Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004401.1 Hibiscus syriacus cultivar Beakdansim tig00009649_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 165641
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:137 original size:68 final size:68
Alignment explanation
Indices: 11--137 Score: 211
Period size: 67 Copynumber: 1.9 Consensus size: 68
1 TTTAATTTTT
11 GTTTCATTTTAGTACCCCCACAGTTAAAAACATTAGTTTTTGTTTCATTCTAGTACCCCTTAAAA
1 GTTTCATTTTAGTACCCCCACAGTTAAAAACATTAGTTTTTGTTTCATTCTAGTACCCCTTAAAA
76 TTG
66 TTG
* * *
79 GTTTCATTTTAGTA-CCCCACCGTTAAAAACTTTAGTTTTTGTTTCATTTTAGTAACCCC
1 GTTTCATTTTAGTACCCCCACAGTTAAAAACATTAGTTTTTGTTTCATTCTAGT-ACCCC
138 ACAGTTAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
67 36 0.65
68 19 0.35
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (68 bp):
GTTTCATTTTAGTACCCCCACAGTTAAAAACATTAGTTTTTGTTTCATTCTAGTACCCCTTAAAA
TTG
Found at i:5569 original size:2 final size:2
Alignment explanation
Indices: 5562--5624 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
5552 TACAAGATGA
5562 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5603 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
5625 GGTAACAAAG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9780 original size:23 final size:23
Alignment explanation
Indices: 9736--9780 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
9726 TGTAAAAAGT
* *
9736 ATTTAGTCATAATAACATATTAA
1 ATTTAGTCAAAATAACAAATTAA
*
9759 ATTTAGTCAAAATAATAAATTA
1 ATTTAGTCAAAATAACAAATTA
9781 TGTAAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (23 bp):
ATTTAGTCAAAATAACAAATTAA
Found at i:12311 original size:2 final size:2
Alignment explanation
Indices: 12304--12338 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12294 TAAGATTAAG
12304 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12339 AGGAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14750 original size:4 final size:4
Alignment explanation
Indices: 14741--14767 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
14731 ATAAATATAT
14741 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
14768 TCTTTTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:16015 original size:27 final size:24
Alignment explanation
Indices: 15952--16023 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 24
15942 ATAAATTCAT
*
15952 AATATTTTATATATATTAATTTAAA
1 AATATTTTAT-TATATTAACTTAAA
*
15977 AATATTTT-TTATATTAACTTATTA
1 AATATTTTATTATATTAACTTA-AA
16001 AATATGCTTTA-T-TATTAACTTAA
1 AATAT--TTTATTATATTAACTTAA
16024 TTTATAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
23 11 0.28
24 7 0.17
25 18 0.45
26 4 0.10
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (24 bp):
AATATTTTATTATATTAACTTAAA
Found at i:16037 original size:27 final size:26
Alignment explanation
Indices: 15967--16040 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 26
15957 TTTATATATA
* *
15967 TTAATTTAAAAATATTTTTTATATTAAC
1 TTAATTT-AAAATACTTTAT-TATTAAC
*
15995 TT-A-TTAAATATGCTTTATTATTAAC
1 TTAATTTAAA-ATACTTTATTATTAAC
16020 TTAATTTATAAATACTTTATT
1 TTAATTTA-AAATACTTTATT
16041 TTTTATTTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
25 12 0.32
26 9 0.24
27 13 0.34
28 4 0.11
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.54
Consensus pattern (26 bp):
TTAATTTAAAATACTTTATTATTAAC
Found at i:16704 original size:1 final size:1
Alignment explanation
Indices: 16698--16727 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
16688 AAAAGTTCAA
16698 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16728 GTAATTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:22936 original size:12 final size:11
Alignment explanation
Indices: 22918--22951 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
22908 CCTCCTTTTG
*
22918 TTTTTATTTTA
1 TTTTTATATTA
22929 TATTTTATATTA
1 T-TTTTATATTA
22941 TTTTTATATTA
1 TTTTTATATTA
22952 AATAATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTATATTA
Found at i:29113 original size:25 final size:24
Alignment explanation
Indices: 29053--29114 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
29043 TTCCAAGAAA
* *
29053 ATTTATTAATTTTTATAAATATAT
1 ATTTATTTATTTTTATAAATAGAT
*
29077 ATTTTTTATATTTTTATAAATAAGAT
1 ATTTATT-TATTTTTATAAAT-AGAT
29103 ATTTATTTATTT
1 ATTTATTTATTT
29115 AGAAATATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 6 0.19
25 17 0.53
26 9 0.28
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
ATTTATTTATTTTTATAAATAGAT
Found at i:29269 original size:148 final size:148
Alignment explanation
Indices: 29100--29481 Score: 611
Period size: 148 Copynumber: 2.6 Consensus size: 148
29090 TTATAAATAA
* * * * * *
29100 GATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGTTACTTTAAGATAGTCATTTTCTTA
1 GATATTTAGTTATTTAAAAATATCAGAAAAAGACTTCTAGTTGCTTTAAGACAATCATTTTCTTA
29165 ATATTAAAAAATAAATAAATAGTAATAAAACATTTCTCTAAAAATAAATAAATAAAATAAATATA
66 ATATTAAAAAATAAATAAATAGTAATAAAACATTTCTCTAAAAATAAATAAATAAAATAAATATA
29230 TATAATTTATAAAAGTAG
131 TATAATTTATAAAAGTAG
* * *
29248 GATATTTAGTTATTAAAAAATATCAGAAAATGAATTCTAGTTGCTTTAAGACAATCATTTTCTTA
1 GATATTTAGTTATTTAAAAATATCAGAAAAAGACTTCTAGTTGCTTTAAGACAATCATTTTCTTA
* * *
29313 ATATTAAAAAATAAATAAATATTAATAAAACATTTCTCTAAAAATAAATAAATTAAATTAATATA
66 ATATTAAAAAATAAATAAATAGTAATAAAACATTTCTCTAAAAATAAATAAATAAAATAAATATA
29378 TATAATTTATAAAAGTAG
131 TATAATTTATAAAAGTAG
* * **
29396 GATATTTAGTTATTTAAAAATATCAGAAAAAGACATCTAGTTGCTTTAAGACAACCCCTTTCTTA
1 GATATTTAGTTATTTAAAAATATCAGAAAAAGACTTCTAGTTGCTTTAAGACAATCATTTTCTTA
*
29461 ATATTTAAAAATAAATAAATA
66 ATATTAAAAAATAAATAAATA
29482 CTATTATTTA
Statistics
Matches: 215, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
148 215 1.00
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.36
Consensus pattern (148 bp):
GATATTTAGTTATTTAAAAATATCAGAAAAAGACTTCTAGTTGCTTTAAGACAATCATTTTCTTA
ATATTAAAAAATAAATAAATAGTAATAAAACATTTCTCTAAAAATAAATAAATAAAATAAATATA
TATAATTTATAAAAGTAG
Found at i:29784 original size:2 final size:2
Alignment explanation
Indices: 29777--29855 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
29767 ATTTATCCTA
29777 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29819 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29856 CATTGCAATG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30587 original size:33 final size:33
Alignment explanation
Indices: 30550--30641 Score: 154
Period size: 33 Copynumber: 2.9 Consensus size: 33
30540 GGCTGTCTGT
30550 AGCTGCAACGTGGAGGGGCTGCTGGAATGTTGA
1 AGCTGCAACGTGGAGGGGCTGCTGGAATGTTGA
30583 AGCTGCAACGTGGAGGGGCTGCTGGAATGTTGA
1 AGCTGCAACGTGGAGGGGCTGCTGGAATGTTGA
*
30616 AGCTGAAACGTGGA---GCTGCTGGAATG
1 AGCTGCAACGTGGAGGGGCTGCTGGAATG
30642 GGGAGGTAGA
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
30 12 0.21
33 46 0.79
ACGTcount: A:0.23, C:0.15, G:0.41, T:0.21
Consensus pattern (33 bp):
AGCTGCAACGTGGAGGGGCTGCTGGAATGTTGA
Found at i:31232 original size:17 final size:17
Alignment explanation
Indices: 31210--31263 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
31200 TTCAAATAAG
31210 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
* *
31227 TTC-T-TCA-GAT-AAG
1 TTCTTCTCATTATGAAC
31240 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
31257 TTCTTCT
1 TTCTTCT
31264 GGAAATGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
13 5 0.17
14 3 0.10
15 6 0.21
16 3 0.10
17 12 0.41
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:31232 original size:30 final size:30
Alignment explanation
Indices: 31198--31262 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
31188 TTCTTCTTTA
31198 TCTTCAAATAAGTTCTTCTCATTATGAACT
1 TCTTCAAATAAGTTCTTCTCATTATGAACT
*
31228 TCTTCAGATAAGTTCTTCTCATTATGAACT
1 TCTTCAAATAAGTTCTTCTCATTATGAACT
31258 TCTTC
1 TCTTC
31263 TGGAAATGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.45
Consensus pattern (30 bp):
TCTTCAAATAAGTTCTTCTCATTATGAACT
Found at i:31406 original size:98 final size:99
Alignment explanation
Indices: 31237--31459 Score: 337
Period size: 98 Copynumber: 2.3 Consensus size: 99
31227 TTCTTCAGAT
* ** *
31237 AAGTTCTTCTCATTATGAAC-TTCTTCTGGAAATGTTGATCCTTAAAAGAGGTGTCGTTGATTCA
1 AAGTTCTTCTCATTATGAACTTTCTTCTGAAAATACTGATCCTCAAAAGAGGTGTCGTTGATTCA
31301 ACTTCATATGTGATAAATTAAGAAAAGATTGAAC
66 ACTTCATATGTGATAAATTAAGAAAAGATTGAAC
*
31335 AAGTTCTTCTCATTATGAACTTTC-TCTGAAAATACTGA-CCATCGAAAGAGGTGTCGTTGATTC
1 AAGTTCTTCTCATTATGAACTTTCTTCTGAAAATACTGATCC-TCAAAAGAGGTGTCGTTGATTC
* * *
31398 AACTTCATATGTGATGAATTAAGACAAGGTTGAAC
65 AACTTCATATGTGATAAATTAAGAAAAGATTGAAC
31433 AAGTTCTTCTCATTATGAAC-TTCTTCT
1 AAGTTCTTCTCATTATGAACTTTCTTCT
31460 TCTTCTTCAG
Statistics
Matches: 114, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
97 5 0.04
98 106 0.93
99 3 0.03
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Consensus pattern (99 bp):
AAGTTCTTCTCATTATGAACTTTCTTCTGAAAATACTGATCCTCAAAAGAGGTGTCGTTGATTCA
ACTTCATATGTGATAAATTAAGAAAAGATTGAAC
Found at i:31582 original size:137 final size:137
Alignment explanation
Indices: 31336--31641 Score: 492
Period size: 137 Copynumber: 2.2 Consensus size: 137
31326 AGATTGAACA
31336 AGTTCTTCTCATTATGAACTTTCTCTGAAAATACTGACCATCGAAAGAGGTGTCGTTGATTCAAC
1 AGTTCTTCTCATTATGAACTTTCTCTGAAAATACTGACCATCGAAAGAGGTGTCGTTGATTCAAC
* * * *
31401 TTCATATGTGATGAATTAAGACAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCT
66 TTCATATATGATGAATTAAGACAAGGTTGAACAAATTATTCTCATTATGAACTTCTTCTTCCTCT
31466 TCAGATG
131 TCAGATG
*
31473 AGTTCTTCTCATTATGAACTTTCTCTGAAAATGCTGATCC-TC-AACAGAGGTGTCGTTGATTCA
1 AGTTCTTCTCATTATGAACTTTCTCTGAAAATACTGA-CCATCGAA-AGAGGTGTCGTTGATTCA
*
31536 ACGTT-ATATATGATGAATTAAGGCAAGGTTGAACAAATTATTCTCATTATGAACTTCTTCTTCC
64 AC-TTCATATATGATGAATTAAGACAAGGTTGAACAAATTATTCTCATTATGAACTTCTTCTTCC
31600 TCTTCAGATG
128 TCTTCAGATG
*
31610 AGTTCTTCTTATTATGAACTTTCTCTGGAAAA
1 AGTTCTTCTCATTATGAACTTTCTCT-GAAAA
31642 GTTGATGCTG
Statistics
Matches: 158, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
136 2 0.01
137 147 0.93
138 9 0.06
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (137 bp):
AGTTCTTCTCATTATGAACTTTCTCTGAAAATACTGACCATCGAAAGAGGTGTCGTTGATTCAAC
TTCATATATGATGAATTAAGACAAGGTTGAACAAATTATTCTCATTATGAACTTCTTCTTCCTCT
TCAGATG
Found at i:31710 original size:123 final size:124
Alignment explanation
Indices: 31560--32137 Score: 936
Period size: 124 Copynumber: 4.7 Consensus size: 124
31550 GAATTAAGGC
* * *
31560 AAGGTTGAACAAATTATTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
31625 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGC-AA
66 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAAA
*
31683 AAGGTTGAAAAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
*
31748 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTTCTTCTGTGATAGAGTCATGCAAA
66 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAAA
* *
31807 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATCTTCAGATAAATTCTTCTCATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* *
31872 GAACTTTCTCTGGAAAAGTTGATGATAATCTATCTCCTTCTGTGATAGAGTCATGCAAA
66 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAAA
* *
31931 AAGGTTGAACAAATTTTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAG---TTCTCATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
31993 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGC-AA
66 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAAA
* * * *
32051 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTC-TCATTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATAAGTTCTTCTCATTA
* * *
32115 TGAAATCT-TCTGGAAATGTTGAT
65 TGAACTTTCTCTGGAAAAGTTGAT
32138 CCATCGAGTG
Statistics
Matches: 426, Mismatches: 24, Indels: 11
0.92 0.05 0.02
Matches are distributed among these distances:
119 2 0.00
120 47 0.11
121 64 0.15
122 14 0.03
123 131 0.31
124 168 0.39
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (124 bp):
AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAAA
Found at i:32292 original size:36 final size:36
Alignment explanation
Indices: 32252--32373 Score: 104
Period size: 36 Copynumber: 3.4 Consensus size: 36
32242 GAGTGAATCT
*
32252 ATCTCAAGAGAAACGCAATTTGTTTTAAGAAAAACA
1 ATCTCAAGAGAGACGCAATTTGTTTTAAGAAAAACA
* * * * ** *
32288 ATCTCAAGTGAGA--TAAATTGTTATTTCGAGTGAAACT
1 ATCTCAAGAGAGACGCAATTTG-T-TTT-AAGAAAAACA
* *
32325 ATCTCAAGCGAGACGCAATTTGTTTTAAGAAAAATA
1 ATCTCAAGAGAGACGCAATTTGTTTTAAGAAAAACA
*
32361 ATCTCAAGTGAGA
1 ATCTCAAGAGAGA
32374 TAAATTGTTA
Statistics
Matches: 64, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
34 5 0.08
35 1 0.02
36 31 0.48
37 21 0.33
38 1 0.02
39 5 0.08
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (36 bp):
ATCTCAAGAGAGACGCAATTTGTTTTAAGAAAAACA
Found at i:32331 original size:37 final size:36
Alignment explanation
Indices: 32221--32337 Score: 94
Period size: 37 Copynumber: 3.2 Consensus size: 36
32211 AACAATCTTG
*
32221 AGTGAGATAAATTGTTGTTTCGAGTGAATCTATCTCA
1 AGTGAGATAAATTGTT-TTTCGAGTGAAACTATCTCA
* * ** * ** *
32258 AGAGAAACGCAATT-TGTTTT-AAGAAAAACAATCTCA
1 AGTGAGA-TAAATTGT-TTTTCGAGTGAAACTATCTCA
32294 AGTGAGATAAATTGTTATTTCGAGTGAAACTATCTCA
1 AGTGAGATAAATTGTT-TTTCGAGTGAAACTATCTCA
*
32331 AGCGAGA
1 AGTGAGA
32338 CGCAATTTGT
Statistics
Matches: 57, Mismatches: 18, Indels: 10
0.67 0.21 0.12
Matches are distributed among these distances:
35 5 0.09
36 20 0.35
37 27 0.47
38 5 0.09
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (36 bp):
AGTGAGATAAATTGTTTTTCGAGTGAAACTATCTCA
Found at i:32383 original size:73 final size:73
Alignment explanation
Indices: 32172--32386 Score: 333
Period size: 73 Copynumber: 2.9 Consensus size: 73
32162 TTGTTTCTAT
* * **
32172 TGAAACTATCTTAAGCGAGAAG-AATCTTGTTTTAAGAAAAACAATCTTGAGTGAGATAAATTGT
1 TGAAACTATCTCAAGCGAGACGCAAT-TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGT
*
32236 TGTTTCGAG
65 TATTTCGAG
* * *
32245 TGAATCTATCTCAAGAGAAACGCAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTT
1 TGAAACTATCTCAAGCGAGACGCAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTT
32310 ATTTCGAG
66 ATTTCGAG
*
32318 TGAAACTATCTCAAGCGAGACGCAATTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAATTGTT
1 TGAAACTATCTCAAGCGAGACGCAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTT
32383 ATTT
66 ATTT
32387 GAAAACATCA
Statistics
Matches: 129, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
73 126 0.98
74 3 0.02
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (73 bp):
TGAAACTATCTCAAGCGAGACGCAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTT
ATTTCGAG
Found at i:33113 original size:22 final size:22
Alignment explanation
Indices: 33055--33113 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
33045 AATAAAGCTT
*
33055 TCATCTTTGAA-AAGAGAATCTA
1 TCATCTTTGAAGAA-TGAATCTA
*
33077 TCACCTTTGAAGAATGAATCTA
1 TCATCTTTGAAGAATGAATCTA
33099 TCATCTTTGAAGAAT
1 TCATCTTTGAAGAAT
33114 ATAGATGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 31 0.94
23 2 0.06
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAGAATGAATCTA
Found at i:34502 original size:19 final size:19
Alignment explanation
Indices: 34475--34526 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
34465 AATGCACTGA
34475 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
* *
34494 GTGCGTCGATGTATGGTAT
1 GTGCATCGATGCATGGTAT
34513 GTGCATCGATGCAT
1 GTGCATCGATGCAT
34527 AAAATGCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.19, C:0.15, G:0.33, T:0.33
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:34582 original size:20 final size:20
Alignment explanation
Indices: 34553--34592 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
34543 TCAAGAAATT
34553 AATTGATGCATCGATGCATG
1 AATTGATGCATCGATGCATG
* *
34573 AATTGGTGCATCGGTGCATG
1 AATTGATGCATCGATGCATG
34593 CCCTTGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (20 bp):
AATTGATGCATCGATGCATG
Found at i:36503 original size:44 final size:44
Alignment explanation
Indices: 36414--36510 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
36404 GCTCTTGTGC
* * *
36414 ATCGATACACATTCAAGGGCGTGCATCGGTGCATCAGCTGATGT
1 ATCGATGCACATTCAAGGGCATGCATCGGTGCATCAGCTAATGT
* *
36458 ATCGATGCACATTCAAAGGG-ATGCATCGGTGCA-CTGTTAAGTGT
1 ATCGATGCACATTC-AAGGGCATGCATCGGTGCATCAGCTAA-TGT
36502 ATCGATGCA
1 ATCGATGCA
36511 TTAAACATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 4 0.09
44 37 0.80
45 5 0.11
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGGCATGCATCGGTGCATCAGCTAATGT
Found at i:42104 original size:46 final size:45
Alignment explanation
Indices: 42045--42132 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 45
42035 TTGAAAAAGC
* * *
42045 CTGAGCGCATCGATGCATAGTCTTGTGCATCGTTGCATCAAATGCA
1 CTGAGCGCATCGATGCATAGT-ATGTGCATCGATGCATAAAATGCA
* *
42091 CTGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAAT
1 CTGAGCGCATCGATGCATAGTATGTGCATCGATGCATAAAAT
42133 ATATTCGATG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 18 0.49
46 19 0.51
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.28
Consensus pattern (45 bp):
CTGAGCGCATCGATGCATAGTATGTGCATCGATGCATAAAATGCA
Found at i:42183 original size:20 final size:20
Alignment explanation
Indices: 42155--42193 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42145 CAAGAAATTA
42155 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
42175 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
42194 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:45124 original size:16 final size:16
Alignment explanation
Indices: 45093--45123 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
45083 TCTTAATTTA
45093 ATTTTTTCCTTTTTTT
1 ATTTTTTCCTTTTTTT
45109 ATTTTTT-CTTTTTTT
1 ATTTTTTCCTTTTTTT
45124 TGATGAACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (16 bp):
ATTTTTTCCTTTTTTT
Found at i:47157 original size:28 final size:26
Alignment explanation
Indices: 47078--47160 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 26
47068 TTATGTAATG
*
47078 ATGCAAATACAAAAATGAAAATGTAA
1 ATGCAAATACAAAAATGAAAATGCAA
* **
47104 ATACAAATGTAAAAATGCAAAGATGCAA
1 ATGCAAATACAAAAATG-AAA-ATGCAA
*
47132 ATGCAAATACAAAGATGTAGAAATGCAA
1 ATGCAAATACAAAAATG-A-AAATGCAA
47160 A
1 A
47161 AATAAGAATG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
26 14 0.31
27 3 0.07
28 26 0.58
29 2 0.04
ACGTcount: A:0.58, C:0.10, G:0.14, T:0.18
Consensus pattern (26 bp):
ATGCAAATACAAAAATGAAAATGCAA
Found at i:47223 original size:6 final size:7
Alignment explanation
Indices: 47207--47238 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
47197 TAAAAGTACG
47207 AATGCAA
1 AATGCAA
47214 AATG-AA
1 AATGCAA
47220 AATGCAA
1 AATGCAA
47227 AATGC-A
1 AATGCAA
47233 AATGCA
1 AATGCA
47239 TGTATGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 12 0.52
7 11 0.48
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (7 bp):
AATGCAA
Found at i:47225 original size:13 final size:13
Alignment explanation
Indices: 47207--47238 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
47197 TAAAAGTACG
47207 AATGCAAAATGAA
1 AATGCAAAATGAA
*
47220 AATGCAAAATGCA
1 AATGCAAAATGAA
47233 AATGCA
1 AATGCA
47239 TGTATGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (13 bp):
AATGCAAAATGAA
Found at i:49283 original size:18 final size:16
Alignment explanation
Indices: 49260--49294 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
49250 AATTCCAAGA
49260 AAATATATTAATTTTTAT
1 AAATATA-T-ATTTTTAT
49278 AAATATATATTTTTAT
1 AAATATATATTTTTAT
49294 A
1 A
49295 TTTTTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATATATATTTTTAT
Found at i:49479 original size:148 final size:147
Alignment explanation
Indices: 49308--49691 Score: 608
Period size: 148 Copynumber: 2.6 Consensus size: 147
49298 TTATAAATAA
* *
49308 GATATTTATTTACTTAGAAATATCAGAAAAAGACTTCTAGTTGCTTTAAGACAGTCATTTTCTTA
1 GATATTTAGTTA-TTAAAAATATCAGAAAAAGACTTCTAGTTGCTTTAAGACAGTCATTTTCTTA
49373 ATATTAAAAAATAAATAAATATTAATAAAACATTTCTCTAAAAATAAATAAATAAAATTAATATA
65 ATATTAAAAAATAAATAAATATTAATAAAACATTTCTCTAAAAATAAATAAATAAAATTAATATA
49438 TATAATTTATAAAAGTAG
130 TATAATTTATAAAAGTAG
*
49456 GATATTTAGTTATTCAAAAATATCA-AAAAATGACTTCTAGTTGCTTTAGGACAGTCATTTTCTT
1 GATATTTAGTTATT-AAAAATATCAGAAAAA-GACTTCTAGTTGCTTTAAGACAGTCATTTTCTT
* *
49520 AATATTAAAAAATAAATAAATATTAATAAAACATTTTTCTAAAAATAAATAAATTAAATTAATAT
64 AATATTAAAAAATAAATAAATATTAATAAAACATTTCTCTAAAAATAAATAAATAAAATTAATAT
*
49585 ATATAATTTATAAAAGTGG
129 ATATAATTTATAAAAGTAG
* * * ** **
49604 GATATTTAGTTATTTAGAATATCAGAAAAGGACTTCTAGTTGCTTTAAGACAACCCCTTTCTTAA
1 GATATTTAGTTATTAAAAATATCAGAAAAAGACTTCTAGTTGCTTTAAGACAGTCATTTTCTTAA
*
49669 TATTTAAAAATAAATAAATATTA
66 TATTAAAAAATAAATAAATATTA
49692 TTATTTAATC
Statistics
Matches: 218, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
147 67 0.31
148 151 0.69
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (147 bp):
GATATTTAGTTATTAAAAATATCAGAAAAAGACTTCTAGTTGCTTTAAGACAGTCATTTTCTTAA
TATTAAAAAATAAATAAATATTAATAAAACATTTCTCTAAAAATAAATAAATAAAATTAATATAT
ATAATTTATAAAAGTAG
Found at i:54975 original size:20 final size:20
Alignment explanation
Indices: 54950--54987 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
54940 AAATCAACGA
*
54950 GTCAAAGTCTACGGTCAATG
1 GTCAAAGTCAACGGTCAATG
54970 GTCAAAGTCAACGGTCAA
1 GTCAAAGTCAACGGTCAA
54988 AGTCAATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (20 bp):
GTCAAAGTCAACGGTCAATG
Found at i:54979 original size:13 final size:13
Alignment explanation
Indices: 54963--55000 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
54953 AAAGTCTACG
54963 GTCAATGGTCAAA
1 GTCAATGGTCAAA
*
54976 GTCAACGGTCAAA
1 GTCAATGGTCAAA
54989 GTCAATGGTCAA
1 GTCAATGGTCAA
55001 TGGGTTGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (13 bp):
GTCAATGGTCAAA
Found at i:55538 original size:2 final size:2
Alignment explanation
Indices: 55533--55566 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55523 ACATATATCC
55533 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55567 CAAATCCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58988 original size:90 final size:91
Alignment explanation
Indices: 58866--59044 Score: 297
Period size: 90 Copynumber: 2.0 Consensus size: 91
58856 TAATCTCGAA
* * * *
58866 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAAT-AAAATCCTTAATATGA
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGA
*
58930 TTAGGGTAACTTTGATATAAAAGGAT
66 TTAGGGTAACTTGGATATAAAAGGAT
58956 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGA
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGA
*
59021 TTAGGGTAACTTGGCTATAAAAGG
66 TTAGGGTAACTTGGATATAAAAGG
59045 GTATGTTAGG
Statistics
Matches: 82, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
90 46 0.56
91 36 0.44
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (91 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGA
TTAGGGTAACTTGGATATAAAAGGAT
Found at i:66305 original size:90 final size:90
Alignment explanation
Indices: 66194--66371 Score: 320
Period size: 90 Copynumber: 2.0 Consensus size: 90
66184 TAATTATGAA
* * *
66194 TATTTAATTTCAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
66259 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
66284 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
66349 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
66372 GTGTGTTAGG
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 84 1.00
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:66993 original size:13 final size:13
Alignment explanation
Indices: 66975--66999 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66965 CCCCTTAAGA
66975 AAAATTTTACCTC
1 AAAATTTTACCTC
66988 AAAATTTTACCT
1 AAAATTTTACCT
67000 GACAGAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATTTTACCTC
Found at i:67366 original size:50 final size:50
Alignment explanation
Indices: 67291--67390 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
67281 ATCATATCGG
67291 AACCTTATAATATGACATTTCAACTTATCTTTCAGAATCTGAATAATTGC
1 AACCTTATAATATGACATTTCAACTTATCTTTCAGAATCTGAATAATTGC
67341 AACCTTATAATATGACATTTCAACTTATCTTTCAGAATCTGAATAATTGC
1 AACCTTATAATATGACATTTCAACTTATCTTTCAGAATCTGAATAATTGC
67391 TCAAATAAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (50 bp):
AACCTTATAATATGACATTTCAACTTATCTTTCAGAATCTGAATAATTGC
Found at i:70036 original size:19 final size:19
Alignment explanation
Indices: 69995--70051 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
69985 CTAGCCCAAG
69995 AGTATCGATAC-TTCTACAAA
1 AGTATCGATACTTTCT--AAA
*
70015 AGTTTCGATACTTTCTAAA
1 AGTATCGATACTTTCTAAA
70034 AGTATCGATACTTT-TAAA
1 AGTATCGATACTTTCTAAA
70052 CATTTCAGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.12
19 16 0.47
20 10 0.29
21 4 0.12
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
AGTATCGATACTTTCTAAA
Found at i:71406 original size:28 final size:28
Alignment explanation
Indices: 71373--71483 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 28
71363 AAACAGAAAC
*
71373 AGGACGGGGACTAAGCCCATGCAGAATT
1 AGGACGGGGACTAAGCCCATGCAGAATA
* * * *
71401 AGGACGGAGCCTAAGCCCATACAGAAAA
1 AGGACGGGGACTAAGCCCATGCAGAATA
** *
71429 AGGATAGGGACTAAGCCCATGCA-AAGTC
1 AGGACGGGGACTAAGCCCATGCAGAA-TA
* *
71457 AGGACGAGGACTAATCCCATGCAGAAT
1 AGGACGGGGACTAAGCCCATGCAGAAT
71484 CAGGGATGCA
Statistics
Matches: 65, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
27 2 0.03
28 61 0.94
29 2 0.03
ACGTcount: A:0.37, C:0.23, G:0.28, T:0.13
Consensus pattern (28 bp):
AGGACGGGGACTAAGCCCATGCAGAATA
Found at i:71476 original size:56 final size:56
Alignment explanation
Indices: 71365--71482 Score: 141
Period size: 56 Copynumber: 2.1 Consensus size: 56
71355 AGGTTCTTAA
* * * *
71365 ACAGAAACAGGACGGGGACTAAGCCCATGCAGAATTAGGACGGAGCCTAAGCCCAT
1 ACAGAAAAAGGACAGGGACTAAGCCCATGCAGAATCAGGACGGAGACTAAGCCCAT
* *
71421 ACAGAAAAAGGATAGGGACTAAGCCCATGCA-AAGTCAGGAC-GAGGACTAATCCCAT
1 ACAGAAAAAGGACAGGGACTAAGCCCATGCAGAA-TCAGGACGGA-GACTAAGCCCAT
*
71477 GCAGAA
1 ACAGAA
71483 TCAGGGATGC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
55 4 0.08
56 49 0.92
ACGTcount: A:0.39, C:0.23, G:0.27, T:0.11
Consensus pattern (56 bp):
ACAGAAAAAGGACAGGGACTAAGCCCATGCAGAATCAGGACGGAGACTAAGCCCAT
Found at i:75202 original size:2 final size:2
Alignment explanation
Indices: 75197--75234 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
75187 TATATTTGTT
75197 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
75235 AGAAAATCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:76023 original size:52 final size:51
Alignment explanation
Indices: 75925--76034 Score: 150
Period size: 52 Copynumber: 2.1 Consensus size: 51
75915 GGGTTGGGGG
*
75925 ATTGGAGTGATGTTAATGGAGTATCGGGGGATTAAGGGATTATATTTTTATT
1 ATTGGAGTGATGTTAATGGAGTATCGCGGGATTAAGGGATTATA-TTTTATT
* * * *
75977 ATTGGAGTCGATGTTATTGGAGTATC-CGGGTTTAGGGGATTGTATTTTATT
1 ATTGGAGT-GATGTTAATGGAGTATCGCGGGATTAAGGGATTATATTTTATT
76028 ATTGGAG
1 ATTGGAG
76035 CCCCTGTTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
51 14 0.27
52 22 0.42
53 16 0.31
ACGTcount: A:0.24, C:0.04, G:0.32, T:0.41
Consensus pattern (51 bp):
ATTGGAGTGATGTTAATGGAGTATCGCGGGATTAAGGGATTATATTTTATT
Found at i:76043 original size:51 final size:53
Alignment explanation
Indices: 75934--76050 Score: 139
Period size: 51 Copynumber: 2.2 Consensus size: 53
75924 GATTGGAGTG
* * * *
75934 ATGTTAATGGAGTATCGGGGGATTAAGGGATTATATTTTTATTATTGGAGTCG
1 ATGTTATTGGAGTATCGCGGGATTAAGGGATTATATTTTTATTATTGGAGCCC
* * *
75987 ATGTTATTGGAGTATC-CGGGTTTAGGGGATTGTA-TTTTATTATTGGAGCCC
1 ATGTTATTGGAGTATCGCGGGATTAAGGGATTATATTTTTATTATTGGAGCCC
* *
76038 CTGTTATTAGAGT
1 ATGTTATTGGAGT
76051 CATTGTTATT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 26 0.47
52 14 0.25
53 15 0.27
ACGTcount: A:0.23, C:0.07, G:0.29, T:0.41
Consensus pattern (53 bp):
ATGTTATTGGAGTATCGCGGGATTAAGGGATTATATTTTTATTATTGGAGCCC
Found at i:76078 original size:15 final size:15
Alignment explanation
Indices: 76060--76094 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
76050 TCATTGTTAT
76060 TGGAGTCGCTATTAA
1 TGGAGTCGCTATTAA
* *
76075 TGGAGTTGCTATTAT
1 TGGAGTCGCTATTAA
76090 TGGAG
1 TGGAG
76095 ATGTTACCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.09, G:0.31, T:0.37
Consensus pattern (15 bp):
TGGAGTCGCTATTAA
Found at i:98594 original size:21 final size:20
Alignment explanation
Indices: 98568--98610 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
98558 ATTTAAAAAT
98568 AAAACTTAAAATAAAAATGAA
1 AAAACTTAAAATAAAAA-GAA
* *
98589 AAAACTTGAAATGAAAAGAA
1 AAAACTTAAAATAAAAAGAA
98609 AA
1 AA
98611 GAGAGAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.70, C:0.05, G:0.09, T:0.16
Consensus pattern (20 bp):
AAAACTTAAAATAAAAAGAA
Found at i:99583 original size:22 final size:21
Alignment explanation
Indices: 99533--99584 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
99523 ACATCACACA
*
99533 TAATATATTAATATTTTTAAT
1 TAATATTTTAATATTTTTAAT
*
99554 AAATTATTTTAATATGTGTTT-AT
1 TAA-TATTTTAATAT-T-TTTAAT
99577 TAATATTT
1 TAATATTT
99585 CATATACACA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 2 0.08
22 15 0.60
23 5 0.20
24 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
TAATATTTTAATATTTTTAAT
Found at i:100741 original size:72 final size:73
Alignment explanation
Indices: 100597--100742 Score: 208
Period size: 72 Copynumber: 2.0 Consensus size: 73
100587 TTTTAAGTTT
* * * *
100597 AATAATTAAAAAATATTTTTAAACATATTTTTTTATTTCAAATATTCGAAAATATGATAATTTAG
1 AATAATTAAAAAATATTTTTAAACATATTTTTTTATTTAAAAAACTCGAAAATATGATAATTCAG
100662 TAGGCCCC
66 TAGGCCCC
*
100670 AATAATT-AAAAATATTTTTAAACATCA-TTTTTTATTTAAAAAACTCGAAAATATGGTAATTCA
1 AATAATTAAAAAATATTTTTAAACAT-ATTTTTTTATTTAAAAAACTCGAAAATATGATAATTCA
100733 GT-GAGCCCC
65 GTAG-GCCCC
100742 A
1 A
100743 TTTTAATGAT
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
71 1 0.02
72 57 0.86
73 8 0.12
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (73 bp):
AATAATTAAAAAATATTTTTAAACATATTTTTTTATTTAAAAAACTCGAAAATATGATAATTCAG
TAGGCCCC
Found at i:103548 original size:46 final size:46
Alignment explanation
Indices: 103481--103573 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
103471 TAGACTATTT
103481 AAGAAAAATATAAAGACTTGTTAAGTATTTAAACTCGAAATTCAGC
1 AAGAAAAATATAAAGACTTGTTAAGTATTTAAACTCGAAATTCAGC
103527 AAGAAAAATATAAAGACTTGTTAAGTATTTAAACTCGAAATTCAGC
1 AAGAAAAATATAAAGACTTGTTAAGTATTTAAACTCGAAATTCAGC
103573 A
1 A
103574 TGAACAAGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (46 bp):
AAGAAAAATATAAAGACTTGTTAAGTATTTAAACTCGAAATTCAGC
Found at i:106373 original size:8 final size:8
Alignment explanation
Indices: 106362--106386 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
106352 TATCTGATAT
106362 GTTGATCC
1 GTTGATCC
106370 GTTGATCC
1 GTTGATCC
106378 GTTGATCC
1 GTTGATCC
106386 G
1 G
106387 ATATAAAAAT
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:0.12, C:0.24, G:0.28, T:0.36
Consensus pattern (8 bp):
GTTGATCC
Found at i:114874 original size:25 final size:25
Alignment explanation
Indices: 114843--114891 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
114833 GGATGAAACA
114843 ACAACTTTTTTATTATGAAATTGAC
1 ACAACTTTTTTATTATGAAATTGAC
114868 ACAACTTTTTTATTATGAAATTGA
1 ACAACTTTTTTATTATGAAATTGA
114892 AGTAAGTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (25 bp):
ACAACTTTTTTATTATGAAATTGAC
Found at i:115466 original size:19 final size:19
Alignment explanation
Indices: 115406--115466 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
115396 TTGGTGCAGA
* *
115406 GGGAATCGATACCCTCATG
1 GGGAATCGATACCCCCCTG
*
115425 AGGGAATCGAT-TCCCCCTAG
1 -GGGAATCGATACCCCCCT-G
115445 GGGAATCGATACCCCCCTG
1 GGGAATCGATACCCCCCTG
115464 GGG
1 GGG
115467 TTCTGGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.18
Consensus pattern (19 bp):
GGGAATCGATACCCCCCTG
Found at i:121862 original size:19 final size:20
Alignment explanation
Indices: 121835--121875 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
121825 TCTACATTGG
*
121835 GAGTGATTTTAT-ATCTTTT
1 GAGTGATTTTATGATATTTT
*
121854 GAGTTATTTTATGATATTTT
1 GAGTGATTTTATGATATTTT
121874 GA
1 GA
121876 TATAATTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.24, C:0.02, G:0.17, T:0.56
Consensus pattern (20 bp):
GAGTGATTTTATGATATTTT
Found at i:122875 original size:64 final size:63
Alignment explanation
Indices: 122738--122893 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 63
122728 ATTGTTCAAG
* * * * *
122738 GTGTATCGATGCACATGAAGTGTATCGATGAACTCCTTTAAATAAAAACATCGAATGCCATAA
1 GTGTATCGATGCACAAGTAGTGCATCGATGAACCCCCTTAAATAAAAACATCGAATGCCATAA
* * ** **
122801 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAGATTAAAACATCGAATGTGATTT
1 GTGTATCGATGCACAAGTAGTGCATCGATGAACCCCCTTAA-ATAAAAACATCGAATGCCATAA
* *
122865 GTGTACCGATGCACAGGTAGTGCATCGAT
1 GTGTATCGATGCACAAGTAGTGCATCGAT
122894 ACACACGGTA
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
63 35 0.44
64 44 0.56
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (63 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGAACCCCCTTAAATAAAAACATCGAATGCCATAA
Found at i:123492 original size:18 final size:19
Alignment explanation
Indices: 123445--123504 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 19
123435 GTCGAGGGTT
123445 ATAGTGGTCCTTCGGGACA
1 ATAGTGGTCCTTCGGGACA
123464 TATCCAGTGGTCCTTCGGGAC-
1 -AT--AGTGGTCCTTCGGGACA
* *
123485 GTAGTGGTCCTTCAGGACA
1 ATAGTGGTCCTTCGGGACA
123504 A
1 A
123505 ATATTCAGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 15 0.44
20 3 0.09
22 16 0.47
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.27
Consensus pattern (19 bp):
ATAGTGGTCCTTCGGGACA
Found at i:126406 original size:2 final size:2
Alignment explanation
Indices: 126399--126425 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
126389 TGTACCAGAG
126399 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
126426 TCCGATATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:137222 original size:45 final size:45
Alignment explanation
Indices: 137171--137494 Score: 400
Period size: 45 Copynumber: 7.2 Consensus size: 45
137161 TGAATTAAAT
* *
137171 AATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAACTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
*
137216 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
*
137261 AATGCATATGGGTTCATTATTGGCATGAAAGGATGCCATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
* ** *
137306 AATGCATATGGGTGCATTATTGACAAT-AAATAATGTCATAATTGA
1 AATGCATATGGGTGCATTATTGGC-ATGAAAGGATGCCATAATTGA
* * * *
137351 AAGGTATATGGGTGCATTATTGGAATGAAAGGATGCTATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
** * * * *
137396 AATAAATATGGGTGCATTAGTGACAAT-AAATGATGCCATAGTTGA
1 AATGCATATGGGTGCATTATTGGC-ATGAAAGGATGCCATAATTGA
* * * * *
137441 AATGCATATTGGTGTATTATGGGCATGAAGGGATGCTATAATTGAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTG-A
137487 AATGCATA
1 AATGCATA
137495 ATGGTATTAT
Statistics
Matches: 236, Mismatches: 38, Indels: 9
0.83 0.13 0.03
Matches are distributed among these distances:
44 4 0.02
45 219 0.93
46 13 0.06
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
Found at i:137511 original size:44 final size:46
Alignment explanation
Indices: 137427--137533 Score: 123
Period size: 44 Copynumber: 2.4 Consensus size: 46
137417 GACAATAAAT
* * * **
137427 GATGCCATAGTTG-AAATGCATATTGGTGTATTATGGGCATGAAGG
1 GATGCTATAATTGAAAATGCATAATGGTGTATTATAAGCATGAAGG
*
137472 GATGCTATAATTGAAAATGCATAAT-G-GTATTATAAGCATGAATG
1 GATGCTATAATTGAAAATGCATAATGGTGTATTATAAGCATGAAGG
137516 GATGCTATTAA-TGAAAAT
1 GATGCTA-TAATTGAAAAT
137534 AAAGAATAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
44 29 0.54
45 15 0.28
46 10 0.19
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.32
Consensus pattern (46 bp):
GATGCTATAATTGAAAATGCATAATGGTGTATTATAAGCATGAAGG
Found at i:143070 original size:45 final size:45
Alignment explanation
Indices: 142971--143352 Score: 448
Period size: 45 Copynumber: 8.5 Consensus size: 45
142961 GCATGAAAGG
* *
142971 GCATTATTGGCATGAAAGAATGCCATAATTG-AATACATATGGGT
1 GCATTATTGGCATGAAAGGATGCCATAATTGAAATGCATATGGGT
143015 GCATTATTGGCATGAAAGGATGCCATAATTGAAATGCATATGGGT
1 GCATTATTGGCATGAAAGGATGCCATAATTGAAATGCATATGGGT
143060 GCATTATTGGCATGAAAGGATGCCATAATTGAAATGCATAT-GGT
1 GCATTATTGGCATGAAAGGATGCCATAATTGAAATGCATATGGGT
* * * * * *
143104 GTATTATTAGCATGAAAAGATGCTATAATTGAAATGCATATTGAT
1 GCATTATTGGCATGAAAGGATGCCATAATTGAAATGCATATGGGT
* ** *
143149 GCATTATTGACAAT-AAATAATGCCATAATTGAAATGCATATAGGT
1 GCATTATTGGC-ATGAAAGGATGCCATAATTGAAATGCATATGGGT
* * * * * *
143194 ACAATATTGGCATGAAATGATGCTATAATTTAAATGTATATGGGT
1 GCATTATTGGCATGAAAGGATGCCATAATTGAAATGCATATGGGT
* ** * *
143239 GCATTAGTGATAAGAAATGATGCCATAATTGAAATGCATATGGGT
1 GCATTATTGGCATGAAAGGATGCCATAATTGAAATGCATATGGGT
* * *
143284 GCATTATTGGCATGAAATGATACTATAATTGAAAATGCATAAT-GGT
1 GCATTATTGGCATGAAAGGATGCCATAATTG-AAATGCAT-ATGGGT
** *
143330 GCATTATAAGCATGAATGGATGC
1 GCATTATTGGCATGAAAGGATGC
143353 TATTAATGAA
Statistics
Matches: 289, Mismatches: 43, Indels: 10
0.85 0.13 0.03
Matches are distributed among these distances:
44 72 0.25
45 184 0.64
46 31 0.11
47 2 0.01
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (45 bp):
GCATTATTGGCATGAAAGGATGCCATAATTGAAATGCATATGGGT
Found at i:143149 original size:24 final size:23
Alignment explanation
Indices: 143122--143189 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 23
143112 AGCATGAAAA
143122 GATGCTATAATTGAAATGCATATT
1 GATGC-ATAATTGAAATGCATATT
* *
143146 GATGCATTATTGACAAT--A-AAT
1 GATGCATAATTGA-AATGCATATT
*
143167 AATGCCATAATTGAAATGCATAT
1 GATG-CATAATTGAAATGCATAT
143190 AGGTACAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
21 8 0.24
22 9 0.26
23 8 0.24
24 9 0.26
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (23 bp):
GATGCATAATTGAAATGCATATT
Found at i:145103 original size:26 final size:26
Alignment explanation
Indices: 145051--145103 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
145041 GGTCTCACGT
* * * *
145051 GGCAGTTTTTAGAAGGTCCAGTTAGC
1 GGCAGTTTCTAGAAGATCCACTCAGC
*
145077 GGCAGTTTCTAGAAGATCTACTCAGC
1 GGCAGTTTCTAGAAGATCCACTCAGC
145103 G
1 G
145104 CTCCTTCTGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (26 bp):
GGCAGTTTCTAGAAGATCCACTCAGC
Found at i:145465 original size:21 final size:22
Alignment explanation
Indices: 145424--145483 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
145414 TCCAATTTAA
*
145424 ACTTTAAATCTCTTCTTTATT-TT
1 ACTTTAAATATC-T-TTTATTATT
145447 ACTTTAAATATCTTTTATTATT
1 ACTTTAAATATCTTTTATTATT
*
145469 A-TTTAAATATATTTT
1 ACTTTAAATATCTTTT
145484 TACCAAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 19 0.56
22 4 0.12
23 11 0.32
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (22 bp):
ACTTTAAATATCTTTTATTATT
Found at i:151879 original size:23 final size:23
Alignment explanation
Indices: 151851--151905 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
151841 TATATTTTCA
151851 ACTTTAAATAT-CTTCTTTATT-TT
1 ACTTTAAATATGC-T-TTTATTATT
151874 ACTTTAAAT-TGCTTTTATTATT
1 ACTTTAAATATGCTTTTATTATT
151896 A-TTTAAATAT
1 ACTTTAAATAT
151906 ATTTTTACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 13 0.45
22 6 0.21
23 10 0.34
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (23 bp):
ACTTTAAATATGCTTTTATTATT
Found at i:156535 original size:45 final size:45
Alignment explanation
Indices: 156471--156906 Score: 572
Period size: 45 Copynumber: 9.7 Consensus size: 45
156461 TTAAATAATA
156471 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGAAATG
1 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGAAATG
*
156516 CATATGGGTGCATTATTGGCATGAAAAGATGCCATAATTGAAATG
1 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGAAATG
*
156561 CATATAGGTGCATTATTGGCATGAAAGGATGCCATAATTGAAATG
1 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGAAATG
* *
156606 CATAT-GGTGCATTATTGGCATGAAATGATGCCATAATTAAAATG
1 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGAAATG
* * *
156650 AATATGGGTGAATTATTGGCATGAAAGGATGCTATAATTGAAATG
1 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGAAATG
* * * *
156695 CATATGGGTTCATTATTGACAAT-AAATGATGCCATAGTTGAAATG
1 CATATGGGTGCATTATTGGC-ATGAAAGGATGCCATAATTGAAATG
* * *
156740 CATATAGGTGCATTATTGGCATGAAAGGATGCAATAATTAAAATG
1 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGAAATG
* * * * * * * *
156785 TATGTGGGTGCATTAGTGACAAGAAATGATGCCACAATTGAAATA
1 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGAAATG
* * *
156830 CATATGGGTGGATTATTAGCATGAAAGGATGCTATAATTGAAAATG
1 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTG-AAATG
** *
156876 CATAAT-GGTGCATTATAAGCATGAATGGATG
1 CAT-ATGGGTGCATTATTGGCATGAAAGGATG
156907 TTATTAATGA
Statistics
Matches: 337, Mismatches: 49, Indels: 9
0.85 0.12 0.02
Matches are distributed among these distances:
44 43 0.13
45 261 0.77
46 31 0.09
47 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (45 bp):
CATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGAAATG
Found at i:156650 original size:22 final size:22
Alignment explanation
Indices: 156491--156739 Score: 87
Period size: 22 Copynumber: 11.1 Consensus size: 22
156481 CATTATTGGC
*
156491 ATGAAAGGATGCCATAATTGAA
1 ATGAAATGATGCCATAATTGAA
* * * **
156513 ATGCATATGGGTG-CATTATTGGC
1 ATG-AAAT-GATGCCATAATTGAA
*
156536 ATGAAAAGATGCCATAATTGAA
1 ATGAAATGATGCCATAATTGAA
* * * **
156558 ATGCATATAGGTG-CATTATTGGC
1 ATG-AAAT-GATGCCATAATTGAA
*
156581 ATGAAAGGATGCCATAATTGAA
1 ATGAAATGATGCCATAATTGAA
* * * **
156603 ATGCATATGGTG-CATTATTGGC
1 ATG-AAATGATGCCATAATTGAA
*
156625 ATGAAATGATGCCATAATTAAA
1 ATGAAATGATGCCATAATTGAA
* * * **
156647 ATGAATATGGGTG-AATTATTGGC
1 ATGAA-AT-GATGCCATAATTGAA
* *
156670 ATGAAAGGATGCTATAATTGAA
1 ATGAAATGATGCCATAATTGAA
* * * *
156692 ATGCATATG-GGTTCATTATTGACA
1 ATG-AAATGATG-CCATAATTGA-A
*
156716 AT-AAATGATGCCATAGTTGAA
1 ATGAAATGATGCCATAATTGAA
156737 ATG
1 ATG
156740 CATATAGGTG
Statistics
Matches: 152, Mismatches: 59, Indels: 32
0.63 0.24 0.13
Matches are distributed among these distances:
21 18 0.12
22 70 0.46
23 52 0.34
24 12 0.08
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (22 bp):
ATGAAATGATGCCATAATTGAA
Found at i:157942 original size:45 final size:43
Alignment explanation
Indices: 157815--157948 Score: 160
Period size: 45 Copynumber: 3.0 Consensus size: 43
157805 GGAAAACAAC
* * * *
157815 AAAAGATTGACTCCTCTTTGAGAGAAAATCAAGAAGGACAACACT
1 AAAATATTGACTCCTC-TTCAGAGAAAGTCAGGAA-GACAACACT
*
157860 AAAATATTGACTCTTCTTCACGAGAAAGTCAAGGAAGACAACACT
1 AAAATATTGACTCCTCTTCA-GAGAAAGTC-AGGAAGACAACACT
*
157905 AAAATATTGACTCCTCTTCATGAGAAAGTCTAGGAAGAAAACAC
1 AAAATATTGACTCCTCTTCA-GAGAAAGTC-AGGAAGACAACAC
157949 CGAACGATTT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
44 3 0.04
45 71 0.91
46 4 0.05
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (43 bp):
AAAATATTGACTCCTCTTCAGAGAAAGTCAGGAAGACAACACT
Found at i:158024 original size:45 final size:45
Alignment explanation
Indices: 157815--158026 Score: 129
Period size: 45 Copynumber: 4.7 Consensus size: 45
157805 GGAAAACAAC
* * *
157815 AAAAGATTGACTCCTCTTTG-A-GAGAAAATCAAGAAGGACAACACT
1 AAAAGATTGACT--TCTTCGCACGAGAAAGTCAAGAAGGACAAAACT
* * *
157860 AAAATATTGAC-TCTTCTTCACGAGAAAGTCAAGGAA-GACAACACT
1 AAAAGATTGACTTCTTC-GCACGAGAAAGTCAA-GAAGGACAAAACT
* * * *
157905 AAAATATTGACTCCTCTT--CATGAGAAAGTCTAGGAA-GA-AAACACC
1 AAAAGATTGACT--TCTTCGCACGAGAAAGTC-AAGAAGGACAAA-ACT
* * * *
157950 GAACGATTTAGTTCTATTCG--CGAGAAAGTCAAGAAGGACAAAACT
1 AAAAGATTGACTTC--TTCGCACGAGAAAGTCAAGAAGGACAAAACT
*
157995 AAAAGATTGACTTCTTCGCACGAGGAAGTCAA
1 AAAAGATTGACTTCTTCGCACGAGAAAGTCAA
158027 AAATAACAAA
Statistics
Matches: 129, Mismatches: 21, Indels: 34
0.70 0.11 0.18
Matches are distributed among these distances:
42 4 0.03
43 6 0.05
44 7 0.05
45 101 0.78
46 7 0.05
48 4 0.03
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (45 bp):
AAAAGATTGACTTCTTCGCACGAGAAAGTCAAGAAGGACAAAACT
Found at i:158126 original size:76 final size:76
Alignment explanation
Indices: 157996--158716 Score: 846
Period size: 76 Copynumber: 9.5 Consensus size: 76
157986 GACAAAACTA
* * * *
157996 AAAGATTGACT--TCTTCGCACGAGGAAGTCAAAAATAACAAAGATTGACTCCTCTTCACGTGGA
1 AAAGATTGACTCCTCTTCG--CGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGA
158059 AGTCAAGAATAAC
64 AGTCAAGAATAAC
* * * * *
158072 AAAGATTGACACATCTTAGCGAGGGAGTCAAGAATAACAGAGATTGAATTCTCTTCACGAGGAAG
1 AAAGATTGACTCCTCTTCGCGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAG
* * *
158137 TAAATAATAAT
66 TCAAGAATAAC
* *
158148 AAAGATTGACTCCTCTTCGCGAGGGAGTC-AGTAATAATAAAGATTGATTTCTCTTCACGAGGAA
1 AAAGATTGACTCCTCTTCGCGAGGGAGTCAAG-AATAACAAAGATTGACTTCTCTTCACGAGGAA
*
158212 GTCGAGAATAAC
65 GTCAAGAATAAC
* * * *
158224 AAAGATTGACTCCTCTTTGCAAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACAAGGAAG
1 AAAGATTGACTCCTCTTCGCGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAG
*
158289 TCAAGGATAAC
66 TCAAGAATAAC
* * * * * *
158300 AAAAAATGACT-CTAAC-TCGCGAGGGAGTCAGGAATAACAAAGATTTACTTCTCTTCATGATGA
1 AAAGATTGACTCCT--CTTCGCGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGA
*
158363 AGTCAACAATAA-
64 AGTCAAGAATAAC
* * *
158375 ATAAGATTGACTCCTCTTCGTGAGGGAGTCAGGAATAACAAAGATTGAATTCTCTTCACGAGGAA
1 A-AAGATTGACTCCTCTTCGCGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAA
*
158440 GTCAAGGATAAC
65 GTCAAGAATAAC
* * * * * * *
158452 AAAGACTGACTCCTCTTCACGAGGGAGT-AGGTAATAATAAAAATTGACTTCTCTTTACGAAGAA
1 AAAGATTGACTCCTCTTCGCGAGGGAGTCAAG-AATAACAAAGATTGACTTCTCTTCACGAGGAA
*
158516 GTCAAGAATAAA
65 GTCAAGAATAAC
* * *
158528 AAAGATTGACTCCTCTTCTCGAGGGAGT-AAGGAATAATAAAGATTGACTTCTGTTCACGAGGAA
1 AAAGATTGACTCCTCTTCGCGAGGGAGTCAA-GAATAACAAAGATTGACTTCTCTTCACGAGGAA
158592 GTCAAGAATAAC
65 GTCAAGAATAAC
* * * * * *
158604 AAAGATTGAATCATCTTCGCGAGGAAGTCAGGAATAACAAAGATTGATTTCTCTTCATGAGGAAG
1 AAAGATTGACTCCTCTTCGCGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAG
*
158669 TCAATAATAAC
66 TCAAGAATAAC
* * *
158680 AAAGAGTGACTCCTCTTCGTGAGGGAGTCGAGAATAA
1 AAAGATTGACTCCTCTTCGCGAGGGAGTCAAGAATAA
158717 GATCGGATTG
Statistics
Matches: 549, Mismatches: 83, Indels: 26
0.83 0.13 0.04
Matches are distributed among these distances:
75 9 0.02
76 528 0.96
77 7 0.01
78 5 0.01
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (76 bp):
AAAGATTGACTCCTCTTCGCGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAG
TCAAGAATAAC
Found at i:158696 original size:38 final size:38
Alignment explanation
Indices: 157996--158716 Score: 677
Period size: 38 Copynumber: 19.0 Consensus size: 38
157986 GACAAAACTA
*
157996 AAAGATTGACT--TCTTCGCACGAGGAAGTCAAAAATAAC
1 AAAGATTGACTCCTCTT--CACGAGGAAGTCAAGAATAAC
*
158034 AAAGATTGACTCCTCTTCACGTGGAAGTCAAGAATAAC
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
* * *
158072 AAAGATTGACACATCTT-AGCGAGGGAGTCAAGAATAAC
1 AAAGATTGACTCCTCTTCA-CGAGGAAGTCAAGAATAAC
* * * * * *
158110 AGAGATTGAATTCTCTTCACGAGGAAGTAAATAATAAT
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
* * *
158148 AAAGATTGACTCCTCTTCGCGAGGGAGTC-AGTAATAAT
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAG-AATAAC
* * *
158186 AAAGATTGATTTCTCTTCACGAGGAAGTCGAGAATAAC
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
** * * *
158224 AAAGATTGACTCCTCTTTGCAAGGGAGTCAGGAATAAC
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
* * *
158262 AAAGATTGACTTCTCTTCACAAGGAAGTCAAGGATAAC
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
* * * * *
158300 AAAAAATGACT-CTAAC-TCGCGAGGGAGTCAGGAATAAC
1 AAAGATTGACTCCT--CTTCACGAGGAAGTCAAGAATAAC
* * * * *
158338 AAAGATTTACTTCTCTTCATGATGAAGTCAACAATAA-
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
** * *
158375 ATAAGATTGACTCCTCTTCGTGAGGGAGTCAGGAATAAC
1 A-AAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
* * *
158414 AAAGATTGAATTCTCTTCACGAGGAAGTCAAGGATAAC
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
158452 AAAGACTGACTCCTCTTCACGAGGGAGT-AGGTAATAAT
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAG-AATAAC
* * * * *
158490 AAAAATTGACTTCTCTTTACGAAGAAGTCAAGAATAAA
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
* * *
158528 AAAGATTGACTCCTCTTCTCGAGGGAGT-AAGGAATAAT
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAA-GAATAAC
* *
158566 AAAGATTGACTTCTGTTCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
158604 AAAGATTGAATCATCTTCGCGAGGAAGTCAGGAATAAC
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
158642 AAAGATTGATTTCTCTTCATGAGGAAGTCAATAATAAC
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
* ** * *
158680 AAAGAGTGACTCCTCTTCGTGAGGGAGTCGAGAATAA
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAA
158717 GATCGGATTG
Statistics
Matches: 549, Mismatches: 118, Indels: 32
0.79 0.17 0.05
Matches are distributed among these distances:
37 10 0.02
38 524 0.95
39 11 0.02
40 4 0.01
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (38 bp):
AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:165004 original size:19 final size:19
Alignment explanation
Indices: 164980--165018 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
164970 GTCCTGTAAA
164980 TGTCTTCCGATCACTTAAG
1 TGTCTTCCGATCACTTAAG
164999 TGTCTTCCGATCACTTAAG
1 TGTCTTCCGATCACTTAAG
165018 T
1 T
165019 ATATGGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTCTTCCGATCACTTAAG
Done.