Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008531.1 Hibiscus syriacus cultivar Beakdansim tig00111409_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: 3817888
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 19
Found at i:919564 original size:134 final size:133
Alignment explanation
Indices: 919324--919867 Score: 586
Period size: 134 Copynumber: 4.1 Consensus size: 133
919314 AGATCTGGTT
* * * **
919324 TCCCCTAAAGAGTAGTGGAGCATATTCTCTTTCTTTTATATTTGGTCTTCCTGAAGAGCAGCAAA
1 TCCCCTAAAGAGTAGTGGAGCAGATTCTCTTTCTTTAAGATTTGGTCTTCCTGAAGAGCAGTGAA
* * * *
919389 ATAAATCACGTTTGATTCAATCTTCACTGAAGAGCAGCGAAGTGGATCAAAATTTTCTCGAGTCT
66 ACAAATCA-GTTCGATTCAATCTTCCCTGAAGAGCAGCGAAGTGGATCAAAATTTTCTCGAGTAT
919454 AATC
130 AATC
* * *
919458 TCCCCTAAAGAGTAGTGTAGCAGATTCT-TCTTCTTTAAGATTTGGTCTTCCTGGAGAGTAGTGA
1 TCCCCTAAAGAGTAGTGGAGCAGATTCTCT-TTCTTTAAGATTTGGTCTTCCTGAAGAGCAGTGA
* * * *
919522 AACAAATC-GATTCCGATTCAGTCTTCCCTGAAGAGCAACGAAGTGGATCAAAA--TT-ACGTGT
65 AACAAATCAG-TT-CGATTCAATCTTCCCTGAAGAGCAGCGAAGTGGATCAAAATTTTCTCGAGT
* *
919583 CTGATC
128 ATAATC
* * * *
919589 TCCCCTAAAGAGTAGTGGAGCATATT-TGTCTTCTTTCAA-ATTTGGTATTCCTGAAAAGCAGTG
1 TCCCCTAAAGAGTAGTGGAGCAGATTCTCT-TTCTTT-AAGATTTGGTCTTCCTGAAGAGCAGTG
* * * *
919652 AAGCAAATCAAGTTCGATTAAATTTTCCCTGAAGAGCAGCGAAGTGGATCAAAATATTCTCGAGT
64 AAACAAATC-AGTTCGATTCAATCTTCCCTGAAGAGCAGCGAAGTGGATCAAAATTTTCTCGAGT
*
919717 ATGATC
128 ATAATC
* * * * * *
919723 TCCCCTTAAA-AATAGTGAAACCGATTCTCTTTCTTTCAGATTTGGTCTT-CTGAAGAGCAG-CA
1 TCCCC-TAAAGAGTAGTGGAGCAGATTCTCTTTCTTTAAGATTTGGTCTTCCTGAAGAGCAGTGA
* ** *
919785 AAGAAAATCACGTTCGATTCAATCTTCCCTGAAGAGCAGTAAAGTTGATCAAAATTTTCTCGAGT
65 AA-CAAATCA-GTTCGATTCAATCTTCCCTGAAGAGCAGCGAAGTGGATCAAAATTTTCTCGAGT
919850 ATAATC
128 ATAATC
*
919856 TCTCCTAAAGAG
1 TCCCCTAAAGAG
919868 AAGCAAAGCA
Statistics
Matches: 343, Mismatches: 51, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
130 1 0.00
131 105 0.31
132 14 0.04
133 80 0.23
134 137 0.40
135 6 0.02
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (133 bp):
TCCCCTAAAGAGTAGTGGAGCAGATTCTCTTTCTTTAAGATTTGGTCTTCCTGAAGAGCAGTGAA
ACAAATCAGTTCGATTCAATCTTCCCTGAAGAGCAGCGAAGTGGATCAAAATTTTCTCGAGTATA
ATC
Found at i:920235 original size:3 final size:3
Alignment explanation
Indices: 920222--920284 Score: 65
Period size: 3 Copynumber: 20.0 Consensus size: 3
920212 TCGTTTGGGT
*
920222 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTAA TT- GTA TATA TATA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA T-TA T-TA
*
920270 TTA TTA TTA GTA TTA
1 TTA TTA TTA TTA TTA
920285 ATTTTATGGG
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
2 1 0.02
3 38 0.73
4 13 0.25
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:930578 original size:21 final size:20
Alignment explanation
Indices: 930530--930580 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
930520 ACAATTTTCG
930530 AATTCGTAACAAGAATTTAC
1 AATTCGTAACAAGAATTTAC
* *
930550 ATTTCGTAACACGAATTTGTA-
1 AATTCGTAACAAGAA-TT-TAC
930571 AATTCGTAAC
1 AATTCGTAAC
930581 TCAGTTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 13 0.50
21 11 0.42
22 2 0.08
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (20 bp):
AATTCGTAACAAGAATTTAC
Found at i:930694 original size:20 final size:20
Alignment explanation
Indices: 930671--930742 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
930661 TTGAAAGTTG
*
930671 AATTCACAACTCGAAACTCA
1 AATTCGCAACTCGAAACTCA
* *
930691 AATTCGCAATTCGAAATTCA
1 AATTCGCAACTCGAAACTCA
* * *
930711 AATTTGCAACTCGAAAATCG
1 AATTCGCAACTCGAAACTCA
*
930731 AATTCGTAACTC
1 AATTCGCAACTC
930743 AAATTTCGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (20 bp):
AATTCGCAACTCGAAACTCA
Found at i:930735 original size:33 final size:33
Alignment explanation
Indices: 930685--930748 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
930675 CACAACTCGA
* *
930685 AACTCAAATTCGCAATTCGAAATTCAAATTTGC
1 AACTCAAAATCGCAATTCGAAACTCAAATTTGC
*
930718 AACTCGAAAATCG-AATTCGTAACTCAAATTT
1 AACTC-AAAATCGCAATTCGAAACTCAAATTT
930749 CGAATTGCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 21 0.78
34 6 0.22
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (33 bp):
AACTCAAAATCGCAATTCGAAACTCAAATTTGC
Found at i:931145 original size:24 final size:24
Alignment explanation
Indices: 931118--931173 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
931108 GAGTGCATTT
** *
931118 ACATGTTTGTGAACATATAATTGA
1 ACATGTTTGCAAACATATAAGTGA
*
931142 ACATGTTCGCAAACATATAAGTGA
1 ACATGTTTGCAAACATATAAGTGA
931166 ACATGTTT
1 ACATGTTT
931174 ACTAACAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (24 bp):
ACATGTTTGCAAACATATAAGTGA
Found at i:939461 original size:17 final size:17
Alignment explanation
Indices: 939439--939479 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
939429 TATAATAAAC
939439 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
939456 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
*
939473 ATATGAT
1 TTATGAT
939480 TACTCTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (17 bp):
TTATGATAATTAAATTA
Found at i:939507 original size:51 final size:52
Alignment explanation
Indices: 939449--939546 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 52
939439 TTATGATAAT
* *
939449 TAAATTATTATGATAATTAAATTAATATGATTAC-TCTTTGAAATTTTATCA
1 TAAATTATTATGATAATCAAATTAATATAATTACTTCTTTGAAATTTTATCA
*
939500 TAAATTATTATGATAATCAAATTAATATAATTACTTTTTTGAAATTT
1 TAAATTATTATGATAATCAAATTAATATAATTACTTCTTTGAAATTT
939547 AATTTTATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
51 32 0.74
52 11 0.26
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (52 bp):
TAAATTATTATGATAATCAAATTAATATAATTACTTCTTTGAAATTTTATCA
Found at i:939575 original size:18 final size:16
Alignment explanation
Indices: 939542--939576 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
939532 ACTTTTTTGA
939542 AATTTAATTTTATATT
1 AATTTAATTTTATATT
939558 AATTATAATTTGTATATT
1 AATT-TAATTT-TATATT
939576 A
1 A
939577 TAAATTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 6 0.35
18 7 0.41
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
AATTTAATTTTATATT
Found at i:940400 original size:20 final size:20
Alignment explanation
Indices: 940375--940425 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
940365 AATATCAAGT
* *
940375 AGAAGCAAGCAATGTCAAAC
1 AGAAGCAAGCAATATAAAAC
* *
940395 ATAAGCAAACAATATAAAAC
1 AGAAGCAAGCAATATAAAAC
940415 AGAAGCAAGCA
1 AGAAGCAAGCA
940426 GAATCAAGCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.57, C:0.18, G:0.16, T:0.10
Consensus pattern (20 bp):
AGAAGCAAGCAATATAAAAC
Found at i:940427 original size:10 final size:10
Alignment explanation
Indices: 940414--940445 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
940404 CAATATAAAA
*
940414 CAGAAGCAAG
1 CAGAATCAAG
940424 CAGAATCAAG
1 CAGAATCAAG
940434 CAGAATCAAG
1 CAGAATCAAG
940444 CA
1 CA
940446 CCAAGTATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.50, C:0.22, G:0.22, T:0.06
Consensus pattern (10 bp):
CAGAATCAAG
Found at i:940602 original size:13 final size:13
Alignment explanation
Indices: 940584--940613 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
940574 AAAGAAGACA
*
940584 AAATCTCCTATTC
1 AAATCTCCAATTC
940597 AAATCTCCAATTC
1 AAATCTCCAATTC
940610 AAAT
1 AAAT
940614 TATTTTAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATCTCCAATTC
Found at i:941520 original size:21 final size:21
Alignment explanation
Indices: 941496--941537 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
941486 CCTTCACATG
941496 GATCATTATGAGCATCACACA
1 GATCATTATGAGCATCACACA
941517 GATCATTATGAGCATCACACA
1 GATCATTATGAGCATCACACA
941538 ATAGTTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (21 bp):
GATCATTATGAGCATCACACA
Found at i:943478 original size:65 final size:63
Alignment explanation
Indices: 943345--943554 Score: 248
Period size: 65 Copynumber: 3.3 Consensus size: 63
943335 TGCACTAAAA
* * **
943345 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGC-CAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATA-CTCTGAGTGCATCGATGCATGTAT
943408 GGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACTCTGAGTGCATCGATGCATAGT
1 -GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATACTCTGAGTGCATCGATGCAT-GT
943472 AT
62 AT
* *
943474 GTGCATCGATGCATGAAATGCATTCGATG-TTCAAAATATTCCATG-GTGCATCGATGCATGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATACT-C-TGAGTGCATCGATGCATGTA-
943537 T
63 T
*
943538 GGTGCATCGGTGCATCA
1 -GTGCATCGATGCATCA
943555 CTCTGAAAAA
Statistics
Matches: 129, Mismatches: 8, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
62 3 0.02
63 9 0.07
64 45 0.35
65 67 0.52
66 5 0.04
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATACTCTGAGTGCATCGATGCATGTAT
Found at i:946231 original size:23 final size:22
Alignment explanation
Indices: 946191--946271 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
946181 CATGGCCTTG
*
946191 TGCATCGATGCAAATTCAAGGCA
1 TGCATCGATGCACATTCAAGG-A
* * *
946214 TGCATCGGTGCACCTTCATGG-
1 TGCATCGATGCACATTCAAGGA
*
946235 TGTATCGATGCACATTCAAGGGGA
1 TGCATCGATGCACATTCAA--GGA
946259 TGCATCGATGCAC
1 TGCATCGATGCAC
946272 TGTTAAGTGT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 15 0.33
23 19 0.41
24 12 0.26
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:946282 original size:44 final size:44
Alignment explanation
Indices: 946194--946290 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
946184 GGCCTTGTGC
* *
946194 ATCGATGCAAATTCAAGGCATGCATCGGTGCACCTTCATGGTGT
1 ATCGATGCAAATTCAAGGCATGCATCGATGCACCTTCATAGTGT
* * *
946238 ATCGATGCACATTCAAGGGGATGCATCGATGCA-CTGTTA-AGTGT
1 ATCGATGCAAATTCAA-GGCATGCATCGATGCACCT-TCATAGTGT
946282 ATCGATGCA
1 ATCGATGCA
946291 TGAAGCAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 30 0.65
45 16 0.35
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (44 bp):
ATCGATGCAAATTCAAGGCATGCATCGATGCACCTTCATAGTGT
Found at i:952699 original size:16 final size:16
Alignment explanation
Indices: 952674--952731 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
952664 TAGTTTACAT
*
952674 TACATCATTAAACCAG
1 TACATAATTAAACCAG
*
952690 TACATAATT-AA-CAT
1 TACATAATTAAACCAG
*
952704 TAACAGGAA-TAAACCAG
1 T-ACA-TAATTAAACCAG
952721 TACATAATTAA
1 TACATAATTAA
952732 CATCAACAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
14 3 0.09
15 8 0.25
16 18 0.56
17 3 0.09
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.26
Consensus pattern (16 bp):
TACATAATTAAACCAG
Found at i:953125 original size:31 final size:31
Alignment explanation
Indices: 952682--953116 Score: 642
Period size: 31 Copynumber: 14.1 Consensus size: 31
952672 ATTACATCAT
* * * **
952682 TAAACCAGTACATAATTAACATTAACAGGAA
1 TAAACCAGTACATCATTTACATCAACAACAA
* *
952713 TAAACCAGTACATAATTAACATCAACAACAA
1 TAAACCAGTACATCATTTACATCAACAACAA
* * *
952744 TAAA-CAGTACATAATTAACATCAACAGCAA
1 TAAACCAGTACATCATTTACATCAACAACAA
* *
952774 TAAATCAGTACATCATTTACATCAACATCAA
1 TAAACCAGTACATCATTTACATCAACAACAA
* *
952805 TAAACTAGTACATAATTTACATCAACAACAA
1 TAAACCAGTACATCATTTACATCAACAACAA
*
952836 TAAACCAGTACATCATTTACATCAAC-ATAA
1 TAAACCAGTACATCATTTACATCAACAACAA
* *
952866 TAAACCAATACATCA-TTATATCAACAACAA
1 TAAACCAGTACATCATTTACATCAACAACAA
952896 TAAACCAGTACATCATTTACATCAACAACAA
1 TAAACCAGTACATCATTTACATCAACAACAA
952927 TAAACCAGTACATCATTTACATCAACAACAA
1 TAAACCAGTACATCATTTACATCAACAACAA
952958 TAAACCAGTACATCATTTACATCAACAACAA
1 TAAACCAGTACATCATTTACATCAACAACAA
** *
952989 TAAACTGGTACATCATTTACATCAACAATAA
1 TAAACCAGTACATCATTTACATCAACAACAA
*
953020 TAAACCAGTACATCATTTACATCAACAGCAA
1 TAAACCAGTACATCATTTACATCAACAACAA
953051 TAAACCAGTACATCATTTACATCAACAACAA
1 TAAACCAGTACATCATTTACATCAACAACAA
* *
953082 TAAACTAGTATATCATTTACATCAACAACAA
1 TAAACCAGTACATCATTTACATCAACAACAA
953113 TAAA
1 TAAA
953117 TCAATATATA
Statistics
Matches: 372, Mismatches: 29, Indels: 6
0.91 0.07 0.01
Matches are distributed among these distances:
29 9 0.02
30 63 0.17
31 300 0.81
ACGTcount: A:0.49, C:0.22, G:0.04, T:0.24
Consensus pattern (31 bp):
TAAACCAGTACATCATTTACATCAACAACAA
Found at i:953146 original size:32 final size:32
Alignment explanation
Indices: 953105--953168 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
953095 CATTTACATC
*
953105 AACAACAATAAATCAATATATATATATATATA
1 AACAACAATAAAACAATATATATATATATATA
*
953137 AACAACAATAAAACTATATATATATATATATA
1 AACAACAATAAAACAATATATATATATATATA
953169 TATATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (32 bp):
AACAACAATAAAACAATATATATATATATATA
Found at i:953158 original size:2 final size:2
Alignment explanation
Indices: 953151--953187 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
953141 ACAATAAAAC
953151 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
953188 CAAACATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:953462 original size:17 final size:16
Alignment explanation
Indices: 953427--953526 Score: 56
Period size: 17 Copynumber: 5.7 Consensus size: 16
953417 GTTTAAGGTC
* *
953427 TGGGTTAGGGTTGGTT
1 TGGGTTTGGGTTAGTT
953443 TGGGTTTGGGTTCAGTT
1 TGGGTTTGGGTT-AGTT
* *
953460 TGGATTTGAGTTCATGTT
1 TGGGTTTGGGTT-A-GTT
*
953478 TAGGAGGGTTAGGGTTAGTT
1 T----GGGTTTGGGTTAGTT
953498 TGGGTTTAGGGTTAGGTT
1 TGGGTTT-GGGTTA-GTT
* *
953516 AGGGTTAGGGT
1 TGGGTTTGGGT
953527 CTGGTTAGGG
Statistics
Matches: 66, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
16 16 0.24
17 25 0.38
18 12 0.18
20 4 0.06
21 1 0.02
22 8 0.12
ACGTcount: A:0.13, C:0.02, G:0.43, T:0.42
Consensus pattern (16 bp):
TGGGTTTGGGTTAGTT
Found at i:953493 original size:6 final size:6
Alignment explanation
Indices: 953482--953543 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
953472 CATGTTTAGG
*
953482 AGGGTT AGGGTT A--GTT TGGGTTT AGGGTT A-GGTT AGGGTT AGGGTCT
1 AGGGTT AGGGTT AGGGTT AGGG-TT AGGGTT AGGGTT AGGGTT AGGGT-T
953529 --GGTT AGGGGTT AGGG
1 AGGGTT A-GGGTT AGGG
953544 AAGATGAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
4 4 0.09
5 8 0.17
6 23 0.50
7 11 0.24
ACGTcount: A:0.15, C:0.02, G:0.48, T:0.35
Consensus pattern (6 bp):
AGGGTT
Found at i:953532 original size:17 final size:16
Alignment explanation
Indices: 953482--953543 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 16
953472 CATGTTTAGG
*
953482 AGGGTTAGGGTTAGTT
1 AGGGTTAGGGTTGGTT
*
953498 TGGGTTTAGGGTTAGGTT
1 AGGG-TTAGGGTT-GGTT
953516 AGGGTTAGGGTCTGGTT
1 AGGGTTAGGGT-TGGTT
953533 AGGGGTTAGGG
1 A-GGGTTAGGG
953544 AAGATGAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
16 3 0.08
17 20 0.51
18 16 0.41
ACGTcount: A:0.15, C:0.02, G:0.48, T:0.35
Consensus pattern (16 bp):
AGGGTTAGGGTTGGTT
Found at i:953887 original size:110 final size:111
Alignment explanation
Indices: 953681--954010 Score: 429
Period size: 111 Copynumber: 3.0 Consensus size: 111
953671 AACAATGGAT
* * * *
953681 GAATTTGTGGGTGTTTGATCGAAATAAATATG-ATATGGTTTAT-GTTTAGGT-TTTTTGAAGAT
1 GAATTT-TGGGTGTTTGATCGAAAAAAACACGAAAAT-GTTT-TGGTTTAGGTGTTTTTGAAGAT
* *
953743 CAAAGGAGGGTTTTGGGGAAGAAT-TGGATGAACAAATTAAGAACACAGAA
63 CAAAGGA-GGTTTTGGGGATG-ATCTGGATGAACAAATGAAGAACACAGAA
* *
953793 GAATATTTGGGTGTTTGATTG-AAAAAACACGAAAATGTTTTGG-TTAGGTGTTTTTGAAGATAA
1 GAAT-TTTGGGTGTTTGATCGAAAAAAACACGAAAATGTTTTGGTTTAGGTGTTTTTGAAGATCA
* * *
953856 AATGAGGTTTTTGGGATGATCTGGATGAACAAATGAAGAACACGGAA
65 AAGGAGGTTTTGGGGATGATCTGGATGAACAAATGAAGAACACAGAA
*
953903 GAATTTTGGGTGTTTGATCGAAAAAAAACACGAAAATGTTTTGGTTTAGGTGTTTTTGAATATCA
1 GAATTTTGGGTGTTTGATCG-AAAAAAACACGAAAATGTTTTGGTTTAGGTGTTTTTGAAGATCA
*
953968 AAGGAGGCTTTTGGGGATGAACTGGATGAACAAATGAAGAACA
65 AAGGAGG-TTTTGGGGATGATCTGGATGAACAAATGAAGAACA
954011 TGATTGATTT
Statistics
Matches: 192, Mismatches: 17, Indels: 17
0.85 0.08 0.08
Matches are distributed among these distances:
109 17 0.09
110 46 0.24
111 50 0.26
112 44 0.23
113 35 0.18
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (111 bp):
GAATTTTGGGTGTTTGATCGAAAAAAACACGAAAATGTTTTGGTTTAGGTGTTTTTGAAGATCAA
AGGAGGTTTTGGGGATGATCTGGATGAACAAATGAAGAACACAGAA
Found at i:954494 original size:51 final size:51
Alignment explanation
Indices: 954438--954566 Score: 159
Period size: 58 Copynumber: 2.4 Consensus size: 51
954428 TAAACTTTTC
*
954438 AATATATAGTTTATATATGCTATATAATTTATATATAATAATGAACTATAT
1 AATATATAGTTTATATATACTATATAATTTATATATAATAATGAACTATAT
* *
954489 AATATATAGTTTGTATATACCATATACTATATAGGTTATATATAGTAATGAACTATAT
1 AATATATAGTTTATATATA-C-TATA-TA-AT---TTATATATAATAATGAACTATAT
*
954547 AATATATAGTTTGTATATAC
1 AATATATAGTTTATATATAC
954567 CATAGTCTAT
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
51 17 0.25
52 1 0.01
53 4 0.06
54 2 0.03
55 2 0.03
57 1 0.01
58 41 0.60
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (51 bp):
AATATATAGTTTATATATACTATATAATTTATATATAATAATGAACTATAT
Found at i:954528 original size:58 final size:58
Alignment explanation
Indices: 954452--954682 Score: 262
Period size: 58 Copynumber: 4.0 Consensus size: 58
954442 TATAGTTTAT
* ** *
954452 ATATGCTATATAATTTATATATAATAATGAACTATATAATATATAGTTTGTATATACC
1 ATATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTGTATATACC
*
954510 ATATACTATATAGGTTATATATAGTAATGAACTATATAATATATAGTTTGTATATACCATAGTC
1 ATATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTGTATATA-C-----C
*
954574 TATATACTATATAGGTTATATATACTAATTAACTATATAATATATA----GT-T-TA-C
1 -ATATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTGTATATACC
* *
954626 ATATACTATATA-TTTGATATATACTAATGAACTATATAATATATAGTTTATATATAC
1 ATATACTATATAGGTT-ATATATACTAATGAACTATATAATATATAGTTTGTATATAC
954683 TAATGAAATA
Statistics
Matches: 149, Mismatches: 9, Indels: 30
0.79 0.05 0.16
Matches are distributed among these distances:
50 2 0.01
51 40 0.27
52 1 0.01
55 1 0.01
56 1 0.01
57 2 0.01
58 52 0.35
59 3 0.02
60 1 0.01
61 2 0.01
64 1 0.01
65 43 0.29
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.43
Consensus pattern (58 bp):
ATATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTGTATATACC
Found at i:954531 original size:18 final size:18
Alignment explanation
Indices: 954440--954808 Score: 156
Period size: 18 Copynumber: 21.2 Consensus size: 18
954430 AACTTTTCAA
*
954440 TATATAGTTTATATATGC
1 TATATAGTTTATATATAC
*
954458 TATATAATTTATATATA-
1 TATATAGTTTATATATAC
** *
954475 -ATA-A-TGAACTATATAA
1 TATATAGTTTA-TATATAC
*
954491 TATATAGTTTGTATATAC
1 TATATAGTTTATATATAC
* * *
954509 CATATACTATATAGGT-TA-
1 TATATAGTTTATA--TATAC
* *
954527 TATATAGTAATGAACTATATAA
1 TATATAGT--T-TA-TATATAC
*
954549 TATATAGTTTGTATATAC
1 TATATAGTTTATATATAC
* *
954567 --CATAG--TCTATATAC
1 TATATAGTTTATATATAC
*
954581 TATATAGGTTATATATAC
1 TATATAGTTTATATATAC
* *
954599 --TA-A-TTAACTATATAA
1 TATATAGTTTA-TATATAC
*
954614 TATATAGTTTACATATAC
1 TATATAGTTTATATATAC
954632 TATATA-TTTGATATATAC
1 TATATAGTTT-ATATATAC
* *
954650 TA-AT-G--AACTATATAA
1 TATATAGTTTA-TATATAC
954665 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
** * * *
954683 TA-AT-GAAATAAAAATAA
1 TATATAG-TTTATATATAC
*
954700 TGTATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
954718 CATATAGTTTATATATAT
1 TATATAGTTTATATATAC
954736 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
***
954754 TA-ATAAACTATATA-A-
1 TATATAGTTTATATATAC
* *
954769 TATATATTTTATATATAT
1 TATATAGTTTATATATAC
* *
954787 TATATAGTTTAAATATAA
1 TATATAGTTTATATATAC
954805 TATA
1 TATA
954809 GTATAAATTA
Statistics
Matches: 257, Mismatches: 59, Indels: 70
0.67 0.15 0.18
Matches are distributed among these distances:
14 13 0.05
15 24 0.09
16 26 0.10
17 30 0.12
18 140 0.54
19 8 0.03
20 3 0.01
21 3 0.01
22 10 0.04
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:954532 original size:25 final size:25
Alignment explanation
Indices: 954485--954532 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
954475 ATAATGAACT
* *
954485 ATATAATATATAGTTTGTATATACC
1 ATATAATATATAGGTTATATATACC
*
954510 ATATACTATATAGGTTATATATA
1 ATATAATATATAGGTTATATATA
954533 GTAATGAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (25 bp):
ATATAATATATAGGTTATATATACC
Found at i:954630 original size:65 final size:65
Alignment explanation
Indices: 954510--954631 Score: 208
Period size: 65 Copynumber: 1.9 Consensus size: 65
954500 TGTATATACC
* **
954510 ATATACTATATAGGTTATATATAGTAATGAACTATATAATATATAGTTTGTATATACCATAGTCT
1 ATATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTACATATACCATAGTCT
*
954575 ATATACTATATAGGTTATATATACTAATTAACTATATAATATATAGTTTACATATAC
1 ATATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTACATATAC
954632 TATATATTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 53 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (65 bp):
ATATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTACATATACCATAGTCT
Found at i:954631 original size:33 final size:33
Alignment explanation
Indices: 954510--954633 Score: 135
Period size: 33 Copynumber: 3.8 Consensus size: 33
954500 TGTATATACC
* * *
954510 ATATACTATATAGGTTATATATAGTAATGAACT
1 ATATAATATATAGGTTATATATACTAATTAACT
* * * *
954543 ATATAATATATAGTTTGTATATAC-CA-TAGTCT
1 ATATAATATATAGGTTATATATACTAATTA-ACT
*
954575 ATATACTATATAGGTTATATATACTAATTAACT
1 ATATAATATATAGGTTATATATACTAATTAACT
* *
954608 ATATAATATATAGTTTACATATACTA
1 ATATAATATATAGGTTATATATACTA
954634 TATATTTGAT
Statistics
Matches: 73, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
31 1 0.01
32 24 0.33
33 46 0.63
34 2 0.03
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (33 bp):
ATATAATATATAGGTTATATATACTAATTAACT
Found at i:954646 original size:51 final size:51
Alignment explanation
Indices: 954574--954803 Score: 236
Period size: 51 Copynumber: 4.5 Consensus size: 51
954564 TACCATAGTC
*
954574 TATATACTATATAGGTTATATATACTAATTAACTATATAATATATAGTTTA
1 TATATACTATATAGTTTATATATACTAATTAACTATATAATATATAGTTTA
* *
954625 CATATACTATATA-TTTGATATATACTAATGAACTATATAATATATAGTTTA
1 TATATACTATATAGTTT-ATATATACTAATTAACTATATAATATATAGTTTA
** * * * *
954676 TATATACTA-AT-G-AAATA-AAAATAATGTATAGTTTATATATACCATATAGTTTA
1 TATATACTATATAGTTTATATATACTAAT-TA-A--CTATATA-A-TATATAGTTTA
* * *
954729 TATATATTATATAGTTTATATATACTAATAAACTATATAATATATATTTTA
1 TATATACTATATAGTTTATATATACTAATTAACTATATAATATATAGTTTA
* *
954780 TATATATTATATAGTTTAAATATA
1 TATATACTATATAGTTTATATATA
954804 ATATAGTATA
Statistics
Matches: 146, Mismatches: 21, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
47 6 0.04
48 4 0.03
49 1 0.01
50 4 0.03
51 91 0.62
52 2 0.01
53 24 0.16
54 2 0.01
55 2 0.01
56 4 0.03
57 6 0.04
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (51 bp):
TATATACTATATAGTTTATATATACTAATTAACTATATAATATATAGTTTA
Found at i:954663 original size:116 final size:120
Alignment explanation
Indices: 954451--954682 Score: 321
Period size: 116 Copynumber: 1.9 Consensus size: 120
954441 ATATAGTTTA
* *
954451 TATATGCTATATAATTTATATATAATAATGAACTATATAATATATAGTTTGTATATACCATATAC
1 TATATACTATATAAGTTATATATAATAATGAACTATATAATATATA---TGTATATACCATATAC
* *
954516 TATATAGGTTATATATAGTAATGAACTATATAATATATAGTTTGTATATACCATAGTC
63 TATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACCATAGTC
* * *
954574 TATATACTATATAGGTTATATATACTAATTAACTATATAATATATA-GT-T-TA-CATATACTAT
1 TATATACTATATAAGTTATATATAATAATGAACTATATAATATATATGTATATACCATATACTAT
*
954635 ATA-TTTGATATATACTAATGAACTATATAATATATAGTTTATATATAC
66 ATAGGTT-ATATATACTAATGAACTATATAATATATAGTTTATATATAC
954683 TAATGAAATA
Statistics
Matches: 100, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
115 2 0.02
116 52 0.52
117 2 0.02
118 1 0.01
119 2 0.02
123 41 0.41
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.43
Consensus pattern (120 bp):
TATATACTATATAAGTTATATATAATAATGAACTATATAATATATATGTATATACCATATACTAT
ATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACCATAGTC
Found at i:954782 original size:69 final size:70
Alignment explanation
Indices: 954658--954808 Score: 207
Period size: 69 Copynumber: 2.2 Consensus size: 70
954648 ACTAATGAAC
*
954658 TATATAATATATAGTTTATATATACTAATGAAATAAAAATAATGTATAGTTTATATATACCATAT
1 TATATAATATATAGTTTATATATACTAATGAAAT-AAAATAATATATAGTTTATATATACCATAT
954723 AGTTTA
65 AGTTTA
* * * **
954729 TATATATTATATAGTTTATATATACTAAT-AAACT-ATATAATATATATTTTATATATATTATAT
1 TATATAATATATAGTTTATATATACTAATGAAA-TAAAATAATATATAGTTTATATATACCATAT
954792 AGTTTA
65 AGTTTA
*
954798 AATATAATATA
1 TATATAATATA
954809 GTATAAATTA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
69 39 0.55
70 3 0.04
71 29 0.41
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (70 bp):
TATATAATATATAGTTTATATATACTAATGAAATAAAATAATATATAGTTTATATATACCATATA
GTTTA
Found at i:954853 original size:104 final size:102
Alignment explanation
Indices: 954633--954854 Score: 216
Period size: 104 Copynumber: 2.1 Consensus size: 102
954623 TACATATACT
* *
954633 ATATATTTGATATATACTAATGAACTATATAATATATAGTTTATATATACTAATGAAATAAAAAT
1 ATATAGTT-ATATATACTAATAAACTATATAATATATAGTTTATATATACTAATGAAATAAAAAT
* * * * *
954698 AATGTATAGTTTATATATACCATATAGTTTATATATATT
65 AA-GTATAGTATAAATATACCATATAGTATATAAATATA
* * ** *
954737 ATATAGTTTATATATACTAATAAACTATATAATATATATTTTATATATATTATAT-AGTTTAAAT
1 ATATAG-TTATATATACTAATAAACTATATAATATATAGTTTATATATACTA-ATGA-AATAAAA
***
954801 ATAA-TATAGTATAAATTATTTTATATAGTATATAAATATCA
63 ATAAGTATAGTATAAA-TATACCATATAGTATATAAATAT-A
954842 ACTATAG-TATATA
1 A-TATAGTTATATA
954855 GTTTATATGG
Statistics
Matches: 97, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
103 9 0.09
104 70 0.72
105 13 0.13
106 5 0.05
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (102 bp):
ATATAGTTATATATACTAATAAACTATATAATATATAGTTTATATATACTAATGAAATAAAAATA
AGTATAGTATAAATATACCATATAGTATATAAATATA
Found at i:954920 original size:20 final size:19
Alignment explanation
Indices: 954890--954960 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 19
954880 ATATGTAAAT
954890 TATACTATATAGTATATATAG
1 TATA-TATATA-TATATATAG
* *
954911 TTTATATATATAATATACAG
1 TATATATATAT-ATATATAG
* *
954931 TATATAAATATAAACTATAG
1 TATATATATATATA-TATAG
954951 TATATATATA
1 TATATATATA
954961 GGTCATATGT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
19 3 0.07
20 35 0.85
21 3 0.07
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (19 bp):
TATATATATATATATATAG
Found at i:954988 original size:33 final size:33
Alignment explanation
Indices: 954951--955157 Score: 143
Period size: 33 Copynumber: 5.8 Consensus size: 33
954941 TAAACTATAG
*
954951 TATATATATAGGTCATATGTAAACTACATAGTT
1 TATATATATAGTTCATATGTAAACTACATAGTT
954984 TATATATATAGTTCATATGTAAA-TATCAGGTATTGTT
1 TATATATATAGTTCATATGTAAACTA-CA--TA--GTT
* * *
955021 TATATGTAAACTATAGTT-AGTATATAAACAATATAGTT
1 TATA--T--A-TATAGTTCA-TATGTAAACTACATAGTT
* *
955059 TATATGTAAACTATAGTTCATATATAAA-TATCA-ACTTT
1 TATA--T--A-TATAGTTCATATGTAAACTA-CATA-GTT
*
955097 AGTATATATATAGTTCATATGTAAACTATATAGTT
1 --TATATATATAGTTCATATGTAAACTACATAGTT
955132 TATATATATAGTTCATATGTAAACTA
1 TATATATATAGTTCATATGTAAACTA
955158 TAGTATATAA
Statistics
Matches: 145, Mismatches: 10, Indels: 38
0.75 0.05 0.20
Matches are distributed among these distances:
32 2 0.01
33 50 0.34
35 21 0.14
36 4 0.03
37 9 0.06
38 33 0.23
39 2 0.01
40 6 0.04
41 2 0.01
42 15 0.10
43 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (33 bp):
TATATATATAGTTCATATGTAAACTACATAGTT
Found at i:955073 original size:18 final size:18
Alignment explanation
Indices: 955018--955166 Score: 84
Period size: 18 Copynumber: 8.4 Consensus size: 18
955008 ATCAGGTATT
955018 GTTTATATGTAAACTATA
1 GTTTATATGTAAACTATA
*
955036 G-TTAGTATATAAACAATATA
1 GTTTA-TATGTAAAC--TATA
955056 GTTTATATGTAAACTATA
1 GTTTATATGTAAACTATA
* *
955074 GTTCATATATAAA-TATCAA
1 GTTTATATGTAAACTAT--A
* *
955093 CTTTAGTA--TATA-TATA
1 GTTTA-TATGTAAACTATA
*
955109 GTTCATATGTAAACTATATA
1 GTTTATATGTAAAC--TATA
955129 GTTTATA--T--A-TATA
1 GTTTATATGTAAACTATA
*
955142 GTTCATATGTAAACTATA
1 GTTTATATGTAAACTATA
*
955160 GTATATA
1 GTTTATA
955167 AATATAAATT
Statistics
Matches: 100, Mismatches: 14, Indels: 34
0.68 0.09 0.23
Matches are distributed among these distances:
13 10 0.10
15 3 0.03
16 5 0.05
17 10 0.10
18 40 0.40
19 4 0.04
20 25 0.25
21 3 0.03
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (18 bp):
GTTTATATGTAAACTATA
Found at i:955160 original size:31 final size:32
Alignment explanation
Indices: 955099--955172 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 32
955089 TCAACTTTAG
*
955099 TATATATATAGTTCATATGTAAACTATATAGTT
1 TATATATATAGTTCATATGTAAAC-ATATAGTA
955132 TATATATATAGTTCATATGTAAAC-TATAGTA
1 TATATATATAGTTCATATGTAAACATATAGTA
*
955163 TATAAATATA
1 TATATATATA
955173 AATTATAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 15 0.38
33 24 0.62
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (32 bp):
TATATATATAGTTCATATGTAAACATATAGTA
Found at i:955217 original size:148 final size:146
Alignment explanation
Indices: 954931--955217 Score: 348
Period size: 148 Copynumber: 1.9 Consensus size: 146
954921 TAATATACAG
954931 TATATAAATATAAACTATAGTATATATATAGGTCATATGTAAACTACATAGTTTATATATATAGT
1 TATATAAATATAAACTATAGTATATATATAGGTCATATGTAAACTACATAGTTTATATATATAGT
* * * * *
954996 TCATATGTAAATATCAGGTATTGTTTATATGTAAACTATAGTTAGTATATAAACAATATAGTTTA
66 TCATATGTAAATATCAGGTA-T-TATAAATATAAACTATAGTTAGTATATAAACAATATAATATA
* *
955061 TATGTAAACTATAGTTCA
129 CATCTAAACTATAGTTCA
* * * *
955079 TATATAAATATCAACTTTAGTATATATATAGTTCATATGTAAACTATATAGTTTATATATATAGT
1 TATATAAATATAAACTATAGTATATATATAGGTCATATGTAAACTACATAGTTTATATATATAGT
* * *
955144 TCATATGTAAACTAT-A-GTA-TATAAATATAAATTATAGTATGTAGTTTATATA-AATATAAAT
66 TCATATGTAAA-TATCAGGTATTATAAATATAAACTATAG--T-TAGTATATAAACAATAT-AAT
955205 ATACACTCTAAAC
126 ATACA-TCTAAAC
955218 CCTAAACTAT
Statistics
Matches: 119, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
144 14 0.12
146 6 0.05
147 17 0.14
148 79 0.66
149 3 0.03
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (146 bp):
TATATAAATATAAACTATAGTATATATATAGGTCATATGTAAACTACATAGTTTATATATATAGT
TCATATGTAAATATCAGGTATTATAAATATAAACTATAGTTAGTATATAAACAATATAATATACA
TCTAAACTATAGTTCA
Found at i:955236 original size:21 final size:21
Alignment explanation
Indices: 955212--955269 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
955202 AATATACACT
*
955212 CTAAACCCTAAACTATAAGCC
1 CTAAACCCTAAACTATAAACC
* *
955233 CTAATA-CTTAAACTCTAAACC
1 CTAA-ACCCTAAACTATAAACC
955254 CTAAACCCTAAA-TATA
1 CTAAACCCTAAACTATA
955270 TATATATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
20 4 0.13
21 25 0.83
22 1 0.03
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24
Consensus pattern (21 bp):
CTAAACCCTAAACTATAAACC
Found at i:955258 original size:14 final size:14
Alignment explanation
Indices: 955209--955265 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
955199 ATAAATATAC
955209 ACTCTAAACCCTAA
1 ACTCTAAACCCTAA
* *
955223 ACTATAAGCCCTAA
1 ACTCTAAACCCTAA
*
955237 TACT-TAAACTCTAA
1 -ACTCTAAACCCTAA
*
955251 ACCCTAAACCCTAA
1 ACTCTAAACCCTAA
955265 A
1 A
955266 TATATATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
13 2 0.06
14 30 0.86
15 3 0.09
ACGTcount: A:0.44, C:0.32, G:0.02, T:0.23
Consensus pattern (14 bp):
ACTCTAAACCCTAA
Found at i:955310 original size:22 final size:23
Alignment explanation
Indices: 955268--955325 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 23
955258 ACCCTAAATA
*
955268 TATATATATATATATATATAAAC
1 TATATATTTATATATATATAAAC
955291 TATATAGTTTATAT-TA-ATAAAC
1 TATATA-TTTATATATATATAAAC
955313 TATATAATTTATA
1 TATAT-ATTTATA
955326 CAATATATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 17 0.53
23 9 0.28
24 6 0.19
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (23 bp):
TATATATTTATATATATATAAAC
Found at i:955473 original size:2 final size:2
Alignment explanation
Indices: 955466--955599 Score: 157
Period size: 2 Copynumber: 67.0 Consensus size: 2
955456 TTATACATGG
955466 TA TA 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 TA TA
* * * *
955508 TA TA TA TA GTT TA TA TA TA TA -A TA TA TA T- TC TT TA TA TA AA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
955549 CTA TA TA GTT TG TA T- TA CA 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 TA TA
955592 TA TA TA TA
1 TA TA TA TA
955600 GTTGTTTTAA
Statistics
Matches: 115, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
1 3 0.03
2 109 0.95
3 3 0.03
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:956386 original size:210 final size:210
Alignment explanation
Indices: 955667--956586 Score: 1332
Period size: 211 Copynumber: 4.3 Consensus size: 210
955657 TATTTTTCAT
*
955667 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTATAATTTCATATTTGTTCAAT
1 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
*
955732 TTAGTCCTCCACATTTTATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTATT-
66 TTAGTCCTCCAAATTTTATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTT-TTA
* * * *
955796 AATTGGCCATAA-ATTTTTAAATGAGTATAATTTAGTACATTTTTGTATTAATTTCAACCTCAAA
130 AATTGGCCATAACTTTTTTAAATGGGTATAATTTAGTACATTTTTGTATTAATTTCAACATCACA
*
955860 ATTTAAAATTATTTCA
195 ATTTAAAATTATTTCG
* *
955876 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGATCAAT
1 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
* * *
955941 TTAGTCCTCCAAAATTTATTTGCATATAAAATTGACCCATTA-TTATTACTTAGTTCTATTTTTA
66 TTAGTCCTCCAAATTTTATTTGCATCTAAAATTGACCCA-TACTTATTACTTATTTCTATTTTTA
* * * *
956005 AATTGGCCCATAACTTTTTTAAGTGGGTATAATTTAATACTTTTTTGTATTAATTTTAACATCAC
130 AATTGG-CCATAACTTTTTTAAATGGGTATAATTTAGTACATTTTTGTATTAATTTCAACATCAC
* *
956070 AATTGAAATTTATTTCG
194 AATTTAAAATTATTTCG
*
956087 ATTTGATCCCTCATCAATGTGTGTT-TTTAATTAATTTAAATTTTTATTTGTAATTTCATATTTG
1 ATTTGATCCCT--T---T-TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTG
* * * *
956151 TTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGATCCATACATT-TTACTTAATTATA
60 TTCAATTTAGTCCTCCAAATTTTATTTGCATCTAAAATTGACCCATAC-TTATTACTTATTTCTA
* *
956215 TTTTTTAATTGGCACATAAC-TTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAA
124 TTTTTAAATTGGC-CATAACTTTTTTAAATGGGTATAATTTAGTACATTTTTGTATTAATTTCAA
*
956279 CATCACAATTTAAAATTATTTTG
188 CATCACAATTTAAAATTATTTCG
956302 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
1 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
* * *
956367 TTAGTCCTCCAATTTTTATTTGCATCTGAAATTAACCCATACTTATTACTTATTTCTATTTTTAA
66 TTAGTCCTCCAAATTTTATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTAA
*
956432 ATTGGCCTATAACTTTTTTAAATGGGTATAATTTAGTACATTTTTGTATTAATTTCAACATCATA
131 ATTGGCC-ATAACTTTTTTAAATGGGTATAATTTAGTACATTTTTGTATTAATTTCAACATCACA
956497 ATTTAAAATTA-TTCTG
195 ATTTAAAATTATTTC-G
* *
956513 ATTTGATACCTCATCAATGTGTGTTGTTTAATTTATTTAAAATTTTATTTGTAATTTCATATTTG
1 ATTTGAT-CC-C-T---TTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTG
956578 TTCAATTTA
60 TTCAATTTA
956587 ATTCTTAAAT
Statistics
Matches: 641, Mismatches: 46, Indels: 40
0.88 0.06 0.06
Matches are distributed among these distances:
208 2 0.00
209 131 0.20
210 122 0.19
211 136 0.21
212 2 0.00
213 3 0.00
214 1 0.00
215 75 0.12
216 106 0.17
217 63 0.10
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (210 bp):
ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
TTAGTCCTCCAAATTTTATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTAA
ATTGGCCATAACTTTTTTAAATGGGTATAATTTAGTACATTTTTGTATTAATTTCAACATCACAA
TTTAAAATTATTTCG
Found at i:956479 original size:426 final size:426
Alignment explanation
Indices: 955680--956586 Score: 1453
Period size: 426 Copynumber: 2.1 Consensus size: 426
955670 TGATCCCTTT
* *
955680 TGTGTTGTTTAATTTATTTAAATTTTTATTTATAATTTCATATTTGTTCAATTTAGTCCTCCACA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
* *
955745 TTTTATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTATTAATTGGCCATAAAT
66 TTTTATTTGCATCTAAAATTGACCCATACTTATTACTTAATTATATTTATTAATTGGCCATAAAT
*
955810 TTTTAAATGAGTATAATTTAGTACATTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTC
131 TTTTAAATGAGTATAATTTAGTACATTTTTGTATTAATTTCAACATCAAAATTTAAAATTATTTC
*
955875 AATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGATCAA
196 AATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGATCAA
*
955940 TTTAGTCCTCCAAAATTTATTTGCATATAAAATTGACCCATTATTATTACTTAGTTCTATTTTTA
261 TTTAGTCCTCCAAAATTTATTTGCATATAAAATTAACCCATTATTATTACTTAGTTCTATTTTTA
* * *
956005 AATTGGCCCATAACTTTTTTAAGTGGGTATAATTTAATACTTTTTTGTATTAATTTTAACATCAC
326 AATTGGCCCATAACTTTTTTAAATGGGTATAATTTAATACATTTTTGTATTAATTTCAACATCAC
* *
956070 AATTGAAATTTATT-TCGATTTGATCCCTCATCAATG
391 AATTGAAAATTATTCT-GATTTGATACCTCATCAATG
*
956106 TGTGTT-TTTAATTAATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
* * *
956170 TTTTATTTGCATCTGAAATTGATCCATACATT-TTACTTAATTATATTTTTTAATTGGCACATAA
66 TTTTATTTGCATCTAAAATTGACCCATAC-TTATTACTTAATTATATTTATTAATTGGC-CATAA
* * * *
956234 CTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATT
129 ATTTTTAAATGAGTATAATTTAGTACATTTTTGTATTAATTTCAACATCAAAATTTAAAATTATT
** *
956299 TTGATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTC
194 TCAATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGATC
** * * *
956364 AATTTAGTCCTCCAATTTTTATTTGCATCTGAAATTAACCCA-TACTTATTACTTATTTCTATTT
259 AATTTAGTCCTCCAAAATTTATTTGCATATAAAATTAACCCATTA-TTATTACTTAGTTCTATTT
* *
956428 TTAAATTGGCCTATAACTTTTTTAAATGGGTATAATTTAGTACATTTTTGTATTAATTTCAACAT
323 TTAAATTGGCCCATAACTTTTTTAAATGGGTATAATTTAATACATTTTTGTATTAATTTCAACAT
* *
956493 CATAATTTAAAATTATTCTGATTTGATACCTCATCAATG
388 CACAATTGAAAATTATTCTGATTTGATACCTCATCAATG
*
956532 TGTGTTGTTTAATTTATTTAAAATTTTATTTGTAATTTCATATTTGTTCAATTTA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
956587 ATTCTTAAAT
Statistics
Matches: 442, Mismatches: 34, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
425 107 0.24
426 288 0.65
427 47 0.11
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (426 bp):
TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
TTTTATTTGCATCTAAAATTGACCCATACTTATTACTTAATTATATTTATTAATTGGCCATAAAT
TTTTAAATGAGTATAATTTAGTACATTTTTGTATTAATTTCAACATCAAAATTTAAAATTATTTC
AATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGATCAA
TTTAGTCCTCCAAAATTTATTTGCATATAAAATTAACCCATTATTATTACTTAGTTCTATTTTTA
AATTGGCCCATAACTTTTTTAAATGGGTATAATTTAATACATTTTTGTATTAATTTCAACATCAC
AATTGAAAATTATTCTGATTTGATACCTCATCAATG
Found at i:957541 original size:61 final size:62
Alignment explanation
Indices: 957393--957541 Score: 178
Period size: 61 Copynumber: 2.4 Consensus size: 62
957383 AGTTGCCACA
* * * *
957393 AAGGCGCATCCCTAGGGATGCACTTT-ATCAGGGTTTTAGCTTACTGGGATGCCACGCGGGT
1 AAGGCGCATCCCTGGGGATGCACTTTCATCAGGGTTTTAGATGACTGGGATGACACGCGGGT
* * * * *
957454 AAGACGCATCCCTGGGGACGCGCTTTCAT-AGGGTTTTAGATGATTGGGATGACATGCGGGT
1 AAGGCGCATCCCTGGGGATGCACTTTCATCAGGGTTTTAGATGACTGGGATGACACGCGGGT
*
957515 AAGGCGCAT-CCTCGGGGGTGCACTTTC
1 AAGGCGCATCCCT-GGGGATGCACTTTC
957542 GCTTGGATTG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
60 3 0.04
61 68 0.93
62 2 0.03
ACGTcount: A:0.19, C:0.22, G:0.33, T:0.26
Consensus pattern (62 bp):
AAGGCGCATCCCTGGGGATGCACTTTCATCAGGGTTTTAGATGACTGGGATGACACGCGGGT
Found at i:957840 original size:15 final size:15
Alignment explanation
Indices: 957822--957870 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
957812 ATTAATATAA
957822 TTTTATAATTATTAT
1 TTTTATAATTATTAT
* *
957837 TTTTATTAAAATAATAT
1 TTTTA-T-AATTATTAT
*
957854 TTATATAATTATTAT
1 TTTTATAATTATTAT
957869 TT
1 TT
957871 ATTTAAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 14 0.52
16 2 0.07
17 11 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTATAATTATTAT
Found at i:957866 original size:32 final size:29
Alignment explanation
Indices: 957807--957878 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
957797 TTCTTATAAT
*
957807 TTTTTATTAATATAATTTTATAATTATTA
1 TTTTTATTAAAATAATTTTATAATTATTA
*
957836 TTTTTATTAAAATAATATTTAT-ATAATTA
1 TTTTTATTAAAATAAT-TTTATAATTATTA
*
957865 TTATTTATTTAAAT
1 TT-TTTATTAAAAT
957879 TTATTAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.61
30 15 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTTATTAAAATAATTTTATAATTATTA
Found at i:958972 original size:17 final size:17
Alignment explanation
Indices: 958950--958984 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
958940 GCTTGATATA
958950 ATTAGAA-TATTATATTT
1 ATTAGAATTA-TATATTT
958967 ATTAGAATTATATATTT
1 ATTAGAATTATATATTT
958984 A
1 A
958985 CATTTCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (17 bp):
ATTAGAATTATATATTT
Found at i:959604 original size:42 final size:42
Alignment explanation
Indices: 959540--959631 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
959530 GATGCCACAG
*
959540 GGGTACATGCCCAACCCTCCAGTTCAGATGCCATCTCCGCAA
1 GGGTACATGCCCAACCCACCAGTTCAGATGCCATCTCCGCAA
* *
959582 GGGTATATG-CCAAGCCCACCAGTTCATATGCCATCTCCGCAA
1 GGGTACATGCCCAA-CCCACCAGTTCAGATGCCATCTCCGCAA
*
959624 GGCTACAT
1 GGGTACAT
959632 TCTTAGCCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 4 0.09
42 40 0.91
ACGTcount: A:0.25, C:0.35, G:0.20, T:0.21
Consensus pattern (42 bp):
GGGTACATGCCCAACCCACCAGTTCAGATGCCATCTCCGCAA
Found at i:960088 original size:14 final size:14
Alignment explanation
Indices: 960053--960089 Score: 53
Period size: 11 Copynumber: 2.9 Consensus size: 14
960043 TCGGTGATCC
960053 AGTTGTATTTAAAT
1 AGTTGTATTTAAAT
960067 -G-T-TATTTAAAT
1 AGTTGTATTTAAAT
960078 AGTTGTATTTAA
1 AGTTGTATTTAA
960090 CAAATTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
11 9 0.45
12 2 0.10
13 2 0.10
14 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (14 bp):
AGTTGTATTTAAAT
Found at i:962421 original size:24 final size:24
Alignment explanation
Indices: 962394--962505 Score: 118
Period size: 24 Copynumber: 4.7 Consensus size: 24
962384 TATATCAAAA
* *
962394 ATCAAAACATAATTCAGGTCAAGT
1 ATCAAATCATAATTCATGTCAAGT
* * *
962418 ATCATATCAAAATTCATATCAAGT
1 ATCAAATCATAATTCATGTCAAGT
* * *
962442 ATCAGATCAGAATCCATGTCAAGT
1 ATCAAATCATAATTCATGTCAAGT
* *
962466 ATCAAATCACAATCCATGTCAAGT
1 ATCAAATCATAATTCATGTCAAGT
962490 ATCATAA-CATAATTCA
1 ATCA-AATCATAATTCA
962506 AATCGGAAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
24 72 0.97
25 2 0.03
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.28
Consensus pattern (24 bp):
ATCAAATCATAATTCATGTCAAGT
Found at i:967142 original size:24 final size:24
Alignment explanation
Indices: 967115--967214 Score: 119
Period size: 24 Copynumber: 4.2 Consensus size: 24
967105 TATATAAAAA
* * *
967115 ATCAAAACATAATTCAAGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
* *
967139 ATCATATCAAAATCCATGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
* *
967163 ATCAGATCAAAATCCAGGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
* *
967187 ATCAAATCAGAATCCATGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
967211 ATCA
1 ATCA
967215 TAACAGAATT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.25
Consensus pattern (24 bp):
ATCAAATCAAAATCCAAGTCAAGT
Found at i:974380 original size:14 final size:15
Alignment explanation
Indices: 974351--974383 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
974341 TCTTCGTTAA
974351 ATTTACTTTTTATTT
1 ATTTACTTTTTATTT
*
974366 ATTTAGTTTTT-TTT
1 ATTTACTTTTTATTT
974380 ATTT
1 ATTT
974384 TTTCAGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (15 bp):
ATTTACTTTTTATTT
Found at i:974380 original size:18 final size:18
Alignment explanation
Indices: 974357--974398 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
974347 TTAAATTTAC
*
974357 TTTTTATTTATTT-AGTTT
1 TTTTTATTT-TTTCAGGTT
974375 TTTTTATTTTTTCAGGTT
1 TTTTTATTTTTTCAGGTT
974393 TTTTTA
1 TTTTTA
974399 AAGTATAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.76
Consensus pattern (18 bp):
TTTTTATTTTTTCAGGTT
Found at i:975427 original size:31 final size:31
Alignment explanation
Indices: 975324--975427 Score: 75
Period size: 31 Copynumber: 3.2 Consensus size: 31
975314 CAGTCGTTGT
*
975324 TGAACCTATACAAGGAATTACCAACAGCGAC
1 TGAACCTATACAAGGAATTACCAGCAGCGAC
* * * * * * *
975355 TGAACCTGCCAGAGATAGGAATTTCTAGTCTGTG-T
1 TGAACCT---ATACA-AGGAATTACCAG-CAGCGAC
*
975390 TAAACCTATACAAGGAATTACCAGCAGCGAC
1 TGAACCTATACAAGGAATTACCAGCAGCGAC
975421 TGAACCT
1 TGAACCT
975428 GCTAGAGTCT
Statistics
Matches: 50, Mismatches: 17, Indels: 12
0.63 0.22 0.15
Matches are distributed among these distances:
30 3 0.06
31 23 0.46
32 3 0.06
34 3 0.06
35 15 0.30
36 3 0.06
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (31 bp):
TGAACCTATACAAGGAATTACCAGCAGCGAC
Found at i:981830 original size:14 final size:14
Alignment explanation
Indices: 981798--981861 Score: 74
Period size: 14 Copynumber: 4.6 Consensus size: 14
981788 AAGTCAACGG
* *
981798 GTTGACTCAAATGA
1 GTTGACTCAGACGA
*
981812 GTTGAATCAGACGA
1 GTTGACTCAGACGA
* *
981826 TTTGACTCAGATGA
1 GTTGACTCAGACGA
*
981840 GTTGACTCAGACGG
1 GTTGACTCAGACGA
981854 GTTGACTC
1 GTTGACTC
981862 GATCAGGTCA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:981839 original size:28 final size:28
Alignment explanation
Indices: 981798--981861 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
981788 AAGTCAACGG
981798 GTTGACTCAAATGAGTTGAATCAGACGA
1 GTTGACTCAAATGAGTTGAATCAGACGA
* * * *
981826 TTTGACTCAGATGAGTTGACTCAGACGG
1 GTTGACTCAAATGAGTTGAATCAGACGA
981854 GTTGACTC
1 GTTGACTC
981862 GATCAGGTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (28 bp):
GTTGACTCAAATGAGTTGAATCAGACGA
Found at i:984009 original size:18 final size:19
Alignment explanation
Indices: 983973--984009 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
983963 AAGAATTATC
983973 TTTAGGAATTATCTCTTGTT
1 TTTAGGAATTA-CTCTTGTT
983993 TTTAGGAATTA-TCTTGT
1 TTTAGGAATTACTCTTGT
984010 CATTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.22, C:0.08, G:0.16, T:0.54
Consensus pattern (19 bp):
TTTAGGAATTACTCTTGTT
Found at i:993066 original size:22 final size:22
Alignment explanation
Indices: 993039--993083 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
993029 AAAAAATAGT
993039 AAGTTAAATAAGCATAAAAAAC
1 AAGTTAAATAAGCATAAAAAAC
993061 AAGTTAAATAAGCATAAAAAAC
1 AAGTTAAATAAGCATAAAAAAC
993083 A
1 A
993084 GTAAAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.64, C:0.09, G:0.09, T:0.18
Consensus pattern (22 bp):
AAGTTAAATAAGCATAAAAAAC
Found at i:993738 original size:14 final size:14
Alignment explanation
Indices: 993721--993756 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
993711 TTTTCATTTA
*
993721 TTTAATTTCAATCC
1 TTTAATTTCAATAC
*
993735 TTTAATTTCACTAC
1 TTTAATTTCAATAC
993749 TTTAATTT
1 TTTAATTT
993757 TCTATCTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTAATTTCAATAC
Found at i:1002965 original size:42 final size:42
Alignment explanation
Indices: 1002901--1003010 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 42
1002891 TCCTTCGGGC
* *
1002901 CATCTGTAAGTCTTTCAAGCATGATGTTTAAAT-TCTTCAGGT
1 CATCTGTAAGTCTTTCGAGCATGATGCTTAAATAT-TTCAGGT
* **
1002943 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATATTTTGGGT
1 CATCTGTAAGTCTTTCGAGCATGATGCTTAAATATTTCAGGT
* *
1002985 CATCTGTAAGACTTTCGAGCAAGATG
1 CATCTGTAAGTCTTTCGAGCATGATG
1003011 ATAATACATT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 58 0.98
43 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (42 bp):
CATCTGTAAGTCTTTCGAGCATGATGCTTAAATATTTCAGGT
Found at i:1003213 original size:42 final size:42
Alignment explanation
Indices: 1003156--1003237 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
1003146 GAGATTAAAG
* * * *
1003156 TAAACCCTTTGGGTCATCA-ATAAGTCTTTCGAGCATGATGCT
1 TAAACCCTTCGGGTCAT-ATATAAGCCTTTCAAGCAAGATGCT
*
1003198 TAAATCCTTCGGGTCATATATAAGCCTTTCAAGCAAGATG
1 TAAACCCTTCGGGTCATATATAAGCCTTTCAAGCAAGATG
1003238 ATAAGACCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.03
42 33 0.97
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (42 bp):
TAAACCCTTCGGGTCATATATAAGCCTTTCAAGCAAGATGCT
Found at i:1003953 original size:17 final size:17
Alignment explanation
Indices: 1003931--1003973 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
1003921 TGAAGAGGAA
* *
1003931 GAAGAAGTTCATAATCT
1 GAAGAACTTCATAATAT
1003948 GAAGAACTTCATAATAT
1 GAAGAACTTCATAATAT
1003965 GAAGAACTT
1 GAAGAACTT
1003974 ATTCAACCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (17 bp):
GAAGAACTTCATAATAT
Found at i:1004061 original size:140 final size:140
Alignment explanation
Indices: 1003809--1004096 Score: 423
Period size: 140 Copynumber: 2.1 Consensus size: 140
1003799 AAAGAGGAAT
* * * * *
1003809 AAGAAGTTCATAATCTGAAGAACTTATTCAACCTTTTGCTCAACTCTATCACAGAATGAGATATA
1 AAGAACTTCATAATATGAAGAACTTATTCAACCATTTGCTCAACTCTATCAAAAAATGAGATATA
* * * * *
1003874 ATAGCATCAATATTTTCATAAAGAGTTCGTAATAAGAATAACTCATCTGAAGAGGAAGAAGAAGT
66 ACAACATCAACATTTCCAGAAAGAGTTCGTAATAAGAATAACTCATCTGAAGAGGAAGAAGAAGT
*
1003939 TCATAATCTG
131 TCATAATCTA
*
1003949 AAGAACTTCATAATATGAAGAACTTATTCAACCATTTGCTCGACTCTATCAAAAAATGAGATATA
1 AAGAACTTCATAATATGAAGAACTTATTCAACCATTTGCTCAACTCTATCAAAAAATGAGATATA
* * * *
1004014 GCAACATCAACATTTCCAGAAGGAGTTCGTAATAAGAATAATTCATCTGAAGATGAAGAAGAAGT
66 ACAACATCAACATTTCCAGAAAGAGTTCGTAATAAGAATAACTCATCTGAAGAGGAAGAAGAAGT
*
1004079 TCATATTCTA
131 TCATAATCTA
1004089 AAGAACTT
1 AAGAACTT
1004097 ATTCATTCGA
Statistics
Matches: 131, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
140 131 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (140 bp):
AAGAACTTCATAATATGAAGAACTTATTCAACCATTTGCTCAACTCTATCAAAAAATGAGATATA
ACAACATCAACATTTCCAGAAAGAGTTCGTAATAAGAATAACTCATCTGAAGAGGAAGAAGAAGT
TCATAATCTA
Found at i:1004210 original size:41 final size:39
Alignment explanation
Indices: 1004153--1004251 Score: 130
Period size: 41 Copynumber: 2.5 Consensus size: 39
1004143 TTCAATGGAA
1004153 GAGTTCATAATGAGAAGAACTT-TCCGAA-AAGGAAAATGAAG
1 GAGTTCATAATGAGAAGAACTTCTCCGAAGAA-G--AA-GAAG
1004194 GAGTTCATAATGAGAAGAACTTCTCCGAAGAAGAAGAAG
1 GAGTTCATAATGAGAAGAACTTCTCCGAAGAAGAAGAAG
* *
1004233 AAGTTCATAATGAAAAGAA
1 GAGTTCATAATGAGAAGAA
1004252 ATTGTTCAAC
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
39 21 0.39
40 2 0.04
41 22 0.41
42 7 0.13
43 2 0.04
ACGTcount: A:0.47, C:0.10, G:0.23, T:0.19
Consensus pattern (39 bp):
GAGTTCATAATGAGAAGAACTTCTCCGAAGAAGAAGAAG
Found at i:1005714 original size:14 final size:14
Alignment explanation
Indices: 1005697--1005732 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1005687 TTTTCATTTA
*
1005697 TTTAATTTCAATCC
1 TTTAATTTCAATAC
*
1005711 TTTAATTTCACTAC
1 TTTAATTTCAATAC
1005725 TTTAATTT
1 TTTAATTT
1005733 TCTATCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTAATTTCAATAC
Found at i:1005822 original size:59 final size:59
Alignment explanation
Indices: 1005702--1005825 Score: 144
Period size: 59 Copynumber: 2.1 Consensus size: 59
1005692 ATTTATTTAA
* * * * *
1005702 TTTCAATCCTTTAATTTCACTACTTTAATTTTCTATCTTTTTATTTTTTTCTTTATATT
1 TTTCAATACTTTAAATTCAATACTTTAATTATCTATCTTTTTATTTTTTTATTTATATT
* *
1005761 TTTCAATATTTTAAATTCAATACTTTAATTAT-TA-CTTTTTATTATATTTTATTTCATTTT
1 TTTCAATACTTTAAATTCAATACTTTAATTATCTATCTTTTTATT-T-TTTTATTT-ATATT
1005821 TTTCA
1 TTTCA
1005826 TTAATTAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
57 9 0.16
58 3 0.05
59 34 0.62
60 9 0.16
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.63
Consensus pattern (59 bp):
TTTCAATACTTTAAATTCAATACTTTAATTATCTATCTTTTTATTTTTTTATTTATATT
Found at i:1009217 original size:3 final size:3
Alignment explanation
Indices: 1009209--1009301 Score: 186
Period size: 3 Copynumber: 31.0 Consensus size: 3
1009199 CTGTTGATGC
1009209 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1009257 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1009302 TCTCACTTGC
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:1009470 original size:3 final size:3
Alignment explanation
Indices: 1009462--1009566 Score: 201
Period size: 3 Copynumber: 35.0 Consensus size: 3
1009452 CTGTTGATGC
1009462 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
1009510 CTT CTT CTT CTT CTT CTT CGT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1009558 CTT CTT CTT
1 CTT CTT CTT
1009567 GGGGTTGGGA
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 100 1.00
ACGTcount: A:0.00, C:0.33, G:0.01, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:1009498 original size:253 final size:253
Alignment explanation
Indices: 1009050--1009554 Score: 1001
Period size: 253 Copynumber: 2.0 Consensus size: 253
1009040 ATCACACCCC
1009050 CTCACTTGCATTTCCTTCAGCGAAGGCCAATTTATAGTAAGCATTTTACGATAGATGCTCTTTAG
1 CTCACTTGCATTTCCTTCAGCGAAGGCCAATTTATAGTAAGCATTTTACGATAGATGCTCTTTAG
1009115 ATTTGGAATATTTTCGAACGTGAAAGTTCATATGTAATGACACCTGATTGAATAAGTTGTGGAGA
66 ATTTGGAATATTTTCGAACGTGAAAGTTCATATGTAATGACACCTGATTGAATAAGTTGTGGAGA
1009180 GAATGATTGCATGGCCCTACTGTTGATGCCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT
131 GAATGATTGCATGGCCCTACTGTTGATGCCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT
*
1009245 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTT
196 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCGTCTTCTTCTTCTTCTTCTTCTTCTTT
1009303 CTCACTTGCATTTCCTTCAGCGAAGGCCAATTTATAGTAAGCATTTTACGATAGATGCTCTTTAG
1 CTCACTTGCATTTCCTTCAGCGAAGGCCAATTTATAGTAAGCATTTTACGATAGATGCTCTTTAG
1009368 ATTTGGAATATTTTCGAACGTGAAAGTTCATATGTAATGACACCTGATTGAATAAGTTGTGGAGA
66 ATTTGGAATATTTTCGAACGTGAAAGTTCATATGTAATGACACCTGATTGAATAAGTTGTGGAGA
1009433 GAATGATTGCATGGCCCTACTGTTGATGCCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT
131 GAATGATTGCATGGCCCTACTGTTGATGCCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT
1009498 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCGTCTTCTTCTTCTTCTTCTTCTTCTT
196 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCGTCTTCTTCTTCTTCTTCTTCTTCTT
1009555 CTTCTTCTTC
Statistics
Matches: 251, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
253 251 1.00
ACGTcount: A:0.18, C:0.23, G:0.14, T:0.46
Consensus pattern (253 bp):
CTCACTTGCATTTCCTTCAGCGAAGGCCAATTTATAGTAAGCATTTTACGATAGATGCTCTTTAG
ATTTGGAATATTTTCGAACGTGAAAGTTCATATGTAATGACACCTGATTGAATAAGTTGTGGAGA
GAATGATTGCATGGCCCTACTGTTGATGCCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT
CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCGTCTTCTTCTTCTTCTTCTTCTTCTTT
Found at i:1009933 original size:7 final size:7
Alignment explanation
Indices: 1009892--1009942 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
1009882 GGGTTTTAAG
1009892 TTAGGGT
1 TTAGGGT
*
1009899 TTATGGT
1 TTAGGGT
*
1009906 TTA-GAT
1 TTAGGGT
*
1009912 ATTATGGGA
1 -TTA-GGGT
1009921 TTAGGGT
1 TTAGGGT
1009928 TTAGGGT
1 TTAGGGT
1009935 TTAGGGT
1 TTAGGGT
1009942 T
1 T
1009943 ATCAATTTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
6 2 0.06
7 30 0.83
8 3 0.08
9 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.45
Consensus pattern (7 bp):
TTAGGGT
Found at i:1010378 original size:23 final size:23
Alignment explanation
Indices: 1010352--1010422 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
1010342 GATGTAAACA
1010352 TAATAATTTGATTTAAATATTTT
1 TAATAATTTGATTTAAATATTTT
* ** * *
1010375 TAATACTCAAGATGTAAACA----
1 TAATAAT-TTGATTTAAATATTTT
1010395 TAATAATTTGATTTAAATATTTT
1 TAATAATTTGATTTAAATATTTT
1010418 TAATA
1 TAATA
1010423 CTCAAGATGT
Statistics
Matches: 33, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 8 0.24
20 6 0.18
23 11 0.33
24 8 0.24
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (23 bp):
TAATAATTTGATTTAAATATTTT
Found at i:1010383 original size:43 final size:43
Alignment explanation
Indices: 1010322--1010454 Score: 259
Period size: 43 Copynumber: 3.1 Consensus size: 43
1010312 TATAAATGAA
1010322 TAAATATTTTTAATACTCAAGATGTAAACATAATAATTTGATT
1 TAAATATTTTTAATACTCAAGATGTAAACATAATAATTTGATT
1010365 TAAATATTTTTAATACTCAAGATGTAAACATAATAATTTGATT
1 TAAATATTTTTAATACTCAAGATGTAAACATAATAATTTGATT
1010408 TAAATATTTTTAATACTCAAGATGTAAACATAATAATTTGA-T
1 TAAATATTTTTAATACTCAAGATGTAAACATAATAATTTGATT
1010450 TAAAT
1 TAAAT
1010455 TAAATATTCT
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
42 6 0.07
43 84 0.93
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (43 bp):
TAAATATTTTTAATACTCAAGATGTAAACATAATAATTTGATT
Found at i:1024312 original size:19 final size:19
Alignment explanation
Indices: 1024277--1024313 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1024267 ATGACCAACA
* *
1024277 AAATCGCAATGCTATCTCT
1 AAATCGCAACGCGATCTCT
1024296 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1024314 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1024410 original size:41 final size:41
Alignment explanation
Indices: 1024358--1024535 Score: 284
Period size: 41 Copynumber: 4.3 Consensus size: 41
1024348 GATTTTGACT
*
1024358 ATCGCAACGCGATTCTGACTATCGCAACGCGATAAAACATA
1 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATA
1024399 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATA
1 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATA
* * *
1024440 ATCGCAACACGATTCTGACTATCGCAACACGATAATATATA
1 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATA
* * *
1024481 ATCGCAATGCAATTCTGACTATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATA
*
1024522 ATCGCAATGCGATT
1 ATCGCAACGCGATT
1024536 TTCAAAGCGC
Statistics
Matches: 126, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 126 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATA
Found at i:1024465 original size:20 final size:20
Alignment explanation
Indices: 1024339--1024513 Score: 160
Period size: 20 Copynumber: 8.6 Consensus size: 20
1024329 GTTTTTAGAT
*
1024339 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
1024359 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
***
1024379 TCGCAACGCGA-TAAAACATAA
1 TCGCAACGCGATTCTGAC-T-A
1024400 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
**
1024420 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTCTGAC-T-A
*
1024441 TCGCAACACGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* *
1024461 TCGCAACACGATAATAT-A-TAA
1 TCGCAACGCGAT--TCTGACT-A
* *
1024482 TCGCAATGCAATTCTGACTA
1 TCGCAACGCGATTCTGACTA
1024502 TCGCAACGCGAT
1 TCGCAACGCGAT
1024514 AATACAAAAT
Statistics
Matches: 125, Mismatches: 19, Indels: 22
0.75 0.11 0.13
Matches are distributed among these distances:
19 7 0.06
20 72 0.58
21 39 0.31
22 7 0.06
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:1024527 original size:21 final size:20
Alignment explanation
Indices: 1024378--1024534 Score: 86
Period size: 21 Copynumber: 7.7 Consensus size: 20
1024368 GATTCTGACT
*
1024378 ATCGCAACGCGATAAAACATA
1 ATCGCAACGCGATAATACA-A
** *
1024399 ATCGCAACGCGATTCTGAC-T
1 ATCGCAACGCGATAAT-ACAA
1024419 ATCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACA-A
* ** *
1024440 ATCGCAACACGATTCTGAC-T
1 ATCGCAACGCGATAAT-ACAA
* *
1024460 ATCGCAACACGATAATATATA
1 ATCGCAACGCGATAATACA-A
* * ** *
1024481 ATCGCAATGCAATTCTGAC-T
1 ATCGCAACGCGATAAT-ACAA
1024501 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATAC-AA
*
1024522 ATCGCAATGCGAT
1 ATCGCAACGCGAT
1024535 TTTCAAAGCG
Statistics
Matches: 99, Mismatches: 28, Indels: 18
0.68 0.19 0.12
Matches are distributed among these distances:
19 5 0.05
20 40 0.40
21 49 0.49
22 5 0.05
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATAATACAA
Found at i:1024704 original size:22 final size:22
Alignment explanation
Indices: 1024679--1024729 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1024669 CTATGGCGAC
*
1024679 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACAAA
*
1024701 ATCCGTCCCCATCTCCGGCAAA
1 ATCCGTCCCCATCTCCGACAAA
1024723 ATCCGTC
1 ATCCGTC
1024730 TATCGCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.45, G:0.14, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACAAA
Found at i:1025152 original size:20 final size:20
Alignment explanation
Indices: 1025113--1025240 Score: 92
Period size: 20 Copynumber: 6.8 Consensus size: 20
1025103 GATAGTCAAA
* *
1025113 TTCGCGTTGCGA-TGTCATT
1 TTCGTGTTGCGATTTTCATT
1025132 TTCGTGTTGCGATTTTCA-T
1 TTCGTGTTGCGATTTTCATT
*
1025151 TTCGCGTTGCGA--TT-A--
1 TTCGTGTTGCGATTTTCATT
* ** **
1025166 -TCTTGTTGCGATAGTCAAA
1 TTCGTGTTGCGATTTTCATT
* * **
1025185 TTCGCGTTGCAATAGTCATT
1 TTCGTGTTGCGATTTTCATT
1025205 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
1025225 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
1025241 AAGTCTCAGA
Statistics
Matches: 87, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
14 9 0.10
16 2 0.02
17 3 0.03
19 23 0.26
20 50 0.57
ACGTcount: A:0.14, C:0.17, G:0.23, T:0.46
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:1027146 original size:20 final size:20
Alignment explanation
Indices: 1027118--1027186 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
1027108 CGAAACTTAA
1027118 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * *
1027138 ATCGTAACGCGGAAATGAAT
1 ATCGCAACGCGAAAATGACT
**
1027158 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1027178 ATCGCAACG
1 ATCGCAACG
1027187 GAATAATCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1027227 original size:14 final size:14
Alignment explanation
Indices: 1027208--1027241 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1027198 ATGCGAAATA
*
1027208 AAAATCGCAACGTG
1 AAAATCGCAACGCG
*
1027222 AAAATCGCAATGCG
1 AAAATCGCAACGCG
1027236 AAAATC
1 AAAATC
1027242 CCATTGCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.15
Consensus pattern (14 bp):
AAAATCGCAACGCG
Found at i:1027826 original size:21 final size:21
Alignment explanation
Indices: 1027775--1027840 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
1027765 GCCCGACTCA
*
1027775 CCTGTCATCGTTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
*
1027796 CCT-CCTATCGTTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* *
1027817 CCTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
1027838 CCT
1 CCT
1027841 CCCACCATTC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
20 1 0.03
21 36 0.95
22 1 0.03
ACGTcount: A:0.18, C:0.33, G:0.21, T:0.27
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:1027852 original size:42 final size:42
Alignment explanation
Indices: 1027775--1027855 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
1027765 GCCCGACTCA
* * *
1027775 CCTGTCATCGTTCAAGAGTCCCCTCCTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCCCACCATTCAAGAGGCC
*
1027817 CCTGTCATCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTGTCATCGTTCAAGA-GTCCCCTCCCACCATTCAAGAG
1027856 CCCGATTCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.21, C:0.35, G:0.20, T:0.25
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGTCCCCTCCCACCATTCAAGAGGCC
Found at i:1029230 original size:14 final size:14
Alignment explanation
Indices: 1029211--1029272 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
1029201 TTGCTTGTTT
1029211 AATTGATTTGTAAA
1 AATTGATTTGTAAA
1029225 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
1029239 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
1029254 TATTGATATGTAAA
1 AATTGATTTGTAAA
1029268 TAATT
1 -AATT
1029273 CTTATTTGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 26 0.67
15 13 0.33
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1029245 original size:28 final size:29
Alignment explanation
Indices: 1029213--1029267 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1029203 GCTTGTTTAA
*
1029213 TTGATTTG-TAAAAATTGATTTGTAAAAG
1 TTGATTTGTTAAAAATTGATATGTAAAAG
* *
1029241 TTGATTTGTTTAATATTGATATGTAAA
1 TTGATTTGTTAAAAATTGATATGTAAA
1029268 TAATTCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.47
Consensus pattern (29 bp):
TTGATTTGTTAAAAATTGATATGTAAAAG
Found at i:1029295 original size:79 final size:77
Alignment explanation
Indices: 1029202--1029374 Score: 292
Period size: 79 Copynumber: 2.2 Consensus size: 77
1029192 TAGCATTTTT
1029202 TGCTTGTTTAATTGATTTGTAAAAATTGATTTGTAAAAGTTGATTTGTTTAATATTGATATGTAA
1 TGCTTGTTTAATTGATTTGTAAAAATTGATTTGTAAAAGTTGATTTGTTT-A-ATTGATATGTAA
1029267 ATAATTCTTATTTG
64 ATAATTCTTATTTG
* *
1029281 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAAT
1 TGCTTGTTTAATTGATTTGTAAAAATTGATTTGTAAAAGTTGATTTGTTTAATTGATATGTAAAT
1029346 AATTCTTATTTG
66 AATTCTTATTTG
* *
1029358 TTCTTATTTAATTGATT
1 TGCTTGTTTAATTGATT
1029375 GAAATGTAAA
Statistics
Matches: 90, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
77 40 0.44
78 1 0.01
79 49 0.54
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (77 bp):
TGCTTGTTTAATTGATTTGTAAAAATTGATTTGTAAAAGTTGATTTGTTTAATTGATATGTAAAT
AATTCTTATTTG
Found at i:1029302 original size:36 final size:36
Alignment explanation
Indices: 1029246--1029374 Score: 98
Period size: 36 Copynumber: 3.4 Consensus size: 36
1029236 AAAAGTTGAT
*
1029246 TTGTTTAATATTGATATGTAAATAATTCTTATTTGTGC
1 TTGTTT-A-ATTGATTTGTAAATAATTCTTATTTGTGC
* *** *
1029284 TTGTTTAATTGATTTGTAAAAGTTGATT-TGTAAAAGTTGAT
1 TTGTTTAATTGATTTGT-AAA--TAATTCT-TATTTG-TG-C
* *
1029325 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTTC
1 TTGTTTAATTGATTTGTAAATAATTCTTATTTGTGC
*
1029361 TTATTTAATTGATT
1 TTGTTTAATTGATT
1029375 GAAATGTAAA
Statistics
Matches: 69, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
36 21 0.30
37 5 0.07
38 14 0.20
39 8 0.12
40 5 0.07
41 16 0.23
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (36 bp):
TTGTTTAATTGATTTGTAAATAATTCTTATTTGTGC
Found at i:1029311 original size:14 final size:14
Alignment explanation
Indices: 1029292--1029328 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1029282 GCTTGTTTAA
1029292 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
1029306 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
1029320 TTGATTTGT
1 TTGATTTGT
1029329 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1029473 original size:20 final size:20
Alignment explanation
Indices: 1029448--1029525 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
1029438 AGGTGTACTT
*
1029448 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACTCAAAA
* *
1029468 TCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAACTCAAAA
*
1029488 TCGCAATGCGAAAGC-CAAAA
1 TCGCAACGCGAAA-CTCAAAA
*
1029508 TCGCAACGCGAAAGTCAA
1 TCGCAACGCGAAACTCAA
1029526 TTCGCGTTGC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.44, C:0.26, G:0.18, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:1029492 original size:40 final size:40
Alignment explanation
Indices: 1029448--1029525 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
1029438 AGGTGTACTT
* *
1029448 TCGCAACGCTAAA-CTCAAAATCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAAGC-CAAAATCGCAACGCGAAAGTCAAAA
*
1029488 TCGCAATGCGAAAGCCAAAATCGCAACGCGAAAGTCAA
1 TCGCAACGCGAAAGCCAAAATCGCAACGCGAAAGTCAA
1029526 TTCGCGTTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.44, C:0.26, G:0.18, T:0.13
Consensus pattern (40 bp):
TCGCAACGCGAAAGCCAAAATCGCAACGCGAAAGTCAAAA
Found at i:1029592 original size:20 final size:20
Alignment explanation
Indices: 1029564--1029660 Score: 149
Period size: 20 Copynumber: 4.8 Consensus size: 20
1029554 GCGATTTTCT
*
1029564 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* * *
1029584 CGTTACGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
1029604 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1029624 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1029644 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
1029661 GAATATGTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1029883 original size:140 final size:140
Alignment explanation
Indices: 1029631--1029913 Score: 494
Period size: 140 Copynumber: 2.0 Consensus size: 140
1029621 TCGCGTTGCG
* *
1029631 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTAAAAAGATCA
1 ATAGTCAAATTCGCATTACGATATTCAAATGAATATGTAATAAGTGATAACAACTAAAAAGATCA
1029696 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1029761 AATACACATA
131 AATACACATA
* * * * * *
1029771 ATAGTCAAATTCGCATTACGATATTCAAATGAATGTGTGATAAGTGATAACAATTGAACATATCA
1 ATAGTCAAATTCGCATTACGATATTCAAATGAATATGTAATAAGTGATAACAACTAAAAAGATCA
1029836 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1029901 AATACACATA
131 AATACACATA
1029911 ATA
1 ATA
1029914 CAACGTTTGC
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
140 135 1.00
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCATTACGATATTCAAATGAATATGTAATAAGTGATAACAACTAAAAAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:1029994 original size:18 final size:18
Alignment explanation
Indices: 1029971--1030005 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1029961 AAGCCAGTTG
*
1029971 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1029989 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1030006 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1033098 original size:20 final size:20
Alignment explanation
Indices: 1033051--1033098 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1033041 GAAATTCAGT
*
1033051 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
1033071 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
1033091 GTTGCGAT
1 GTTGCGAT
1033099 TTACATATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.25
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:1039166 original size:66 final size:67
Alignment explanation
Indices: 1039020--1039190 Score: 222
Period size: 66 Copynumber: 2.6 Consensus size: 67
1039010 GTCCATCTTT
* * * *
1039020 AGAGACAAAACTCGTTTCAAGGGAAACAATCTCAAAG--ATGATGTTTCAATAGAAACTGTATCA
1 AGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAAGTTTTGATGTTTCAAGAGAAACTATATCA
1039083 AG
66 AG
* * *
1039085 AGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGTTTTG-TGTTTCAAGGGAAACTATCTCA
1 AGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAAGTTTTGATGTTTCAAGAGAAACTATATCA
1039149 AG
66 AG
* * * *
1039151 AGAGAAAAAACTTGTTTCAAGAGAAACAATATCAGAGTTT
1 AGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAAGTTT
1039191 ATTAATTTTG
Statistics
Matches: 92, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
65 35 0.38
66 55 0.60
67 2 0.02
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (67 bp):
AGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAAGTTTTGATGTTTCAAGAGAAACTATATCA
AG
Found at i:1039382 original size:35 final size:35
Alignment explanation
Indices: 1039300--1039374 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 35
1039290 TTCTTAAAGG
* *
1039300 GAAAATGTCTCAAGTGAGATGAAATTTGTTTTTAGA
1 GAAAATGTCTCAAGAGAGAT-AAATTTATTTTTAGA
1039336 GAAAACTGTCTCAAGAGAGAT-AATTTATTTTTA-A
1 GAAAA-TGTCTCAAGAGAGATAAATTTATTTTTAGA
1039370 GAAAA
1 GAAAA
1039375 ATTGTCTCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
34 6 0.17
35 11 0.31
36 5 0.14
37 14 0.39
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (35 bp):
GAAAATGTCTCAAGAGAGATAAATTTATTTTTAGA
Found at i:1039703 original size:16 final size:16
Alignment explanation
Indices: 1039682--1039721 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
1039672 TGAAAAATTC
1039682 ATGTATGTATGTGTTA
1 ATGTATGTATGTGTTA
*
1039698 ATGTATGTATGTGTTG
1 ATGTATGTATGTGTTA
1039714 ATGTATGT
1 ATGTATGT
1039722 TTTCTCAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.50
Consensus pattern (16 bp):
ATGTATGTATGTGTTA
Found at i:1043780 original size:23 final size:23
Alignment explanation
Indices: 1043741--1043890 Score: 108
Period size: 23 Copynumber: 6.4 Consensus size: 23
1043731 GAGTCGAGGG
* *
1043741 TTCTACGCGGTCATTCGGGATAA
1 TTCTACGTGGTCCTTCGGGATAA
* * *
1043764 TTCTATGTGGTTCTTCGGGAAAAA
1 TTCTACGTGGTCCTTCGGG-ATAA
* *
1043788 TTCTACGCGGTCCTTCGGGATAT
1 TTCTACGTGGTCCTTCGGGATAA
* * *
1043811 TTCTACGTAGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGATAA
*
1043834 TTCTACATGG-CACTTCGGTGCAT-A
1 TTCTACGTGGTC-CTTCGG-G-ATAA
* *
1043858 TTCTACGCGG-CACTTCGGTATAA
1 TTCTACGTGGTC-CTTCGGGATAA
*
1043881 TTCTATGTGG
1 TTCTACGTGG
1043891 CAGTTTCTAC
Statistics
Matches: 100, Mismatches: 22, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
22 3 0.03
23 60 0.60
24 36 0.36
25 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.35
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGATAA
Found at i:1043794 original size:47 final size:47
Alignment explanation
Indices: 1043741--1043830 Score: 135
Period size: 47 Copynumber: 1.9 Consensus size: 47
1043731 GAGTCGAGGG
* * *
1043741 TTCTACGCGGTCATTCGGGATAATTCTATGTGGTTCTTCGGGAAAAA
1 TTCTACGCGGTCATTCGGGATAATTCTACGTAGTCCTTCGGGAAAAA
* *
1043788 TTCTACGCGGTCCTTCGGGATATTTCTACGTAGTCCTTCGGGA
1 TTCTACGCGGTCATTCGGGATAATTCTACGTAGTCCTTCGGGA
1043831 CATTTCTACA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 38 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (47 bp):
TTCTACGCGGTCATTCGGGATAATTCTACGTAGTCCTTCGGGAAAAA
Found at i:1043892 original size:23 final size:23
Alignment explanation
Indices: 1043834--1043892 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
1043824 TTCGGGACAT
*
1043834 TTCTACATGGCACTTCGGTGCATA
1 TTCTACGTGGCACTTCGGT-CATA
*
1043858 TTCTACGCGGCACTTCGGT-ATAA
1 TTCTACGTGGCACTTCGGTCAT-A
*
1043881 TTCTATGTGGCA
1 TTCTACGTGGCA
1043893 GTTTCTACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 2 0.07
23 11 0.37
24 17 0.57
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (23 bp):
TTCTACGTGGCACTTCGGTCATA
Found at i:1050795 original size:24 final size:23
Alignment explanation
Indices: 1050737--1050803 Score: 80
Period size: 24 Copynumber: 2.9 Consensus size: 23
1050727 GAGTCGAGGG
* * *
1050737 TTCTACGCGGTTATTTGGGACAA
1 TTCTATGCGGTTCTTCGGGACAA
**
1050760 TTCTATATGGTTCTTCGGGACAAA
1 TTCTATGCGGTTCTTCGGGAC-AA
1050784 TTCTATGCGGTTCTTCGGGA
1 TTCTATGCGGTTCTTCGGGA
1050804 TATTTCTACG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 16 0.44
24 20 0.56
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.37
Consensus pattern (23 bp):
TTCTATGCGGTTCTTCGGGACAA
Found at i:1050822 original size:23 final size:23
Alignment explanation
Indices: 1050796--1050856 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
1050786 CTATGCGGTT
*
1050796 CTTCGGGATATTTCTACGTGGTC
1 CTTCGGGATATTTCTACGTGGTA
* *
1050819 CTTCGAGACATTTCTACGTGGTA
1 CTTCGGGATATTTCTACGTGGTA
1050842 CTTCGGTGCATATTT
1 CTTCGG-G-ATATTT
1050857 TATGCGGCAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 25 0.81
24 1 0.03
25 5 0.16
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.39
Consensus pattern (23 bp):
CTTCGGGATATTTCTACGTGGTA
Found at i:1053182 original size:21 final size:20
Alignment explanation
Indices: 1053144--1053182 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1053134 CTTTTTTTTA
*
1053144 AAAAACAATTATGTTTTATT
1 AAAAACAATTATGCTTTATT
1053164 AAAAACAATTATGACTTTA
1 AAAAACAATTATG-CTTTA
1053183 CTAGTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAAACAATTATGCTTTATT
Found at i:1055565 original size:3 final size:3
Alignment explanation
Indices: 1055557--1055611 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
1055547 AATGTTATAT
* * *
1055557 TAA TAA TAA TAT TAA TAA TAA TAA TAA TAAA TGA TAA -AA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
1055602 TAA TAA TAA T
1 TAA TAA TAA T
1055612 TTATAATATT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1055570 original size:12 final size:12
Alignment explanation
Indices: 1055553--1055586 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1055543 TAAAAATGTT
1055553 ATATTAATAATA
1 ATATTAATAATA
1055565 ATATTAATAATA
1 ATATTAATAATA
*
1055577 ATAATAATAA
1 ATATTAATAA
1055587 ATGATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATTAATAATA
Found at i:1056913 original size:21 final size:20
Alignment explanation
Indices: 1056874--1056914 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1056864 ACTTTTTTTT
*
1056874 AAAACAATTATGTTTTATTA
1 AAAACAATTATGCTTTATTA
1056894 AAAACAATTATGACTTTATTA
1 AAAACAATTATG-CTTTATTA
1056915 TTTGAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (20 bp):
AAAACAATTATGCTTTATTA
Found at i:1058589 original size:12 final size:13
Alignment explanation
Indices: 1058573--1058605 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1058563 TTTTTTCCTT
1058573 ATTTTTTCTTTTG
1 ATTTTTTCTTTTG
*
1058586 -TTTTCTCTTTTG
1 ATTTTTTCTTTTG
1058598 ATTTTTTC
1 ATTTTTTC
1058606 GAATGCTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 2
0.81 0.10 0.10
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.06, C:0.12, G:0.06, T:0.76
Consensus pattern (13 bp):
ATTTTTTCTTTTG
Found at i:1059308 original size:3 final size:3
Alignment explanation
Indices: 1059300--1059360 Score: 95
Period size: 3 Copynumber: 19.7 Consensus size: 3
1059290 AATGTTATAT
*
1059300 TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1059346 TAA TAA TTAA TAA TA
1 TAA TAA -TAA TAA TA
1059361 TTTTTTAAGA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
3 48 0.89
4 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1060311 original size:41 final size:41
Alignment explanation
Indices: 1060246--1060343 Score: 101
Period size: 41 Copynumber: 2.4 Consensus size: 41
1060236 AAAGACTCAG
* * *
1060246 ACTTTCGTGGTGTTTGTGAACAAACACCGCTATAG-AATTAT
1 ACTTTAGTGGTGTTTTTGAACAAACACCGCAATAGTAA-TAT
** * * *
1060287 ACTTTAGTGGTGTTTTTGTTCAAACGCCGCAATAGTCATGT
1 ACTTTAGTGGTGTTTTTGAACAAACACCGCAATAGTAATAT
1060328 ACTTTAGTGGT-TTTTT
1 ACTTTAGTGGTGTTTTT
1060344 AATAAACGTT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
40 5 0.10
41 42 0.88
42 1 0.02
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.41
Consensus pattern (41 bp):
ACTTTAGTGGTGTTTTTGAACAAACACCGCAATAGTAATAT
Found at i:1060358 original size:39 final size:40
Alignment explanation
Indices: 1060286--1060383 Score: 108
Period size: 39 Copynumber: 2.4 Consensus size: 40
1060276 TATAGAATTA
** *
1060286 TACTTTAGTGGTGTTTTTGTTCAAACGCCGCAATAGTCATG
1 TACTTTAGTGGT-TTTTTAATCAAACGCCGCAATAATCATG
**
1060327 TACTTTAGTGGTTTTTTAAT-AAACGTTGCAATAATCATG
1 TACTTTAGTGGTTTTTTAATCAAACGCCGCAATAATCATG
* *
1060366 TAATTTAGTAAGTTTTTT
1 TACTTTAGT-GGTTTTTT
1060384 TTTTTGTAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
39 24 0.49
40 13 0.27
41 12 0.24
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (40 bp):
TACTTTAGTGGTTTTTTAATCAAACGCCGCAATAATCATG
Found at i:1064041 original size:17 final size:17
Alignment explanation
Indices: 1064021--1064062 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
1064011 GATGAAGTTT
1064021 AAGATATGATATTAGAA
1 AAGATATGATATTAGAA
1064038 AAGATATGATATTAGAA
1 AAGATATGATATTAGAA
1064055 AAGATATG
1 AAGATATG
1064063 TAAGGATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.29
Consensus pattern (17 bp):
AAGATATGATATTAGAA
Found at i:1064789 original size:20 final size:20
Alignment explanation
Indices: 1064753--1064791 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1064743 TTAATGAATA
*
1064753 ATTTTAATTTGAGTAAATTT
1 ATTTTAATTAGAGTAAATTT
1064773 ATTTATAATTAGA-TAAATT
1 ATTT-TAATTAGAGTAAATT
1064792 ATATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTTTAATTAGAGTAAATTT
Found at i:1064793 original size:19 final size:21
Alignment explanation
Indices: 1064753--1064800 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1064743 TTAATGAATA
*
1064753 ATTT-TAATTTGAGTAAATTT
1 ATTTATAATTAGAGTAAATTT
1064773 ATTTATAATTAGA-TAAATTAT
1 ATTTATAATTAGAGTAAATT-T
*
1064794 ATATATA
1 ATTTATA
1064801 TATATATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (21 bp):
ATTTATAATTAGAGTAAATTT
Found at i:1069226 original size:18 final size:17
Alignment explanation
Indices: 1069187--1069240 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
1069177 TTGAAAAGTA
1069187 TAATAGTTTATTAAAAAT-
1 TAATA-TTTATT-AAAATC
1069205 TAATCATTTATTAAAATC
1 TAAT-ATTTATTAAAATC
* *
1069223 TAATTTTTATTATAATC
1 TAATATTTATTAAAATC
1069240 T
1 T
1069241 TCTTTTTGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 17 0.53
18 14 0.44
19 1 0.03
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.50
Consensus pattern (17 bp):
TAATATTTATTAAAATC
Found at i:1069856 original size:40 final size:40
Alignment explanation
Indices: 1069812--1069914 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
1069802 CATACTTTCG
*
1069812 TGACGTTTTTATATAAAT-CCGTTATAGAC-TAGTACGTCAT
1 TGACGTTTTTATATAAATGCCGCTATA-ACTTA-TACGTCAT
* *
1069852 TGACGTTTTTATATAAATGCTGCTATAACTTATGCGTCAT
1 TGACGTTTTTATATAAATGCCGCTATAACTTATACGTCAT
* *
1069892 TGACGTTTTTATACAAATACCGC
1 TGACGTTTTTATATAAATGCCGC
1069915 AAATTTATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
40 47 0.85
41 8 0.15
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (40 bp):
TGACGTTTTTATATAAATGCCGCTATAACTTATACGTCAT
Found at i:1071793 original size:49 final size:48
Alignment explanation
Indices: 1071712--1071806 Score: 154
Period size: 49 Copynumber: 2.0 Consensus size: 48
1071702 ACGTTTGACG
*
1071712 TCTTTGTGACGTGGAGTTACTATTAATGATGATTTAGCACGTCTGAAA
1 TCTTTGTGACGTGGAGCTACTATTAATGATGATTTAGCACGTCTGAAA
* *
1071760 TCTTTTTGACGGTGGTGCTACTATTAATGATGATTTAGCACGTCTGA
1 TCTTTGTGAC-GTGGAGCTACTATTAATGATGATTTAGCACGTCTGA
1071807 CTTATGTAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
48 9 0.21
49 34 0.79
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.39
Consensus pattern (48 bp):
TCTTTGTGACGTGGAGCTACTATTAATGATGATTTAGCACGTCTGAAA
Found at i:1072932 original size:21 final size:21
Alignment explanation
Indices: 1072906--1072945 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1072896 TTTTTATCCT
1072906 TACTATTCTTTAATTCTTGAA
1 TACTATTCTTTAATTCTTGAA
1072927 TACTATTCTTTAATTCTTG
1 TACTATTCTTTAATTCTTG
1072946 TATAATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.05, T:0.55
Consensus pattern (21 bp):
TACTATTCTTTAATTCTTGAA
Found at i:1074297 original size:40 final size:40
Alignment explanation
Indices: 1074242--1074321 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
1074232 TAGTAGATAC
*
1074242 CGAAATAAGTGTACACGAAGGAGGAACGAATACAAACCTT
1 CGAAATAAGTGTACACAAAGGAGGAACGAATACAAACCTT
*
1074282 CGAAATAAGTGTACACAAAGGAGGAACGAATATAAACCTT
1 CGAAATAAGTGTACACAAAGGAGGAACGAATACAAACCTT
1074322 TATACGTTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.16
Consensus pattern (40 bp):
CGAAATAAGTGTACACAAAGGAGGAACGAATACAAACCTT
Found at i:1076014 original size:17 final size:18
Alignment explanation
Indices: 1075975--1076016 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1075965 AAGTAGTGTT
*
1075975 CTTGAAAGAAAAATGAAT
1 CTTGAAAGAAAAATGAAG
* *
1075993 ATTGAATGAAAAAT-AAG
1 CTTGAAAGAAAAATGAAG
1076010 CTTGAAA
1 CTTGAAA
1076017 TGCTCAAACT
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.55, C:0.05, G:0.17, T:0.24
Consensus pattern (18 bp):
CTTGAAAGAAAAATGAAG
Done.