Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006332.1 Corchorus capsularis cultivar CVL-1 contig06353, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 98684
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:10835 original size:16 final size:16
Alignment explanation
Indices: 10814--10854 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
10804 ACTAGTAATG
*
10814 AATGAATGAAAATGAA
1 AATGAATGAAAACGAA
10830 AATGAAT-AAAACGAA
1 AATGAATGAAAACGAA
10845 AA--AATGAAAA
1 AATGAATGAAAA
10855 AAATGTATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 3 0.13
14 4 0.17
15 9 0.39
16 7 0.30
ACGTcount: A:0.68, C:0.02, G:0.15, T:0.15
Consensus pattern (16 bp):
AATGAATGAAAACGAA
Found at i:17410 original size:17 final size:19
Alignment explanation
Indices: 17378--17415 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
17368 TGCAAAATGC
*
17378 AAAGCGAAAGAAC-AAAGA
1 AAAGCGAAACAACAAAAGA
17396 AAAGC-AAACAACAAAAGA
1 AAAGCGAAACAACAAAAGA
17414 AA
1 AA
17416 TTAGTTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.71, C:0.13, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAGCGAAACAACAAAAGA
Found at i:18669 original size:27 final size:27
Alignment explanation
Indices: 18636--18724 Score: 83
Period size: 27 Copynumber: 3.2 Consensus size: 27
18626 TTTCTTACTC
*
18636 TTTTTACTGATTACAATTTTTTTCTTT
1 TTTTTACTGATTACCATTTTTTTCTTT
* *
18663 TTTTTACTTATTACCCCTTTCTTTTC-TT
1 TTTTTACTGATTA-CCATTT-TTTTCTTT
*
18691 CTTTTACTGGA-TACCATTTTTTTACTCTT
1 TTTTTACT-GATTACCATTTTTTT-CT-TT
18720 TTTTT
1 TTTTT
18725 TCTTTACTGA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
26 4 0.08
27 18 0.37
28 15 0.31
29 12 0.24
ACGTcount: A:0.15, C:0.18, G:0.03, T:0.64
Consensus pattern (27 bp):
TTTTTACTGATTACCATTTTTTTCTTT
Found at i:18750 original size:32 final size:34
Alignment explanation
Indices: 18684--18753 Score: 99
Period size: 32 Copynumber: 2.1 Consensus size: 34
18674 TACCCCTTTC
*
18684 TTTTCTTCTTTTACTGGATACCATTTTTTTACTCT
1 TTTTCTTCTTTTACTGAATACCA-TTTTTTACTCT
*
18719 TTTTTTTC-TTTACTGAATACCA-TTTTTACTCT
1 TTTTCTTCTTTTACTGAATACCATTTTTTACTCT
18751 TTT
1 TTT
18754 CTACCGATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 13 0.39
34 13 0.39
35 7 0.21
ACGTcount: A:0.16, C:0.19, G:0.04, T:0.61
Consensus pattern (34 bp):
TTTTCTTCTTTTACTGAATACCATTTTTTACTCT
Found at i:18983 original size:32 final size:33
Alignment explanation
Indices: 18915--18987 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
18905 TTCTTAATTA
* * *
18915 TTAATTTACTGATTAGTCCTTTCTACTTCCTTTC
1 TTAA-TTACTGATTACTCATTTCTACTTCCTCTC
*
18949 TTAATTACTGATTACTCATTT-TACTTTCTCTC
1 TTAATTACTGATTACTCATTTCTACTTCCTCTC
18981 TTAATTA
1 TTAATTA
18988 TCAATTTACT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 16 0.46
33 15 0.43
34 4 0.11
ACGTcount: A:0.22, C:0.21, G:0.04, T:0.53
Consensus pattern (33 bp):
TTAATTACTGATTACTCATTTCTACTTCCTCTC
Found at i:18997 original size:40 final size:40
Alignment explanation
Indices: 18953--19107 Score: 152
Period size: 40 Copynumber: 3.9 Consensus size: 40
18943 CCTTTCTTAA
* *
18953 TTACTGATTACTCATTTTACTTTCTCTCTTAATTATCAAT
1 TTACTGATTAATCATTTTACTTCCTCTCTTAATTATCAAT
* * *** *
18993 TTACTAATTAATCCTTTTACTTTGACTCTTAATTA-CTGAT
1 TTACTGATTAATCATTTTACTTCCTCTCTTAATTATC-AAT
* * * *
19033 TTACTTATTACT-ACTTTTACTTCCTCTATTGATTATCAAT
1 TTACTGATTAATCA-TTTTACTTCCTCTCTTAATTATCAAT
* *
19073 TTACTGATTAATCTTTTTACTTCCTTTCTTAATTA
1 TTACTGATTAATCATTTTACTTCCTCTCTTAATTA
19108 CTGATTACTA
Statistics
Matches: 90, Mismatches: 21, Indels: 8
0.76 0.18 0.07
Matches are distributed among these distances:
39 1 0.01
40 88 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (40 bp):
TTACTGATTAATCATTTTACTTCCTCTCTTAATTATCAAT
Found at i:19043 original size:80 final size:80
Alignment explanation
Indices: 18953--19113 Score: 216
Period size: 80 Copynumber: 2.0 Consensus size: 80
18943 CCTTTCTTAA
* * **
18953 TTACTGATTACT-CATTTTACTTTCTCTCTTAATTATCAATTTACTAATTAATCCTTTTACTTTG
1 TTACTGATTACTAC-TTTTACTTCCTCTATTAATTATCAATTTACTAATTAATCCTTTTACTTCC
19017 ACTCTTAATTACTGAT
65 ACTCTTAATTACTGAT
* * * * *
19033 TTACTTATTACTACTTTTACTTCCTCTATTGATTATCAATTTACTGATTAATCTTTTTACTTCCT
1 TTACTGATTACTACTTTTACTTCCTCTATTAATTATCAATTTACTAATTAATCCTTTTACTTCCA
*
19098 TTCTTAATTACTGAT
66 CTCTTAATTACTGAT
19113 T
1 T
19114 ACTACCTTTA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
80 69 0.99
81 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.53
Consensus pattern (80 bp):
TTACTGATTACTACTTTTACTTCCTCTATTAATTATCAATTTACTAATTAATCCTTTTACTTCCA
CTCTTAATTACTGAT
Found at i:19142 original size:17 final size:16
Alignment explanation
Indices: 19120--19175 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
19110 GATTACTACC
19120 TTTACTTTCTTAATCCT
1 TTTAC-TTCTTAATCCT
*
19137 TTTAC-TCTT-ATTCT
1 TTTACTTCTTAATCCT
*
19151 CATTACTTCATTAATCCT
1 -TTTACTTC-TTAATCCT
19169 TTTACTT
1 TTTACTT
19176 TACTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 4 0.13
15 8 0.26
16 2 0.06
17 13 0.42
18 4 0.13
ACGTcount: A:0.20, C:0.23, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTACTTCTTAATCCT
Found at i:24090 original size:12 final size:12
Alignment explanation
Indices: 24073--24098 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
24063 AGAAGTGTCA
24073 GGATGCTTGATG
1 GGATGCTTGATG
24085 GGATGCTTGATG
1 GGATGCTTGATG
24097 GG
1 GG
24099 TTCTTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.46, T:0.31
Consensus pattern (12 bp):
GGATGCTTGATG
Found at i:26112 original size:9 final size:9
Alignment explanation
Indices: 26081--26121 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
26071 TTGTATGAAA
*
26081 AAAAAAAGT
1 AAAAAAATT
*
26090 AAATAAATT
1 AAAAAAATT
*
26099 GAAAAAATT
1 AAAAAAATT
26108 AAAAAAATT
1 AAAAAAATT
26117 AAAAA
1 AAAAA
26122 GAAAAGTAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (9 bp):
AAAAAAATT
Found at i:26979 original size:2 final size:2
Alignment explanation
Indices: 26972--26997 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26962 TGATAGTAAG
26972 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
26998 TAGAAATCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30039 original size:86 final size:86
Alignment explanation
Indices: 29877--30041 Score: 298
Period size: 86 Copynumber: 1.9 Consensus size: 86
29867 TCCCTAAGGG
*
29877 ACACATGTCACCCTTCAAGACCCGCTTGTATAGTCTGCTAAACTTGACTAACGGTGTATTGTATA
1 ACACATGTCACCCTTCAAGACCCGCTTGTATAGTCTGCTAAACTTCACTAACGGTGTATTGTATA
29942 ATTTGCCATATATATATATAT
66 ATTTGCCATATATATATATAT
*
29963 ACACATGTCACCCTTCAAGACCCGCTTGTGTAGTCTGCTAAACTTCACTAA-GG-GTATTGTATA
1 ACACATGTCACCCTTCAAGACCCGCTTGTATAGTCTGCTAAACTTCACTAACGGTGTATTGTATA
30026 ATTTGCCATATATATA
66 ATTTGCCATATATATA
30042 AGATAAAAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
84 26 0.34
85 2 0.03
86 49 0.64
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.34
Consensus pattern (86 bp):
ACACATGTCACCCTTCAAGACCCGCTTGTATAGTCTGCTAAACTTCACTAACGGTGTATTGTATA
ATTTGCCATATATATATATAT
Found at i:43941 original size:3 final size:3
Alignment explanation
Indices: 43931--44002 Score: 85
Period size: 3 Copynumber: 23.0 Consensus size: 3
43921 ACTACTACAT
43931 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
43977 CTACA TTAA TAA TACA TTAA TAA TAA
1 -TA-A -TAA TAA TA-A -TAA TAA TAA
44003 ACTGGTTTCT
Statistics
Matches: 62, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
2 4 0.06
3 49 0.79
4 4 0.06
5 5 0.08
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:57132 original size:32 final size:32
Alignment explanation
Indices: 57092--57196 Score: 120
Period size: 32 Copynumber: 3.2 Consensus size: 32
57082 AGTAAATTGA
* * **
57092 TAATTAAGAGAGAAAGTAAAATTAGTAATCAG
1 TAATTAAGAAAGGAAGTAAAAGGAGTAATCAG
* *
57124 TAATTAAGAAAGGAAGTAAAAGGATTAATCGG
1 TAATTAAGAAAGGAAGTAAAAGGAGTAATCAG
* *
57156 TAATTAAGAAAGGAAGTAAAAAGGACTAATAAG
1 TAATTAAGAAAGGAAGT-AAAAGGAGTAATCAG
57189 TAAATTAA
1 T-AATTAA
57197 TAATTAAGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 43 0.69
33 13 0.21
34 6 0.10
ACGTcount: A:0.54, C:0.03, G:0.20, T:0.23
Consensus pattern (32 bp):
TAATTAAGAAAGGAAGTAAAAGGAGTAATCAG
Found at i:57324 original size:32 final size:32
Alignment explanation
Indices: 57274--57446 Score: 154
Period size: 32 Copynumber: 5.2 Consensus size: 32
57264 TAGCTAAAAA
*
57274 GAGTAGAAGTAAAAGAAGTAATCAGTAGAAAG
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGAAAG
* * * *
57306 GAGTAAAAGTGAATGAAGTAATCAGAAAATTGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAG-----TAG-AA--AG
57346 GAGTAAAAGTAAAAGAAGTAATCAGTAGAATA-
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGAA-AG
* * *
57378 GAGTAAAAGTGAAAGAAATAATCAGTAAGAATG
1 GAGTAAAAGTAAAAGAAGTAATCAGT-AGAAAG
*
57411 GAGTAAAAGTAAAAGAAGTAA-AAGTA-AAAG
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGAAAG
57441 GAGTAA
1 GAGTAA
57447 TTAGTAGAAG
Statistics
Matches: 116, Mismatches: 15, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
30 9 0.08
31 1 0.01
32 49 0.42
33 25 0.22
34 2 0.02
35 2 0.02
37 2 0.02
38 2 0.02
40 24 0.21
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.18
Consensus pattern (32 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAGAAAG
Found at i:57337 original size:112 final size:110
Alignment explanation
Indices: 57212--57522 Score: 316
Period size: 112 Copynumber: 2.8 Consensus size: 110
57202 AAGAAGGGAT
* * * *
57212 TAATCAGTAAATTGGTAATTGAGAGTCAAAGTAAGAGAAGTAATTAGAAAAATAGCTAAAAAGAG
1 TAATCAGAAAATTGGTAATTGAGAGTAAAAGTAAAAGAAGTAATCAG--AAATAGCTAAAAAGAG
* *
57277 TAGAAGTAAAAGAAGTAATCAGTAGAAAGGAGTAAAAGTGAATGAAG
64 TAGAAGTAAAAGAAGTAATCAGTAGAAAGGAGTAAAAGTAAAAGAAG
* *
57324 TAATCAGAAAATTGGTAATTAAGAGTAAAAGTAAAAGAAGTAATCAG---TAG---AATAGAGTA
1 TAATCAGAAAATTGGTAATTGAGAGTAAAAGTAAAAGAAGTAATCAGAAATAGCTAAAAAGAGTA
* * * *
57383 AAAGTGAAAGAAATAATCAGTAAGAATGGAGTAAAAGTAAAAGAAG
66 GAAGTAAAAGAAGTAATCAGT-AGAAAGGAGTAAAAGTAAAAGAAG
* *
57429 TAA-AAGTAAAA-GGAGTAATTAGTAGAAGGGAGTAAAAGTAAAAGAAGTAATCAGTAAA-AGCT
1 TAATCAG-AAAATTG-GTAA-T--T-G-A--GAGTAAAAGTAAAAGAAGTAATCAG-AAATAGCT
57491 AAAAAGAGTAGAAGTAAAAGAAGTAATCAGTA
56 AAAAAGAGTAGAAGTAAAAGAAGTAATCAGTA
57523 AAAACTAAAG
Statistics
Matches: 163, Mismatches: 19, Indels: 29
0.77 0.09 0.14
Matches are distributed among these distances:
104 29 0.18
105 32 0.20
106 1 0.01
107 3 0.02
108 1 0.01
110 1 0.01
112 67 0.41
115 2 0.01
117 1 0.01
118 26 0.16
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.20
Consensus pattern (110 bp):
TAATCAGAAAATTGGTAATTGAGAGTAAAAGTAAAAGAAGTAATCAGAAATAGCTAAAAAGAGTA
GAAGTAAAAGAAGTAATCAGTAGAAAGGAGTAAAAGTAAAAGAAG
Found at i:57465 original size:47 final size:48
Alignment explanation
Indices: 57379--57488 Score: 150
Period size: 48 Copynumber: 2.3 Consensus size: 48
57369 AGTAGAATAG
* *
57379 AGTAAAAGTGAAAGAAATAATCAGTAAGAATGGAGTAAAAGTAAAAGA
1 AGTAAAAGTAAAAGAAATAATCAGTAAGAAGGGAGTAAAAGTAAAAGA
* * *
57427 AGTAAAAGTAAAAGGAGTAATTAGT-AGAAGGGAGTAAAAGTAAAAGA
1 AGTAAAAGTAAAAGAAATAATCAGTAAGAAGGGAGTAAAAGTAAAAGA
*
57474 AGTAATCAGTAAAAG
1 AGTAA-AAGTAAAAG
57489 CTAAAAAGAG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
47 26 0.47
48 29 0.53
ACGTcount: A:0.56, C:0.02, G:0.25, T:0.17
Consensus pattern (48 bp):
AGTAAAAGTAAAAGAAATAATCAGTAAGAAGGGAGTAAAAGTAAAAGA
Found at i:57485 original size:22 final size:21
Alignment explanation
Indices: 57459--57642 Score: 79
Period size: 22 Copynumber: 9.4 Consensus size: 21
57449 AGTAGAAGGG
57459 AGTAAAAGTAAAAGAAGTAATC
1 AGTAAAAGTAAAAGAAGTAA-C
57481 AGTAAAAGCT-AAA-AAG----
1 AGTAAAAG-TAAAAGAAGTAAC
*
57497 AGTAGAAGTAAAAGAAGTAATC
1 AGTAAAAGTAAAAGAAGTAA-C
* *
57519 AGTAAAAACT-AAAGAGAGTAAA
1 AGT-AAAAGTAAAAGA-AGTAAC
57541 AGTAAAAGTAAAAG-AG----
1 AGTAAAAGTAAAAGAAGTAAC
*
57557 -G-AAGAGTAAAAGAAGTAATC
1 AGTAAAAGTAAAAGAAGTAA-C
57577 AGTAAAAGTAAAAG-AGT---
1 AGTAAAAGTAAAAGAAGTAAC
*
57594 A--AAAA-TAAAAGAAGCAATC
1 AGTAAAAGTAAAAGAAGTAA-C
*
57613 AGTAAAAGTAATTAAG-AGTAAA
1 AGTAAAAGTAA--AAGAAGTAAC
57635 AGTAAAAG
1 AGTAAAAG
57643 AAGTAATCAG
Statistics
Matches: 123, Mismatches: 10, Indels: 58
0.64 0.05 0.30
Matches are distributed among these distances:
14 16 0.13
15 10 0.08
16 10 0.08
17 4 0.03
19 1 0.01
20 2 0.02
21 16 0.13
22 47 0.38
23 14 0.11
24 3 0.02
ACGTcount: A:0.60, C:0.04, G:0.20, T:0.16
Consensus pattern (21 bp):
AGTAAAAGTAAAAGAAGTAAC
Found at i:57500 original size:38 final size:38
Alignment explanation
Indices: 57458--57548 Score: 155
Period size: 38 Copynumber: 2.4 Consensus size: 38
57448 TAGTAGAAGG
*
57458 GAGTAAAAGTAAAAGAAGTAATCAGTAAAAGCTAAAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAAACTAAAAA
* *
57496 GAGTAGAAGTAAAAGAAGTAATCAGTAAAAACTAAAGA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAAACTAAAAA
57534 GAGTAAAAGTAAAAG
1 GAGTAAAAGTAAAAG
57549 TAAAAGAGGA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.59, C:0.04, G:0.21, T:0.15
Consensus pattern (38 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAAAAACTAAAAA
Found at i:57573 original size:58 final size:58
Alignment explanation
Indices: 57459--57604 Score: 181
Period size: 58 Copynumber: 2.5 Consensus size: 58
57449 AGTAGAAGGG
* * *
57459 AGTAAAAGTAAAAGAAGTAATCAGTAAAAGCTAAAAAGAGTAGAAGTAAAAGAAGTAATC
1 AGTAAAACTAAAAG-AGTAA-AAGTAAAAGCTAAAAAGAGAAGAAGTAAAAGAAGTAATC
57519 AGTAAAAACTAAAGAGAGTAAAAGTAAAAG-T-AAAAGAGGAAG-AGTAAAAGAAGTAATC
1 AGT-AAAACTAAA-AGAGTAAAAGTAAAAGCTAAAAAGA-GAAGAAGTAAAAGAAGTAATC
* *
57577 AGTAAAAGTAAAAGAGTAAAAATAAAAG
1 AGTAAAACTAAAAGAGTAAAAGTAAAAG
57605 AAGCAATCAG
Statistics
Matches: 78, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
56 15 0.19
57 8 0.10
58 25 0.32
59 4 0.05
60 11 0.14
61 13 0.17
62 2 0.03
ACGTcount: A:0.61, C:0.03, G:0.21, T:0.15
Consensus pattern (58 bp):
AGTAAAACTAAAAGAGTAAAAGTAAAAGCTAAAAAGAGAAGAAGTAAAAGAAGTAATC
Found at i:57616 original size:132 final size:129
Alignment explanation
Indices: 57412--57652 Score: 333
Period size: 132 Copynumber: 1.8 Consensus size: 129
57402 GTAAGAATGG
* * * ** * *
57412 AGTAAAAGTAAAAGAAGTAAAAGTAAAAGGAGTAATTAGTAGAAGGGAGTAAAAGTAAAAGAAGT
1 AGTAAAAGTAAAAGAAGGAAAAGTAAAAGAAGTAATCAGTAGAAAAGAGTAAAAATAAAAGAAGC
*
57477 AATCAGTAAAAGCTAA-AAAGAGTAGAAGTAAAAGAAGTAATCAGTAAAAACTAAAGAGAGTAAA
66 AATCAGTAAAAG-TAATAAAGAGTAAAAGTAAAAGAAGTAATCAGTAAAAACTAAAGAGAGTAAA
*
57541 AGTAAAAGTAAAAG-AGGAAGAGTAAAAGAAGTAATCAGTAAAAGTAAAAGAGTAAAAATAAAAG
1 AGTAAAAGTAAAAGAAGGAAAAGTAAAAGAAGTAATCAGT---AG-AAAAGAGTAAAAATAAAAG
*
57605 AAGCAATCAGTAAAAGTAATTAAGAGTAAAAGTAAAAGAAGTAATCAG
62 AAGCAATCAGTAAAAGTAATAAAGAGTAAAAGTAAAAGAAGTAATCAG
57653 AGAAATAGTA
Statistics
Matches: 97, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
128 21 0.22
129 14 0.14
131 5 0.05
132 57 0.59
ACGTcount: A:0.59, C:0.03, G:0.22, T:0.16
Consensus pattern (129 bp):
AGTAAAAGTAAAAGAAGGAAAAGTAAAAGAAGTAATCAGTAGAAAAGAGTAAAAATAAAAGAAGC
AATCAGTAAAAGTAATAAAGAGTAAAAGTAAAAGAAGTAATCAGTAAAAACTAAAGAGAGTAAA
Found at i:57623 original size:58 final size:58
Alignment explanation
Indices: 57483--57623 Score: 153
Period size: 58 Copynumber: 2.4 Consensus size: 58
57473 AAGTAATCAG
* * *
57483 TAAAAGCTAAAAAGAGTAGAAGTAAAAGAAGTAATCAGTAAAAACTAAAGAGAGTAAAAG
1 TAAAAG-T-AAAACAGTAAAAGTAAAAGAAGTAATCAGTAAAAACTAAAGAGAGTAAAAA
* * * *
57543 TAAAAGTAAAAGAGGAAGAGTAAAAGAAGTAATCAGT-AAAAGTAAA-AGAGTAAAAA
1 TAAAAGTAAAACAGTAAAAGTAAAAGAAGTAATCAGTAAAAACTAAAGAGAGTAAAAA
57599 TAAAAG-AAGCAATCAGTAAAAGTAA
1 TAAAAGTAA--AA-CAGTAAAAGTAA
57624 TTAAGAGTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
55 2 0.03
56 15 0.21
57 10 0.14
58 36 0.51
59 1 0.01
60 6 0.09
ACGTcount: A:0.61, C:0.04, G:0.20, T:0.15
Consensus pattern (58 bp):
TAAAAGTAAAACAGTAAAAGTAAAAGAAGTAATCAGTAAAAACTAAAGAGAGTAAAAA
Found at i:57674 original size:40 final size:37
Alignment explanation
Indices: 57519--57735 Score: 208
Period size: 36 Copynumber: 5.7 Consensus size: 37
57509 AGAAGTAATC
*
57519 AGTAAAAACT-AAAGAGAGTAA-AAGTAAAAGTAA-AAG
1 AGTAAAAA-TAAAAGA-AGTAATCAGTAAAAGTAATAAG
* * *
57555 AGGAAGAGTAAAAGAAGTAATCAGTAAAAGTAA-AAG
1 AGTAAAAATAAAAGAAGTAATCAGTAAAAGTAATAAG
*
57591 AGTAAAAATAAAAGAAGCAATCAGTAAAAGTAATTAAG
1 AGTAAAAATAAAAGAAGTAATCAGTAAAAGTAA-TAAG
* *
57629 AGTAAAAGTAAAAGAAGTAATCAGAGAAATAGTAAGTAAG
1 AGTAAAAATAAAAGAAGTAATCAG-TAAA-AGTAA-TAAG
* * * * *
57669 CGTAAAAACAAAAAGGAGTAAGCAGTAAATTGATAATCAAG
1 AGTAAAAA-TAAAAGAAGTAATCAGTAAA-AG-TAAT-AAG
57710 AGTAAAAATAAAAGAAGTAATCAGTA
1 AGTAAAAATAAAAGAAGTAATCAGTA
57736 GAAGGGAGTA
Statistics
Matches: 149, Mismatches: 23, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
35 6 0.04
36 53 0.36
38 25 0.17
39 3 0.02
40 36 0.24
41 26 0.17
ACGTcount: A:0.59, C:0.05, G:0.20, T:0.17
Consensus pattern (37 bp):
AGTAAAAATAAAAGAAGTAATCAGTAAAAGTAATAAG
Found at i:57722 original size:81 final size:75
Alignment explanation
Indices: 57541--57738 Score: 204
Period size: 81 Copynumber: 2.6 Consensus size: 75
57531 AGAGAGTAAA
* * * * *
57541 AGTAAAAGTAA--AAGAGGAAGAGTAAAAGAAGTAATCAG-TAAAAGTAAAAGAGTAAAAATAAA
1 AGTAAAAGTAATCAAGAGTAAAAATAAAAGAAGTAATCAGAGAAAAGTAAAAGAGTAAAAAAAAA
*
57603 AGAAGCAATC
66 AGAAGCAAGC
* * *
57613 AGTAAAAGTAATTAAGAGTAAAAGTAAAAGAAGTAATCAGAGAAATAGTAAGTAAGCGTAAAAAC
1 AGTAAAAGTAATCAAGAGTAAAAATAAAAGAAGTAATCAGAGAAA-AGTAA--AAGAGTAAAAA-
* *
57678 AAAAAGGAGTAAGC
62 AAAAAGAAGCAAGC
*
57692 AGTAAATTGATAATCAAGAGTAAAAATAAAAGAAGTAATCAGTAGAA
1 AGTAAA-AG-TAATCAAGAGTAAAAATAAAAGAAGTAATCAG-AGAA
57739 GGGAGTAAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
72 11 0.10
74 25 0.24
75 3 0.03
76 5 0.05
78 10 0.10
79 16 0.15
80 1 0.01
81 30 0.29
82 4 0.04
ACGTcount: A:0.59, C:0.05, G:0.20, T:0.17
Consensus pattern (75 bp):
AGTAAAAGTAATCAAGAGTAAAAATAAAAGAAGTAATCAGAGAAAAGTAAAAGAGTAAAAAAAAA
AGAAGCAAGC
Found at i:57745 original size:32 final size:32
Alignment explanation
Indices: 57709--57800 Score: 89
Period size: 32 Copynumber: 2.9 Consensus size: 32
57699 TGATAATCAA
57709 GAGTAAAAATAAAAGAAGTAATCAGTAGAAGG
1 GAGTAAAAATAAAAGAAGTAATCAGTAGAAGG
* * * *
57741 GAGTAAAAGA-AGAAGAAGTAATCAACT-CAATG
1 GAGTAAAA-ATAAAAGAAGTAATC-AGTAGAAGG
* * *
57773 GAGTAAAAGTAAAAGGAGTAAACAGTAG
1 GAGTAAAAATAAAAGAAGTAATCAGTAG
57801 TAACAGTAGT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
31 2 0.04
32 41 0.89
33 3 0.07
ACGTcount: A:0.54, C:0.05, G:0.25, T:0.15
Consensus pattern (32 bp):
GAGTAAAAATAAAAGAAGTAATCAGTAGAAGG
Found at i:62770 original size:74 final size:75
Alignment explanation
Indices: 62649--62797 Score: 230
Period size: 74 Copynumber: 2.0 Consensus size: 75
62639 TTATCTCGAC
*
62649 TGTGAGCAAAGGAATGATTGGTTTTAATCAAAACATGTTTCAAAATCAGTTTCAATCAAAGCAAT
1 TGTGAGCAAAAGAATGATTGGTTTTAATCAAAACATGTTTCAAAATCAGTTTCAATCAAAGCAAT
62714 G-TTTCGAGG
66 GATTTCGAGG
* * * *
62723 TGTGAGCAAAAGAATGA-TGAGTTTTAATCAAAAGATGTTTCAAAATCAGTTTTAGTCGAAGCAA
1 TGTGAGCAAAAGAATGATTG-GTTTTAATCAAAACATGTTTCAAAATCAGTTTCAATCAAAGCAA
62787 TGATTTCGAGG
65 TGATTTCGAGG
62798 GGACTAAAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
73 2 0.03
74 58 0.85
75 8 0.12
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (75 bp):
TGTGAGCAAAAGAATGATTGGTTTTAATCAAAACATGTTTCAAAATCAGTTTCAATCAAAGCAAT
GATTTCGAGG
Found at i:63169 original size:7 final size:7
Alignment explanation
Indices: 63157--63226 Score: 56
Period size: 7 Copynumber: 10.0 Consensus size: 7
63147 ATTTCCCAAA
63157 AAAAAAG
1 AAAAAAG
63164 -AAAAA-
1 AAAAAAG
*
63169 AAGAAAG
1 AAAAAAG
* *
63176 ATAAATG
1 AAAAAAG
*
63183 AAAAATG
1 AAAAAAG
63190 AAAAAAG
1 AAAAAAG
63197 AGAAAAA-
1 A-AAAAAG
63204 AAATAAAG
1 AAA-AAAG
63212 AAAAAAG
1 AAAAAAG
63219 AGAAAAAG
1 A-AAAAAG
63227 CAACGGTGGT
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
6 11 0.22
7 26 0.51
8 14 0.27
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.06
Consensus pattern (7 bp):
AAAAAAG
Found at i:63286 original size:45 final size:45
Alignment explanation
Indices: 63237--63323 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
63227 CAACGGTGGT
* *
63237 TTTCAAAAAGAGTTATGGTTTTTAAAAGGTTTTGATAAAATGATA
1 TTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGATA
63282 TTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATG
1 TTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATG
63324 GTTTTCCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.38
Consensus pattern (45 bp):
TTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGATA
Found at i:64039 original size:13 final size:11
Alignment explanation
Indices: 64019--64068 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 11
64009 CAAGTGCATG
64019 AAAAAAATGTAA
1 AAAAAAATG-AA
64031 AAGAAAAATGAA
1 AA-AAAAATGAA
64043 AAAAAAA-GAA
1 AAAAAAATGAA
*
64053 AAAAGAATGAA
1 AAAAAAATGAA
64064 GAAAA
1 -AAAA
64069 GAGGCTCTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
10 9 0.26
11 8 0.24
12 10 0.29
13 7 0.21
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (11 bp):
AAAAAAATGAA
Found at i:64061 original size:21 final size:23
Alignment explanation
Indices: 64019--64068 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
64009 CAAGTGCATG
*
64019 AAAAAAATGTAAAAGAAAAATGA
1 AAAAAAAAGTAAAAGAAAAATGA
*
64042 AAAAAAAAG-AAAA-AAGAATGA
1 AAAAAAAAGTAAAAGAAAAATGA
*
64063 AGAAAA
1 AAAAAA
64069 GAGGCTCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.50
22 4 0.17
23 8 0.33
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (23 bp):
AAAAAAAAGTAAAAGAAAAATGA
Found at i:64400 original size:50 final size:50
Alignment explanation
Indices: 64340--64440 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 50
64330 GAAGTTTTAT
*
64340 AATAAGATTGCATTTCATTTGTGAGTCCAAGATCGAAATTCGCTTTTCAA
1 AATAAGATTGCATTTCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
* *
64390 AATAGGATTGCATTTCATTTGTGAGTCTAAGATCAAAATTCGCTTTTCAA
1 AATAAGATTGCATTTCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
64440 A
1 A
64441 GGGCATTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (50 bp):
AATAAGATTGCATTTCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
Found at i:65126 original size:69 final size:69
Alignment explanation
Indices: 64962--65136 Score: 185
Period size: 69 Copynumber: 2.5 Consensus size: 69
64952 AATGCTTCGA
* * * ** *
64962 CTTTTCCATAAATCAAACTCATTTCCATATGAGTCAGTTTAAGTTTTGGTTCCATCCAAGCATTC
1 CTTTTCCAT-AAGCCAACTCATTTCCATATGAGTCAGGTTAAGCCTTGGTTCCATCCAAGCATGC
65027 AGGGG
65 AGGGG
* ** * *
65032 CTTTTTCA-AGAGCCATACTTGTTTCCATACGAGTTAGGTT-AGCCTTGGTTCCATCCAAGCA-G
1 CTTTTCCATA-AGCCA-ACTCATTTCCATATGAGTCAGGTTAAGCCTTGGTTCCATCCAAGCATG
65094 CAAGGGG
64 C-AGGGG
65101 CTTTTCCATAAGCCAAGCTCATTTCCATATGAGTCA
1 CTTTTCCATAAGCCAA-CTCATTTCCATATGAGTCA
65137 AGCCTTACTT
Statistics
Matches: 84, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
68 3 0.04
69 54 0.64
70 27 0.32
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (69 bp):
CTTTTCCATAAGCCAACTCATTTCCATATGAGTCAGGTTAAGCCTTGGTTCCATCCAAGCATGCA
GGGG
Found at i:65287 original size:47 final size:47
Alignment explanation
Indices: 65204--65567 Score: 415
Period size: 47 Copynumber: 7.7 Consensus size: 47
65194 CTAGGTAATA
* * * ** *
65204 TTTTCTAGCTTCCATGCGAGTCGACAATGAAATGACCAAAGTTGGTC
1 TTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGGTC
* * *
65251 TTTTCTCGCTTCCGCACGAGTCTACCATTTAGTGACCAAAGTTGGTC
1 TTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGGTC
** * * *
65298 TTTTCTCGCTTCCGTGCGAGTCTACCATATAGCGACCAAAGTTGGTC
1 TTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGGTC
* *
65345 TTTTTCTCGTTTCCACGCGAGTCTACAATTTAGTGACCAAAGCTGGTC
1 -TTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGGTC
* * * * * *
65393 TTTTCTCACTTTCATGCGAGTGTACGATTTAGTGACCAAAATTGGTC
1 TTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGGTC
* * *
65440 TTTTCTCGCTTCCACGCAAGTCTACGACTTAGTGACCAAAGTTGGTC
1 TTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGGTC
* * * *
65487 TTTTCTCACTTCCACGTGAGTTTACAATGTCT-TTGACCAAAGTTGGTC
1 TTTTCTCGCTTCCACGCGAGTCTACAAT-T-TAGTGACCAAAGTTGGTC
*
65535 TTTTCTCGCTTCCACGCGAGTCTTCAATCTTAG
1 TTTTCTCGCTTCCACGCGAGTCTACAAT-TTAG
65568 ACCGTGGAAT
Statistics
Matches: 265, Mismatches: 48, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
47 183 0.69
48 81 0.31
49 1 0.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (47 bp):
TTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGGTC
Found at i:65393 original size:95 final size:94
Alignment explanation
Indices: 65204--65567 Score: 435
Period size: 95 Copynumber: 3.8 Consensus size: 94
65194 CTAGGTAATA
* * * *
65204 TTTTCT-AGCTTCCATGCGAGTCGACAATGA-AATGACCAAAGTTGGTCTTTTCTCGCTTCCGCA
1 TTTTCTCA-CTTCCATGCGAGTCTACAAT-ATAGTGACCAAAGTTGGTCTTTTCTCGCTTCCACG
*
65267 CGAGTCTACCATTTAGTGACCAAAGTTGGTC
64 CGAGTCTACAATTTAGTGACCAAAGTTGGTC
* * * * *
65298 TTTTCTCGCTTCCGTGCGAGTCTACCATATAGCGACCAAAGTTGGTCTTTTTCTCGTTTCCACGC
1 TTTTCTCACTTCCATGCGAGTCTACAATATAGTGACCAAAGTTGGTC-TTTTCTCGCTTCCACGC
*
65363 GAGTCTACAATTTAGTGACCAAAGCTGGTC
65 GAGTCTACAATTTAGTGACCAAAGTTGGTC
* * * * * *
65393 TTTTCTCACTTTCATGCGAGTGTACGATTTAGTGACCAAAATTGGTCTTTTCTCGCTTCCACGCA
1 TTTTCTCACTTCCATGCGAGTCTACAATATAGTGACCAAAGTTGGTCTTTTCTCGCTTCCACGCG
* *
65458 AGTCTACGACTTAGTGACCAAAGTTGGTC
66 AGTCTACAATTTAGTGACCAAAGTTGGTC
* * * * **
65487 TTTTCTCACTTCCACGTGAGTTTACAATGTCTTTGACCAAAGTTGGTCTTTTCTCGCTTCCACGC
1 TTTTCTCACTTCCATGCGAGTCTACAATAT-AGTGACCAAAGTTGGTCTTTTCTCGCTTCCACGC
*
65552 GAGTCTTCAATCTTAG
65 GAGTCTACAAT-TTAG
65568 ACCGTGGAAT
Statistics
Matches: 228, Mismatches: 37, Indels: 8
0.84 0.14 0.03
Matches are distributed among these distances:
93 1 0.00
94 104 0.46
95 119 0.52
96 4 0.02
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (94 bp):
TTTTCTCACTTCCATGCGAGTCTACAATATAGTGACCAAAGTTGGTCTTTTCTCGCTTCCACGCG
AGTCTACAATTTAGTGACCAAAGTTGGTC
Found at i:65462 original size:142 final size:141
Alignment explanation
Indices: 65204--65557 Score: 433
Period size: 142 Copynumber: 2.5 Consensus size: 141
65194 CTAGGTAATA
* * * ** * *
65204 TTTTCTAGCTTCCATGCGAGTCGACAATGAAATGACCAAAGTTGGTCTTTTCTCGCTTCCGCACG
1 TTTTCTCGCTTCCACGCGAGTCTACAATTTAATGACCAAAGTTGGTCTTTTCTCGCTTCCACGCG
* ** *
65269 AGTCTACCATTTAGTGACCAAAGTTGGTCTTTTCTCGCTTCCGTGCGAGTCTACCA-TATAGCGA
66 AGTCTACCATTTAGTGACCAAAATTGGTCTTTTCTCGCTTCCACGCAAGTCTACCACT-TAGCGA
65333 CCAAAGTTGGTC
130 CCAAAGTTGGTC
* * * * * *
65345 TTTTTCTCGTTTCCACGCGAGTCTACAATTTAGTGACCAAAGCTGGTCTTTTCTCACTTTCATGC
1 -TTTTCTCGCTTCCACGCGAGTCTACAATTTAATGACCAAAGTTGGTCTTTTCTCGCTTCCACGC
* * * *
65410 GAGTGTACGATTTAGTGACCAAAATTGGTCTTTTCTCGCTTCCACGCAAGTCTACGACTTAGTGA
65 GAGTCTACCATTTAGTGACCAAAATTGGTCTTTTCTCGCTTCCACGCAAGTCTACCACTTAGCGA
65475 CCAAAGTTGGTC
130 CCAAAGTTGGTC
* * * *
65487 TTTTCTCACTTCCACGTGAGTTTACAATGTCT-TTGACCAAAGTTGGTCTTTTCTCGCTTCCACG
1 TTTTCTCGCTTCCACGCGAGTCTACAAT-T-TAATGACCAAAGTTGGTCTTTTCTCGCTTCCACG
65551 CGAGTCT
64 CGAGTCT
65558 TCAATCTTAG
Statistics
Matches: 178, Mismatches: 31, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
141 24 0.13
142 152 0.85
143 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (141 bp):
TTTTCTCGCTTCCACGCGAGTCTACAATTTAATGACCAAAGTTGGTCTTTTCTCGCTTCCACGCG
AGTCTACCATTTAGTGACCAAAATTGGTCTTTTCTCGCTTCCACGCAAGTCTACCACTTAGCGAC
CAAAGTTGGTC
Found at i:66327 original size:30 final size:30
Alignment explanation
Indices: 66288--66345 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
66278 ACACCAGAAA
*
66288 TACATGTCATCAGAGA-GCCAAATAAGCAAG
1 TACAGGTCATCAGA-ATGCCAAATAAGCAAG
*
66318 TACAGGTCATCAGAATGCCACATAAGCA
1 TACAGGTCATCAGAATGCCAAATAAGCA
66346 TTAATAGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.17
Consensus pattern (30 bp):
TACAGGTCATCAGAATGCCAAATAAGCAAG
Found at i:67543 original size:21 final size:21
Alignment explanation
Indices: 67517--67565 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
67507 ACACTGGAGT
* *
67517 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCGAAGCAAACC
67538 ACATGGGGCGCGAAGCAAACC
1 ACATGGGGCGCGAAGCAAACC
67559 ACATGGG
1 ACATGGG
67566 CGCCCAGCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.27, G:0.35, T:0.08
Consensus pattern (21 bp):
ACATGGGGCGCGAAGCAAACC
Found at i:70712 original size:40 final size:39
Alignment explanation
Indices: 70640--70716 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 39
70630 AAGTAAAAGG
* * *
70640 ATTAAGAGTCAAAGTAAAAGGATTAATTAGTAAATTAATA
1 ATTAAGAGACAAAGTAAAAGGAGTAATCAGT-AATTAATA
* **
70680 ATTAAGAGAGAAAGTAAAATTAGTAATCAGTAATTAA
1 ATTAAGAGACAAAGTAAAAGGAGTAATCAGTAATTAA
70717 GAAAGGAAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
39 6 0.19
40 25 0.81
ACGTcount: A:0.53, C:0.03, G:0.16, T:0.29
Consensus pattern (39 bp):
ATTAAGAGACAAAGTAAAAGGAGTAATCAGTAATTAATA
Found at i:70718 original size:32 final size:32
Alignment explanation
Indices: 70664--70763 Score: 110
Period size: 32 Copynumber: 3.1 Consensus size: 32
70654 TAAAAGGATT
* * *
70664 AATTAGTAAATTAATAATTAAGAGAGAAAGTAA
1 AATTAGT-AATCAGTAATTAAGAAAGAAAGTAA
*
70697 AATTAGTAATCAGTAATTAAGAAAGGAAGTAA
1 AATTAGTAATCAGTAATTAAGAAAGAAAGTAA
** * *
70729 AAGGATTAATCAGTAATTAAGAAAGGAAGTTAA
1 AATTAGTAATCAGTAATTAAGAAAGAAAG-TAA
70762 AA
1 AA
70764 GGACTAATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
32 47 0.80
33 12 0.20
ACGTcount: A:0.55, C:0.02, G:0.18, T:0.25
Consensus pattern (32 bp):
AATTAGTAATCAGTAATTAAGAAAGAAAGTAA
Found at i:70777 original size:33 final size:32
Alignment explanation
Indices: 70678--70782 Score: 129
Period size: 32 Copynumber: 3.2 Consensus size: 32
70668 AGTAAATTAA
* * ** *
70678 TAATTAAGAGAGAAAGTAAAATTAGTAATCAG
1 TAATTAAGAAAGGAAGTAAAAGGACTAATCAG
*
70710 TAATTAAGAAAGGAAGTAAAAGGATTAATCAG
1 TAATTAAGAAAGGAAGTAAAAGGACTAATCAG
*
70742 TAATTAAGAAAGGAAGTTAAAAGGACTAATAAG
1 TAATTAAGAAAGGAAG-TAAAAGGACTAATCAG
70775 TAAATTAA
1 T-AATTAA
70783 TAATTAAGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
32 43 0.67
33 15 0.23
34 6 0.09
ACGTcount: A:0.54, C:0.03, G:0.19, T:0.24
Consensus pattern (32 bp):
TAATTAAGAAAGGAAGTAAAAGGACTAATCAG
Found at i:70907 original size:32 final size:31
Alignment explanation
Indices: 70857--71474 Score: 316
Period size: 32 Copynumber: 19.0 Consensus size: 31
70847 AAATAGCTAA
*
70857 AAAGAGTAGAAGTAAAAGAAGTAATCAGTAG
1 AAAGAGTAAAAGTAAAAGAAGTAATCAGTAG
* *
70888 AAAGGAGTAAAAGTGAAAGAAGTAATCAGAAAATTGG
1 AAA-GAGTAAAAGTAAAAGAAGTAATCAG-----TAG
* *
70925 TAATTAAGAGTAAAAGTAAAGGAGGTAATCAGTAG
1 --A--AAGAGTAAAAGTAAAAGAAGTAATCAGTAG
*
70960 AATAGAGTAAAAGTAAAAGAAATAATCAGTAAG
1 AA-AGAGTAAAAGTAAAAGAAGTAATCAGT-AG
*
70993 AATAGAGTAAAAGTAAAAGAAGTAA-AAGTA-
1 AA-AGAGTAAAAGTAAAAGAAGTAATCAGTAG
* *
71023 AAAGAGTAAAAGTAAAAGGAGTAATTAGTAG
1 AAAGAGTAAAAGTAAAAGAAGTAATCAGTAG
* *
71054 AAGGGAGTAAAAGTAAAAGAAGTAATCAGTAAAAATA
1 AA-AGAGTAAAAGTAAAAGAAGTAATCAGT----A-G
71091 AAAGAGTAAAAGTAAAAGAAGTAATCAGTAAAAG
1 AAAGAGTAAAAGTAAAAGAAGTAATCAGT---AG
* *
71125 CTAAAAAGAGTAGAAGCAAAAGAAGTAATCAGTAAAAG
1 ----AAAGAGTAAAAGTAAAAGAAGTAATCAGT---AG
*
71163 CTAAAAAGAGTAGAAGTAAAAGAAGTAATCAGT--
1 ----AAAGAGTAAAAGTAAAAGAAGTAATCAGTAG
* *
71196 AAA-AGTAAAAG-AAGTAATAAGTAA-GAGTA-
1 AAAGAGTAAAAGTAA--AAGAAGTAATCAGTAG
* *
71225 AAAGAGTAAGAGTAAAAGAAGTAATCTGTGAAAG
1 AAAGAGTAAAAGTAAAAGAAGTAATCAGT---AG
* *
71259 TAAAAGAGTAAAAATAAAAGAAGCAATCAGTAAAAG
1 --AAAGAGTAAAAGTAAAAGAAGTAATCAGT---AG
71295 TAATTAAGAGTAAAAGTAAAAGAAGTAATCAG-AG
1 --A--AAGAGTAAAAGTAAAAGAAGTAATCAGTAG
* * *
71329 AAATAGT--AAGT--AAG-AGTAA-AAGTAA
1 AAAGAGTAAAAGTAAAAGAAGTAATCAGTAG
* *
71354 AAAGGAGTAAGCAGTAAATTG-A-TAAT---T--
1 AAA-GAGTAA-AAGTAAA-AGAAGTAATCAGTAG
*
71381 -AAGAGTAAAAGTAAAACAAGTAATCAGTAG
1 AAAGAGTAAAAGTAAAAGAAGTAATCAGTAG
71411 AAAGGAGTAAAAG-AAGAAGAAGTAATCAGTA-
1 AAA-GAGTAAAAGTAA-AAGAAGTAATCAGTAG
*
71442 AAATGTAGTAAAAGTAAATAG-AGTAAACAGTAG
1 AAA-G-AGTAAAAGTAAA-AGAAGTAATCAGTAG
71475 TAACAGTAGT
Statistics
Matches: 477, Mismatches: 49, Indels: 120
0.74 0.08 0.19
Matches are distributed among these distances:
24 9 0.02
25 19 0.04
26 8 0.02
27 2 0.00
28 15 0.03
29 47 0.10
30 20 0.04
31 21 0.04
32 119 0.25
33 32 0.07
34 2 0.00
35 6 0.01
36 59 0.12
37 4 0.01
38 89 0.19
39 1 0.00
40 22 0.05
41 2 0.00
ACGTcount: A:0.57, C:0.03, G:0.22, T:0.18
Consensus pattern (31 bp):
AAAGAGTAAAAGTAAAAGAAGTAATCAGTAG
Found at i:70991 original size:94 final size:91
Alignment explanation
Indices: 70930--71111 Score: 240
Period size: 94 Copynumber: 1.9 Consensus size: 91
70920 ATTGGTAATT
*
70930 AAGAGTAAAAGT-AAAGGAGGTAATCAGTAGAATAGAGTAAAAGTAAAAGAAATAATCAGTAAGA
1 AAGAGTAAAAGTAAAAGGA-GTAATCAGTAGAAGAGAGTAAAAGTAAAAGAAATAATCAGTAA-A
70994 ATAGAGTAAAAGTAAAAGAAGTAAAAGTAA
64 ATAGAG-AAAAGTAAAAGAAG-AAAAGTAA
* * *
71024 AAGAGTAAAAGTAAAAGGAGTAATTAGTAGAAGGGAGTAAAAGTAAAAGAAGTAATCAGTAAAAA
1 AAGAGTAAAAGTAAAAGGAGTAATCAGTAGAAGAGAGTAAAAGTAAAAGAAATAATCAGT-AAAA
71089 TAAAAGAGTAAAAGTAAAAGAAG
65 T---AGAG-AAAAGTAAAAGAAG
71112 TAATCAGTAA
Statistics
Matches: 79, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
94 52 0.66
95 8 0.10
97 19 0.24
ACGTcount: A:0.59, C:0.02, G:0.23, T:0.16
Consensus pattern (91 bp):
AAGAGTAAAAGTAAAAGGAGTAATCAGTAGAAGAGAGTAAAAGTAAAAGAAATAATCAGTAAAAT
AGAGAAAAGTAAAAGAAGAAAAGTAA
Found at i:71085 original size:22 final size:22
Alignment explanation
Indices: 71059--71242 Score: 119
Period size: 22 Copynumber: 9.4 Consensus size: 22
71049 AGTAGAAGGG
71059 AGTAAAAGTAAAAGAAGTAATC
1 AGTAAAAGTAAAAGAAGTAATC
*
71081 AGTAAAAATAAAAG-AG---T-
1 AGTAAAAGTAAAAGAAGTAATC
71098 A--AA-AGTAAAAGAAGTAATC
1 AGTAAAAGTAAAAGAAGTAATC
71117 AGTAAAAGCT-AAA-AAG-----
1 AGTAAAAG-TAAAAGAAGTAATC
* *
71133 AGTAGAAGCAAAAGAAGTAATC
1 AGTAAAAGTAAAAGAAGTAATC
71155 AGTAAAAGCT-AAA-AAG-----
1 AGTAAAAG-TAAAAGAAGTAATC
*
71171 AGTAGAAGTAAAAGAAGTAATC
1 AGTAAAAGTAAAAGAAGTAATC
*
71193 AGTAAAAGTAAAAGAAGTAATA
1 AGTAAAAGTAAAAGAAGTAATC
* *
71215 AGTAAGAGTAAAAG-AGTAA-G
1 AGTAAAAGTAAAAGAAGTAATC
71235 AGTAAAAG
1 AGTAAAAG
71243 AAGTAATCTG
Statistics
Matches: 126, Mismatches: 12, Indels: 50
0.67 0.06 0.27
Matches are distributed among these distances:
14 7 0.06
15 5 0.04
16 20 0.16
17 7 0.06
18 2 0.02
19 1 0.01
20 7 0.06
21 15 0.12
22 61 0.48
23 1 0.01
ACGTcount: A:0.60, C:0.04, G:0.21, T:0.16
Consensus pattern (22 bp):
AGTAAAAGTAAAAGAAGTAATC
Found at i:71146 original size:38 final size:38
Alignment explanation
Indices: 71058--71219 Score: 242
Period size: 38 Copynumber: 4.3 Consensus size: 38
71048 TAGTAGAAGG
*
71058 GAGTAAAAGTAAAAGAAGTAATCAGTAAAA-AT-AAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAAGCTAAAAA
71094 GAGTAAAAGTAAAAGAAGTAATCAGTAAAAGCTAAAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAAGCTAAAAA
* *
71132 GAGTAGAAGCAAAAGAAGTAATCAGTAAAAGCTAAAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAAGCTAAAAA
*
71170 GAGTAGAAGTAAAAGAAGTAATCAGTAAAAG-T-AAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAAGCTAAAAA
71206 GAAGTAATAAGTAA
1 G-AGTAA-AAGTAA
71220 GAGTAAAAGA
Statistics
Matches: 117, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
36 35 0.30
37 6 0.05
38 76 0.65
ACGTcount: A:0.60, C:0.04, G:0.20, T:0.16
Consensus pattern (38 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAAAAGCTAAAAA
Found at i:71159 original size:60 final size:57
Alignment explanation
Indices: 71095--71245 Score: 146
Period size: 60 Copynumber: 2.5 Consensus size: 57
71085 AAAATAAAAG
* * *
71095 AGTAAAAGTAAAAGAAGTAATCAGTAAAAGCTAA-AAAGAGTAGAAGCAAAAGAAGTAATC
1 AGTAAAAGTAAAAGAAGTAA--AGTAAAAG--AAGAAACAGTAAAAGCAAAAGAAGTAATA
* *
71155 AGTAAAAGCTAAAA-AGAGTAGAAGTAAAAGAAGTAATCAGTAAAAGTAAAAGAAGTAATA
1 AGTAAAAG-TAAAAGA-AGTA-AAGTAAAAGAAG-AAACAGTAAAAGCAAAAGAAGTAATA
*
71215 AGTAAGAGTAAAAG-AGTAAGAGTAAAAGAAG
1 AGTAAAAGTAAAAGAAGTAA-AGTAAAAGAAG
71246 TAATCTGTGA
Statistics
Matches: 78, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
57 1 0.01
58 17 0.22
59 5 0.06
60 45 0.58
61 9 0.12
62 1 0.01
ACGTcount: A:0.59, C:0.04, G:0.22, T:0.15
Consensus pattern (57 bp):
AGTAAAAGTAAAAGAAGTAAAGTAAAAGAAGAAACAGTAAAAGCAAAAGAAGTAATA
Found at i:71233 original size:36 final size:36
Alignment explanation
Indices: 71193--71443 Score: 237
Period size: 36 Copynumber: 6.8 Consensus size: 36
71183 AGAAGTAATC
*
71193 AGTAAAAGTAAAAGAAGTAATAAGTAAGAGTAA-AAG
1 AGTAAAAGTAAAAGAAGTAATCAGTAA-AGTAATAAG
* *
71229 AGTAAGAGTAAAAGAAGTAATCTGTGAAAGTAA-AAG
1 AGTAAAAGTAAAAGAAGTAATCAGT-AAAGTAATAAG
* *
71265 AGTAAAAATAAAAGAAGCAATCAGTAAAAGTAATTAAG
1 AGTAAAAGTAAAAGAAGTAATCAGT-AAAGTAA-TAAG
*
71303 AGTAAAAGTAAAAGAAGTAATCAGAGAAATAGTAAGTAAG
1 AGTAAAAGTAAAAGAAGTAATC--AGTAA-AGTAA-TAAG
* *
71343 AGTAAAAGTAAAAAGGAGTAAGCAGTAAATTGATAATTAAG
1 AGTAAAAGT-AAAAGAAGTAATCAGTAAA--G-TAA-TAAG
* *
71384 AGTAAAAGTAAAACAAGTAATCAGT--AG-AA-AGG
1 AGTAAAAGTAAAAGAAGTAATCAGTAAAGTAATAAG
71416 AGTAAAAG-AAGAAGAAGTAATCAGTAAA
1 AGTAAAAGTAA-AAGAAGTAATCAGTAAA
71444 ATGTAGTAAA
Statistics
Matches: 181, Mismatches: 21, Indels: 28
0.79 0.09 0.12
Matches are distributed among these distances:
31 2 0.01
32 23 0.13
34 3 0.02
36 59 0.33
37 2 0.01
38 25 0.14
39 6 0.03
40 34 0.19
41 27 0.15
ACGTcount: A:0.57, C:0.03, G:0.22, T:0.18
Consensus pattern (36 bp):
AGTAAAAGTAAAAGAAGTAATCAGTAAAGTAATAAG
Found at i:71244 original size:58 final size:60
Alignment explanation
Indices: 71133--71278 Score: 185
Period size: 58 Copynumber: 2.5 Consensus size: 60
71123 AGCTAAAAAG
* * *
71133 AGTAGAAGCAAAAGAAGTAATCAGTAAAAGCTAAAAAGAGTAGAAGTAAAAGAAGTAATC
1 AGTAAAAGTAAAAGAAGTAATAAGTAAAAGCTAAAAAGAGTAGAAGTAAAAGAAGTAATC
*
71193 AGTAAAAGTAAAAGAAGTAATAAGTAAGAG-T-AAAAGAGTA-AGAGTAAAAGAAGTAATC
1 AGTAAAAGTAAAAGAAGTAATAAGTAAAAGCTAAAAAGAGTAGA-AGTAAAAGAAGTAATC
* * *
71251 TGTGAAAGTAAAAG-AGTAA-AAATAAAAG
1 AGTAAAAGTAAAAGAAGTAATAAGTAAAAG
71279 AAGCAATCAG
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
56 7 0.09
57 6 0.08
58 37 0.48
59 1 0.01
60 26 0.34
ACGTcount: A:0.58, C:0.03, G:0.22, T:0.16
Consensus pattern (60 bp):
AGTAAAAGTAAAAGAAGTAATAAGTAAAAGCTAAAAAGAGTAGAAGTAAAAGAAGTAATC
Found at i:71269 original size:170 final size:173
Alignment explanation
Indices: 71058--71371 Score: 449
Period size: 170 Copynumber: 1.8 Consensus size: 173
71048 TAGTAGAAGG
* *
71058 GAGTAAAAGTAAAAGAAGTAATCAGTAAAAATAAAAGAGTAAAAGTAAAAGAAGTAATCAGTAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAAATAAAAGAGTAAAAATAAAAGAAGCAATCAGTAAA
* * *
71123 AGCTAA-AAAGAGTAGAAGCAAAAGAAGTAATCAG-TAAA-AGCTAA-AAAGAGTAGAAGT-AAA
66 AG-TAATAAAGAGTAAAAGCAAAAGAAGTAATCAGAGAAATAG-TAAGAAAGAGTAAAAGTAAAA
*
71183 AGAAGTAATCAGTAAAAGTAAAAGAAGTAATAAGTAAGAGTAAAA
129 AGAAGTAAGCAGTAAAAGTAAAAGAAGTAATAAGTAAGAGTAAAA
* * * *
71228 GAGTAAGAGTAAAAGAAGTAATCTGTGAAAGTAAAAGAGTAAAAATAAAAGAAGCAATCAGTAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAAATAAAAGAGTAAAAATAAAAGAAGCAATCAGTAAA
* * *
71293 AGTAATTAAGAGTAAAAGTAAAAGAAGTAATCAGAGAAATAGTAAGTAAGAGTAAAAGTAAAAAG
66 AGTAATAAAGAGTAAAAGCAAAAGAAGTAATCAGAGAAATAGTAAGAAAGAGTAAAAGTAAAAAG
*
71358 GAGTAAGCAGTAAA
131 AAGTAAGCAGTAAA
71372 TTGATAATTA
Statistics
Matches: 125, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
169 3 0.02
170 86 0.69
171 6 0.05
172 13 0.10
173 17 0.14
ACGTcount: A:0.59, C:0.04, G:0.21, T:0.17
Consensus pattern (173 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAAAAATAAAAGAGTAAAAATAAAAGAAGCAATCAGTAAA
AGTAATAAAGAGTAAAAGCAAAAGAAGTAATCAGAGAAATAGTAAGAAAGAGTAAAAGTAAAAAG
AAGTAAGCAGTAAAAGTAAAAGAAGTAATAAGTAAGAGTAAAA
Found at i:71291 original size:58 final size:58
Alignment explanation
Indices: 71133--71371 Score: 159
Period size: 58 Copynumber: 4.1 Consensus size: 58
71123 AGCTAAAAAG
* * * * * *
71133 AGTAGAAGCAAAAGAAGTAATCAGTAAAAGCTAAAAAGAGTAGAAGTAAAAGAAGTAATC
1 AGTAAAAGTAAAAGAAGTAATAAATAAAAG-T-AAAACAGTAAAAGTAAAAGAAGTAATC
* * * *
71193 AGTAAAAGTAAAAGAAGTAATAAGTAAGAGTAAAAGAGTAAGAGTAAAAGAAGTAATC
1 AGTAAAAGTAAAAGAAGTAATAAATAAAAGTAAAACAGTAAAAGTAAAAGAAGTAATC
* * * ** * *
71251 TGTGAAAGTAAAAG-AGTAA-AAATAAAAG--AAGCA--ATCAGTAAAAGTAATTAA-G
1 AGTAAAAGTAAAAGAAGTAATAAATAAAAGTAAAACAGTAAAAGTAAAAG-AAGTAATC
* * * * *
71303 AGTAAAAGTAAAAGAAGTAATCAGAGAAATAGTAAGTAAGAGTAAAAGTAAAAAGGAGTAAGC
1 AGTAAAAGTAAAAGAAGTAAT-AAATAAA-AGTAA--AACAGTAAAAGT-AAAAGAAGTAATC
71366 AGTAAA
1 AGTAAA
71372 TTGATAATTA
Statistics
Matches: 139, Mismatches: 27, Indels: 23
0.74 0.14 0.12
Matches are distributed among these distances:
52 21 0.15
53 10 0.07
54 3 0.02
55 5 0.04
56 9 0.06
57 5 0.04
58 38 0.27
59 1 0.01
60 28 0.20
62 8 0.06
63 11 0.08
ACGTcount: A:0.58, C:0.04, G:0.22, T:0.17
Consensus pattern (58 bp):
AGTAAAAGTAAAAGAAGTAATAAATAAAAGTAAAACAGTAAAAGTAAAAGAAGTAATC
Found at i:71384 original size:41 final size:39
Alignment explanation
Indices: 71193--71409 Score: 241
Period size: 36 Copynumber: 5.7 Consensus size: 39
71183 AGAAGTAATC
* *
71193 AGTAAAAGTAAAAGAAGTAATAAGT-AAGAGTAA--AAG
1 AGTAAAAGTAAAAGAAGTAATCAGTAAATAGTAATTAAG
* * *
71229 AGTAAGAGTAAAAGAAGTAATCTGTGAA-AGTAA--AAG
1 AGTAAAAGTAAAAGAAGTAATCAGTAAATAGTAATTAAG
* *
71265 AGTAAAAATAAAAGAAGCAATCAGTAAA-AGTAATTAAG
1 AGTAAAAGTAAAAGAAGTAATCAGTAAATAGTAATTAAG
* *
71303 AGTAAAAGTAAAAGAAGTAATCAGAGAAATAGTAAGTAAG
1 AGTAAAAGTAAAAGAAGTAATCAG-TAAATAGTAATTAAG
* * *
71343 AGTAAAAGTAAAAAGGAGTAAGCAGTAAATTGATAATTAAG
1 AGTAAAAGT-AAAAGAAGTAATCAGTAAATAG-TAATTAAG
*
71384 AGTAAAAGTAAAACAAGTAATCAGTA
1 AGTAAAAGTAAAAGAAGTAATCAGTA
71410 GAAAGGAGTA
Statistics
Matches: 154, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
36 58 0.38
37 2 0.01
38 25 0.16
39 3 0.02
40 37 0.24
41 29 0.19
ACGTcount: A:0.57, C:0.03, G:0.21, T:0.19
Consensus pattern (39 bp):
AGTAAAAGTAAAAGAAGTAATCAGTAAATAGTAATTAAG
Found at i:71390 original size:81 final size:75
Alignment explanation
Indices: 71193--71424 Score: 236
Period size: 81 Copynumber: 3.0 Consensus size: 75
71183 AGAAGTAATC
* * ** * * * *
71193 AGTAAAAGTAAAAGAAGTAATAAGTAAGAGTAA--AAGAGTAAGAGTAAAAGAAGTAATCTGTG-
1 AGTAAAAATAAAAGAAGCAAGCAGTAAAAGTAATTAAGAGTAAAAGTAAAAGAAGTAATCAGAGA
71255 AAAGTAAAAG
66 AAAGTAAAAG
*
71265 AGTAAAAATAAAAGAAGCAATCAGTAAAAGTAATTAAGAGTAAAAGTAAAAGAAGTAATCAGAGA
1 AGTAAAAATAAAAGAAGCAAGCAGTAAAAGTAATTAAGAGTAAAAGTAAAAGAAGTAATCAGAGA
71330 AATAGTAAGTAAG
66 AA-AGTAA--AAG
* * * * *
71343 AGTAAAAGTAAAAAGGAGTAAGCAGTAAATTGATAATTAAGAGTAAAAGTAAAACAAGTAATCAG
1 AGTAAAAAT-AAAAGAAGCAAGCAGTAAA-AG-TAATTAAGAGTAAAAGTAAAAGAAGTAATCAG
71408 TAGAAAGGAGTAAAAG
63 -AGAAA--AGTAAAAG
71424 A
1 A
71425 AGAAGAAGTA
Statistics
Matches: 135, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
72 29 0.21
74 26 0.19
75 2 0.01
76 5 0.04
78 11 0.08
79 16 0.12
80 1 0.01
81 35 0.26
82 5 0.04
83 5 0.04
ACGTcount: A:0.57, C:0.03, G:0.22, T:0.18
Consensus pattern (75 bp):
AGTAAAAATAAAAGAAGCAAGCAGTAAAAGTAATTAAGAGTAAAAGTAAAAGAAGTAATCAGAGA
AAAGTAAAAG
Found at i:82806 original size:12 final size:12
Alignment explanation
Indices: 82789--82823 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
82779 CTTGAGAAAA
82789 TATTTTCCTTGG
1 TATTTTCCTTGG
82801 TATTTTCCATT-G
1 TATTTTCC-TTGG
82813 TATTTTCCTTG
1 TATTTTCCTTG
82824 ACACCAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.11, C:0.17, G:0.11, T:0.60
Consensus pattern (12 bp):
TATTTTCCTTGG
Found at i:83550 original size:22 final size:21
Alignment explanation
Indices: 83500--83557 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
83490 AAAATTTTGA
83500 TTTC-AAAATTAAAAGAAATT
1 TTTCAAAAATTAAAAGAAATT
* **
83520 TTTCTAAAATTGAAAAGACTTAT
1 TTTCAAAAATT-AAAAGAAAT-T
83543 TTTCAAAAATTAAAA
1 TTTCAAAAATTAAAA
83558 AGAATTTCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 4 0.12
21 6 0.19
22 11 0.34
23 11 0.34
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (21 bp):
TTTCAAAAATTAAAAGAAATT
Found at i:87213 original size:18 final size:18
Alignment explanation
Indices: 87187--87224 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
87177 ATCCACGCCT
87187 CCCAAACCAAGCTTTACA
1 CCCAAACCAAGCTTTACA
* *
87205 CCCAGACCAAGCTTTGCA
1 CCCAAACCAAGCTTTACA
87223 CC
1 CC
87225 ATCATACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.42, G:0.11, T:0.16
Consensus pattern (18 bp):
CCCAAACCAAGCTTTACA
Found at i:91635 original size:42 final size:42
Alignment explanation
Indices: 91558--91637 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
91548 GATGTTTTTA
* * * *
91558 TGTCATGTCATCATGTCAAGTGATATTTTAGATGATATGGCC
1 TGTCATATCATCATGTCAAGTGACATATGAGATGATATGGCC
*
91600 TGTCATATCATCATGTCACGTGACATGATGA-ATGATAT
1 TGTCATATCATCATGTCAAGTGACAT-ATGAGATGATAT
91638 AGACGTGTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
42 30 0.94
43 2 0.06
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (42 bp):
TGTCATATCATCATGTCAAGTGACATATGAGATGATATGGCC
Found at i:91897 original size:33 final size:33
Alignment explanation
Indices: 91860--91925 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
91850 AGGTTTTATT
* *
91860 CTAATTGTTGTTTAGTAGAGAGAAAATTCGGTG
1 CTAATTGTTATTTACTAGAGAGAAAATTCGGTG
* * *
91893 CTAATTGTTATTTACTGGTGAGAAAATTTGGTG
1 CTAATTGTTATTTACTAGAGAGAAAATTCGGTG
91926 TGCGCAGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.39
Consensus pattern (33 bp):
CTAATTGTTATTTACTAGAGAGAAAATTCGGTG
Found at i:93808 original size:17 final size:17
Alignment explanation
Indices: 93770--93802 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
93760 CTTATAGTAC
*
93770 CTAGGTATTATGAGGTA
1 CTAGGTAGTATGAGGTA
93787 CTAGGTAGTATGAGGT
1 CTAGGTAGTATGAGGT
93803 GATAGGCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.06, G:0.33, T:0.33
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTA
Found at i:94392 original size:156 final size:155
Alignment explanation
Indices: 94154--94517 Score: 389
Period size: 156 Copynumber: 2.3 Consensus size: 155
94144 GAGCTTCTCA
*
94154 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTAAATGAGCTAAAA
1 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTAAACGAGCT-AAA
* * * *
94219 TTTTGCCAAGGGTCTTAGAATATC-CACAT-GAGACTATGGAAAAAATTATAAGTAAAACCGAGC
65 TTTTGCCAAGAGACTTAGAATATCAC-CATAAAG-CTATGGAAAAAATTATAAGTAAAACCGAAC
* * * *
94282 TCCCCTTG-ATGGTGAACTAGGTTTCTCT
128 T-CCCTAGCATAGAGAACTAGGTTTCACT
** * * *
94310 CCTTGAGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAAGCT-GA
1 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTAAACG-AGCTAAA
* * *
94373 TTTT-CCACCAGTAGACTTAGATTATCACCATAAAGCTATGGGAAAAATTCTAAGTAAAACCGAA
65 TTTTGCCA--AG-AGACTTAGAATATCACCATAAAGCTATGGAAAAAATTATAAGTAAAACCGAA
* * * *
94437 CTCTCTAGCATAGAGAAGTTGGTTTGACT
127 CTCCCTAGCATAGAGAACTAGGTTTCACT
* * * *
94466 CCTCAAACTGTCCTTAACTGAAAAACTAGCTTAAGTTTTTCATACTAAGTCT
1 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCT
94518 GTTTGAGATG
Statistics
Matches: 172, Mismatches: 28, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
153 3 0.02
154 5 0.03
155 9 0.05
156 152 0.88
157 3 0.02
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (155 bp):
CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTAAACGAGCTAAAT
TTTGCCAAGAGACTTAGAATATCACCATAAAGCTATGGAAAAAATTATAAGTAAAACCGAACTCC
CTAGCATAGAGAACTAGGTTTCACT
Done.