Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007760.1 Hibiscus syriacus cultivar Beakdansim tig00110029_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: 2010226
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:736842 original size:18 final size:18
Alignment explanation
Indices: 736821--736871 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
736811 AAGATTACAA
*
736821 GTGGGAATATGATTAACG
1 GTGGGAATAAGATTAACG
736839 GTGGGAATAAGATTAACG
1 GTGGGAATAAGATTAACG
*
736857 GCGGGAATAAGATTA
1 GTGGGAATAAGATTA
736872 CGGGGAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.24
Consensus pattern (18 bp):
GTGGGAATAAGATTAACG
Found at i:740951 original size:21 final size:20
Alignment explanation
Indices: 740927--740973 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
740917 TAAAAGAATC
*
740927 AAAAATAATTCAAAAATAATA
1 AAAAATAAAT-AAAAATAATA
740948 AAAAGATAAATAAAAAT--TA
1 AAAA-ATAAATAAAAATAATA
740967 AAAAATA
1 AAAAATA
740974 TTAGAATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 3 0.12
19 6 0.25
21 10 0.42
22 5 0.21
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (20 bp):
AAAAATAAATAAAAATAATA
Found at i:745951 original size:21 final size:21
Alignment explanation
Indices: 745927--745969 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
745917 TATTGAAGTT
745927 TATTGAAACTATATCAAAAAA
1 TATTGAAACTATATCAAAAAA
745948 TATTGAAACTATATCAAAAAA
1 TATTGAAACTATATCAAAAAA
745969 T
1 T
745970 TTATATTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (21 bp):
TATTGAAACTATATCAAAAAA
Found at i:751956 original size:29 final size:29
Alignment explanation
Indices: 751914--751984 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
751904 TAGATGGGGT
*
751914 AGGTCGCCATGCACGCCCAGCGACCTACC
1 AGGTCGCCATGCACGCCCAACGACCTACC
751943 AGGTCGCCATGCACGCCCAACGACCTACC
1 AGGTCGCCATGCACGCCCAACGACCTACC
751972 AGGTCGCCATGCA
1 AGGTCGCCATGCA
751985 ATCCATGCAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.23, C:0.42, G:0.24, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAACGACCTACC
Found at i:755533 original size:139 final size:140
Alignment explanation
Indices: 755353--755612 Score: 339
Period size: 139 Copynumber: 1.9 Consensus size: 140
755343 AGATGAATAC
* *
755353 TTGCCTAATTGATTAAAATTAATTAGGATTAATATTTGAGCCTCCACTTTAGGCT-TAATTTCA-
1 TTGCATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCACTTTAGG-TATAATTTCAT
* * * * * *
755416 AATATAGTCC-TTAAATTAGGTGAATTCTTAATTTGGTCCTGGCTTTTGCTCGAGGTTCCATATT
65 AA-ATAGTCCTTTAAACTAGGGGAATTCTTAATTTGGGCCTCGATTATGCTCGAGGTTCCATATT
755480 AAATTATTCAAA
129 AAATTATTCAAA
* *
755492 TTGCATAATTGATTGAAATTAATTAGG-TTAATAATTAGAGCCTCCATTTTAGGTATAATTTCAT
1 TTGCATAATTGATTAAAATTAATTAGGATTAAT-ATTAGAGCCTCCACTTTAGGTATAATTTCAT
* * * *
755556 AACTAGTCCTTTAACCTAGGGGAATTTTTGATTTGGGCCTCGATTATGCTCGAGGTT
65 AAATAGTCCTTTAAACTAGGGGAATTCTTAATTTGGGCCTCGATTATGCTCGAGGTT
755613 TCATTTTGAC
Statistics
Matches: 103, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
138 6 0.06
139 57 0.55
140 40 0.39
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (140 bp):
TTGCATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCACTTTAGGTATAATTTCATA
AATAGTCCTTTAAACTAGGGGAATTCTTAATTTGGGCCTCGATTATGCTCGAGGTTCCATATTAA
ATTATTCAAA
Found at i:756500 original size:2 final size:2
Alignment explanation
Indices: 756493--756537 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
756483 TTAATTTTTG
756493 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
756535 TA T
1 TA T
756538 TATTTTATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:756663 original size:18 final size:18
Alignment explanation
Indices: 756642--756682 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
756632 TTTTTCGAAT
*
756642 TATTTTAT-ATTTTTTTAA
1 TATTTTATCA-TTTTATAA
756660 TA-TTTATCATTTTATAA
1 TATTTTATCATTTTATAA
756677 TATTTT
1 TATTTT
756683 TTAAATTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTTTATCATTTTATAA
Found at i:756699 original size:28 final size:27
Alignment explanation
Indices: 756634--756712 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 27
756624 GCTCTTATTT
*
756634 TTTCGAATTATTTTATATTTTTTTAATA
1 TTTC-AATAATTTTATATTTTTTTAATA
*
756662 TTT--ATCATTTTATAATATTTTTTAA-A
1 TTTCAATAATTTTAT-AT-TTTTTTAATA
756688 TTTCAATAATTTTA-ATTTTTCTTAA
1 TTTCAATAATTTTATATTTTT-TTAA
756713 AGATTAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
25 13 0.30
26 12 0.27
27 8 0.18
28 11 0.25
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (27 bp):
TTTCAATAATTTTATATTTTTTTAATA
Found at i:756732 original size:29 final size:29
Alignment explanation
Indices: 756699--756757 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
756689 TTCAATAATT
* * * *
756699 TTAATTTTTCTTAAAGATTAAATAAGCCC
1 TTAATCTTTCTAAAAAAATAAATAAGCCC
*
756728 TTAATCTTTCTAAAAAAATAATTAAGCCC
1 TTAATCTTTCTAAAAAAATAAATAAGCCC
756757 T
1 T
756758 CATACTTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (29 bp):
TTAATCTTTCTAAAAAAATAAATAAGCCC
Found at i:765854 original size:29 final size:29
Alignment explanation
Indices: 765821--765880 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
765811 TACTCCAAGC
*
765821 CCAAATCAGGCCTCAAATTACAAACAACA
1 CCAAATCAGGCCCCAAATTACAAACAACA
765850 CCAAATCAGGCCCCAAATTACAAACAACA
1 CCAAATCAGGCCCCAAATTACAAACAACA
765879 CC
1 CC
765881 CCGGTCGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.35, G:0.07, T:0.12
Consensus pattern (29 bp):
CCAAATCAGGCCCCAAATTACAAACAACA
Found at i:767491 original size:12 final size:12
Alignment explanation
Indices: 767474--767498 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
767464 TATAATTAAG
767474 ATGTTCAATTTT
1 ATGTTCAATTTT
767486 ATGTTCAATTTT
1 ATGTTCAATTTT
767498 A
1 A
767499 ATTAGTCCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (12 bp):
ATGTTCAATTTT
Found at i:769598 original size:55 final size:55
Alignment explanation
Indices: 769534--769673 Score: 199
Period size: 55 Copynumber: 2.5 Consensus size: 55
769524 ATATTCAAGT
* *
769534 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAACCTGATTCAAGAAC
1 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTCAAGAAC
* * *
769589 GATTCATGAAGATGGACATCCGATGAATGAAGAAATCTGAAACTGATTGAAGATC
1 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTCAAGAAC
* * **
769644 GATCCACGAAGAAATACATCCGATGAATGA
1 GATTCATGAAGAAGGACATCCGATGAATGA
769674 TGTTTGAGAT
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 75 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.21
Consensus pattern (55 bp):
GATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTCAAGAAC
Found at i:774043 original size:125 final size:126
Alignment explanation
Indices: 773814--774062 Score: 353
Period size: 125 Copynumber: 2.0 Consensus size: 126
773804 ATACACACAC
* ** *
773814 TGGGGGCATGACTGAACCCACATCATGTTGAGAGGACGAGACTTAGAACAAGAAGGCGTTGAGAA
1 TGGGGGCATGACTCAACCCACATCATGTTGAGAGGAAAAGACTTAGAACAAGAAGGCATTGAGAA
* *
773879 TGAGCGTTACAATTTGATGTGTTGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATGT
66 TGAGCCTTACAATCTGATGTGTTGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATGT
* *
773940 TGGGGG-ATGACTCAACCCACATCATGTTGAGATGAAAAGA-TTCAGACCAAGAAGGCATTGAGA
1 TGGGGGCATGACTCAACCCACATCATGTTGAGAGGAAAAGACTT-AGAACAAGAAGGCATTGAGA
* *
774003 GTGAGCCTTACAATCTGA-GTTGTTGGGG-ATTTTTGAAGGCCTGTACCAGTATAAGATAAT
65 ATGAGCCTTACAATCTGATG-TGTTGGGGCA-TTTTGAAGGCCCGTACCAGTATAAGATAAT
774063 ATTGCGGCAC
Statistics
Matches: 110, Mismatches: 10, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
124 4 0.04
125 100 0.91
126 6 0.05
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (126 bp):
TGGGGGCATGACTCAACCCACATCATGTTGAGAGGAAAAGACTTAGAACAAGAAGGCATTGAGAA
TGAGCCTTACAATCTGATGTGTTGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATGT
Found at i:786443 original size:21 final size:23
Alignment explanation
Indices: 786417--786467 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
786407 AGGGAATCGA
*
786417 TCCCCCCTTG-A-GGGAACTAAT
1 TCCCCCCTTGAAGGGGAACCAAT
* *
786438 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCTTGAAGGGGAACCAAT
786461 TCCCCCC
1 TCCCCCC
786468 ACAGGGGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 9 0.38
22 1 0.04
23 14 0.58
ACGTcount: A:0.20, C:0.39, G:0.20, T:0.22
Consensus pattern (23 bp):
TCCCCCCTTGAAGGGGAACCAAT
Found at i:786475 original size:21 final size:21
Alignment explanation
Indices: 786449--786488 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
786439 CCCCCTTTGA
*
786449 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
786470 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
786489 CTGGGGTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:787771 original size:12 final size:12
Alignment explanation
Indices: 787732--787764 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
787722 AGATGAGCCT
787732 GAGCAGCCCGAG
1 GAGCAGCCCGAG
*
787744 GAGCAGACCGAG
1 GAGCAGCCCGAG
787756 GAGCAGCCC
1 GAGCAGCCC
787765 AAAGAGCGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.27, C:0.33, G:0.39, T:0.00
Consensus pattern (12 bp):
GAGCAGCCCGAG
Found at i:791808 original size:55 final size:55
Alignment explanation
Indices: 790263--791789 Score: 2360
Period size: 55 Copynumber: 27.8 Consensus size: 55
790253 GTGAAGCAAA
* * *
790263 TGAAGATTGTTCGAGTCTTATCCTCTCTGAAGGAATAGGGAGCAAATACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* * *
790318 TGAAGATTGTTTGAGTCTTATACTCTCTGAAGGAATAGGTAGCAGATACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
*
790373 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAAGGAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* *
790428 T-ATAGATTGTTCGAGT-TTATACTCTCTGAAGGAATAGGGGGCAAACACGATTGT
1 TGA-AGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* *
790482 TGAAGATTGTTTGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACATGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* *
790537 TGAAGATTGTTCGAGTCTTATACTCTCTCAAGGAATAGGGAGCAGACACAATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* * *
790592 TGAAGATTGTTAGAGTCTTATACTCTCTCAAGGAATAGAGAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* * * * * *
790647 TGAAGATTGTTCGAATCTTGTACTCTCTGTAGGAATAAGGAACATACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* * *
790702 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATATGAAACAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
** * *
790757 TGAAGATTGTTCGAGTCTTATACTCTCTGAAAAAATAGGGAGAAGACATGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
*
790812 TAAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* *
790867 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAAGGAGAAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
*
790922 TGAAGATTATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
*
790977 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCATACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* *
791032 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGAAACAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
** *
791087 TGAAGATTGTTCGAGTCTTATACTCTCTGAAAAAATAGGGAGCATACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
*
791142 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCATACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* *
791197 TAAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGAAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* * * *
791252 TAAAGATTATTTGAGTCTTATACTCTCTGAAGGAATAGGAAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* *
791307 TGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGGGAGCATACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* *
791362 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGAAACAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* * * *
791417 TGAAGATTGTTCGAGTCTTATACTCTCTAAAGGAATAGGGAACATACACGGTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* * *
791472 TGAAGATTGTTCGAGTCTTATACTCTCTAAAGGAATAGGGAGCAGCCACGATCGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* * *
791527 GGAAGATTGTTCGAGTCTTGTACTCTCTGAAGGAATAGGGAGCAGACATGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* * *
791582 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATATGAAGCAGCCACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* * * * *
791637 TGAAGATTTTTTGAGTCTTATACTCTCTGAAGGAATAAGGAGCATACACGGTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* *
791692 TGAAGATTGTTCGATTCTTATACTCTCTGAAGGAATAGGGAGCA-ACCACGATCG-
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGA-CACGATTGT
*
791746 TGAAAGATTGTTCGAGTCTTATACTCTTTGAAGGAATAGGGAGC
1 TG-AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGC
791790 GAACCCATTG
Statistics
Matches: 1347, Mismatches: 120, Indels: 10
0.91 0.08 0.01
Matches are distributed among these distances:
54 52 0.04
55 1295 0.96
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
Found at i:793953 original size:13 final size:13
Alignment explanation
Indices: 793928--793956 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
793918 GATAATATAA
793928 TATTAGTAATTTT
1 TATTAGTAATTTT
793941 TATTA-TAATTTT
1 TATTAGTAATTTT
793953 TATT
1 TATT
793957 TTATTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (13 bp):
TATTAGTAATTTT
Found at i:794123 original size:4 final size:4
Alignment explanation
Indices: 794114--794161 Score: 96
Period size: 4 Copynumber: 12.0 Consensus size: 4
794104 TACGTATAGT
794114 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
794162 TATATATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:794168 original size:2 final size:2
Alignment explanation
Indices: 794161--794229 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
794151 TAAATAAATA
794161 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
794203 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 A
794230 GGTTGTACAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:795328 original size:43 final size:43
Alignment explanation
Indices: 795267--795352 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
795257 CCACTTCTTT
795267 TGAGTGATTTTTCCTCAAATCGTCGTTGTCTTCAAATGGTGAA
1 TGAGTGATTTTTCCTCAAATCGTCGTTGTCTTCAAATGGTGAA
795310 TGAGTGATTTTTCCTCAAATCGTCGTTGTCTTCAAATGGTGAA
1 TGAGTGATTTTTCCTCAAATCGTCGTTGTCTTCAAATGGTGAA
795353 AGATCTGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (43 bp):
TGAGTGATTTTTCCTCAAATCGTCGTTGTCTTCAAATGGTGAA
Found at i:799054 original size:18 final size:17
Alignment explanation
Indices: 799033--799066 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
799023 TGAAATTATT
799033 TTTTTCTTCTTTGTCTTC
1 TTTTTCTTC-TTGTCTTC
799051 TTTTTCTTCTTGTCTT
1 TTTTTCTTCTTGTCTT
799067 TGAACTCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.00, C:0.21, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTTTCTTCTTGTCTTC
Found at i:809341 original size:2 final size:2
Alignment explanation
Indices: 809334--809377 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
809324 AAACCAATGA
809334 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
809376 AT
1 AT
809378 CTTTAAAACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:815862 original size:12 final size:12
Alignment explanation
Indices: 815793--815861 Score: 68
Period size: 12 Copynumber: 5.8 Consensus size: 12
815783 ATGGAGATAT
*
815793 CAGAAATCAAAA
1 CAGAATTCAAAA
815805 CAGAATTCAAAA
1 CAGAATTCAAAA
*
815817 CAG-ATATCATAA
1 CAGAAT-TCAAAA
* *
815829 CAGAATACAAAT
1 CAGAATTCAAAA
* *
815841 CAGAAATCAGAA
1 CAGAATTCAAAA
815853 CAGAATTCA
1 CAGAATTCA
815862 GGTCATGTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 41 0.91
13 2 0.04
ACGTcount: A:0.57, C:0.17, G:0.10, T:0.16
Consensus pattern (12 bp):
CAGAATTCAAAA
Found at i:815897 original size:24 final size:24
Alignment explanation
Indices: 815791--815886 Score: 104
Period size: 24 Copynumber: 4.0 Consensus size: 24
815781 AAATGGAGAT
*
815791 ATCAGAAATCAAAACAGAATTCAA
1 ATCAGAAATCATAACAGAATTCAA
* * *
815815 AACAGATATCATAACAGAATACAA
1 ATCAGAAATCATAACAGAATTCAA
* *
815839 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCATAACAGAATTCAA
* *
815863 GTCATG-TATCATAACAGAATTCAA
1 ATCA-GAAATCATAACAGAATTCAA
815887 GTCGAAAATC
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
24 57 0.98
25 1 0.02
ACGTcount: A:0.52, C:0.17, G:0.11, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCATAACAGAATTCAA
Found at i:820775 original size:12 final size:12
Alignment explanation
Indices: 820758--820792 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
820748 TGTTAAAATC
820758 ACTGTAGCAGTT
1 ACTGTAGCAGTT
*
820770 ACTGTAGCCGTT
1 ACTGTAGCAGTT
820782 ACTGTAGCAGT
1 ACTGTAGCAGT
820793 GCATCGATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (12 bp):
ACTGTAGCAGTT
Found at i:823346 original size:21 final size:23
Alignment explanation
Indices: 823305--823347 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
823295 TTATGCCATA
823305 TCGATCGACCATTTAAACTTCAT
1 TCGATCGACCATTTAAACTTCAT
*
823328 TCGATCG-CC-TTTGAACTTCA
1 TCGATCGACCATTTAAACTTCA
823348 ATCTAATGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 2 0.11
23 7 0.37
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.35
Consensus pattern (23 bp):
TCGATCGACCATTTAAACTTCAT
Found at i:823562 original size:6 final size:6
Alignment explanation
Indices: 823551--823611 Score: 50
Period size: 6 Copynumber: 9.2 Consensus size: 6
823541 TAACTTTTTG
* *
823551 GTCAAA GTCAAA CGGTCAAGG GTCAAA GTCAACT GTCAAA GTCAACA GGTCAAA
1 GTCAAA GTCAAA --GTCAA-A GTCAAA GTCAA-A GTCAAA GTCAA-A -GTCAAA
823605 GTCAAA G
1 GTCAAA G
823612 GGTTGCCTCG
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
6 23 0.51
7 12 0.27
8 10 0.22
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (6 bp):
GTCAAA
Found at i:823588 original size:13 final size:14
Alignment explanation
Indices: 823571--823609 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
823561 AACGGTCAAG
823571 GGTCAAAGTCAAC-
1 GGTCAAAGTCAACA
*
823584 TGTCAAAGTCAACA
1 GGTCAAAGTCAACA
823598 GGTCAAAGTCAA
1 GGTCAAAGTCAA
823610 AGGGTTGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (14 bp):
GGTCAAAGTCAACA
Found at i:823643 original size:14 final size:14
Alignment explanation
Indices: 823626--823661 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
823616 GCCTCGGACT
**
823626 AGTTGACTGGGATG
1 AGTTGACTAAGATG
823640 AGTTGACTAAGATG
1 AGTTGACTAAGATG
823654 AGTTGACT
1 AGTTGACT
823662 CAGTCTAGGT
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:0.08, G:0.33, T:0.31
Consensus pattern (14 bp):
AGTTGACTAAGATG
Found at i:827102 original size:2 final size:2
Alignment explanation
Indices: 827095--827136 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
827085 AACCTGAATA
827095 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
827137 TTCATTCAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:839403 original size:18 final size:18
Alignment explanation
Indices: 839380--839424 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
839370 ACCAGTCACA
*
839380 ACCCGACCCGACCTGTTG
1 ACCCGACCCGACCCGTTG
*
839398 ACCCGACCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
839416 ACCCGACCC
1 ACCCGACCC
839425 ATTGACCGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.18, C:0.49, G:0.20, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:841916 original size:24 final size:24
Alignment explanation
Indices: 841885--842000 Score: 137
Period size: 24 Copynumber: 4.8 Consensus size: 24
841875 TTCGATTTAA
*
841885 ATTTTGATCTGATACTTGACATGG
1 ATTTTGATATGATACTTGACATGG
*
841909 ATTCTGATATGATA-TCTGACATGG
1 ATTTTGATATGATACT-TGACATGG
* * *
841933 ATTATGATCTGATACTTGACTTGG
1 ATTTTGATATGATACTTGACATGG
* *
841957 ATTTTGATATGTTACTTGACCT-G
1 ATTTTGATATGATACTTGACATGG
841980 ATTTTTGATATGATACTTGAC
1 A-TTTTGATATGATACTTGAC
842001 TTGAATTATG
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 3 0.04
24 75 0.95
25 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (24 bp):
ATTTTGATATGATACTTGACATGG
Found at i:841994 original size:48 final size:48
Alignment explanation
Indices: 841885--842003 Score: 152
Period size: 48 Copynumber: 2.5 Consensus size: 48
841875 TTCGATTTAA
*
841885 ATTTTGATCTGATACTTGACATGGATTCTGATATGATATCTGACATGG
1 ATTTTGATCTGATACTTGACTTGGATTCTGATATGATATCTGACATGG
* * * *
841933 ATTATGATCTGATACTTGACTTGGATTTTGATATGTTA-CTTGACCT-G
1 ATTTTGATCTGATACTTGACTTGGATTCTGATATGATATC-TGACATGG
*
841980 ATTTTTGATATGATACTTGACTTG
1 A-TTTTGATCTGATACTTGACTTG
842004 AATTATGTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
47 3 0.05
48 59 0.95
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (48 bp):
ATTTTGATCTGATACTTGACTTGGATTCTGATATGATATCTGACATGG
Found at i:842124 original size:35 final size:35
Alignment explanation
Indices: 842077--842151 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
842067 TGGAGGAAGA
* * * *
842077 TTACTTGGAGGCTCCTTGGTTTTGTGCTCATGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
842112 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
842147 TTACT
1 TTACT
842152 GTTTGTGACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.09, C:0.27, G:0.27, T:0.37
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
Found at i:845178 original size:18 final size:17
Alignment explanation
Indices: 845124--845172 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 17
845114 TTGGACCCTT
*
845124 AGTGCATCGATGCACTAA
1 AGTGCATCGATGCA-TCA
845142 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
845160 AGTGCATTCGATG
1 AGTGCA-TCGATG
845173 TTTCAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 6 0.21
18 8 0.29
19 14 0.50
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:845281 original size:65 final size:64
Alignment explanation
Indices: 845124--845303 Score: 204
Period size: 65 Copynumber: 2.8 Consensus size: 64
845114 TTGGACCCTT
* *
845124 AGTGCATCGATGCACTAAGA-GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCA
1 AGTGCATCGATGCA-T-GGATGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCA
*
845187 G
64 C
* * * * * *
845188 AGTGCATCGATGCATTGCTGCTGTATCGATGCATCAAATGCATTTGATGTTTTCATAAA-ATCCT
1 AGTGCATCGATGCATGGATG-TGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCA
845252 C
64 C
*
845253 AGTGCATCGATGCATGGTATGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATGG-ATGTGCATCGATGCATCAAATGCATTCGATGTT
845304 CAATTTAATT
Statistics
Matches: 98, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 39 0.40
65 51 0.52
66 5 0.05
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (64 bp):
AGTGCATCGATGCATGGATGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAC
Found at i:847863 original size:19 final size:19
Alignment explanation
Indices: 847839--847876 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
847829 AAAAATCGTT
847839 GATTTTGAGCAAGA-ATGGA
1 GATTTT-AGCAAGAGATGGA
*
847858 GATTTTAGGAAGAGATGGA
1 GATTTTAGCAAGAGATGGA
847877 TGGATGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.37, C:0.03, G:0.34, T:0.26
Consensus pattern (19 bp):
GATTTTAGCAAGAGATGGA
Found at i:853895 original size:18 final size:17
Alignment explanation
Indices: 853841--853889 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
853831 TTGGACCCTT
* *
853841 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
853859 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
853877 AGTGCATTCGATG
1 AGTGCA-TCGATG
853890 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:853958 original size:46 final size:45
Alignment explanation
Indices: 853860--853965 Score: 142
Period size: 45 Copynumber: 2.3 Consensus size: 45
853850 GTGCACTAAG
* *
853860 AGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
* *
853905 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTC
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCAC
*
853951 AGTGCATCGGTGCAT
1 AGTGCATCGATGCAT
853966 GTTATGTGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 29 0.54
46 22 0.41
47 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (45 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
Found at i:854039 original size:20 final size:20
Alignment explanation
Indices: 854014--854089 Score: 143
Period size: 20 Copynumber: 3.8 Consensus size: 20
854004 ATTTAATTCA
854014 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
854034 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
854054 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
*
854074 TGGTGCATCGGTGCAT
1 TGGTGCATCGATGCAT
854090 CACTCTGAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.18, C:0.16, G:0.36, T:0.30
Consensus pattern (20 bp):
TGGTGCATCGATGCATGGAT
Found at i:854040 original size:65 final size:63
Alignment explanation
Indices: 853906--854050 Score: 161
Period size: 65 Copynumber: 2.2 Consensus size: 63
853896 AATAGCCAGA
* * *
853906 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGTTAT
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGTTAG
**
853971 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCAT-G-T
854034 T-G
61 TAG
854036 GTGCATCGATGCATG
1 GTGCATCGATGCATG
854051 GATTGGTGCA
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 18 0.26
65 44 0.63
66 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGTTAG
Found at i:858228 original size:3 final size:3
Alignment explanation
Indices: 858214--858414 Score: 350
Period size: 3 Copynumber: 67.0 Consensus size: 3
858204 ATGAATGAAT
*
858214 GAA GAA GGA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
858262 GAA GAA GAA GAA GAA GAA GAA GAA GAA G-A GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * *
858309 GAA GAA GAA GAG GAA GAG GAA GAA GAA GAA GAA GAA GAA TAA GAA GGAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA
858358 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
858406 GAA GAA GAA
1 GAA GAA GAA
858415 AACACATAAT
Statistics
Matches: 188, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
2 2 0.01
3 183 0.97
4 3 0.02
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:862770 original size:31 final size:31
Alignment explanation
Indices: 862700--862762 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
862690 TACATCAGGA
*
862700 ACCATATTGCAAACGGACTAAATGTTGAGGG
1 ACCATATTGCAAACGGACTAAATATTGAGGG
* * *
862731 ACCATATTGCAAATGGACTAATTATTGGGGG
1 ACCATATTGCAAACGGACTAAATATTGAGGG
862762 A
1 A
862763 TTATATTGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.25
Consensus pattern (31 bp):
ACCATATTGCAAACGGACTAAATATTGAGGG
Found at i:866377 original size:31 final size:31
Alignment explanation
Indices: 866309--866384 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
866299 TTTTAAAACA
**
866309 TGTAATATAATCCCTAAATATTTAGTCTATT
1 TGTAATATGGTCCCTAAATATTTAGTCTATT
* * *
866340 TATAATATGGTCCCTCAATATTTAGT-TCGTT
1 TGTAATATGGTCCCTAAATATTTAGTCT-ATT
866371 TGTAATATGGTCCC
1 TGTAATATGGTCCC
866385 CAACGTAACT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 1 0.03
31 37 0.97
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (31 bp):
TGTAATATGGTCCCTAAATATTTAGTCTATT
Found at i:872082 original size:20 final size:21
Alignment explanation
Indices: 872053--872095 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
872043 CTTTTGTTCA
872053 AAATCAATTAA-TTTTGCTTTC
1 AAATCAATTAACTTTT-CTTTC
872074 AAATC-ATTAACTTTTCTTTC
1 AAATCAATTAACTTTTCTTTC
872094 AA
1 AA
872096 GTTTATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.35, C:0.16, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATCAATTAACTTTTCTTTC
Found at i:874735 original size:25 final size:23
Alignment explanation
Indices: 874691--874736 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
874681 CAAAAAAATA
874691 ATTGAATTTTTAGAAAATTAATT
1 ATTGAATTTTTAGAAAATTAATT
874714 ATTGAAATGTTTT-GAAATATTAA
1 ATTG-AAT-TTTTAGAAA-ATTAA
874737 ATATGATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 7 0.35
25 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (23 bp):
ATTGAATTTTTAGAAAATTAATT
Found at i:876808 original size:37 final size:38
Alignment explanation
Indices: 876741--876827 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 38
876731 ACTAAATCTA
* * *
876741 AAATTTAAATAATGAAACAAAATAATTAATAATAAACT
1 AAATTAAAATAATGAAACAAAATAATTAATAAAAAAAT
* *
876779 TAATTAAAATAATGAAAACAACA-AA-TAATAAAAAAAT
1 AAATTAAAATAATG-AAACAAAATAATTAATAAAAAAAT
*
876816 AAAATAAAATAA
1 AAATTAAAATAA
876828 AATAAAATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
37 20 0.49
38 14 0.34
39 7 0.17
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (38 bp):
AAATTAAAATAATGAAACAAAATAATTAATAAAAAAAT
Found at i:876817 original size:42 final size:38
Alignment explanation
Indices: 876741--876832 Score: 94
Period size: 42 Copynumber: 2.3 Consensus size: 38
876731 ACTAAATCTA
* * * *
876741 AAATTTAAATAATGAAACAAAATAATTAATAATAAACT
1 AAATTAAAATAATGAAACAAAATAATAAAAAATAAAAT
*
876779 TAATTAAAATAATGAAAACAACAAATAATAAAAAAATAAAAT
1 AAATTAAAATAATG-AAAC-A-AAATAAT-AAAAAATAAAAT
*
876821 AAAATAAAATAA
1 AAATTAAAATAA
876833 AATAAACATA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
38 12 0.28
39 4 0.09
40 1 0.02
41 7 0.16
42 19 0.44
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (38 bp):
AAATTAAAATAATGAAACAAAATAATAAAAAATAAAAT
Found at i:876820 original size:16 final size:16
Alignment explanation
Indices: 876783--876837 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 16
876773 TAAACTTAAT
*
876783 TAAAATAATGAAAACAA
1 TAAAATAAT-AAAAAAA
*
876800 -CAAATAATAAAAAAA
1 TAAAATAATAAAAAAA
*
876815 TAAAATAA-AATAAAA
1 TAAAATAATAAAAAAA
876830 TAAAATAA
1 TAAAATAA
876838 ACATAAATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 20 0.61
16 13 0.39
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (16 bp):
TAAAATAATAAAAAAA
Found at i:876821 original size:5 final size:5
Alignment explanation
Indices: 876801--876844 Score: 61
Period size: 5 Copynumber: 8.4 Consensus size: 5
876791 TGAAAACAAC
*
876801 AAATA ATAAAA AAATA AAATA AAATA AAATA AAATA AACATA AA
1 AAATA A-AATA AAATA AAATA AAATA AAATA AAATA AA-ATA AA
876845 TACAATGACC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
5 26 0.74
6 9 0.26
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:878211 original size:22 final size:22
Alignment explanation
Indices: 878185--878236 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
878175 GACATGGAGT
878185 GGTGGTGTTTGGTTGGGCAGTG
1 GGTGGTGTTTGGTTGGGCAGTG
878207 GGTGGTGTTTGGTTGGGCAGTG
1 GGTGGTGTTTGGTTGGGCAGTG
878229 GGTGGTGT
1 GGTGGTGT
878237 GTGTTGATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.04, C:0.04, G:0.56, T:0.37
Consensus pattern (22 bp):
GGTGGTGTTTGGTTGGGCAGTG
Found at i:878724 original size:59 final size:60
Alignment explanation
Indices: 878607--878799 Score: 180
Period size: 59 Copynumber: 3.2 Consensus size: 60
878597 CTTTCCACTG
* * *
878607 GAAATGTTGATCCC-TCGATTGA-GCATTGCTGATTCGAAGTGTTGTGTGAATTAAGCAAAA
1 GAAATGTTGATCCCTTCCAATGAGGCATTGCTGATTCGAAGTG-T-TGTGAATCAAGCAAAA
**** * *
878667 GAAATGTT-ATCCCTTTTGGTGGGGCATTGCTGATTCGAAGTGTTGTGAATCGAGC-AAA
1 GAAATGTTGATCCCTTCCAATGAGGCATTGCTGATTCGAAGTGTTGTGAATCAAGCAAAA
* * * * ** *
878725 GTAAATATTGATCCC-TCCAATGAGGTATTACTGATTTGAAGTGTTGTGAATCTTGCAAAG
1 G-AAATGTTGATCCCTTCCAATGAGGCATTGCTGATTCGAAGTGTTGTGAATCAAGCAAAA
878785 GAAATGTTGATCCCT
1 GAAATGTTGATCCCT
878800 CAAGTGAGGC
Statistics
Matches: 107, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
58 4 0.04
59 64 0.60
60 20 0.19
61 19 0.18
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (60 bp):
GAAATGTTGATCCCTTCCAATGAGGCATTGCTGATTCGAAGTGTTGTGAATCAAGCAAAA
Found at i:878912 original size:39 final size:39
Alignment explanation
Indices: 878833--879078 Score: 282
Period size: 39 Copynumber: 6.3 Consensus size: 39
878823 AGAAAAATAT
* *
878833 TCTCAAGTGAGAT-AAATCTTCTGTTT-GAGTGAAACTA
1 TCTCAAGCGAGATAAAATCTTCTATTTCGAGTGAAACTA
* * *
878870 TCTCAAGCGAGATAAAATATTCAATTCCGAGTGAAACTA
1 TCTCAAGCGAGATAAAATCTTCTATTTCGAGTGAAACTA
* * *
878909 TCTCAAGCGAAATTAAATCTTCTATTTCGAGTGAAACCA
1 TCTCAAGCGAGATAAAATCTTCTATTTCGAGTGAAACTA
* * * * *
878948 TCTCAAGCAAGATAAAATCTTTTGTTTCGGGTGAAACAA
1 TCTCAAGCGAGATAAAATCTTCTATTTCGAGTGAAACTA
* * * *
878987 TCTCAAAG-GAGATAAAAATCATATATTTCGAGCGAAACCA
1 TCTC-AAGCGAGAT-AAAATCTTCTATTTCGAGTGAAACTA
* *
879027 TCTCAAGCAAGATAAAATCTTCTGTTTCGAGTGAAACTA
1 TCTCAAGCGAGATAAAATCTTCTATTTCGAGTGAAACTA
879066 TCTCAAGCGAGAT
1 TCTCAAGCGAGAT
879079 GTTGACCCCT
Statistics
Matches: 172, Mismatches: 32, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
37 12 0.07
38 9 0.05
39 120 0.70
40 31 0.18
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.29
Consensus pattern (39 bp):
TCTCAAGCGAGATAAAATCTTCTATTTCGAGTGAAACTA
Found at i:879045 original size:118 final size:114
Alignment explanation
Indices: 878833--879078 Score: 300
Period size: 118 Copynumber: 2.1 Consensus size: 114
878823 AGAAAAATAT
* *
878833 TCTCAAGTGAGATAAATCTTCTGTTTGAGTGAAACTATCTCAAGCGAGATAAAATATTCAATTCC
1 TCTCAAGCGAGATAAATCTTCTGTTTGAGTGAAACAATCTCAAGCGAGATAAAATATT-AATTCC
* * *
878898 GAGTGAAACTATCTCAAGCGAAATTAAATCTTCTATTTCGAGTGAAACCA
65 GAGCGAAACCATCTCAAGCGAAATAAAATCTTCTATTTCGAGTGAAACCA
* * *
878948 TCTCAAGCAAGATAAAATCTTTTGTTTCGGGTGAAACAATCTCAAAG-GAGATAAAA-ATCATAT
1 TCTCAAGCGAGAT-AAATCTTCTGTTT-GAGTGAAACAATCTC-AAGCGAGATAAAATAT--TA-
* * *
879011 ATTTCGAGCGAAACCATCTCAAGC-AAGATAAAATCTTCTGTTTCGAGTGAAACTA
60 ATTCCGAGCGAAACCATCTCAAGCGAA-ATAAAATCTTCTATTTCGAGTGAAACCA
879066 TCTCAAGCGAGAT
1 TCTCAAGCGAGAT
879079 GTTGACCCCT
Statistics
Matches: 112, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
115 11 0.10
116 14 0.12
117 25 0.22
118 62 0.55
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.29
Consensus pattern (114 bp):
TCTCAAGCGAGATAAATCTTCTGTTTGAGTGAAACAATCTCAAGCGAGATAAAATATTAATTCCG
AGCGAAACCATCTCAAGCGAAATAAAATCTTCTATTTCGAGTGAAACCA
Found at i:879078 original size:79 final size:78
Alignment explanation
Indices: 878833--879078 Score: 282
Period size: 79 Copynumber: 3.2 Consensus size: 78
878823 AGAAAAATAT
* * * * * * * * **
878833 TCTCAAGTGAGAT-AAATCTTCTGTTT-GAGTGAAACTATCTCAAGCGAGATAAAATATTCAATT
1 TCTCAAGCGAGATAAAATCATATATTTCGAGCGAAACCATCTCAAGCAAGATAAAATCTTCTGTT
*
878896 CCGAGTGAAACTA
66 TCGAGTGAAACTA
* * * * * *
878909 TCTCAAGCGAAATTAAATCTTCTATTTCGAGTGAAACCATCTCAAGCAAGATAAAATCTTTTGTT
1 TCTCAAGCGAGATAAAATCATATATTTCGAGCGAAACCATCTCAAGCAAGATAAAATCTTCTGTT
* *
878974 TCGGGTGAAACAA
66 TCGAGTGAAACTA
878987 TCTCAAAG-GAGATAAAAATCATATATTTCGAGCGAAACCATCTCAAGCAAGATAAAATCTTCTG
1 TCTC-AAGCGAGAT-AAAATCATATATTTCGAGCGAAACCATCTCAAGCAAGATAAAATCTTCTG
879051 TTTCGAGTGAAACTA
64 TTTCGAGTGAAACTA
879066 TCTCAAGCGAGAT
1 TCTCAAGCGAGAT
879079 GTTGACCCCT
Statistics
Matches: 145, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
76 11 0.08
77 12 0.08
78 52 0.36
79 70 0.48
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.29
Consensus pattern (78 bp):
TCTCAAGCGAGATAAAATCATATATTTCGAGCGAAACCATCTCAAGCAAGATAAAATCTTCTGTT
TCGAGTGAAACTA
Found at i:879361 original size:59 final size:59
Alignment explanation
Indices: 879277--879408 Score: 151
Period size: 59 Copynumber: 2.2 Consensus size: 59
879267 AGATATTGAT
* * * * *
879277 CCCTCAAGTGAGGCGTCGCTAATTCGATA-T-ACCGTGAATTGAGCAAAGAAAAAGTTAAC
1 CCCTCTAGTGGGGCGTCACTAATTCGA-AGTGA-CATGAATCGAGCAAAGAAAAAGTTAAC
* ** *
879336 CCCTCTAGTGGGGCGTCACTGATTCGAAGTGACATGAATCGAGTGAAGAAAATGTTAAC
1 CCCTCTAGTGGGGCGTCACTAATTCGAAGTGACATGAATCGAGCAAAGAAAAAGTTAAC
879395 CCCTCTAGTGGGGC
1 CCCTCTAGTGGGGC
879409 ATTGTTCGTT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
58 1 0.02
59 60 0.97
60 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (59 bp):
CCCTCTAGTGGGGCGTCACTAATTCGAAGTGACATGAATCGAGCAAAGAAAAAGTTAAC
Found at i:879482 original size:38 final size:39
Alignment explanation
Indices: 879426--879521 Score: 131
Period size: 39 Copynumber: 2.5 Consensus size: 39
879416 GTTTTAAGAA
* *
879426 AAACAATCTCAAGTGAGAT-AAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
879464 AAACTATCTCAAGCGAGATAAAATCTTCTTTTTTGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
879503 AAATTATCTCAAGCAAGAT
1 AAACTATCTCAAGCGAGAT
879522 GTTGATCCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 17 0.33
39 34 0.67
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (39 bp):
AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
Found at i:879529 original size:251 final size:251
Alignment explanation
Indices: 879083--879543 Score: 699
Period size: 251 Copynumber: 1.8 Consensus size: 251
879073 CGAGATGTTG
* * *
879083 ACCCCTCAAGTGACGCGTCGCTGATTCGAAATGTCATGAATCAAGCAAAGGAAAAGTTAACCCTT
1 ACCCCTCAAGTGACGCGTCACTGATTCGAAATGACATGAATCAAGCAAAGGAAAAGTTAACCCCT
* * * *
879148 CTGGTGGGGCATTGTTCGTTTTAAGAAAAATAATCTTAAGTGAGATAAATCTTTTCTTTCGAGTG
66 CTAGTGGGGCATTGTTCGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTCTTTCGAGTG
*
879213 AAACTATCTAAACCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCACAAGCGAGATATTGATC
131 AAACTATCTAAACCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCACAAGCAAGATATTGATC
879278 CCTCAAGTGAGGCGTCGCTAATTCGATATACCGTGAATTGAGCAAAGAAAAAGTTA
196 CCTCAAGTGAGGCGTCGCTAATTCGATATACCGTGAATTGAGCAAAGAAAAAGTTA
* ** * * **
879334 ACCCCTCTAGTGGGGCGTCACTGATTCGAAGTGACATGAATCGAGTGAA-GAAAATGTTAACCCC
1 ACCCCTCAAGTGACGCGTCACTGATTCGAAATGACATGAATCAAGCAAAGGAAAA-GTTAACCCC
*
879398 TCTAGTGGGGCATTGTTCGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGT
65 TCTAGTGGGGCATTGTTCGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTCTTTCGAGT
* * * * * * *
879463 GAAACTATCTCAAGCGAGATAAAATCTTCTTTTTTGAGTGAAATTATCTCAAGCAAGATGTTGAT
130 GAAACTATCTAAACCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCACAAGCAAGATATTGAT
879528 CCCTCAAGTGAGGCGT
195 CCCTCAAGTGAGGCGT
879544 TTCTGATTCA
Statistics
Matches: 186, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
250 5 0.03
251 181 0.97
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (251 bp):
ACCCCTCAAGTGACGCGTCACTGATTCGAAATGACATGAATCAAGCAAAGGAAAAGTTAACCCCT
CTAGTGGGGCATTGTTCGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTCTTTCGAGTG
AAACTATCTAAACCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCACAAGCAAGATATTGATC
CCTCAAGTGAGGCGTCGCTAATTCGATATACCGTGAATTGAGCAAAGAAAAAGTTA
Found at i:879842 original size:57 final size:58
Alignment explanation
Indices: 879713--879861 Score: 191
Period size: 57 Copynumber: 2.6 Consensus size: 58
879703 AAGGACTTAC
* * *
879713 TCATCAAGAAACCCTTAAAAATCAAGCTTAGTTTCTTAAAATCTTTCTTTTTCAGTTA
1 TCATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTAAAATCTTTCTTTATCAGTTA
*
879771 TCATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTCTAAAA-C-TTCTTTGGAATCA-TT-
1 TCATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCT-TAAAATCTTTCTTT---ATCAGTTA
879829 T-ATCAAGAAACCCCTAAAAATCAGGCTTAGTTT
1 TCATCAAGAAACCCCTAAAAATCAGGCTTAGTTT
879862 ATTTAAAAAA
Statistics
Matches: 82, Mismatches: 5, Indels: 9
0.85 0.05 0.09
Matches are distributed among these distances:
57 37 0.45
58 35 0.43
59 7 0.09
60 3 0.04
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (58 bp):
TCATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTAAAATCTTTCTTTATCAGTTA
Found at i:881839 original size:7 final size:7
Alignment explanation
Indices: 881827--881875 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
881817 TTGATCAGTT
881827 TTCTTTC
1 TTCTTTC
881834 TTCTTTC
1 TTCTTTC
881841 TT-TTT-
1 TTCTTTC
881846 TTCTTTC
1 TTCTTTC
* *
881853 TTTTTTA
1 TTCTTTC
881860 TTCTTAT-
1 TTCTT-TC
881867 TTCTTTC
1 TTCTTTC
881874 TT
1 TT
881876 TTCTATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
5 2 0.06
6 7 0.20
7 25 0.71
8 1 0.03
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (7 bp):
TTCTTTC
Found at i:881842 original size:11 final size:10
Alignment explanation
Indices: 881825--881912 Score: 60
Period size: 10 Copynumber: 8.8 Consensus size: 10
881815 ATTTGATCAG
881825 TTTTCTTTCT
1 TTTTCTTTCT
881835 TCTTTC-TT-T
1 T-TTTCTTTCT
881844 TTTTCTTTCT
1 TTTTCTTTCT
881854 TTTT-TATTCT
1 TTTTCT-TTCT
881864 TATTTCTTTC-
1 T-TTTCTTTCT
* *
881874 TTTTCTATAT
1 TTTTCTTTCT
881884 TTTT-TTTGCT
1 TTTTCTTT-CT
* *
881894 ATATCTCTTCT
1 TTTTCT-TTCT
881905 TTTTCTTT
1 TTTTCTTT
881913 ATGTGTTGTC
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
8 4 0.07
9 13 0.22
10 23 0.38
11 17 0.28
12 3 0.05
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.75
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:881851 original size:12 final size:12
Alignment explanation
Indices: 881834--881858 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
881824 GTTTTCTTTC
881834 TTCTTTCTTTTT
1 TTCTTTCTTTTT
881846 TTCTTTCTTTTT
1 TTCTTTCTTTTT
881858 T
1 T
881859 ATTCTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTCTTTCTTTTT
Found at i:881871 original size:17 final size:17
Alignment explanation
Indices: 881849--881890 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
881839 TCTTTTTTTC
881849 TTTCTTTTTTATTCT-TA
1 TTTCTTTTTT-TTCTATA
*
881866 TTTCTTTCTTTTCTATA
1 TTTCTTTTTTTTCTATA
881883 TTT-TTTTT
1 TTTCTTTTT
881891 GCTATATCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTTTTTTTTCTATA
Found at i:881886 original size:29 final size:29
Alignment explanation
Indices: 881831--881910 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
881821 TCAGTTTTCT
* * *
881831 TTCTTCTTTCTTTTTTTCTTTCTTTTTTA
1 TTCTTATTTCTTTTTTTCTATCATTTTTA
*
881860 TTCTTATTTCTTTCTTTTCTAT-ATTTTTT
1 TTCTTATTTCTTT-TTTTCTATCATTTTTA
*
881889 TTGCTATATCTCTTCTTTTTCT
1 TT-CT-TATTTCTT-TTTTTCT
881911 TTATGTGTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
29 19 0.45
30 9 0.21
31 13 0.31
32 1 0.02
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.74
Consensus pattern (29 bp):
TTCTTATTTCTTTTTTTCTATCATTTTTA
Found at i:888363 original size:12 final size:12
Alignment explanation
Indices: 888326--888388 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
888316 GATCTGAACT
888326 TGACATGGATTC
1 TGACATGGATTC
*
888338 TGATAT-GATATC
1 TGACATGGAT-TC
888350 TGACATGGATTC
1 TGACATGGATTC
* *
888362 TGATAT-GATAC
1 TGACATGGATTC
*
888373 TTGACTTGGATTC
1 -TGACATGGATTC
888386 TGA
1 TGA
888389 TATGATACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 7 0.17
12 26 0.65
13 7 0.17
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:888442 original size:24 final size:24
Alignment explanation
Indices: 888311--888428 Score: 177
Period size: 24 Copynumber: 5.0 Consensus size: 24
888301 TTTTATTTGA
*
888311 ATTCTGATCTGA-ACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
888334 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
*
888358 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
*
888382 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
*
888406 ATTTTGATATGATACTTGACATG
1 ATTCTGATATGATACTTGACATG
888429 AATTATGTTT
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
23 12 0.14
24 74 0.85
25 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:892981 original size:24 final size:24
Alignment explanation
Indices: 892933--893050 Score: 157
Period size: 24 Copynumber: 5.0 Consensus size: 24
892923 TTCGATTTGA
*
892933 ATTCTGATATGA-ACTTCACATGG
1 ATTCTGATATGATACTTGACATGG
* *
892956 ATTCTGATCTGATATTTGACATGG
1 ATTCTGATATGATACTTGACATGG
* * *
892980 ATTCTGGTCTGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
*
893004 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
*
893028 ATTTTGATATGATACTTGACATG
1 ATTCTGATATGATACTTGACATG
893051 AATTATTTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
23 11 0.13
24 72 0.87
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:893562 original size:35 final size:35
Alignment explanation
Indices: 893516--893585 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
893506 TATGCACGTT
893516 CTTCAACATCATCTGGTAGTTCTGTATTACTGAGC
1 CTTCAACATCATCTGGTAGTTCTGTATTACTGAGC
893551 CTTCAACATCATCTGGTAGTTCTGTATTACTGAGC
1 CTTCAACATCATCTGGTAGTTCTGTATTACTGAGC
893586 TTTCCGAAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (35 bp):
CTTCAACATCATCTGGTAGTTCTGTATTACTGAGC
Found at i:895717 original size:25 final size:25
Alignment explanation
Indices: 895667--895717 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
895657 CAGTATGTAT
*
895667 GGCAGGGAGTGGTGGTGTTTGGTTG
1 GGCAGGGAGTGGTGGTGTTTGATTG
895692 GGCAGTGG-GTGGT-GTGTGTTGATTG
1 GGCAG-GGAGTGGTGGTGT-TTGATTG
895717 G
1 G
895718 TGGGTTGAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 4 0.17
25 17 0.74
26 2 0.09
ACGTcount: A:0.08, C:0.04, G:0.55, T:0.33
Consensus pattern (25 bp):
GGCAGGGAGTGGTGGTGTTTGATTG
Found at i:896858 original size:42 final size:41
Alignment explanation
Indices: 896768--896866 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 41
896758 TAAATGGTTT
* *
896768 GGTTGGTGTGTTGAGATTTATTCCGAGAATAACGAGCGGTA
1 GGTTGGTGCGTTGAGATTTATTCCGAGAATAACAAGCGGTA
* * * *
896809 GGATTGGTGCGTTGAGCTTTACTT-TGAGAATAATAAGTGGTAA
1 GG-TTGGTGCGTTGAGATTTA-TTCCGAGAATAACAAGCGGT-A
*
896852 GGTTGGTGCATTGAG
1 GGTTGGTGCGTTGAG
896867 TTTTGCTCCG
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
41 2 0.04
42 41 0.85
43 5 0.10
ACGTcount: A:0.24, C:0.08, G:0.34, T:0.33
Consensus pattern (41 bp):
GGTTGGTGCGTTGAGATTTATTCCGAGAATAACAAGCGGTA
Found at i:913388 original size:34 final size:33
Alignment explanation
Indices: 913346--913441 Score: 97
Period size: 34 Copynumber: 2.8 Consensus size: 33
913336 ATAGAGATAT
*
913346 TATTTTAATATTCAAATTTAAACATATAATAAT-A
1 TATTTTAATATTCAAATTTAAA-AGATAA-AATCA
913380 TATTTTAAT-TTCAAATATTCAAAAGATAAAATCA
1 TATTTTAATATTCAAAT-TT-AAAAGATAAAATCA
** *
913414 CCTTTTACTATTCAAATTTAAATAGATA
1 TATTTTAATATTCAAATTTAAA-AGATA
913442 TTATTTTAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
33 13 0.25
34 30 0.57
35 10 0.19
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (33 bp):
TATTTTAATATTCAAATTTAAAAGATAAAATCA
Found at i:913459 original size:63 final size:62
Alignment explanation
Indices: 913373--913504 Score: 178
Period size: 63 Copynumber: 2.1 Consensus size: 62
913363 TTAAACATAT
* *
913373 AATA-ATATATTTTAATTTCAAATATTCAAAA-GATAAAATCACCTTTTACTATTCAAATTTA
1 AATAGATATATTTTAATTTCAAATATTCAAAAGGATAAAATCACC-TTTAATATTCAAAGTTA
* * * *
913434 AATAGATATTATTTTAATTTGAAATATTCAAAAGGATATAATTATCTTTAATATTCAAAGTTA
1 AATAGATA-TATTTTAATTTCAAATATTCAAAAGGATAAAATCACCTTTAATATTCAAAGTTA
913497 AATAGATA
1 AATAGATA
913505 GCAAATACCT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
61 4 0.06
62 3 0.05
63 46 0.74
64 9 0.15
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (62 bp):
AATAGATATATTTTAATTTCAAATATTCAAAAGGATAAAATCACCTTTAATATTCAAAGTTA
Found at i:913504 original size:97 final size:97
Alignment explanation
Indices: 913340--913518 Score: 210
Period size: 97 Copynumber: 1.8 Consensus size: 97
913330 TTTTCAATAG
*
913340 AGATATTATTTTAATATTCAAATTTAAACATATAATAATATATTTTAATTTCAAATATTCAAAAG
1 AGATATTATTTTAATATTCAAATTTAAACAGATAATAATATATTTTAATTTCAAATATTCAAAAG
913405 ATA-AAATCACCTTTTACTATTCAAATTTAAAT
66 ATACAAAT-ACCTTTTACTATTCAAATTTAAAT
* *
913437 AGATATTATTTTAAT-TTGAAATATTCAAA-AGGAT-ATAAT-TATCTTTAATATTCAAA-GTT-
1 AGATATTATTTTAATATTCAAAT-TT-AAACA-GATAATAATATAT-TTTAAT-TTCAAATATTC
913496 AAATAGATAGCAAATACCTTTTA
61 AAA-AGATA-CAAATACCTTTTA
913519 ATTTGACATA
Statistics
Matches: 71, Mismatches: 3, Indels: 15
0.80 0.03 0.17
Matches are distributed among these distances:
96 12 0.17
97 36 0.51
98 19 0.27
99 4 0.06
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.41
Consensus pattern (97 bp):
AGATATTATTTTAATATTCAAATTTAAACAGATAATAATATATTTTAATTTCAAATATTCAAAAG
ATACAAATACCTTTTACTATTCAAATTTAAAT
Found at i:920490 original size:24 final size:24
Alignment explanation
Indices: 920458--920576 Score: 143
Period size: 24 Copynumber: 5.0 Consensus size: 24
920448 TTCAATTTGA
920458 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
920482 ATTCTGATCTGATA-TCTGATATGG
1 ATTCTGATCTGATACT-TGACATGG
*
920506 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* * *
920530 ATTCTGGTATGATACTTGAC-TCAG
1 ATTCTGATCTGATACTTGACAT-GG
* *
920554 ATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATG
920577 ATTTATGTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
23 2 0.02
24 78 0.95
25 2 0.02
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:925089 original size:24 final size:24
Alignment explanation
Indices: 925062--925183 Score: 133
Period size: 24 Copynumber: 5.1 Consensus size: 24
925052 TTCAATTTGA
*
925062 ATTCTGATCTGATACTTGACATTG
1 ATTCTGATATGATACTTGACATTG
* *
925086 ATTCTGATATGATA-TCTGATATGG
1 ATTCTGATATGATACT-TGACATTG
*
925110 ATTCTGATCTGATACTTGAC-TTGG
1 ATTCTGATATGATACTTGACATT-G
* * *
925134 ATTCTAATATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATTG
*
925158 ATTTTGATATGATACTTGACA-TG
1 ATTCTGATATGATACTTGACATTG
925181 ATT
1 ATT
925184 TATGTTTTGA
Statistics
Matches: 81, Mismatches: 13, Indels: 9
0.79 0.13 0.09
Matches are distributed among these distances:
23 6 0.07
24 73 0.90
25 2 0.02
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATTG
Found at i:925105 original size:12 final size:11
Alignment explanation
Indices: 925084--925122 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
925074 TACTTGACAT
925084 TGATTCTGATA
1 TGATTCTGATA
925095 TGATATCTGATA
1 TGAT-TCTGATA
*
925107 TGGATTCTGATC
1 T-GATTCTGATA
925119 TGAT
1 TGAT
925123 ACTTGACTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 7 0.28
12 15 0.60
13 3 0.12
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.44
Consensus pattern (11 bp):
TGATTCTGATA
Found at i:925121 original size:48 final size:48
Alignment explanation
Indices: 925062--925183 Score: 160
Period size: 48 Copynumber: 2.6 Consensus size: 48
925052 TTCAATTTGA
* *
925062 ATTCTGATCTGATACTTGACATTGATTCTGATATGATA-TCTGATATGG
1 ATTCTGATCTGATACTTGACATTGATTCTAATATGATACT-TGACATGG
*
925110 ATTCTGATCTGATACTTGAC-TTGGATTCTAATATGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATT-GATTCTAATATGATACTTGACATGG
* *
925158 ATTTTGATATGATACTTGACA-TGATT
1 ATTCTGATCTGATACTTGACATTGATT
925184 TATGTTTTGA
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
47 6 0.09
48 59 0.89
49 1 0.02
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (48 bp):
ATTCTGATCTGATACTTGACATTGATTCTAATATGATACTTGACATGG
Found at i:928819 original size:21 final size:21
Alignment explanation
Indices: 928743--928818 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
928733 GATCCCCTTA
* * *
928743 AAAAGGATCGATCCCTCGAGG
1 AAAAGGATCAATCCCTTGATG
* * *
928764 AAAATGATCAATCCCTTCATC
1 AAAAGGATCAATCCCTTGATG
* ** *
928785 AAAAAGATTGATCTCTTGATG
1 AAAAGGATCAATCCCTTGATG
928806 AAAAGGATCAATC
1 AAAAGGATCAATC
928819 TTTCCCCTAA
Statistics
Matches: 40, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (21 bp):
AAAAGGATCAATCCCTTGATG
Found at i:937253 original size:46 final size:46
Alignment explanation
Indices: 937145--937255 Score: 118
Period size: 46 Copynumber: 2.4 Consensus size: 46
937135 TAATCGATTT
* * * *
937145 ACAGGCTGGTGCATCCTTAACAGATAGTAATCTCAATTACTGATAT
1 ACAGGCTGGTGCATCCTTAACAGATAGTAAACCCAATTACGGATAC
* * *
937191 ACATGCTGATGCATCCTTATCAGAT-GATAAACCCAATTACGGACT-C
1 ACAGGCTGGTGCATCCTTAACAGATAG-TAAACCCAATTACGGA-TAC
*
937237 ACAGGCTGGTGAATCCTTA
1 ACAGGCTGGTGCATCCTTA
937256 GCGGATGGGA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
45 1 0.02
46 51 0.96
47 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (46 bp):
ACAGGCTGGTGCATCCTTAACAGATAGTAAACCCAATTACGGATAC
Found at i:937486 original size:3 final size:3
Alignment explanation
Indices: 937480--937524 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
937470 ATTTTTCAGT
* * *
937480 TTA TTA TTA TTA TTA TTA TTA TTC TTA TAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
937525 ATATATATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:937532 original size:2 final size:2
Alignment explanation
Indices: 937525--937566 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
937515 ATTATTATTA
937525 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
937567 TATTAAACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:938075 original size:11 final size:11
Alignment explanation
Indices: 938051--938087 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
938041 CCATAACAGC
*
938051 AAACAGAAAAG
1 AAACAGAGAAG
*
938062 AAAGAGAGAAG
1 AAACAGAGAAG
938073 AAACAGAGAAG
1 AAACAGAGAAG
938084 AAAC
1 AAAC
938088 TTACCACCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.68, C:0.08, G:0.24, T:0.00
Consensus pattern (11 bp):
AAACAGAGAAG
Found at i:939044 original size:11 final size:11
Alignment explanation
Indices: 938987--939054 Score: 54
Period size: 11 Copynumber: 6.3 Consensus size: 11
938977 TTATTTGCAA
938987 TATTATTTTAT
1 TATTATTTTAT
938998 TATTACTTTTA-
1 TATTA-TTTTAT
*
939009 TA-T-TTTGAT
1 TATTATTTTAT
*
939018 TATTGCA-TTAAT
1 TATT--ATTTTAT
939030 TATTATTTTAT
1 TATTATTTTAT
*
939041 TATTATTTTTT
1 TATTATTTTAT
939052 TAT
1 TAT
939055 CTTAGTTATA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
8 4 0.09
9 2 0.04
10 3 0.07
11 24 0.52
12 13 0.28
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:939351 original size:143 final size:142
Alignment explanation
Indices: 939098--939359 Score: 341
Period size: 142 Copynumber: 1.8 Consensus size: 142
939088 ATTTAAATAA
* * * * *
939098 TAATGTTTATTTATTTCTAATATCTAAGAAAAGGGTTGTCTTAAAGCACCTAGAAATCCTTTTTT
1 TAATATTTATTTATTTCTAATATCTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAATCATTTTCT
* **
939163 GGTATTCTTAAATAAATAAATATCCTATTTTTTATATAAATTATATATATTAATTTATTTTAATA
66 GATATTCTTAAATAAATAAATATCCTATAATTTATATAAATTATATATATTAATTTATTTTAATA
939228 GAAATGTTTTAT
131 GAAATGTTTTAT
* * *
939240 TAATATTTATTTATTTTTTAATAT-TAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCATTTTC
1 TAATATTTATTTA-TTTCTAATATCTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAATCATTTTC
** *
939304 TGATATT-TCTAAAGTAAATAAATATTTTATAAATTTATATATA-TATATATATTAAT
65 TGATATTCT-TAAA-TAAATAAATATCCTAT-AATTTATATAAATTATATATATTAAT
939360 AGATTTTCTT
Statistics
Matches: 102, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
141 1 0.01
142 56 0.55
143 36 0.35
144 9 0.09
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (142 bp):
TAATATTTATTTATTTCTAATATCTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAATCATTTTCT
GATATTCTTAAATAAATAAATATCCTATAATTTATATAAATTATATATATTAATTTATTTTAATA
GAAATGTTTTAT
Found at i:944351 original size:7 final size:7
Alignment explanation
Indices: 944333--944370 Score: 53
Period size: 6 Copynumber: 5.6 Consensus size: 7
944323 ATTAGGTAAA
944333 AAAAAGG
1 AAAAAGG
944340 AAAAAAGG
1 -AAAAAGG
944348 AAAAA-G
1 AAAAAGG
944354 AAAAA-G
1 AAAAAGG
944360 AAAAAGG
1 AAAAAGG
944367 AAAA
1 AAAA
944371 TTGAATCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.41
7 10 0.34
8 7 0.24
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:944357 original size:12 final size:13
Alignment explanation
Indices: 944333--944370 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
944323 ATTAGGTAAA
944333 AAAAAGGAAAAAAGG
1 AAAAAGG-AAAAA-G
944348 AAAAA-GAAAAAG
1 AAAAAGGAAAAAG
944360 AAAAAGGAAAA
1 AAAAAGGAAAA
944371 TTGAATCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.27
13 10 0.45
14 1 0.05
15 5 0.23
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAAGGAAAAAG
Found at i:945017 original size:32 final size:32
Alignment explanation
Indices: 944976--945038 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
944966 GTCAGACACA
**
944976 AGAAATATCTCTATGAGATGAGCATAACAATG
1 AGAAATATCTCTACAAGATGAGCATAACAATG
*
945008 AGAAGTATCTCTACAAGATGAGCATAACAAT
1 AGAAATATCTCTACAAGATGAGCATAACAAT
945039 CATTTCTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.24
Consensus pattern (32 bp):
AGAAATATCTCTACAAGATGAGCATAACAATG
Found at i:949085 original size:22 final size:22
Alignment explanation
Indices: 949054--949111 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
949044 TACATCTACA
949054 CTTTTCAAAGATGATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
*
949076 CTTTTTAAAGATGATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
949098 CTTTTCAAAGATGA
1 CTTTTCAAAGATGA
949112 AAGCTTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (22 bp):
CTTTTCAAAGATGATAGATTCT
Found at i:949809 original size:45 final size:45
Alignment explanation
Indices: 949740--950272 Score: 843
Period size: 45 Copynumber: 11.8 Consensus size: 45
949730 CTATTTCCCA
*
949740 CATCTGTAAGCCCTTCAGTTCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
949785 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCATT-GGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACC-TTCGGGT
* *
949831 CATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * **
949876 CATCTGTAATCCCTTCAGTGCATGATGTTTTAAAAACCTTCAAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
949921 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
949966 CATCTGTAAGCCCTTCAATGCATGATGTTTTCGAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
950012 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
950057 TATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
950102 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
950147 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* * *
950193 TATCTGTAAGCCCTTCAATGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * *
950238 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
950273 TAAGATAATA
Statistics
Matches: 451, Mismatches: 32, Indels: 10
0.91 0.06 0.02
Matches are distributed among these distances:
44 2 0.00
45 323 0.72
46 124 0.27
47 2 0.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:950003 original size:136 final size:135
Alignment explanation
Indices: 949740--950272 Score: 834
Period size: 136 Copynumber: 3.9 Consensus size: 135
949730 CTATTTCCCA
* * *
949740 CATCTGTAAGCCCTTCAGTTCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTAAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTG
*
949805 CATGATGTTTTCAAAAACCATT-GGGTCATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAACC
66 CATGATGTTTTC-AAAACC-TTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACC
*
949869 TTTGGGT
129 TTCGGGT
* *
949876 CATCTGTAATCCCTTCAGTGCATGATGTTTTAAAAACCTTCAAGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTAAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTG
* *
949941 CATGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAATGCATGATGTTTTCGAAAACCT
66 CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCT
950006 TCGGGT
130 TCGGGT
* * * *
950012 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTAAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTG
*
950077 CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTT
66 CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTT
950142 CGGGT
131 CGGGT
* *
950147 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGAGTTATCTGTAAGCCCTTCAAT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTT-AAAAACCTTCGAGTCATCTGTAAGCCCTTCAGT
* * * * *
950212 GCTTGATGTTTTCAAAACCTTCGGGTCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAA
65 GCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
950273 TAAGATAATA
Statistics
Matches: 366, Mismatches: 28, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
134 2 0.01
135 82 0.22
136 282 0.77
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (135 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTAAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTG
CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTT
CGGGT
Found at i:950269 original size:181 final size:181
Alignment explanation
Indices: 949740--950272 Score: 861
Period size: 181 Copynumber: 2.9 Consensus size: 181
949730 CTATTTCCCA
*
949740 CATCTGTAAGCCCTTCAGTTCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
*
949805 CATGATGTTTTCAAAAACCATT-GGGTCATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAACC
66 CATGATGTTTTCAAAAACC-TTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACC
* * *
949869 TTTGGGTCATCTGTAATCCCTTCAGTGCATGATGTTTTAAAAACCTTCAAGT
130 TTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAAGT
* *
949921 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAATG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
* *
949986 CATGATGTTTTCGAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCT
66 CATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCT
* **
950051 TCGGGTTATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
131 TCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAAGT
*
950102 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
* * * *
950167 CATGATGTTTTCAAAAACCTTCGAGTTATCTGTAAGCCCTTCAATGCTTGATGTTTTCAAAACCT
66 CATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCT
* * * *
950232 TCGGGTCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAA
131 TCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
950273 TAAGATAATA
Statistics
Matches: 325, Mismatches: 26, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
180 2 0.01
181 323 0.99
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (181 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
CATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCT
TCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAAGT
Found at i:950542 original size:6 final size:6
Alignment explanation
Indices: 950525--950600 Score: 53
Period size: 6 Copynumber: 11.5 Consensus size: 6
950515 TTTTTTCAGT
* * * *
950525 TTATTT TTATTA TTATTA TTCTTA TAAATA TTATTA TTATTA TATATATA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA T-TAT-TA
950575 TATATATA TATATATA TATATTA TTA
1 T-TAT-TA T-TAT-TA T-TATTA TTA
950601 AACAAAATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
6 32 0.52
7 6 0.10
8 23 0.38
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (6 bp):
TTATTA
Found at i:950558 original size:18 final size:18
Alignment explanation
Indices: 950535--950600 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 18
950525 TTATTTTTAT
*
950535 TATTATTATTCTTATAAA
1 TATTATTATTATTATAAA
*
950553 TATTATTATTATTATATA
1 TATTATTATTATTATAAA
*
950571 TATATATATATATATATATATA
1 TAT-TAT-TAT-TAT-TATAAA
950593 TATTATTA
1 TATTATTA
950601 AACAAAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
18 19 0.45
19 3 0.07
20 5 0.12
21 6 0.14
22 9 0.21
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTATTATTATTATAAA
Found at i:950572 original size:2 final size:2
Alignment explanation
Indices: 950565--950595 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
950555 TTATTATTAT
950565 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 T
950596 TATTAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:951145 original size:11 final size:11
Alignment explanation
Indices: 951129--951154 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
951119 AAACAAAAAT
951129 GAAAGAGAGAA
1 GAAAGAGAGAA
951140 GAAAGAGAGAA
1 GAAAGAGAGAA
951151 GAAA
1 GAAA
951155 CTTACCACCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (11 bp):
GAAAGAGAGAA
Found at i:951848 original size:12 final size:12
Alignment explanation
Indices: 951831--951863 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
951821 TTAATCACTG
951831 TTTATATATATA
1 TTTATATATATA
*
951843 TTTATATATATG
1 TTTATATATATA
951855 TTTATATAT
1 TTTATATAT
951864 TTTAGGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (12 bp):
TTTATATATATA
Found at i:975959 original size:2 final size:2
Alignment explanation
Indices: 975952--975996 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
975942 TGCTTATTTC
* *
975952 AT AT AT AT TT AT TT CAT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
975994 AT A
1 AT A
975997 GTTATTATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.95
3 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:975965 original size:15 final size:15
Alignment explanation
Indices: 975945--975989 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
975935 ATAAAAATGC
975945 TTATTTCATATATAT
1 TTATTTCATATATAT
975960 TTATTTCATATATAT
1 TTATTTCATATATAT
* *
975975 ATATAT-ATATATAT
1 TTATTTCATATATAT
975989 T
1 T
975990 ATATATAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATTTCATATATAT
Found at i:975978 original size:21 final size:19
Alignment explanation
Indices: 975952--975996 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
975942 TGCTTATTTC
* *
975952 ATATATATTTATTTCATA-T
1 ATATATATATATAT-ATATT
975971 ATATATATATATATATATT
1 ATATATATATATATATATT
975990 ATATATA
1 ATATATA
975997 GTTATTATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATATATATATATATATT
Found at i:976004 original size:13 final size:13
Alignment explanation
Indices: 975952--975996 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
975942 TGCTTATTTC
*
975952 ATATATATTTATT
1 ATATATATATATT
975965 -TCATATATATA-T
1 AT-ATATATATATT
975977 ATATATATATATT
1 ATATATATATATT
975990 ATATATA
1 ATATATA
975997 GTTATTATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (13 bp):
ATATATATATATT
Found at i:977268 original size:22 final size:21
Alignment explanation
Indices: 977232--977276 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
977222 CATCTACATT
977232 TCATCATCAACACCA-ACAACA
1 TCATCATCAACACCATA-AACA
*
977253 TCATCCATCAAGACCATAAACA
1 TCAT-CATCAACACCATAAACA
977275 TC
1 TC
977277 TTCTTAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 16 0.76
23 1 0.05
ACGTcount: A:0.44, C:0.36, G:0.02, T:0.18
Consensus pattern (21 bp):
TCATCATCAACACCATAAACA
Found at i:980465 original size:15 final size:15
Alignment explanation
Indices: 980445--980474 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
980435 ATAAAAATGC
980445 TTATTTCATATATAT
1 TTATTTCATATATAT
980460 TTATTTCATATATAT
1 TTATTTCATATATAT
980475 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTTCATATATAT
Found at i:985876 original size:51 final size:51
Alignment explanation
Indices: 985785--985881 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 51
985775 AGAATTAGAT
* * *
985785 TTATCATTTTATTAGGAATTAAGATAGAGTTGAAATATTATTTTTAGTTAA
1 TTATCATTTTATTAGGAATTAAGATAGAGTCGAAACATTATCTTTAGTTAA
* * *
985836 TTATTATTTTATTATGAATTAAGATTGAAG-CGAAACATTATCTTTA
1 TTATCATTTTATTAGGAATTAAGATAG-AGTCGAAACATTATCTTTA
985882 TCCATTAGTC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 37 0.95
52 2 0.05
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.46
Consensus pattern (51 bp):
TTATCATTTTATTAGGAATTAAGATAGAGTCGAAACATTATCTTTAGTTAA
Found at i:988009 original size:90 final size:90
Alignment explanation
Indices: 987856--988026 Score: 297
Period size: 90 Copynumber: 1.9 Consensus size: 90
987846 CAAATATTTT
* *
987856 AATTCTAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAGGG
1 AATTCCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAGGG
*
987921 TAACTTGGATATAAAATGATTATTA
66 TAACTCGGATATAAAATGATTATTA
* *
987946 AATTCCAATTCATTAAATATAAATTTAATTAATTTGAAATAATAAAATCCCTAATGTGATTAGGG
1 AATTCCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAGGG
988011 TAACTCGGATATAAAA
66 TAACTCGGATATAAAA
988027 GGACGTGTTA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 76 1.00
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.37
Consensus pattern (90 bp):
AATTCCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAGGG
TAACTCGGATATAAAATGATTATTA
Found at i:994870 original size:89 final size:90
Alignment explanation
Indices: 994714--994892 Score: 279
Period size: 89 Copynumber: 2.0 Consensus size: 90
994704 TAATCCCAAA
* * * * *
994714 TATTTAATTCCAATTAATTAAATATATATTTAATTGATTTTAAATATTAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
* *
994779 TAGGGTAACTTGGATAT-AAAGGAT
66 TAGGATAACTCGGATATAAAAGGAT
*
994803 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATGTGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
994868 TAGGATAACTCGGATATAAAAGGAT
66 TAGGATAACTCGGATATAAAAGGAT
994893 GTGTTAGGTC
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
89 74 0.91
90 7 0.09
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.39
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
TAGGATAACTCGGATATAAAAGGAT
Found at i:995933 original size:25 final size:25
Alignment explanation
Indices: 995905--995953 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
995895 GGCCTTCCCT
995905 CACA-CTTTTCACATCTTATTTTCTA
1 CACATCTTTTC-CATCTTATTTTCTA
* *
995930 CACATTTTTTCCATTTTATTTTCT
1 CACATCTTTTCCATCTTATTTTCT
995954 TTTTTTCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.20, C:0.24, G:0.00, T:0.55
Consensus pattern (25 bp):
CACATCTTTTCCATCTTATTTTCTA
Found at i:999487 original size:17 final size:19
Alignment explanation
Indices: 999448--999493 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
999438 TTTTTTTATT
*
999448 TTTTATTACTATTTTGTTTA
1 TTTTATTA-GATTTTGTTTA
999468 TTTT-TTAGATTTTG-TTA
1 TTTTATTAGATTTTGTTTA
999485 TTTTATTAG
1 TTTTATTAG
999494 TTTATTTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.29
18 10 0.42
19 3 0.12
20 4 0.17
ACGTcount: A:0.20, C:0.02, G:0.09, T:0.70
Consensus pattern (19 bp):
TTTTATTAGATTTTGTTTA
Found at i:999538 original size:16 final size:16
Alignment explanation
Indices: 999517--999549 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
999507 TTTCTTGAGA
999517 TTTCTTTCTTTCATTC
1 TTTCTTTCTTTCATTC
*
999533 TTTCTTTCTTTTATTC
1 TTTCTTTCTTTCATTC
999549 T
1 T
999550 CTTTTCAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTCTTTCTTTCATTC
Found at i:1004667 original size:21 final size:21
Alignment explanation
Indices: 1004612--1004651 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1004602 AAGAGCCAAT
1004612 GAGCATTGTTGCAAAGTCAAG
1 GAGCATTGTTGCAAAGTCAAG
1004633 GAGCATTGTTGCAAAGTCA
1 GAGCATTGTTGCAAAGTCA
1004652 TAGATCATCT
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:0.33, C:0.15, G:0.28, T:0.25
Consensus pattern (21 bp):
GAGCATTGTTGCAAAGTCAAG
Found at i:1015104 original size:21 final size:23
Alignment explanation
Indices: 1015067--1015120 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
1015057 CATCTCTATC
1015067 CTTTT-TTTATTTCATTTCAATT
1 CTTTTCTTTATTTCATTTCAATT
1015089 CTTTTCTTTA-TT-ATTTCAATT
1 CTTTTCTTTATTTCATTTCAATT
*
1015110 ATTTTCCTTTA
1 CTTTT-CTTTA
1015121 CTAATCATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 13 0.45
22 12 0.41
23 4 0.14
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.67
Consensus pattern (23 bp):
CTTTTCTTTATTTCATTTCAATT
Found at i:1019767 original size:2 final size:2
Alignment explanation
Indices: 1019755--1019789 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
1019745 TCACATGTTC
1019755 AT AT CAT 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
1019790 CATGTAACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1019861 original size:16 final size:16
Alignment explanation
Indices: 1019823--1019866 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
1019813 CATTTTCTGA
*
1019823 CATTCATATAGACATG
1 CATTCACATAGACATG
* * *
1019839 TAATCACATATACATG
1 CATTCACATAGACATG
1019855 CATTCACATAGA
1 CATTCACATAGA
1019867 TCACATATGG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (16 bp):
CATTCACATAGACATG
Found at i:1025615 original size:11 final size:11
Alignment explanation
Indices: 1025599--1025628 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1025589 AGTACATCAA
1025599 TTACACAACAC
1 TTACACAACAC
1025610 TTACACAACAC
1 TTACACAACAC
*
1025621 TTAAACAA
1 TTACACAA
1025629 TAACCCATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (11 bp):
TTACACAACAC
Found at i:1031869 original size:25 final size:25
Alignment explanation
Indices: 1031841--1031914 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
1031831 CCATTTAATA
1031841 CAATAAGCTCGTAAGCTTATTTTAC
1 CAATAAGCTCGTAAGCTTATTTTAC
*
1031866 CAATATA-CT--T-A-C-CA-TTTATC
1 CAATA-AGCTCGTAAGCTTATTTTA-C
1031886 C-ATAAGCTCGTAAGCTTATTTTAC
1 CAATAAGCTCGTAAGCTTATTTTAC
1031910 CAATA
1 CAATA
1031915 CACCTGCCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 20
0.63 0.03 0.34
Matches are distributed among these distances:
18 1 0.03
19 9 0.24
20 3 0.08
21 2 0.05
22 2 0.05
23 2 0.05
24 3 0.08
25 14 0.38
26 1 0.03
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (25 bp):
CAATAAGCTCGTAAGCTTATTTTAC
Found at i:1031896 original size:44 final size:46
Alignment explanation
Indices: 1031828--1031914 Score: 151
Period size: 44 Copynumber: 1.9 Consensus size: 46
1031818 GTGCAATATT
1031828 TTACCATTTAATACAATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTAATACAATAAGCTCGTAAGCTTATTTTACCAATATAC
*
1031874 TTACCATTT-AT-CCATAAGCTCGTAAGCTTATTTTACCAATA
1 TTACCATTTAATACAATAAGCTCGTAAGCTTATTTTACCAATA
1031915 CACCTGCCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 29 0.73
45 2 0.05
46 9 0.22
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (46 bp):
TTACCATTTAATACAATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:1031925 original size:44 final size:44
Alignment explanation
Indices: 1031843--1031934 Score: 141
Period size: 44 Copynumber: 2.1 Consensus size: 44
1031833 ATTTAATACA
* *
1031843 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATT-TATCC
1 ATAAGCTCGTAAGCTTATTTTACCAATACACCTACCATTAT-TCC
*
1031887 ATAAGCTCGTAAGCTTATTTTACCAATACACCTGCCATTATTCC
1 ATAAGCTCGTAAGCTTATTTTACCAATACACCTACCATTATTCC
1031931 ATAA
1 ATAA
1031935 CCATATACCA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 43 0.98
45 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.36
Consensus pattern (44 bp):
ATAAGCTCGTAAGCTTATTTTACCAATACACCTACCATTATTCC
Found at i:1041452 original size:21 final size:22
Alignment explanation
Indices: 1041411--1041461 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
1041401 GAACAATATT
1041411 GATACCATATGGAAGGAGTATC
1 GATACCATATGGAAGGAGTATC
1041433 GATACC-TATGTGAAGG-GTATC
1 GATACCATATG-GAAGGAGTATC
1041454 GATACCAT
1 GATACCAT
1041462 GGAAACATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (22 bp):
GATACCATATGGAAGGAGTATC
Found at i:1041550 original size:20 final size:20
Alignment explanation
Indices: 1041525--1041595 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
1041515 TAGCATAGAG
*
1041525 GTATCGATATTGCGAGGATA
1 GTATCGATACTGCGAGGATA
** *
1041545 GTATCGATACTGTTAGGGTA
1 GTATCGATACTGCGAGGATA
** *
1041565 GTATCGATACTATGAGGGTA
1 GTATCGATACTGCGAGGATA
*
1041585 GTACCGATACT
1 GTATCGATACT
1041596 AATTAAGTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (20 bp):
GTATCGATACTGCGAGGATA
Found at i:1041596 original size:20 final size:20
Alignment explanation
Indices: 1041538--1041596 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
1041528 TCGATATTGC
* *
1041538 GAGGATAGTATCGATACTGT
1 GAGGGTAGTATCGATACTAT
*
1041558 TAGGGTAGTATCGATACTAT
1 GAGGGTAGTATCGATACTAT
*
1041578 GAGGGTAGTACCGATACTA
1 GAGGGTAGTATCGATACTA
1041597 ATTAAGTTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.29
Consensus pattern (20 bp):
GAGGGTAGTATCGATACTAT
Done.