Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002932.1 Hibiscus syriacus cultivar Beakdansim tig00006058_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: 153390
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1265 original size:15 final size:15
Alignment explanation
Indices: 1232--1262 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1222 CATAGATACT
1232 AATAAAACTAAACTA
1 AATAAAACTAAACTA
1247 AATAAAA-TAAACTA
1 AATAAAACTAAACTA
1261 AA
1 AA
1263 ATAGTTCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (15 bp):
AATAAAACTAAACTA
Found at i:6679 original size:15 final size:16
Alignment explanation
Indices: 6643--6679 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
6633 AGTGCTTCGA
*
6643 GATGATGACCAAGATG
1 GATGATGAACAAGATG
6659 GA-GATGAAC-AGATG
1 GATGATGAACAAGATG
6673 GATGATG
1 GATGATG
6680 CTCACAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 7 0.37
15 10 0.53
16 2 0.11
ACGTcount: A:0.38, C:0.08, G:0.35, T:0.19
Consensus pattern (16 bp):
GATGATGAACAAGATG
Found at i:7665 original size:21 final size:20
Alignment explanation
Indices: 7615--7665 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
7605 TTAGTCATAT
*
7615 GATCGATCCCTTAGCAAAAG
1 GATCGATCCCTTAACAAAAG
* *
7635 GATTGGTCCCTTTAACAAAAG
1 GATCGATCCC-TTAACAAAAG
7656 GATCGATCCC
1 GATCGATCCC
7666 CTTGTAAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (20 bp):
GATCGATCCCTTAACAAAAG
Found at i:7798 original size:42 final size:41
Alignment explanation
Indices: 7709--7801 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 41
7699 AGTTTTTGAC
* * *
7709 CGATCCCTTCACAAAAGGATCAATCCCTCGAGGAAAATGAT
1 CGATCCATTCACAAAAGAATCAAGCCCTCGAGGAAAATGAT
* * *
7750 CAATCCATTCATCAAAAGAATCAAGCCTTCGATGAAACA-GAT
1 CGATCCATTCA-CAAAAGAATCAAGCCCTCGAGGAAA-ATGAT
7792 CGATCCATTC
1 CGATCCATTC
7802 CCCTAAATGA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 9 0.21
42 33 0.77
43 1 0.02
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.22
Consensus pattern (41 bp):
CGATCCATTCACAAAAGAATCAAGCCCTCGAGGAAAATGAT
Found at i:11427 original size:9 final size:9
Alignment explanation
Indices: 11413--11442 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
11403 TCAGTATGCA
11413 ATCTCTTCG
1 ATCTCTTCG
11422 ATCTCTTCG
1 ATCTCTTCG
11431 ATCTCTTCG
1 ATCTCTTCG
11440 ATC
1 ATC
11443 CCATGTTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.13, C:0.33, G:0.10, T:0.43
Consensus pattern (9 bp):
ATCTCTTCG
Found at i:14462 original size:31 final size:31
Alignment explanation
Indices: 14424--14531 Score: 153
Period size: 31 Copynumber: 3.5 Consensus size: 31
14414 ATTTATTTTA
*
14424 TTATTATTTATATTCAATTCATTTTGTTTCT
1 TTATTATTTATATTTAATTCATTTTGTTTCT
*
14455 TTATTATTTATGTTTAATTCATTTTGTTTCT
1 TTATTATTTATATTTAATTCATTTTGTTTCT
* * *
14486 TTATTGTTTATATTTAATTCATTTTATTGCT
1 TTATTATTTATATTTAATTCATTTTGTTTCT
* *
14517 TTCTTATTTGTATTT
1 TTATTATTTATATTT
14532 GGTTTAACAT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.20, C:0.07, G:0.06, T:0.67
Consensus pattern (31 bp):
TTATTATTTATATTTAATTCATTTTGTTTCT
Found at i:14760 original size:20 final size:21
Alignment explanation
Indices: 14728--14773 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
14718 TTAATTTCCT
*
14728 TTATTTATAAAAATAAA-ATTC
1 TTATTTATAAAAA-AAATATCC
14749 TTATTT-TAAAAAAAATATCC
1 TTATTTATAAAAAAAATATCC
14769 TTATT
1 TTATT
14774 ATTTAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 3 0.13
20 14 0.61
21 6 0.26
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (21 bp):
TTATTTATAAAAAAAATATCC
Found at i:14783 original size:23 final size:23
Alignment explanation
Indices: 14728--14785 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
14718 TTAATTTCCT
*
14728 TTATTTATAAAAATAAAATTCTTA
1 TTATTTA-AAAAATAAAATCCTTA
*
14752 -T-TTTAAAAAA-AATATCCTTA
1 TTATTTAAAAAATAAAATCCTTA
*
14772 TTATTTAGAAAATA
1 TTATTTAAAAAATA
14786 TCTAAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 8 0.29
21 6 0.21
22 12 0.43
23 2 0.07
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (23 bp):
TTATTTAAAAAATAAAATCCTTA
Found at i:15042 original size:34 final size:34
Alignment explanation
Indices: 14999--15063 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
14989 TGCAAAATGT
14999 TGTAAGGCTTACCCTTGCACACAA-CAAAGGAAAC
1 TGTAAGGCTTACCCTTGCACA-AAGCAAAGGAAAC
15033 TGTAAGGCTTACCCTTGCACAAAGCAAAGGA
1 TGTAAGGCTTACCCTTGCACAAAGCAAAGGA
15064 GCATGCGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 2 0.07
34 28 0.93
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (34 bp):
TGTAAGGCTTACCCTTGCACAAAGCAAAGGAAAC
Found at i:17480 original size:30 final size:30
Alignment explanation
Indices: 17444--17518 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
17434 TTGACTCTTT
* *
17444 GGTCAAAGTCAACGATCAACGGTTTGACTC
1 GGTCAAAGTCAACGATCAACAGATTGACTC
* *
17474 GGTCAAAGTCAACGGTCAATAGATTGACTC
1 GGTCAAAGTCAACGATCAACAGATTGACTC
*
17504 GGTCAAAGTTAACGA
1 GGTCAAAGTCAACGA
17519 GTTGACCAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (30 bp):
GGTCAAAGTCAACGATCAACAGATTGACTC
Found at i:19651 original size:44 final size:44
Alignment explanation
Indices: 19518--19893 Score: 474
Period size: 44 Copynumber: 8.6 Consensus size: 44
19508 AACATATTTT
* * *
19518 CCCTGTGCACAAAGCAGAGGAGCCT-GGGGAAA-TGGTAAGGTCTTA
1 CCCT-TGCACACAGCAAAGGAACCTGGGGGAAACT-GTAAGG-CTTA
* *
19563 TCCTCTGCACACAGCAAAGAAACCT-GGGGAAACTGTAAGGCTTA
1 CCCT-TGCACACAGCAAAGGAACCTGGGGGAAACTGTAAGGCTTA
19607 CCCTTGCACACAGCAAAGGAACCTGGGGGAAACTGTAAGGCTTA
1 CCCTTGCACACAGCAAAGGAACCTGGGGGAAACTGTAAGGCTTA
*
19651 CCCTTGCACACAGCAAAGGAACTTGGGGGAAACTGTAAGGCTTA
1 CCCTTGCACACAGCAAAGGAACCTGGGGGAAACTGTAAGGCTTA
* **
19695 CCCTTGCACACAACAAAGGAACCTGGGGGAAACTACAAGGCTTA
1 CCCTTGCACACAGCAAAGGAACCTGGGGGAAACTGTAAGGCTTA
* * *
19739 CCCTTGCACACAGCAAAGGAAGCT-GAGGAAAATGTAAGGCTTA
1 CCCTTGCACACAGCAAAGGAACCTGGGGGAAACTGTAAGGCTTA
* * * * *
19782 CCCTTGAACACGGCACATGAACCTGGGGGAAAATGTAAGGCTTA
1 CCCTTGCACACAGCAAAGGAACCTGGGGGAAACTGTAAGGCTTA
* * * * *
19826 CCCTTACACACAGTAAAGAAACAT-GAGGAAACTGTAAGGCTTA
1 CCCTTGCACACAGCAAAGGAACCTGGGGGAAACTGTAAGGCTTA
*
19869 CCCTTGCACACAGCAAAGGAGCCTG
1 CCCTTGCACACAGCAAAGGAACCTG
19894 CGGTAAATGT
Statistics
Matches: 287, Mismatches: 40, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
43 89 0.31
44 165 0.57
45 32 0.11
46 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.17
Consensus pattern (44 bp):
CCCTTGCACACAGCAAAGGAACCTGGGGGAAACTGTAAGGCTTA
Found at i:19681 original size:88 final size:86
Alignment explanation
Indices: 19518--19893 Score: 477
Period size: 87 Copynumber: 4.3 Consensus size: 86
19508 AACATATTTT
* * * *
19518 CCCTGTGCACAAAGCAGAGGAGCCT-GGGGAAA-TGGTAAGGTCTTATCCTCTGCACACAGCAAA
1 CCCT-TGCACACAGCAAAGGAACCTGGGGGAAACT-GTAAGG-CTTACCCT-TGCACACAGCAAA
*
19581 GAAACCTGGGGAAACTGTAAGGCTTA
62 GAAA-CTGAGGAAACTGTAAGGCTTA
*
19607 CCCTTGCACACAGCAAAGGAACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAA
1 CCCTTGCACACAGCAAAGGAACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGAAA
*
19672 CTTGGGGGAAACTGTAAGGCTTA
66 C-T-GAGGAAACTGTAAGGCTTA
* **
19695 CCCTTGCACACAACAAAGGAACCTGGGGGAAACTACAAGGCTTACCCTTGCACACAGCAAAGGAA
1 CCCTTGCACACAGCAAAGGAACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAA-GAA
* *
19760 GCTGAGGAAAATGTAAGGCTTA
65 ACTGAGGAAACTGTAAGGCTTA
* * * * * * *
19782 CCCTTGAACACGGCACATGAACCTGGGGGAAAATGTAAGGCTTACCCTTACACACAGTAAAGAAA
1 CCCTTGCACACAGCAAAGGAACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGAAA
19847 CATGAGGAAACTGTAAGGCTTA
66 C-TGAGGAAACTGTAAGGCTTA
*
19869 CCCTTGCACACAGCAAAGGAGCCTG
1 CCCTTGCACACAGCAAAGGAACCTG
19894 CGGTAAATGT
Statistics
Matches: 252, Mismatches: 29, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
86 5 0.02
87 124 0.49
88 102 0.40
89 20 0.08
90 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.17
Consensus pattern (86 bp):
CCCTTGCACACAGCAAAGGAACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGAAA
CTGAGGAAACTGTAAGGCTTA
Found at i:24749 original size:21 final size:21
Alignment explanation
Indices: 24723--24767 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
24713 ATATATGAGT
24723 TTCATGCAATATAAATAGTCA
1 TTCATGCAATATAAATAGTCA
24744 TTCATGCAATATAAATAGTCA
1 TTCATGCAATATAAATAGTCA
24765 TTC
1 TTC
24768 TCATACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (21 bp):
TTCATGCAATATAAATAGTCA
Found at i:25818 original size:2 final size:2
Alignment explanation
Indices: 25811--26021 Score: 415
Period size: 2 Copynumber: 106.0 Consensus size: 2
25801 GTTATTAATA
25811 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25853 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25895 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25937 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25979 AG AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
26020 AG
1 AG
26022 GTATTCGGTG
Statistics
Matches: 208, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
1 1 0.00
2 207 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28215 original size:2 final size:2
Alignment explanation
Indices: 28208--28244 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28198 TTTTAATAAT
28208 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28245 GAAATCATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28580 original size:7 final size:7
Alignment explanation
Indices: 28568--28601 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
28558 TATCATTAAC
28568 TATAATA
1 TATAATA
28575 TATAATA
1 TATAATA
28582 TAT-ATA
1 TATAATA
28588 TATAATA
1 TATAATA
28595 TTATAAT
1 -TATAAT
28602 TGGTTCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.24
7 13 0.52
8 6 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TATAATA
Found at i:28590 original size:13 final size:13
Alignment explanation
Indices: 28568--28599 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
28558 TATCATTAAC
28568 TATA-ATATATAA
1 TATATATATATAA
28580 TATATATATATAA
1 TATATATATATAA
28593 TAT-TATA
1 TATATATA
28600 ATTGGTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TATATATATATAA
Found at i:29535 original size:20 final size:20
Alignment explanation
Indices: 29510--29623 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
29500 AATTGGGAAA
*
29510 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
29530 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * * *
29550 ATCGCAATGCAATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
29571 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
29591 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
29611 TTCGCAACGCGAT
1 ATCGCAACGCGAT
29624 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:30166 original size:19 final size:19
Alignment explanation
Indices: 30142--30188 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
30132 TTCGAGAATG
* *
30142 AAAATCGCAACGCGAAATA
1 AAAATCGCAACACGAAACA
*
30161 AAAATCGCAACACGAAACC
1 AAAATCGCAACACGAAACA
30180 AAAATCGCA
1 AAAATCGCA
30189 TTGCGATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.53, C:0.26, G:0.13, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACACGAAACA
Found at i:30235 original size:33 final size:33
Alignment explanation
Indices: 30198--30285 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
30188 ATTGCGATTT
30198 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
30231 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
30264 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
30286 ATTATCTCGT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 38 0.72
34 15 0.28
ACGTcount: A:0.11, C:0.27, G:0.23, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:30287 original size:20 final size:20
Alignment explanation
Indices: 30253--30310 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
30243 GCGATTCTCT
**
30253 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
30273 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
30293 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
30311 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:32468 original size:21 final size:21
Alignment explanation
Indices: 32444--32510 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
32434 TCATTCCTCG
32444 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
32465 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
32486 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
32507 AGAG
1 AGAG
32511 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:33881 original size:14 final size:14
Alignment explanation
Indices: 33862--33897 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
33852 ATTGTTTAAT
33862 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
33876 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
33890 TGATTTGT
1 TGATTTGT
33898 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:34041 original size:14 final size:14
Alignment explanation
Indices: 34022--34078 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
34012 GCGAAATGAA
34022 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
34036 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
34055 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
34069 AATGGCAACG
1 AATCGCAACG
34079 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.21, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:34049 original size:33 final size:33
Alignment explanation
Indices: 34004--34093 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
33994 AAAAAGTACT
*
34004 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
34037 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
34070 ATGGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
34094 GTTGCGATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:34063 original size:19 final size:19
Alignment explanation
Indices: 34004--34064 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
33994 AAAAAGTACT
*
34004 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
34023 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
34037 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
34056 ATCGCAACG
1 ATCGCAACG
34065 AGAGAATGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:34111 original size:19 final size:19
Alignment explanation
Indices: 34089--34219 Score: 103
Period size: 19 Copynumber: 7.7 Consensus size: 19
34079 CGAAATTAAA
*
34089 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
34108 TTCGCATTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
* *
34123 -CCTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
34141 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
*
34155 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
34174 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
34190 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
34207 TTCGCATTGCGAT
1 TTCGCATTGCGAT
34220 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 11, Indels: 30
0.68 0.09 0.24
Matches are distributed among these distances:
14 27 0.31
16 10 0.12
17 10 0.12
19 39 0.45
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:34137 original size:33 final size:32
Alignment explanation
Indices: 34093--34219 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
34083 ATTAAATTCG
34093 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* *
34126 CATTGCGATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
34159 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
34192 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
34220 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:34164 original size:66 final size:66
Alignment explanation
Indices: 34086--34218 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
34076 ACGCGAAATT
34086 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGCATTGC
34151 G
66 G
* *
34152 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGCATTGC
34217 G
66 G
34218 A
1 A
34219 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGCATTGC
G
Found at i:36527 original size:12 final size:12
Alignment explanation
Indices: 36510--36534 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36500 TCTTCGGGGA
36510 CTTTTTCTTCTT
1 CTTTTTCTTCTT
36522 CTTTTTCTTCTT
1 CTTTTTCTTCTT
36534 C
1 C
36535 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:36743 original size:24 final size:24
Alignment explanation
Indices: 36709--36762 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
36699 CTGAAACATC
*
36709 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
*
36733 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
36757 ATCAAA
1 ATCAAA
36763 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:36776 original size:24 final size:24
Alignment explanation
Indices: 36709--36776 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
36699 CTGAAACATC
* * * *
36709 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAGTCCGAATACTGACCAAG
* *
36733 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
36757 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
36777 TAGTACTCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:37615 original size:20 final size:20
Alignment explanation
Indices: 37501--37614 Score: 140
Period size: 20 Copynumber: 5.7 Consensus size: 20
37491 GATTCTGTAT
*
37501 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
37521 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
37541 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
37561 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
37582 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
37602 TATCGCATTGCGA
1 TATCGCGTTGCGA
37615 TTTTACCAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.77
21 14 0.17
22 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:37617 original size:41 final size:41
Alignment explanation
Indices: 37481--37618 Score: 172
Period size: 41 Copynumber: 3.4 Consensus size: 41
37471 AACTTTGAAA
* * *
37481 ATCGCATTGCGATTCTGTATTATCTCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** *
37522 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGT-ATTATCGCGTTGCGAAAGTCAGT
* *
37562 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
37603 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
37619 ACCAATTCGC
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.02
40 32 0.39
41 47 0.57
42 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:37629 original size:41 final size:41
Alignment explanation
Indices: 37481--37636 Score: 136
Period size: 41 Copynumber: 3.8 Consensus size: 41
37471 AACTTTGAAA
* ** * * * *
37481 ATCGCATTGCGATTCTGTATTATCTCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* *** * *
37522 ATCGCGTTGCGAAAGT-CAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* ** *
37562 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
37603 ATCGCATTGCGATTTTACCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
37637 TTACTTATTC
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
40 33 0.35
41 60 0.63
42 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
Found at i:37646 original size:20 final size:21
Alignment explanation
Indices: 37604--37655 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
37594 ATAGTCAGTA
37604 TCGCATTGCGATTTTACCAAT
1 TCGCATTGCGATTTTACCAAT
* **
37625 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
37645 TCGCATTGCGA
1 TCGCATTGCGA
37656 ATTGGGAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:43845 original size:3 final size:3
Alignment explanation
Indices: 43831--43920 Score: 78
Period size: 3 Copynumber: 30.0 Consensus size: 3
43821 TTTCTCCATT
*
43831 TTA TTCA TTA TTA TTA TTTA TTA TTA TT- CTA TTA TTA TTA TTA TT-
1 TTA TT-A TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
43876 TTAA TTA -TA ATA ATA ATA TTA TTA TTA ATA ATA TTA TTA TTA TTA
1 TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43921 CATACCCAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
2 5 0.07
3 63 0.83
4 8 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:43865 original size:11 final size:10
Alignment explanation
Indices: 43838--43919 Score: 62
Period size: 10 Copynumber: 8.1 Consensus size: 10
43828 ATTTTATTCA
43838 TTATTATTAT
1 TTATTATTAT
43848 TTATTATTAT
1 TTATTATTAT
43858 TCTATTATTA-
1 T-TATTATTAT
43868 TTATTATT-T
1 TTATTATTAT
* *
43877 TAATTATAAT
1 TTATTATTAT
* *
43887 AATAATATTA-
1 -TTATTATTAT
*
43897 TTATTAATAAT
1 TTATT-ATTAT
43908 ATTATTATTAT
1 -TTATTATTAT
43919 T
1 T
43920 ACATACCCAA
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
9 16 0.29
10 17 0.31
11 17 0.31
12 5 0.09
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (10 bp):
TTATTATTAT
Found at i:45823 original size:17 final size:18
Alignment explanation
Indices: 45803--45838 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
45793 TTTATAAAAA
45803 TATAAAAAAT-ATATATT
1 TATAAAAAATAATATATT
*
45820 TATAAAAATTAATATATT
1 TATAAAAAATAATATATT
45838 T
1 T
45839 TTCTTGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAAAAAATAATATATT
Found at i:47907 original size:13 final size:15
Alignment explanation
Indices: 47880--47912 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
47870 CATGCATTTA
47880 CATTTTGCATCTTTG
1 CATTTTGCATCTTTG
47895 CATTTT-CAT-TTTG
1 CATTTTGCATCTTTG
47908 CATTT
1 CATTT
47913 GTACTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 3 0.17
15 6 0.33
ACGTcount: A:0.15, C:0.18, G:0.09, T:0.58
Consensus pattern (15 bp):
CATTTTGCATCTTTG
Found at i:47913 original size:6 final size:7
Alignment explanation
Indices: 47880--47912 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
47870 CATGCATTTA
47880 CATTTTG
1 CATTTTG
47887 CATCTTTG
1 CAT-TTTG
47895 CATTTT-
1 CATTTTG
47901 CATTTTG
1 CATTTTG
47908 CATTT
1 CATTT
47913 GTACTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
7 11 0.46
8 7 0.29
ACGTcount: A:0.15, C:0.18, G:0.09, T:0.58
Consensus pattern (7 bp):
CATTTTG
Found at i:52502 original size:118 final size:117
Alignment explanation
Indices: 52279--52502 Score: 262
Period size: 118 Copynumber: 1.9 Consensus size: 117
52269 ATCCATATGG
*
52279 GACATCTTGAAGGCCCATTTCAACGAGAAATAGAATGGTGGGGTATTTTGAAGGCTCACGACAAT
1 GACATCTTGAAGGCCCATTTCAACGAGAAATAGAATGGTGGGGCATTTTGAAGGCTCACGACAAT
* * *
52344 ATGAATATTTGGGCATTCTTAGAGGCTCATCTCAGCAAGAAAAAAATGTTGA
66 ATGAATATTTGGGCATTCTTAGAAGCTAATATCAGCAAGAAAAAAATGTTGA
* *
52396 GACATTTTGAATGCCCATTTCAAAC-AGAAAT-GATCCAT-GTGGGGCATTTTGAAGGAC-CAC-
1 GACATCTTGAAGGCCCATTTC-AACGAGAAATAGA---ATGGTGGGGCATTTTGAAGG-CTCACG
* * *
52456 ATCAATATGAATATTTGGGCA-TCTTTGAAAGCTAATATTAGTAAGAA
61 A-CAATATGAATATTTGGGCATTCTTAG-AAGCTAATATCAGCAAGAA
52503 GCAAATGCTG
Statistics
Matches: 91, Mismatches: 9, Indels: 13
0.81 0.08 0.12
Matches are distributed among these distances:
116 2 0.02
117 31 0.34
118 55 0.60
119 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (117 bp):
GACATCTTGAAGGCCCATTTCAACGAGAAATAGAATGGTGGGGCATTTTGAAGGCTCACGACAAT
ATGAATATTTGGGCATTCTTAGAAGCTAATATCAGCAAGAAAAAAATGTTGA
Found at i:52509 original size:118 final size:117
Alignment explanation
Indices: 52279--52544 Score: 258
Period size: 118 Copynumber: 2.3 Consensus size: 117
52269 ATCCATATGG
* * *
52279 GACATCTTGAAGGCCCATTTC-AACGAGAAATAGAATGGTGGGGTATTTTGAAGGCTCACGACAA
1 GACATATTGAAAGCCCATTTCAAAC-AGAAATAGAATGGTGGGGCATTTTGAAGGCTCACGACAA
* * * *
52343 TATGAATATTTGGGCATTCTTAGAGGCTCATCTCAGCAAGAAAAAAATGTTGA
65 TATGAATATTTGGGCATTCTTAGAAGCTAATATCAGCAAGAAAAAAATGCTGA
* *
52396 GACATTTTGAATGCCCATTTCAAACAGAAAT-GATCCAT-GTGGGGCATTTTGAAGGAC-CAC-A
1 GACATATTGAAAGCCCATTTCAAACAGAAATAGA---ATGGTGGGGCATTTTGAAGG-CTCACGA
* * * ** *
52457 TCAATATGAATATTTGGGCA-TCTTTGAAAGCTAATATTAGTAAGAAGCAAATGCTGG
62 -CAATATGAATATTTGGGCATTCTTAG-AAGCTAATATCAGCAAGAAAAAAATGCTGA
* *
52514 GGCATACTGAAAGCCCATTTCAATA-AGAAAT
1 GACATATTGAAAGCCCATTTCAA-ACAGAAAT
52545 TGGAATATTA
Statistics
Matches: 124, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
116 2 0.02
117 31 0.25
118 87 0.70
119 4 0.03
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (117 bp):
GACATATTGAAAGCCCATTTCAAACAGAAATAGAATGGTGGGGCATTTTGAAGGCTCACGACAAT
ATGAATATTTGGGCATTCTTAGAAGCTAATATCAGCAAGAAAAAAATGCTGA
Found at i:54713 original size:17 final size:16
Alignment explanation
Indices: 54687--54718 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
54677 GATTTCCAAA
54687 GTTTCTTCTTTCATGT
1 GTTTCTTCTTTCATGT
54703 GTTTGCTTCTTTCATG
1 GTTT-CTTCTTTCATG
54719 GTTCACCGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.06, C:0.19, G:0.16, T:0.59
Consensus pattern (16 bp):
GTTTCTTCTTTCATGT
Found at i:56049 original size:20 final size:20
Alignment explanation
Indices: 56024--56070 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
56014 TGGCAGTTTT
56024 CCACTTCTTGTCTCGCTACG
1 CCACTTCTTGTCTCGCTACG
* *
56044 CCACTTCTTGTTTTGCTACG
1 CCACTTCTTGTCTCGCTACG
*
56064 CCTCTTC
1 CCACTTC
56071 AAAGTTGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.09, C:0.38, G:0.13, T:0.40
Consensus pattern (20 bp):
CCACTTCTTGTCTCGCTACG
Found at i:66269 original size:18 final size:17
Alignment explanation
Indices: 66239--66272 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
66229 ATAGTTAGAA
66239 GGTTGTTAATCTGTTAG
1 GGTTGTTAATCTGTTAG
*
66256 GGTTGGTTACTCTGTTA
1 GGTT-GTTAATCTGTTA
66273 TAACTATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.15, C:0.09, G:0.29, T:0.47
Consensus pattern (17 bp):
GGTTGTTAATCTGTTAG
Found at i:67508 original size:56 final size:58
Alignment explanation
Indices: 67448--67571 Score: 150
Period size: 57 Copynumber: 2.2 Consensus size: 58
67438 AACTTTCAAC
* *
67448 AATATATTTTATTATT-ATTTTAATTTTTAAAG-TA-TATATT-TTATATTAATTTACTA
1 AATATATTTTATTATTGATTTAAATTATTAAAGATATTATATTATTATATTAATTT--TA
* * *
67504 AATATATTATATTATTGCTTTAAATTATTAAAGATATTTTATTATTATATTAATTTTA
1 AATATATTTTATTATTGATTTAAATTATTAAAGATATTATATTATTATATTAATTTTA
67562 AA-ATATTTTA
1 AATATATTTTA
67572 GCATAAAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
56 15 0.26
57 20 0.34
58 6 0.10
59 5 0.09
60 12 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (58 bp):
AATATATTTTATTATTGATTTAAATTATTAAAGATATTATATTATTATATTAATTTTA
Found at i:67567 original size:27 final size:28
Alignment explanation
Indices: 67451--67571 Score: 108
Period size: 30 Copynumber: 4.3 Consensus size: 28
67441 TTTCAACAAT
*
67451 ATATTTTATTATTATTTTAATTTTTAAAG
1 ATATTTTATTATTATATTAA-TTTTAAAG
* *
67480 -TA-TATATT-TTATATTAATTTACTAAAT
1 ATATTTTATTATTATATTAATTT--TAAAG
* *
67507 ATATTATATTATTGCT-TTAAATTATTAAAG
1 ATATTTTATTATT-ATATT-AATT-TTAAAG
67537 ATATTTTATTATTATATTAATTTTAAA-
1 ATATTTTATTATTATATTAATTTTAAAG
67564 ATATTTTA
1 ATATTTTA
67572 GCATAAAAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
25 3 0.04
26 8 0.11
27 17 0.22
28 9 0.12
29 11 0.14
30 22 0.29
31 5 0.07
32 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (28 bp):
ATATTTTATTATTATATTAATTTTAAAG
Found at i:67633 original size:27 final size:27
Alignment explanation
Indices: 67603--67682 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
67593 TTAAAATAGA
*
67603 AATAAAATATTTTTAGATTAGGTT-A-AT
1 AATAAAATATTTTTA-A-TAAGTTGATAT
*
67630 AATAAAATATATTTAATAAGTTGATAT
1 AATAAAATATTTTTAATAAGTTGATAT
* *
67657 AA-AAAATATTTTTTA-AAGTTAATAT
1 AATAAAATATTTTTAATAAGTTGATAT
67682 A
1 A
67683 TATATATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
25 15 0.33
26 13 0.28
27 18 0.39
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (27 bp):
AATAAAATATTTTTAATAAGTTGATAT
Found at i:69825 original size:14 final size:14
Alignment explanation
Indices: 69806--69841 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
69796 CAAACCAAAA
69806 TCCAACAATATAAG
1 TCCAACAATATAAG
69820 TCCAACAATATAAG
1 TCCAACAATATAAG
*
69834 TCTAACAA
1 TCCAACAA
69842 AGTGAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (14 bp):
TCCAACAATATAAG
Found at i:71096 original size:26 final size:26
Alignment explanation
Indices: 71067--71186 Score: 168
Period size: 26 Copynumber: 4.4 Consensus size: 26
71057 CAAAATCTAA
*
71067 TTTAAAACAAAGCATAATCCTCTGTT
1 TTTAAAACAGAGCATAATCCTCTGTT
*
71093 TTTAAAACATAGCATAATCCTCTGTT
1 TTTAAAACAGAGCATAATCCTCTGTT
71119 TTTAAAACAGAGCATAATCCTCTCCTCTGTT
1 TTTAAAACAGAGCATAA-----TCCTCTGTT
*
71150 TTTAAAACAGAGCATAATCCTCTATT
1 TTTAAAACAGAGCATAATCCTCTGTT
71176 TTTAAAACAGA
1 TTTAAAACAGA
71187 ACACAAACGC
Statistics
Matches: 86, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
26 60 0.70
31 26 0.30
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (26 bp):
TTTAAAACAGAGCATAATCCTCTGTT
Found at i:71145 original size:31 final size:31
Alignment explanation
Indices: 71084--71172 Score: 134
Period size: 31 Copynumber: 3.0 Consensus size: 31
71074 CAAAGCATAA
*
71084 TCCTCTGTTTTTAAAACATAGCATAA-----
1 TCCTCTGTTTTTAAAACAGAGCATAATCCTC
71110 TCCTCTGTTTTTAAAACAGAGCATAATCCTC
1 TCCTCTGTTTTTAAAACAGAGCATAATCCTC
71141 TCCTCTGTTTTTAAAACAGAGCATAATCCTC
1 TCCTCTGTTTTTAAAACAGAGCATAATCCTC
71172 T
1 T
71173 ATTTTTAAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
26 25 0.44
31 32 0.56
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.37
Consensus pattern (31 bp):
TCCTCTGTTTTTAAAACAGAGCATAATCCTC
Found at i:76662 original size:29 final size:31
Alignment explanation
Indices: 76616--76688 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
76606 AAAATTTGGC
* * * *
76616 TAGTGACCAAAATGTAAA-ATATGAA-AGTT
1 TAGTGACTAAAGTATAAACATAAGAATAGTT
*
76645 TAGTGACTAAAGTATAAACTTAAGAATAGTT
1 TAGTGACTAAAGTATAAACATAAGAATAGTT
*
76676 TAGGGACTAAAGT
1 TAGTGACTAAAGT
76689 GTAATTTCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 15 0.42
30 5 0.14
31 16 0.44
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.29
Consensus pattern (31 bp):
TAGTGACTAAAGTATAAACATAAGAATAGTT
Found at i:77595 original size:21 final size:21
Alignment explanation
Indices: 77553--77591 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
77543 GTTCAAGATG
77553 AATTGAAATTGATATGGAATT
1 AATTGAAATTGATATGGAATT
77574 AATTGAAATTGA-ATGGAA
1 AATTGAAATTGATATGGAA
77592 ATTATAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.33
Consensus pattern (21 bp):
AATTGAAATTGATATGGAATT
Found at i:78111 original size:6 final size:6
Alignment explanation
Indices: 78103--78175 Score: 83
Period size: 6 Copynumber: 11.8 Consensus size: 6
78093 ATATTTTTTT
* *
78103 TTATTT TTATTG TTACTTGC TTATTC TTATTC TTATTC TTATTC TTATTC
1 TTATTC TTATTC TTA-TT-C TTATTC TTATTC TTATTC TTATTC TTATTC
* * *
78153 TTATTA TTATTA TTATTA TTATT
1 TTATTC TTATTC TTATTC TTATT
78176 ACTACTACTT
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
6 55 0.89
7 4 0.06
8 3 0.05
ACGTcount: A:0.21, C:0.10, G:0.03, T:0.67
Consensus pattern (6 bp):
TTATTC
Found at i:78161 original size:3 final size:3
Alignment explanation
Indices: 78123--78204 Score: 85
Period size: 3 Copynumber: 27.7 Consensus size: 3
78113 TGTTACTTGC
* * * * *
78123 TTA TTC TTA TTC TTA TTC TTA TTC TTA TTC TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
78171 TTA TTA CTA CTA CT- TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
78205 TATTTAAATT
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
2 1 0.02
3 65 0.98
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:78468 original size:22 final size:22
Alignment explanation
Indices: 78426--78469 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
78416 CGTCGCCGTC
*
78426 ACCTTCTGTCACTATCATCGCT
1 ACCTTCTGTCACTACCATCGCT
*
78448 ACCTTCTG-CTACTACCGTCGCT
1 ACCTTCTGTC-ACTACCATCGCT
78470 TTTACTGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.16, C:0.39, G:0.11, T:0.34
Consensus pattern (22 bp):
ACCTTCTGTCACTACCATCGCT
Found at i:83680 original size:18 final size:18
Alignment explanation
Indices: 83652--83698 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
83642 CCCATGATTT
83652 CAGAA-GAAAGACCAATG
1 CAGAATGAAAGACCAATG
83669 CAGAATGAAAGACCAATG
1 CAGAATGAAAGACCAATG
83687 CAGAATGAAAGA
1 CAGAATGAAAGA
83699 TCTGCTTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 5 0.17
18 24 0.83
ACGTcount: A:0.53, C:0.15, G:0.23, T:0.09
Consensus pattern (18 bp):
CAGAATGAAAGACCAATG
Found at i:85614 original size:29 final size:31
Alignment explanation
Indices: 85568--85630 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
85558 AAATTTTAGC
* * *
85568 TAGTGATCAAAATGTAAA-TTT-TAAAAGTT
1 TAGTGACCAAAATATAAACTTTAGAAAAGTT
*
85597 TAGTGACCAAAGTATAAACTTTAGAAAAGTT
1 TAGTGACCAAAATATAAACTTTAGAAAAGTT
85628 TAG
1 TAG
85631 GAATTAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.54
30 3 0.11
31 10 0.36
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.33
Consensus pattern (31 bp):
TAGTGACCAAAATATAAACTTTAGAAAAGTT
Found at i:93514 original size:81 final size:81
Alignment explanation
Indices: 93397--93955 Score: 794
Period size: 81 Copynumber: 6.9 Consensus size: 81
93387 CGTTCAGAGG
* * * * **
93397 CATTTAACCTTTCATCTAACTTGCATTATTGGCACCTTTCTGCTAAATGCACAGTTAGAATTTTA
1 CATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTTTTA
* *
93462 GTCTTTGACTCAAAGT
66 GTCTTTTACTCAAAGA
* *
93478 CATTTAACCTTTCATCTTACTGGCATGATTGACACCTTTTTGCCAAATGCACAGTTAGGCTTTTA
1 CATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTTTTA
* *
93543 GTCTTTTACTTAAAGG
66 GTCTTTTACTCAAAGA
* * *
93559 CATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGCCAAATACACAGTTAGGATTTTA
1 CATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTTTTA
93624 GTCTTTTACTCAAAGA
66 GTCTTTTACTCAAAGA
* * *
93640 CATTTAACATTTCATCTAACTGGCATGATTGACACATTTCTGCCAAATGCACAATTAGGCTTTTA
1 CATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTTTTA
* *
93705 GTTTTTTACTCAAAGG
66 GTCTTTTACTCAAAGA
* * * *
93721 CATTTAACCTTTCATCTAAGTGGCATGATTGACACCTTTCTGTCAAATGCACAATTAGACTTTTA
1 CATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTTTTA
*
93786 GTCTTTTACTCAAGGA
66 GTCTTTTACTCAAAGA
* * ** * *
93802 AATTTAACCTATCATCTAACTGAAATGATTTACACCTTTATGCCAAATGCACAGTTAGGCTTTTA
1 CATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTTTTA
*
93867 GTATTTTACTCAAAGA
66 GTCTTTTACTCAAAGA
* * *
93883 CATTTAACCTTTCATCTAATTGGTATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTTTAA
1 CATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTTTTA
*
93948 GTATTTTA
66 GTCTTTTA
93956 TTTTAGAACA
Statistics
Matches: 426, Mismatches: 52, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 426 1.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (81 bp):
CATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTTTTA
GTCTTTTACTCAAAGA
Found at i:94185 original size:54 final size:53
Alignment explanation
Indices: 94041--94205 Score: 186
Period size: 53 Copynumber: 3.1 Consensus size: 53
94031 TTGCACCCGT
* * * * * * * *
94041 AGTGTCAATACGATAATCCAAAACTTACTATGAATTACGTGGGTTGCACATAC
1 AGTGCCAATACGAAAATTCTAAACTTATTATGAATTTCTTGGGTTGCACACAC
* * *
94094 AGTGCTAATACGAAAATTCTAAACTTATTATGAATTTCTTGGGTTTCACGCAC
1 AGTGCCAATACGAAAATTCTAAACTTATTATGAATTTCTTGGGTTGCACACAC
* * * *
94147 AGTGCCAATATGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAT
1 AGTGCCAATACGAAAATTC-TAAACTTATTATGAATTTCTTGGGTTGCACACAC
94201 AGTGC
1 AGTGC
94206 TCATTCAATA
Statistics
Matches: 93, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
53 58 0.62
54 35 0.38
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (53 bp):
AGTGCCAATACGAAAATTCTAAACTTATTATGAATTTCTTGGGTTGCACACAC
Found at i:98095 original size:81 final size:80
Alignment explanation
Indices: 98010--98829 Score: 1026
Period size: 81 Copynumber: 10.2 Consensus size: 80
98000 TTGTTATACA
* * * * *
98010 TTTAGTCTTTCA-TCCAGAAGCATTTAACCTTTTATATAACCT-GCATTATTGGCACTTTTATGC
1 TTTAGTCTTTTACT-CA-AAGCATTTAACCTTTCATCTAA-CTGGCATGATTGACACTTTTATGC
98073 CAAATGCACAGTTAGGCT
63 CAAATGCACAGTTAGGCT
* ** *
98091 TTTAGTCTTTTACTCAAAGACATTTAACCTTTCATCTAACTGGCATGATTGACACATTCCTACCA
1 TTTAGTCTTTTACTCAAAG-CATTTAACCTTTCATCTAACTGGCATGATTGACACTTTTATGCCA
98156 AATGCACAGTTAGGCT
65 AATGCACAGTTAGGCT
* *
98172 TTTAGTCTTTTACTCAAAAGCATTTAACCTTTCATCTAACTGCCATGATTGACA-TCTTTATACC
1 TTTAGTCTTTTACTC-AAAGCATTTAACCTTTCATCTAACTGGCATGATTGACACT-TTTATGCC
*
98236 AAATGCCCAGTTAGGCT
64 AAATGCACAGTTAGGCT
* *
98253 TTTAGCCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATGATTGACAGC-TTTCTGCC
1 TTTAGTCTTTTACTCAAA-GCATTTAACCTTTCATCTAACTGGCATGATTGACA-CTTTTATGCC
* *
98317 AAATACACAGTTAGACT
64 AAATGCACAGTTAGGCT
* * * * *
98334 TTTAGTCTTTTACTCAAATGCATTTAACTTTTCATCTAATTGGCATGACTGACACATTTCTGCCA
1 TTTAGTCTTTTACTCAAA-GCATTTAACCTTTCATCTAACTGGCATGATTGACACTTTTATGCCA
98399 AATGCACAGTTAGGCT
65 AATGCACAGTTAGGCT
* * *
98415 TTTAGTCTTTTACTCAGAGGCATTTAACCTTTCATCTAACTGGCATGATTGATACCTTTT-TTCC
1 TTTAGTCTTTTACTCA-AAGCATTTAACCTTTCATCTAACTGGCATGATTGACA-CTTTTATGCC
*
98479 AAATGCACAATTAGGCT
64 AAATGCACAGTTAGGCT
* * * * *
98496 TTTAGTCTTTTATTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTAACACCTTTATACCA
1 TTTAGTCTTTTACTCAAA-GCATTTAACCTTTCATCTAACTGGCATGATTGACACTTTTATGCCA
* *
98561 AATACACA-TTAGGTT
65 AATGCACAGTTAGGCT
* * * * * *
98576 TTTAGTCTTTTACTCAAAAGCATTGAAACTTTCATCTAATTGGCTTGATTGAAAC-CTTACTGCC
1 TTTAGTCTTTTACTC-AAAGCATTTAACCTTTCATCTAACTGGCATGATTGACACTTTTA-TGCC
98640 AAATGCACAGTTAGGCT
64 AAATGCACAGTTAGGCT
* * *
98657 TTTAGTATTTTACTCAAAGACATTTAACCATTCATCTAACTGGCATGATTGACACTTTT-TTCCA
1 TTTAGTCTTTTACTCAAAG-CATTTAACCTTTCATCTAACTGGCATGATTGACACTTTTATGCCA
98721 AATGCACAGTTAGGCT
65 AATGCACAGTTAGGCT
* * * *
98737 TTTAGTCTTTTACTTAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTGTGCCA
1 TTTAGTCTTTTACTCAAA-GCATTTAACCTTTCATCTAACTGGCATGATTGACACTTTTATGCCA
*
98802 AATGCACAGTTAGACT
65 AATGCACAGTTAGGCT
98818 TTTAGTCTTTTA
1 TTTAGTCTTTTA
98830 TTTTAGAACA
Statistics
Matches: 646, Mismatches: 73, Indels: 40
0.85 0.10 0.05
Matches are distributed among these distances:
79 3 0.00
80 150 0.23
81 481 0.74
82 12 0.02
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (80 bp):
TTTAGTCTTTTACTCAAAGCATTTAACCTTTCATCTAACTGGCATGATTGACACTTTTATGCCAA
ATGCACAGTTAGGCT
Found at i:98464 original size:243 final size:240
Alignment explanation
Indices: 98029--98829 Score: 1147
Period size: 243 Copynumber: 3.3 Consensus size: 240
98019 TCATCCAGAA
* * * * * * *
98029 GCATTTAACCTTTTATATAACCT-GCATTATTGGCACTTTTATGCCAAATGCACAGTTAGGCTTT
1 GCATTTAACCTTTCATCTAA-CTGGCATGATTGACACCTTTATGCCAAATACACAGTTAGACTTT
* * *
98093 TAGTCTTTTACTCAAAGACATTTAACCTTTCATCTAACTGGCATGATTGACACATTCCTACCAAA
65 TAGTCTTTTACTCAAAG-CATTTAA-CTTTCATCTAATTGGCATGATTGACACATTACTGCCAAA
* *
98158 TGCACAGTTAGGCTTTTAGTCTTTTACTCAAAAGCATTTAACCTTTCATCTAACTGCCATGATTG
128 TGCACAGTTAGGCTTTTAGTCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATGATTG
* * * *
98223 ACATCTTTATACCAAATGCCCAGTTAGGCTTTTAGCCTTTTACTCAAAG
193 ACA-CTTTTTTCCAAATGCACAGTTAGGCTTTTAGTCTTTTACTCAAAG
* *
98272 GCATTTAACCTTTCATCTAACTGGCATGATTGACAGCTTTCTGCCAAATACACAGTTAGACTTTT
1 GCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTATGCCAAATACACAGTTAGACTTTT
* *
98337 AGTCTTTTACTCAAATGCATTTAACTTTTCATCTAATTGGCATGACTGACACATTTCTGCCAAAT
66 AGTCTTTTACTCAAA-GCATTTAAC-TTTCATCTAATTGGCATGATTGACACATTACTGCCAAAT
*
98402 GCACAGTTAGGCTTTTAGTCTTTTACTCAGAGGCATTTAACCTTTCATCTAACTGGCATGATTGA
129 GCACAGTTAGGCTTTTAGTCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATGATTGA
* * *
98467 TACCTTTTTTCCAAATGCACAATTAGGCTTTTAGTCTTTTATTCAAAG
194 CA-CTTTTTTCCAAATGCACAGTTAGGCTTTTAGTCTTTTACTCAAAG
* * * **
98515 GCATTTAACCTTTCATCTAACTAGCATGATTAACACCTTTATACCAAATACACA-TTAGGTTTTT
1 GCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTATGCCAAATACACAGTTAGACTTTT
* * * *
98579 AGTCTTTTACTCAAAAGCATTGAAACTTTCATCTAATTGGCTTGATTGAAACCTTACTGCCAAAT
66 AGTCTTTTACTC-AAAGCATT-TAACTTTCATCTAATTGGCATGATTGACACATTACTGCCAAAT
* * *
98644 GCACAGTTAGGCTTTTAGTATTTTACTCAAAGACATTTAACCATTCATCTAACTGGCATGATTGA
129 GCACAGTTAGGCTTTTAGTCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATGATTGA
*
98709 CACTTTTTTCCAAATGCACAGTTAGGCTTTTAGTCTTTTACTTAAAG
194 CACTTTTTTCCAAATGCACAGTTAGGCTTTTAGTCTTTTACTCAAAG
* * *
98756 GTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTGTGCCAAATGCACAGTTAGACTTTT
1 GCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTATGCCAAATACACAGTTAGACTTTT
98821 AGTCTTTTA
66 AGTCTTTTA
98830 TTTTAGAACA
Statistics
Matches: 499, Mismatches: 53, Indels: 13
0.88 0.09 0.02
Matches are distributed among these distances:
241 90 0.18
242 141 0.28
243 267 0.54
244 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (240 bp):
GCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTATGCCAAATACACAGTTAGACTTTT
AGTCTTTTACTCAAAGCATTTAACTTTCATCTAATTGGCATGATTGACACATTACTGCCAAATGC
ACAGTTAGGCTTTTAGTCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATGATTGACA
CTTTTTTCCAAATGCACAGTTAGGCTTTTAGTCTTTTACTCAAAG
Found at i:99014 original size:54 final size:54
Alignment explanation
Indices: 98915--99080 Score: 255
Period size: 54 Copynumber: 3.1 Consensus size: 54
98905 TTGCACCCGT
* * * * *
98915 AGTGCCAATACGATAATCCA-AAACTTACTATGAATTAT-GTGGGTTGCACACAC
1 AGTGCCAATACGAAAATTCATAAACTTATTATGAATT-TCTTAGGTTGCACACAC
98968 AGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAC
1 AGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAC
*
99022 AGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAT
1 AGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAC
99076 AGTGC
1 AGTGC
99081 TCATTCGGTA
Statistics
Matches: 105, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
53 19 0.18
54 86 0.82
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (54 bp):
AGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAC
Found at i:103079 original size:81 final size:81
Alignment explanation
Indices: 102975--105874 Score: 3799
Period size: 81 Copynumber: 35.9 Consensus size: 81
102965 TTTCATCCAG
* * * * * *
102975 AGGCATTTAACTTTTCATCTAACTTGCATTATTGTCGCCTTTCTGCCAAATGCACTGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
103040 TTAGTCTTTTACTCAA
66 TTAGTCTTTTACTCAA
* * * * * *
103056 AGGCATTTAACCTTTCATTTAACTGGCATGATTGACACCTTTATTCCAAATACACGGTTAGGGTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
*
103121 TTAGTCTTTTAATCAA
66 TTAGTCTTTTACTCAA
* * * **
103137 AGGCATTTAACCTTTTATCTAACTAGCATGATTGACGCCTTTCTGTAAAATGCACAGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
*
103202 TTAGTCTTTAACTCAA
66 TTAGTCTTTTACTCAA
* *
103218 AAGCATTTAACCTTTCTTCTAACTGGCATGATTGACACCTTTCTGCCAAAT-C-CA--TA-G---
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
103275 TTAGTCTTTTACTCAA
66 TTAGTCTTTTACTCAA
* * ** *
103291 AGGCATTTAACCTTTC-TCTAACTAGCATGATTGATATATTTCTACCAAATGCACAGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
* *
103355 TTAGTCTTTAACTCGA
66 TTAGTCTTTTACTCAA
* * *
103371 AGGCATTTAACTTTTCATCTAACTAGCATGATTAACACCTTTCTGCCAAATGCACAGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
* * *
103436 TAAGTCTTCTAATCAA
66 TTAGTCTTTTACTCAA
* *
103452 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACATTTATGCCAAATGCACAGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
*
103517 TTAGTCTTTTACACAA
66 TTAGTCTTTTACTCAA
* *
103533 AGGCATTTAACCATTCATCTAACTGACATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
*
103598 TTAGTTTTTTACTCAA
66 TTAGTCTTTTACTCAA
* * * * **
103614 AGTCATTTAACCTTTCAACTAACTGGCATGATTGACACCTATATGCCAAATATACAGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
* **
103679 TAAGAATTTTACTCAA
66 TTAGTCTTTTACTCAA
* * * * * *
103695 ATGCATTTCACATTTCATCTAATTGGCATGATTGACACCTTTCTACCAAATACACAGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
103760 TTAGTCTTTTACTCAA
66 TTAGTCTTTTACTCAA
* * * * * * ** * *
103776 AGGCAATTAAACTTTCATCTGACTGGCATGATTGAAACCTTTATTCCAAATGCGTAATTAAGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
**
103841 TTAGGGTTTTACTCAA
66 TTAGTCTTTTACTCAA
* * * * * *
103857 GGGAATTTAACCTTTCATCTAACTGGTATGATTGACACATTTCTTCCAAATGCATAGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
103922 TTAGTCTTTTACTCAA
66 TTAGTCTTTTACTCAA
* * *
103938 ACGCATTTAACATTTCTTCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
*
104003 TAAGTCTTTTACTCAA
66 TTAGTCTTTTACTCAA
* *** * *
104019 AGGCATTTAACCTTTCATCTAAATATAATGATTGATACATTTCTGCCAAATGCACAGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
* *
104084 TTATTCTTTTTCTCAA
66 TTAGTCTTTTACTCAA
*
104100 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGCCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
104165 TTAGTCTTTTACTCAA
66 TTAGTCTTTTACTCAA
* **
104181 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTACCAAATGCATTGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
104246 TTAGTCTTTTACTCAA
66 TTAGTCTTTTACTCAA
** * **
104262 AGGCATTTAACCTTTCATCTAACTATCATGATTGACACCTTTTTAACAAATGCACAGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
104327 TTAGTCTTTTACTCAA
66 TTAGTCTTTTACTCAA
* * * * ** *
104343 AGGCATTTAACATTTCATCTAACTGGCATGATCGATACCTTTTTGATAAATACACAGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
*
104408 TTAGTCTTCTACTCAA
66 TTAGTCTTTTACTCAA
* *
104424 AGGCATTTAACCTTTCATCTAACTGACATGATTGACACCTTTCTGCCAAATTCACAGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
104489 TTAGTCTTTTACTCAA
66 TTAGTCTTTTACTCAA
** *
104505 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACATATTTCT-CTCAAATGCACATTTAGGCT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGC-CAAATGCACAGTTAGGCT
104569 TTTAGTCTTTTACTCAA
65 TTTAGTCTTTTACTCAA
* * * *
104586 AGACATTTAACCTTTCATCTAACTGGCATAATTGACACCTATCTGCCAAATGCATAGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
* *
104651 TTAGTATTTTACTGAA
66 TTAGTCTTTTACTCAA
* * * * *
104667 AGGCATTTCACCTTTCATCTAATTGGCATGATTGACACATTTCTACCAAATACACAGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
*
104732 TTAATCTTTTACTCAA
66 TTAGTCTTTTACTCAA
* * * * *
104748 AGGCATTTAACATTTCATCTAACTGGCATGATTGACACCTTTTTTCCAAATTCACAATTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
*
104813 TTAGTGTTTTACTCAA
66 TTAGTCTTTTACTCAA
* * * *
104829 AGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTATGCCAAATGCACAGTTAGCCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
104894 TTAGTCTTTTACTCAA
66 TTAGTCTTTTACTCAA
* ** * * * * * *
104910 AGGCATTTAACCTTTCATCTAACTGGTATGATTGACATATTTTTTCTAAATACATAGTTAGGGTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
104975 TTAGTCTTTTACTCAA
66 TTAGTCTTTTACTCAA
* * * **
104991 AGGCATTTAACCTTTCTTCTAACTGGCATGAATGACACATTTCTGCCAAATGCACAACTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
* *
105056 TTAGTCTTTTTCTCTA
66 TTAGTCTTTTACTCAA
* * * * * * *
105072 AGGAATTTAGCATTTCATCTAACTAGCATGAGTGACACCTTTCTACCAAATGCAAAGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
105137 TTAGTCTTTTACTCAA
66 TTAGTCTTTTACTCAA
** * * * * * *
105153 AGGCATTTAATATTTCATCTAACTGGCATGATTTACACCTTTCTTCCAAATTCACTGGTAGGGTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
105218 TTAGTCTTTTACTCAA
66 TTAGTCTTTTACTCAA
* * * **
105234 ATGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATACACATTTATTCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
105299 TTAGTCTTTTACTCAA
66 TTAGTCTTTTACTCAA
* ** * ** *
105315 AGGCATTTAACCTTTCATCTAACTGGTATGATTGACACCAATCTGCTAAATGCACAGTTATTC-A
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
*
105379 TTAGTATTTTACTCAA
66 TTAGTCTTTTACTCAA
* * * * **
105395 AGGCATTTCACCTTTCATCTAATTGGCATGATTGACACCTTTCCGCCAAATGCACATTTAGAATT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
* * *
105460 TTAGTCGTTAACTTAA
66 TTAGTCTTTTACTCAA
** * * * * *
105476 AGTTATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTTCCAAATGTATATTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
* *
105541 CTAGTATTTTACTCAA
66 TTAGTCTTTTACTCAA
* * * *
105557 AGGCATTTAACCTTCCATCTAACTGGCATGATTGACATCTTTCTGCCAAATACACCGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
105622 TTAGTCTTTTACTCAA
66 TTAGTCTTTTACTCAA
* * * * * *
105638 AGGTAATTAACCTTTTATCTAACTGGCATGATTGACACCTTTCTTCCAAATGCACAATTAGGGTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
*
105703 TTAGTGTTTTACTCAA
66 TTAGTCTTTTACTCAA
* ** * *
105719 AGGCATTTAACCTTTCATCTAACTGGCATGTTTGACATATTTATACCAAATGCACAGTTA-GCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
105783 TTAGTCTTTTACTCAA
66 TTAGTCTTTTACTCAA
* * * *
105799 AGGCATTTAACCTTTCATCTAATTTGTATGATTGACACATTTCTGCCAAATGCACAGTTAGGCTT
1 AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
*
105864 TTAGTCCTTTA
66 TTAGTCTTTTA
105875 TTTTAGAATA
Statistics
Matches: 2435, Mismatches: 371, Indels: 26
0.86 0.13 0.01
Matches are distributed among these distances:
72 29 0.01
73 31 0.01
74 2 0.00
76 3 0.00
77 3 0.00
79 2 0.00
80 169 0.07
81 2195 0.90
82 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (81 bp):
AGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTTAGGCTT
TTAGTCTTTTACTCAA
Found at i:106048 original size:54 final size:52
Alignment explanation
Indices: 105959--106125 Score: 210
Period size: 54 Copynumber: 3.1 Consensus size: 52
105949 TTTTCACCCG
* * * * *
105959 TAGTGCCAATACGGTAATCCA-CAACTTACTATGAATTACATAGATTGCACACA
1 TAGTGCCAATACGG-AATTCATAAACTTATTATGAATTTC-TAGGTTGCACACA
* *
106012 CAGTGCCAATACGGAAGTTCATGAACTTATTATGAATTTCTTAGGTTGCACACA
1 TAGTGCCAATACGGAA-TTCATAAACTTATTATGAATTTC-TAGGTTGCACACA
106066 TAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTAAGGTTGCACACA
1 TAGTGCCAATACGG-AATTCATAAACTTATTATGAATTTCT-AGGTTGCACACA
106120 TAGTGC
1 TAGTGC
106126 TCATTCGGTA
Statistics
Matches: 101, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
52 2 0.02
53 17 0.17
54 80 0.79
55 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (52 bp):
TAGTGCCAATACGGAATTCATAAACTTATTATGAATTTCTAGGTTGCACACA
Found at i:111662 original size:2 final size:2
Alignment explanation
Indices: 111655--111708 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
111645 AGCGAAATTG
111655 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
111697 AT AT AT AT AT AT
1 AT AT AT AT AT AT
111709 TAACCAAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:111909 original size:27 final size:27
Alignment explanation
Indices: 111864--111919 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
111854 TTAAACTAAA
*
111864 GACTAAATTTTAAAATTTAAAAGATTG
1 GACTAAATTATAAAATTTAAAAGATTG
* *
111891 GACTAAATTATAGATTTTAAAAGATTG
1 GACTAAATTATAAAATTTAAAAGATTG
111918 GA
1 GA
111920 GGAAGTGATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.36
Consensus pattern (27 bp):
GACTAAATTATAAAATTTAAAAGATTG
Found at i:119983 original size:178 final size:181
Alignment explanation
Indices: 119684--120046 Score: 705
Period size: 178 Copynumber: 2.0 Consensus size: 181
119674 AATAGAATAA
119684 TCAATCCTTAGCCAAATTGGCTAAGGAAAAAGGAAAAATGCGATGTTTAATCTCATCCTCATATA
1 TCAATCCTTAGCCAAATTGGCTAAGGAAAAAGGAAAAATGCGATGTTTAATCTCATCCTCATATA
119749 CTCCCTATTATTTCATGCTAGAGTAAACCATGTGAAATTCAGTAAGGTACTTGTGAGGATTTTTA
66 CTCCCTATTATTTCATGCTAGAGTAAACCATGTGAAATTCAGTAAGGTACTTGTGAGGATTTTTA
119814 ATGGATAGTCCAT-GG-AGTCGG-ATAATATGGATTAAACTCATTTTCAGC
131 ATGGATAGTCCATGGGAAGTCGGTATAATATGGATTAAACTCATTTTCAGC
119862 TCAATCCTTAGCCAAATTGGCTAAGGAAAAAGGAAAAATGCGATGTTTAATCTCATCCTCATATA
1 TCAATCCTTAGCCAAATTGGCTAAGGAAAAAGGAAAAATGCGATGTTTAATCTCATCCTCATATA
119927 CTCCCTATTATTTCATGCTAGAGTAAACCATGTGAAATTCAGTAAGGTACTTGTGAGGATTTTTA
66 CTCCCTATTATTTCATGCTAGAGTAAACCATGTGAAATTCAGTAAGGTACTTGTGAGGATTTTTA
119992 ATGGATAGTCCATGGGAAGTCGGTATAATATGGATTAAACTCATTTTCAGC
131 ATGGATAGTCCATGGGAAGTCGGTATAATATGGATTAAACTCATTTTCAGC
120043 TCAA
1 TCAA
120047 ACGATGTCTC
Statistics
Matches: 182, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
178 143 0.79
179 2 0.01
180 6 0.03
181 31 0.17
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (181 bp):
TCAATCCTTAGCCAAATTGGCTAAGGAAAAAGGAAAAATGCGATGTTTAATCTCATCCTCATATA
CTCCCTATTATTTCATGCTAGAGTAAACCATGTGAAATTCAGTAAGGTACTTGTGAGGATTTTTA
ATGGATAGTCCATGGGAAGTCGGTATAATATGGATTAAACTCATTTTCAGC
Found at i:122874 original size:21 final size:21
Alignment explanation
Indices: 122845--122896 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
122835 TGCAAGAAAT
* **
122845 GGATTGATCCTTTAGGGGAAG
1 GGATCGATCCTTTAGGCAAAG
* *
122866 GGATCGATCATTTTGGCAAAG
1 GGATCGATCCTTTAGGCAAAG
122887 GGATCGATCC
1 GGATCGATCC
122897 AAACCCTACT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (21 bp):
GGATCGATCCTTTAGGCAAAG
Found at i:122962 original size:21 final size:19
Alignment explanation
Indices: 122913--122963 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
122903 TACTAGAATC
* *
122913 CAAGGGATCAATCCTTTTT
1 CAAGGGATCGATCCTTTGT
122932 CAAGGAGATCGATCCTTTAGT
1 CAAGG-GATCGATCCTTT-GT
122953 CAAAGGGATCG
1 C-AAGGGATCG
122964 GTTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 5 0.19
20 11 0.41
21 7 0.26
22 4 0.15
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (19 bp):
CAAGGGATCGATCCTTTGT
Found at i:123402 original size:2 final size:2
Alignment explanation
Indices: 123395--123472 Score: 92
Period size: 2 Copynumber: 41.0 Consensus size: 2
123385 TACTTTTGAA
*
123395 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
123436 TT AA AT -T AT A- AT AT AA AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
123473 TGAAAGCTTA
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
1 4 0.06
2 62 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123506 original size:18 final size:18
Alignment explanation
Indices: 123461--123508 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
123451 AATAATATAT
123461 ATATATATATATTGAAAGC
1 ATATATA-ATATTGAAAGC
* * * *
123480 TTATTTAATTTTTAAAGC
1 ATATATAATATTGAAAGC
123498 ATATATAATAT
1 ATATATAATAT
123509 ACAGTTTTGA
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (18 bp):
ATATATAATATTGAAAGC
Found at i:123612 original size:14 final size:14
Alignment explanation
Indices: 123589--123623 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
123579 TTATATTTCC
*
123589 TATTTCTATTTTAT
1 TATTTTTATTTTAT
123603 TATTTTTATTTTAT
1 TATTTTTATTTTAT
*
123617 TGTTTTT
1 TATTTTT
123624 CAGGTCCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (14 bp):
TATTTTTATTTTAT
Found at i:127646 original size:64 final size:64
Alignment explanation
Indices: 127567--127760 Score: 388
Period size: 64 Copynumber: 3.0 Consensus size: 64
127557 GTTGTATGGC
127567 GCGCACCATGGTTTGATCAATACAAATTTCTGTGCAAGTGTGGTAATGATCATTAGGTAAATTT
1 GCGCACCATGGTTTGATCAATACAAATTTCTGTGCAAGTGTGGTAATGATCATTAGGTAAATTT
127631 GCGCACCATGGTTTGATCAATACAAATTTCTGTGCAAGTGTGGTAATGATCATTAGGTAAATTT
1 GCGCACCATGGTTTGATCAATACAAATTTCTGTGCAAGTGTGGTAATGATCATTAGGTAAATTT
127695 GCGCACCATGGTTTGATCAATACAAATTTCTGTGCAAGTGTGGTAATGATCATTAGGTAAATTT
1 GCGCACCATGGTTTGATCAATACAAATTTCTGTGCAAGTGTGGTAATGATCATTAGGTAAATTT
127759 GC
1 GC
127761 TAAGACTTTG
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 130 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.34
Consensus pattern (64 bp):
GCGCACCATGGTTTGATCAATACAAATTTCTGTGCAAGTGTGGTAATGATCATTAGGTAAATTT
Found at i:127649 original size:31 final size:31
Alignment explanation
Indices: 127613--127713 Score: 89
Period size: 31 Copynumber: 3.2 Consensus size: 31
127603 AGTGTGGTAA
127613 TGATCATTAGGTAAATTTGCGCACCATGGTT
1 TGATCATTAGGTAAATTTGCGCACCATGGTT
* * * *** *
127644 TGATCAATA--CAAATTTCTGTGCAAGTGTGGTAA
1 TGATCATTAGGTAAA-TT-TGCGC-ACCATGGT-T
127677 TGATCATTAGGTAAATTTGCGCACCATGGTT
1 TGATCATTAGGTAAATTTGCGCACCATGGTT
127708 TGATCA
1 TGATCA
127714 ATACAAATTT
Statistics
Matches: 50, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
29 3 0.06
30 2 0.04
31 18 0.36
32 10 0.20
33 12 0.24
34 2 0.04
35 3 0.06
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.35
Consensus pattern (31 bp):
TGATCATTAGGTAAATTTGCGCACCATGGTT
Found at i:127659 original size:29 final size:29
Alignment explanation
Indices: 127625--127723 Score: 81
Period size: 31 Copynumber: 3.2 Consensus size: 29
127615 ATCATTAGGT
127625 AAATTTGCGCACCATGGTTTGATCAATAC
1 AAATTTGCGCACCATGGTTTGATCAATAC
* *** * * *
127654 AAATTTCTGTGCAAGTGTGGTAATGATCATTAGGT
1 AAA-TT-TGCGC-ACCATGGT-TTGATCAATA--C
127689 AAATTTGCGCACCATGGTTTGATCAATAC
1 AAATTTGCGCACCATGGTTTGATCAATAC
127718 AAATTT
1 AAATTT
127724 CTGTGCAAGT
Statistics
Matches: 50, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
29 9 0.18
30 2 0.04
31 12 0.24
32 10 0.20
33 12 0.24
34 2 0.04
35 3 0.06
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (29 bp):
AAATTTGCGCACCATGGTTTGATCAATAC
Found at i:127682 original size:33 final size:33
Alignment explanation
Indices: 127580--127746 Score: 116
Period size: 33 Copynumber: 5.2 Consensus size: 33
127570 CACCATGGTT
127580 TGATCAATACAAATTTCTGTGCAAGTGTGGTAA
1 TGATCAATACAAATTTCTGTGCAAGTGTGGTAA
* * * *** *
127613 TGATCATTAGGTAAA-TT-TGCGC-ACCATGGT-T
1 TGATCAATA--CAAATTTCTGTGCAAGTGTGGTAA
127644 TGATCAATACAAATTTCTGTGCAAGTGTGGTAA
1 TGATCAATACAAATTTCTGTGCAAGTGTGGTAA
* * * *** *
127677 TGATCATTAGGTAAA-TT-TGCGC-ACCATGGT-T
1 TGATCAATA--CAAATTTCTGTGCAAGTGTGGTAA
127708 TGATCAATACAAATTTCTGTGCAAGTGTGGTAA
1 TGATCAATACAAATTTCTGTGCAAGTGTGGTAA
127741 TGATCA
1 TGATCA
127747 TTAGGTAAAT
Statistics
Matches: 94, Mismatches: 28, Indels: 24
0.64 0.19 0.16
Matches are distributed among these distances:
29 6 0.06
30 4 0.04
31 24 0.26
32 20 0.21
33 30 0.32
34 4 0.04
35 6 0.06
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34
Consensus pattern (33 bp):
TGATCAATACAAATTTCTGTGCAAGTGTGGTAA
Found at i:131878 original size:14 final size:14
Alignment explanation
Indices: 131859--131896 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
131849 GTAAAATACG
*
131859 GTATGAACATTACC
1 GTATGAACAGTACC
131873 GTATGAACAGTACC
1 GTATGAACAGTACC
131887 G--TGAACAGTA
1 GTATGAACAGTA
131897 TTGATTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 9 0.39
14 14 0.61
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (14 bp):
GTATGAACAGTACC
Found at i:132817 original size:18 final size:18
Alignment explanation
Indices: 132796--132863 Score: 82
Period size: 18 Copynumber: 3.6 Consensus size: 18
132786 ATTTGTCTTG
132796 AAGGACCACTATGTCCCA
1 AAGGACCACTATGTCCCA
*
132814 AAGGACCACTATATATGTCCCC
1 AAGGACCAC----TATGTCCCA
*
132836 AAGGACCACTATGTCCCG
1 AAGGACCACTATGTCCCA
132854 AAGGACCACT
1 AAGGACCACT
132864 GTATACCCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
18 27 0.61
22 17 0.39
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (18 bp):
AAGGACCACTATGTCCCA
Found at i:132830 original size:22 final size:22
Alignment explanation
Indices: 132805--132847 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
132795 GAAGGACCAC
132805 TATGTCCCAAAGGACCACTATA
1 TATGTCCCAAAGGACCACTATA
*
132827 TATGTCCCCAAGGACCACTAT
1 TATGTCCCAAAGGACCACTAT
132848 GTCCCGAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.23
Consensus pattern (22 bp):
TATGTCCCAAAGGACCACTATA
Found at i:134089 original size:3 final size:3
Alignment explanation
Indices: 134083--134139 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
134073 CGGGGAGGAG
* * *
134083 GAA GAA GAA G-G GAA -AA GAA GAA GAA GGGA GAA GAA GAA GAA GGGA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA -GAA
134128 GAA GAA GAA GAA
1 GAA GAA GAA GAA
134140 AGAGTTTTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 3 0.07
3 37 0.84
4 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:134104 original size:16 final size:16
Alignment explanation
Indices: 134083--134139 Score: 105
Period size: 16 Copynumber: 3.6 Consensus size: 16
134073 CGGGGAGGAG
*
134083 GAAGAAGAAGGGAAAA
1 GAAGAAGAAGGGAGAA
134099 GAAGAAGAAGGGAGAA
1 GAAGAAGAAGGGAGAA
134115 GAAGAAGAAGGGAGAA
1 GAAGAAGAAGGGAGAA
134131 GAAGAAGAA
1 GAAGAAGAA
134140 AGAGTTTTAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (16 bp):
GAAGAAGAAGGGAGAA
Found at i:149452 original size:22 final size:22
Alignment explanation
Indices: 149426--149468 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
149416 ATTTTAGAAA
* *
149426 AAATATAAATCATATACTTTTG
1 AAATATAAATAATATAATTTTG
*
149448 AAATATATATAATATAATTTT
1 AAATATAAATAATATAATTTT
149469 AGTAACATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (22 bp):
AAATATAAATAATATAATTTTG
Found at i:149537 original size:24 final size:25
Alignment explanation
Indices: 149498--149560 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
149488 AAGTATATTT
*
149498 AAAATATATATAATATA-AGTTTTG
1 AAAATATATATAATATACAATTTTG
* *
149522 AAAGTATATATTATATACAATTTTG
1 AAAATATATATAATATACAATTTTG
149547 AAAATATATATAAT
1 AAAATATATATAAT
149561 TTTGAAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
24 15 0.45
25 18 0.55
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (25 bp):
AAAATATATATAATATACAATTTTG
Found at i:149554 original size:25 final size:24
Alignment explanation
Indices: 149416--149560 Score: 91
Period size: 25 Copynumber: 5.8 Consensus size: 24
149406 TTAAATTTTT
*
149416 ATTTTAGAAAAAATATA-AATCATATA
1 ATTTT-GAAAATATATATAAT-ATA-A
*
149442 CTTTTG-AAATATATATAATAT-A
1 ATTTTGAAAATATATATAATATAA
* * * *
149464 ATTTTAGTAACATATATGT-TTTTAA
1 ATTTT-G-AAAATATATATAATATAA
*
149489 AGTATATTTAAAATATATATAATATAA
1 A-T-T-TTGAAAATATATATAATATAA
* * *
149516 GTTTTGAAAGTATATATTATATACA
1 ATTTTGAAAATATATATAATATA-A
149541 ATTTTGAAAATATATATAAT
1 ATTTTGAAAATATATATAAT
149561 TTTGAAATTA
Statistics
Matches: 90, Mismatches: 19, Indels: 21
0.69 0.15 0.16
Matches are distributed among these distances:
22 5 0.06
23 1 0.01
24 29 0.32
25 33 0.37
26 15 0.17
27 5 0.06
28 2 0.02
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (24 bp):
ATTTTGAAAATATATATAATATAA
Found at i:149572 original size:16 final size:18
Alignment explanation
Indices: 149533--149572 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
149523 AAGTATATAT
149533 TATATACAATTTTGAAAA
1 TATATACAATTTTGAAAA
* *
149551 TATATATAATTTTGAAAT
1 TATATACAATTTTGAAAA
149569 TATA
1 TATA
149573 ATATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (18 bp):
TATATACAATTTTGAAAA
Found at i:149598 original size:30 final size:29
Alignment explanation
Indices: 149550--149608 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
149540 AATTTTGAAA
*
149550 ATATATATAATTTTGAAATTATAATATAT
1 ATATATATAATATTGAAATTATAATATAT
149579 ATATATATATATATTGAAATTATAATATAT
1 ATATATATA-ATATTGAAATTATAATATAT
149609 GGTTTTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (29 bp):
ATATATATAATATTGAAATTATAATATAT
Found at i:149607 original size:51 final size:47
Alignment explanation
Indices: 149499--149618 Score: 113
Period size: 51 Copynumber: 2.5 Consensus size: 47
149489 AGTATATTTA
149499 AAATATATATAATATAAGTTTTGAAAGTATATATTATATACAAT-T-TTG
1 AAATATA-AT-ATATAA-TTTTGAAAGTATATATTATATACAATATATTG
* *
149547 AAA-AT-ATATATAATTTTGAAATTATAATATATATATATATATATATTG
1 AAATATAATATATAATTTTGAAAGTAT-ATAT-TATATACA-ATATATTG
**
149595 AAATTATAATATATGGTTTTGAAA
1 AAA-TATAATATATAATTTTGAAA
149619 AAAAATATGC
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
43 11 0.18
44 10 0.17
45 9 0.15
46 2 0.03
47 3 0.05
48 9 0.15
50 2 0.03
51 14 0.23
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (47 bp):
AAATATAATATATAATTTTGAAAGTATATATTATATACAATATATTG
Found at i:149728 original size:14 final size:15
Alignment explanation
Indices: 149711--149743 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
149701 ATTTCCATTG
149711 TTTTATTTT-ATTAT
1 TTTTATTTTGATTAT
149725 TTTTATTTTGATTAT
1 TTTTATTTTGATTAT
149740 TTTT
1 TTTT
149744 TAGGTCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTATTTTGATTAT
Found at i:152449 original size:15 final size:15
Alignment explanation
Indices: 152429--152458 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
152419 TGAAATTGAT
152429 GATTTTATCAAAAAC
1 GATTTTATCAAAAAC
152444 GATTTTATCAAAAAC
1 GATTTTATCAAAAAC
152459 TTTCGACACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (15 bp):
GATTTTATCAAAAAC
Done.