Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008662.1 Hibiscus syriacus cultivar Beakdansim tig00111662_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: 1703488
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1400468 original size:21 final size:21
Alignment explanation
Indices: 1400443--1400490 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
1400433 ATGATGACAT
1400443 AAATAAAAGACAAAACAAAAA
1 AAATAAAAGACAAAACAAAAA
* * *
1400464 TAATAAAAAGAGAAAAGAAAAA
1 AAAT-AAAAGACAAAACAAAAA
1400486 AAATA
1 AAATA
1400491 GAATAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.79, C:0.04, G:0.08, T:0.08
Consensus pattern (21 bp):
AAATAAAAGACAAAACAAAAA
Found at i:1400499 original size:4 final size:4
Alignment explanation
Indices: 1400486--1400521 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
1400476 AAAAGAAAAA
1400486 AAAT AGAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1400522 GTACAAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1400696 original size:108 final size:108
Alignment explanation
Indices: 1400566--1400826 Score: 302
Period size: 108 Copynumber: 2.4 Consensus size: 108
1400556 TAAAGTAAAT
*
1400566 AAAAAA-AATCAGATACAAATAATTAGAATATATATAATAATAATAATAGACGTATAAATAAAAT
1 AAAAAATAATCAAATA-AAATAATTAGAATATATATAATAATAATAATAGACGTATAAATAAAAT
* *
1400630 A-TTAAAAGTATATATATATATATAT-ATAATGATAAAATATAGT-
65 ATTTAAAAATATATATATACATATATGA-AATGAT-AAATATAGTA
* * ** *** *
1400673 AGAAAATAATCAAATAAAGATAATAAGAATATACGT-ATAATAATAATAGGTTTATAAATGAAAT
1 AAAAAATAATCAAATAAA-ATAATTAGAATATATATAATAATAATAATAGACGTATAAATAAAAT
1400737 ATTTAAAAATATATATATACATATATGAAATGATAAATATAGTA
65 ATTTAAAAATATATATATACATATATGAAATGATAAATATAGTA
*
1400781 AAAAAATAATCAAATAAAA-AATAATAAAATAATATATAAT-ATAATA
1 AAAAAATAATCAAATAAAATAAT--TAGAAT-ATATATAATAATAATA
1400827 CAAATAATAA
Statistics
Matches: 129, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
106 3 0.02
107 42 0.33
108 71 0.55
109 11 0.09
110 2 0.02
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.31
Consensus pattern (108 bp):
AAAAAATAATCAAATAAAATAATTAGAATATATATAATAATAATAATAGACGTATAAATAAAATA
TTTAAAAATATATATATACATATATGAAATGATAAATATAGTA
Found at i:1400797 original size:8 final size:8
Alignment explanation
Indices: 1400783--1400838 Score: 51
Period size: 8 Copynumber: 6.5 Consensus size: 8
1400773 ATATAGTAAA
1400783 AAAATAAT
1 AAAATAAT
*
1400791 CAAATAA-
1 AAAATAAT
1400798 AAAATAAT
1 AAAATAAT
1400806 AAAATAATAT
1 AAAAT-A-AT
1400816 ATAATATAAT
1 A-AA-ATAAT
1400826 ACAAATAAT
1 A-AAATAAT
1400835 AAAA
1 AAAA
1400839 GGAAATAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
7 6 0.15
8 14 0.35
9 7 0.17
10 8 0.20
11 3 0.08
12 2 0.05
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (8 bp):
AAAATAAT
Found at i:1400801 original size:15 final size:15
Alignment explanation
Indices: 1400781--1400838 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
1400771 AAATATAGTA
*
1400781 AAAAAATAATCAAAT
1 AAAAAATAATAAAAT
1400796 AAAAAATAATAAAAT
1 AAAAAATAATAAAAT
* * *
1400811 AATATATAATATAAT
1 AAAAAATAATAAAAT
*
1400826 -ACAAATAATAAAA
1 AAAAAATAATAAAA
1400839 GGAAATAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
14 10 0.28
15 26 0.72
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAAATAATAAAAT
Found at i:1400844 original size:108 final size:106
Alignment explanation
Indices: 1400565--1400863 Score: 281
Period size: 108 Copynumber: 2.8 Consensus size: 106
1400555 ATAAAGTAAA
* * * **
1400565 TAAAAAA-AATCAGATACAAATAATTAGAATATA-TATAATAATAATAATAGACGT-ATAAATAA
1 TAAAAAATAATCAAATAAAAATAATAAGAATATACTATAATAATAATAA-A-A--TAATAAAGGA
* *
1400627 AATATTAAAAGTATATATATATATATATATAATGATAAAATATAG
62 AATATTAAAAATATATATATACATATATATAATGATAAAATATAG
* * *** * *
1400672 TAGAAAATAATCAAATAAAGATAATAAGAATATACGTATAATAATAATAGGTTTATAAATGAAAT
1 TAAAAAATAATCAAATAAAAATAATAAGAATATAC-TATAATAATAATAAAATAATAAAGGAAAT
1400737 ATTTAAAAATATATATATACATATATGA-AATGAT-AAATATAG
65 A-TTAAAAATATATATATACATATAT-ATAATGATAAAATATAG
1400779 TAAAAAAATAATCAAATAAAAAATAATAA-AATAATA-TATAAT-ATAATACAAATAATAAAAGG
1 T-AAAAAATAATCAAAT-AAAAATAATAAGAAT-ATACTATAATAATAATA-AAATAAT-AAAGG
* *
1400841 AAATAAATAAAAATATCTATATA
61 AAAT-ATTAAAAATATATATATA
1400864 ATAAATAAAG
Statistics
Matches: 160, Mismatches: 20, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
106 7 0.04
107 35 0.22
108 90 0.56
109 15 0.09
110 13 0.08
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (106 bp):
TAAAAAATAATCAAATAAAAATAATAAGAATATACTATAATAATAATAAAATAATAAAGGAAATA
TTAAAAATATATATATACATATATATAATGATAAAATATAG
Found at i:1401905 original size:2 final size:2
Alignment explanation
Indices: 1401898--1401951 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1401888 GAAATAAGCA
1401898 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
1401940 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1401952 GTGACAGAAA
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:1402643 original size:43 final size:43
Alignment explanation
Indices: 1402577--1402705 Score: 177
Period size: 43 Copynumber: 3.0 Consensus size: 43
1402567 TGGATGCTGC
* * *
1402577 TTGTGTGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGAT
1 TTGTGGGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
**
1402620 TTGTGGGCACGATATCCTCCGTCGTGGAGTTGAAATTATGGAT
1 TTGTGGGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
* * * *
1402663 TTATGGGTACGATATCCTCTGTCATGGAGTTGAAATCGTGGAT
1 TTGTGGGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
1402706 GACCCCTTCG
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.34
Consensus pattern (43 bp):
TTGTGGGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
Found at i:1403705 original size:12 final size:12
Alignment explanation
Indices: 1403688--1403730 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
1403678 CCCTAAACGT
*
1403688 TTCTTTTTTTTG
1 TTCTTTTTTTTC
1403700 TTCTTTTCTTTTC
1 TTCTTTT-TTTTC
*
1403713 TTTTTTCTTTTTC
1 TTCTTT-TTTTTC
1403726 TTCTT
1 TTCTT
1403731 CGACTTAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 7 0.27
13 18 0.69
14 1 0.04
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.81
Consensus pattern (12 bp):
TTCTTTTTTTTC
Found at i:1403709 original size:17 final size:17
Alignment explanation
Indices: 1403687--1403723 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1403677 ACCCTAAACG
1403687 TTTCTTTT-TTTTGTTCT
1 TTTCTTTTCTTTT-TTCT
1403704 TTTCTTTTCTTTTTTCT
1 TTTCTTTTCTTTTTTCT
1403721 TTT
1 TTT
1403724 TCTTCTTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.84
Consensus pattern (17 bp):
TTTCTTTTCTTTTTTCT
Found at i:1412174 original size:14 final size:14
Alignment explanation
Indices: 1412136--1412175 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1412126 CTCCCAAAGG
* *
1412136 TGAATAGGTGATGC
1 TGAATCGGTGGTGC
1412150 TGAATCGGTGGTGC
1 TGAATCGGTGGTGC
1412164 TGAATCGGTGGT
1 TGAATCGGTGGT
1412176 AGACAACCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.20, C:0.10, G:0.40, T:0.30
Consensus pattern (14 bp):
TGAATCGGTGGTGC
Found at i:1412631 original size:8 final size:8
Alignment explanation
Indices: 1412618--1412642 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1412608 TGATGCTTTT
1412618 GCAGTGTA
1 GCAGTGTA
1412626 GCAGTGTA
1 GCAGTGTA
1412634 GCAGTGTA
1 GCAGTGTA
1412642 G
1 G
1412643 TATATTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.40, T:0.24
Consensus pattern (8 bp):
GCAGTGTA
Found at i:1414101 original size:15 final size:14
Alignment explanation
Indices: 1414081--1414118 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
1414071 GGGAAAAATG
*
1414081 ATAAAATAAGAGAAA
1 ATAAAATAA-ACAAA
1414096 ATAAAATAAACAAA
1 ATAAAATAAACAAA
1414110 AT-AAATAAA
1 ATAAAATAAA
1414119 TGCTGACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.32
14 6 0.27
15 9 0.41
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (14 bp):
ATAAAATAAACAAA
Found at i:1414385 original size:99 final size:102
Alignment explanation
Indices: 1414208--1414477 Score: 283
Period size: 97 Copynumber: 2.7 Consensus size: 102
1414198 TGAAAAAAAA
* ** *
1414208 ATATACATATATG-AT-ATAAAGTA-AAT-AAAAA-AATCAGCTAAAAATAATTAGAATATATAT
1 ATATACATATATGAATAATAAA-TATAGTAAAAAATAATCAAATAAAAATAATAAGAATATATAT
*
1414268 AATAATAATAGACGTATAAATAAAATA-TTAAAAGTAT
65 AATAATAATAGACGTATAAATAAAATATTTAAAAATAT
* * *
1414305 ATATATATA-ATG-AT-A-AAATATAGTAGAAAATAATCAAATAAAGATAATAAGAATATACGTA
1 ATATACATATATGAATAATAAATATAGTAAAAAATAATCAAATAAAAATAATAAGAATATA--TA
*** *
1414366 TAATAATAATAGGTTTATAAATGAAATATTTAAAAATAT
64 TAATAATAATAGACGTATAAATAAAATATTTAAAAATAT
* *
1414405 ATATACATATTTGAAATAATAAATATAGTAAAAAATAATCAAATAAAAAATAATTAA-AAAATAT
1 ATATACATATATG-AATAATAAATATAGTAAAAAATAATCAAAT-AAAAATAA-TAAGAATATAT
1414469 ATAATAATA
63 ATAATAATA
1414478 CAAATAATAA
Statistics
Matches: 143, Mismatches: 17, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
94 2 0.01
95 5 0.03
96 10 0.07
97 30 0.21
99 26 0.18
100 17 0.12
101 2 0.01
103 2 0.01
104 11 0.08
105 23 0.16
106 12 0.08
107 3 0.02
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.31
Consensus pattern (102 bp):
ATATACATATATGAATAATAAATATAGTAAAAAATAATCAAATAAAAATAATAAGAATATATATA
ATAATAATAGACGTATAAATAAAATATTTAAAAATAT
Found at i:1414416 original size:20 final size:22
Alignment explanation
Indices: 1414391--1414431 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1414381 TATAAATGAA
*
1414391 ATATTT-AAA-AATATATATAC
1 ATATTTGAAATAATAAATATAC
1414411 ATATTTGAAATAATAAATATA
1 ATATTTGAAATAATAAATATA
1414432 GTAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATTTGAAATAATAAATATAC
Found at i:1415585 original size:2 final size:2
Alignment explanation
Indices: 1415578--1415606 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1415568 GAAATAAGCA
1415578 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 A
1415607 ATCAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1416523 original size:3 final size:3
Alignment explanation
Indices: 1416515--1416555 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1416505 TTTTTCACCA
1416515 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1416556 ATTACAAGGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1423807 original size:21 final size:23
Alignment explanation
Indices: 1423731--1423797 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
1423721 AGGATTTTAG
* * *
1423731 TGAAGAGGGAATCGATACCCCCCT
1 TGAAG-GGGAACCGATTCCCCCTT
* *
1423755 CGAAAGGGAACCGATTCCCCCTT
1 TGAAGGGGAACCGATTCCCCCTT
1423778 TGAAGGGGAACCGATTCCCC
1 TGAAGGGGAACCGATTCCCC
1423798 TTGTAGGGGA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 33 0.92
24 3 0.08
ACGTcount: A:0.27, C:0.31, G:0.25, T:0.16
Consensus pattern (23 bp):
TGAAGGGGAACCGATTCCCCCTT
Found at i:1423813 original size:21 final size:22
Alignment explanation
Indices: 1423760--1423807 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
1423750 CCCCTCGAAA
1423760 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATT-CCCCTTTGAAG
*
1423783 GGGAACCGATTCCCC-TTGTAG
1 GGGAACCGATTCCCCTTTGAAG
1423804 GGGA
1 GGGA
1423808 TTCGATACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 9 0.38
22 4 0.17
23 11 0.46
ACGTcount: A:0.21, C:0.27, G:0.31, T:0.21
Consensus pattern (22 bp):
GGGAACCGATTCCCCTTTGAAG
Found at i:1425406 original size:18 final size:17
Alignment explanation
Indices: 1425378--1425425 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 17
1425368 ATGAACTAGA
1425378 ACAGCACGAGGAACAAGC
1 ACAGCA-GAGGAACAAGC
1425396 ACGAGCAGAGGAACAAGC
1 AC-AGCAGAGGAACAAGC
1425414 ACAGCCAGAGGA
1 ACAG-CAGAGGA
1425426 TCAAATGCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 2 0.07
18 22 0.79
19 4 0.14
ACGTcount: A:0.44, C:0.25, G:0.31, T:0.00
Consensus pattern (17 bp):
ACAGCAGAGGAACAAGC
Found at i:1427974 original size:18 final size:18
Alignment explanation
Indices: 1427948--1427989 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1427938 TTTTTAGGAA
*
1427948 AATAATTATATTATT-ATT
1 AATATTTAT-TTATTAATT
1427966 AATATTTATTTATTAATT
1 AATATTTATTTATTAATT
1427984 AATATT
1 AATATT
1427990 AAAGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATATTTATTTATTAATT
Found at i:1429750 original size:12 final size:12
Alignment explanation
Indices: 1429733--1429757 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1429723 ATGGTGACAA
1429733 CTGTAAAAGCTC
1 CTGTAAAAGCTC
1429745 CTGTAAAAGCTC
1 CTGTAAAAGCTC
1429757 C
1 C
1429758 CAGAGATGAG
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:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (12 bp):
CTGTAAAAGCTC
Found at i:1434845 original size:22 final size:22
Alignment explanation
Indices: 1434814--1434863 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
1434804 GACAGAAATA
1434814 ATCCACGTGTGGCATTTTAAAG
1 ATCCACGTGTGGCATTTTAAAG
* *
1434836 ATCCATGTGTGGCATTTTGAAG
1 ATCCACGTGTGGCATTTTAAAG
*
1434858 GTCCAC
1 ATCCAC
1434864 ATCAATATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (22 bp):
ATCCACGTGTGGCATTTTAAAG
Found at i:1435965 original size:54 final size:54
Alignment explanation
Indices: 1435879--1435989 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
1435869 TTCACTGGTA
*
1435879 AACATCTTGGCAGAAACCACAAGAAAAGATGAATATGTTGTCAAATATTTTATG
1 AACATCTTGGCAGAAACCACAAGAAAAGATGAATATGTTGTCAAATATTTTACG
* *
1435933 AACATC-TGTGCAGAAACCACAAG-AAAGAATGAATGTGTTGTCAAATGTTTTACG
1 AACATCTTG-GCAGAAACCACAAGAAAAG-ATGAATATGTTGTCAAATATTTTACG
1435987 AAC
1 AAC
1435990 CAGTTATTCT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
53 6 0.12
54 46 0.88
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.26
Consensus pattern (54 bp):
AACATCTTGGCAGAAACCACAAGAAAAGATGAATATGTTGTCAAATATTTTACG
Found at i:1436426 original size:20 final size:21
Alignment explanation
Indices: 1436356--1436451 Score: 131
Period size: 22 Copynumber: 4.5 Consensus size: 21
1436346 ATCCACATTC
1436356 TTCAAAGATGATAGATCTCTT
1 TTCAAAGATGATAGATCTCTT
1436377 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGA-TCTCTT
* *
1436399 TTCAAAGATGATAGA-CACTC
1 TTCAAAGATGATAGATCTCTT
*
1436419 TCCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGA-TCTCTT
*
1436441 TTAAAAGATGA
1 TTCAAAGATGA
1436452 AAGCTTTATT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
20 17 0.26
21 15 0.23
22 33 0.51
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (21 bp):
TTCAAAGATGATAGATCTCTT
Found at i:1436435 original size:42 final size:43
Alignment explanation
Indices: 1436356--1436451 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 43
1436346 ATCCACATTC
* * *
1436356 TTCAAAGATGATAGATCTCTTTTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATCACTCTCCAAAGATGATAGATTCTCTT
1436399 TTCAAAGATGATAGA-CACTCTCCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATCACTCTCCAAAGATGATAGATTCTCTT
*
1436441 TTAAAAGATGA
1 TTCAAAGATGA
1436452 AAGCTTTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 34 0.69
43 15 0.31
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (43 bp):
TTCAAAGATGATAGATCACTCTCCAAAGATGATAGATTCTCTT
Found at i:1437177 original size:31 final size:32
Alignment explanation
Indices: 1437139--1437220 Score: 127
Period size: 31 Copynumber: 2.7 Consensus size: 32
1437129 CTACAGTGCA
1437139 TGATGTTTTCAAAAAGCCTTCGA-GAGCTTTT
1 TGATGTTTTCAAAAAGCCTTCGAGGAGCTTTT
*
1437170 TGATGTTTCCAAAAAGCCTTC-AGGAGCTTTT
1 TGATGTTTTCAAAAAGCCTTCGAGGAGCTTTT
1437201 TGATGTTTTC--AAAGCCTTCG
1 TGATGTTTTCAAAAAGCCTTCG
1437221 GGTCATCTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
29 9 0.19
30 1 0.02
31 37 0.79
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (32 bp):
TGATGTTTTCAAAAAGCCTTCGAGGAGCTTTT
Found at i:1437300 original size:76 final size:76
Alignment explanation
Indices: 1437170--1437343 Score: 262
Period size: 76 Copynumber: 2.3 Consensus size: 76
1437160 GAGAGCTTTT
* * * * * *
1437170 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
1 TGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGA
*
1437235 CCTACAGTGCA
66 CCTACAATGCA
*
1437246 TGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGATGTTTTTAAAACCTTAGGGTCATCTGTAAGA
1 TGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGA
1437311 CCTACAATGCA
66 CCTACAATGCA
1437322 TGATGTTTTC-AAAA-CCTTCGGG
1 TGATGTTTTCAAAAAGCCTTCGGG
1437344 TCATCTATAA
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
74 8 0.09
75 4 0.04
76 78 0.87
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (76 bp):
TGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGA
CCTACAATGCA
Found at i:1437345 original size:45 final size:45
Alignment explanation
Indices: 1437277--1437380 Score: 154
Period size: 45 Copynumber: 2.3 Consensus size: 45
1437267 GGGAGATTTT
* *
1437277 TGATGTTTTTAAAACCTTAGGGTCATCTGTAAGACCTACAATGCA
1 TGATGTTTTCAAAACCTTAGGGTCATCTATAAGACCTACAATGCA
* * *
1437322 TGATGTTTTCAAAACCTTCGGGTCATCTATAATACCTACAGTGCA
1 TGATGTTTTCAAAACCTTAGGGTCATCTATAAGACCTACAATGCA
*
1437367 GGATGTTTTCAAAA
1 TGATGTTTTCAAAA
1437381 AGCCTTCAGG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTAGGGTCATCTATAAGACCTACAATGCA
Found at i:1437415 original size:121 final size:121
Alignment explanation
Indices: 1437201--1437769 Score: 687
Period size: 121 Copynumber: 4.6 Consensus size: 121
1437191 AGGAGCTTTT
* *
1437201 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
* * * *
1437266 CGGGAGATTTTTGATGTTTTTAAAACCTTAGGGTCATCTGTAAGACCTACAATGCA
66 CGGGAGATTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* * *
1437322 TGATGTTTTCAAAACCTTCGGGTCATCTATAATACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
* * *
1437387 CAGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
66 CGGGAGATTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* **
1437443 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
* *
1437508 CGGGAGTTTTTTGATGTTATTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
66 CGGGAGATTTTTGATGTT-TTC-AAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* *
1437566 TGATGTTATTCAAAAACCTTTGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTC-AAAA-CC
1 TGATGTT-TTC-AAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCC
* * * *
1437629 TTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTATCAAAACCTTCGGGTTATCTGTAAGCCC
64 TTC-GG------G--AGA--TT---T--TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACC
*
1437694 TTCAGTGTA
113 TTCAGTGCA
* * *
1437703 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
1437766 CGGG
66 CGGG
1437770 TCATCTGTAA
Statistics
Matches: 395, Mismatches: 33, Indels: 33
0.86 0.07 0.07
Matches are distributed among these distances:
121 183 0.46
122 3 0.01
123 46 0.12
124 9 0.02
125 42 0.11
128 1 0.00
130 1 0.00
132 2 0.01
134 4 0.01
135 51 0.13
136 3 0.01
137 41 0.10
138 2 0.01
139 7 0.02
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (121 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
CGGGAGATTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
Found at i:1437454 original size:45 final size:45
Alignment explanation
Indices: 1437398--1437511 Score: 183
Period size: 45 Copynumber: 2.5 Consensus size: 45
1437388 AGGAGCTTTT
*
1437398 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* *
1437443 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1437488 TGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
1437512 AGTTTTTTGA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
45 52 0.81
46 4 0.06
47 8 0.12
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
Found at i:1437642 original size:45 final size:45
Alignment explanation
Indices: 1437519--1437862 Score: 499
Period size: 45 Copynumber: 7.5 Consensus size: 45
1437509 GGGAGTTTTT
1437519 TGATGTTATTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTT-TTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
1437566 TGATGTTATTCAAAAACCTTTGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTT-TTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1437613 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
1437658 TGATGTTATCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTGTA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1437703 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1437748 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * ** * *
1437793 TGATGTTATCAAAACCTTCGGGCCATCCATAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
1437838 GGACGTTTTCAAAAAGCCTTCGGGT
1 TGATGTTTTC-AAAA-CCTTCGGGT
1437863 GCTTTTTGAT
Statistics
Matches: 273, Mismatches: 22, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
45 206 0.75
46 7 0.03
47 60 0.22
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:1438092 original size:3 final size:3
Alignment explanation
Indices: 1438086--1438133 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
1438076 TTTTTCATCA
* *
1438086 TAT TAT TAT TAT TAT TAC TAT TAT TAT TAA TA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1438133 T
1 T
1438134 TTTAATTACA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1445037 original size:24 final size:24
Alignment explanation
Indices: 1444975--1445039 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
1444965 TTCGATTTGA
*
1444975 ATTCTGTTATGATACCTAACATGG
1 ATTCTGTTATGATATCTAACATGG
* *
1444999 ATTCTGTTATGATATCTGATATGG
1 ATTCTGTTATGATATCTAACATGG
*
1445023 ATTCTGTTATAATATCT
1 ATTCTGTTATGATATCT
1445040 TACCTGAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (24 bp):
ATTCTGTTATGATATCTAACATGG
Found at i:1449909 original size:23 final size:21
Alignment explanation
Indices: 1449861--1449909 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
1449851 AATATTTGAA
*
1449861 AAATGATCAATCCCTTTTAAT
1 AAATGATCAATCCCTTTCAAT
*
1449882 AAATGATCGATCCCTTGTGCAAT
1 AAATGATCAATCCCTT-T-CAAT
1449905 AAATG
1 AAATG
1449910 TTGTTTTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 15 0.62
22 1 0.04
23 8 0.33
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (21 bp):
AAATGATCAATCCCTTTCAAT
Found at i:1462684 original size:33 final size:33
Alignment explanation
Indices: 1462620--1462696 Score: 79
Period size: 33 Copynumber: 2.4 Consensus size: 33
1462610 AAATATAGAT
* *
1462620 ATCAGAAATCAGAGCAGAGATCATAGATCAAAA
1 ATCAGAAATCAGAACAGAGATCAAAGATCAAAA
* *
1462653 ATCAGAGATCAGAACAG-GTATCAAAGTTC--AA
1 ATCAGAAATCAGAACAGAG-ATCAAAGATCAAAA
*
1462684 AGCAGAAATCAGA
1 ATCAGAAATCAGA
1462697 GGCTAGACTA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
31 13 0.35
32 1 0.03
33 23 0.62
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (33 bp):
ATCAGAAATCAGAACAGAGATCAAAGATCAAAA
Found at i:1471168 original size:18 final size:18
Alignment explanation
Indices: 1471145--1471201 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
1471135 CAGTATTGTT
1471145 CATGAAGTATCGATACTA
1 CATGAAGTATCGATACTA
1471163 CATGAAGTATCGATACTA
1 CATGAAGTATCGATACTA
* *
1471181 TAAGAACAGTATCGATACTA
1 CATG-A-AGTATCGATACTA
1471201 C
1 C
1471202 TTTTCCATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 20 0.59
19 1 0.03
20 13 0.38
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (18 bp):
CATGAAGTATCGATACTA
Found at i:1472098 original size:21 final size:19
Alignment explanation
Indices: 1472074--1472131 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
1472064 ATTTTTGGCT
*
1472074 CAAAGGATCTATCCCTTTGA
1 CAAAGGATCGATCCCTTT-A
*
1472094 CCAAAGAATCGATCCCCTTTA
1 -CAAAGGATCGAT-CCCTTTA
*
1472115 AAAAGGATCGATCCCTT
1 CAAAGGATCGATCCCTT
1472132 GGACAACAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.16
20 10 0.31
21 11 0.34
22 6 0.19
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.26
Consensus pattern (19 bp):
CAAAGGATCGATCCCTTTA
Found at i:1473117 original size:35 final size:35
Alignment explanation
Indices: 1473039--1473124 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 35
1473029 ATGAAGGATT
* * * * *
1473039 ATGACTCTTTATCAAGAGATGTCTCACCAAAAGTT
1 ATGACTCTTCACCAAAAGGTGTCTCACCAAAAGTC
* *
1473074 GTGACTCTTCACCAAAAGGTGTCTCACCATAAGTC
1 ATGACTCTTCACCAAAAGGTGTCTCACCAAAAGTC
* *
1473109 ATGCCTCTTCATCAAA
1 ATGACTCTTCACCAAA
1473125 GGTTACTTCA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (35 bp):
ATGACTCTTCACCAAAAGGTGTCTCACCAAAAGTC
Found at i:1476090 original size:19 final size:20
Alignment explanation
Indices: 1476062--1476099 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1476052 ATTAATAAGC
1476062 TTTAATTTTATATAAATATT
1 TTTAATTTTATATAAATATT
*
1476082 TTTAA-TTTATATACATAT
1 TTTAATTTTATATAAATAT
1476100 GGTTTATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAATTTTATATAAATATT
Found at i:1476105 original size:20 final size:20
Alignment explanation
Indices: 1476062--1476105 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1476052 ATTAATAAGC
*
1476062 TTTAATTTTATATAAATATT
1 TTTAATTTTATATAAATATG
*
1476082 TTTAA-TTTATATACATATGG
1 TTTAATTTTATATAAATAT-G
1476102 TTTA
1 TTTA
1476106 TTACAAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (20 bp):
TTTAATTTTATATAAATATG
Found at i:1485650 original size:18 final size:19
Alignment explanation
Indices: 1485629--1485666 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1485619 GTTTATAAAA
1485629 ATTATATTTTT-TAT-GAAT
1 ATTA-ATTTTTCTATCGAAT
1485647 ATTAATTTTTCTATCGAAT
1 ATTAATTTTTCTATCGAAT
1485666 A
1 A
1485667 GTACAGGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 7 0.39
19 5 0.28
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTAATTTTTCTATCGAAT
Found at i:1486600 original size:39 final size:42
Alignment explanation
Indices: 1486556--1486649 Score: 104
Period size: 45 Copynumber: 2.2 Consensus size: 42
1486546 TCTTACTTGT
1486556 TATAAAAATATT-A-GATTTATAATAG-AAATATAAGAGAAA
1 TATAAAAATATTAATGATTTATAATAGAAAATATAAGAGAAA
** * *
1486595 TATAAATTTATTAAAATTTATTTATAATAGAAAATTTAAGAGAAA
1 TATAAAAATATT--AA-TGATTTATAATAGAAAATATAAGAGAAA
1486640 TATAAAAATA
1 TATAAAAATA
1486650 AGAATCATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
39 10 0.23
42 1 0.02
44 11 0.26
45 21 0.49
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (42 bp):
TATAAAAATATTAATGATTTATAATAGAAAATATAAGAGAAA
Found at i:1491708 original size:27 final size:28
Alignment explanation
Indices: 1491678--1491734 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
1491668 AAATTGAATT
* *
1491678 TTAAAAA-TATATCCCTAATAACATATA
1 TTAAAAATTAGATCCATAATAACATATA
*
1491705 TTAAAAATTAGATCCATAATAACATGTA
1 TTAAAAATTAGATCCATAATAACATATA
1491733 TT
1 TT
1491735 GAGAAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35
Consensus pattern (28 bp):
TTAAAAATTAGATCCATAATAACATATA
Found at i:1491871 original size:32 final size:30
Alignment explanation
Indices: 1491833--1491920 Score: 106
Period size: 30 Copynumber: 2.9 Consensus size: 30
1491823 GAGTATGATC
1491833 TAATAATAAATATTTGAAAAAAATTA-AACCT
1 TAATAATAAATA-TT-AAAAAAATTAGAACCT
* *
1491864 ATAATAATAAGTATTAAAAAAATTAGATCCT
1 -TAATAATAAATATTAAAAAAATTAGAACCT
* *
1491895 TAATATTAGATATTAAAAAAATTAGA
1 TAATAATAAATATTAAAAAAATTAGA
1491921 TTATTTTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
30 33 0.66
31 6 0.12
32 11 0.22
ACGTcount: A:0.57, C:0.05, G:0.06, T:0.33
Consensus pattern (30 bp):
TAATAATAAATATTAAAAAAATTAGAACCT
Found at i:1495567 original size:12 final size:12
Alignment explanation
Indices: 1495550--1495582 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1495540 AAGTAATAGC
1495550 AAATATCCAACA
1 AAATATCCAACA
*
1495562 AAATATTCAACA
1 AAATATCCAACA
1495574 AAATATCCA
1 AAATATCCA
1495583 TCATATCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (12 bp):
AAATATCCAACA
Found at i:1499421 original size:20 final size:20
Alignment explanation
Indices: 1499396--1499433 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1499386 TGATTCAATC
1499396 AGTATCGATACCGAAGGGTG
1 AGTATCGATACCGAAGGGTG
1499416 AGTATCGATACCGAAGGG
1 AGTATCGATACCGAAGGG
1499434 AAGGTATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.34, T:0.18
Consensus pattern (20 bp):
AGTATCGATACCGAAGGGTG
Found at i:1499440 original size:20 final size:20
Alignment explanation
Indices: 1499396--1499447 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1499386 TGATTCAATC
*
1499396 AGTATCGATACCGAAGGGTG
1 AGTATCGATACCGAAGGGAG
1499416 AGTATCGATACCGAAGGGA-
1 AGTATCGATACCGAAGGGAG
*
1499435 AGGTATTGATACC
1 A-GTATCGATACC
1499448 ATTCAAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Consensus pattern (20 bp):
AGTATCGATACCGAAGGGAG
Found at i:1499485 original size:17 final size:18
Alignment explanation
Indices: 1499463--1499500 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1499453 AAACAAAATG
1499463 CAAAAT-AGTATCGGTAC
1 CAAAATAAGTATCGGTAC
1499480 CAAAATAAAGTATCGGTAC
1 CAAAAT-AAGTATCGGTAC
1499499 CA
1 CA
1499501 TAGCATAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.21
Consensus pattern (18 bp):
CAAAATAAGTATCGGTAC
Found at i:1499516 original size:22 final size:20
Alignment explanation
Indices: 1499467--1499523 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
1499457 AAAATGCAAA
1499467 ATAGTATCGGTACCA-AAAT
1 ATAGTATCGGTACCATAAAT
* *
1499486 AAAGTATCGGTACCATAGCAT
1 ATAGTATCGGTACCATA-AAT
*
1499507 AGTAGTATCGATACCAT
1 A-TAGTATCGGTACCAT
1499524 GGTAGGGGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 14 0.45
20 1 0.03
21 3 0.10
22 13 0.42
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.26
Consensus pattern (20 bp):
ATAGTATCGGTACCATAAAT
Found at i:1500120 original size:54 final size:55
Alignment explanation
Indices: 1499867--1500189 Score: 454
Period size: 55 Copynumber: 5.9 Consensus size: 55
1499857 CTAAGTGTAC
* * * * * *
1499867 TACAAGCACTATGTGTGCAATTCCATGAAATTCATCATGAATTGATGAATAACTG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* * *
1499922 TACAAGCACTAAT-TGTGCAAATCTACGGAATTCATCATGAGTTGATGAATAATCG
1 TACAGGCACT-ATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* *
1499977 TACAGGCACTATGTGTGAAAATCCACGGAATTCATCATGAGTTGATGAATAATCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* *
1500032 TACAGGCACTATGTGTGCAAGTCCACGGACTTCATCATGAGTTGATGAATAACCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* * *
1500087 TAC-TGCACTATGTATGCAAATCCATGGAATTCATCATGAGTTGATGAATAACCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* *
1500141 TACATGCACTATGTGTGC-AACCCACGGAATTCATCATGAGTTGATGAAT
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAAT
1500190 TATCGTATAT
Statistics
Matches: 243, Mismatches: 22, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
54 80 0.33
55 161 0.66
56 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (55 bp):
TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
Found at i:1501272 original size:2 final size:2
Alignment explanation
Indices: 1501265--1501310 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1501255 TCCTGCAACA
1501265 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
1501307 AT AT
1 AT AT
1501311 GATTCTAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1518056 original size:23 final size:23
Alignment explanation
Indices: 1518028--1518085 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
1518018 TATTTATTTC
1518028 TTAAATTATTTCAATCTAAAGAT
1 TTAAATTATTTCAATCTAAAGAT
*
1518051 TTAAATTATTTCAATCTAACGAT
1 TTAAATTATTTCAATCTAAAGAT
1518074 TTAAATTATTTC
1 TTAAATTATTTC
1518086 TCAAATTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (23 bp):
TTAAATTATTTCAATCTAAAGAT
Found at i:1519980 original size:59 final size:60
Alignment explanation
Indices: 1519879--1519996 Score: 166
Period size: 59 Copynumber: 2.0 Consensus size: 60
1519869 GCTATCACTG
* * * * *
1519879 ATTTCTGTATGGTATTACTGATGGGGAATGGTAGTTTTAGTATTGATGA-TTTATTATTC
1 ATTTCTGTATGGTATTACTAATAGGGAATGGTAGTTTAAGTATCGACGATTTTATTATTC
* *
1519938 ATTTTTGTATGGTATTGCTAATAGGGAATGGTAGTTTAAGTATCGACGATTTTATTATT
1 ATTTCTGTATGGTATTACTAATAGGGAATGGTAGTTTAAGTATCGACGATTTTATTATT
1519997 TAACTTTGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 42 0.82
60 9 0.18
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.47
Consensus pattern (60 bp):
ATTTCTGTATGGTATTACTAATAGGGAATGGTAGTTTAAGTATCGACGATTTTATTATTC
Found at i:1530331 original size:47 final size:48
Alignment explanation
Indices: 1530262--1530360 Score: 164
Period size: 49 Copynumber: 2.1 Consensus size: 48
1530252 AGTTCACCGC
* *
1530262 TGTCTTTAACCTGTTCGATTCGAT-CACCTTTGATCATTATCTCTTTT
1 TGTCTTCAACCTATTCGATTCGATACACCTTTGATCATTATCTCTTTT
1530309 TGTCTTCAACCTATTCGATTCGATCACACCTTTGATCATTATCTCTTTT
1 TGTCTTCAACCTATTCGATTCGAT-ACACCTTTGATCATTATCTCTTTT
1530358 TGT
1 TGT
1530361 TAATCTCAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 22 0.46
49 26 0.54
ACGTcount: A:0.18, C:0.24, G:0.10, T:0.47
Consensus pattern (48 bp):
TGTCTTCAACCTATTCGATTCGATACACCTTTGATCATTATCTCTTTT
Found at i:1532775 original size:21 final size:21
Alignment explanation
Indices: 1532749--1532793 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1532739 TGAGGAGTCC
1532749 TTTCTTGCTTTTCATAAAGTT
1 TTTCTTGCTTTTCATAAAGTT
*
1532770 TTTCTTGTTTTTCATAAAGTT
1 TTTCTTGCTTTTCATAAAGTT
1532791 TTT
1 TTT
1532794 GTCGAAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTCTTGCTTTTCATAAAGTT
Found at i:1533411 original size:22 final size:22
Alignment explanation
Indices: 1533383--1533427 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1533373 GTCTAAAAGA
1533383 ATTTTCAAGATGGATAGTAAGT
1 ATTTTCAAGATGGATAGTAAGT
1533405 ATTTTCAAGATGGATAGTAAGT
1 ATTTTCAAGATGGATAGTAAGT
1533427 A
1 A
1533428 CATATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (22 bp):
ATTTTCAAGATGGATAGTAAGT
Found at i:1534559 original size:31 final size:33
Alignment explanation
Indices: 1534509--1534574 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 33
1534499 ATATAATTTA
**
1534509 TAATATTTTTATTTCAATAAAATATACCAATAT
1 TAATATTTTTATTTCAATAAAATATAAAAATAT
*
1534542 TAATATTTTTA-TT-AATAAATTATAAAAATAT
1 TAATATTTTTATTTCAATAAAATATAAAAATAT
1534573 TA
1 TA
1534575 TTTTAATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 17 0.57
32 2 0.07
33 11 0.37
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (33 bp):
TAATATTTTTATTTCAATAAAATATAAAAATAT
Found at i:1539544 original size:36 final size:35
Alignment explanation
Indices: 1539490--1539560 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 35
1539480 ATGGTTGAAC
1539490 TCTAATTTGTATCAGTGAGAGGTTCTAGGTTAAAAA
1 TCTAATTTGTATCAGTGAGAGGTT-TAGGTTAAAAA
* *
1539526 TCTAATTTGTCTCGGTGAGAGGTTTAGGTTAAAAA
1 TCTAATTTGTATCAGTGAGAGGTTTAGGTTAAAAA
1539561 GTAAACGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 11 0.33
36 22 0.67
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.37
Consensus pattern (35 bp):
TCTAATTTGTATCAGTGAGAGGTTTAGGTTAAAAA
Found at i:1540072 original size:22 final size:21
Alignment explanation
Indices: 1540049--1540101 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 21
1540039 TAATGAAATA
1540049 TTATAAGATATTTATTAATTTATT
1 TTATAAGAT-TTTA-TAATTTA-T
*
1540073 TTATAAGATTTTATAATTAAT
1 TTATAAGATTTTATAATTTAT
1540094 TTAATAAG
1 TT-ATAAG
1540102 TTTAATGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 3 0.11
22 11 0.41
23 4 0.15
24 9 0.33
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (21 bp):
TTATAAGATTTTATAATTTAT
Found at i:1541235 original size:35 final size:35
Alignment explanation
Indices: 1541192--1541310 Score: 107
Period size: 35 Copynumber: 3.3 Consensus size: 35
1541182 TGAAATATAT
* * *
1541192 ATATAATATGGTTTTGAAAACACGTTTTTGAAAAC
1 ATATAATATAGTTTTAAAAACACATTTTTGAAAAC
* *
1541227 GTATAATATAGTTTTAAAAACATATTTTTGAAAAC
1 ATATAATATAGTTTTAAAAACACATTTTTGAAAAC
* *
1541262 ATATATAATATA-TAATGTTTAAAAC-CAGTTTTGGAAAAC
1 --ATATAATATAGT--T-TTAAAAACACA-TTTTTGAAAAC
1541301 ATATAATATA
1 ATATAATATA
1541311 TAATTTGTAA
Statistics
Matches: 69, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
35 30 0.43
36 1 0.01
37 19 0.28
38 2 0.03
39 17 0.25
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (35 bp):
ATATAATATAGTTTTAAAAACACATTTTTGAAAAC
Found at i:1541286 original size:39 final size:38
Alignment explanation
Indices: 1541243--1541382 Score: 128
Period size: 39 Copynumber: 3.7 Consensus size: 38
1541233 TATAGTTTTA
1541243 AAAACATATTTTTGAAAACATATATAATATATAATGTTT
1 AAAACAT-TTTTTGAAAACATATATAATATATAATGTTT
* *
1541282 AAAACCAGTTTTGGAAAAC--ATATAATATATAAT-TTGT
1 AAAA-CATTTTTTGAAAACATATATAATATATAATGTT-T
* * *
1541319 AAAATATTTTTTGAAAACGTATATATAATACA-ACATG-TG
1 AAAACATTTTTTGAAAAC--ATATATAATATATA-ATGTTT
* *
1541358 AAAACGTTTTTTTAAAACATATATA
1 AAAACATTTTTTGAAAACATATATA
1541383 GTTTTTAAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
36 13 0.16
37 26 0.31
39 30 0.36
40 14 0.17
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (38 bp):
AAAACATTTTTTGAAAACATATATAATATATAATGTTT
Found at i:1541331 original size:37 final size:36
Alignment explanation
Indices: 1541216--1541345 Score: 101
Period size: 37 Copynumber: 3.6 Consensus size: 36
1541206 TGAAAACACG
* * *
1541216 TTTTTGAAAACGTATAATATAGT--T-TTAAAAACATA
1 TTTTTGAAAACATATAATATA-TAATGTTTAAAAC-CA
1541251 TTTTTGAAAACATATATAATATATAATGTTTAAAACCA
1 TTTTTGAAAAC--ATATAATATATAATGTTTAAAACCA
* *
1541289 GTTTTGGAAAACATATAATATATAAT-TTGTAAAA-TA
1 -TTTTTGAAAACATATAATATATAATGTT-TAAAACCA
*
1541325 TTTTTTGAAAACGTAT-ATATA
1 -TTTTTGAAAACATATAATATA
1541346 ATACAACATG
Statistics
Matches: 80, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
35 16 0.20
36 17 0.21
37 28 0.35
38 2 0.03
39 17 0.21
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.41
Consensus pattern (36 bp):
TTTTTGAAAACATATAATATATAATGTTTAAAACCA
Found at i:1541367 original size:74 final size:72
Alignment explanation
Indices: 1541213--1541367 Score: 156
Period size: 74 Copynumber: 2.1 Consensus size: 72
1541203 TTTTGAAAAC
* * *
1541213 ACGTTTTTGAAAACGTATAATATAGTTTTAAAAACATATTTTTGAAAACATATATAATATATAAT
1 ACGTTTTGGAAAACATATAATATAGTTTTAAAAACATATTTTTGAAAACATATATAATACATAAT
*
1541278 GTTTAAA
66 GTTGAAA
**
1541285 ACCAGTTTTGGAAAACATATAATATA-TAATTTGTAAA-ATATTTTTTGAAAACGTATATATAAT
1 A-C-GTTTTGGAAAACATATAATATAGT--TTTAAAAACATA-TTTTTGAAAAC--ATATATAAT
1541348 ACA-ACATG-TGAAA
59 ACATA-ATGTTGAAA
1541361 ACGTTTT
1 ACGTTTT
1541368 TTTAAAACAT
Statistics
Matches: 69, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
72 1 0.01
73 2 0.03
74 28 0.41
75 18 0.26
76 6 0.09
77 14 0.20
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.39
Consensus pattern (72 bp):
ACGTTTTGGAAAACATATAATATAGTTTTAAAAACATATTTTTGAAAACATATATAATACATAAT
GTTGAAA
Found at i:1541464 original size:5 final size:5
Alignment explanation
Indices: 1541449--1541498 Score: 59
Period size: 5 Copynumber: 10.0 Consensus size: 5
1541439 AGTATATACA
*
1541449 TATTAT TATTT TATTT TATTT TATTT T-TTG T-TTT TATTTT TATTT TATTT
1 TATT-T TATTT TATTT TATTT TATTT TATTT TATTT TA-TTT TATTT TATTT
1541499 ACTTATTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
4 6 0.15
5 25 0.62
6 9 0.22
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:1541507 original size:23 final size:24
Alignment explanation
Indices: 1541458--1541515 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
1541448 ATATTATTAT
** *
1541458 TTTA-TTTTATTTTATTTTTTGTT
1 TTTATTTTTATTTTATTTACTGTA
1541481 TTTATTTTTATTTTATTTACT-TA
1 TTTATTTTTATTTTATTTACTGTA
*
1541504 TTTATTCTTATT
1 TTTATTTTTATT
1541516 ATCATTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 16 0.53
24 14 0.47
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (24 bp):
TTTATTTTTATTTTATTTACTGTA
Found at i:1541514 original size:29 final size:29
Alignment explanation
Indices: 1541449--1541515 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
1541439 AGTATATACA
*
1541449 TATTATTA-TTTTATTTTATTTTATTTTT
1 TATTATTATTTTTATTTTATTTTATTATT
* *
1541477 TGTTTTTATTTTTATTTTA-TTTACTTATT
1 TATTATTATTTTTATTTTATTTTA-TTATT
*
1541506 TATTCTTATT
1 TATTATTATT
1541516 ATCATTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
28 10 0.31
29 22 0.69
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.76
Consensus pattern (29 bp):
TATTATTATTTTTATTTTATTTTATTATT
Found at i:1544050 original size:12 final size:12
Alignment explanation
Indices: 1544033--1544063 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1544023 AGTAGGTCTT
*
1544033 TTATTTTCATTA
1 TTATTTTAATTA
1544045 TTATTTTAATTA
1 TTATTTTAATTA
1544057 TTATTTT
1 TTATTTT
1544064 TATCTTACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTTTAATTA
Found at i:1555064 original size:76 final size:75
Alignment explanation
Indices: 1554984--1555251 Score: 233
Period size: 76 Copynumber: 3.5 Consensus size: 75
1554974 TTTTTGAAAA
*
1554984 ATATATA-ATTTTTAGAAAATATTTTTTAAAAACATATAATATATAGTTTTTTAAAAA-AAATCG
1 ATATATATATTTTT-GAAAATATTTTTTGAAAACATATAATATATAG-TTTTTAAAAACAAAT--
*
1555047 GTTTTGAAAATATAT
62 -TTTTGAAAACATAT
** * * * *
1555062 ATA-ATATGGTTTTGAAAACACGTTTTTGAAAACGTATAATATATAG-TTTTAAAAACATATTTT
1 ATATATATATTTTTGAAAATA-TTTTTTGAAAACATATAATATATAGTTTTTAAAAACAAATTTT
1555125 TGAAAACATAT
65 TGAAAACATAT
* * * *
1555136 ATAATATATAGTTTTT-AAAATCGTTTTTGGAAAACATATAATATATAGTTTTTAAAAA-TATTT
1 AT-ATATATA-TTTTTGAAAAT-ATTTTTTGAAAACATATAATATATAGTTTTTAAAAACAAATT
*
1555199 TTTGAAAACGTAT
63 TTTGAAAACATAT
** * * *
1555212 ATATAATATAGCCTATGAAAATGTTTTTTTAAAACATATA
1 ATAT-ATATA-TTTTTGAAAATATTTTTTGAAAACATATA
1555252 TATTTTTAAA
Statistics
Matches: 156, Mismatches: 24, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
74 15 0.10
75 3 0.02
76 79 0.51
77 30 0.19
78 29 0.19
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (75 bp):
ATATATATATTTTTGAAAATATTTTTTGAAAACATATAATATATAGTTTTTAAAAACAAATTTTT
GAAAACATAT
Found at i:1555150 original size:39 final size:38
Alignment explanation
Indices: 1554983--1555221 Score: 179
Period size: 37 Copynumber: 6.2 Consensus size: 38
1554973 TTTTTTGAAA
* * * *
1554983 AATATATAATTTTTAGAAAATATTTTTTAAAA-ACATAT
1 AATATAT-AGTTTTAAAAAATATTTTTGAAAACATATAT
* *
1555021 AATATATAGTTTTTTAAAAAAAATCGGTTTTGAAAATATATAT
1 AATATATAG--TTTTAAAAAATAT---TTTTGAAAACATATAT
* * ** *
1555064 -A-ATATGGTTTTGAAAACACGTTTTTGAAAAC--GTAT
1 AATATATAGTTTT-AAAAAATATTTTTGAAAACATATAT
1555099 AATATATAGTTTTAAAAACATATTTTTGAAAACATATAT
1 AATATATAGTTTTAAAAA-ATATTTTTGAAAACATATAT
* *
1555138 AATATATAGTTTT-TAAAATCGTTTTTGGAAAAC--ATAT
1 AATATATAGTTTTAAAAAAT-ATTTTT-GAAAACATATAT
*
1555175 AATATATAGTTTTTAAAAATATTTTTTGAAAACGTATATAT
1 AATATATAGTTTTAAAAAATA-TTTTTGAAAAC--ATATAT
1555216 AATATA
1 AATATA
1555222 GCCTATGAAA
Statistics
Matches: 161, Mismatches: 20, Indels: 37
0.74 0.09 0.17
Matches are distributed among these distances:
35 3 0.02
36 5 0.03
37 56 0.35
38 25 0.16
39 37 0.23
40 6 0.04
41 15 0.09
42 9 0.06
43 5 0.03
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (38 bp):
AATATATAGTTTTAAAAAATATTTTTGAAAACATATAT
Found at i:1555233 original size:39 final size:37
Alignment explanation
Indices: 1554984--1555254 Score: 210
Period size: 39 Copynumber: 7.1 Consensus size: 37
1554974 TTTTTGAAAA
* *
1554984 ATATATA-ATTTTTAGAAAATATTTTTTAAAAACATAT
1 ATATATATAGTTTTA-AAAATATTTTTTGAAAACATAT
* * *
1555021 A-ATATATAGTTTTTTAAAAAAAATCGGTTTTGAAAATATAT
1 ATATATATAG--TTTT-AAAAATAT--TTTTTGAAAACATAT
* * * * *
1555062 ATA-ATATGGTTTTGAAAACACGTTTTTGAAAACGTAT
1 ATATATATAGTTTTAAAAATA-TTTTTTGAAAACATAT
*
1555099 A-ATATATAGTTTTAAAAACATATTTTTGAAAACATAT
1 ATATATATAGTTTTAAAAATAT-TTTTTGAAAACATAT
* * *
1555136 ATAATATATAGTTTTTAAAATCGTTTTTGGAAAACATAT
1 AT-ATATATAGTTTTAAAAAT-ATTTTTTGAAAACATAT
*
1555175 A-ATATATAGTTTTTAAAAATATTTTTTGAAAACGTAT
1 ATATATATAG-TTTTAAAAATATTTTTTGAAAACATAT
* * * * *
1555212 ATATAATATAGCCTATGAAAATGTTTTTTTAAAACATAT
1 ATAT-ATATAG-TTTTAAAAATATTTTTTGAAAACATAT
1555251 ATAT
1 ATAT
1555255 TTTTAAAAAA
Statistics
Matches: 187, Mismatches: 31, Indels: 30
0.75 0.12 0.12
Matches are distributed among these distances:
36 6 0.03
37 68 0.36
38 16 0.09
39 76 0.41
40 2 0.01
41 18 0.10
42 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (37 bp):
ATATATATAGTTTTAAAAATATTTTTTGAAAACATAT
Found at i:1555274 original size:17 final size:17
Alignment explanation
Indices: 1555229--1555274 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
1555219 ATAGCCTATG
1555229 AAAATG-TTTTTTTAAA
1 AAAATGATTTTTTTAAA
* *
1555245 ACATAT-ATATTTTTAAA
1 A-AAATGATTTTTTTAAA
1555262 AAAATGATTTTTT
1 AAAATGATTTTTT
1555275 GGAAAACATC
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (17 bp):
AAAATGATTTTTTTAAA
Found at i:1555347 original size:15 final size:15
Alignment explanation
Indices: 1555319--1555369 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
1555309 AGTATATACA
1555319 TATTATTATTTTCTTT
1 TATT-TTATTTTCTTT
* *
1555335 TCTTTTCTTTTCTTT
1 TATTTTATTTTCTTT
*
1555350 TATTTTATTTTATTT
1 TATTTTATTTTCTTT
1555365 TATTT
1 TATTT
1555370 ACTTATTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 27 0.90
16 3 0.10
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (15 bp):
TATTTTATTTTCTTT
Found at i:1555366 original size:5 final size:5
Alignment explanation
Indices: 1555319--1555369 Score: 57
Period size: 5 Copynumber: 10.0 Consensus size: 5
1555309 AGTATATACA
* * * *
1555319 TATTAT TATTT TCTTT TCTTT TCTTT TCTTT TATTT TATTT TATTT TATTT
1 TATT-T TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT
1555370 ACTTATTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
5 39 0.91
6 4 0.09
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:1556736 original size:14 final size:13
Alignment explanation
Indices: 1556712--1556754 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
1556702 TAAAAGTTAA
1556712 TATTTTCTTAATTT
1 TATTTT-TTAATTT
1556726 TATTATTTTAATTT
1 TATT-TTTTAATTT
*
1556740 TCTTTTTTAAATTT
1 TATTTTTT-AATTT
1556754 T
1 T
1556755 TTTCTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 4 0.15
14 20 0.77
15 2 0.08
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTTTTTAATTT
Found at i:1561953 original size:3 final size:3
Alignment explanation
Indices: 1561939--1562035 Score: 105
Period size: 3 Copynumber: 33.7 Consensus size: 3
1561929 TAATATTTTA
* * * *
1561939 AAT AAT ACT AAT AAT AAT GAT AAC AATT AAT AAT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT
*
1561985 AAT AAT AAT AAT AA- AAT AAT GAT AAT AA- AA- AAT AA- AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1562028 AAT AAT AA
1 AAT AAT AA
1562036 ATCAATATGG
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
2 10 0.12
3 68 0.85
4 2 0.03
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1562036 original size:23 final size:23
Alignment explanation
Indices: 1561966--1562034 Score: 52
Period size: 23 Copynumber: 2.9 Consensus size: 23
1561956 TGATAACAAT
*
1561966 TAATAATAATGATAATAATAATA-A
1 TAATAATAA-AATAATAA-AATAGA
* *
1561990 TAATAATAAAATAATGATAATAAA
1 TAATAATAAAATAAT-AAAATAGA
*
1562014 AAATAA-AAAATAATAATAATA
1 TAATAATAAAATAATAA-AATA
1562035 AATCAATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 1 0.03
23 21 0.55
24 16 0.42
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (23 bp):
TAATAATAAAATAATAAAATAGA
Found at i:1562447 original size:40 final size:40
Alignment explanation
Indices: 1562392--1562541 Score: 147
Period size: 40 Copynumber: 3.5 Consensus size: 40
1562382 ATCTAAACAA
1562392 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTCGATGAG
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTCGATGAG
* *** * *
1562432 TTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATCTATCAAGTCTTGAG
1 TTCTTCTCATTATGAAC-TTCT-T----CA-TCCTTCTTTC--G--ATGAG
1562483 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTCGATGAG
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTCGATGAG
1562523 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAACTT
1562542 TCTCTAGAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
40 40 0.46
41 4 0.05
42 2 0.02
44 6 0.07
45 1 0.01
46 1 0.01
47 6 0.07
49 2 0.02
50 4 0.05
51 21 0.24
ACGTcount: A:0.21, C:0.22, G:0.11, T:0.46
Consensus pattern (40 bp):
TTCTTCTCATTATGAACTTCTTCATCCTTCTTTCGATGAG
Found at i:1562488 original size:51 final size:50
Alignment explanation
Indices: 1562427--1562567 Score: 149
Period size: 40 Copynumber: 3.0 Consensus size: 50
1562417 CCTTCTTTCG
1562427 ATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATCTATCAAGT
1 ATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATCTATCAAGT
* * *** *
1562477 CTTGAGTTCTTCTCATTATGAAC-TTCT-T----CA-TCCTTCTTTC--G-
1 -ATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATCTATCAAGT
1562518 ATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATCTATCAAGT
1 ATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATCTATCAAGT
1562568 GATGGATTTG
Statistics
Matches: 68, Mismatches: 12, Indels: 21
0.67 0.12 0.21
Matches are distributed among these distances:
40 21 0.31
41 4 0.06
42 2 0.03
44 6 0.09
45 1 0.01
46 1 0.01
47 6 0.09
49 2 0.03
50 4 0.06
51 21 0.31
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (50 bp):
ATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATCTATCAAGT
Found at i:1562500 original size:91 final size:91
Alignment explanation
Indices: 1562392--1562567 Score: 352
Period size: 91 Copynumber: 1.9 Consensus size: 91
1562382 ATCTAAACAA
1562392 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTCGATGAGTTCTTCTCATTATGAACTTTCTCTA
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTCGATGAGTTCTTCTCATTATGAACTTTCTCTA
1562457 GAAAAGTTGATCTATCAAGTCTTGAG
66 GAAAAGTTGATCTATCAAGTCTTGAG
1562483 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTCGATGAGTTCTTCTCATTATGAACTTTCTCTA
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTCGATGAGTTCTTCTCATTATGAACTTTCTCTA
1562548 GAAAAGTTGATCTATCAAGT
66 GAAAAGTTGATCTATCAAGT
1562568 GATGGATTTG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.44
Consensus pattern (91 bp):
TTCTTCTCATTATGAACTTCTTCATCCTTCTTTCGATGAGTTCTTCTCATTATGAACTTTCTCTA
GAAAAGTTGATCTATCAAGTCTTGAG
Found at i:1562609 original size:113 final size:113
Alignment explanation
Indices: 1562483--1563248 Score: 940
Period size: 113 Copynumber: 6.8 Consensus size: 113
1562473 AAGTCTTGAG
*
1562483 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCATTATGAACTTTCTCT
1 TTCTTCTCATTATGAACTTCTTCATCCTTC-TTCAGATGAGTTCTTCTCATTATGAACTTACTCT
* * * *
1562547 AGAAAAGTTGATCTATCAAGTGATGGATTTGAGCAAAA-ATCTAAACAAA
65 GGAAAAGTTAATCTATCAAGTGATGGATTTGAGCAAAAGGT-TGAACAAA
*
1562596 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCATTATGAACTTTCTCT
1 TTCTTCTCATTATGAACTTCTTCATCCTTC-TTCAGATGAGTTCTTCTCATTATGAACTTACTCT
* * *
1562660 AGAAAAGTTGATCTATCAAGTGATGGATTTGAGCAAAA-ATCTGAACAAA
65 GGAAAAGTTAATCTATCAAGTGATGGATTTGAGCAAAAGGT-TGAACAAA
* *
1562709 -TCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTC-T-T-ATTA-GAACTCGA-ACT
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TACTCT
* *
1562768 GGAAAAGCTAATCTATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
65 GGAAAAGTTAATCTATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
* * *
1562817 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAAT-T
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TACTCT
** *
1562881 GGAAAAAATAATCTATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
65 GGAAAAGTTAATCTATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
*
1562930 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TAC
* * * * * *
1562995 -CTGGCAATGTTAATCCATCATA-TGATGAATTTAAACAAAAGGTTGAACAAA
62 TCTGGAAAAGTTAATCTATCA-AGTGATGGATTTGAGCAAAAGGTTGAACAAA
* *
1563046 TTCTTCTCATTATGAGCTTCTTCATCCTTCTTCAGATGAGTTCTTCTC---ATGAACTTCCTCTG
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTG
* * * * *
1563108 G-AAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAGA
66 GAAAAGTTAATCTATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
* * *
1563155 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGA-ACT
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TACTCT
* *
1563219 GGAAAA-TCTAATCCATCAAGTAATGGATTT
65 GGAAAAGT-TAATCTATCAAGTGATGGATTT
1563249 AAATCTTTGC
Statistics
Matches: 588, Mismatches: 43, Indels: 44
0.87 0.06 0.07
Matches are distributed among these distances:
108 50 0.09
109 131 0.22
110 13 0.02
111 5 0.01
112 53 0.09
113 238 0.40
116 97 0.16
117 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTG
GAAAAGTTAATCTATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
Found at i:1562628 original size:204 final size:206
Alignment explanation
Indices: 1562280--1562874 Score: 793
Period size: 221 Copynumber: 2.8 Consensus size: 206
1562270 TAAGTCTTGA
1562280 TGAGTTCTTCTCATTATGAACTTCTTCATCCTTC-TCGATGAGTTCTTCTCATTATGAAC-TTCT
1 TGAGTTCTTCTCATTATGAACTTCTTCATCCTTCTTCGATGAGTTCTTCTCATTATGAACTTTCT
1562343 CTAGAAAAGTTGATCTATC-AGTGATGGATTTGAGCAAAAATCTAAAC-AATTCTTCTCATTATG
66 CTAGAAAAGTTGATCTATCAAGTGATGGATTTGAGCAAAAATCTAAACAAATTCTTCTCATTATG
1562406 AACTTCTTCATCCTTCTTTCGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATCTA
131 AACTTCTTCATCCTTCTTTCGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATCTA
1562471 TCAA-G-T-CT
196 TCAAGGATGCT
1562479 TGAGTTCTTCTCATTATGAACTTCTTCATCCTTCTTTCGATGAGTTCTTCTCATTATGAACTTTC
1 TGAGTTCTTCTCATTATGAACTTCTTCATCCTTC-TTCGATGAGTTCTTCTCATTATGAACTTTC
1562544 TCTAGAAAAGTTGATCTATCAAGTGATGGATTTGAGCAAAAATCTAAACAAATTCTTCTCATTAT
65 TCTAGAAAAGTTGATCTATCAAGTGATGGATTTGAGCAAAAATCTAAACAAATTCTTCTCATTAT
1562609 GAACTTCTTCATCCTTCTTTCGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATCT
130 GAACTTCTTCATCCTTCTTTCGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATCT
*
1562674 ATCAAGTGATGGATT
195 ATCAAG-GAT-G-CT
1562689 TGAGCAAAAATCTGAACAAATCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTC-T-
1 TGAG--------T-------TCTTCTCATTATGAACTTCTTCATCCTTCTTC-GATGAGTTCTTC
**** * * * * * *
1562752 T-ATTA-GAACTCGAACTGGAAAAGCTAATCTATCAAGTGATAGATTTGAGCAAAAGGT-TGAAC
50 TCATTATGAACTTTCTCTAGAAAAGTTGATCTATCAAGTGATGGATTTGAGCAAAA-ATCTAAAC
*
1562814 AAATTCTTCTCATTATGAACTTCTTCTTCCTTC-TTCAGATGAGTTCTTCTCATTATGAACT
114 AAATTCTTCTCATTATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCATTATGAACT
1562875 CGAATTGGAA
Statistics
Matches: 355, Mismatches: 12, Indels: 36
0.88 0.03 0.09
Matches are distributed among these distances:
199 34 0.10
201 25 0.07
202 23 0.06
203 28 0.08
204 85 0.24
206 1 0.00
207 1 0.00
210 5 0.01
218 1 0.00
220 3 0.01
221 101 0.28
222 5 0.01
223 1 0.00
224 4 0.01
225 38 0.11
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (206 bp):
TGAGTTCTTCTCATTATGAACTTCTTCATCCTTCTTCGATGAGTTCTTCTCATTATGAACTTTCT
CTAGAAAAGTTGATCTATCAAGTGATGGATTTGAGCAAAAATCTAAACAAATTCTTCTCATTATG
AACTTCTTCATCCTTCTTTCGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATCTA
TCAAGGATGCT
Found at i:1563182 original size:338 final size:334
Alignment explanation
Indices: 1562483--1563248 Score: 1019
Period size: 338 Copynumber: 2.3 Consensus size: 334
1562473 AAGTCTTGAG
* ***
1562483 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCATTATGAACT-TTCTC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTC-TTCAGATGAGTTCTTCTCATTATGAACTCGAAT-
* ** *
1562546 TAGAAAAGTTGATCTATCAAGTGATGGATTTGAGCAAAAATCTAAACAAATTCTTCTCATTATGA
64 TGGAAAAAATAATCTATCAAGTGATGGATTTGAGCAAAAATCTAAACAAATTCTTCTCATTATGA
* * *
1562611 ACTTCTTCATCCTTCTTTCGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATCTAT
129 ACTTCTTCATCCTTCTTTCGATGAGTTCTTCTCATTATGAACTTACTCTAGAAAAGTTAATCCAT
* * *
1562676 CAAGTGATGGATTTGAGCAAAAATCTGAACAAATCTTCTCATTATGAACTTCTTCATCCTTCTTC
194 CAAGTGATGAATTTAAACAAAAATCTGAACAAATCTTCTCATTATGAACTTCTTCATCCTTCTTC
* * *
1562741 AGATGAGTTCTTATTAGAACTCGAACTGGAAAAGCTAATCTATCAAGTGATAGATTTGAGCAAAA
259 AGATGAGTTCTTATCAGAACTCGAACTGGAAAAGCTAATCCATCAAATGATAGATTTGAGCAAAA
1562806 GGTTGAACAAA
324 GGTTGAACAAA
1562817 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAATTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAATTG
* * *
1562882 GAAAAAATAATCTATCAAGTGATAGATTTGAGCAAAAGGT-TGAACAAATTCTTCTCATTATGAA
66 GAAAAAATAATCTATCAAGTGATGGATTTGAGCAAAA-ATCTAAACAAATTCTTCTCATTATGAA
* * * *
1562946 CTTCTTCTTCCTTC-TTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTAAT
130 CTTCTTCATCCTTCTTTC-GAT---GAGTTCTTCTCATTATGAACT-TACTCTAGAAAAGTTAAT
* *
1563009 CCATCATA-TGATGAATTTAAACAAAAGGT-TGAACAAATTCTTCTCATTATGAGCTTCTTCATC
190 CCATCA-AGTGATGAATTTAAACAAAA-ATCTGAACAAA-TCTTCTCATTATGAACTTCTTCATC
* ** * *
1563072 CTTCTTCAGATGAGTTCTTCTCATGAACTTC-CTCTGG-AAAGCTGATCCATCAAATGATGGATT
252 CTTCTTCAGATGAGTTCTTATCA-GAAC-TCGAACTGGAAAAGCTAATCCATCAAATGATAGATT
*
1563135 TGAGCAAAAGGTTGAACAGA
315 TGAGCAAAAGGTTGAACAAA
*
1563155 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAATTG
** * *
1563220 GAAAATCTAATCCATCAAGTAATGGATTT
66 GAAAAAATAATCTATCAAGTGATGGATTT
1563249 AAATCTTTGC
Statistics
Matches: 381, Mismatches: 38, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
333 6 0.02
334 126 0.33
335 2 0.01
337 59 0.15
338 178 0.47
339 8 0.02
340 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (334 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAATTG
GAAAAAATAATCTATCAAGTGATGGATTTGAGCAAAAATCTAAACAAATTCTTCTCATTATGAAC
TTCTTCATCCTTCTTTCGATGAGTTCTTCTCATTATGAACTTACTCTAGAAAAGTTAATCCATCA
AGTGATGAATTTAAACAAAAATCTGAACAAATCTTCTCATTATGAACTTCTTCATCCTTCTTCAG
ATGAGTTCTTATCAGAACTCGAACTGGAAAAGCTAATCCATCAAATGATAGATTTGAGCAAAAGG
TTGAACAAA
Found at i:1563187 original size:225 final size:222
Alignment explanation
Indices: 1562483--1563248 Score: 923
Period size: 221 Copynumber: 3.4 Consensus size: 222
1562473 AAGTCTTGAG
*
1562483 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCATTATGAACT-TTCTC
1 TTCTTCTCATTATGAACTTCTTCATCCTTC-TTCAGATGAGTTCTTCTCATTATGAACTCTAC-C
* * * * *
1562546 TAGAAAAGTTGATCTATCAAGTGATGGATTTGAGCAAAA-ATCTAAACAAATTCTTCTCATTATG
64 TGGAAAAGTTAATCTATCAAGTGATGAATTTGAGCAAAAGGT-TGAACAAATTCTTCTCATTATG
* * *
1562610 AACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATCT
128 AACTTCTTCATCCTTC-TTCAGATGAGTTCTTCTC--TATGAACTTCCTCT-GGAAAGATGATCT
*
1562674 ATCAAGTGATGGATTTGAGCAAAA-ATCTGAACAA
189 ATCAAGTGATGGATTTGAGCAAAAGGT-TGAACAA
* * *
1562708 ATCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTC-T-T-ATTA-GAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
*
1562769 GAAAAGCTAATCTATCAAGTGAT-AGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
66 GAAAAGTTAATCTATCAAGTGATGA-ATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
* * * *
1562833 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCGAAT-TGGAAAAAATAATCTA
130 CTTCTTCATCCTTCTTCAGATGAGTTCTTCTC--TATGAACTTC--CTCTGG-AAAGATGATCTA
*
1562896 TCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
190 TCAAGTGATGGATTTGAGCAAAAGGTTGAAC-AA
*
1562930 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTAC
* * * * *
1562995 CTGGCAATGTTAATCCATCATA-TGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTAT
63 CTGGAAAAGTTAATCTATCA-AGTGATGAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTAT
* * *
1563059 GAGCTTCTTCATCCTTCTTCAGATGAGTTCTTCTC-ATGAACTTCCTCTGGAAAGCTGATCCATC
127 GAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCTATGAACTTCCTCTGGAAAGATGATCTATC
*
1563123 AAATGATGGATTTGAGCAAAAGGTTGAACAGA
192 AAGTGATGGATTTGAGCAAAAGGTTGAACA-A
* * *
1563155 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
* * *
1563220 GAAAA-TCTAATCCATCAAGTAATGGATTT
66 GAAAAGT-TAATCTATCAAGTGATGAATTT
1563249 AAATCTTTGC
Statistics
Matches: 473, Mismatches: 44, Indels: 51
0.83 0.08 0.09
Matches are distributed among these distances:
220 5 0.01
221 138 0.29
222 91 0.19
223 1 0.00
224 5 0.01
225 120 0.25
226 10 0.02
227 3 0.01
228 4 0.01
229 94 0.20
230 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (222 bp):
TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
GAAAAGTTAATCTATCAAGTGATGAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
TTCTTCATCCTTCTTCAGATGAGTTCTTCTCTATGAACTTCCTCTGGAAAGATGATCTATCAAGT
GATGGATTTGAGCAAAAGGTTGAACAA
Found at i:1564276 original size:82 final size:82
Alignment explanation
Indices: 1564004--1564433 Score: 707
Period size: 82 Copynumber: 5.2 Consensus size: 82
1563994 CTTATTTTTA
* * * * * *
1564004 CTATGAGCAAATTCATCTTTCAATTTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATC-TTCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAAA
1564069 GAACACTTCCAGAAGATG
65 GAACACTTCCAGAAGATG
* * * *
1564087 CTATGAGCACATTCCTCTTTCAAATTCAATGATTGGTTTTACCAAACCAGATTAGATAACTCAAA
1 CTATGAGCACATTCATC-TTCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTC--A
*
1564152 AAAAACACTTCCAGAAGATG
63 AAGAACACTTCCAGAAGATG
*
1564172 CTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAG
1 CTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAAAG
1564237 AACACTTCCAGAAGATG
66 AACACTTCCAGAAGATG
1564254 CTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAAAG
1 CTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAAAG
1564319 AACACTTCCAGAAGATG
66 AACACTTCCAGAAGATG
*
1564336 CTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTTCCAAACCAGATCAGATAACTCAAAG
1 CTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAAAG
1564401 AACACTTCCAGAAGATG
66 AACACTTCCAGAAGATG
1564418 CTATGAGCACATTCAT
1 CTATGAGCACATTCAT
1564434 TTGTTTCAGT
Statistics
Matches: 330, Mismatches: 15, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
82 198 0.60
83 56 0.17
84 40 0.12
85 36 0.11
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (82 bp):
CTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATG
Found at i:1565239 original size:16 final size:18
Alignment explanation
Indices: 1565198--1565245 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
1565188 AATTCATAGA
*
1565198 AAAATAAATTGAATTTCC
1 AAAATAAATTGAATCTCC
1565216 AAAAATAAATTGAATCT-C
1 -AAAATAAATTGAATCTCC
1565234 -AAATAAATTGAA
1 AAAATAAATTGAA
1565246 CTTGAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 12 0.43
18 1 0.04
19 15 0.54
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.29
Consensus pattern (18 bp):
AAAATAAATTGAATCTCC
Found at i:1565579 original size:1 final size:1
Alignment explanation
Indices: 1565575--1565650 Score: 62
Period size: 1 Copynumber: 76.0 Consensus size: 1
1565565 TTGACCCCCC
* * * * * * * *
1565575 TTTTTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTTTTCTTTTTTCTTTTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
1565640 CTTTTCTTTTT
1 TTTTTTTTTTT
1565651 CTCTTCAAGC
Statistics
Matches: 55, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:1565591 original size:7 final size:7
Alignment explanation
Indices: 1565575--1565655 Score: 110
Period size: 7 Copynumber: 11.0 Consensus size: 7
1565565 TTGACCCCCC
1565575 TTTT-TT
1 TTTTCTT
1565581 TTTTCTT
1 TTTTCTT
1565588 TTTTCTT
1 TTTTCTT
1565595 TTTTCTT
1 TTTTCTT
1565602 TTTTCTT
1 TTTTCTT
1565609 TTTTCTTTTT
1 TTTTC---TT
1565619 TTTTCTT
1 TTTTCTT
1565626 TTTTCTT
1 TTTTCTT
1565633 TTTTCTT
1 TTTTCTT
1565640 CTTTTCTT
1 -TTTTCTT
1565648 TTTCTCTT
1 TTT-TCTT
1565656 CAAGCATAAT
Statistics
Matches: 69, Mismatches: 0, Indels: 10
0.87 0.00 0.13
Matches are distributed among these distances:
6 4 0.06
7 47 0.68
8 11 0.16
10 7 0.10
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTCTT
Found at i:1565618 original size:38 final size:40
Alignment explanation
Indices: 1565576--1565655 Score: 146
Period size: 38 Copynumber: 2.0 Consensus size: 40
1565566 TGACCCCCCT
1565576 TTTTTTTTTCTTTTTTCTTTTTTCTT-TTTTCTTTTT-TC
1 TTTTTTTTTCTTTTTTCTTTTTTCTTCTTTTCTTTTTCTC
1565614 TTTTTTTTTCTTTTTTCTTTTTTCTTCTTTTCTTTTTCTC
1 TTTTTTTTTCTTTTTTCTTTTTTCTTCTTTTCTTTTTCTC
1565654 TT
1 TT
1565656 CAAGCATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 26 0.65
39 10 0.25
40 4 0.10
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (40 bp):
TTTTTTTTTCTTTTTTCTTTTTTCTTCTTTTCTTTTTCTC
Found at i:1573774 original size:78 final size:79
Alignment explanation
Indices: 1573623--1573780 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
1573613 CGCTCTCTTC
1573623 TGTCGACCTCAAAATCTTCCATTTTTTGCTTTCCTTTCTCAAGGCTTTGAGTAGACGGCTATTCT
1 TGTCGACCTCAAAATCTTCCATTTTTTGCTTTCCTTTCTCAAGGCTTTGAGTAGACGGCTATTCT
1573688 TTCCTTTCAGATCT
66 TTCCTTTCAGATCT
1573702 TGTCGACCTCAAAATCTTCCATTTTTTGCTTTCCTTTCTCAAGGC-TTGAGTAGACGGCTATTCT
1 TGTCGACCTCAAAATCTTCCATTTTTTGCTTTCCTTTCTCAAGGCTTTGAGTAGACGGCTATTCT
1573766 TTCCTTTCAGATCT
66 TTCCTTTCAGATCT
1573780 T
1 T
1573781 CAACTCGACT
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 34 0.43
79 45 0.57
ACGTcount: A:0.18, C:0.25, G:0.14, T:0.43
Consensus pattern (79 bp):
TGTCGACCTCAAAATCTTCCATTTTTTGCTTTCCTTTCTCAAGGCTTTGAGTAGACGGCTATTCT
TTCCTTTCAGATCT
Found at i:1573916 original size:58 final size:59
Alignment explanation
Indices: 1573844--1573960 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 59
1573834 CTTGGTCTGA
1573844 TGCTTTCCCGGGATTTATATAACTCCTGGTAATTTTCTGTAATACTCTGATTCATCATC
1 TGCTTTCCCGGGATTTATATAACTCCTGGTAATTTTCTGTAATACTCTGATTCATCATC
1573903 TGCTTT-CCGGGATTTATATAACTCCTGGTAATTTTCTGTAATACTCTGATTCATCATC
1 TGCTTTCCCGGGATTTATATAACTCCTGGTAATTTTCTGTAATACTCTGATTCATCATC
1573961 AACTTTTTCT
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 52 0.90
59 6 0.10
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.43
Consensus pattern (59 bp):
TGCTTTCCCGGGATTTATATAACTCCTGGTAATTTTCTGTAATACTCTGATTCATCATC
Found at i:1576032 original size:22 final size:21
Alignment explanation
Indices: 1576007--1576069 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
1575997 ATGAAATATT
1576007 AATAATATATAAATACTATAAA
1 AATAATATATAAATA-TATAAA
* *
1576029 AATAATATGTATATATATAAAA
1 AATAATATATAAATATAT-AAA
* *
1576051 AATTATAAATTAAATATAT
1 AATAATATA-TAAATATAT
1576070 GAAATTTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.09
22 22 0.67
23 8 0.24
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
AATAATATATAAATATATAAA
Found at i:1576698 original size:15 final size:15
Alignment explanation
Indices: 1576666--1576706 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1576656 TCGATATTGC
1576666 AAAATAAA-TATT--
1 AAAATAAATTATTAA
*
1576678 AAAATAATTTATTAA
1 AAAATAAATTATTAA
1576693 AAAATAAATTATTA
1 AAAATAAATTATTA
1576707 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 4 0.17
15 13 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAATAAATTATTAA
Found at i:1578122 original size:3 final size:3
Alignment explanation
Indices: 1578114--1578198 Score: 152
Period size: 3 Copynumber: 28.3 Consensus size: 3
1578104 AATATATTAT
1578114 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
1578162 ATA ATA ATA ATA ATG ATA ATA AAA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1578199 ATCAATATGG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1588027 original size:37 final size:38
Alignment explanation
Indices: 1587986--1588075 Score: 139
Period size: 37 Copynumber: 2.4 Consensus size: 38
1587976 ATGTAAAACT
**
1587986 AAAACTTACCCTTTTTCTTTTCTT-TTCTTTTTAGT-AA
1 AAAACTTACCCTTTTTCTTTT-TTACCCTTTTTAGTAAA
1588023 AAAACTTACCCTTTTTCTTTTTTACCCTTTTTAGTAAA
1 AAAACTTACCCTTTTTCTTTTTTACCCTTTTTAGTAAA
1588061 AAAACTTACCCTTTT
1 AAAACTTACCCTTTT
1588076 CATAAAAGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
36 2 0.04
37 30 0.61
38 17 0.35
ACGTcount: A:0.26, C:0.21, G:0.02, T:0.51
Consensus pattern (38 bp):
AAAACTTACCCTTTTTCTTTTTTACCCTTTTTAGTAAA
Found at i:1592314 original size:25 final size:25
Alignment explanation
Indices: 1592256--1592314 Score: 59
Period size: 25 Copynumber: 2.3 Consensus size: 25
1592246 AATCAAAAGA
1592256 TAAATTTATGATATGAATTTTAAATT
1 TAAA-TTATGATATGAATTTTAAATT
* *
1592282 TTATTTATGATTAT-AA-TTTAAATAT
1 TAAATTATGA-TATGAATTTTAAAT-T
1592307 TAAATTAT
1 TAAATTAT
1592315 TCTTTAACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
24 7 0.26
25 15 0.56
26 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (25 bp):
TAAATTATGATATGAATTTTAAATT
Found at i:1592502 original size:14 final size:14
Alignment explanation
Indices: 1592466--1592503 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
1592456 TTGGCCTAGA
*
1592466 TGTAAGTTCTCACT
1 TGTAAGTTTTCACT
1592480 TGTAAGTTTTCACT
1 TGTAAGTTTTCACT
1592494 TGTAAGTTTT
1 TGTAAGTTTT
1592504 TATTTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.50
Consensus pattern (14 bp):
TGTAAGTTTTCACT
Found at i:1592529 original size:2 final size:2
Alignment explanation
Indices: 1592524--1592563 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1592514 TCATTAACTA
1592524 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1592564 ATTGATTCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1593085 original size:20 final size:19
Alignment explanation
Indices: 1593018--1593084 Score: 107
Period size: 19 Copynumber: 3.4 Consensus size: 19
1593008 AATCAGATTG
1593018 CCCAGGGGGTACAGATTCCCC
1 CCCA-GGGGTACAGATT-CCC
1593039 CCCAGGGGTACAGATTCCC
1 CCCAGGGGTACAGATTCCC
*
1593058 CCCAGGGGAACAGATTCCC
1 CCCAGGGGTACAGATTCCC
1593077 CCCAGGGG
1 CCCAGGGG
1593085 GTATTCATTC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 29 0.64
20 12 0.27
21 4 0.09
ACGTcount: A:0.21, C:0.37, G:0.30, T:0.12
Consensus pattern (19 bp):
CCCAGGGGTACAGATTCCC
Found at i:1593095 original size:39 final size:40
Alignment explanation
Indices: 1593018--1593098 Score: 103
Period size: 39 Copynumber: 2.0 Consensus size: 40
1593008 AATCAGATTG
* *
1593018 CCCAGGGGGTACAGATTCCCCCCCAGGGGTACAGATTCCC
1 CCCAGGGGGAACAGATTCCCCCCCAGGGGTACACATTCCC
**
1593058 CCCA-GGGGAACAGATT-CCCCCCAGGGGGTATTCATTCCC
1 CCCAGGGGGAACAGATTCCCCCCCA-GGGGTACACATTCCC
1593097 CC
1 CC
1593099 TGTCTAACGG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 7 0.19
39 25 0.69
40 4 0.11
ACGTcount: A:0.20, C:0.38, G:0.26, T:0.16
Consensus pattern (40 bp):
CCCAGGGGGAACAGATTCCCCCCCAGGGGTACACATTCCC
Found at i:1594398 original size:19 final size:20
Alignment explanation
Indices: 1594374--1594421 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1594364 AACGATTTTC
*
1594374 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1594393 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1594413 TTTTGAAAA
1 TTTTGAAAA
1594422 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1595888 original size:20 final size:20
Alignment explanation
Indices: 1595863--1595921 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
1595853 TTAGATTGCT
1595863 CAGGGGGTACAGATTCCCCC
1 CAGGGGGTACAGATTCCCCC
* *
1595883 CAGGGGGAATAGATTCCCCC
1 CAGGGGGTACAGATTCCCCC
*
1595903 CAGGGGGTACCGATTCCCC
1 CAGGGGGTACAGATTCCCC
1595922 TGTCTAACGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.20, C:0.34, G:0.31, T:0.15
Consensus pattern (20 bp):
CAGGGGGTACAGATTCCCCC
Found at i:1596993 original size:19 final size:21
Alignment explanation
Indices: 1596928--1597007 Score: 101
Period size: 23 Copynumber: 3.8 Consensus size: 21
1596918 CCGTTAGACA
*
1596928 GGGGGAATCTGTACCCCTTGGGG
1 GGGGGAATCTGTACCCCTT--AG
*
1596951 GGGGGAATCTGTTCCCCTTAG
1 GGGGGAATCTGTACCCCTTAG
*
1596972 GGGGGAATCTATACCCC-T-G
1 GGGGGAATCTGTACCCCTTAG
1596991 GGGGGAATCTGTACCCC
1 GGGGGAATCTGTACCCC
1597008 CTGGACAATC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 17 0.33
20 1 0.02
21 16 0.31
23 18 0.35
ACGTcount: A:0.16, C:0.25, G:0.36, T:0.23
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCTTAG
Found at i:1597373 original size:21 final size:22
Alignment explanation
Indices: 1597347--1597397 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 22
1597337 TTTGAAATTA
*
1597347 CTCCCCTTT-ACTTTAACACTT
1 CTCCCCTTTAACCTTAACACTT
1597368 CTCCCCTTTAACACCTTAACACTT
1 CTCCCCTTT-A-ACCTTAACACTT
1597392 CTCCCC
1 CTCCCC
1597398 CTTTTTGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 9 0.35
24 17 0.65
ACGTcount: A:0.20, C:0.45, G:0.00, T:0.35
Consensus pattern (22 bp):
CTCCCCTTTAACCTTAACACTT
Found at i:1599763 original size:20 final size:20
Alignment explanation
Indices: 1599738--1599778 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1599728 CCGTTAGACA
1599738 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
* *
1599758 GGGGGAATCTGTACTCCCTG
1 GGGGGAATCGGTACCCCCTG
1599778 G
1 G
1599779 ACAATCTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.27, G:0.39, T:0.20
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:1601838 original size:29 final size:29
Alignment explanation
Indices: 1601801--1601898 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 29
1601791 TTTTAAATTG
1601801 ATCCTTAAACTTTTAAACATTTCAATTTC
1 ATCCTTAAACTTTTAAACATTTCAATTTC
* * * ** *
1601830 ATCCCTAAACTATGACTCATTTCAAATT-
1 ATCCTTAAACTTTTAAACATTTCAATTTC
* * *
1601858 AGTCCTTAATCTTTTGAACATTCCAATTTC
1 A-TCCTTAAACTTTTAAACATTTCAATTTC
*
1601888 ATCCTCAAACT
1 ATCCTTAAACT
1601899 ATGAATCTCA
Statistics
Matches: 50, Mismatches: 17, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
28 1 0.02
29 48 0.96
30 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (29 bp):
ATCCTTAAACTTTTAAACATTTCAATTTC
Found at i:1601864 original size:58 final size:60
Alignment explanation
Indices: 1601794--1601956 Score: 176
Period size: 58 Copynumber: 2.8 Consensus size: 60
1601784 AGCCTCGTTT
*
1601794 TAAATT-GATCCTTAAACTTTTAAACATTTCAATTTCATCC-CTAAACTATG-A-CTCATT-
1 TAAATTAG-TCCTTAAACTTTTAAACATTCCAATTTCATCCTC-AAACTATGAATCTCATTC
* *
1601851 TCAAATTAGTCCTTAATCTTTTGAACATTCCAATTTCATCCTCAAACTATGAATCTCATTC
1 T-AAATTAGTCCTTAAACTTTTAAACATTCCAATTTCATCCTCAAACTATGAATCTCATTC
* * * * *
1601912 TAAATTGGTACATAAACTTTTAGATC-TTCTAATTTCATCCTCAAA
1 TAAATTAGTCCTTAAACTTTTA-AACATTCCAATTTCATCCTCAAA
1601957 TTCATCCAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
57 1 0.01
58 42 0.47
59 3 0.03
60 40 0.45
61 3 0.03
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (60 bp):
TAAATTAGTCCTTAAACTTTTAAACATTCCAATTTCATCCTCAAACTATGAATCTCATTC
Found at i:1601946 original size:60 final size:58
Alignment explanation
Indices: 1601806--1601956 Score: 164
Period size: 60 Copynumber: 2.6 Consensus size: 58
1601796 AATTGATCCT
* * * *
1601806 TAAACTTTTAAACATTTCAATTTCATCC-CTAAACTATGACTCATTTCAAATTAGTCCT
1 TAAACTTTTGAACATTCCAATTTCATCCTC-AAACTATGACTCATTTCAAATTAGTACA
* *
1601864 TAATCTTTTGAACATTCCAATTTCATCCTCAAACTATGAATCTCA-TTCTAAATTGGTACA
1 TAAACTTTTGAACATTCCAATTTCATCCTCAAACTATG-A-CTCATTTC-AAATTAGTACA
* *
1601924 TAAACTTTTAGATC-TTCTAATTTCATCCTCAAA
1 TAAACTTTT-GAACATTCCAATTTCATCCTCAAA
1601957 TTCATCCAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
58 33 0.42
59 5 0.06
60 38 0.48
61 3 0.04
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.40
Consensus pattern (58 bp):
TAAACTTTTGAACATTCCAATTTCATCCTCAAACTATGACTCATTTCAAATTAGTACA
Found at i:1603565 original size:20 final size:20
Alignment explanation
Indices: 1603515--1603556 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1603505 GAGTATAATA
1603515 TGATGAGGCATCCAACATGT
1 TGATGAGGCATCCAACATGT
1603535 TGATGAGGCATCCAACATGT
1 TGATGAGGCATCCAACATGT
1603555 TG
1 TG
1603557 CTGTGGCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (20 bp):
TGATGAGGCATCCAACATGT
Found at i:1611070 original size:10 final size:10
Alignment explanation
Indices: 1611055--1611079 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1611045 ATACTCTATG
1611055 TTATACATGC
1 TTATACATGC
1611065 TTATACATGC
1 TTATACATGC
1611075 TTATA
1 TTATA
1611080 TTACTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (10 bp):
TTATACATGC
Found at i:1626683 original size:16 final size:16
Alignment explanation
Indices: 1626659--1626692 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1626649 TATCGCCGAT
*
1626659 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
1626675 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
1626691 CG
1 CG
1626693 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:1631070 original size:30 final size:30
Alignment explanation
Indices: 1631036--1631121 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 30
1631026 AACTTTCAAA
*
1631036 AGTTACAAAGCTATCATTAAATTTTTGGA-T
1 AGTTACAAA-CTATCATTAAATTTTTGAACT
*
1631066 AGTTACAAAATAATCATTAAATTTCTTGAACT
1 AGTTACAAACT-ATCATTAAATTT-TTGAACT
*
1631098 A-TTACAAAACAATCATTAAATTTT
1 AGTTAC-AAACTATCATTAAATTTT
1631122 ATCGAAATGT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
29 1 0.02
30 22 0.46
31 20 0.42
32 5 0.10
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (30 bp):
AGTTACAAACTATCATTAAATTTTTGAACT
Found at i:1631106 original size:31 final size:30
Alignment explanation
Indices: 1631036--1631121 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 30
1631026 AACTTTCAAA
* * *
1631036 AGTTACAAAGCTATCATTAAATTTTTGGAT
1 AGTTACAAAACAATCATTAAATTTTTGAAT
*
1631066 AGTTACAAAATAATCATTAAATTTCTTGAACT
1 AGTTACAAAACAATCATTAAATTT-TTGAA-T
1631098 A-TTACAAAACAATCATTAAATTTT
1 AGTTACAAAACAATCATTAAATTTT
1631122 ATCGAAATGT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 22 0.45
31 25 0.51
32 2 0.04
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (30 bp):
AGTTACAAAACAATCATTAAATTTTTGAAT
Found at i:1631234 original size:62 final size:62
Alignment explanation
Indices: 1631098--1631224 Score: 218
Period size: 62 Copynumber: 2.0 Consensus size: 62
1631088 TTCTTGAACT
* *
1631098 ATTACAAAACAATCATTAAATTTTATCGAAATGTTACAGATTGTTATAACGACAAAGTGACC
1 ATTACAAAACAATCATTAAATTTTATCGAAATGTTACAAATTATTATAACGACAAAGTGACC
* *
1631160 ATTACAAAACAATCATTAAATTTTATCGAAATGTTACAAATTATTATAACGACAGAGTGGCC
1 ATTACAAAACAATCATTAAATTTTATCGAAATGTTACAAATTATTATAACGACAAAGTGACC
1631222 ATT
1 ATT
1631225 TTGTAACAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.31
Consensus pattern (62 bp):
ATTACAAAACAATCATTAAATTTTATCGAAATGTTACAAATTATTATAACGACAAAGTGACC
Found at i:1637583 original size:26 final size:26
Alignment explanation
Indices: 1637530--1637579 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
1637520 AATGAATATA
*
1637530 AAAGGAGTGTGTTTGTGTAACAGATG
1 AAAGGAGTGTGTTTATGTAACAGATG
*
1637556 AAAGGAGTGTG-TTATGTAAGAGAT
1 AAAGGAGTGTGTTTATGTAACAGAT
1637580 TGAAGATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.34, C:0.02, G:0.34, T:0.30
Consensus pattern (26 bp):
AAAGGAGTGTGTTTATGTAACAGATG
Found at i:1640790 original size:2 final size:2
Alignment explanation
Indices: 1640783--1640834 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1640773 TCATTCATCA
1640783 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
1640825 AT AT AT AT AT
1 AT AT AT AT AT
1640835 GTCTGTGTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1644752 original size:20 final size:20
Alignment explanation
Indices: 1644729--1644772 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1644719 CATCAGTACT
* *
1644729 GATATTGGACCCTTAGTATC
1 GATATTGAACCATTAGTATC
*
1644749 GATATTGAACCATTGGTATC
1 GATATTGAACCATTAGTATC
1644769 GATA
1 GATA
1644773 CCCGCCTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (20 bp):
GATATTGAACCATTAGTATC
Found at i:1662959 original size:15 final size:16
Alignment explanation
Indices: 1662923--1662960 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1662913 AGAGCCTCTA
*
1662923 AATCATTCAACATTTG
1 AATCATTCAACACTTG
*
1662939 AATCATTCAGCACTT-
1 AATCATTCAACACTTG
1662954 AATCATT
1 AATCATT
1662961 ATGAAGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (16 bp):
AATCATTCAACACTTG
Found at i:1663073 original size:2 final size:2
Alignment explanation
Indices: 1663066--1663100 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1663056 AGAAACCCTA
1663066 AT 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 AT A
1663101 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1663105 original size:2 final size:2
Alignment explanation
Indices: 1663100--1663128 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1663090 ATATATATAT
1663100 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1663129 TTTGTAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.