCAAAATC
706495 TAAAAGGACTAAAATAGTAATTAC
1 TAAAAGGACTAAAATAGTAATTAC
706519 AAATAAACCA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 11 0.26
29 13 0.30
30 13 0.30
31 6 0.14
ACGTcount: A:0.57, C:0.11, G:0.10, T:0.23
Consensus pattern (31 bp):
TAAAAGGACTAAAATAGTAATTACCAAAATC
Found at i:706521 original size:30 final size:30
Alignment explanation
Indices: 706436--706521 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
706426 AAATAGAAAG
* *
706436 TAAAAGGACTAAAATAGTAATTACCAACATT
1 TAAAAGGACTAAAATAGTAATTA-CAAAATC
**
706467 TAAAA-GACT-AAATAGTAAAAACAAAATC
1 TAAAAGGACTAAAATAGTAATTACAAAATC
706495 TAAAAGGACTAAAATAGTAATTACAAA
1 TAAAAGGACTAAAATAGTAATTACAAA
706522 TAAACCAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
28 10 0.21
29 14 0.30
30 18 0.38
31 5 0.11
ACGTcount: A:0.58, C:0.10, G:0.09, T:0.22
Consensus pattern (30 bp):
TAAAAGGACTAAAATAGTAATTACAAAATC
Found at i:709604 original size:7 final size:7
Alignment explanation
Indices: 709592--709624 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
709582 TCATTTGTTT
709592 GCAACAA
1 GCAACAA
709599 GCAACAA
1 GCAACAA
709606 GCAACAA
1 GCAACAA
709613 GCAACAA
1 GCAACAA
709620 GCAAC
1 GCAAC
709625 CAGGACCTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.55, C:0.30, G:0.15, T:0.00
Consensus pattern (7 bp):
GCAACAA
Found at i:709944 original size:3 final size:3
Alignment explanation
Indices: 709936--709988 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
709926 TTTGTTTTAT
*
709936 TTA TTA TTA TTA TTA TTA TT- TTG TT- TTA TTA TTA -TA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
709980 TTA TTA TTA
1 TTA TTA TTA
709989 AATAATTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 8 0.17
3 38 0.83
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:709956 original size:19 final size:19
Alignment explanation
Indices: 709932--709988 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
709922 TTCATTTGTT
709932 TTATTTATTATTATTATTA
1 TTATTTATTATTATTATTA
*
709951 TTATTT-TGTTTTATTATTA
1 TTATTTAT-TATTATTATTA
709970 -TATTATATTATTATTATTA
1 TTATT-TATTATTATTATTA
709989 AATAATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 5 0.15
19 27 0.82
20 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TTATTTATTATTATTATTA
Found at i:709964 original size:16 final size:16
Alignment explanation
Indices: 709943--709987 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
709933 TATTTATTAT
*
709943 TATTATTATTATTTTG
1 TATTATTATTATTTTA
* *
709959 TTTTATTATTATATTA
1 TATTATTATTATTTTA
709975 TATTATTATTATT
1 TATTATTATTATT
709988 AAATAATTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TATTATTATTATTTTA
Found at i:709984 original size:29 final size:29
Alignment explanation
Indices: 709926--709981 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
709916 AATTATTTCA
709926 TTTGTTTTATTTATTATTATTATTATTAT
1 TTTGTTTTATTTATTATTATTATTATTAT
709955 TTTGTTTTA-TTATTA-TATTA-TATTAT
1 TTTGTTTTATTTATTATTATTATTATTAT
709981 T
1 T
709982 ATTATTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 7 0.26
27 5 0.19
28 6 0.22
29 9 0.33
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (29 bp):
TTTGTTTTATTTATTATTATTATTATTAT
Found at i:711823 original size:2 final size:2
Alignment explanation
Indices: 711816--711841 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
711806 TAAAGAAATA
711816 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
711842 TAATATCTTT
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):
AT
Found at i:713839 original size:43 final size:44
Alignment explanation
Indices: 713772--713855 Score: 125
Period size: 43 Copynumber: 1.9 Consensus size: 44
713762 TGGCTTTAGA
* *
713772 GAAGTTAGGAGGGAAAGTTATCCCCTATATGT-AAAGTTTTACT
1 GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAAGTTTTACT
* *
713815 GAAGTTAGGACTGAAAGATGTCCCCTATATGTAAAAGTTTT
1 GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAAGTTTT
713856 GTTTGATGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 28 0.78
44 8 0.22
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAAGTTTTACT
Found at i:714031 original size:14 final size:14
Alignment explanation
Indices: 714009--714044 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
713999 ATGCATTAAA
714009 ACATATTTACATTT
1 ACATATTTACATTT
*
714023 ACATTTTTACATTT
1 ACATATTTACATTT
*
714037 GCATATTT
1 ACATATTT
714045 TTAAATAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.53
Consensus pattern (14 bp):
ACATATTTACATTT
Found at i:714161 original size:14 final size:14
Alignment explanation
Indices: 714129--714167 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
714119 ATTTTAAATA
* *
714129 ATTTACGTTTACAT
1 ATTTACATTTGCAT
*
714143 TTTTACATTTGCAT
1 ATTTACATTTGCAT
714157 ATTTACATTTG
1 ATTTACATTTG
714168 GAATCTTTGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.08, T:0.54
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:717720 original size:21 final size:19
Alignment explanation
Indices: 717690--717770 Score: 80
Period size: 21 Copynumber: 4.3 Consensus size: 19
717680 ATGGGAAAGG
*
717690 AAAAAGGGGAAAAAAAGAAA
1 AAAAAAGGG-AAAAAAGAAA
717710 AAAAAATGGG--AAAA-AAA
1 AAAAAA-GGGAAAAAAGAAA
717727 AAAAAA-GGAAAAAAGAAA
1 AAAAAAGGGAAAAAAGAAA
*
717745 AAAAAAGGAAGAAAAAATAAA
1 AAAAAAGG--GAAAAAAGAAA
717766 AAAAA
1 AAAAA
717771 TTGAACCAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
15 2 0.04
17 13 0.25
18 13 0.25
19 1 0.02
20 5 0.10
21 18 0.35
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (19 bp):
AAAAAAGGGAAAAAAGAAA
Found at i:717727 original size:15 final size:15
Alignment explanation
Indices: 717702--717767 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 15
717692 AAAGGGGAAA
717702 AAAAGAAAAAAAAATGGG
1 AAAA-AAAAAAAAA--GG
717720 AAAAAAAAAAAAAGG
1 AAAAAAAAAAAAAGG
717735 AAAAAAGAAAAAAAAAGG
1 --AAAA-AAAAAAAAAGG
717753 AAGAAAAAATAAAAA
1 AA-AAAAAA-AAAAA
717768 AAATTGAACC
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
15 2 0.05
16 6 0.14
17 20 0.47
18 15 0.35
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAAAAGG
Found at i:717730 original size:36 final size:35
Alignment explanation
Indices: 717674--717769 Score: 106
Period size: 35 Copynumber: 2.7 Consensus size: 35
717664 CATATGTTGT
** **
717674 AAAAAAATGGG-AAAGGAAAAAGGGGAAAAAAAGAA
1 AAAAAAATGGGAAAAAAAAAAAAAGG-AAAAAAGAA
717709 AAAAAAATGGGAAAAAAAAAAAAAGGAAAAAAGAA
1 AAAAAAATGGGAAAAAAAAAAAAAGGAAAAAAGAA
717744 AAAAAAA-GGAAGAAAAAATAAAAAAA
1 AAAAAAATGG--GAAAAAA-AAAAAAA
717770 ATTGAACCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
34 2 0.04
35 27 0.51
36 17 0.32
37 7 0.13
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (35 bp):
AAAAAAATGGGAAAAAAAAAAAAAGGAAAAAAGAA
Found at i:721313 original size:70 final size:72
Alignment explanation
Indices: 721150--721323 Score: 219
Period size: 70 Copynumber: 2.4 Consensus size: 72
721140 ATCAACAAGA
* * *
721150 AGCAAATGTTGGGGTATGCTGAAAACCCATTTTAATCATAATCAGGAATATTGACGCATTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTTAATCAAAATCAGGAATA-T-AC-CATTTTGAA
721215 TATTCACATC
63 TATTCACATC
* * *
721225 AACAAATGTTGGGGCATGCTGAAAGCCCATTTTAATTAGAAAT-TGGAATA-A-CATTTTGAATA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTTAATCA-AAATCAGGAATATACCATTTTGAATA
*
721287 TTCATATC
65 TTCACATC
*
721295 AGCAAATGTTGGGGCATGCTGAAGGCCCA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCA
721324 CATCATTATG
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
70 45 0.51
72 1 0.01
75 40 0.45
76 3 0.03
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (72 bp):
AGCAAATGTTGGGGCATGCTGAAAGCCCATTTTAATCAAAATCAGGAATATACCATTTTGAATAT
TCACATC
Found at i:723543 original size:122 final size:123
Alignment explanation
Indices: 723280--724052 Score: 987
Period size: 123 Copynumber: 6.4 Consensus size: 123
723270 CACTCGATGG
*
723280 ATCAAC-TTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCA
1 ATCAACTTTTTC-AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* *
723344 TAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
65 TAATGAGAAGAACTTGTTCAACCTTTT-CTTGACTCTATCACAGAAGGAGATAGATCAGC
* * * *
723404 ATAAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCAT
1 ATCAACTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
723468 AATGAGAAGAACGTGTTCAACCTTTAT-TTGAATCTATCACAGAAGGAGATATATCAGC
66 AATGAGAAGAACTTGTTCAACCTTT-TCTTGACTCTATCACAGAAGGAGATAGATCAGC
* * * *
723526 ATCAACTTTTTCAGAGAACGTTCGTAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAATTCAT
1 ATCAACTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * * *
723590 AATGAGAAGAATTTGTTCAACCTTTTGCTTAAAT-TCATCAC---------TCGAT--GG
66 AATGAGAAGAACTTGTTCAACCTTTT-CTTGACTCT-ATCACAGAAGGAGATAGATCAGC
*
723638 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
723703 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
66 AATGAGAAGAACTTGTTCAACCTTTT-CTTGACTCTATCACAGAAGGAGATAGATCAGC
* * *
723762 ATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCAT
1 ATCAACTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
723826 AATGAGAAGAACTTGTTCAACCTTTAT-TTGACTTTATCACAGAAGGAGATAGATCAGC
66 AATGAGAAGAACTTGTTCAACCTTT-TCTTGACTCTATCACAGAAGGAGATAGATCAGC
*
723884 ATCAA-TTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCTGAAGAAGGAAGAAGAAGTTCA
1 ATCAACTTTTT-CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * * *
723948 TAATGAGAATAGCTTGTTCAACCTTTGT-TTGATTCTATCACAGAAGGAGATAGATCAGT
65 TAATGAGAAGAACTTGTTCAACCTTT-TCTTGACTCTATCACAGAAGGAGATAGATCAGC
* * *
724007 ATC-AGTATTTCTAGA-AGGAGTTCATAATGAGAAGAACTCATCTGAA
1 ATCAACTTTTTC-AGAGA-AAGTTCATAATGAGAAGAACTCATCTGAA
724053 AAAAGAGAAG
Statistics
Matches: 575, Mismatches: 50, Indels: 49
0.85 0.07 0.07
Matches are distributed among these distances:
112 44 0.08
113 50 0.09
114 4 0.01
121 5 0.01
122 186 0.32
123 196 0.34
124 86 0.15
125 4 0.01
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (123 bp):
ATCAACTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTTTCTTGACTCTATCACAGAAGGAGATAGATCAGC
Found at i:723710 original size:358 final size:359
Alignment explanation
Indices: 723076--723973 Score: 1423
Period size: 358 Copynumber: 2.5 Consensus size: 359
723066 TTCCAGAAGT
* * * * *
723076 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTTA
1 GTTCGTAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACGTGTTCA
* * * * *
723141 ACCTTT-TGTTCAA---ATC-CATAA-CA-ATGGATCA--A-C-A--TTTCTAGA-AAAGTTCAT
65 ACCTTTAT-TTGAATCTATCACAGAAGGAGATAGATCAGCATCAATTTTTCCAGAGAAAGTTCAT
*
723192 AATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTT
129 AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTT
*
723257 TGCTTAAATTCATCACTCGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATC
194 TGCTTAAATTCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATC
723322 TGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACA
259 TGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACA
723387 GAAGGAGATAGATCAGCATAAACTTTTCCAGAGAAA
324 GAAGGAGATAGATCAGCATAAACTTTTCCAGAGAAA
723423 GTTCGTAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACGTGTTCAA
1 GTTCGTAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACGTGTTCAA
* * *
723488 CCTTTATTTGAATCTATCACAGAAGGAGATATATCAGCATCAACTTTTT-CAGAGAACGTTCGTA
66 CCTTTATTTGAATCTATCACAGAAGGAGATAGATCAGCATCAA-TTTTTCCAGAGAAAGTTCATA
*
723552 ATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT
130 ATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT
723616 GCTTAAATTCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
195 GCTTAAATTCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
*
723681 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAG
260 GAAGAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAG
*
723746 AAGGAGATAGATCAGCATCAACTTTTCCAGAGAAA
325 AAGGAGATAGATCAGCATAAACTTTTCCAGAGAAA
*
723781 GTTCGTAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1 GTTCGTAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACGTGTTCAA
* *
723846 CCTTTATTTGACTTTATCACAGAAGGAGATAGATCAGCATCAATTTTTCCAGAGAAAGTTCATAA
66 CCTTTATTTGAATCTATCACAGAAGGAGATAGATCAGCATCAATTTTTCCAGAGAAAGTTCATAA
* * * **
723911 TGAGAAGAACTCGTCTGAAGAAGGAAGAAGAAGTTCATAATGAGAATAGCTTGTTCAACCTTT
131 TGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTT
723974 GTTTGATTCT
Statistics
Matches: 504, Mismatches: 30, Indels: 22
0.91 0.05 0.04
Matches are distributed among these distances:
346 43 0.09
347 27 0.05
349 3 0.01
350 4 0.01
351 1 0.00
352 6 0.01
354 1 0.00
355 1 0.00
356 1 0.00
357 5 0.01
358 343 0.68
359 69 0.14
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (359 bp):
GTTCGTAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACGTGTTCAA
CCTTTATTTGAATCTATCACAGAAGGAGATAGATCAGCATCAATTTTTCCAGAGAAAGTTCATAA
TGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
CTTAAATTCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
AAGAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGA
AGGAGATAGATCAGCATAAACTTTTCCAGAGAAA
Found at i:724314 original size:3 final size:3
Alignment explanation
Indices: 724308--724351 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
724298 TTTTTTTTAT
*
724308 TTA TTA TTA TTA TT- TTG TT- TTA TTA TTA -TA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
724352 ATTAATTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 8 0.22
3 29 0.78
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:724332 original size:16 final size:16
Alignment explanation
Indices: 724305--724359 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
724295 TCATTTTTTT
724305 TATT-TATTATTATTA
1 TATTATATTATTATTA
* * *
724320 TTTTGTTTTATTATTA
1 TATTATATTATTATTA
724336 TATTATATTATTATTA
1 TATTATATTATTATTA
724352 -ATTA-ATTA
1 TATTATATTA
724360 ATTTTAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 4 0.12
15 7 0.21
16 23 0.68
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TATTATATTATTATTA
Done.