Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008284.1 Hibiscus syriacus cultivar Beakdansim tig00110946_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: 665325
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:588755 original size:63 final size:62
Alignment explanation
Indices: 588653--589011 Score: 194
Period size: 63 Copynumber: 5.6 Consensus size: 62
588643 GATGAGATCC
** *
588653 ATCTTTGAGTCAGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAA
1 ATCTTTGAGTTTGTTTC-TTTGAAACAAAATTTTGTCTCTTAAAGACAATTTCTTTTGAAAAA
** *
588716 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC-TCGAGACAACTTCTTTTGAAAATA
1 ATCTTTGAGTTTGTTT-CTTTGAAACAAAATTTTGTCTCTTAAAGACAATTTCTTTTGAAAA-A
* * * * ** * * * *
588779 CCCACCTTTGAGATTGTTTCTATTAAAAC-TAATTTTGTCTCGCATGAGACAGTTTCCTTTCAAT
1 ---ATCTTTGAGTTTGTTTCT-TTGAAACAAAATTTTGTCTCTTA-AAGACAATTTCTTTTGAA-
* *
588843 GAC
60 AAA
* * * * * * **
588846 ATCTTTGAG-TCGTTTCCCTTCAAAC-GAATTTTGTCTCTTGAA-ACATTTTCTCTTAAAATAAG
1 ATCTTTGAGTTTGTTT-CTTTGAAACAAAATTTTGTCTCTTAAAGACAATTTCT-TTTGAA-AA-
588908 A
62 A
* ** * * *
588909 TCATCTTTGAGTTTGTTTCTCTGGAAACAAGGTTTTATCCCTTAAA-ACAGTTTCTTTTGAAGAA
1 --ATCTTTGAGTTTGTTTCT-TTGAAACAAAATTTTGTCTCTTAAAGACAATTTCTTTTG-A-AA
588973 AA
61 AA
*
588975 ATC--TGAGTCTGTTTCTTTGAAAACAAAATTTTGTCTC
1 ATCTTTGAGTTTGTTTCTTTG-AAACAAAATTTTGTCTC
589012 ACTAAGATAC
Statistics
Matches: 224, Mismatches: 52, Indels: 41
0.71 0.16 0.13
Matches are distributed among these distances:
61 9 0.04
62 51 0.23
63 57 0.25
64 13 0.06
65 23 0.10
66 33 0.15
67 36 0.16
68 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.42
Consensus pattern (62 bp):
ATCTTTGAGTTTGTTTCTTTGAAACAAAATTTTGTCTCTTAAAGACAATTTCTTTTGAAAAA
Found at i:589233 original size:35 final size:36
Alignment explanation
Indices: 589162--589236 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
589152 TGTTTCTTTG
* * *
589162 GAAACAAAATTTACCATCTTTGAATCTGTTTCCCTT
1 GAAACAAAATTAAACATCTTTGAATCTGTTTACCTT
589198 GAAACAAAA-TAAACATCTTTGAGATC-GTTTACCTT
1 GAAACAAAATTAAACATCTTTGA-ATCTGTTTACCTT
589233 GAAA
1 GAAA
589237 TGAATTTCGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (36 bp):
GAAACAAAATTAAACATCTTTGAATCTGTTTACCTT
Found at i:589332 original size:66 final size:65
Alignment explanation
Indices: 589211--589349 Score: 154
Period size: 66 Copynumber: 2.1 Consensus size: 65
589201 ACAAAATAAA
* * ** *
589211 CATCTTTGAGATCGTTTACCTTGAAATGAATTTCGTCTCATTTGAGACAATTTCCCATGAAATAC
1 CATCTTTGAGAACGTTTACCTTAAAACAAATTTCGTCTCACTTGAGACAATTTCCCATGAAATAC
* * * * *
589276 CGATCTTTGAGAACGTTTCCCTTAAAAACAAATTTTGTCTCGCTTGAGACAA-TTCCCTTTAAAT
1 C-ATCTTTGAGAACGTTTACCTT-AAAACAAATTTCGTCTCACTTGAGACAATTTCCCATGAAAT
*
589340 GC
64 AC
589342 CATCTTTG
1 CATCTTTG
589350 GGTTGTTTCC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
65 8 0.13
66 31 0.51
67 22 0.36
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (65 bp):
CATCTTTGAGAACGTTTACCTTAAAACAAATTTCGTCTCACTTGAGACAATTTCCCATGAAATAC
Found at i:589726 original size:46 final size:45
Alignment explanation
Indices: 589630--589868 Score: 180
Period size: 46 Copynumber: 5.5 Consensus size: 45
589620 CCATCTCCTT
* ** * *
589630 ATCACGTAGGAGCCGTGTCA--ACCATAGATAACCAG-CCGTCCTC
1 ATCACGTAGGAGCCGTGTCATCACCTTAGATGGCCAGAAC-TCTTC
* *
589673 ATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAGAACTCTTC
1 ATCACGTAGGAGCCGTGTCATCACCTT-AGATGGCCAGAACTCTTC
* *
589719 ATCACGTATGAGCCGTGTCATTC-CC--AGA---CCAGATCTCCTT-
1 ATCACGTAGGAGCCGTGTCA-TCACCTTAGATGGCCAGAACT-CTTC
* ** * *
589759 ATCACGTAGGAGCCGTGTCA--ACCATAGATAACCAG-CCGTCCTC
1 ATCACGTAGGAGCCGTGTCATCACCTTAGATGGCCAGAAC-TCTTC
* *
589802 ATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTC
1 ATCACGTAGGAGCCGTGTCATCACC-TTAGATGGCCAGAACTCTTC
*
589848 ATCACGTATGAGCCGTGTCAT
1 ATCACGTAGGAGCCGTGTCAT
589869 TCCCCGACCA
Statistics
Matches: 154, Mismatches: 24, Indels: 33
0.73 0.11 0.16
Matches are distributed among these distances:
38 2 0.01
40 29 0.19
41 3 0.02
42 3 0.02
43 44 0.29
45 7 0.05
46 62 0.40
47 4 0.03
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.24
Consensus pattern (45 bp):
ATCACGTAGGAGCCGTGTCATCACCTTAGATGGCCAGAACTCTTC
Found at i:589801 original size:129 final size:129
Alignment explanation
Indices: 589573--589907 Score: 523
Period size: 129 Copynumber: 2.6 Consensus size: 129
589563 ATAGCTTCTA
* * * * * *
589573 AAGATGGCCAG-CCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACC--ATCTCCTTATCAC
1 AAGATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCAC
589635 GTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
65 GTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
589700 AAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACG
1 AAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACG
589765 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
66 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
* * * * *
589829 TAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATGTCCTCATCATG
1 AAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACG
* *
589894 TAGGAACCTTGTCA
66 TAGGAGCCGTGTCA
589908 CTTTTAGACG
Statistics
Matches: 192, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
127 41 0.21
128 1 0.01
129 150 0.78
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (129 bp):
AAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACG
TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
Found at i:589807 original size:43 final size:41
Alignment explanation
Indices: 589580--589819 Score: 159
Period size: 43 Copynumber: 5.7 Consensus size: 41
589570 CTAAAGATGG
* * **
589580 CCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAG--A
1 CCAGCC-TCCTCATCACGTAGGAACCGTGTCAACCATAGATA
* * *
589620 CCA-TCTCCTTATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAGCCTCCTCATCACGTAGGAACCGTGTCAACCATAGAT-A
* * *
589661 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGG
1 CCAGCC-TCCTCATCACGTAGGAACCGTGTCA--ACCAT-AGAT-A
* * * * * *
589707 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCC-CAG--A
1 CCAG-CCTCCTCATCACGTAGGAACCGTGTCA-ACCATAGATA
* * *
589747 CCAGATCTCCTTATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAG-CCTCCTCATCACGTAGGAACCGTGTCAACCATAGAT-A
589790 CCAGCCGTCCTCATCACGTAGGAACCGTGT
1 CCAGCC-TCCTCATCACGTAGGAACCGTGT
589820 TATCACCTTT
Statistics
Matches: 154, Mismatches: 32, Indels: 25
0.73 0.15 0.12
Matches are distributed among these distances:
38 26 0.17
39 3 0.02
40 33 0.21
41 4 0.03
42 2 0.01
43 50 0.32
45 6 0.04
46 29 0.19
47 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (41 bp):
CCAGCCTCCTCATCACGTAGGAACCGTGTCAACCATAGATA
Found at i:590131 original size:3 final size:3
Alignment explanation
Indices: 590123--590164 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
590113 AATTTTAATT
*
590123 TTA TTA TTA TTA TTA TTG TTA TTTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
590165 ATTACATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:590150 original size:16 final size:16
Alignment explanation
Indices: 590123--590160 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
590113 AATTTTAATT
590123 TTATTA-TTATTATTA
1 TTATTATTTATTATTA
*
590138 TTGTTATTTATTATTA
1 TTATTATTTATTATTA
590154 TTATTAT
1 TTATTAT
590161 ATTAATTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTATTATTTATTATTA
Found at i:590174 original size:22 final size:22
Alignment explanation
Indices: 590127--590175 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
590117 TTAATTTTAT
* * *
590127 TATTATTATTATTGTTATTTAT
1 TATTATTATTATTATTAATTAA
590149 TATTATTATTA-TATTAATTACA
1 TATTATTATTATTATTAATTA-A
590171 TATTA
1 TATTA
590176 CAATATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
TATTATTATTATTATTAATTAA
Found at i:594043 original size:32 final size:31
Alignment explanation
Indices: 594002--594077 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 31
593992 TTTAAATAGT
* *
594002 TATTATTTTTTATATTAATATATTTATGTAAA
1 TATTATTTTTTATATTAAAATA-ATATGTAAA
* * *
594034 TATTATTTTTTTTATTAAAATAATATTTATA
1 TATTATTTTTTATATTAAAATAATATGTAAA
594065 TATTATTTATTTA
1 TATTATTT-TTTA
594078 GAATTATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
31 14 0.38
32 23 0.62
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (31 bp):
TATTATTTTTTATATTAAAATAATATGTAAA
Found at i:594045 original size:34 final size:33
Alignment explanation
Indices: 593969--594048 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 33
593959 GTGGTAAGAA
* * *
593969 ATTTATTTTTATGTTAGTATTTTTTTAAATAGTT
1 ATTT-TTTTTATATTAATATTTTTGTAAATAGTT
594003 ATTATTTTTTATATTAATATATTTATGTAAATA-TT
1 ATT-TTTTTTATATTAATAT-TTT-TGTAAATAGTT
594038 ATTTTTTTTAT
1 ATTTTTTTTAT
594049 TAAAATAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 24 0.60
35 9 0.22
36 7 0.17
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (33 bp):
ATTTTTTTTATATTAATATTTTTGTAAATAGTT
Found at i:595841 original size:20 final size:21
Alignment explanation
Indices: 595797--595843 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
595787 GCAGGGGTAC
* *
595797 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
*
595818 ATGCCAAGCCCACCAGTT-AT
1 ATGCCAAGCCCACCACTTCAT
595838 ATGCCA
1 ATGCCA
595844 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.26, C:0.40, G:0.13, T:0.21
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:595871 original size:21 final size:21
Alignment explanation
Indices: 595847--595940 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
595837 TATGCCATCT
* *
595847 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
595868 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
595889 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
595910 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
*
595931 CCGTAGGGTT
1 CCGCAGGGTT
595941 TTATACCATA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 1 0.01
21 65 0.96
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:596513 original size:34 final size:34
Alignment explanation
Indices: 596463--596559 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
596453 AAATGTTTTT
*
596463 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
596497 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
596530 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
596560 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:596566 original size:34 final size:33
Alignment explanation
Indices: 596461--596566 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
596451 ATAAATGTTT
*
596461 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
596495 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
596527 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
596562 TTAAA
1 TTAAA
596567 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:597172 original size:126 final size:126
Alignment explanation
Indices: 596947--597550 Score: 1183
Period size: 126 Copynumber: 4.8 Consensus size: 126
596937 TTTAAGTTAT
596947 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
597012 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
597073 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
597138 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
597199 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
597264 GCG-CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
597324 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
597389 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
597450 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
597515 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
597551 CCGATTATAG
Statistics
Matches: 474, Mismatches: 3, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
125 125 0.26
126 349 0.74
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (126 bp):
TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:597391 original size:251 final size:252
Alignment explanation
Indices: 596947--597550 Score: 1183
Period size: 251 Copynumber: 2.4 Consensus size: 252
596937 TTTAAGTTAT
596947 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
597012 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
597077 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
131 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
597142 CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
196 CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
597199 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
597264 GCG-CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
*
597328 CGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
131 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
597393 CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
196 CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
597450 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
597515 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
597551 CCGATTATAG
Statistics
Matches: 349, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
251 249 0.71
252 100 0.29
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (252 bp):
TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:597631 original size:8 final size:8
Alignment explanation
Indices: 597618--597666 Score: 73
Period size: 8 Copynumber: 6.2 Consensus size: 8
597608 TCACAATCTT
597618 TCAAATTC
1 TCAAATTC
597626 TCAAATTC
1 TCAAATTC
* *
597634 CCAAACTC
1 TCAAATTC
597642 T-AAATTC
1 TCAAATTC
597649 TCAAATTC
1 TCAAATTC
597657 TCAAATTC
1 TCAAATTC
597665 TC
1 TC
597667 TGAAAATGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
7 6 0.17
8 30 0.83
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.35
Consensus pattern (8 bp):
TCAAATTC
Found at i:597648 original size:15 final size:16
Alignment explanation
Indices: 597619--597664 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
597609 CACAATCTTT
*
597619 CAAATTCTCAAATTCC
1 CAAACTCTCAAATTCC
*
597635 CAAACTCT-AAATTCT
1 CAAACTCTCAAATTCC
*
597650 CAAATTCTCAAATTC
1 CAAACTCTCAAATTC
597665 TCTGAAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (16 bp):
CAAACTCTCAAATTCC
Found at i:600680 original size:13 final size:12
Alignment explanation
Indices: 600662--600701 Score: 62
Period size: 13 Copynumber: 3.2 Consensus size: 12
600652 TACATAAATA
600662 TATTTAATATATT
1 TATTTAATATA-T
600675 TATTTAATATAT
1 TATTTAATATAT
600687 TATTTAATATTAT
1 TATTTAATA-TAT
600700 TA
1 TA
600702 GTTATAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTAATATAT
Found at i:612331 original size:22 final size:24
Alignment explanation
Indices: 612305--612356 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
612295 TTGGTCTTTG
612305 TGTTGTTTTGTCTCCTT-GG-TTT
1 TGTTGTTTTGTCTCCTTAGGATTT
* *
612327 TGTTGTTTTGTTTCTTTAGGATTT
1 TGTTGTTTTGTCTCCTTAGGATTT
612351 TGTTGT
1 TGTTGT
612357 ACTTGATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 15 0.58
23 2 0.08
24 9 0.35
ACGTcount: A:0.04, C:0.08, G:0.23, T:0.65
Consensus pattern (24 bp):
TGTTGTTTTGTCTCCTTAGGATTT
Found at i:614175 original size:23 final size:23
Alignment explanation
Indices: 614144--614212 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
614134 CACCACAACT
* * *
614144 CGTATAATTGTACTGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
614167 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
614190 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
614213 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:614401 original size:103 final size:103
Alignment explanation
Indices: 614228--614543 Score: 578
Period size: 103 Copynumber: 3.1 Consensus size: 103
614218 TAATGTCCAT
* * * *
614228 AAGGACTACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
614293 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
614331 AAGGACCACATATCATTCTTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
614396 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
614434 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
614499 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
614537 AAGGACC
1 AAGGACC
614544 GCGTAGACCC
Statistics
Matches: 205, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 205 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:620594 original size:20 final size:20
Alignment explanation
Indices: 620571--620762 Score: 59
Period size: 20 Copynumber: 9.5 Consensus size: 20
620561 TAAAATTTGT
620571 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTCGAAAATCGA
** *
620591 GTTGCGAAAAC-AAAATTCGT
1 GTTGCGAATTCGAAAA-TCGA
** * **
620611 GTTGCGGTTTAGAAAATCTT
1 GTTGCGAATTCGAAAATCGA
*** * * *
620631 GTTGCGAAAAGGAAACTTGT
1 GTTGCGAATTCGAAAATCGA
*** * *
620651 GTTGCGAAAAAGAAATTCGC
1 GTTGCGAATTCGAAAATCGA
*
620671 GTTGAGAATTC-AGAAATCGA
1 GTTGCGAATTCGA-AAATCGA
* * *
620691 GTTGCGAATTTGAAATTCTA
1 GTTGCGAATTCGAAAATCGA
* * *
620711 TATTGCGAATTTGGAAAATCGC
1 -GTTGCGAA-TTCGAAAATCGA
*
620733 GTTGCG-ATT-GCAGAAATTGA
1 GTTGCGAATTCG-A-AAATCGA
620753 GTTGCGAATT
1 GTTGCGAATT
620763 TGGAAACTGT
Statistics
Matches: 124, Mismatches: 39, Indels: 17
0.69 0.22 0.09
Matches are distributed among these distances:
18 1 0.01
19 8 0.06
20 87 0.70
21 20 0.16
22 8 0.06
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (20 bp):
GTTGCGAATTCGAAAATCGA
Found at i:620599 original size:40 final size:40
Alignment explanation
Indices: 620551--620658 Score: 117
Period size: 40 Copynumber: 2.7 Consensus size: 40
620541 AATAAAAGCT
** *
620551 GTTGCGAAATTAAAATTTGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAAACAAAATTTGTGTTGCGAATTAGAAAATCGA
* ** **
620591 GTTGCGAAAACAAAATTCGTGTTGCGGTTTAGAAAATCTT
1 GTTGCGAAAACAAAATTTGTGTTGCGAATTAGAAAATCGA
** *
620631 GTTGCGAAAAGGAAACTTGTGTTGCGAA
1 GTTGCGAAAACAAAATTTGTGTTGCGAA
620659 AAAGAAATTC
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (40 bp):
GTTGCGAAAACAAAATTTGTGTTGCGAATTAGAAAATCGA
Found at i:620768 original size:20 final size:20
Alignment explanation
Indices: 620683--620786 Score: 70
Period size: 20 Copynumber: 5.1 Consensus size: 20
620673 TGAGAATTCA
*
620683 GAAATCGAGTTGCGAATTT-
1 GAAATTGAGTTGCGAATTTG
* *
620702 GAAATTCTATATTGCGAATTTG
1 GAAATT-GA-GTTGCGAATTTG
* *
620724 GAAAATCGCGTTGCG-A-TTG
1 G-AAATTGAGTTGCGAATTTG
620743 CAGAAATTGAGTTGCGAATTTG
1 --GAAATTGAGTTGCGAATTTG
* * *
620765 GAAACTGTGTTGCGAAATTG
1 GAAATTGAGTTGCGAATTTG
620785 GA
1 GA
620787 GTTCGCGTTA
Statistics
Matches: 65, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
19 8 0.12
20 32 0.49
21 17 0.26
22 4 0.06
23 4 0.06
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.32
Consensus pattern (20 bp):
GAAATTGAGTTGCGAATTTG
Found at i:630398 original size:60 final size:60
Alignment explanation
Indices: 630330--630510 Score: 267
Period size: 60 Copynumber: 3.0 Consensus size: 60
630320 TTTGGATGAA
* * *
630330 TTTGGGGATGAAATTGGAA-GAATCAAAAGTTTG-GGGACAAATTTAGAATGAGAGTCATAG
1 TTTGGGGATGAAATTGGAATG-TTCAAAAG-TTGAAGGACCAATTTAGAATGAGAGTCATAG
* *
630390 TTTGGGGATGAAATTGGAATGTTCAAAAGTTGAAGGACCAATTTAAAATGAGAGTCACAG
1 TTTGGGGATGAAATTGGAATGTTCAAAAGTTGAAGGACCAATTTAGAATGAGAGTCATAG
* *
630450 TTTGGGGATGAAATTGGAATGTTCAAAAATTGAAGGACCAATTTAGAATGAGATTCATAG
1 TTTGGGGATGAAATTGGAATGTTCAAAAGTTGAAGGACCAATTTAGAATGAGAGTCATAG
630510 T
1 T
630511 ATTTAGATAA
Statistics
Matches: 110, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
59 3 0.03
60 106 0.96
61 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.28
Consensus pattern (60 bp):
TTTGGGGATGAAATTGGAATGTTCAAAAGTTGAAGGACCAATTTAGAATGAGAGTCATAG
Found at i:630410 original size:31 final size:30
Alignment explanation
Indices: 630330--630420 Score: 91
Period size: 31 Copynumber: 3.1 Consensus size: 30
630320 TTTGGATGAA
630330 TTTGGGGATGAAATTGGAA-GAATCAAAAG
1 TTTGGGGATGAAATTGGAATGAATCAAAAG
* * *
630359 TTTGGGGA-CAAATTTAGAATGAGAGTC-ATAG
1 TTTGGGGATGAAA-TTGGAATGA-A-TCAAAAG
*
630390 TTTGGGGATGAAATTGGAATG-TTCAAAAG
1 TTTGGGGATGAAATTGGAATGAATCAAAAG
630419 TT
1 TT
630421 GAAGGACCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
28 5 0.10
29 18 0.37
30 2 0.04
31 19 0.39
32 5 0.10
ACGTcount: A:0.36, C:0.04, G:0.30, T:0.30
Consensus pattern (30 bp):
TTTGGGGATGAAATTGGAATGAATCAAAAG
Found at i:632796 original size:18 final size:17
Alignment explanation
Indices: 632773--632808 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
632763 GTAATTATAG
632773 TGATTGAATATTACTTAA
1 TGATTGAAT-TTACTTAA
*
632791 TGATTGAATTTATTTAA
1 TGATTGAATTTACTTAA
632808 T
1 T
632809 AAGTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.36, C:0.03, G:0.11, T:0.50
Consensus pattern (17 bp):
TGATTGAATTTACTTAA
Found at i:636515 original size:31 final size:30
Alignment explanation
Indices: 636472--636587 Score: 123
Period size: 31 Copynumber: 3.8 Consensus size: 30
636462 AATAAAATTT
636472 ATTTCTTAAATTAAAATAAGAATAAAATATAC
1 ATTT-TTAAATTAAAATAAGAATAAAA-ATAC
636504 ATTTTTAAATTAAAATTAA-AATAATAAAT--
1 ATTTTTAAATTAAAA-TAAGAATAA-AAATAC
* *
636533 ATATTTAAATTAAGATAAGAAT-AAAATAC
1 ATTTTTAAATTAAAATAAGAATAAAAATAC
* *
636562 ATATTTTAAGTTAAAATAAAAATAAA
1 AT-TTTTAAATTAAAATAAGAATAAA
636588 TATTAATAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
27 4 0.06
28 4 0.06
29 18 0.25
30 16 0.23
31 20 0.28
32 9 0.13
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (30 bp):
ATTTTTAAATTAAAATAAGAATAAAAATAC
Found at i:636583 original size:25 final size:25
Alignment explanation
Indices: 636542--636591 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
636532 TATATTTAAA
*
636542 TTAAGATAAGAATAAAATACATATT
1 TTAAGATAAGAATAAAATAAATATT
*
636567 TTAAGTTAA-AATAAAAATAAATATT
1 TTAAGATAAGAAT-AAAATAAATATT
636592 AATAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (25 bp):
TTAAGATAAGAATAAAATAAATATT
Found at i:636602 original size:31 final size:30
Alignment explanation
Indices: 636411--636601 Score: 137
Period size: 30 Copynumber: 6.4 Consensus size: 30
636401 TTTTTTCTTA
* *
636411 TAATATTTTAAAATTAAGATGAAAAT-AAA-
1 TAATATTTT-AAATTAAAATAAAAATAAAAT
* * *
636440 T-ATTTTTTATAGTTAAGATAAAAATAAAAT
1 TAATATTTTA-AATTAAAATAAAAATAAAAT
* *
636470 TTAT-TTCTTAAATTAAAATAAGAATAAAAT
1 TAATATT-TTAAATTAAAATAAAAATAAAAT
*
636500 ATACAT-TTTTAAATTAAAATTAAAAT--AAT
1 -TA-ATATTTTAAATTAAAATAAAAATAAAAT
* * *
636529 AAATATATTTAAATTAAGATAAGAATAAAA-
1 TAATAT-TTTAAATTAAAATAAAAATAAAAT
*
636559 TACATATTTTAAGTTAAAATAAAAATAAATAT
1 TA-ATATTTTAAATTAAAATAAAAATAAA-AT
*
636591 TAATAATTTAA
1 TAATATTTTAA
636602 GGTAGGAATA
Statistics
Matches: 130, Mismatches: 18, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
27 3 0.02
28 21 0.16
29 23 0.18
30 40 0.31
31 37 0.28
32 6 0.05
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (30 bp):
TAATATTTTAAATTAAAATAAAAATAAAAT
Found at i:636686 original size:28 final size:30
Alignment explanation
Indices: 636412--636819 Score: 110
Period size: 30 Copynumber: 13.6 Consensus size: 30
636402 TTTTTCTTAT
636412 AATAT-TTTAA-AA-TTAAGATGAA-AAT-A
1 AATATATTTAATAAGTTAAGAT-AAGAATAA
* * *
636438 AATATTTTTTAT-AGTTAAGATAAAAATAA
1 AATATATTTAATAAGTTAAGATAAGAATAA
* ** * *
636467 AATTTATTTCTTAAATTAAAATAAGAATAA
1 AATATATTTAATAAGTTAAGATAAGAATAA
* * *
636497 AATATACATTT-TTAAATTAAAATTAA-AATAATA
1 AATAT--ATTTAATAAGTTAAGA-TAAGAAT-A-A
636530 AATATATTT-A-AA-TTAAGATAAGAATAA
1 AATATATTTAATAAGTTAAGATAAGAATAA
* *
636557 AATACATATTT--TAAGTTAAAATAA-AA-AT
1 AAT--ATATTTAATAAGTTAAGATAAGAATAA
* * *
636585 AA-ATA-TTAATAATTTAAGGTAGGAATATAA
1 AATATATTTAATAAGTTAAGATAAG-A-ATAA
* * *
636615 TATATATATATTAAT-ATTTAATAATTTAAGTTAAGAA
1 -A-ATATAT-TTAATAAGTTAA-GA--TAAG--AATAA
*
636652 TATAATATATGTAATAAGTTAAGATAA-AA-AA
1 AAT-ATAT-T-TAATAAGTTAAGATAAGAATAA
*
636683 AATATTTTTAA-AAGTTAAAGATAAGAATAA
1 AATATATTTAATAAGTT-AAGATAAGAATAA
* * * * *
636713 GATATATCTT-TTAAGTTACGGTAGGAATAA
1 AATATAT-TTAATAAGTTAAGATAAGAATAA
* * * * *
636743 AATATAAATT-CTGAGTTAAGATAATATTAA
1 AATAT-ATTTAATAAGTTAAGATAAGAATAA
* * *
636773 AATA-ATTT-TTTAGTTAACATAAGAATAA
1 AATATATTTAATAAGTTAAGATAAGAATAA
*
636801 AACATATTTAATAAGTTAA
1 AATATATTTAATAAGTTAA
636820 AAATAAAATA
Statistics
Matches: 288, Mismatches: 52, Indels: 80
0.69 0.12 0.19
Matches are distributed among these distances:
24 2 0.01
25 3 0.01
26 14 0.05
27 16 0.06
28 49 0.17
29 35 0.12
30 79 0.27
31 31 0.11
32 11 0.04
33 9 0.03
34 6 0.02
35 10 0.03
36 6 0.02
37 11 0.04
38 6 0.02
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (30 bp):
AATATATTTAATAAGTTAAGATAAGAATAA
Found at i:636868 original size:18 final size:18
Alignment explanation
Indices: 636842--636884 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
636832 TTGTTTAATG
636842 TTAAGATGTGAATTTAAC
1 TTAAGATGTGAATTTAAC
* *
636860 TTAATATGTGAATTTAAG
1 TTAAGATGTGAATTTAAC
636878 TTAAGAT
1 TTAAGAT
636885 ATAATATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (18 bp):
TTAAGATGTGAATTTAAC
Found at i:637199 original size:23 final size:23
Alignment explanation
Indices: 637173--637220 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
637163 ATAAAGTACA
*
637173 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
637196 ATAATGTAATAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
637219 AT
1 AT
637221 TTACCTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:637464 original size:30 final size:29
Alignment explanation
Indices: 637424--637490 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
637414 TCATTTGCAC
* * *
637424 AAAAAATTATTT-GATTTTTTGATATTTTAT
1 AAAATATTATTTAGAATTTTT-A-ATTTAAT
637454 AAAATATTATTTAGAATTTTTAATTTAAT
1 AAAATATTATTTAGAATTTTTAATTTAAT
637483 AATAATAT
1 AA-AATAT
637491 ATATCGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (29 bp):
AAAATATTATTTAGAATTTTTAATTTAAT
Found at i:637675 original size:23 final size:23
Alignment explanation
Indices: 637645--637707 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
637635 AATATACCAC
637645 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
637668 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
637691 TACCTATTACATCATAT
1 TACCTATTACATTATAT
637708 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:638099 original size:23 final size:23
Alignment explanation
Indices: 638073--638135 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
638063 ATATAACCAC
638073 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
638096 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
638119 TACCTATTACATCATAT
1 TACCTATTACATTATAT
638136 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:638146 original size:428 final size:432
Alignment explanation
Indices: 637287--638345 Score: 1978
Period size: 427 Copynumber: 2.5 Consensus size: 432
637277 TATTACAATA
637287 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
637352 TTATGTTTCAATTTTTTGAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
637417 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT--
131 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
*
637480 -AATAAT-AATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAA
196 CAATATTAAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAA
637543 ATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGTATGGACA
261 ATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGTATGGACA
637608 CTTTTATAAAAAGGATAGACACTTTACAATATACCACTACCTATTACATTATATAAACGATACCT
326 CTTTTATAAAAAGGATAGACACTTTACAATATACCACTACCTATTACATTATATAAACGATACCT
637673 ATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 ATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
637715 TATTATATTGAAAGTGTCCATACTTTTTAT-AAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
637779 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTAC-A-A-T-A-TTAATAATTTC
66 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
637839 ATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
130 ATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
637904 ACAATATTAAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAA
195 ACAATATTAAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAA
*
637969 AATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGAC
260 AATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGTATGGAC
638034 ACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATAC
325 ACTTTTATAAAAAGGATAGACACTTTACAATAT-ACCACTACCTATTACATTATATAAACGATAC
638099 CTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
389 CTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
*
638143 TATTATATTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
638208 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
638273 TTTGCACAAAAAATTATTTGA-TTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
131 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
*
638337 CAACATTAA
196 CAATATTAA
638346 CCAAAGAATA
Statistics
Matches: 614, Mismatches: 5, Indels: 20
0.96 0.01 0.03
Matches are distributed among these distances:
423 75 0.12
424 1 0.00
425 1 0.00
426 6 0.01
427 199 0.32
428 199 0.32
429 46 0.07
430 1 0.00
431 1 0.00
432 52 0.08
433 33 0.05
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (432 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
CAATATTAAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAA
ATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGTATGGACA
CTTTTATAAAAAGGATAGACACTTTACAATATACCACTACCTATTACATTATATAAACGATACCT
ATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
Found at i:638431 original size:427 final size:424
Alignment explanation
Indices: 637287--638362 Score: 1855
Period size: 428 Copynumber: 2.5 Consensus size: 424
637277 TATTACAATA
637287 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
637352 TTATGTTTCAATTTTTTGAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
637417 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
131 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
* *
637482 TAATAATATATATCGTAACG--TAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAAT
196 CAA-AAT-TA-A-C-TAAAGAATAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAAT
637545 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGTATGGACACT
256 CTTAAAAC-CACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGTATGGACACT
637610 TTTATAAAAAGGATAGACACTTTACAATATACCACTACCTATTACATTATATAAACGATACCTAT
320 TTTATAAAAAGGATAGACACTTTACAATATACCACTACCTATTACATTATATAAACGATACCTAT
637675 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
385 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
637715 TATTATATTGAAAGTGTCCATACTTTTTAT-AAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
637779 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTAC-A-A-T-A-TTAATAATTTC
66 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
637839 ATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
130 ATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
* *
637904 ACAATATTAAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAA
195 ACAAAATTAACTA-A-A--G-AA--TAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAA
*
637969 AATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGAC
253 AATCTTAAAAC-CACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGTATGGAC
638034 ACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATAC
317 ACTTTTATAAAAAGGATAGACACTTTACAATAT-ACCACTACCTATTACATTATATAAACGATAC
638099 CTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
381 CTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
*
638143 TATTATATTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
638208 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
638273 TTTGCACAAAAAATTATTTGA-TTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
131 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
* * *
638337 CAACATTAACCAAAGAATAATAAATA
196 CAAAATTAACTAAAGAATAAAAAATA
638363 TGTAATATAT
Statistics
Matches: 620, Mismatches: 11, Indels: 37
0.93 0.02 0.06
Matches are distributed among these distances:
418 2 0.00
419 1 0.00
420 1 0.00
421 2 0.00
422 3 0.00
423 79 0.13
424 1 0.00
425 9 0.01
426 1 0.00
427 185 0.30
428 200 0.32
429 46 0.07
430 2 0.00
431 2 0.00
432 53 0.09
433 33 0.05
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (424 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
CAAAATTAACTAAAGAATAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTAA
AACCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGTATGGACACTTTTATA
AAAAGGATAGACACTTTACAATATACCACTACCTATTACATTATATAAACGATACCTATTACATT
ATATAAGCGCTACCTATTACATCATATTTTTACC
Found at i:638602 original size:39 final size:39
Alignment explanation
Indices: 638548--638633 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
638538 CAAGTTGTAG
*
638548 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
638587 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
638626 ATTTTGAT
1 ATTTTGAT
638634 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:638913 original size:18 final size:18
Alignment explanation
Indices: 638890--638926 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
638880 CGAAATATAT
638890 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
638908 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
638926 A
1 A
638927 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:639381 original size:23 final size:23
Alignment explanation
Indices: 639355--639408 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
639345 CTTTACAATT
* *
639355 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAACGATACCTATTAC
639378 ATTATATAAACGATACCTATTAC
1 ATTATATAAACGATACCTATTAC
639401 ATTATATA
1 ATTATATA
639409 CTTGTAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.37
Consensus pattern (23 bp):
ATTATATAAACGATACCTATTAC
Found at i:642410 original size:183 final size:183
Alignment explanation
Indices: 641885--642508 Score: 1101
Period size: 183 Copynumber: 3.4 Consensus size: 183
641875 CGACACATTT
*
641885 TAGGTTGTAGACATATTCGCGCATAAAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
1 TAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
641950 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
66 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
642015 TTTTCTTCCAATATGGACATAAAGTACCGACACAATA-TAAAAAGTGTCG-TA
131 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
* *
642066 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATA-TTATACCTGTTATATTACAAAATTATCT
1 TAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
642130 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
66 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
642195 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
131 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
* *
642248 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
1 TAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
642313 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
66 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
** *
642378 TTTAATTCCAATATTGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
131 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
* * * *
642431 TAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTGCAAATTTACCT
1 TAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
**
642496 ATTTTATTATAAT
66 ATTACATTATAAT
642509 ATGTTGAAAG
Statistics
Matches: 426, Mismatches: 14, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
180 130 0.31
181 45 0.11
182 38 0.09
183 213 0.50
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (183 bp):
TAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
Found at i:642578 original size:11 final size:11
Alignment explanation
Indices: 642562--642600 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
642552 TTTTTAAAGA
642562 TATGTTTTAAG
1 TATGTTTTAAG
*
642573 TATGTTTCAA-
1 TATGTTTTAAG
*
642583 TATTTTTTAAG
1 TATGTTTTAAG
642594 TATGTTT
1 TATGTTT
642601 CATGTTTTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.59
Consensus pattern (11 bp):
TATGTTTTAAG
Found at i:642608 original size:20 final size:21
Alignment explanation
Indices: 642561--642602 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
642551 TTTTTTAAAG
*
642561 ATATGTTTTAAGTATGTTTCA
1 ATATTTTTTAAGTATGTTTCA
642582 ATATTTTTTAAGTATGTTTCA
1 ATATTTTTTAAGTATGTTTCA
642603 TGTTTTCCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.55
Consensus pattern (21 bp):
ATATTTTTTAAGTATGTTTCA
Found at i:643977 original size:3 final size:3
Alignment explanation
Indices: 643969--644043 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
643959 ACTTGTTTGG
* * * ** * *
643969 ATC ATC ATC TTC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
644017 ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
644044 GTCAGCTTCA
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.23, C:0.35, G:0.07, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:643986 original size:12 final size:12
Alignment explanation
Indices: 643973--644055 Score: 94
Period size: 12 Copynumber: 6.9 Consensus size: 12
643963 GTTTGGATCA
*
643973 TCATCTTCATCA
1 TCATCTTCATCG
* * *
643985 TCATCATCGTCA
1 TCATCTTCATCG
643997 TCATCTTCATCG
1 TCATCTTCATCG
* *
644009 CCAGCTTCATCG
1 TCATCTTCATCG
*
644021 TCATCATCATCG
1 TCATCTTCATCG
644033 TCATCTTCATCG
1 TCATCTTCATCG
*
644045 TCAGCTTCATC
1 TCATCTTCATC
644056 TTCTGCGACC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.20, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:644017 original size:36 final size:36
Alignment explanation
Indices: 643977--644055 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
643967 GGATCATCAT
*
643977 CTTCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
644013 CTTCATCGTCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAG
644049 CTTCATC
1 CTTCATC
644056 TTCTGCGACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.20, C:0.35, G:0.09, T:0.35
Consensus pattern (36 bp):
CTTCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:644056 original size:18 final size:18
Alignment explanation
Indices: 643997--644058 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
643987 ATCATCGTCA
*
643997 TCATCTTCATCGCCAGCT
1 TCATCTTCATCGTCAGCT
* * * *
644015 TCATCGTCATCATCATCG
1 TCATCTTCATCGTCAGCT
644033 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGTCAGCT
644051 TCATCTTC
1 TCATCTTC
644059 TGCGACCGCT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.18, C:0.35, G:0.10, T:0.37
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCT
Found at i:644058 original size:6 final size:6
Alignment explanation
Indices: 643973--644058 Score: 64
Period size: 6 Copynumber: 14.3 Consensus size: 6
643963 GTTTGGATCA
* * * * * * * *
643973 TCATCT TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
644021 TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
644059 TGCGACCGCT
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.20, C:0.35, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:645832 original size:194 final size:196
Alignment explanation
Indices: 645510--646559 Score: 1606
Period size: 194 Copynumber: 5.5 Consensus size: 196
645500 TTTAAATTAG
645510 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
645575 ATTGTACC-GTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
645639 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATAT-T-AAATT
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCAT-TCTGAAATA
*
645702 AG
195 AA
645704 TATCGACACAAAC-ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
645768 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATGTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
645833 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATAT-TTAAATT
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCAT-TCTGAAATA
*
645897 AG
195 AA
* * ** ** * ** *
645899 TATCGACAC--A-T-TA-T--T-T--AGACA-TATTCT-CACATAAAC-C-GGTATAA-TTGTAC
1 TATCGACACAAACTATATTAGTGTCGACACATTATT-TAGACATATTCTCACATAAAACCGGTAT
*** * *
645949 CGGT-TA--GATT-GA----AAAATTACATATTACATTATAATTTTGGGTTCGATGATTTTGGGA
65 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
646006 TCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCT-GAAAT
646071 AAA
194 AAA
646074 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACC-GTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
646138 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
646203 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
131 CGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCT-GAAAT
646268 AAA
194 AAA
646271 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
646336 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
646401 CGACAC-TTTT-TATATGGATCGACACTTTATGGTGCACCCTG-TTTCCATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCT-G-AAAT
646463 AAA
194 AAA
646466 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
646531 ATTGTACCGGTTAGATTGAAAAATTACAT
66 ATTGTACCGGTTAGATTGAAAAATTACAT
646560 CCTTTTGGCC
Statistics
Matches: 789, Mismatches: 35, Indels: 63
0.89 0.04 0.07
Matches are distributed among these distances:
173 1 0.00
174 100 0.13
175 14 0.02
177 1 0.00
178 3 0.00
179 5 0.01
180 1 0.00
181 2 0.00
182 5 0.01
183 5 0.01
184 1 0.00
185 15 0.02
186 15 0.02
187 1 0.00
188 9 0.01
189 3 0.00
191 4 0.01
192 4 0.01
193 60 0.08
194 142 0.18
195 127 0.16
196 97 0.12
197 98 0.12
198 76 0.10
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (196 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGAAATAA
A
Found at i:645963 original size:174 final size:187
Alignment explanation
Indices: 645750--646559 Score: 1134
Period size: 174 Copynumber: 4.3 Consensus size: 187
645740 AGACATATTC
645750 TCACATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG
1 TCACATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG
*
645815 GTTCGATGATGTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTT
66 GTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTT
* * * *
645880 CCATTCATAT-T-TAAATTAGTATCGACAC-A-T-TA-T-T-T-AGACA-TA-TT-C-
131 CCATTCAT-TCTGGAAATAAATATCGACACAACTATATTATGTCACACATTATTTACT
*
645925 TCACAT-AAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAATTTTGG
1 TCACATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG
645989 GTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTT
66 GTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTT
646054 CCATTCATTCTGGAAATAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATAT
131 CCATTCATTCTGGAAATAAATATCGACAC-AACTATATTA-TGTC-ACACATTATTT--AC----
646119 T
187 T
646120 CTCACATAAAACC-GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTG
1 -TCACATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTG
646184 GGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
65 GGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTT
646249 TTCCATTCATTCTGGAAATAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACAT
129 TTCCATTCATTCTGGAAATAAATATCGACAC-AACTATATTA-TGTC-ACACATTATTT--AC--
646314 ATT
187 --T
646317 CTCACATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTG
1 -TCACATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTG
646382 GGTTCGATGATTTTGGGATCGACAC-TTTT-TATATGGATCGACACTTTATGGTGCACCCTG-TT
65 GGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTT
*
646444 TCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACAT
130 TCCATTCATTCTGG-AAATAAATATCGACAC-AACTATATTA-TGTC-ACACATTATTT--AC--
646509 ATT
187 --T
646512 CTCACATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACAT
1 -TCACATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACAT
646560 CCTTTTGGCC
Statistics
Matches: 600, Mismatches: 8, Indels: 34
0.93 0.01 0.05
Matches are distributed among these distances:
173 1 0.00
174 130 0.22
175 20 0.03
177 1 0.00
178 1 0.00
179 2 0.00
180 1 0.00
182 1 0.00
183 1 0.00
185 4 0.01
186 2 0.00
187 2 0.00
190 1 0.00
194 16 0.03
195 111 0.19
196 127 0.21
197 103 0.17
198 76 0.13
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (187 bp):
TCACATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG
GTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTT
CCATTCATTCTGGAAATAAATATCGACACAACTATATTATGTCACACATTATTTACT
Found at i:646533 original size:195 final size:197
Alignment explanation
Indices: 645894--646559 Score: 1252
Period size: 196 Copynumber: 3.4 Consensus size: 197
645884 TCATATTTAA
*
645894 ATTAGTATCGACACATTATTTAGACATATTCTCACAT-AAACCGGTATAATTGTACCGGTTAGAT
1 ATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAGAT
*
645958 TGAAAAATTACATATTACATTATAATTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATA
66 TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATA
646023 TGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAAATATCGACACAAACT
131 TGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAAATATCGACACAAACT
646088 AT
196 AT
646090 ATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACC-GTATAATTGTACCGGTTAGAT
1 ATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAGAT
646154 TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATA
66 TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATA
646219 TGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAATAAATATCGACACAAAC
131 TGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGGAAATAAATATCGACACAAAC
646284 TAT
195 TAT
646287 ATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAGAT
1 ATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAGAT
646352 TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC-TTTT-TATA
66 TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATA
*
646415 TGGATCGACACTTTATGGTGCACCCTG-TTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
131 TGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGG-AAATAAATATCGACACAAAC
646479 TAT
195 TAT
646482 ATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAGAT
1 ATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAGAT
646547 TGAAAAATTACAT
66 TGAAAAATTACAT
646560 CCTTTTGGCC
Statistics
Matches: 463, Mismatches: 3, Indels: 9
0.97 0.01 0.02
Matches are distributed among these distances:
194 16 0.03
195 111 0.24
196 157 0.34
197 103 0.22
198 76 0.16
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Consensus pattern (197 bp):
ATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAGAT
TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATA
TGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAAATATCGACACAAACT
AT
Found at i:646714 original size:19 final size:19
Alignment explanation
Indices: 646683--646731 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
646673 TTATATTCAC
646683 ATACGAAAA-TATAAATCGT
1 ATAC-AAAATTATAAATCGT
*
646702 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
646721 ATACAAAATTA
1 ATACAAAATTA
646732 ACCCTACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:648553 original size:32 final size:32
Alignment explanation
Indices: 648511--648571 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
648501 TTAATATCAC
*
648511 CCCTTAACACCCCAACTTCTTTCACCACTTCA
1 CCCTCAACACCCCAACTTCTTTCACCACTTCA
* *
648543 CCCTCAACACCTCTACTTCTTTCACCACT
1 CCCTCAACACCCCAACTTCTTTCACCACT
648572 CCATCTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.30
Consensus pattern (32 bp):
CCCTCAACACCCCAACTTCTTTCACCACTTCA
Found at i:648645 original size:21 final size:21
Alignment explanation
Indices: 648605--648669 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
648595 CCCCTTATGC
* *
648605 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
648626 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
648647 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
648668 CT
1 CT
648670 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:650897 original size:17 final size:18
Alignment explanation
Indices: 650875--650917 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
650865 AATATATCCG
650875 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
650892 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
650912 TATCAT
1 TATCAT
650918 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:650935 original size:20 final size:19
Alignment explanation
Indices: 650880--650926 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
650870 ATCCGTATCA
650880 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
650899 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
650920 TTTTACC
1 TTTTACC
650927 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:661155 original size:9 final size:9
Alignment explanation
Indices: 661137--661178 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
661127 CATTTTAACC
661137 TTTAAATAT
1 TTTAAATAT
*
661146 TTTAATTAT
1 TTTAAATAT
*
661155 TTAAAATA-
1 TTTAAATAT
661163 TTTAAATAT
1 TTTAAATAT
*
661172 TTAAAAT
1 TTTAAAT
661179 TGTTTGTACA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TTTAAATAT
Found at i:661159 original size:17 final size:17
Alignment explanation
Indices: 661140--661178 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
661130 TTTAACCTTT
*
661140 AAATATTTTAATTATTTA
1 AAATA-TTTAAATATTTA
661158 AAATATTTAAATATTTA
1 AAATATTTAAATATTTA
661175 AAAT
1 AAAT
661179 TGTTTGTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATATTTAAATATTTA
Found at i:661169 original size:8 final size:8
Alignment explanation
Indices: 661137--661176 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
661127 CATTTTAACC
661137 TTTAAATA
1 TTTAAATA
*
661145 TTTTAATTA
1 -TTTAAATA
661154 TTTAAAATA
1 TTT-AAATA
661163 TTTAAATA
1 TTTAAATA
661171 TTTAAA
1 TTTAAA
661177 ATTGTTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 14 0.50
9 14 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTAAATA
Found at i:661843 original size:24 final size:20
Alignment explanation
Indices: 661790--661847 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
661780 TTTCCCTTGA
*
661790 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
661810 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
661833 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
661848 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Done.