Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 63 of 143
Found at i:20411211 original size:24 final size:24
Alignment explanation
Indices: 20411150--20411212 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
20411140 TAGACTAATA
* *
20411150 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
20411174 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
20411198 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
20411213 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:20416739 original size:19 final size:19
Alignment explanation
Indices: 20416683--20416741 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
20416673 TTAACCCAAA
** *
20416683 AAGTCAACGGTCAACAGTC
1 AAGTCAACGACCAACGGTC
20416702 AAGTCAACGACCAACGGTC
1 AAGTCAACGACCAACGGTC
* * *
20416721 AAGTCAATGATCAATGGTC
1 AAGTCAACGACCAACGGTC
20416740 AA
1 AA
20416742 CGGTCAATGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (19 bp):
AAGTCAACGACCAACGGTC
Found at i:20432651 original size:20 final size:18
Alignment explanation
Indices: 20432626--20432662 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
20432616 TTTTTTAATA
20432626 TTAAATAAATAAATTTTTTT
1 TTAAAT-AAT-AATTTTTTT
20432646 TTAAATAATAATTTTTT
1 TTAAATAATAATTTTTT
20432663 AAAAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 3 0.18
20 6 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAATAATAATTTTTTT
Found at i:20432652 original size:16 final size:16
Alignment explanation
Indices: 20432631--20432672 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
20432621 TAATATTAAA
*
20432631 TAAATAAATTTTTTTT
1 TAAATAAATTATTTTT
*
20432647 TAAAT-AATAATTTTT
1 TAAATAAATTATTTTT
*
20432662 TAAAAAAATTA
1 TAAATAAATTA
20432673 CTAAAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAATAAATTATTTTT
Found at i:20432901 original size:17 final size:17
Alignment explanation
Indices: 20432865--20432903 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
20432855 AGGTAAGGTA
20432865 AAAT-GGGGGGAAGGGT
1 AAATGGGGGGGAAGGGT
20432881 AAATGGGGGGGAAGGGT
1 AAATGGGGGGGAAGGGT
20432898 AAATGG
1 AAATGG
20432904 TCCCCAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.33, C:0.00, G:0.54, T:0.13
Consensus pattern (17 bp):
AAATGGGGGGGAAGGGT
Found at i:20433125 original size:17 final size:17
Alignment explanation
Indices: 20433103--20433136 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20433093 AAAAAAATTC
*
20433103 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
20433120 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
20433137 TTATTGTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:20433289 original size:27 final size:27
Alignment explanation
Indices: 20433259--20433342 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 27
20433249 ATATATAATC
20433259 TAATTTTTATTTGAAATATAAAATATA
1 TAATTTTTATTTGAAATATAAAATATA
* * * *
20433286 TAATCATTTATTT---AT-TTAACTAAA
1 TAAT-TTTTATTTGAAATATAAAATATA
*
20433310 TTATTTTTATTTGAAATATAAAATATA
1 TAATTTTTATTTGAAATATAAAATATA
20433337 T-ATTTT
1 TAATTTT
20433343 AAAAAATACA
Statistics
Matches: 43, Mismatches: 9, Indels: 11
0.68 0.14 0.17
Matches are distributed among these distances:
23 7 0.16
24 9 0.21
25 2 0.05
26 7 0.16
27 11 0.26
28 7 0.16
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (27 bp):
TAATTTTTATTTGAAATATAAAATATA
Found at i:20433730 original size:23 final size:25
Alignment explanation
Indices: 20433704--20433754 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
20433694 TTAAAAATGC
20433704 TTAAAA-TT-AAATTAT-TAATATTT
1 TTAAAACTTGAAATTATAT-ATATTT
20433727 TTAAAACTTTGAAATTATATATATTT
1 TTAAAAC-TTGAAATTATATATATTT
20433753 TT
1 TT
20433755 TCATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.25
25 2 0.08
26 15 0.62
27 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (25 bp):
TTAAAACTTGAAATTATATATATTT
Found at i:20433828 original size:31 final size:29
Alignment explanation
Indices: 20433790--20433847 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 29
20433780 TGAATTGAAT
*
20433790 ATTTCAATTTTAAATTTTCAATAAATAATAA
1 ATTTCAATTTAAAATTTT-AA-AAATAATAA
20433821 ATTTCAATTTAAAATTTTAAAAATAAT
1 ATTTCAATTTAAAATTTTAAAAATAAT
20433848 TAAGGATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.27
30 2 0.08
31 17 0.65
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTTCAATTTAAAATTTTAAAAATAATAA
Found at i:20435457 original size:6 final size:6
Alignment explanation
Indices: 20435446--20435472 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
20435436 ACTTTTAGTC
20435446 GCCTGA GCCTGA GCCTGA GCCTGA GCC
1 GCCTGA GCCTGA GCCTGA GCCTGA GCC
20435473 GCAGCACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (6 bp):
GCCTGA
Found at i:20436056 original size:26 final size:26
Alignment explanation
Indices: 20436000--20436084 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
20435990 GCTAAACCTC
*
20436000 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAATA
* ** *
20436026 GTTAAATAAATTCAAATTTAAACATA
1 ATTAAATAAATTCAAACATAAAAATA
* * **
20436052 ATTAATTCCAAATTCAATCATAAACTTA
1 ATTAAAT--AAATTCAAACATAAAAATA
20436080 ATTAA
1 ATTAA
20436085 TTCCAATAGA
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
26 26 0.57
28 20 0.43
ACGTcount: A:0.54, C:0.11, G:0.01, T:0.34
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAATA
Found at i:20436064 original size:22 final size:21
Alignment explanation
Indices: 20436034--20436074 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
20436024 TTGTTAAATA
*
20436034 AATTCAAATTTAAACATAATT
1 AATTCAAATTCAAACATAATT
*
20436055 AATTCCAAATTCAATCATAA
1 AATT-CAAATTCAAACATAA
20436075 ACTTAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (21 bp):
AATTCAAATTCAAACATAATT
Found at i:20440322 original size:27 final size:27
Alignment explanation
Indices: 20440284--20440364 Score: 126
Period size: 27 Copynumber: 3.0 Consensus size: 27
20440274 AAAATACGGG
*
20440284 TTGGTGCCGCCTGACAGGAAGGCACCA
1 TTGGTGCCGCCTGACAGGTAGGCACCA
20440311 TTGGTGCCGCCTGACAGGTAGGCACCA
1 TTGGTGCCGCCTGACAGGTAGGCACCA
* * *
20440338 CTAGTGCCGCCTGTCAGGTAGGCACCA
1 TTGGTGCCGCCTGACAGGTAGGCACCA
20440365 CCCCTTGTAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.20, C:0.31, G:0.32, T:0.17
Consensus pattern (27 bp):
TTGGTGCCGCCTGACAGGTAGGCACCA
Found at i:20449246 original size:21 final size:21
Alignment explanation
Indices: 20449222--20449276 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
20449212 TAGAGGTAAG
**
20449222 ACTTGTATTGGTAGAGGAGTC
1 ACTTGTATTGGTAGAACAGTC
* *
20449243 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATTGGTAGAACAGTC
20449264 ACTTGTATTGGTA
1 ACTTGTATTGGTA
20449277 CAAATCTGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (21 bp):
ACTTGTATTGGTAGAACAGTC
Found at i:20450518 original size:29 final size:29
Alignment explanation
Indices: 20450485--20450568 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 29
20450475 CACGATTTGA
*
20450485 CACACGATCTGAGACACGATCGTGTGATC
1 CACACGATCTGGGACACGATCGTGTGATC
*
20450514 CACACGGTCTGGGACACGATCGTGTGATC
1 CACACGATCTGGGACACGATCGTGTGATC
* *
20450543 CACATGATCTGGGACACGGTCGTGTG
1 CACACGATCTGGGACACGATCGTGTG
20450569 TATCGAGTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.23, C:0.26, G:0.30, T:0.21
Consensus pattern (29 bp):
CACACGATCTGGGACACGATCGTGTGATC
Found at i:20455505 original size:28 final size:30
Alignment explanation
Indices: 20455474--20455547 Score: 98
Period size: 28 Copynumber: 2.5 Consensus size: 30
20455464 GACTTACCCC
*
20455474 GTGTTTACTATCCTGATGGACT-CTAT-TT
1 GTGTTTACTATCCTAATGGACTACTATCTT
* *
20455502 GTGTTTACTGTCCCAATGGACTACCTATCTT
1 GTGTTTACTATCCTAATGGACTA-CTATCTT
20455533 GTGTTTACTATCCTA
1 GTGTTTACTATCCTA
20455548 GCGGACTATC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
28 19 0.50
30 4 0.11
31 15 0.39
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (30 bp):
GTGTTTACTATCCTAATGGACTACTATCTT
Found at i:20455554 original size:31 final size:29
Alignment explanation
Indices: 20455474--20455555 Score: 87
Period size: 31 Copynumber: 2.8 Consensus size: 29
20455464 GACTTACCCC
20455474 GTGTTTACTATCCT-GATGGACT-CTATTT
1 GTGTTTACTATCCTAG-TGGACTACTATTT
* * *
20455502 GTGTTTACTGTCCCAATGGACTACCTATCTT
1 GTGTTTACTATCCTAGTGGACTA-CTAT-TT
*
20455533 GTGTTTACTATCCTAGCGGACTA
1 GTGTTTACTATCCTAGTGGACTA
20455556 TCTCTATAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
28 18 0.42
30 4 0.09
31 21 0.49
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (29 bp):
GTGTTTACTATCCTAGTGGACTACTATTT
Found at i:20457347 original size:16 final size:16
Alignment explanation
Indices: 20457328--20457363 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
20457318 ACTTGGGTTT
* *
20457328 GGTTTGGTTTTTAAAG
1 GGTTTGGGTTTAAAAG
20457344 GGTTTGGGTTTAAAAG
1 GGTTTGGGTTTAAAAG
20457360 GGTT
1 GGTT
20457364 ATTGGATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.36, T:0.44
Consensus pattern (16 bp):
GGTTTGGGTTTAAAAG
Found at i:20460701 original size:132 final size:132
Alignment explanation
Indices: 20460464--20460729 Score: 532
Period size: 132 Copynumber: 2.0 Consensus size: 132
20460454 TTGAACTCAA
20460464 CTCTGATACCATTAAATATAACCCCTTTTTACTCGATCTAGAGTATTTGACCAGATCCAGAAGGT
1 CTCTGATACCATTAAATATAACCCCTTTTTACTCGATCTAGAGTATTTGACCAGATCCAGAAGGT
20460529 TATTTAAGTAATTTCATCCACACACAACTCGATAGTCCAAAATCATTCATAAATATAAATATAAA
66 TATTTAAGTAATTTCATCCACACACAACTCGATAGTCCAAAATCATTCATAAATATAAATATAAA
20460594 GT
131 GT
20460596 CTCTGATACCATTAAATATAACCCCTTTTTACTCGATCTAGAGTATTTGACCAGATCCAGAAGGT
1 CTCTGATACCATTAAATATAACCCCTTTTTACTCGATCTAGAGTATTTGACCAGATCCAGAAGGT
20460661 TATTTAAGTAATTTCATCCACACACAACTCGATAGTCCAAAATCATTCATAAATATAAATATAAA
66 TATTTAAGTAATTTCATCCACACACAACTCGATAGTCCAAAATCATTCATAAATATAAATATAAA
20460726 GT
131 GT
20460728 CT
1 CT
20460730 ATAATTAAAA
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
132 134 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.32
Consensus pattern (132 bp):
CTCTGATACCATTAAATATAACCCCTTTTTACTCGATCTAGAGTATTTGACCAGATCCAGAAGGT
TATTTAAGTAATTTCATCCACACACAACTCGATAGTCCAAAATCATTCATAAATATAAATATAAA
GT
Found at i:20462049 original size:16 final size:16
Alignment explanation
Indices: 20462030--20462065 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
20462020 ACTTGGGTTT
*
20462030 GGTTTGGGTTTTAAAG
1 GGTTTGGGTTTAAAAG
20462046 GGTTTGGGTTTAAAAG
1 GGTTTGGGTTTAAAAG
20462062 GGTT
1 GGTT
20462066 ATTGGATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.39, T:0.42
Consensus pattern (16 bp):
GGTTTGGGTTTAAAAG
Found at i:20463525 original size:30 final size:30
Alignment explanation
Indices: 20463489--20463589 Score: 94
Period size: 30 Copynumber: 3.4 Consensus size: 30
20463479 TGGTCTACAA
* *
20463489 ATAGCCACGAAGGCATCCATACATCATTAG
1 ATAGCCACAAAGGCATCCAGACATCATTAG
* ** *
20463519 ATAGCCATAAAGGTGTCCAGATATCATTAG
1 ATAGCCACAAAGGCATCCAGACATCATTAG
* * ** *
20463549 ATAGACAGAAAGGTGTCCAGATATCATTAG
1 ATAGCCACAAAGGCATCCAGACATCATTAG
*
20463579 GTAGCCACAAA
1 ATAGCCACAAA
20463590 TGCGTCAATA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (30 bp):
ATAGCCACAAAGGCATCCAGACATCATTAG
Found at i:20463802 original size:30 final size:30
Alignment explanation
Indices: 20463768--20463869 Score: 95
Period size: 30 Copynumber: 3.5 Consensus size: 30
20463758 GAGTAGCCAT
20463768 AAAGGCTTTCACATATTAGAGAACAACCAC
1 AAAGGCTTTCACATATTAGAGAACAACCAC
* * *
20463798 AAAGGCTTCCAC-TTTTCAGAGGACCAACCAC
1 AAAGGCTTTCACATATT-AGA-GAACAACCAC
* *
20463829 AAAGGC-TT-ACATATCA-AGAACAACCAA
1 AAAGGCTTTCACATATTAGAGAACAACCAC
**
20463856 AAACACTTTCACAT
1 AAAGGCTTTCACAT
20463870 TTCGATATCT
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
27 12 0.21
28 3 0.05
29 10 0.18
30 17 0.30
31 15 0.26
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.20
Consensus pattern (30 bp):
AAAGGCTTTCACATATTAGAGAACAACCAC
Found at i:20464092 original size:55 final size:55
Alignment explanation
Indices: 20463996--20464136 Score: 160
Period size: 55 Copynumber: 2.6 Consensus size: 55
20463986 CATAGTCCCA
* * * * * *
20463996 AACTAGGTCTTACACTATGTGGTCTTC-ACTTGCCCATATGATGTCATAGCC-CTCC
1 AACTAGGTCTTACACGATATGGTCTTCGA-TTCCCCAAATGATGCCAAAGCCACT-C
*
20464051 AACTAGGTCTTACACGATATGGTCTTCGATTCCCCAAATGATGCCAAATCCACTC
1 AACTAGGTCTTACACGATATGGTCTTCGATTCCCCAAATGATGCCAAAGCCACTC
* * *
20464106 GACTAGGTCTTACATGATATGGCCTTCGATT
1 AACTAGGTCTTACACGATATGGTCTTCGATT
20464137 TTCATGACCA
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
55 71 0.96
56 3 0.04
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (55 bp):
AACTAGGTCTTACACGATATGGTCTTCGATTCCCCAAATGATGCCAAAGCCACTC
Found at i:20467907 original size:17 final size:18
Alignment explanation
Indices: 20467872--20467909 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
20467862 GTTATTTGTT
20467872 TTTAAATTGATTATTAAA
1 TTTAAATTGATTATTAAA
20467890 TTTAAATT-A-TATTTAAA
1 TTTAAATTGATTA-TTAAA
20467907 TTT
1 TTT
20467910 TTTATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.11
17 9 0.47
18 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
TTTAAATTGATTATTAAA
Found at i:20472400 original size:22 final size:22
Alignment explanation
Indices: 20472375--20472426 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
20472365 TACAAAACAT
*
20472375 TATTTTGTAACTCTCCTCATAC
1 TATTTTGTAACTCTCCTCATAA
*
20472397 TATTTTGTAGCTCTCCTCATAA
1 TATTTTGTAACTCTCCTCATAA
*
20472419 TGTTTTGT
1 TATTTTGT
20472427 TTTAAATTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.10, T:0.50
Consensus pattern (22 bp):
TATTTTGTAACTCTCCTCATAA
Found at i:20473429 original size:20 final size:20
Alignment explanation
Indices: 20473390--20473459 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 20
20473380 AAATAAACAA
*
20473390 TTATAATA-TTAGAT-TTTT
1 TTATAATATTTAAATATTTT
20473408 TTATAATATTTAAATATTTT
1 TTATAATATTTAAATATTTT
20473428 TT-TAA-ATTT-AATAATTCTT
1 TTATAATATTTAAAT-ATT-TT
*
20473447 TTAAAAT-TTTAAA
1 TTATAATATTTAAA
20473460 ATTGAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
17 3 0.07
18 15 0.35
19 12 0.28
20 11 0.26
21 2 0.05
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (20 bp):
TTATAATATTTAAATATTTT
Found at i:20473462 original size:19 final size:18
Alignment explanation
Indices: 20473404--20473462 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 18
20473394 AATATTAGAT
*
20473404 TTTTTTATAATATTTAAATA
1 TTTTTTAAAAT-TTTAAA-A
*
20473424 TTTTTTTAAA-TTTAATAA
1 TTTTTTAAAATTTTAA-AA
20473442 TTCTTTTAAAATTTTAAAA
1 TT-TTTTAAAATTTTAAAA
20473461 TT
1 TT
20473463 GAAAAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 8 0.24
19 12 0.36
20 13 0.39
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTTAAAATTTTAAAA
Found at i:20478444 original size:91 final size:90
Alignment explanation
Indices: 20478278--20478450 Score: 283
Period size: 91 Copynumber: 1.9 Consensus size: 90
20478268 TAACCATCCA
* *
20478278 ATAACACCCAGTTTGCTTATAAGAGCTTTCCAACCGATAACACACCAGATGCAAATAATGCAAAG
1 ATAACACCCAATTTGCTCATAAGAGCTTTCCAACCGATAACACACCAGATGCAAATAATGCAAAG
20478343 CCCGTAGGCTAAACATTATCCCCCG
66 CCCGTAGGCTAAACATTATCCCCCG
* * *
20478368 ATAACACGCCAATTTGCTCATAAGAGCTTTCCAACCGATAACACGCCAGATGCACATAGTGCAAA
1 ATAACAC-CCAATTTGCTCATAAGAGCTTTCCAACCGATAACACACCAGATGCAAATAATGCAAA
*
20478433 GCTCGTAGGCTAAACATT
65 GCCCGTAGGCTAAACATT
20478451 TTCTATCACA
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
90 7 0.09
91 69 0.91
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (90 bp):
ATAACACCCAATTTGCTCATAAGAGCTTTCCAACCGATAACACACCAGATGCAAATAATGCAAAG
CCCGTAGGCTAAACATTATCCCCCG
Found at i:20483336 original size:69 final size:69
Alignment explanation
Indices: 20483210--20483345 Score: 204
Period size: 69 Copynumber: 2.0 Consensus size: 69
20483200 TAATTAAACT
* *
20483210 TAATCACTTTAATATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTAATAAAATACTTATCAAGATAAATATTAGATTAAATTTAACATT
20483275 AAGA
66 AAGA
* *
20483279 TAATCACTTTAATATTAAATTAATAAAATAC-TATTAAGATAAGTATT-GAATTAAAATTTAACA
1 TAATCACTTTAATATTAAATTAATAAAATACTTATCAAGATAAATATTAG-ATT-AAATTTAACA
20483342 TTAA
64 TTAA
20483346 ATCTTTTAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
67 1 0.02
68 17 0.28
69 43 0.70
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (69 bp):
TAATCACTTTAATATTAAATTAATAAAATACTTATCAAGATAAATATTAGATTAAATTTAACATT
AAGA
Found at i:20486994 original size:17 final size:17
Alignment explanation
Indices: 20486937--20486981 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
20486927 ATATATATGG
**
20486937 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
*
20486954 AGATGCAATGACAATAA
1 AAATGCAATGACAATAA
20486971 AAATGCAATGA
1 AAATGCAATGA
20486982 TATTAATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.20
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:20496503 original size:16 final size:17
Alignment explanation
Indices: 20496467--20496505 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
20496457 ACATTGTCGT
*
20496467 TGCATTTTAATTGTTAT
1 TGCATTTTAATTGTTAG
20496484 TGCATTTTAA-TGTTAG
1 TGCATTTTAATTGTTAG
20496500 TGCATT
1 TGCATT
20496506 GGGGACAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (17 bp):
TGCATTTTAATTGTTAG
Found at i:20497055 original size:14 final size:15
Alignment explanation
Indices: 20497036--20497068 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
20497026 TTCACATAAA
20497036 AAAAAGAAAG-AAAG
1 AAAAAGAAAGAAAAG
20497050 AAAAAGAAAGAAAAG
1 AAAAAGAAAGAAAAG
20497065 AAAA
1 AAAA
20497069 GAGATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAGAAAAG
Found at i:20497069 original size:14 final size:14
Alignment explanation
Indices: 20497033--20497070 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
20497023 TAGTTCACAT
20497033 AAAA-AAAAGAAAG
1 AAAAGAAAAGAAAG
20497046 -AAAGAAAAAGAAAG
1 AAAAG-AAAAGAAAG
20497060 AAAAGAAAAGA
1 AAAAGAAAAGA
20497071 GATAAATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
14 15 0.68
15 4 0.18
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:20501506 original size:31 final size:31
Alignment explanation
Indices: 20501457--20501516 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
20501447 AGATTGCTCA
* *
20501457 CCCTTTATAAAAGACATTTTGAATTTAAGCC
1 CCCTATATAAAAGACATTTTCAATTTAAGCC
20501488 CCCTATATAAAA-ATCATTTTCAATTTAAG
1 CCCTATATAAAAGA-CATTTTCAATTTAAG
20501517 GCATAAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (31 bp):
CCCTATATAAAAGACATTTTCAATTTAAGCC
Found at i:20504257 original size:22 final size:22
Alignment explanation
Indices: 20504198--20504257 Score: 88
Period size: 21 Copynumber: 2.8 Consensus size: 22
20504188 TACTTGATAG
*
20504198 AAGGTATCGATAC-TTCTTGAA
1 AAGGTATCGATACTTTTTTGAA
*
20504219 AAGGTAACGATACTTTTTTG-A
1 AAGGTATCGATACTTTTTTGAA
20504240 AAGGTATCGATACTTTTT
1 AAGGTATCGATACTTTTT
20504258 GTCATTGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 30 0.86
22 5 0.14
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (22 bp):
AAGGTATCGATACTTTTTTGAA
Found at i:20509285 original size:209 final size:209
Alignment explanation
Indices: 20508920--20509334 Score: 758
Period size: 209 Copynumber: 2.0 Consensus size: 209
20508910 AATATTACCC
20508920 GTTTCATTAGAAGCTATGTAAAGGAGATTGAATCTACTAAAGAAAAGCGACTTATCTTGTCAAAA
1 GTTTCATTAGAAGCTATGTAAAGGAGATTGAATCTACTAAAGAAAAGCGACTTATCTTGTCAAAA
*
20508985 AGGAATGCCCGTTGGGATCCTCCTCCAAGGAATGTCGTAAAAATCAACTTTGATGCCAGCTTTGA
66 AGGAACGCCCGTTGGGATCCTCCTCCAAGGAATGTCGTAAAAATCAACTTTGATGCCAGCTTTGA
* * *
20509050 CTTTTGTAGTTGTAAAGCAAGAATGGGAATAGTTATCAGGGACATGCATGGAAGTGTTCTAGCCT
131 CTTTGGTAGTTGTAAAGCAAGAATGGGAATAGTTATCAAGGACATGCATGGAAGTGTTCTAACCT
20509115 CCAGAATGATGCAT
196 CCAGAATGATGCAT
20509129 GTTTCATTAGAAGCTATGTAAAGGAGATTGAATCTACTAAAGAAAAGCGACTTATCTTGTCAAAA
1 GTTTCATTAGAAGCTATGTAAAGGAGATTGAATCTACTAAAGAAAAGCGACTTATCTTGTCAAAA
*
20509194 AGGAACGCCCGTTGGGATCCTTCTCCAAGGAATGTCGTAAAAATCAACTTTGATGCCAGCTTTGA
66 AGGAACGCCCGTTGGGATCCTCCTCCAAGGAATGTCGTAAAAATCAACTTTGATGCCAGCTTTGA
* *
20509259 CTTTGGTAGTTGTAAAGCAGGAATGGGAATAGTTATCAAGGACATGCATGGAAGTGTTCTAATCT
131 CTTTGGTAGTTGTAAAGCAAGAATGGGAATAGTTATCAAGGACATGCATGGAAGTGTTCTAACCT
*
20509324 CTAGAATGATG
196 CCAGAATGATG
20509335 ACTCAATCAC
Statistics
Matches: 198, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
209 198 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (209 bp):
GTTTCATTAGAAGCTATGTAAAGGAGATTGAATCTACTAAAGAAAAGCGACTTATCTTGTCAAAA
AGGAACGCCCGTTGGGATCCTCCTCCAAGGAATGTCGTAAAAATCAACTTTGATGCCAGCTTTGA
CTTTGGTAGTTGTAAAGCAAGAATGGGAATAGTTATCAAGGACATGCATGGAAGTGTTCTAACCT
CCAGAATGATGCAT
Found at i:20510083 original size:8 final size:8
Alignment explanation
Indices: 20510072--20510096 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
20510062 GTTTTTCAAA
20510072 AAAATATT
1 AAAATATT
20510080 AAAATATT
1 AAAATATT
20510088 AAAATATT
1 AAAATATT
20510096 A
1 A
20510097 TTATTTTTGA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAAATATT
Found at i:20511972 original size:25 final size:25
Alignment explanation
Indices: 20511880--20511970 Score: 119
Period size: 25 Copynumber: 3.6 Consensus size: 25
20511870 AATTTCTAAA
20511880 GTCTGGCTCATAAGAGCGATATTCT
1 GTCTGGCTCATAAGAGCGATATTCT
**
20511905 GTAAGGCTCATAAGAGCGATATTCT
1 GTCTGGCTCATAAGAGCGATATTCT
* * *
20511930 GTCTGGCTCGTAAGAGTGATACTCT
1 GTCTGGCTCATAAGAGCGATATTCT
* *
20511955 ATCTGGCTCGTAAGAG
1 GTCTGGCTCATAAGAG
20511971 TGTAAATTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (25 bp):
GTCTGGCTCATAAGAGCGATATTCT
Found at i:20521265 original size:25 final size:25
Alignment explanation
Indices: 20521236--20521333 Score: 124
Period size: 25 Copynumber: 3.9 Consensus size: 25
20521226 TTAAAGTCTT
*
20521236 GCTCGTAAGAGCGATATTCTATCTA
1 GCTCGTAAGAGCGATATTCTATCTG
*
20521261 GCTCGTAAGAGCGATATTCTGTCTG
1 GCTCGTAAGAGCGATATTCTATCTG
* * *
20521286 GCTCGTAAGAGAGATATTCTGTTTG
1 GCTCGTAAGAGCGATATTCTATCTG
* *
20521311 GCTCATAAGAGCGTAAATTCTAT
1 GCTCGTAAGAGCG-ATATTCTAT
20521334 TTGGGCTCAT
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
25 57 0.89
26 7 0.11
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (25 bp):
GCTCGTAAGAGCGATATTCTATCTG
Found at i:20521356 original size:27 final size:26
Alignment explanation
Indices: 20521236--20521353 Score: 82
Period size: 25 Copynumber: 4.7 Consensus size: 26
20521226 TTAAAGTCTT
* * * *
20521236 GCTCGTAAGAGCG-ATATTCTATCTA
1 GCTCATAAGAGCGTAAATTCTATTTG
* * * *
20521261 GCTCGTAAGAGCG-ATATTCTGTCTG
1 GCTCATAAGAGCGTAAATTCTATTTG
* * * *
20521286 GCTCGTAAGAGAG-ATATTCTGTTTG
1 GCTCATAAGAGCGTAAATTCTATTTG
20521311 GCTCATAAGAGCGTAAATTCTATTTGG
1 GCTCATAAGAGCGTAAATTCTATTT-G
*
20521338 GCTCATATGAGC-TAAA
1 GCTCATAAGAGCGTAAA
20521354 ATTTCTAGAA
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
25 57 0.70
26 13 0.16
27 12 0.15
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (26 bp):
GCTCATAAGAGCGTAAATTCTATTTG
Found at i:20526068 original size:58 final size:57
Alignment explanation
Indices: 20525989--20526135 Score: 174
Period size: 58 Copynumber: 2.6 Consensus size: 57
20525979 ATTGAATCTT
* *
20525989 TAAAAAAATTTAGATACCAAATTAGAAAAAAATGTC-AATTCAAGTATCAAATTAGA
1 TAAAAAAATTTAGATACCAAATTAGAAAAAAATATCAAATTCAAGTACCAAATTAGA
* * * * * *
20526045 TCCAAAAAAATTTAGGTATCAAATTAGGAAAAAGTATCAAATTTAAGTACCAAATTGGA
1 T--AAAAAAATTTAGATACCAAATTAGAAAAAAATATCAAATTCAAGTACCAAATTAGA
20526104 TAAAAAAACTTTAGATACCAAA-TA-AAAAAAAT
1 TAAAAAAA-TTTAGATACCAAATTAGAAAAAAAT
20526136 CAAGTTCAGG
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
56 7 0.09
57 9 0.12
58 41 0.55
59 18 0.24
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.26
Consensus pattern (57 bp):
TAAAAAAATTTAGATACCAAATTAGAAAAAAATATCAAATTCAAGTACCAAATTAGA
Found at i:20528490 original size:16 final size:16
Alignment explanation
Indices: 20528466--20528500 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20528456 TTAAATTTTG
20528466 AAAAGAAAATAAAATA
1 AAAAGAAAATAAAATA
* *
20528482 AAAATAAAATAGAATA
1 AAAAGAAAATAAAATA
20528498 AAA
1 AAA
20528501 GGTCTCAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (16 bp):
AAAAGAAAATAAAATA
Found at i:20530450 original size:42 final size:42
Alignment explanation
Indices: 20530394--20531016 Score: 524
Period size: 42 Copynumber: 15.6 Consensus size: 42
20530384 CTTTGATTTA
* * * *
20530394 GGGGTAAAAGATTGGATGATGTCTTCAATCCGTCTCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* *
20530436 GGGATAAGAGATTGGATG--G-CTTCAAACTGCCCCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* ** *
20530475 GGGGTAAGAGACTGG-TG-TGTCTTCAATCTGCCCTTTGATT
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * *
20530515 AGGGTAAAAGATT-G--GATG-CTTCAATCTGCCCCATGATT
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
*
20530553 GGGGTAAGAGATTGGATGATGT-TTACAATCTACCCCATGATC
1 GGGGTAAGAGATTGGATGATGTCTT-CAATCTGCCCCATGATC
* * * * *
20530595 -GAGAAAAAGATT--AAG-TG-CTTCAATCTGACCCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * ** *
20530632 GGGGTAAGAGATTGG-T-ATGTCTTCAATTTGCTCTTTGATT
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* *
20530672 AGGGTAAAAGATT-GA--ATG-CTGT-AATCTGCCCCATGATC
1 GGGGTAAGAGATTGGATGATGTCT-TCAATCTGCCCCATGATC
* * * * *
20530710 GGGGTAAGAGATTGGATGAGGTCTTCAATTTACCCTC-TTATT
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCC-CATGATC
* * * * *
20530752 AGGGTAAAAGATT-GA--ATG-CTTCAATCTGCACCATAATT
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * * *
20530790 GGGGTAAGAGATT-G--G-TGTCTTTAATCTACCTCATGATT
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * * *
20530828 GGGGTAAGAGATTGGATGATGTCTTTAATCTGTCTCATGGTC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* *
20530870 GGGGTAAGAGATTGGATGAGGTCTTCAATCTGCCTCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
*
20530912 GGGG-AAGAGATTGGATGA---CTTCAATCTGCCCCATGGTC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * *
20530950 GAGGTAAGAGATTGGATAATGTCTTCAATCTACCCCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
20530992 GGGGTAAGAGATTGGATGATGTCTT
1 GGGGTAAGAGATTGGATGATGTCTT
20531017 TGCTTTGCTC
Statistics
Matches: 467, Mismatches: 81, Indels: 66
0.76 0.13 0.11
Matches are distributed among these distances:
37 18 0.04
38 144 0.31
39 61 0.13
40 52 0.11
41 35 0.07
42 156 0.33
43 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (42 bp):
GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
Found at i:20530544 original size:38 final size:38
Alignment explanation
Indices: 20530411--20531009 Score: 400
Period size: 38 Copynumber: 15.1 Consensus size: 38
20530401 AAGATTGGAT
* * * * *
20530411 GATGTCTTCAATCCGTCTCATGATCGGGATAAGAGATTG
1 GATG-CTTCAATCTGCCCCATGATTGGGGTAAGAGATTG
* * *
20530450 GATGGCTTCAAACTGCCCCATGATCGGGGTAAGAGACTG
1 GAT-GCTTCAATCTGCCCCATGATTGGGGTAAGAGATTG
* ** * *
20530489 GTGTGTCTTCAATCTGCCCTTTGATTAGGGTAAAAGATTG
1 G-ATG-CTTCAATCTGCCCCATGATTGGGGTAAGAGATTG
20530529 GATGCTTCAATCTGCCCCATGATTGGGGTAAGAGATTGG
1 GATGCTTCAATCTGCCCCATGATTGGGGTAAGAGATT-G
* * * * * *
20530568 ATGATGTTTACAATCTACCCCATGA-TCGAGAAAAAGATT-
1 --GATGCTT-CAATCTGCCCCATGATTGGGGTAAGAGATTG
* * *
20530607 AAGTGCTTCAATCTGACCCATGATCGGGGTAAGAGATTG
1 GA-TGCTTCAATCTGCCCCATGATTGGGGTAAGAGATTG
* * ** * *
20530646 GTATGTCTTCAATTTGCTCTTTGATTAGGGTAAAAGATTG
1 G-ATG-CTTCAATCTGCCCCATGATTGGGGTAAGAGATTG
* *
20530686 AATGCTGT-AATCTGCCCCATGATCGGGGTAAGAGATTG
1 GATGCT-TCAATCTGCCCCATGATTGGGGTAAGAGATTG
* * * * *
20530724 GATGAGGTCTTCAATTTACCCTC-TTATTAGGGTAAAAGATTG
1 GAT---G-CTTCAATCTGCCC-CATGATTGGGGTAAGAGATTG
* * *
20530766 AATGCTTCAATCTGCACCATAATTGGGGTAAGAGATTG
1 GATGCTTCAATCTGCCCCATGATTGGGGTAAGAGATTG
* * *
20530804 G-TGTCTTTAATCTACCTCATGATTGGGGTAAGAGATTGG
1 GATG-CTTCAATCTGCCCCATGATTGGGGTAAGAGATT-G
* * * * *
20530843 ATGATGTCTTTAATCTGTCTCATGGTCGGGGTAAGAGATTG
1 --GATG-CTTCAATCTGCCCCATGATTGGGGTAAGAGATTG
* *
20530884 GATGAGGTCTTCAATCTGCCTCATGATCGGGG-AAGAGATTG
1 GAT---G-CTTCAATCTGCCCCATGATTGGGGTAAGAGATTG
* * *
20530925 GATGACTTCAATCTGCCCCATGGTCGAGGTAAGAGATTG
1 GATG-CTTCAATCTGCCCCATGATTGGGGTAAGAGATTG
* *
20530964 GATAATGTCTTCAATCTACCCCATGATCGGGGTAAGAGATTG
1 G---ATG-CTTCAATCTGCCCCATGATTGGGGTAAGAGATTG
20531006 GATG
1 GATG
20531010 ATGTCTTTGC
Statistics
Matches: 442, Mismatches: 86, Indels: 64
0.75 0.15 0.11
Matches are distributed among these distances:
37 17 0.04
38 145 0.33
39 60 0.14
40 57 0.13
41 32 0.07
42 130 0.29
43 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (38 bp):
GATGCTTCAATCTGCCCCATGATTGGGGTAAGAGATTG
Found at i:20530682 original size:157 final size:155
Alignment explanation
Indices: 20530394--20530980 Score: 585
Period size: 157 Copynumber: 3.7 Consensus size: 155
20530384 CTTTGATTTA
* * *** * * *
20530394 GGGGTAAAAGATTGGATGATGTCTTCAATCCGTCTCATGATCGGGATAAGAGATT-GGATGGCTT
1 GGGGTAAGAGATTGGATGAGGTCTTCAATCTACCCCATGATCGGGA-AAAAGATTAAG-T-GCTT
* * *
20530458 CAAACTGCCCCATGATCGGGGTAAGAGACTGGTGTGTCTTCAATCTGCCCTTTGATTAGGGTAAA
63 CAATCTGCCCCATGATCGGGGTAAGAGATTGGTATGTCTTCAATCTG-CCTTTGATTAGGGTAAA
*
20530523 AGATTGGATGCTTCAATCTGCCCCATGATT
127 AGATTGGATGCTT-AATCTGCCCCATGATC
* *
20530553 GGGGTAAGAGATTGGATGATGT-TTACAATCTACCCCATGATCGAGAAAAAGATTAAGTGCTTCA
1 GGGGTAAGAGATTGGATGAGGTCTT-CAATCTACCCCATGATCGGGAAAAAGATTAAGTGCTTCA
* *
20530617 ATCTGACCCATGATCGGGGTAAGAGATTGGTATGTCTTCAATTTGCTCTTTGATTAGGGTAAAAG
65 ATCTGCCCCATGATCGGGGTAAGAGATTGGTATGTCTTCAATCTGC-CTTTGATTAGGGTAAAAG
*
20530682 ATTGAATGCTGTAATCTGCCCCATGATC
129 ATTGGATGCT-TAATCTGCCCCATGATC
* * * *
20530710 GGGGTAAGAGATTGGATGAGGTCTTCAATTTACCCTC-TTATTAGGGTAAAAGATTGAA-TGCTT
1 GGGGTAAGAGATTGGATGAGGTCTTCAATCTACCC-CATGA-TCGGGAAAAAGATT-AAGTGCTT
* * * * * * * *
20530773 CAATCTGCACCATAATTGGGGTAAGAGATTGG--TGTCTTTAATCTACCTCATGATTGGGGTAAG
63 CAATCTGCCCCATGATCGGGGTAAGAGATTGGTATGTCTTCAATCTGCCT-TTGATTAGGGTAAA
* * *
20530836 AGATTGGATGATGTCTTTAATCTGTCTCATGGTC
127 AGATT-G--GATG-C-TTAATCTGCCCCATGATC
* * * * *
20530870 GGGGTAAGAGATTGGATGAGGTCTTCAATCTGCCTCATGATCGGGGAAGAGATT-GGATGACTTC
1 GGGGTAAGAGATTGGATGAGGTCTTCAATCTACCCCATGATCGGGAAAAAGATTAAG-TG-CTTC
* *
20530934 AATCTGCCCCATGGTCGAGGTAAGAGATTGGATAATGTCTTCAATCT
64 AATCTGCCCCATGATCGGGGTAAGAGATTGG-T-ATGTCTTCAATCT
20530981 ACCCCATGAT
Statistics
Matches: 357, Mismatches: 49, Indels: 39
0.80 0.11 0.09
Matches are distributed among these distances:
155 2 0.01
156 28 0.08
157 121 0.34
158 58 0.16
159 57 0.16
160 79 0.22
161 1 0.00
164 11 0.03
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (155 bp):
GGGGTAAGAGATTGGATGAGGTCTTCAATCTACCCCATGATCGGGAAAAAGATTAAGTGCTTCAA
TCTGCCCCATGATCGGGGTAAGAGATTGGTATGTCTTCAATCTGCCTTTGATTAGGGTAAAAGAT
TGGATGCTTAATCTGCCCCATGATC
Found at i:20530767 original size:80 final size:81
Alignment explanation
Indices: 20530394--20531005 Score: 568
Period size: 80 Copynumber: 7.7 Consensus size: 81
20530384 CTTTGATTTA
* * * * *
20530394 GGGGTAAAAGATTGGATGATGTCTTCAATC--CGTCTCATGA-TCGGGATAAGAGATTGGATGGC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTAC-CCTCATGATTAGGG-TAAAAGATTGAAT-GC
*
20530456 TTCAAACTGCCCCATGATC
63 TTCAATCTGCCCCATGATC
* * * *
20530475 GGGGTAAGAGACTGG-TG-TGTCTTCAATCTGCCCT-TTGATTAGGGTAAAAGATTGGATGCTTC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTACCCTCATGATTAGGGTAAAAGATTGAATGCTTC
*
20530537 AATCTGCCCCATGATT
66 AATCTGCCCCATGATC
* * *
20530553 GGGGTAAGAGATTGGATGATGT-TTACAATCTACCC-CATGA-TCGAGAAAAAGATT-AAGTGCT
1 GGGGTAAGAGATTGGATGATGTCTT-CAATCTACCCTCATGATTAGGGTAAAAGATTGAA-TGCT
*
20530614 TCAATCTGACCCATGATC
64 TCAATCTGCCCCATGATC
* * * *
20530632 GGGGTAAGAGATTGG-T-ATGTCTTCAATTTGCTCT-TTGATTAGGGTAAAAGATTGAATGCTGT
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTACCCTCATGATTAGGGTAAAAGATTGAATGCT-T
20530694 -AATCTGCCCCATGATC
65 CAATCTGCCCCATGATC
* * *
20530710 GGGGTAAGAGATTGGATGAGGTCTTCAATTTACCCTC-TTATTAGGGTAAAAGATTGAATGCTTC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTACCCTCATGATTAGGGTAAAAGATTGAATGCTTC
* * *
20530774 AATCTGCACCATAATT
66 AATCTGCCCCATGATC
* * *
20530790 GGGGTAAGAGATT-G--G-TGTCTTTAATCTA-CCTCATGATTGGGGTAAGAGATTGGATGATGT
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTACCCTCATGATTAGGGTAAAAGATT-GA--ATG-
* * * *
20530850 CTTTAATCTGTCTCATGGTC
62 CTTCAATCTGCCCCATGATC
* * * * * *
20530870 GGGGTAAGAGATTGGATGAGGTCTTCAATCT-GCCTCATGA-TCGGGGAAGAGATTGGATGACTT
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTACCCTCATGATTAGGGTAAAAGATTGAATG-CTT
*
20530933 CAATCTGCCCCATGGTC
65 CAATCTGCCCCATGATC
* * ** *
20530950 GAGGTAAGAGATTGGATAATGTCTTCAATCTACCC-CATGATCGGGGTAAGAGATTG
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTACCCTCATGATTAGGGTAAAAGATTG
20531006 GATGATGTCT
Statistics
Matches: 441, Mismatches: 61, Indels: 58
0.79 0.11 0.10
Matches are distributed among these distances:
75 4 0.01
76 25 0.06
77 17 0.04
78 82 0.19
79 85 0.19
80 167 0.38
81 29 0.07
82 1 0.00
83 13 0.03
84 18 0.04
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (81 bp):
GGGGTAAGAGATTGGATGATGTCTTCAATCTACCCTCATGATTAGGGTAAAAGATTGAATGCTTC
AATCTGCCCCATGATC
Found at i:20531195 original size:49 final size:49
Alignment explanation
Indices: 20531144--20531454 Score: 241
Period size: 49 Copynumber: 6.4 Consensus size: 49
20531134 TTATCTTCAA
* * * * * *
20531144 GGTATAAGATTCGCCGTTGTGGCCTCAATCTTTCCCTTCACATCTCTAA
1 GGTATAAGATTCACCATTGCGACTTCAATCTTTCCCTTCACATCTCTAG
* * *
20531193 GGTATAAGGTTCACCATTGCGACTTCAACCTTT-CCTTCCATATCTCTAG
1 GGTATAAGATTCACCATTGCGACTTCAATCTTTCCCTT-CACATCTCTAG
* * * * * * * *
20531242 GGTATAAGGTTCGCCGTTGCGGCTTC-ATCCTTTCCCTCCACGTCTTTGG
1 GGTATAAGATTCACCATTGCGACTTCAAT-CTTTCCCTTCACATCTCTAG
* ** * *
20531291 GGTTTAAGATTCGTCATTGCGACTTCAATCTTTCCC-CCATATCTCTAG
1 GGTATAAGATTCACCATTGCGACTTCAATCTTTCCCTTCACATCTCTAG
* * * * * *
20531339 GGTATAAGATTCACCATTACGACTTCAATCATTCCCTTTATATTTCTAA
1 GGTATAAGATTCACCATTGCGACTTCAATCTTTCCCTTCACATCTCTAG
* * * * * * * *
20531388 GGTATAGGATTCATCGTTGTGGCTTCAATCTTTCCTTTTACATCTTTAG
1 GGTATAAGATTCACCATTGCGACTTCAATCTTTCCCTTCACATCTCTAG
* *
20531437 GGTATAGGATTCAACATT
1 GGTATAAGATTCACCATT
20531455 TCCTCGGTTC
Statistics
Matches: 207, Mismatches: 50, Indels: 10
0.78 0.19 0.04
Matches are distributed among these distances:
48 44 0.21
49 158 0.76
50 5 0.02
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.37
Consensus pattern (49 bp):
GGTATAAGATTCACCATTGCGACTTCAATCTTTCCCTTCACATCTCTAG
Found at i:20531399 original size:97 final size:98
Alignment explanation
Indices: 20531168--20531423 Score: 259
Period size: 97 Copynumber: 2.6 Consensus size: 98
20531158 CGTTGTGGCC
* * * *
20531168 TCAATCTTTCCCTTCACATCTCTAAGGTATAAGG-TTCACCATTGCGACTTCAACCTTTCCTTCC
1 TCAATCTTTCCCTTCACATTTCTAAGGTAT-AGGATTCATCATTGCGACTTCAATCTTTCCTCCC
* * * * *
20531232 ATATCTCTAGGGTATAAGGTTCGCCGTTGCGGCT
65 ATATCTCTAGGGTATAAGATTCACCATTACGACT
* * ** * * *
20531266 TC-ATCCTTTCCCTCCACGTCTT-TGGGGTTTAAGATTCGTCATTGCGACTTCAATCTTTCC-CC
1 TCAAT-CTTTCCCTTCACAT-TTCTAAGGTATAGGATTCATCATTGCGACTTCAATCTTTCCTCC
20531328 CATATCTCTAGGGTATAAGATTCACCATTACGACT
64 CATATCTCTAGGGTATAAGATTCACCATTACGACT
* * * * * *
20531363 TCAATCATTCCCTTTATATTTCTAAGGTATAGGATTCATCGTTGTGGCTTCAATCTTTCCT
1 TCAATCTTTCCCTTCACATTTCTAAGGTATAGGATTCATCATTGCGACTTCAATCTTTCCT
20531424 TTTACATCTT
Statistics
Matches: 123, Mismatches: 29, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
96 2 0.02
97 76 0.62
98 44 0.36
99 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.38
Consensus pattern (98 bp):
TCAATCTTTCCCTTCACATTTCTAAGGTATAGGATTCATCATTGCGACTTCAATCTTTCCTCCCA
TATCTCTAGGGTATAAGATTCACCATTACGACT
Found at i:20531434 original size:146 final size:147
Alignment explanation
Indices: 20531144--20531448 Score: 330
Period size: 146 Copynumber: 2.1 Consensus size: 147
20531134 TTATCTTCAA
* * * * * * *
20531144 GGTATAAGATTCGCCGTTGTGGCCTCAATCTTTCCCTTCACATCTCTAAGGTATAAGGTTCACCA
1 GGTATAAGATTCGTCATTGCGACTTCAATCTTTCCCTCCACATCTCTAAGGTATAAGATTCACCA
* * * * *
20531209 TTGCGACTTCAACCTTTCCTTCCATATCTCTAGGGTATAAGGTTCGCCGTTGCGGCTTCATCCTT
66 TTACGACTTCAACATTCCCTTCCATATCTCTAAGGTATAAGGTTCACCGTTGCGGCTTCATCCTT
* *
20531274 TCCCTCCACGTCTTTGG
131 TCCCTCCACATCTTTAG
* * *
20531291 GGTTTAAGATTCGTCATTGCGACTTCAATCTTTCCC-CCATATCTCTAGGGTATAAGATTCACCA
1 GGTATAAGATTCGTCATTGCGACTTCAATCTTTCCCTCCACATCTCTAAGGTATAAGATTCACCA
* * * *
20531355 TTACGACTTCAATCATTCCCTT-TATATTTCTAAGGTAT-AGGATTCATCGTTGTGGCTTCAAT-
66 TTACGACTTCAA-CATTCCCTTCCATATCTCTAAGGTATAAGG-TTCACCGTTGCGGCTTC-ATC
* **
20531417 CTTTCCTTTTACATCTTTAG
128 CTTTCCCTCCACATCTTTAG
*
20531437 GGTATAGGATTC
1 GGTATAAGATTC
20531449 AACATTTCCT
Statistics
Matches: 129, Mismatches: 26, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
145 3 0.02
146 87 0.67
147 39 0.30
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (147 bp):
GGTATAAGATTCGTCATTGCGACTTCAATCTTTCCCTCCACATCTCTAAGGTATAAGATTCACCA
TTACGACTTCAACATTCCCTTCCATATCTCTAAGGTATAAGGTTCACCGTTGCGGCTTCATCCTT
TCCCTCCACATCTTTAG
Found at i:20544256 original size:52 final size:52
Alignment explanation
Indices: 20544178--20544281 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
20544168 AAAGAAAAAG
*
20544178 AAGATGAAAGCTAAAGCAGCCACTGCATCGACTACTGCACAATGAGTTAGTT
1 AAGATGAAAGCTAAAGCAGCCACTGCATCGACTACTGCACAATAAGTTAGTT
20544230 AAGATGAAAGCTAAAGCAGCCACTGCATCGACTACTGCACAATAAGTTAGTT
1 AAGATGAAAGCTAAAGCAGCCACTGCATCGACTACTGCACAATAAGTTAGTT
20544282 TTACTTTTCA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (52 bp):
AAGATGAAAGCTAAAGCAGCCACTGCATCGACTACTGCACAATAAGTTAGTT
Found at i:20544951 original size:10 final size:11
Alignment explanation
Indices: 20544936--20544981 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
20544926 CACTTATAAA
20544936 AAAAAG-AAAG
1 AAAAAGAAAAG
20544946 AAAAAG-AAAG
1 AAAAAGAAAAG
*
20544956 AAGAAGAAAAG
1 AAAAAGAAAAG
20544967 AGAAAAGAAAAG
1 A-AAAAGAAAAG
20544979 AAA
1 AAA
20544982 TATATTACCG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 15 0.47
11 7 0.22
12 10 0.31
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:20550272 original size:10 final size:11
Alignment explanation
Indices: 20550242--20550287 Score: 69
Period size: 10 Copynumber: 4.3 Consensus size: 11
20550232 TGGCAATATA
20550242 TTTCTTTTCTT
1 TTTCTTTTCTT
20550253 TTCTCTTTTCTT
1 TT-TCTTTTCTT
20550265 TTTC-TTTCTT
1 TTTCTTTTCTT
20550275 TTTC-TTTCTT
1 TTTCTTTTCTT
20550285 TTT
1 TTT
20550288 GTGATTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
10 19 0.56
11 4 0.12
12 11 0.32
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:20571838 original size:23 final size:22
Alignment explanation
Indices: 20571812--20571855 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
20571802 AAAATATTTC
*
20571812 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
20571835 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
20571856 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:20572346 original size:159 final size:159
Alignment explanation
Indices: 20572057--20572368 Score: 615
Period size: 159 Copynumber: 2.0 Consensus size: 159
20572047 AGATTTACAT
20572057 TTGACCAAGTCTCAATCCTGAGTTGTTATGGCATTTAAATTGTTTAAAAATCAAGCAAAATTCAA
1 TTGACCAAGTCTCAATCCTGAGTTGTTATGGCATTTAAATTGTTTAAAAATCAAGCAAAATTCAA
20572122 CTCAAAATCCACTAATCATGGTCAACCACTCATTGAAGAAGCTTGAAGAGACTAAACCTCTCTAT
66 CTCAAAATCCACTAATCATGGTCAACCACTCATTGAAGAAGCTTGAAGAGACTAAACCTCTCTAT
20572187 TTTTAGCAAACTACTCTACTCTCCACTCA
131 TTTTAGCAAACTACTCTACTCTCCACTCA
20572216 TTGACCAAGTCTCAATCCTGAGTTGTTATGGCATTTAAATTGTTTAAAAATCAAGCAAAATTCAA
1 TTGACCAAGTCTCAATCCTGAGTTGTTATGGCATTTAAATTGTTTAAAAATCAAGCAAAATTCAA
20572281 CTCAAAATCCACTAATCATGGTCAACCACTCATTGAAGAAGCTTGAAGAGACTAAACCTCTCTAT
66 CTCAAAATCCACTAATCATGGTCAACCACTCATTGAAGAAGCTTGAAGAGACTAAACCTCTCTAT
*
20572346 TTTTAGCAAACTACTCTCCTCTC
131 TTTTAGCAAACTACTCTACTCTC
20572369 TTCACCTATA
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
159 152 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (159 bp):
TTGACCAAGTCTCAATCCTGAGTTGTTATGGCATTTAAATTGTTTAAAAATCAAGCAAAATTCAA
CTCAAAATCCACTAATCATGGTCAACCACTCATTGAAGAAGCTTGAAGAGACTAAACCTCTCTAT
TTTTAGCAAACTACTCTACTCTCCACTCA
Found at i:20574213 original size:28 final size:28
Alignment explanation
Indices: 20574044--20574220 Score: 97
Period size: 28 Copynumber: 6.3 Consensus size: 28
20574034 TTACGTCCGT
* * * *
20574044 CATAAAGGCTTCCTTCAATAGAGATGGC
1 CATAAAGGCTTCCTTTAACAGAGTTAGC
* * * * *
20574072 CACAAAGG-ATCCTTTTAAAAAAATTAGC
1 CATAAAGGCTTCC-TTTAACAGAGTTAGC
** * * * *
20574100 CACGAAGACTTCTTTTAACAGAATTAAC
1 CATAAAGGCTTCCTTTAACAGAGTTAGC
* * *
20574128 CATGAAGGCTTCCTTTAATAGAATTCA-C
1 CATAAAGGCTTCCTTTAACAGAGTT-AGC
* * * *
20574156 CACAAAGGTTTCCTTTAACATAGATAGC
1 CATAAAGGCTTCCTTTAACAGAGTTAGC
* *
20574184 CATAAAGGCTTCCTTTTACAGAGTTTGC
1 CATAAAGGCTTCCTTTAACAGAGTTAGC
*
20574212 CATAGAGGC
1 CATAAAGGC
20574221 AGTTCCCTTG
Statistics
Matches: 112, Mismatches: 33, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
27 4 0.04
28 105 0.94
29 3 0.03
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (28 bp):
CATAAAGGCTTCCTTTAACAGAGTTAGC
Found at i:20574383 original size:28 final size:28
Alignment explanation
Indices: 20574317--20574395 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
20574307 TTTAACGGAA
**
20574317 ACAACCACAAATACTCACTTTTACAAAG
1 ACAACCACAAAGGCTCACTTTTACAAAG
*
20574345 ACAACCACAAAGGCTCACTTTTACAGAG
1 ACAACCACAAAGGCTCACTTTTACAAAG
* * *
20574373 ATAGCCGCAAAGGCTCACTTTTA
1 ACAACCACAAAGGCTCACTTTTA
20574396 TGGAAATTGG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (28 bp):
ACAACCACAAAGGCTCACTTTTACAAAG
Found at i:20576726 original size:40 final size:41
Alignment explanation
Indices: 20576671--20576772 Score: 156
Period size: 40 Copynumber: 2.5 Consensus size: 41
20576661 AATAAACTTA
20576671 TGTATGCACTTCGGTGCCCCTGA-ATGCAGTTC-GATGCCCC
1 TGTATGCACTTCGGTGCCCCTGATATGCAGTTCAG-TGCCCC
* *
20576711 TGTATGCACTTCGGTGCCCGT-ATGTGCAGTTCAGTGCCCC
1 TGTATGCACTTCGGTGCCCCTGATATGCAGTTCAGTGCCCC
20576751 TGTATGCACTTCGGTGCCCCTG
1 TGTATGCACTTCGGTGCCCCTG
20576773 TTTAATTTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
39 1 0.02
40 54 0.96
41 1 0.02
ACGTcount: A:0.13, C:0.31, G:0.26, T:0.29
Consensus pattern (41 bp):
TGTATGCACTTCGGTGCCCCTGATATGCAGTTCAGTGCCCC
Found at i:20576773 original size:20 final size:20
Alignment explanation
Indices: 20576671--20576773 Score: 134
Period size: 20 Copynumber: 5.2 Consensus size: 20
20576661 AATAAACTTA
20576671 TGTATGCACTTCGGTGCCCC
1 TGTATGCACTTCGGTGCCCC
* * *
20576691 TGAATGCAGTTCGATGCCCC
1 TGTATGCACTTCGGTGCCCC
*
20576711 TGTATGCACTTCGGTGCCCG
1 TGTATGCACTTCGGTGCCCC
* * * *
20576731 TATGTGCAGTTCAGTGCCCC
1 TGTATGCACTTCGGTGCCCC
20576751 TGTATGCACTTCGGTGCCCC
1 TGTATGCACTTCGGTGCCCC
20576771 TGT
1 TGT
20576774 TTAATTTTAA
Statistics
Matches: 67, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.13, C:0.31, G:0.26, T:0.30
Consensus pattern (20 bp):
TGTATGCACTTCGGTGCCCC
Found at i:20579193 original size:25 final size:25
Alignment explanation
Indices: 20579165--20579214 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
20579155 ATGGTGATTG
*
20579165 TGGCAAGAAGCATTTTGGTTAATCT
1 TGGCAAGAAGCATTTTGGTGAATCT
20579190 TGGCAAGAAGCATTTTGGTGAATCT
1 TGGCAAGAAGCATTTTGGTGAATCT
20579215 AGATCAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (25 bp):
TGGCAAGAAGCATTTTGGTGAATCT
Found at i:20582663 original size:79 final size:79
Alignment explanation
Indices: 20582435--20582724 Score: 404
Period size: 79 Copynumber: 3.7 Consensus size: 79
20582425 CAGTTTAACT
*
20582435 AACTAGAGCTGGGCTCACATTTGCGGTTTATTCGCTAGGCACTAGGTGCCAGGATTTGACGGATA
1 AACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTAGGTGCCAGGATTTGACGGATA
20582500 TTGTTGGTTAATCC
66 TTGTTGGTTAATCC
** * * * * *
20582514 AACTAGAGCTGGGCTCATTTTTTGTGTTTTATCCGTTAGGCACTCGGTGCTAGGATTTGACGGAT
1 AACTAGAGCTGGGCTCA-CATTTGCGGTTTATCCGCTAGGCACTAGGTGCCAGGATTTGACGGAT
* *
20582579 TTTGTTGGTTAATCA
65 ATTGTTGGTTAATCC
* * *
20582594 AACTAGAGCTGGGCTCACATTTGCGGTTTATCCACTAGGCACTGGGTGCCAGGATTTGACGGATG
1 AACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTAGGTGCCAGGATTTGACGGATA
20582659 TTGTTGGTTAATCC
66 TTGTTGGTTAATCC
* *
20582673 AACTAGA-CTTGAGCTCAC-TTTAGCGGTTTATCCGCTAGGCACTAGGTTCCAG
1 AACTAGAGC-TGGGCTCACATTT-GCGGTTTATCCGCTAGGCACTAGGTGCCAG
20582725 AATCGTTGGT
Statistics
Matches: 184, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
78 4 0.02
79 111 0.60
80 69 0.38
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (79 bp):
AACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTAGGTGCCAGGATTTGACGGATA
TTGTTGGTTAATCC
Found at i:20587595 original size:19 final size:20
Alignment explanation
Indices: 20587518--20587609 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
20587508 CAATAAATTT
* *
20587518 CTGTATGCACTTCAGTGGCC
1 CTGTATGCACTTCGGTAGCC
* *
20587538 CTGTATGCACTTCGATAACC
1 CTGTATGCACTTCGGTAGCC
20587558 CTGTATGCACTTCGGT-GCC
1 CTGTATGCACTTCGGTAGCC
20587577 ACTGTATGCACTT-GGT-GCC
1 -CTGTATGCACTTCGGTAGCC
*
20587596 CTTGAATGCACTTC
1 C-TGTATGCACTTC
20587610 TATGCCCTTG
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
18 1 0.02
19 18 0.29
20 43 0.69
ACGTcount: A:0.17, C:0.29, G:0.22, T:0.32
Consensus pattern (20 bp):
CTGTATGCACTTCGGTAGCC
Found at i:20591652 original size:22 final size:21
Alignment explanation
Indices: 20591611--20591652 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
20591601 CTCTTTGGTT
20591611 ATACTAGAATTACATAAGTTA
1 ATACTAGAATTACATAAGTTA
20591632 ATACTATGAACTTAC-TAAGTT
1 ATACTA-GAA-TTACATAAGTT
20591653 TTGTGACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (21 bp):
ATACTAGAATTACATAAGTTA
Found at i:20596491 original size:28 final size:28
Alignment explanation
Indices: 20596460--20596521 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
20596450 TCCATTTGAC
20596460 AGAATTAGAAACGAAGACATT-CTTTAAT
1 AGAATTAGAAACGAAGAC-TTCCTTTAAT
**
20596488 AGAATTAGTCACGAAGACTTCCTTTAAT
1 AGAATTAGAAACGAAGACTTCCTTTAAT
*
20596516 AAAATT
1 AGAATT
20596522 CACCATAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 2 0.07
28 28 0.93
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (28 bp):
AGAATTAGAAACGAAGACTTCCTTTAAT
Found at i:20609642 original size:21 final size:21
Alignment explanation
Indices: 20609625--20609739 Score: 194
Period size: 21 Copynumber: 5.5 Consensus size: 21
20609615 AAGACTTGTT
20609625 TCGGTAGAAGAGTCACTTATA
1 TCGGTAGAAGAGTCACTTATA
20609646 TCGGTAGAAGAGTCACTTATA
1 TCGGTAGAAGAGTCACTTATA
20609667 TCGGTAGAAGAGTCACTTATA
1 TCGGTAGAAGAGTCACTTATA
20609688 TCGGTAGAAGAGTCACTTATA
1 TCGGTAGAAGAGTCACTTATA
** *
20609709 TCGGTAGAATTGTCACTTGTA
1 TCGGTAGAAGAGTCACTTATA
*
20609730 TCGATAGAAG
1 TCGGTAGAAG
20609740 CATGCACCAT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 89 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (21 bp):
TCGGTAGAAGAGTCACTTATA
Found at i:20611472 original size:28 final size:28
Alignment explanation
Indices: 20611440--20611495 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
20611430 TTAAAAGTGC
20611440 ACCATTCAAGTTTTATGTCCATTAATCA
1 ACCATTCAAGTTTTATGTCCATTAATCA
20611468 ACCATTCAAGTTTTATGTCCATTAATCA
1 ACCATTCAAGTTTTATGTCCATTAATCA
20611496 CAACCCTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.39
Consensus pattern (28 bp):
ACCATTCAAGTTTTATGTCCATTAATCA
Found at i:20617783 original size:238 final size:238
Alignment explanation
Indices: 20617360--20617824 Score: 725
Period size: 238 Copynumber: 2.0 Consensus size: 238
20617350 TGCCTCCAAT
* * *
20617360 TTACTTGTAACTTAACTAAGACGTATACACCAAACTTATCTAATTTACAACTTAAATTAGAGATT
1 TTACGTGTAACTTAACTAAGACGTATACACCAAACTTATCTAATTGAAAACTTAAATTAGAGATT
* *
20617425 TTTACTTCTAACAAGAACCCTAAAGGATACCTAAATAATTCTAGTAAAATACTTTCAATTCTTAA
66 TTTACTTCTAACAAGAACCCTAAAGGATACCTAAATAACTCTAGTAAAATACATTCAATTCTTAA
*
20617490 AATTAATTCTATTTTAAAATCTTAAAAAAACCTAATAAATTACTAATAAATTAAGAGAAATATTA
131 AATTAATTCTATTTTAAAATCTAAAAAAAACCTAATAAATTACTAATAAATTAAGAGAAATATTA
* * *
20617555 AAATTCATCTCCAACTTATTTGATTTTTTATCATTACTCTGAC
196 AAATTCATCTACAACTTATTCGATCTTTTATCATTACTCTGAC
* * * * *
20617598 TTACGTGTAACTTGACTAAGACGTGTTCACCAAAGTTATCTAATTGAAAACTTGAATTAGAGATT
1 TTACGTGTAACTTAACTAAGACGTATACACCAAACTTATCTAATTGAAAACTTAAATTAGAGATT
* *
20617663 TTTACTTCTAACGAGAATCCTAAAGGATACCTAAATAACTCTAGTAAAATACATTCAATTCTTAA
66 TTTACTTCTAACAAGAACCCTAAAGGATACCTAAATAACTCTAGTAAAATACATTCAATTCTTAA
* * * * *
20617728 AATTAGTTTTATTTTAGAATCCTAAAAAAAACCTAA-AAATTACTAATGAATTAAGAGGAATATT
131 AATTAATTCTATTTTAAAAT-CTAAAAAAAACCTAATAAATTACTAATAAATTAAGAGAAATATT
20617792 AAAATTCATCTACAACTTATTCGATCTTTTATC
195 AAAATTCATCTACAACTTATTCGATCTTTTATC
20617825 TTTATTATTA
Statistics
Matches: 205, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
238 191 0.93
239 14 0.07
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (238 bp):
TTACGTGTAACTTAACTAAGACGTATACACCAAACTTATCTAATTGAAAACTTAAATTAGAGATT
TTTACTTCTAACAAGAACCCTAAAGGATACCTAAATAACTCTAGTAAAATACATTCAATTCTTAA
AATTAATTCTATTTTAAAATCTAAAAAAAACCTAATAAATTACTAATAAATTAAGAGAAATATTA
AAATTCATCTACAACTTATTCGATCTTTTATCATTACTCTGAC
Found at i:20618278 original size:16 final size:16
Alignment explanation
Indices: 20618259--20618312 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
20618249 ATACATAGAC
20618259 ATGAAAATGAATAAAT
1 ATGAAAATGAATAAAT
*
20618275 ATGAAATAAGAATAAAT
1 ATGAAA-ATGAATAAAT
* *
20618292 A-AAAAATTATATAAAT
1 ATGAAAATGA-ATAAAT
20618308 ATGAA
1 ATGAA
20618313 TAAATTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 2 0.07
16 16 0.53
17 12 0.40
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (16 bp):
ATGAAAATGAATAAAT
Found at i:20618323 original size:26 final size:26
Alignment explanation
Indices: 20618273--20618331 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
20618263 AAATGAATAA
*
20618273 ATATGAAATAAGAATAAATAAAAAATT
1 ATAT-AAATAAGAATAAATAAAAAAAT
* **
20618300 ATATAAATATGAATAAATTTAAAAAT
1 ATATAAATAAGAATAAATAAAAAAAT
20618326 AT-TAAA
1 ATATAAA
20618332 ATAAAATGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 4 0.14
26 20 0.71
27 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (26 bp):
ATATAAATAAGAATAAATAAAAAAAT
Found at i:20618985 original size:151 final size:147
Alignment explanation
Indices: 20618830--20619373 Score: 697
Period size: 151 Copynumber: 3.7 Consensus size: 147
20618820 AAATTTCTTC
* * * * * * *
20618830 TTTTTTTAAATCAAAAGTTTTCTTTTGATTAAAACAAAATCACTACTTTGCTTTTAAAA-TCAAA
1 TTTTTTAAAATCTAAA-TTTTCTTTT-TTTTAAAGAAAATCACTACTTTAC-TTAAAAATTC-AA
*
20618894 ACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTGTTTCTTTAC
62 ACTTTTATTTCGAAATAGTT--AAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAC
20618959 AATCACT-AAAAACAGATTTTTA
125 AATCACTAAAAAACAGATTTTTA
* * * * *
20618981 TTTTTTAAAAATTTAAACTTTCTTTCTTTTTTAATGAAAATTACTACTTTACTAAAAAATTCAAA
1 TTTTTT-AAAATCTAAATTTTC-TT-TTTTTTAAAGAAAATCACTACTTTACTTAAAAATTCAAA
20619046 CTTTTATTTCGAAATAGTTAAAAAATCAAAACTTT-TTTAAAAATTTAAACTTTTTCTTTACAAT
63 CTTTTATTTCGAAATAGTTAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTACAAT
* *
20619110 CATTAAAAAATAGATTTTTA
128 CACTAAAAAACAGATTTTTA
* *
20619130 TTTTTAAAAATCTAAA----CTTTTTTTTAAAGAAAATCACTATTTTACTTAAAAATTCAAACTT
1 TTTTTTAAAATCTAAATTTTCTTTTTTTTAAAGAAAATCACTACTTTACTTAAAAATTCAAACTT
* * *
20619191 TTATTTTGAAATAGTTTAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATA
66 TTATTTCGAAATAG-TT-AAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTACAATC
20619256 ACTAAAAAACAGATTTTTA
129 ACTAAAAAACAGATTTTTA
* * * *
20619275 TTTTTTAAAATCTAAACTTTCTCTTTTTTTTAAATAAAATCACTAATTTACTTAAAAATTTAAAA
1 TTTTTTAAAATCTAAA-TTT-TCTTTTTTTTAAAGAAAATCACTACTTTACTTAAAAATTCAAAC
*
20619340 TTTTATTTCAAAATAGTTAAAAAATCAAAACTTT
64 TTTTATTTCGAAATAGTTAAAAAATCAAAACTTT
20619374 TTCTTTAAAA
Statistics
Matches: 346, Mismatches: 33, Indels: 30
0.85 0.08 0.07
Matches are distributed among these distances:
142 51 0.15
143 4 0.01
144 17 0.05
145 60 0.17
148 40 0.12
149 51 0.15
150 2 0.01
151 90 0.26
152 29 0.08
153 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (147 bp):
TTTTTTAAAATCTAAATTTTCTTTTTTTTAAAGAAAATCACTACTTTACTTAAAAATTCAAACTT
TTATTTCGAAATAGTTAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTACAATCAC
TAAAAAACAGATTTTTA
Found at i:20619089 original size:18 final size:18
Alignment explanation
Indices: 20619066--20619100 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20619056 GAAATAGTTA
20619066 AAAAATCAAAACTTTTTT
1 AAAAATCAAAACTTTTTT
**
20619084 AAAAATTTAAACTTTTT
1 AAAAATCAAAACTTTTT
20619101 CTTTACAATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAAATCAAAACTTTTTT
Found at i:20619116 original size:49 final size:49
Alignment explanation
Indices: 20618916--20619120 Score: 113
Period size: 49 Copynumber: 4.1 Consensus size: 49
20618906 AAATAGTTAA
*
20618916 AAAAAATCAAAACTTTGTTTAAAAATTTAAACTGTTTCTTTACAATCAC-T
1 AAAAAATCAAAACTTTATTTAAAAATTTAAACT-TTTCTTT-CAATCACTT
* ** ***
20618966 -AAAAA-CAGATTTTTATTTTTTAAAAATTTAAAC-TTTCTTTC--TTTTTT
1 AAAAAATCAAAACTTTA---TTTAAAAATTTAAACTTTTCTTTCAATCACTT
* ** * * * * *
20619013 AATGAAAATTACTACTTTACTAAAAAATTCAAACTTTTATTTCGAAAT-AGTT
1 AA--AAAATCAAAACTTTATTTAAAAATTTAAACTTTTCTTTC--AATCACTT
20619065 AAAAAATCAAAACTTT-TTTAAAAATTTAAACTTTTTCTTTACAATCA-TT
1 AAAAAATCAAAACTTTATTTAAAAATTTAAAC-TTTTCTTT-CAATCACTT
20619114 AAAAAAT
1 AAAAAAT
20619121 AGATTTTTAT
Statistics
Matches: 114, Mismatches: 25, Indels: 33
0.66 0.15 0.19
Matches are distributed among these distances:
46 1 0.01
47 1 0.01
48 20 0.18
49 43 0.38
50 23 0.20
51 21 0.18
52 4 0.04
53 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.42
Consensus pattern (49 bp):
AAAAAATCAAAACTTTATTTAAAAATTTAAACTTTTCTTTCAATCACTT
Found at i:20619490 original size:127 final size:129
Alignment explanation
Indices: 20619223--20619490 Score: 380
Period size: 127 Copynumber: 2.1 Consensus size: 129
20619213 AATCAAAACT
** * *
20619223 TTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTAAAATCT
1 TTGTTTAAAAATCAAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATAT
* * * *
20619288 AAACTTTCTCTTTTTTTTAAATAAAATCACTAATTTACTTAAAAATTTAAAATTTTATTTCAAAA
66 AAAATTTCTC-TTTTTTAAAAGAAAATCACTAATTTACTTAAAAATTCAAAATTTTATTTCAAAA
* * *
20619353 TAGTTAAAAAATCAAAACTTTTTCTTTAAAATAACTAAAAAA-ATATTTTTATTTTTAAAAATAT
1 TTGTTTAAAAATCAAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATAT
* *
20619417 AAAATTTCTC-TTTTTAAAAGAAAATCACTATTTTACTTAAAAA-TCAAAACTTTTATTTCGAAA
66 AAAATTTCTCTTTTTTAAAAGAAAATCACTAATTTACTTAAAAATTCAAAA-TTTTATTTCAAAA
20619480 TTGTTTAAAAA
1 TTGTTTAAAAA
20619491 AACCAAAAAC
Statistics
Matches: 122, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
126 5 0.04
127 51 0.42
129 28 0.23
130 38 0.31
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (129 bp):
TTGTTTAAAAATCAAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATAT
AAAATTTCTCTTTTTTAAAAGAAAATCACTAATTTACTTAAAAATTCAAAATTTTATTTCAAAA
Found at i:20620458 original size:42 final size:42
Alignment explanation
Indices: 20620380--20620967 Score: 722
Period size: 42 Copynumber: 14.0 Consensus size: 42
20620370 CAACAATGAA
* ** * *
20620380 AAAAATAAATGGACC-CCATGCCTAGGTCTCTGAATGCAATG
1 AAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATG
*
20620421 AAAAGTAAATGGACCTCCACACCTAGCCCTCTAAATGCAATG
1 AAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATG
* * *
20620463 AAAAGTAAATGGGCCTCCACATCTGGGCCTCTAAATGCAATG
1 AAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATG
* *
20620505 AAAAGTAAATGGGCCTTCACACCTAGGCCTCTAAATGCAATG
1 AAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATG
* * * *
20620547 AAAAGTAAATGGACCTCTACACCTGGGTCTCTAAGTGCAATG
1 AAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATG
* *
20620589 AAAAGTAAATGGACCTCTACACCTAAGCCTCTAAATGCAATG
1 AAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATG
* * ** *
20620631 AAAAGTAAATGGACCTCCACACTTGGGCCAATAAATGCAATA
1 AAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATG
*
20620673 AAAAATAAATGTG-CCTCCACACCTAGGCCTCTAAATGCAATG
1 AAAAGTAAATG-GACCTCCACACCTAGGCCTCTAAATGCAATG
* * * * *
20620715 AAAATTAAATGGACCTTCATACGTGGGCCTCTAAATGCAATG
1 AAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATG
20620757 AAAAGTAAAT-GAGCCTCCACACCTA-GCCTCTAAATGCAATG
1 AAAAGTAAATGGA-CCTCCACACCTAGGCCTCTAAATGCAATG
* * * * **
20620798 AAAAGTAAATGGGCCTCCACACTTTGGCCGCTAAATAAAATG
1 AAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATG
* *
20620840 AAAAGTAAAT-GAGCCTCCACACCT-GAACCTCTAAATGCGATG
1 AAAAGTAAATGGA-CCTCCACACCTAG-GCCTCTAAATGCAATG
* *
20620882 AAAAGTAAAT-GAGCTTCCACACCTTGGCCTCTAAATGCAATG
1 AAAAGTAAATGGA-CCTCCACACCTAGGCCTCTAAATGCAATG
* *
20620924 AAAAGTAAATGGACCTCCATACCTGGGCCTCTAAATGCAATG
1 AAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATG
20620966 AA
1 AA
20620968 TGCTTTCCTT
Statistics
Matches: 472, Mismatches: 65, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
41 55 0.12
42 413 0.88
43 4 0.01
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (42 bp):
AAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATG
Found at i:20622449 original size:29 final size:29
Alignment explanation
Indices: 20622419--20622578 Score: 113
Period size: 29 Copynumber: 5.5 Consensus size: 29
20622409 TTCGAGGTTA
*
20622419 AAAATGG-AATTTTGGAAAGTTTTGGGGT
1 AAAATGGTAATTTTGGAAAGTTTAGGGGT
**
20622447 AAAATGGTAATTTTTGGTGAAA---CCGGGGTT
1 AAAATGGTAA-TTTT-G-GAAAGTTTAGGGG-T
20622477 AAAAAT-G-AGATTTTGGAAAGTTTAGGGGT
1 -AAAATGGTA-ATTTTGGAAAGTTTAGGGGT
* *
20622506 AAAATGGTAATTTTGGGTGAAA--TCAGGGTT
1 AAAATGGTAATTTT--G-GAAAGTTTAGGGGT
*
20622536 AAAAAT-GAAATTTTGGAAAGTTTAGGGGT
1 -AAAATGGTAATTTTGGAAAGTTTAGGGGT
20622565 AAAATGGTAATTTT
1 AAAATGGTAATTTT
20622579 TAGAAGTTTC
Statistics
Matches: 103, Mismatches: 10, Indels: 37
0.69 0.07 0.25
Matches are distributed among these distances:
27 8 0.08
28 19 0.18
29 31 0.30
30 25 0.24
31 12 0.12
32 8 0.08
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAAAGTTTAGGGGT
Found at i:20622457 original size:59 final size:59
Alignment explanation
Indices: 20622389--20622578 Score: 246
Period size: 59 Copynumber: 3.2 Consensus size: 59
20622379 CTCGATGGCA
*
20622389 AAAAT-GTAATTTTGAG-AAAATTCGAGGTTAAAAATGGAATTTTGGAAAGTTTTGGGGT
1 AAAATGGTAATTTTGAGTAAAA-TCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* * *
20622447 AAAATGGTAATTTTTG-GTGAAACCGGGGTTAAAAAT-GAGATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAA-TTTTGAGTAAAATCGAGGTTAAAAATGGA-ATTTTGGAAAGTTTAGGGGT
* * *
20622506 AAAATGGTAATTTTGGGTGAAATC-AGGGTTAAAAATGAAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTGAGTAAAATCGA-GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
20622565 AAAATGGTAATTTT
1 AAAATGGTAATTTT
20622579 TAGAAGTTTC
Statistics
Matches: 118, Mismatches: 7, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
58 12 0.10
59 97 0.82
60 9 0.08
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTGAGTAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:20622585 original size:29 final size:28
Alignment explanation
Indices: 20622471--20622651 Score: 91
Period size: 29 Copynumber: 6.1 Consensus size: 28
20622461 TGGTGAAACC
*
20622471 GGGGTTAAAAATG-AGATTTTGGAAAGTTTA
1 GGGG-TAAAAATGTA-ATTTTTG-AAGTTTA
* *
20622501 GGGGT-AAAATGGTAATTTTGGGTGAA-ATCA
1 GGGGTAAAAAT-GTAATTTT---TGAAGTTTA
* * *
20622531 GGGTTAAAAATGAAATTTTGGAAAGTTTA
1 GGGGTAAAAATGTAATTTTTG-AAGTTTA
*
20622560 GGGGT-AAAATGGTAATTTTTAGAAGTTTC
1 GGGGTAAAAAT-GTAATTTTT-GAAGTTTA
* * *
20622589 GGGGTCAAAATATAATTTTTTGAAGTTTT
1 GGGGTAAAAATGTAA-TTTTTGAAGTTTA
* * *
20622618 GGGATGACAAATATAATTTTTGAATAGTTTA
1 GGGGT-AAAAATGTAATTTTTG-A-AGTTTA
20622649 GGG
1 GGG
20622652 ACCTATAAGC
Statistics
Matches: 118, Mismatches: 18, Indels: 29
0.72 0.11 0.18
Matches are distributed among these distances:
27 1 0.01
28 12 0.10
29 51 0.43
30 38 0.32
31 15 0.13
32 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (28 bp):
GGGGTAAAAATGTAATTTTTGAAGTTTA
Found at i:20622609 original size:30 final size:28
Alignment explanation
Indices: 20622553--20622651 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 28
20622543 AAATTTTGGA
* *
20622553 AAGTTTAGGGGTAAAATGGTAATTTTTAG
1 AAGTTTAGGGGTAAAAT-ATAATTTTTTG
*
20622582 AAGTTTCGGGGTCAAAATATAATTTTTTG
1 AAGTTTAGGGGT-AAAATATAATTTTTTG
* *
20622611 AAGTTTTGGGATGACAAATATAA-TTTTTG
1 AAGTTTAGGGGT-A-AAATATAATTTTTTG
20622640 AATAGTTTAGGG
1 -A-AGTTTAGGG
20622652 ACCTATAAGC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
29 37 0.63
30 14 0.24
31 8 0.14
ACGTcount: A:0.33, C:0.03, G:0.24, T:0.39
Consensus pattern (28 bp):
AAGTTTAGGGGTAAAATATAATTTTTTG
Found at i:20624569 original size:17 final size:17
Alignment explanation
Indices: 20624547--20624622 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 17
20624537 AATTTAATTT
*
20624547 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* **
20624564 TAAATTTAAATTTTATG
1 TAAATTTAAATTTAAAA
* *
20624581 CAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
*
20624598 TAAATCT-AATTTAAAA
1 TAAATTTAAATTTAAAA
20624614 CTAAATTTA
1 -TAAATTTA
20624623 TCTCATTGGA
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
16 8 0.18
17 36 0.82
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:20624620 original size:34 final size:35
Alignment explanation
Indices: 20624547--20624622 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 35
20624537 AATTTAATTT
* * * * **
20624547 TAAATTTAAATTTATAATAAATTTAAATTTTATGC
1 TAAATTTAAATTCAAAATAAATCTAAATTTAAAAC
20624582 -AAATTTAAATTCAAAATAAATCT-AATTTAAAAC
1 TAAATTTAAATTCAAAATAAATCTAAATTTAAAAC
20624615 TAAATTTA
1 TAAATTTA
20624623 TCTCATTGGA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
33 7 0.21
34 27 0.79
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (35 bp):
TAAATTTAAATTCAAAATAAATCTAAATTTAAAAC
Found at i:20625313 original size:200 final size:200
Alignment explanation
Indices: 20624952--20625993 Score: 1548
Period size: 200 Copynumber: 5.2 Consensus size: 200
20624942 TTCATTGACC
* * * * * *
20624952 TGGTCTTCTTCCCTGTGTCTCATCAGGAAGATGACCGCAATCAT-CTATTTTAATTCGCTTCTCT
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGC-CTC-TGTTGTTTTAATTCGCTTCTCT
* * * * * *
20625016 GGATCTCCTCAAGAAGACGAATTTGGTCCACTTCTTTGTGTCTTATTAGGAAGCTAACCTTTTTA
64 GGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTA
* * **
20625081 TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTTGAAGATTTGCTCGCGTTGAGC
129 TTGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCGTTGAGC
20625146 GTTGAGT
194 GTTGAGT
* *
20625153 TGGTATTCTTCTCTATATCTCATCAGGAAGATGACCGCCTCTGTTGTTTTAATTCGCTTCTCTGA
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCTGTTGTTTTAATTCGCTTCTCTGG
* *
20625218 ATCTCCTCAAGAAGACGAATTCGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
66 ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
* * *
20625283 GTTTTGACCTGCTTCTCAGTGTCTCATCAGGAAGCTTGGTACGAAGATTTGCTCGCTTTGAGCGT
131 GTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCGTTGAGCGT
20625348 TGAGT
196 TGAGT
* * *
20625353 TGGTATTCTTCTCTATATCTCATTAGGAAGATGACTGCCTCTGTTGTTTTAATTCGCTTCTCTGG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCTGTTGTTTTAATTCGCTTCTCTGG
* * *
20625418 ATCTCCTCAGGAAGACAAATTTGGTCCACTTCTCTATATCTCATCCGGAAGCTAACCATTTTATT
66 ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
* *** **
20625483 GTTTCGACCTGCTTCTCAATGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCATATTGAGCAC
131 GTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCGTTGAGCGT
20625548 TGAGT
196 TGAGT
* *
20625553 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGATCGTCTC-GCTTGTTTTAATTCGCTTCTCTG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCTG-TTGTTTTAATTCGCTTCTCTG
20625617 GATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTAT
65 GATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTAT
* * * *
20625682 TGCTTCGACCTGCTTCTCAGTGTCTCATCAAGAAGTTGGGTACGAAGATTTGCTCGCTTTGAGCG
130 TGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCGTTGAGCG
*
20625747 TTAAGT
195 TTGAGT
* * * * ** **
20625753 TGGTATTCTTCTCTGTATCTCATCAAGAAGATAACCACATCACTTGTTTTAATAAGCTTCTCTGG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCTGTTGTTTTAATTCGCTTCTCTGG
20625818 ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
66 ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
* * *
20625883 GTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTGGCTCGTGTTGAGCAT
131 GTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCGTTGAGCGT
20625948 TGAGT
196 TGAGT
* *
20625953 TGGTATTCTTCTCTGTGTCTCATTAGGAAGATGACCGCCTC
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTC
20625994 GCTGTCTTGT
Statistics
Matches: 760, Mismatches: 78, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
199 2 0.00
200 724 0.95
201 34 0.04
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (200 bp):
TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCTGTTGTTTTAATTCGCTTCTCTGG
ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
GTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCGTTGAGCGT
TGAGT
Found at i:20637849 original size:59 final size:59
Alignment explanation
Indices: 20637529--20637854 Score: 389
Period size: 59 Copynumber: 5.6 Consensus size: 59
20637519 TCTTGATGGC
* *
20637529 AAAAT-GTAATTTTTGGAAAATT-TAGGGTTAAAAATGGAATTTTGGAAAGTTTTGGGGT
1 AAAATGGTAATTTTTGGAAAATTCGA-GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* *
20637587 AAAATGGTAATTTTTGGCAAAA-TCGAGGTTAAAAAT-GAGATTTTGGAAAGTTCAGGGGC
1 AAAATGGTAATTTTTGG-AAAATTCGAGGTTAAAAATGGA-ATTTTGGAAAGTTTAGGGGT
* * *
20637646 AAAATGGTAATTTTTGGTAAAA-TCGAGGTT-AAAATGGGATTTTGGAATGTTTGGGGGT
1 AAAATGGTAATTTTTGG-AAAATTCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
** * *
20637704 AAAATGGTAA-TTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTGAAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGAAAATTCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* * * *
20637762 AAAATGGTAATTTTGGGTGAAATT-GAGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGG-AAAATTCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
** *
20637821 AAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAA
1 AAAATGGTAATTTTTGGAAAATTCGAGGTTAAAA
20637855 TATAATTTTC
Statistics
Matches: 228, Mismatches: 30, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
56 2 0.01
57 13 0.06
58 75 0.33
59 130 0.57
60 8 0.04
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAAATTCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:20638271 original size:28 final size:28
Alignment explanation
Indices: 20638238--20638291 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
20638228 GAAGTACCAA
20638238 ACGCGCAAATAACCCATTAATCCAAAAC
1 ACGCGCAAATAACCCATTAATCCAAAAC
20638266 ACGCGCAAATAACCCATTAATCCAAA
1 ACGCGCAAATAACCCATTAATCCAAA
20638292 TCTCTCTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.46, C:0.31, G:0.07, T:0.15
Consensus pattern (28 bp):
ACGCGCAAATAACCCATTAATCCAAAAC
Found at i:20639714 original size:28 final size:28
Alignment explanation
Indices: 20639657--20639715 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
20639647 TTTGGACATT
* * * *
20639657 AATTTTATCCAATTTAATTTTAAATTTA
1 AATTTTATCAAATTTAAATTCAAATATA
20639685 AATTTTATGCAAATTTAAATTCAAA-ATA
1 AATTTTAT-CAAATTTAAATTCAAATATA
20639713 AAT
1 AAT
20639716 CTAATCTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (28 bp):
AATTTTATCAAATTTAAATTCAAATATA
Found at i:20639890 original size:21 final size:21
Alignment explanation
Indices: 20639852--20639892 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20639842 TTTCTTTCTA
* *
20639852 TTTTTTTCTTTTTTTTTCTTC
1 TTTTTTTCTATTTGTTTCTTC
*
20639873 TTTTTTTGTATTTGTTTCTT
1 TTTTTTTCTATTTGTTTCTT
20639893 GATTTAAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.02, C:0.10, G:0.05, T:0.83
Consensus pattern (21 bp):
TTTTTTTCTATTTGTTTCTTC
Found at i:20649686 original size:7 final size:7
Alignment explanation
Indices: 20649674--20649743 Score: 53
Period size: 7 Copynumber: 10.9 Consensus size: 7
20649664 TTTCGAAAAA
20649674 GTCAACG
1 GTCAACG
*
20649681 GTCAACA
1 GTCAACG
20649688 GTC-A--
1 GTCAACG
20649692 GTCAACG
1 GTCAACG
*
20649699 GTCAATG
1 GTCAACG
20649706 GTCAACG
1 GTCAACG
20649713 GTC-A--
1 GTCAACG
20649717 GTCAACG
1 GTCAACG
*
20649724 GTCAACA
1 GTCAACG
*
20649731 GACAACG
1 GTCAACG
*
20649738 ATCAAC
1 GTCAAC
20649744 AAGCAACGAC
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
4 6 0.12
5 2 0.04
6 2 0.04
7 39 0.80
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:20649697 original size:11 final size:11
Alignment explanation
Indices: 20649681--20649727 Score: 58
Period size: 11 Copynumber: 4.0 Consensus size: 11
20649671 AAAGTCAACG
*
20649681 GTCAACAGTCA
1 GTCAACGGTCA
20649692 GTCAACGGTCAA
1 GTCAACGGTC-A
20649704 TGGTCAACGGTCA
1 --GTCAACGGTCA
20649717 GTCAACGGTCA
1 GTCAACGGTCA
20649728 ACAGACAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 20 0.62
12 1 0.03
13 1 0.03
14 10 0.31
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (11 bp):
GTCAACGGTCA
Found at i:20649737 original size:25 final size:25
Alignment explanation
Indices: 20649674--20649729 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
20649664 TTTCGAAAAA
*
20649674 GTCAACGGTCAACAGTCAGTCAACG
1 GTCAACGGTCAACGGTCAGTCAACG
*
20649699 GTCAATGGTCAACGGTCAGTCAACG
1 GTCAACGGTCAACGGTCAGTCAACG
20649724 GTCAAC
1 GTCAAC
20649730 AGACAACGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.18
Consensus pattern (25 bp):
GTCAACGGTCAACGGTCAGTCAACG
Found at i:20649771 original size:11 final size:11
Alignment explanation
Indices: 20649754--20649816 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
20649744 AAGCAACGAC
20649754 CGATCAACGGT
1 CGATCAACGGT
*
20649765 CGGTCAACGG-
1 CGATCAACGGT
* *
20649775 CCATTCAACAGT
1 CGA-TCAACGGT
* *
20649787 CAATCAATGGT
1 CGATCAACGGT
*
20649798 CGGTCAACGGT
1 CGATCAACGGT
20649809 CGATCAAC
1 CGATCAAC
20649817 AATTGGTCAA
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
10 1 0.03
11 36 0.92
12 2 0.05
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.19
Consensus pattern (11 bp):
CGATCAACGGT
Found at i:20657121 original size:152 final size:151
Alignment explanation
Indices: 20656912--20657615 Score: 929
Period size: 152 Copynumber: 4.7 Consensus size: 151
20656902 TTCTTCTTTC
* * * * * * *
20656912 TTTTTAAAATCAAAAGTTT-TCTTTTGATTAAAACAAAATCACAACTTTACTTCAAAATCAAAAC
1 TTTTTAAAATCTAAACTTTCTCTTTT-TTTTAAAGAAAATCACTACTTTACTTAAAAATCAAAAC
*
20656976 TTTTATTTCGAAATAGTT-AAAAAAATCAAAATTTTGTTTAAAAATTTAAACTTTTTCTTTAAAA
65 TTTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAA
*
20657040 TCACTAAAAAACAGATTTTTATT
130 TAACTAAAAAACAGATTTTTA-T
* * * * * * * * *
20657063 TTTTTTAAATCTAAACTTTCTTTTTTTTTTTAATGAAAATAACAACTTTGCTAAAAAATCTAAAT
1 TTTTTAAAATCTAAACTTTC-TCTTTTTTTTAAAGAAAATCACTACTTTACTTAAAAATCAAAAC
20657128 TTTTATTTCGAAATAGTT-AAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAA
65 TTTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAA
* * *
20657192 TCATTTAAAAACAGATTTTTAT
130 TAACTAAAAAACAGATTTTTAT
* * *
20657214 TTTTTAAAATCTAAATTTTCTCTTTTTTTTAAAGAAAATCACTATTTTACTTAAAAATCTAAACT
1 TTTTTAAAATCTAAACTTTCTCTTTTTTTTAAAGAAAATCACTACTTTACTTAAAAATCAAAACT
* *
20657279 TTTATTTCGAAACAGTTAAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTTTCTTAAAA
66 TTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCT-TTAAAA
20657344 TAACTAAAAAACAGATTTTTAT
130 TAACTAAAAAACAGATTTTTAT
* * * * *
20657366 TTTTTAAAATCTAAACTTTTTCTTTTTTTTAAAGCAAATTACTA-TTCTACTTAAAAATCCAAAT
1 TTTTTAAAATCTAAACTTTCTCTTTTTTTTAAAGAAAATCACTACTT-TACTTAAAAATCAAAAC
*
20657430 TTTTATTTCGAAATAATTAAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAA
65 TTTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAA
20657495 TAACT-AAAAACAGATTTTTAT
130 TAACTAAAAAACAGATTTTTAT
* * * *
20657516 TTTTAAAAATATAAACTTTCTC--TTTTTTAAAG-AAATTACTATTTTACTTAAAAATCAAAACT
1 TTTTTAAAATCTAAACTTTCTCTTTTTTTTAAAGAAAATCACTACTTTACTTAAAAATCAAAACT
* * *
20657578 TTTATTTTGAAATTGTTTTAAAAAAAAACCAAAACTTT
66 TTTATTTCGAAATAG--TT-AAAAAAAATCAAAACTTT
20657616 TCCCAAAATC
Statistics
Matches: 494, Mismatches: 50, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
147 37 0.07
148 12 0.02
149 2 0.00
150 105 0.21
151 87 0.18
152 246 0.50
153 5 0.01
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.43
Consensus pattern (151 bp):
TTTTTAAAATCTAAACTTTCTCTTTTTTTTAAAGAAAATCACTACTTTACTTAAAAATCAAAACT
TTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAAT
AACTAAAAAACAGATTTTTAT
Found at i:20657613 original size:302 final size:302
Alignment explanation
Indices: 20656946--20657615 Score: 985
Period size: 302 Copynumber: 2.2 Consensus size: 302
20656936 TGATTAAAAC
* * * *
20656946 AAAATCACAACTTTACTTCAAAATCAAAACTTTTATTTCGAAATAGTT-AAAAAAATCAAAATTT
1 AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
* *
20657010 TGTTTAAAAATTTAAACTTTTTCTTTAAAATCACTAAAAAACAGATTTTTATTTTTTTTAAATCT
66 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTTAAAATCT
* * * *
20657075 AAACTTTCTTTTTTTTTTTAATGAAAATAACAACTTTGCTAAAAAATCTAAATTTTTATTTCGAA
131 AAACTTTCTTCTTTTTTTTAAAGAAAATAACAACTTTACTAAAAAATCCAAATTTTTATTTCGAA
* **
20657140 ATAGTTAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATCATTTAAAAACA
196 ATAATTAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATCAACTAAAAACA
* * *
20657205 GATTTTTATTTTTTAAAATCTAAATTTTCTCTTTTTTTTAAAG
261 GATTTTTATTTTTAAAAATATAAACTTTCTC-TTTTTTTAAAG
* *
20657248 AAAATCACTATTTTACTTAAAAATCTAAACTTTTATTTCGAAACAGTTAAAAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
*
20657313 TGTTTAAAAATTTAAACTTTTTTTCTTAAAATAACTAAAAAACAGATTTTTA-TTTTTTAAAATC
66 TGTTTAAAAATTTAAACTTTTTCT-TTAAAATAACTAAAAAACAGATTTTTATTTTTTTAAAATC
* * * *
20657377 TAAACTTT-TTCTTTTTTTTAAAGCAAATTACTA-TTCTACTTAAAAATCCAAATTTTTATTTCG
130 TAAACTTTCTTCTTTTTTTTAAAGAAAATAACAACTT-TACTAAAAAATCCAAATTTTTATTTCG
20657440 AAATAATTAAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAAT-AACTAAAA
194 AAATAATT-AAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATCAACTAAAA
20657504 ACAGATTTTTATTTTTAAAAATATAAACTTTCTC-TTTTTTAAAG
258 ACAGATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTTAAAG
* * * *
20657548 -AAATTACTATTTTACTTAAAAATCAAAACTTTTATTTTGAAATTGTTTTAAAAAAAAACCAAAA
1 AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAG--TT-AAAAAAAATCAAAA
20657612 CTTT
63 CTTT
20657616 TCCCAAAATC
Statistics
Matches: 332, Mismatches: 29, Indels: 14
0.89 0.08 0.04
Matches are distributed among these distances:
299 40 0.12
300 10 0.03
301 4 0.01
302 148 0.45
303 104 0.31
304 26 0.08
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.43
Consensus pattern (302 bp):
AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTTAAAATCT
AAACTTTCTTCTTTTTTTTAAAGAAAATAACAACTTTACTAAAAAATCCAAATTTTTATTTCGAA
ATAATTAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATCAACTAAAAACA
GATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTTAAAG
Found at i:20669772 original size:14 final size:16
Alignment explanation
Indices: 20669742--20669773 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
20669732 AACTTTGGGG
20669742 ATATTAGGTTGCTTCA
1 ATATTAGGTTGCTTCA
20669758 ATATTA-GTT-CTTCA
1 ATATTAGGTTGCTTCA
20669772 AT
1 AT
20669774 TGTTGGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (16 bp):
ATATTAGGTTGCTTCA
Found at i:20672766 original size:32 final size:32
Alignment explanation
Indices: 20672730--20672794 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
20672720 ATCGAACCCT
*
20672730 TTAATCCGTAATAAAATTTATATAACTCACGA
1 TTAATCCGTAATAAAATTCATATAACTCACGA
**
20672762 TTAATCCGTAATAGCATTCATATAACTCACGA
1 TTAATCCGTAATAAAATTCATATAACTCACGA
20672794 T
1 T
20672795 GACACAACGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (32 bp):
TTAATCCGTAATAAAATTCATATAACTCACGA
Found at i:20676263 original size:14 final size:14
Alignment explanation
Indices: 20676230--20676269 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
20676220 AAAAATTATC
*
20676230 AAAAAAATTTATTT
1 AAAAATATTTATTT
20676244 --AAATATTTATTT
1 AAAAATATTTATTT
20676256 AAAAATATTTATTT
1 AAAAATATTTATTT
20676270 TAATTTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 11 0.48
14 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAAAATATTTATTT
Found at i:20680783 original size:14 final size:14
Alignment explanation
Indices: 20680764--20680794 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
20680754 GATACTTAAA
20680764 AAATTTAATTAATT
1 AAATTTAATTAATT
*
20680778 AAATTTATTTAATT
1 AAATTTAATTAATT
20680792 AAA
1 AAA
20680795 AAATCAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:20683201 original size:177 final size:177
Alignment explanation
Indices: 20682900--20683248 Score: 644
Period size: 177 Copynumber: 2.0 Consensus size: 177
20682890 CTTTGTCCTC
*
20682900 ATATATATATTATCTCAATTAAGCAAAATAAATACACATACATGGTAAATTTAATTATTTGGCTC
1 ATATATATATTATCTCAATTAAGCAAAATAAATACACATACATAGTAAATTTAATTATTTGGCTC
*
20682965 TCGATCTAGTTTGATGGTTTGGGTTACTTGGTTCAGAGTAATCGAGGGCCACAGGTCACAGGTTC
66 TCGATCTAGTTTGATGGTTTGGGTTACTTGGTTCAGAGTAACCGAGGGCCACAGGTCACAGGTTC
* *
20683030 GAGGGCCTTGAGAGAGATGAGAGAGGATGAAGCAAACTAAGATATAT
131 GAGGGCCGTGAGAGAGATGAGAGAGGATGAAGCAAACAAAGATATAT
20683077 ATATATATATTATCTCAATTAAGCAAAATAAATACACATACATAGTAAATTTAATTATTTGGCTC
1 ATATATATATTATCTCAATTAAGCAAAATAAATACACATACATAGTAAATTTAATTATTTGGCTC
*
20683142 TCGATCTAGTTTGATGGTTTGGGTTACTTGGTTCAGAGTAACCGAGGGCCACGGGTCACAGGTTC
66 TCGATCTAGTTTGATGGTTTGGGTTACTTGGTTCAGAGTAACCGAGGGCCACAGGTCACAGGTTC
*
20683207 GATGGCCGTGAGAGAGATGAGAGAGGATGAAGCAAACAAAGA
131 GAGGGCCGTGAGAGAGATGAGAGAGGATGAAGCAAACAAAGA
20683249 AAAACCAATT
Statistics
Matches: 166, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
177 166 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.29
Consensus pattern (177 bp):
ATATATATATTATCTCAATTAAGCAAAATAAATACACATACATAGTAAATTTAATTATTTGGCTC
TCGATCTAGTTTGATGGTTTGGGTTACTTGGTTCAGAGTAACCGAGGGCCACAGGTCACAGGTTC
GAGGGCCGTGAGAGAGATGAGAGAGGATGAAGCAAACAAAGATATAT
Found at i:20686485 original size:58 final size:60
Alignment explanation
Indices: 20686351--20686497 Score: 192
Period size: 58 Copynumber: 2.5 Consensus size: 60
20686341 ATAATATAAT
* **
20686351 ATTTGGTACTTGAACTTGATATTTTTTTTCTTAATTTGGTTCCTAAATCTTTTTTTTACCCA
1 ATTTGGTACTTGAACTTGATA--TTTTTTCCTAATTTGGTTCCTAAATCTTTTTTGGACCCA
* *
20686413 ATTTGATACTTGAACTTGACATTTTTTCCTAATTTGGTAT-CT-AAT-TTTTTTGGACCCA
1 ATTTGGTACTTGAACTTGATATTTTTTCCTAATTTGGT-TCCTAAATCTTTTTTGGACCCA
*
20686471 ATTTGGTACCTGAACTTGATATTTTTT
1 ATTTGGTACTTGAACTTGATATTTTTT
20686498 TTTCTAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
58 35 0.46
59 3 0.04
60 18 0.24
61 1 0.01
62 19 0.25
ACGTcount: A:0.22, C:0.14, G:0.12, T:0.52
Consensus pattern (60 bp):
ATTTGGTACTTGAACTTGATATTTTTTCCTAATTTGGTTCCTAAATCTTTTTTGGACCCA
Found at i:20686498 original size:60 final size:62
Alignment explanation
Indices: 20686351--20686508 Score: 209
Period size: 60 Copynumber: 2.6 Consensus size: 62
20686341 ATAATATAAT
* **
20686351 ATTTGGTACTTGAACTTGATATTTTTTTTCTTAATTTGGTTCCTAAATCTTTTTTTTACCCA
1 ATTTGGTACTTGAACTTGATATTTTTTTTCCTAATTTGGTTCCTAAATCTTTTTTGGACCCA
* *
20686413 ATTTGATACTTGAACTTGACA--TTTTTTCCTAATTTGGTAT-CT-AAT-TTTTTTGGACCCA
1 ATTTGGTACTTGAACTTGATATTTTTTTTCCTAATTTGGT-TCCTAAATCTTTTTTGGACCCA
* *
20686471 ATTTGGTACCTGAACTTGATATTTTTTTTTCTAATTTG
1 ATTTGGTACTTGAACTTGATATTTTTTTTCCTAATTTG
20686509 ATACATAAGC
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
58 29 0.35
59 3 0.04
60 32 0.38
61 1 0.01
62 19 0.23
ACGTcount: A:0.22, C:0.14, G:0.11, T:0.53
Consensus pattern (62 bp):
ATTTGGTACTTGAACTTGATATTTTTTTTCCTAATTTGGTTCCTAAATCTTTTTTGGACCCA
Found at i:20687243 original size:3 final size:3
Alignment explanation
Indices: 20687235--20687302 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
20687225 GGAAATGACT
20687235 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
20687283 TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TT
20687303 TTGCTTTTAC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:20687967 original size:24 final size:24
Alignment explanation
Indices: 20687939--20687995 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
20687929 GGGTTACAAA
20687939 AAGATGAAAGGTTAAAAGCTAAAG
1 AAGATGAAAGGTTAAAAGCTAAAG
20687963 AAGATGAAAGGTTAAAAGCTAAAG
1 AAGATGAAAGGTTAAAAGCTAAAG
20687987 AAGATGAAA
1 AAGATGAAA
20687996 AGTGAAAGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.56, C:0.04, G:0.25, T:0.16
Consensus pattern (24 bp):
AAGATGAAAGGTTAAAAGCTAAAG
Found at i:20690333 original size:16 final size:17
Alignment explanation
Indices: 20690305--20690338 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
20690295 TGATAATTCA
*
20690305 TTCCAATCTATTTCTTT
1 TTCCAATCTATTTATTT
20690322 TTCCAA-CTATTTATTT
1 TTCCAATCTATTTATTT
20690338 T
1 T
20690339 CTTCCCCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (17 bp):
TTCCAATCTATTTATTT
Found at i:20693582 original size:31 final size:32
Alignment explanation
Indices: 20693547--20693617 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 32
20693537 TTGCTCCTTT
* *
20693547 AACTTGTCC-AAAAGTACCTAGTTGGTA-TATG
1 AACTTGTCCAAAAAGTACCTAATTGATACT-TG
20693578 AACTTGTCCAAAAAGTACCTAATTGATACTTG
1 AACTTGTCCAAAAAGTACCTAATTGATACTTG
20693610 AACTTGTC
1 AACTTGTC
20693618 TCGAAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 9 0.25
32 26 0.72
33 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (32 bp):
AACTTGTCCAAAAAGTACCTAATTGATACTTG
Found at i:20698688 original size:24 final size:24
Alignment explanation
Indices: 20698661--20698715 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
20698651 CACAGACAAC
* *
20698661 TTAGCTCACATGAGCCCAAAATGG
1 TTAGCTCACAAGAGCCCAAAATGA
** *
20698685 TTAGCTCTTAAGAGCCCAGAATGA
1 TTAGCTCACAAGAGCCCAAAATGA
20698709 TTAGCTC
1 TTAGCTC
20698716 TTACGAGCCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (24 bp):
TTAGCTCACAAGAGCCCAAAATGA
Found at i:20698716 original size:24 final size:24
Alignment explanation
Indices: 20698672--20698730 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
20698662 TAGCTCACAT
* *
20698672 GAGCCCAAAATGGTTAGCTCTTAA
1 GAGCCCAGAATGATTAGCTCTTAA
*
20698696 GAGCCCAGAATGATTAGCTCTTAC
1 GAGCCCAGAATGATTAGCTCTTAA
20698720 GAGCCCAGAAT
1 GAGCCCAGAAT
20698731 CAGAATAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (24 bp):
GAGCCCAGAATGATTAGCTCTTAA
Found at i:20698770 original size:27 final size:27
Alignment explanation
Indices: 20698712--20698788 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
20698702 AGAATGATTA
* *
20698712 GCTCTTACGAGCCCAGAATCAGAATAAC
1 GCTCTTTCGAG-CCAAAATCAGAATAAC
*
20698740 GCTCTTTCGAGCCAAAATCAGAATAAT
1 GCTCTTTCGAGCCAAAATCAGAATAAC
*
20698767 GCTCTTTTGAGCCAAAATCAGA
1 GCTCTTTCGAGCCAAAATCAGA
20698789 TTACTCCTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 35 0.78
28 10 0.22
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (27 bp):
GCTCTTTCGAGCCAAAATCAGAATAAC
Found at i:20700118 original size:3 final size:3
Alignment explanation
Indices: 20700112--20700173 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
20700102 AATCATCATA
20700112 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20700160 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
20700174 AGATCCTCAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20704409 original size:28 final size:29
Alignment explanation
Indices: 20704368--20704460 Score: 116
Period size: 28 Copynumber: 3.0 Consensus size: 29
20704358 GATTATTCGA
20704368 TTTACTCCCTATTGACCCAAAGGTCATGC
1 TTTACTCCCTATTGACCCAAAGGTCATGC
20704397 -TTACTCCCTATTGACCCAAAGGTCATGATGTTC
1 TTTACTCCCTATTGACCCAAAGGTC---ATG--C
20704430 ATTTTACTCCCTATTGACCCAAAGGTCATGC
1 --TTTACTCCCTATTGACCCAAAGGTCATGC
20704461 CTGTTGCCAG
Statistics
Matches: 56, Mismatches: 0, Indels: 14
0.80 0.00 0.20
Matches are distributed among these distances:
28 24 0.43
31 4 0.07
33 4 0.07
36 24 0.43
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (29 bp):
TTTACTCCCTATTGACCCAAAGGTCATGC
Found at i:20708767 original size:49 final size:49
Alignment explanation
Indices: 20708705--20709248 Score: 303
Period size: 49 Copynumber: 10.9 Consensus size: 49
20708695 CATAGAGTTG
* * * *
20708705 AAGAGGGATAGATTGAAGCTGCAAC-AGTGGATCTAACACCTTAAAACTT
1 AAGAGGGAAAGATTGAAGCCGCAACGA-CGGATCTAACACCTTAAAACTA
* *
20708754 AAGAGGGAAAGATTGAAGCCGCAACGACAGATCTTACACCTTAAAACTA
1 AAGAGGGAAAGATTGAAGCCGCAACGACGGATCTAACACCTTAAAACTA
* * * *
20708803 AAGAGGGATAGGTAAGTTGAAGCCGTAACGACGGACCTAACACCTTAAAACTG
1 AAGAGGGA-AAG--A-TTGAAGCCGCAACGACGGATCTAACACCTTAAAACTA
* * ** * * * * * * *
20708856 AAGAGAGAAAGATTGAAGTCATAATGATGAATCTTATACCTTAAAATTT
1 AAGAGGGAAAGATTGAAGCCGCAACGACGGATCTAACACCTTAAAACTA
** * * * * * * * * *
20708905 AAGAGGGGTAGGTTGAAGTCGTAATGGCAGA-CTTAAAACCCTAAAA-TCG
1 AAGAGGGAAAGATTGAAGCCGCAACGACGGATC-TAACACCTTAAAACT-A
* * * ** *
20708954 AAGAGGAAAAGATTAAAGCCGCAATGATAGATCTTACACCTTAAAACTA
1 AAGAGGGAAAGATTGAAGCCGCAACGACGGATCTAACACCTTAAAACTA
* * * *
20709003 AAGAGGGATAGGTTGAAGTCGCAACGACGGA-CTTAACATCC-TAAAATCGA
1 AAGAGGGAAAGATTGAAGCCGCAACGACGGATC-TAACA-CCTTAAAA-CTA
* * * ** * *
20709053 AA-AGGGATAA-ATTAAAGCCACAACGGCAAATCTAACACCCTAAAACCA
1 AAGAGGGA-AAGATTGAAGCCGCAACGACGGATCTAACACCTTAAAACTA
* * * * *
20709101 AAAAAGGATAA-ATTGAAGTCGTAACGACGGATCTAACACCTTAAAACTG
1 AAGAGGGA-AAGATTGAAGCCGCAACGACGGATCTAACACCTTAAAACTA
* * *** * *
20709150 AAGAGGGAAACATTGAAGCCGCAACAATAAATCTTACACCCTAAAGAAACTA
1 AAGAGGGAAAGATTGAAGCCGCAACGACGGATCTAACA-CCT-TA-AAACTA
* ** *
20709202 AAGAGGTAACAGATTGAAGCCGCAACGACAAATCTTACACCTTAAAA
1 AAGAGGGAA-AGATTGAAGCCGCAACGACGGATCTAACACCTTAAAA
20709249 GAATTGAATA
Statistics
Matches: 378, Mismatches: 96, Indels: 41
0.73 0.19 0.08
Matches are distributed among these distances:
48 11 0.03
49 261 0.69
50 20 0.05
51 2 0.01
52 19 0.05
53 65 0.17
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (49 bp):
AAGAGGGAAAGATTGAAGCCGCAACGACGGATCTAACACCTTAAAACTA
Found at i:20709339 original size:45 final size:45
Alignment explanation
Indices: 20709280--20709844 Score: 545
Period size: 45 Copynumber: 12.8 Consensus size: 45
20709270 CCACATCTAG
*
20709280 TCTTTTACCCCTAATCTAGAGGGGTAGATTGAAGCCACCATCCAA
1 TCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCCACCATCCAA
* * * * * * *
20709325 TCTTTTACCCCTAATCTAAAAGGGAAAATTAAAGCCACCAACCGA
1 TCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCCACCATCCAA
* * * * * * **
20709370 TCTTTCA-CCCTAATCCA-AAGGGCAAATTAAAACCACCATCTGA
1 TCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCCACCATCCAA
* * * *
20709413 TCTTTTA-CCCTAATCTA-AAGGGCAAATTGAAGCAACCAACCAA
1 TCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCCACCATCCAA
* * ** * * * *
20709456 TCTTTCA-CCCTAATCCA-AAAGGAAAATTAAAGCCACCATCCGA
1 TCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCCACCATCCAA
*
20709499 TCTTTTA-CCCTAATCTAGA-GGGCAGATTGAAGCAACCATCCAA
1 TCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCCACCATCCAA
* * * * *
20709542 TCTTTTACCCCTAATCCAGAGGGGCAGATTAAAACCACCATCTAG
1 TCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCCACCATCCAA
* *
20709587 TCTTTTACCCCTAATCTAGAGGGGTAGATAGAAGCCACCATCCAA
1 TCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCCACCATCCAA
* * ** *
20709632 TCTTTTACCCTTAATCTAGAGAGGCAGATTGAAGCCATTATTCAA
1 TCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCCACCATCCAA
* * * * * *
20709677 TCTTTTACCCGTAATCCAGTGAGGCAGATTAAAGCCATCATCCAA
1 TCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCCACCATCCAA
* * * * * *
20709722 TCTCTTACCCTTAATCCAAAAGGGCAGATTGAAGCCATCATCCAA
1 TCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCCACCATCCAA
* * *
20709767 TCTCTTACCCCTAATCTCGAGGGGCAGATTGAAGCCATCATCCAA
1 TCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCCACCATCCAA
* *
20709812 TATCTTACCCCTAATCTAGA-GGGCAGATTGAAG
1 TCTTTTACCCCTAATCTAGAGGGGCAGATTGAAG
20709845 TTATAACACC
Statistics
Matches: 440, Mismatches: 77, Indels: 7
0.84 0.15 0.01
Matches are distributed among these distances:
43 132 0.30
44 34 0.08
45 274 0.62
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (45 bp):
TCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCCACCATCCAA
Found at i:20709492 original size:129 final size:133
Alignment explanation
Indices: 20709280--20709567 Score: 377
Period size: 129 Copynumber: 2.2 Consensus size: 133
20709270 CCACATCTAG
* * * * * * *
20709280 TCTTTTACCCCTAATCTAGAGGGGTAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCTAAA
1 TCTTTTACCCCTAATCTAGAAGGGCAAATTGAAGCAACCAACCAATCTTTCACCCCTAATCCAAA
*
20709345 AGGGAAAATTAAAGCCACCAACCGATCTTTCACCCTAATCCAAAGGGCAAATTAAAACCACCATC
66 AGGGAAAATTAAAGCCACCAACCGATCTTTCACCCTAATCCAAAGGGCAAATTAAAACAACCATC
**
20709410 TGA
131 CAA
20709413 TCTTTTA-CCCTAATCTA-AAGGGCAAATTGAAGCAACCAACCAATCTTTCA-CCCTAATCCAAA
1 TCTTTTACCCCTAATCTAGAAGGGCAAATTGAAGCAACCAACCAATCTTTCACCCCTAATCCAAA
* * * * * * *
20709475 A-GGAAAATTAAAGCCACCATCCGATCTTTTACCCTAATCTAGAGGGCAGATTGAAGCAACCATC
66 AGGGAAAATTAAAGCCACCAACCGATCTTTCACCCTAATCCAAAGGGCAAATTAAAACAACCATC
20709539 CAA
131 CAA
* *
20709542 TCTTTTACCCCTAATCCAGAGGGGCA
1 TCTTTTACCCCTAATCTAGAAGGGCA
20709568 GATTAAAACC
Statistics
Matches: 134, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
129 63 0.47
130 21 0.16
131 33 0.25
132 10 0.07
133 7 0.05
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (133 bp):
TCTTTTACCCCTAATCTAGAAGGGCAAATTGAAGCAACCAACCAATCTTTCACCCCTAATCCAAA
AGGGAAAATTAAAGCCACCAACCGATCTTTCACCCTAATCCAAAGGGCAAATTAAAACAACCATC
CAA
Found at i:20710335 original size:28 final size:26
Alignment explanation
Indices: 20710288--20710339 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
20710278 GATTCAGAGA
*
20710288 TTTTTTTATACAACACTCAAAGAATT
1 TTTTTTTAGACAACACTCAAAGAATT
*
20710314 TTTTTTTGAGACATACATTCAAAGAA
1 TTTTTTT-AGACA-ACACTCAAAGAA
20710340 AATTCAAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 4 0.18
28 11 0.50
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (26 bp):
TTTTTTTAGACAACACTCAAAGAATT
Found at i:20728025 original size:30 final size:30
Alignment explanation
Indices: 20727991--20728048 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
20727981 GATAAATTGG
20727991 TAAATTATGAT-AAATTAAGGG-CTTAATTCA
1 TAAATTAT-ATAAAATT-AGGGACTTAATTCA
*
20728021 TAAATTCTATAAAATTAGGGACTTAATT
1 TAAATTATATAAAATTAGGGACTTAATT
20728049 GAACTCTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (30 bp):
TAAATTATATAAAATTAGGGACTTAATTCA
Found at i:20729513 original size:12 final size:12
Alignment explanation
Indices: 20729496--20729537 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
20729486 TATATTAGCA
20729496 TGAGATTAAGAT
1 TGAGATTAAGAT
*
20729508 TGAGATTAAGGT
1 TGAGATTAAGAT
*
20729520 TGAGATTAAGAC
1 TGAGATTAAGAT
20729532 TGAGAT
1 TGAGAT
20729538 ATACATGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.38, C:0.02, G:0.29, T:0.31
Consensus pattern (12 bp):
TGAGATTAAGAT
Found at i:20729925 original size:3 final size:3
Alignment explanation
Indices: 20729917--20729950 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
20729907 TCCAATTATG
20729917 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20729951 TTGGGATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:20731264 original size:51 final size:51
Alignment explanation
Indices: 20731146--20731383 Score: 261
Period size: 51 Copynumber: 4.6 Consensus size: 51
20731136 TTTCATTTAA
* * * * *
20731146 TACTCACGATGAC-GTATAGTCATCGAACCCCTT-GTTCCGTATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGA-CCCTTAATT-CGTAAAGG-ATTCATT
* * * *
20731199 TACTCACGATGACACTGAGTCATCGGACCCTTAATTCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTAATTCGTAAAGGATTCATT
20731250 TACTCACGATGACACTTAGTCATCGGA-CCTATAA-TCTGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCT-TAATTC-GTAAAGGATTCATT
* * *
20731301 TACTCATGATGACACTTAGTCATCGGACCTTTAATAT-GTAAAAGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTAAT-TCGTAAAGGATTCATT
*
20731352 TACTCACGATGACACTTAGTCATCGAACCCTT
1 TACTCACGATGACACTTAGTCATCGGACCCTT
20731384 TCGTTTATAG
Statistics
Matches: 159, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
50 5 0.03
51 117 0.74
52 11 0.07
53 25 0.16
54 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCCTTAATTCGTAAAGGATTCATT
Found at i:20735207 original size:16 final size:16
Alignment explanation
Indices: 20735184--20735239 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
20735174 CGTTTGATCC
*
20735184 GCTGTAATAAAATAGA
1 GCTGTAATGAAATAGA
* *
20735200 GTTGTAATGTAATAGA
1 GCTGTAATGAAATAGA
20735216 GCTGTAATGAAATATGA
1 GCTGTAATGAAATA-GA
20735233 -CTGTAAT
1 GCTGTAAT
20735240 CAATAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
16 32 0.94
17 2 0.06
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.32
Consensus pattern (16 bp):
GCTGTAATGAAATAGA
Found at i:20735530 original size:59 final size:60
Alignment explanation
Indices: 20735397--20735567 Score: 208
Period size: 59 Copynumber: 2.9 Consensus size: 60
20735387 TTGTTATTAA
* * *
20735397 ATTTTAATAAGATTATTATTAAATATAATTTAATAAAA-AATAATAAATAATTTAATAAC
1 ATTTTAATAATATTATTATTAAATACAATTTAATAAAATAATAATATATAATTTAATAAC
* *
20735456 ATTATAA-CATAATTATTATTAAATACAATTTAATAAAATAAT-ATATA-AATTTAATAAC
1 ATTTTAATAAT-ATTATTATTAAATACAATTTAATAAAATAATAATATATAATTTAATAAC
* *
20735514 ATTTTTAATAATATTATTATTAAAATATGAA-TTAATAAAATCATAATATATAAT
1 A-TTTTAATAATATTATTATT-AAATA-CAATTTAATAAAATAATAATATATAAT
20735568 ATTAGAAAAA
Statistics
Matches: 95, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
58 13 0.14
59 50 0.53
60 22 0.23
61 7 0.07
62 3 0.03
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (60 bp):
ATTTTAATAATATTATTATTAAATACAATTTAATAAAATAATAATATATAATTTAATAAC
Found at i:20746249 original size:19 final size:19
Alignment explanation
Indices: 20746225--20746270 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
20746215 TTGGCTCGTT
20746225 GAGCAATACTAGCTCGTAA
1 GAGCAATACTAGCTCGTAA
20746244 GAGCAATACTAGCTCGTAA
1 GAGCAATACTAGCTCGTAA
20746263 GAGCAATA
1 GAGCAATA
20746271 TTGGATCGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.20
Consensus pattern (19 bp):
GAGCAATACTAGCTCGTAA
Found at i:20777112 original size:22 final size:22
Alignment explanation
Indices: 20777080--20777123 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
20777070 TGAATGCAAG
*
20777080 AAATGATATAAATTTCATGATTT
1 AAATGATATAAA-TTAATGATTT
20777103 AAATG-TATAAATTAATGATTT
1 AAATGATATAAATTAATGATTT
20777124 GTTGTTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 6 0.30
23 5 0.25
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (22 bp):
AAATGATATAAATTAATGATTT
Found at i:20777350 original size:18 final size:18
Alignment explanation
Indices: 20777327--20777389 Score: 81
Period size: 18 Copynumber: 3.4 Consensus size: 18
20777317 TAGCTCGTAA
20777327 GAGTAATACTGGCTCGTT
1 GAGTAATACTGGCTCGTT
* *
20777345 GAGTAATACTGACTCATT
1 GAGTAATACTGGCTCGTT
* *
20777363 GAGCAATACTGGCTCGTAA
1 GAGTAATACTGGCTCGT-T
20777382 GAGTAATA
1 GAGTAATA
20777390 TTAGATCACA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
18 30 0.81
19 7 0.19
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (18 bp):
GAGTAATACTGGCTCGTT
Found at i:20783061 original size:40 final size:40
Alignment explanation
Indices: 20783030--20783128 Score: 171
Period size: 40 Copynumber: 2.5 Consensus size: 40
20783020 TTGACCACAT
* *
20783030 TACTTGCAGTTTATCTGCAATATTGACAGCTTGTTTGCAC
1 TACTGGCAGTTTATCTGCAATATTGACAGCTTGTTTACAC
*
20783070 TACTGGCATTTTATCTGCAATATTGACAGCTTGTTTACAC
1 TACTGGCAGTTTATCTGCAATATTGACAGCTTGTTTACAC
20783110 TACTGGCAGTTTATCTGCA
1 TACTGGCAGTTTATCTGCA
20783129 TTCCTGGTGG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.39
Consensus pattern (40 bp):
TACTGGCAGTTTATCTGCAATATTGACAGCTTGTTTACAC
Done.