Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 110 of 216
Found at i:34974752 original size:44 final size:44
Alignment explanation
Indices: 34974704--34974804 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 44
34974694 GAGAGAGGAT
* ** *
34974704 TTGTTTATTTAATCTGCCCCACTGCAATTTCAGGGGGATAAGAC
1 TTGTTTATTCAATCTGCCCCACTGCAACCTCAGGGAGATAAGAC
** *
34974748 TTGTTTATTCGGTCTGCTCCACTGCAACCTCAGGGAGATAAGAC
1 TTGTTTATTCAATCTGCCCCACTGCAACCTCAGGGAGATAAGAC
*
34974792 TTGATTTTTTCAA
1 TTG-TTTATTCAA
34974805 CCTTTTTAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
44 40 0.87
45 6 0.13
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (44 bp):
TTGTTTATTCAATCTGCCCCACTGCAACCTCAGGGAGATAAGAC
Found at i:34975093 original size:94 final size:94
Alignment explanation
Indices: 34974948--34975171 Score: 272
Period size: 94 Copynumber: 2.4 Consensus size: 94
34974938 CTAAGGAGAT
* * * *
34974948 AAGATTCGTCGTCGT-GACTTCAATCTGCTCCGCTACAACGCTAGGGAAATAAGATTCGCCATTG
1 AAGATTCGTCGTCGTAG-CTTCAATCTGCTCCACTACAACACCAGGGAAATAAGATTCACCATTG
* * *
34975012 TGGCTTCAATCTTTGCAATGTTGGGGAAAT
65 CGGCTTCAATCTTCGCAATGTTGGGGAAAC
* * * *
34975042 GAGATTCGTCGTCGTAGCTTTAATCTGCTCCACTACATCACCAGAGG-AATAAGATTCACCGTTG
1 AAGATTCGTCGTCGTAGCTTCAATCTGCTCCACTACAACACCAG-GGAAATAAGATTCACCATTG
*
34975106 CGGCTTCAATCTTCGCAATGTTGGGGTAAC
65 CGGCTTCAATCTTCGCAATGTTGGGGAAAC
** **
34975136 AAGATTCACCGTCGTAGCTTCAATCTTTTCCACTAC
1 AAGATTCGTCGTCGTAGCTTCAATCTGCTCCACTAC
34975172 CCCGCCAGGG
Statistics
Matches: 110, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
94 107 0.97
95 3 0.03
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (94 bp):
AAGATTCGTCGTCGTAGCTTCAATCTGCTCCACTACAACACCAGGGAAATAAGATTCACCATTGC
GGCTTCAATCTTCGCAATGTTGGGGAAAC
Found at i:34975189 original size:94 final size:94
Alignment explanation
Indices: 34974948--34975211 Score: 271
Period size: 94 Copynumber: 2.8 Consensus size: 94
34974938 CTAAGGAGAT
** * * * * *
34974948 AAGATTCGTCGTCGT-GACTTCAATCTGCTCCGCTACAACGCTAG-GGAAATAAGATTCGCCATT
1 AAGATTCACCGTCGTAG-CTTCAATCTGCTCCACTACACCACCAGAGG-AATAAGATTCGCCGTT
* * *
34975011 GTGGCTTCAATCTTTGCAATGTTGGGGAAAT
64 GCGGCTTCAATCTTCGCAATGTTGGGGAAAC
* ** * * *
34975042 GAGATTCGTCGTCGTAGCTTTAATCTGCTCCACTACATCACCAGAGGAATAAGATTCACCGTTGC
1 AAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACACCACCAGAGGAATAAGATTCGCCGTTGC
*
34975107 GGCTTCAATCTTCGCAATGTTGGGGTAAC
66 GGCTTCAATCTTCGCAATGTTGGGGAAAC
** * * * * *
34975136 AAGATTCACCGTCGTAGCTTCAATCTTTTCCACTACCCCGCCAGGGGAGTAAGATTCGTCGTTGC
1 AAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACACCACCAGAGGAATAAGATTCGCCGTTGC
*
34975201 AGCTTCAATCT
66 GGCTTCAATCT
34975212 GCTCCACTGC
Statistics
Matches: 142, Mismatches: 26, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
94 139 0.98
95 3 0.02
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (94 bp):
AAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACACCACCAGAGGAATAAGATTCGCCGTTGC
GGCTTCAATCTTCGCAATGTTGGGGAAAC
Found at i:34975405 original size:50 final size:50
Alignment explanation
Indices: 34975297--34975408 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 50
34975287 TTAACGCTAG
* *
34975297 GGAGATAAGATTCGCCGTCGTGGCTTCAATCTGCTCCGCTACAACGCCAA
1 GGAGATAAGACTCGCCGTCGTGGCTTCAATCTGCTCCACTACAACGCCAA
* * * ** * * *
34975347 GGAAATAAGACTCGCCGTTGTGGCTTTAATCTTTTCCATTGCAACGTCAA
1 GGAGATAAGACTCGCCGTCGTGGCTTCAATCTGCTCCACTACAACGCCAA
*
34975397 GGTGATAAGACT
1 GGAGATAAGACT
34975409 AATGTCTTCG
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (50 bp):
GGAGATAAGACTCGCCGTCGTGGCTTCAATCTGCTCCACTACAACGCCAA
Found at i:34975539 original size:87 final size:88
Alignment explanation
Indices: 34975413--34975581 Score: 232
Period size: 87 Copynumber: 1.9 Consensus size: 88
34975403 AAGACTAATG
* * * * *
34975413 TCTTCGATCTGCTTCACTGCCAGCACAGGAAGGCGAGATCTGCTA-CTTCAACGTACTCCAGTGC
1 TCTTCGATCTACTTCACTGCCAACACAGGAAGACGAGATCTGCTATCTTCAACCTACTCCACTGC
34975477 TACTCAAGGAGACAAGGCTGGTA
66 TACTCAAGGAGACAAGGCTGGTA
* * *
34975500 TCTTCGATCTACTTCACTGCCAATACAGGAAGACGAGATCTGCTATTTTTAACCTACTCCACTGC
1 TCTTCGATCTACTTCACTGCCAACACAGGAAGACGAGATCTGCTATCTTCAACCTACTCCACTGC
* * *
34975565 TGCTCAGGGAGATAAGG
66 TACTCAAGGAGACAAGG
34975582 TTAAAGTTTC
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
87 41 0.59
88 29 0.41
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (88 bp):
TCTTCGATCTACTTCACTGCCAACACAGGAAGACGAGATCTGCTATCTTCAACCTACTCCACTGC
TACTCAAGGAGACAAGGCTGGTA
Found at i:34979215 original size:21 final size:21
Alignment explanation
Indices: 34979182--34979234 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
34979172 TACCAATTTG
* *
34979182 TACCAAATACCATATCATTTCA
1 TACC-AATTCCATACCATTTCA
*
34979204 TACCAATTCCATACCATTTCG
1 TACCAATTCCATACCATTTCA
34979225 TACCAATTCC
1 TACCAATTCC
34979235 CAAATACCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.34, C:0.32, G:0.02, T:0.32
Consensus pattern (21 bp):
TACCAATTCCATACCATTTCA
Found at i:34980197 original size:15 final size:15
Alignment explanation
Indices: 34980165--34980198 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
34980155 GTTCAACGAA
*
34980165 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
34980180 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
34980195 GAGG
1 GAGG
34980199 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:34983928 original size:21 final size:21
Alignment explanation
Indices: 34983895--34983947 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
34983885 TACCAATTTG
*
34983895 TACCAAATACCATACCATTTCA
1 TACC-AATTCCATACCATTTCA
*
34983917 TACCAATTCCATACCATTTCG
1 TACCAATTCCATACCATTTCA
34983938 TACCAATTCC
1 TACCAATTCC
34983948 CAAATACCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.34, C:0.34, G:0.02, T:0.30
Consensus pattern (21 bp):
TACCAATTCCATACCATTTCA
Found at i:34992524 original size:20 final size:21
Alignment explanation
Indices: 34992499--34992538 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
34992489 AAAAGTCAGT
34992499 ATCAAAAAACA-TAAAATATA
1 ATCAAAAAACAGTAAAATATA
*
34992519 ATCAAAAAATAGTAAAATAT
1 ATCAAAAAACAGTAAAATAT
34992539 CTAATCGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.68, C:0.07, G:0.03, T:0.23
Consensus pattern (21 bp):
ATCAAAAAACAGTAAAATATA
Found at i:34995013 original size:12 final size:12
Alignment explanation
Indices: 34994996--34995020 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34994986 GTTTTATTTT
34994996 AGTAAATAAATA
1 AGTAAATAAATA
34995008 AGTAAATAAATA
1 AGTAAATAAATA
34995020 A
1 A
34995021 CATATAAAAA
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
AGTAAATAAATA
Found at i:34997238 original size:22 final size:21
Alignment explanation
Indices: 34997192--34997246 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
34997182 AAAATTTAGT
* *
34997192 ATTTAAAGTTTACTATTTAAG
1 ATTTAAAGTTTACCATTTAAA
*
34997213 ATTTAAAGTTTAGCCCTTTAAA
1 ATTTAAAGTTTA-CCATTTAAA
*
34997235 ATTTAAGGTTTA
1 ATTTAAAGTTTA
34997247 AATTTTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (21 bp):
ATTTAAAGTTTACCATTTAAA
Found at i:34997254 original size:22 final size:23
Alignment explanation
Indices: 34997229--34997279 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
34997219 AGTTTAGCCC
34997229 TTTAAAATTTAAGGTTTAA-ATT
1 TTTAAAATTTAAGGTTTAAGATT
* *
34997251 TTTAATATTTAATGTTTAAGATT
1 TTTAAAATTTAAGGTTTAAGATT
*
34997274 TATAAA
1 TTTAAA
34997280 TAAATTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (23 bp):
TTTAAAATTTAAGGTTTAAGATT
Found at i:35005093 original size:59 final size:60
Alignment explanation
Indices: 35004960--35005130 Score: 152
Period size: 58 Copynumber: 2.9 Consensus size: 60
35004950 TTAATATAAC
* * * * ****
35004960 ATTTGGTACTTAAACTT-AACATTTTTCTTAATTTAGTA-CTTAA-TTTTTTTTTTGCACA
1 ATTTGGTACTTAAACTTGAA-TTTTTTCCTAATTTGGTACCTAAACTTTTTTGGGGGCACA
* *
35005018 ATTTGGTATTTGAACTTGAATTTTTTCCTAATTTGGTACCTAAACTTTTTTGGGGGC-CA
1 ATTTGGTACTTAAACTTGAATTTTTTCCTAATTTGGTACCTAAACTTTTTTGGGGGCACA
* * * *
35005077 ATTTGGTACTTAAACTTAGCATTTTTTTTTCTAATTTGGTACTTAAGCTTTTTT
1 ATTTGGTACTTAAACTT-G-A-ATTTTTTCCTAATTTGGTACCTAAACTTTTTT
35005131 TAGGTTCAAT
Statistics
Matches: 91, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
58 30 0.33
59 23 0.25
60 9 0.10
61 1 0.01
62 28 0.31
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.51
Consensus pattern (60 bp):
ATTTGGTACTTAAACTTGAATTTTTTCCTAATTTGGTACCTAAACTTTTTTGGGGGCACA
Found at i:35016099 original size:25 final size:25
Alignment explanation
Indices: 35016048--35016132 Score: 71
Period size: 30 Copynumber: 3.2 Consensus size: 25
35016038 TGTATAACCA
* **
35016048 AAAACAATTCGAATTCGACAAAATAT
1 AAAAC-ATTCAAATTCGACAATGTAT
35016074 AAAACATTCAAATTCGACAATGTAT
1 AAAACATTCAAATTCGACAATGTAT
* *
35016099 ATCTATAATTAATCAAATTCGACAATGTAT
1 A---A-AA-CATTCAAATTCGACAATGTAT
35016129 AAAA
1 AAAA
35016133 TATTTATATT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
25 18 0.37
26 7 0.14
27 1 0.02
28 1 0.02
29 2 0.04
30 20 0.41
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (25 bp):
AAAACATTCAAATTCGACAATGTAT
Found at i:35018136 original size:4 final size:4
Alignment explanation
Indices: 35018119--35018155 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
35018109 TCATAAAAAA
*
35018119 ATTT ATTCT ATTT ATTT ATTT ATGT ATTT ATTT ATTT
1 ATTT ATT-T ATTT ATTT ATTT ATTT ATTT ATTT ATTT
35018156 CTTACTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:35018237 original size:17 final size:18
Alignment explanation
Indices: 35018215--35018253 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
35018205 GCACATTTTG
35018215 TTATTAT-CATTATTATT-
1 TTATTATGCA-TATTATTA
35018232 TTATTATGCATATTATTA
1 TTATTATGCATATTATTA
35018250 TTAT
1 TTAT
35018254 GATTTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (18 bp):
TTATTATGCATATTATTA
Found at i:35018309 original size:3 final size:3
Alignment explanation
Indices: 35018215--35018299 Score: 56
Period size: 3 Copynumber: 29.3 Consensus size: 3
35018205 GCACATTTTG
* * *
35018215 TTA TTA TCA TTA TTA TT- TTA TTA TGCA -TA TTA TTA TTA TGA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA -TTA
* *
35018260 TTA TTA -TA CTT- TTA -TA TT- TTA TTA TGA GTA TTA TTA TTA T
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
35018300 GCCATTATTA
Statistics
Matches: 63, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
2 11 0.17
3 48 0.76
4 4 0.06
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:35028672 original size:21 final size:21
Alignment explanation
Indices: 35028632--35028695 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
35028622 GTTATTTTTT
*
35028632 TAATT-TTATGATTTTCATATG
1 TAATTATTATTATTTT-ATATG
*
35028653 TAATTATTATTATTTTATATA
1 TAATTATTATTATTTTATATG
*
35028674 T-ATGTATTTTTATTTT-TATG
1 TAAT-TATTATTATTTTATATG
35028694 TA
1 TA
35028696 CGTATTTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 6 0.17
21 21 0.58
22 9 0.25
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (21 bp):
TAATTATTATTATTTTATATG
Found at i:35028702 original size:20 final size:21
Alignment explanation
Indices: 35028657--35028702 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
35028647 CATATGTAAT
* *
35028657 TATTATTATTTTATATATATG
1 TATTTTTATTTTATATATACG
*
35028678 TATTTTTATTTT-TATGTACG
1 TATTTTTATTTTATATATACG
35028698 TATTT
1 TATTT
35028703 ATACCCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.65
Consensus pattern (21 bp):
TATTTTTATTTTATATATACG
Found at i:35032287 original size:44 final size:44
Alignment explanation
Indices: 35032216--35032477 Score: 211
Period size: 44 Copynumber: 5.8 Consensus size: 44
35032206 CTCTTTGAAG
* **
35032216 AAGTTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTA
1 AAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTA
* * * **
35032260 AAGTTGCAAATATTATCTCTCTGAAGTTATAGTGGAATAGATTAAAGCTA
1 AAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGA-T-----TA
* * * * ** * *
35032310 CAAGTTACGAATCTCATGTCCCTGAAGTTGTAGTGGAGCAAATTG
1 -AAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTA
*
35032355 AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTA
1 AAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTA
* * **
35032399 AGGTTACAAATCTAATCTATCTGAAGTTGCAGTGGAATAGATTA
1 AAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTA
** * * *
35032443 AAGCGACAAATCCTATAC-CTCTGAAGTTACAGTGG
1 AAGTTACAAATCTTAT-CTCCCTGAAGTTGCAGTGG
35032478 GTCGGATTAA
Statistics
Matches: 170, Mismatches: 40, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
44 133 0.78
45 3 0.02
50 3 0.02
51 31 0.18
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (44 bp):
AAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTA
Found at i:35032407 original size:95 final size:95
Alignment explanation
Indices: 35032216--35032399 Score: 251
Period size: 95 Copynumber: 1.9 Consensus size: 95
35032206 CTCTTTGAAG
* * * * *
35032216 AAGTTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGTTGCAAATATTATCTCTC
1 AAGTTACAAATCTCATCTCCCTAAAGTTGCAGTGGAGCAAATTAAAGCTACAAATATTATCTCCC
*
35032281 TGAAGTTATAGTGGAATAGATTAAAGCTAC
66 TGAAGTTACAGTGGAATAGATTAAAGCTAC
* * * * * *
35032311 AAGTTACGAATCTCATGTCCCTGAAGTTGTAGTGGAGCAAATTGAAGCTACAAATCTTATCTCCC
1 AAGTTACAAATCTCATCTCCCTAAAGTTGCAGTGGAGCAAATTAAAGCTACAAATATTATCTCCC
*
35032376 TGAAGTTGCAGTGGAATAGATTAA
66 TGAAGTTACAGTGGAATAGATTAA
35032400 GGTTACAAAT
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
95 76 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (95 bp):
AAGTTACAAATCTCATCTCCCTAAAGTTGCAGTGGAGCAAATTAAAGCTACAAATATTATCTCCC
TGAAGTTACAGTGGAATAGATTAAAGCTAC
Found at i:35034170 original size:30 final size:32
Alignment explanation
Indices: 35034134--35034217 Score: 113
Period size: 31 Copynumber: 2.7 Consensus size: 32
35034124 ATTTTAAAAT
**
35034134 ATTTTTAAAATACTTTTTTTAA-A-TTTTTTTA
1 ATTTTTAAAATA-TTTTTAAAATACTTTTTTTA
35034165 A-TTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATATTTTTAAAATACTTTTTTTA
35034196 ATTTTTAAAAT-TTTTTAAAATA
1 ATTTTTAAAATATTTTTAAAATA
35034218 AAAATGGGCC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
29 7 0.15
30 11 0.23
31 21 0.44
32 9 0.19
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (32 bp):
ATTTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:35034209 original size:40 final size:40
Alignment explanation
Indices: 35034039--35034201 Score: 269
Period size: 41 Copynumber: 4.1 Consensus size: 40
35034029 AATATATTTA
* *
35034039 TTTTTTAATTTTAAAATATTTTTTACATAC-TTTTTTAA-
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
35034077 TTTTTTAATTTTAAAATA-TTTTAAAATACTTTTTTTTAAT
1 TTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTTTAAT
35034117 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAAT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT-AAT
35034158 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
35034198 TTTT
1 TTTT
35034202 AAAATTTTTT
Statistics
Matches: 118, Mismatches: 2, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
37 9 0.08
38 18 0.15
39 8 0.07
40 32 0.27
41 51 0.43
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (40 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
Found at i:35034661 original size:3 final size:3
Alignment explanation
Indices: 35034561--35034651 Score: 68
Period size: 3 Copynumber: 31.3 Consensus size: 3
35034551 CACATTTTTG
* * *
35034561 TTA TTA TCA TTA TTA TTA TT- TTA TTA TGTA -TA TTA GTA TTA TGA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
* *
35034605 TTTA TTA TTA TTA -TA CTT- TTA -TA TT- TTA TTA TGA GTA TTA TTA
1 -TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
35034648 TTA T
1 TTA T
35034652 GCCATTATTA
Statistics
Matches: 69, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
2 12 0.17
3 52 0.75
4 5 0.07
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:35040268 original size:21 final size:23
Alignment explanation
Indices: 35040244--35040294 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
35040234 CTAAATCACT
35040244 AACTCTTAATCC-C-AAACCCC-A
1 AACTCTTAA-CCACTAAACCCCTA
*
35040265 AACTCCTAACCACTAAACCCCTA
1 AACTCTTAACCACTAAACCCCTA
35040288 AAC-CTTA
1 AACTCTTA
35040295 TTTAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 2 0.08
21 9 0.36
22 10 0.40
23 4 0.16
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (23 bp):
AACTCTTAACCACTAAACCCCTA
Found at i:35040588 original size:14 final size:15
Alignment explanation
Indices: 35040571--35040603 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
35040561 CTTAAATCAG
35040571 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
35040585 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
35040600 AATC
1 AATC
35040604 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:35041276 original size:41 final size:41
Alignment explanation
Indices: 35041220--35041455 Score: 279
Period size: 41 Copynumber: 5.9 Consensus size: 41
35041210 TTTTATTATT
* * *
35041220 ATTAGCGGCGCTTTTTCAAAAACGCTGCTAAAGGCCTGAGT
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
*
35041261 ATTAGAGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* * * * * *
35041302 ATTAGCGGTGCTTATCCAAAAACACCGCTGAAGGCCCAAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
35041343 ATTAGCGACGCTTCTTCAAAAACGCCGC---A---CCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
*
35041378 ATTAGCGGCG-TTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTT-TTCAAAAACGCCGCTAAAGGCCCGAGC
* *
35041419 ATTAGCAGCGCTTTTTCAAAAACGTCGCTAAAGGCCC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCC
35041456 TAAGGCTTTT
Statistics
Matches: 164, Mismatches: 23, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
34 2 0.01
35 28 0.17
38 2 0.01
41 129 0.79
42 3 0.02
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:35041585 original size:40 final size:38
Alignment explanation
Indices: 35041479--35041585 Score: 97
Period size: 40 Copynumber: 2.7 Consensus size: 38
35041469 GGCGCTTTTC
* *
35041479 AAAAGACGCCACTAATGCTTATTTTTAGCGTCATTTCCA
1 AAAAG-CGCCGCTAATGCTTATTTTTAGCGACATTTCCA
* * ** **
35041518 AAATGCGCCGCTAATGCTCAACCTTTAGCGACATTTTTA
1 AAAAGCGCCGCTAATGCT-TATTTTTAGCGACATTTCCA
*
35041557 TAAAAGTGCCGCTAATGCTTGATTTTTAG
1 -AAAAGCGCCGCTAATGCTT-ATTTTTAG
35041586 TAGCGTTTTT
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
38 12 0.23
39 18 0.35
40 22 0.42
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (38 bp):
AAAAGCGCCGCTAATGCTTATTTTTAGCGACATTTCCA
Found at i:35043506 original size:1 final size:1
Alignment explanation
Indices: 35043500--35043525 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
35043490 TAAAATTCTC
35043500 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
35043526 CAACAACAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:35047512 original size:31 final size:31
Alignment explanation
Indices: 35047451--35047627 Score: 221
Period size: 31 Copynumber: 5.7 Consensus size: 31
35047441 ATCCACTGCT
* *
35047451 CAAATC-AATTAGGCAATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* * * *
35047481 CGAATCAAATTCGGTAATGTACATCTATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
35047512 CAAATCAAATTAGGCAATGAATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* * *
35047543 CAAATCGAATTCGACAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
35047574 CAAATCAAATTCGGTAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
35047605 CAAATCAAATTCGGAAATGTATA
1 CAAATCAAATTCGGCAATGTATA
35047628 AAACATATAC
Statistics
Matches: 123, Mismatches: 23, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
30 5 0.04
31 118 0.96
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCCATATA
Found at i:35047647 original size:93 final size:93
Alignment explanation
Indices: 35047451--35047638 Score: 252
Period size: 93 Copynumber: 2.0 Consensus size: 93
35047441 ATCCACTGCT
* * * *
35047451 CAAATC-AATTAGGCAATATATATCCATATACGAATCAAATTCGGTAATGTACATCTATATACAA
1 CAAATCAAATTCGACAATATATAACCATATACAAATCAAATTCGGTAATGTACATCTATATACAA
* **
35047515 ATCAAATTAGGCAATGAATATCCATATA
66 ATCAAATTAGGAAATGAATAAACATATA
* * *
35047543 CAAATCGAATTCGACAATGTATAACCATATACAAATCAAATTCGGTAATGTATATCTATATACAA
1 CAAATCAAATTCGACAATATATAACCATATACAAATCAAATTCGGTAATGTACATCTATATACAA
* *
35047608 ATCAAATTCGGAAATGTATAAAACATATA
66 ATCAAATTAGGAAATGAAT-AAACATATA
35047637 CA
1 CA
35047639 TTTAAATTCA
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
92 6 0.07
93 68 0.82
94 9 0.11
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.29
Consensus pattern (93 bp):
CAAATCAAATTCGACAATATATAACCATATACAAATCAAATTCGGTAATGTACATCTATATACAA
ATCAAATTAGGAAATGAATAAACATATA
Found at i:35051914 original size:56 final size:56
Alignment explanation
Indices: 35051828--35052003 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
35051818 ACAAGGGATG
*
35051828 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
35051884 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
35051940 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
35051996 ATGGGCAA
1 ATGGGCAA
35052004 TAAACTAATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:35053268 original size:79 final size:81
Alignment explanation
Indices: 35053132--35053314 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
35053122 TCGAATGATG
* *
35053132 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
35053196 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
35053211 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
35053273 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
35053291 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
35053315 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:35053330 original size:40 final size:40
Alignment explanation
Indices: 35053133--35053316 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
35053123 CGAATGATGT
* * * *
35053133 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
35053173 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
35053213 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
35053251 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
35053292 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
35053317 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:35053338 original size:79 final size:79
Alignment explanation
Indices: 35053185--35053339 Score: 208
Period size: 79 Copynumber: 2.0 Consensus size: 79
35053175 GGACTAAGAT
* **
35053185 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
35053250 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
35053264 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
35053327 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
35053340 ATTCTGAAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
78 2 0.03
79 41 0.61
80 24 0.36
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:35055256 original size:42 final size:42
Alignment explanation
Indices: 35055144--35055256 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
35055134 TGGCATACAC
* * * * * *
35055144 AGCCCAACAGGATTGTTCATAACCATGTGTGGAGGAGGAGCA
1 AGCCCAACAGAATGGTGCATACCCATGTGTGGAGAAGGAACA
* * *
35055186 AGCCCAACAGAATGGTGTAGACCTATGTGTGGAGAAGGAACA
1 AGCCCAACAGAATGGTGCATACCCATGTGTGGAGAAGGAACA
*
35055228 GGCCCAACAGAATGGTGCATACCCATGTG
1 AGCCCAACAGAATGGTGCATACCCATGTG
35055257 CAGGGAAGGA
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.32, C:0.20, G:0.30, T:0.18
Consensus pattern (42 bp):
AGCCCAACAGAATGGTGCATACCCATGTGTGGAGAAGGAACA
Found at i:35065266 original size:27 final size:27
Alignment explanation
Indices: 35065236--35065410 Score: 136
Period size: 27 Copynumber: 6.5 Consensus size: 27
35065226 CATCGAGACG
* *
35065236 GTAAAAACGAGGTAGTCCACTAGGATA
1 GTAAACACGAGGTAGTCCACCAGGATA
*** * *
35065263 GTAAACACGAGGTAGTATGCTAGGA-C
1 GTAAACACGAGGTAGTCCACCAGGATA
** * *
35065289 GTAAACATAAGGTAGTCTACCAAGATA
1 GTAAACACGAGGTAGTCCACCAGGATA
** ** *
35065316 GTAAACACGAGGTAGTCTGCTGGGACA
1 GTAAACACGAGGTAGTCCACCAGGATA
** **
35065343 GTAAACATAATATAGTCCACCAGGATA
1 GTAAACACGAGGTAGTCCACCAGGATA
* *
35065370 GTAAACACAAGGTGGTCCACCAGGATA
1 GTAAACACGAGGTAGTCCACCAGGATA
*
35065397 GTAAACAAGAGGTA
1 GTAAACACGAGGTA
35065411 ATTTGTTAGG
Statistics
Matches: 112, Mismatches: 35, Indels: 2
0.75 0.23 0.01
Matches are distributed among these distances:
26 19 0.17
27 93 0.83
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (27 bp):
GTAAACACGAGGTAGTCCACCAGGATA
Found at i:35065302 original size:53 final size:54
Alignment explanation
Indices: 35065245--35065382 Score: 197
Period size: 53 Copynumber: 2.6 Consensus size: 54
35065235 GGTAAAAACG
*
35065245 AGGTAGTCCACTAGGATAGTAAACACGAGGTAGTATGCTAGGAC-GTAAACATA
1 AGGTAGTCCACCAGGATAGTAAACACGAGGTAGTATGCTAGGACAGTAAACATA
* * * *
35065298 AGGTAGTCTACCAAGATAGTAAACACGAGGTAGTCTGCTGGGACAGTAAACATA
1 AGGTAGTCCACCAGGATAGTAAACACGAGGTAGTATGCTAGGACAGTAAACATA
** *
35065352 ATATAGTCCACCAGGATAGTAAACACAAGGT
1 AGGTAGTCCACCAGGATAGTAAACACGAGGT
35065383 GGTCCACCAG
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
53 39 0.53
54 35 0.47
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (54 bp):
AGGTAGTCCACCAGGATAGTAAACACGAGGTAGTATGCTAGGACAGTAAACATA
Found at i:35067354 original size:41 final size:42
Alignment explanation
Indices: 35067309--35067390 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 42
35067299 GCCTGGGCTG
* * *
35067309 TGTGATAGC-CTACACGCTCATGTGGAAG-AGGCACACACCCA
1 TGTGA-AGCACTAAACGCCCATGTGAAAGCAGGCACACACCCA
* *
35067350 TGTGAAGCAGTAAATGCCCATGTGAAAGCAGGCACACACCC
1 TGTGAAGCACTAAACGCCCATGTGAAAGCAGGCACACACCC
35067391 TTATGACGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
40 3 0.09
41 19 0.56
42 12 0.35
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (42 bp):
TGTGAAGCACTAAACGCCCATGTGAAAGCAGGCACACACCCA
Found at i:35073055 original size:16 final size:15
Alignment explanation
Indices: 35073028--35073057 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
35073018 TAAGTCTGAA
35073028 AAATAAAATAAAAAC
1 AAATAAAATAAAAAC
35073043 AAATAACAATAAAAA
1 AAATAA-AATAAAAA
35073058 TAAAAGATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (15 bp):
AAATAAAATAAAAAC
Found at i:35081222 original size:117 final size:113
Alignment explanation
Indices: 35081022--35081480 Score: 663
Period size: 117 Copynumber: 4.1 Consensus size: 113
35081012 GGAAAAAATT
35081022 TTTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAAATTTTTTTTTGAATTTTTTCT
1 TTTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGT-AA--TTTTTTT-AATTTTTTCT
* *
35081087 TTTTTTTTCGTGTTAGAATCAGATATAAATATACGAAAAATGTAAAAAAAAA
62 TTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTAAAAAAAAA
*
35081139 TTTTTTTTGGATGCTGGCCTGTCAATGGCCGGCACCCAACAGTAAATTTTTTTTGAATTTTTTCT
1 -TTTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGT-AA-TTTTTTT-AATTTTTTCT
* * *
35081204 TTTTTTTTCATATCAGAATCAAATATAAATATACGAAAAAAGTAAAAAAAAA
62 TTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTAAAAAAAAA
35081256 --TTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAA-------AATTTTTTCTTTTT
1 TTTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAATTTTTTTAATTTTTTCTTTTT
*
35081312 TTTTCGTGTTAGAATCAGATATAAATATACGAAAAAAGTAAAAAAAAA
66 TTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTAAAAAAAAA
***
35081360 -TTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAATTTTTTT--TTTTGAATTTTT
1 TTTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAATTTTTTTAATTTTTTCTTTTT
35081422 TTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTAAAAAAAAAA
66 TTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGT-AAAAAAAAA
35081471 TTTTTTTGGG
1 TTTTTTTGGG
35081481 ACCCAACAGT
Statistics
Matches: 316, Mismatches: 15, Indels: 26
0.89 0.04 0.07
Matches are distributed among these distances:
104 58 0.18
105 42 0.13
110 47 0.15
111 9 0.03
112 9 0.03
113 2 0.01
114 39 0.12
117 66 0.21
118 44 0.14
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (113 bp):
TTTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAATTTTTTTAATTTTTTCTTTTT
TTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTAAAAAAAAA
Found at i:35081316 original size:104 final size:105
Alignment explanation
Indices: 35081194--35081475 Score: 440
Period size: 104 Copynumber: 2.6 Consensus size: 105
35081184 ATTTTTTTTG
* * *
35081194 AATTTTTTCTTTTTTTTTCATATCAGAATCAAATATAAATATACGAAAAAAGTAAAAAAAAATTT
1 AATTTTTTCTTTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTAAAAAAAAATTT
35081259 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAA-
66 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAAT
*
35081298 AATTTTTTCTTTTTTTTTCGTGTTAGAATCAGATATAAATATACGAAAAAAGTAAAAAAAAATTT
1 AATTTTTTCTTTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTAAAAAAAAA-TT
35081363 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAATTT
65 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAA--T
** *
35081406 TTTTTTTTGAATTTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTAAAAAAAAAA
1 AATTTTTT--CTTTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGT-AAAAAAAAA
35081471 TTTTT
63 TTTTT
35081476 TTGGGACCCA
Statistics
Matches: 163, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
104 58 0.36
105 42 0.26
108 6 0.04
110 48 0.29
111 9 0.06
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (105 bp):
AATTTTTTCTTTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTAAAAAAAAATTT
TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAAT
Found at i:35081828 original size:112 final size:112
Alignment explanation
Indices: 35081609--35081957 Score: 576
Period size: 112 Copynumber: 3.1 Consensus size: 112
35081599 TTTTATTGTT
*
35081609 AGCACCCAAATTTTTTTTTTAATTTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAA
1 AGCACCCAAA-TTTTTTTTTAA-TTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAG
*
35081674 AGAAAAATTCAAATTTTTTTTTACTGTTGGGTGCCGGCCATTGACAGGTC
64 A-AAAAATTCAAATTTTTTTTTACTGTTGGGTGCCGGCCATTGACAGGCC
*
35081724 AGCACCCAAATTTTTTTTTAATTTTTTCGTATATTTATATTTGATTCTGACACGAAAAAAAAGAA
1 AGCACCCAAATTTTTTTTTAATTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAA
* *
35081789 AAAATTCAAATTTTTTTTTACTGTTGGGTGTCGGACATTGACAGGCC
66 AAAATTCAAATTTTTTTTTACTGTTGGGTGCCGGCCATTGACAGGCC
* *
35081836 AGCACTCAAAATTTTTTTTACA-TTTTTCGTATATTTATATCTGATTCTGACACG-AAAAAAAGA
1 AGCACCCAAATTTTTTTTTA-ATTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGA
35081899 AAAAATTCAAAATTTTTTTTTACTGTTGGGTGCCGGCCATTGACAGGCC
65 AAAAATTC-AAATTTTTTTTTACTGTTGGGTGCCGGCCATTGACAGGCC
35081948 AGCACCCAAA
1 AGCACCCAAA
35081958 AAAATTTCTT
Statistics
Matches: 221, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
111 17 0.08
112 141 0.64
113 42 0.19
114 11 0.05
115 10 0.05
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (112 bp):
AGCACCCAAATTTTTTTTTAATTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAA
AAAATTCAAATTTTTTTTTACTGTTGGGTGCCGGCCATTGACAGGCC
Found at i:35081984 original size:17 final size:17
Alignment explanation
Indices: 35081962--35081994 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
35081952 CCCAAAAAAA
35081962 TTTCTTTTTCCTTTTTT
1 TTTCTTTTTCCTTTTTT
35081979 TTTCTTTTTCCTTTTT
1 TTTCTTTTTCCTTTTT
35081995 CGTATATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTCTTTTTCCTTTTTT
Found at i:35082359 original size:29 final size:30
Alignment explanation
Indices: 35082315--35082371 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
35082305 TTAATCATTT
35082315 AATAGTTCAATAACTTAAATAAAAACTTCG
1 AATAGTTCAATAACTTAAATAAAAACTTCG
*
35082345 AATAGTT-TATAACTTAAATAAAAACTT
1 AATAGTTCAATAACTTAAATAAAAACTT
35082372 TCAAATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.33
Consensus pattern (30 bp):
AATAGTTCAATAACTTAAATAAAAACTTCG
Found at i:35085820 original size:5 final size:5
Alignment explanation
Indices: 35085810--35085835 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
35085800 TATTAATATA
35085810 TAATT TAATT TAATT TAATT TAATT T
1 TAATT TAATT TAATT TAATT TAATT T
35085836 TTATCCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TAATT
Found at i:35088429 original size:21 final size:21
Alignment explanation
Indices: 35088405--35088447 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
35088395 GAATTTAACT
*
35088405 CAATTTAATACAATTCACATC
1 CAATTCAATACAATTCACATC
* *
35088426 CAATTCCATCCAATTCACATC
1 CAATTCAATACAATTCACATC
35088447 C
1 C
35088448 TAGGAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (21 bp):
CAATTCAATACAATTCACATC
Found at i:35088435 original size:10 final size:11
Alignment explanation
Indices: 35088415--35088447 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
35088405 CAATTTAATA
35088415 CAATTCACATC
1 CAATTCACATC
35088426 CAATTC-CATC
1 CAATTCACATC
35088436 CAATTCACATC
1 CAATTCACATC
35088447 C
1 C
35088448 TAGGAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.33, C:0.39, G:0.00, T:0.27
Consensus pattern (11 bp):
CAATTCACATC
Found at i:35098802 original size:30 final size:30
Alignment explanation
Indices: 35098767--35098825 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
35098757 AATTATTTGC
* *
35098767 AAAATTTAGTTAT-TCTTTTTGTAAATATT
1 AAAAATTAGCTATCTCTTTTTGTAAATATT
*
35098796 AAAAATTAGCTGTCTCTTTTTGTAAATATT
1 AAAAATTAGCTATCTCTTTTTGTAAATATT
35098826 TTTAAGGCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (30 bp):
AAAAATTAGCTATCTCTTTTTGTAAATATT
Found at i:35102226 original size:56 final size:50
Alignment explanation
Indices: 35102163--35102351 Score: 175
Period size: 50 Copynumber: 3.7 Consensus size: 50
35102153 GGGAATGAGA
*
35102163 TCCCATGTAAGACCATGTCTGGGACATGGCATT-GACATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTAG-C---ACTGA-G--ATGAGAGG
* * *
35102219 TCCCATGTAAGACCATGTTTGGGATATGGCGTTAGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTAGCACTGAGATGAGAGG
* * ** * **
35102269 TCCCCTGTAAAACCATGTCTGGGACATGGCATGGGCA-TCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTAGCACT-GAGATGAGAGG
* *
35102319 TCCCATGTAAGACCATATCTGGGATATGGCATT
1 TCCCATGTAAGACCATGTCTGGGACATGGCATT
35102352 GGTAGTTCAG
Statistics
Matches: 112, Mismatches: 19, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
49 1 0.01
50 74 0.66
52 1 0.01
53 4 0.04
56 31 0.28
57 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTAGCACTGAGATGAGAGG
Found at i:35102632 original size:20 final size:20
Alignment explanation
Indices: 35102607--35102645 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
35102597 TGAGTTATTT
35102607 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
35102627 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
35102646 GAAGAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:35117525 original size:45 final size:45
Alignment explanation
Indices: 35117461--35117549 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
35117451 AACAGATACT
* * *
35117461 CGGTGGATTCAGCAAATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACAAATAGCAACCACCTTACTAATCAATGATGTC
*
35117506 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGT
1 CGGTGGAATCAACAAATAGCAACCACCTTACTAATCAATGATGT
35117550 TCAGTTCACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (45 bp):
CGGTGGAATCAACAAATAGCAACCACCTTACTAATCAATGATGTC
Found at i:35128955 original size:28 final size:28
Alignment explanation
Indices: 35128915--35128970 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
35128905 AGAATGTTAG
35128915 TGAAATTCAGAGTTTTCTCAGACTTGCT
1 TGAAATTCAGAGTTTTCTCAGACTTGCT
*
35128943 TGAAATTCAGAGTTTTCTCGGACTTGCT
1 TGAAATTCAGAGTTTTCTCAGACTTGCT
35128971 GGCTATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (28 bp):
TGAAATTCAGAGTTTTCTCAGACTTGCT
Found at i:35132725 original size:16 final size:17
Alignment explanation
Indices: 35132699--35132731 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
35132689 TATGAGCATA
35132699 AATATGTGAAAAATATG
1 AATATGTGAAAAATATG
*
35132716 AATA-GTGAAACATATG
1 AATATGTGAAAAATATG
35132732 TGTTTAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.52, C:0.03, G:0.18, T:0.27
Consensus pattern (17 bp):
AATATGTGAAAAATATG
Found at i:35132889 original size:22 final size:22
Alignment explanation
Indices: 35132864--35132932 Score: 57
Period size: 26 Copynumber: 3.0 Consensus size: 22
35132854 ATATGCCAGC
35132864 TCATCAGTATCTATGTGGTGGT
1 TCATCAGTATCTATGTGGTGGT
* * *
35132886 TCATCCATGATGTGCTATGTGATCGT
1 TCAT-CA-G-TAT-CTATGTGGTGGT
**
35132912 TCATTGGTATCTATGTGGTGG
1 TCATCAGTATCTATGTGGTGG
35132933 CTTGTCCACA
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
22 13 0.37
23 4 0.11
24 2 0.06
25 2 0.06
26 14 0.40
ACGTcount: A:0.17, C:0.14, G:0.28, T:0.41
Consensus pattern (22 bp):
TCATCAGTATCTATGTGGTGGT
Found at i:35137539 original size:3 final size:3
Alignment explanation
Indices: 35137531--35137574 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
35137521 TTCTTGACTT
*
35137531 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
35137575 TATTTGCATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:35142350 original size:26 final size:27
Alignment explanation
Indices: 35142298--35142360 Score: 119
Period size: 26 Copynumber: 2.4 Consensus size: 27
35142288 ATAAAAAATA
35142298 ACCAAAATATTATAACTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTATTT
35142325 ACCAAAATATTATAA-TTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTATTT
35142351 ACCAAAATAT
1 ACCAAAATAT
35142361 ACTAAAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 21 0.58
27 15 0.42
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (27 bp):
ACCAAAATATTATAACTTTTTTTATTT
Found at i:35142389 original size:15 final size:16
Alignment explanation
Indices: 35142365--35142394 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35142355 AAATATACTA
35142365 AAAAACAAAAACCTGC
1 AAAAACAAAAACCTGC
35142381 AAAAA-AAAAACCTG
1 AAAAACAAAAACCTG
35142395 TGGCGGCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.07
Consensus pattern (16 bp):
AAAAACAAAAACCTGC
Found at i:35143066 original size:15 final size:15
Alignment explanation
Indices: 35143026--35143075 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
35143016 AACTCTATTT
35143026 TAATTTAATAAACTATTC
1 TAATTTAATAAAC---TC
*
35143044 TCATTTAATAAACTC
1 TAATTTAATAAACTC
35143059 TAATTTAATAAACTC
1 TAATTTAATAAACTC
35143074 TA
1 TA
35143076 TTTTGGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 18 0.60
18 12 0.40
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATTTAATAAACTC
Found at i:35143816 original size:27 final size:28
Alignment explanation
Indices: 35143786--35143851 Score: 107
Period size: 29 Copynumber: 2.4 Consensus size: 28
35143776 TGTTTTTGGC
*
35143786 ATATTTTGGTAAAT-AAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
35143813 ATATTTTGGTAAATAAAAAAAAAGTTATA
1 ATATTTTGGTAAAT-AAAAAAAAGTTATA
35143842 ATATTTTGGT
1 ATATTTTGGT
35143852 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 14 0.39
29 22 0.61
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:35152527 original size:22 final size:22
Alignment explanation
Indices: 35152501--35152545 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
35152491 ATTACATGTA
*
35152501 TTAATTCATAATATAA-TTAATT
1 TTAATT-ATAATAAAATTTAATT
*
35152523 TTAATTTTAATAAAATTTAATT
1 TTAATTATAATAAAATTTAATT
35152545 T
1 T
35152546 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTATAATAAAATTTAATT
Found at i:35158205 original size:13 final size:13
Alignment explanation
Indices: 35158187--35158211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35158177 TAATTTATAT
35158187 GTGTGAAAATTTC
1 GTGTGAAAATTTC
35158200 GTGTGAAAATTT
1 GTGTGAAAATTT
35158212 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:35159408 original size:42 final size:43
Alignment explanation
Indices: 35159307--35159455 Score: 146
Period size: 42 Copynumber: 3.5 Consensus size: 43
35159297 TGTGATTTCG
* *
35159307 TGTAAGACCACGTCTGGGACGA-TGGCATTGACT-TGA-GATTTACA
1 TGTAAGACCATGTCTGGGAC-ACTGGCATCGA-TAT-ATGA-TTACA
* *
35159351 TGTAAGACCATGTCTGGGACATTGGCATC-ATATATGAATT-CG
1 TGTAAGACCATGTCTGGGACACTGGCATCGATATATG-ATTACA
* *
35159393 TGTAAGACCCTGTCTGGGACACTGGCATCGATATTTGATTACA
1 TGTAAGACCATGTCTGGGACACTGGCATCGATATATGATTACA
* *
35159436 TGTAAGACCACGTCTAGGAC
1 TGTAAGACCATGTCTGGGAC
35159456 GATGACATTG
Statistics
Matches: 89, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
42 33 0.37
43 30 0.34
44 26 0.29
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACACTGGCATCGATATATGATTACA
Found at i:35163291 original size:16 final size:15
Alignment explanation
Indices: 35163264--35163297 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
35163254 ATAACTAGTA
*
35163264 TATAATTATATTTAT
1 TATAATTATATTAAT
35163279 TATAATATATATTAAT
1 TATAAT-TATATTAAT
35163295 TAT
1 TAT
35163298 TATCAACTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:35166819 original size:9 final size:10
Alignment explanation
Indices: 35166772--35166820 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
35166762 ATGAACAAGT
*
35166772 TTAATTTTAA
1 TTAATTTTTA
35166782 TTAATTTTATA
1 TTAATTTT-TA
*
35166793 TCAAATTTTTA
1 T-TAATTTTTA
35166804 TTAATTTTTA
1 TTAATTTTTA
35166814 TT-ATTTT
1 TTAATTTT
35166821 CGACAGATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 5 0.15
10 18 0.53
11 5 0.15
12 6 0.18
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (10 bp):
TTAATTTTTA
Found at i:35184640 original size:15 final size:15
Alignment explanation
Indices: 35184620--35184653 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
35184610 GATTTTCTGA
35184620 TGTAAACTTAAATAT
1 TGTAAACTTAAATAT
35184635 TGTAAACTTAAATAT
1 TGTAAACTTAAATAT
35184650 TGTA
1 TGTA
35184654 GATAGCGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (15 bp):
TGTAAACTTAAATAT
Found at i:35185579 original size:2 final size:2
Alignment explanation
Indices: 35185574--35185613 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
35185564 TCTATATATA
35185574 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
35185614 CAGATCATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:35194224 original size:48 final size:48
Alignment explanation
Indices: 35194153--35194250 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
35194143 AAATAATAGA
35194153 AAAATGTATATTATTTAAGCTTAGGGAAGAATCAATTATCATGGGTTT
1 AAAATGTATATTATTTAAGCTTAGGGAAGAATCAATTATCATGGGTTT
*
35194201 AAAATGTATATTATTTAAGCTTAGGGAAGAATCAGTTATCATGGGTTT
1 AAAATGTATATTATTTAAGCTTAGGGAAGAATCAATTATCATGGGTTT
35194249 AA
1 AA
35194251 GTTAAAATGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (48 bp):
AAAATGTATATTATTTAAGCTTAGGGAAGAATCAATTATCATGGGTTT
Found at i:35195874 original size:54 final size:54
Alignment explanation
Indices: 35195816--35195928 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 54
35195806 TCGTGTATGT
* *
35195816 CAAGTCA-ATGAGTTACATGGTCTAGCACACGGCCTGCGACACAACCATGTGACA
1 CAAGTCAGA-GAGTTACACGGTCTAGCACACGGCCTACGACACAACCATGTGACA
* * * * *
35195870 CAAGTCAGAGAGTTACACGGTCTGGCACATGGCCTACGACACGACCGTGTGACC
1 CAAGTCAGAGAGTTACACGGTCTAGCACACGGCCTACGACACAACCATGTGACA
35195924 CAAGT
1 CAAGT
35195929 TAGTGAGTCA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 50 0.98
55 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.25, T:0.18
Consensus pattern (54 bp):
CAAGTCAGAGAGTTACACGGTCTAGCACACGGCCTACGACACAACCATGTGACA
Found at i:35196132 original size:21 final size:21
Alignment explanation
Indices: 35196099--35196138 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
35196089 TATCCTAAAC
*
35196099 TGTTCTTAGGGCCCCAAATGCT
1 TGTTCTTAAGG-CCCAAATGCT
35196121 TGTT-TTAAGGCCCAAATG
1 TGTTCTTAAGGCCCAAATG
35196139 TGAATGCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.33
Consensus pattern (21 bp):
TGTTCTTAAGGCCCAAATGCT
Found at i:35197275 original size:15 final size:15
Alignment explanation
Indices: 35197255--35197285 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35197245 AAGATAAAAA
35197255 TAAAATTAGAAATTT
1 TAAAATTAGAAATTT
35197270 TAAAATTAGAAATTT
1 TAAAATTAGAAATTT
35197285 T
1 T
35197286 CTTCTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
TAAAATTAGAAATTT
Found at i:35201148 original size:57 final size:57
Alignment explanation
Indices: 35201081--35201194 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 57
35201071 ATTTCCAAAC
* * * *
35201081 CATTTCATTTTGGAGAAAACTACATTCATTTTCAAATGTTTC-CATTTCTCCATTTT
1 CATTTCATTTTGAAGAAAACCACATTCATTTCCAAATGTTTCTCATTTATCCATTTT
35201137 CATTTCCATTTTGAAGAAAACCACATTCATTTCCAAATGTTTCTCATTTATCCATTTT
1 CATTT-CATTTTGAAGAAAACCACATTCATTTCCAAATGTTTCTCATTTATCCATTTT
35201195 TACCATTTCT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 5 0.10
57 34 0.65
58 13 0.25
ACGTcount: A:0.28, C:0.21, G:0.06, T:0.45
Consensus pattern (57 bp):
CATTTCATTTTGAAGAAAACCACATTCATTTCCAAATGTTTCTCATTTATCCATTTT
Found at i:35204190 original size:18 final size:19
Alignment explanation
Indices: 35204164--35204200 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
35204154 AAGGAAAGGT
35204164 AACTAAGTAAGTT-TAGAG
1 AACTAAGTAAGTTCTAGAG
*
35204182 AACTTAGTAAGTTCTAGAG
1 AACTAAGTAAGTTCTAGAG
35204201 TAGGCACTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (19 bp):
AACTAAGTAAGTTCTAGAG
Found at i:35209943 original size:21 final size:20
Alignment explanation
Indices: 35209914--35209957 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
35209904 TTATAATGAC
*
35209914 AAAATAAATTATTTTAATTTAT
1 AAAATAAA-TAATTTAATTT-T
35209936 AAAA-AAATAATTTAATTTT
1 AAAATAAATAATTTAATTTT
35209955 AAA
1 AAA
35209958 TTTCCGTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 10 0.48
21 3 0.14
22 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAAATAAATAATTTAATTTT
Found at i:35211353 original size:13 final size:13
Alignment explanation
Indices: 35211335--35211359 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35211325 ACTTTATTTG
35211335 TTATTTACTTTAT
1 TTATTTACTTTAT
35211348 TTATTTACTTTA
1 TTATTTACTTTA
35211360 CCACTTTCGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTTACTTTAT
Found at i:35212998 original size:12 final size:12
Alignment explanation
Indices: 35212967--35213000 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
35212957 AAAAATTCCT
*
35212967 TCAAAGAAAAAC
1 TCAAAGAGAAAC
35212979 TCAAAGAGAAAC
1 TCAAAGAGAAAC
35212991 TCAAAGAGAA
1 TCAAAGAGAA
35213001 TTTTATTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.09
Consensus pattern (12 bp):
TCAAAGAGAAAC
Found at i:35214031 original size:9 final size:9
Alignment explanation
Indices: 35213961--35214077 Score: 58
Period size: 10 Copynumber: 12.1 Consensus size: 9
35213951 ACATTCTTGG
35213961 ATTATAAAA
1 ATTATAAAA
*
35213970 AGTA-AAAA
1 ATTATAAAA
*
35213978 ATATAAAAAAA
1 AT-T-ATAAAA
*
35213989 ATTATTAAA
1 ATTATAAAA
35213998 ATTATAAAAGA
1 ATTAT-AAA-A
*
35214009 ACTT-TAAAT
1 A-TTATAAAA
*
35214018 TTTATAAAA
1 ATTATAAAA
35214027 ATTATTAAAAA
1 ATTA-T-AAAA
*
35214038 ATCATTAAAA
1 ATTA-TAAAA
*
35214048 ATCATAAAA
1 ATTATAAAA
*
35214057 TTTTATAAAA
1 -ATTATAAAA
35214067 ATCTATAAAA
1 AT-TATAAAA
35214077 A
1 A
35214078 ATAATGTATT
Statistics
Matches: 84, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
8 7 0.08
9 26 0.31
10 31 0.37
11 18 0.21
12 2 0.02
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.32
Consensus pattern (9 bp):
ATTATAAAA
Found at i:35214039 original size:40 final size:40
Alignment explanation
Indices: 35213985--35214079 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 40
35213975 AAAATATAAA
* * *
35213985 AAAAATTATT--AAAATTA-TAAAAGAACTTTAAATTTTAT
1 AAAAATTATTAAAAAATCATTAAAA-AACATAAAATTTTAT
*
35214023 AAAAATTATTAAAAAATCATTAAAAATCATAAAATTTTAT
1 AAAAATTATTAAAAAATCATTAAAAAACATAAAATTTTAT
35214063 AAAAATCTA-TAAAAAAT
1 AAAAAT-TATTAAAAAAT
35214080 AATGTATTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
38 10 0.20
40 32 0.65
41 7 0.14
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (40 bp):
AAAAATTATTAAAAAATCATTAAAAAACATAAAATTTTAT
Found at i:35214055 original size:30 final size:30
Alignment explanation
Indices: 35214024--35214079 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
35214014 AAATTTTATA
*
35214024 AAAATTATTA-AAAAATC-ATTAAAAATCAT
1 AAAATT-TTATAAAAATCTATAAAAAATCAT
35214053 AAAATTTTATAAAAATCTATAAAAAAT
1 AAAATTTTATAAAAATCTATAAAAAAT
35214080 AATGTATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 3 0.12
29 13 0.54
30 8 0.33
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (30 bp):
AAAATTTTATAAAAATCTATAAAAAATCAT
Found at i:35214417 original size:20 final size:19
Alignment explanation
Indices: 35214360--35214417 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
35214350 AAATTCTATA
35214360 AAATTTTATGATTTTTTAAT
1 AAATTTTATGA-TTTTTAAT
* *
35214380 TAATTTCTAAT-AATTTTAAT
1 AAATTT-T-ATGATTTTTAAT
35214400 AAATTTTGATGATTTTTA
1 AAATTTT-ATGATTTTTA
35214418 TAAGGGTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 3 0.10
20 23 0.77
21 2 0.07
22 2 0.07
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (19 bp):
AAATTTTATGATTTTTAAT
Found at i:35215094 original size:12 final size:12
Alignment explanation
Indices: 35215074--35215119 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
35215064 ATTTTGGGTT
* *
35215074 ATTTCGATTTCA
1 ATTTTGATTTCG
35215086 ATTTTGATTTCG
1 ATTTTGATTTCG
*
35215098 ATTTTGATTTTG
1 ATTTTGATTTCG
35215110 ATTTTGATTT
1 ATTTTGATTT
35215120 AGGGTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.61
Consensus pattern (12 bp):
ATTTTGATTTCG
Found at i:35215095 original size:6 final size:6
Alignment explanation
Indices: 35215086--35215119 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
35215076 TTCGATTTCA
*
35215086 ATTTTG ATTTCG ATTTTG ATTTTG ATTTTG ATTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTT
35215120 AGGGTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.03, G:0.15, T:0.65
Consensus pattern (6 bp):
ATTTTG
Found at i:35215097 original size:18 final size:18
Alignment explanation
Indices: 35215074--35215227 Score: 66
Period size: 18 Copynumber: 8.6 Consensus size: 18
35215064 ATTTTGGGTT
35215074 ATTTCGATTTCAATTTTG
1 ATTTCGATTTCAATTTTG
**
35215092 ATTTCGATTTTGATTTTG
1 ATTTCGATTTCAATTTTG
*
35215110 ATTTTGATTT-AGGGTTATTTTG
1 ATTTCGATTTCA-----ATTTTG
** * **
35215132 GGTT--ATTTAAATTTCA
1 ATTTCGATTTCAATTTTG
***
35215148 ATTTCGATTT-AGGGTT-
1 ATTTCGATTTCAATTTTG
* * *
35215164 ATTTTGATTTCGATTTCG
1 ATTTCGATTTCAATTTTG
*
35215182 ATTTTGATTTCAATTTTG
1 ATTTCGATTTCAATTTTG
**
35215200 ATTTCGATTTCGGTTTTG
1 ATTTCGATTTCAATTTTG
*
35215218 ATTTCAATTT
1 ATTTCGATTT
35215228 TGGTTTTATT
Statistics
Matches: 100, Mismatches: 26, Indels: 20
0.68 0.18 0.14
Matches are distributed among these distances:
16 15 0.15
17 3 0.03
18 69 0.69
20 4 0.04
21 1 0.01
22 8 0.08
ACGTcount: A:0.20, C:0.07, G:0.16, T:0.56
Consensus pattern (18 bp):
ATTTCGATTTCAATTTTG
Found at i:35215157 original size:28 final size:28
Alignment explanation
Indices: 35215126--35215187 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
35215116 ATTTAGGGTT
35215126 ATTTTGGGTTATTTAAATTTCAATTTCG
1 ATTTTGGGTTATTTAAATTTCAATTTCG
* ** *
35215154 ATTTAGGGTTATTTTGATTTCGATTTCG
1 ATTTTGGGTTATTTAAATTTCAATTTCG
35215182 ATTTTG
1 ATTTTG
35215188 ATTTCAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.06, G:0.18, T:0.55
Consensus pattern (28 bp):
ATTTTGGGTTATTTAAATTTCAATTTCG
Found at i:35215173 original size:6 final size:6
Alignment explanation
Indices: 35215164--35215227 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
35215154 ATTTAGGGTT
* * * *
35215164 ATTTTG ATTTCG ATTTCG ATTTTG ATTTCA ATTTTG ATTTCG ATTTCG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
* * *
35215212 GTTTTG ATTTCA ATTT
1 ATTTCG ATTTCG ATTT
35215228 TGGTTTTATT
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.19, C:0.09, G:0.14, T:0.58
Consensus pattern (6 bp):
ATTTCG
Found at i:35215232 original size:18 final size:18
Alignment explanation
Indices: 35215195--35215238 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
35215185 TTGATTTCAA
*
35215195 TTTTGATTTCGATTTCGG
1 TTTTGATTTCAATTTCGG
*
35215213 TTTTGATTTCAATTTTGG
1 TTTTGATTTCAATTTCGG
35215231 TTTT-ATTT
1 TTTTGATTT
35215239 GTTATTAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.14, C:0.07, G:0.16, T:0.64
Consensus pattern (18 bp):
TTTTGATTTCAATTTCGG
Found at i:35215721 original size:15 final size:15
Alignment explanation
Indices: 35215701--35215730 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
35215691 GAAGAAGAAA
35215701 TGTCTGGTAGTGATG
1 TGTCTGGTAGTGATG
35215716 TGTCTGGTAGTGATG
1 TGTCTGGTAGTGATG
35215731 CATCTAAAAG
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:0.13, C:0.07, G:0.40, T:0.40
Consensus pattern (15 bp):
TGTCTGGTAGTGATG
Found at i:35217516 original size:25 final size:26
Alignment explanation
Indices: 35217458--35217518 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
35217448 CTATGACTGT
**
35217458 TTTTTTAATATACATGTTGTTGACTA
1 TTTTTTAATATACATGCAGTTGACTA
* * *
35217484 TTTCTTAATATGCATGCAG-TGAGTA
1 TTTTTTAATATACATGCAGTTGACTA
35217509 TTTTTTAATA
1 TTTTTTAATA
35217519 ATATGCATGC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
25 14 0.48
26 15 0.52
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.51
Consensus pattern (26 bp):
TTTTTTAATATACATGCAGTTGACTA
Found at i:35217536 original size:96 final size:96
Alignment explanation
Indices: 35217421--35217623 Score: 345
Period size: 96 Copynumber: 2.1 Consensus size: 96
35217411 GAGTGTTTTT
* *
35217421 TAATATGCATGCAGTGATTGTTAGTGTCTATGACTGTTTTTTTAATATACATGTTGTTGACTATT
1 TAATATGCATGCAGCGATTGTTAGTGTCTATGACTATTTTTTTAATATACATGTTGTTGACT-TT
35217486 TCTTAATATGCATGCAGTGAGTA-TTTTTTAA
65 TCTTAATATGCATGCAGTGAGTATTTTTTTAA
* *
35217517 TAATATGCATGCAGCGATTGTTGGTGTGTATGACTATTTTTTTAATATACATGTTGTTGACTTTT
1 TAATATGCATGCAGCGATTGTTAGTGTCTATGACTATTTTTTTAATATACATGTTGTTGACTTTT
*
35217582 TTTAATATGCATGCAGTGAGTATTTTTTTAA
66 CTTAATATGCATGCAGTGAGTATTTTTTTAA
35217613 TAATATGCATG
1 TAATATGCATG
35217624 TAGTGACTTT
Statistics
Matches: 101, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
95 24 0.24
96 77 0.76
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.47
Consensus pattern (96 bp):
TAATATGCATGCAGCGATTGTTAGTGTCTATGACTATTTTTTTAATATACATGTTGTTGACTTTT
CTTAATATGCATGCAGTGAGTATTTTTTTAA
Found at i:35217620 original size:25 final size:27
Alignment explanation
Indices: 35217553--35217639 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 27
35217543 TGTATGACTA
*
35217553 TTTTTTTAATAT-A--CATGTTGTTGAC
1 TTTTTTTAATATCATGCATGTAG-TGAC
35217578 TTTTTTTAATATGCATGCA-GTGAGT-A-
1 TTTTTTTAATAT-CATGCATGT-AGTGAC
35217604 TTTTTTTAATAAT-ATGCATGTAGTGAC
1 TTTTTTTAAT-ATCATGCATGTAGTGAC
35217631 TTTTTTTAA
1 TTTTTTTAA
35217640 GTAGGTGTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 16
0.75 0.01 0.23
Matches are distributed among these distances:
25 20 0.38
26 13 0.25
27 13 0.25
28 3 0.06
29 3 0.06
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.53
Consensus pattern (27 bp):
TTTTTTTAATATCATGCATGTAGTGAC
Found at i:35219134 original size:36 final size:36
Alignment explanation
Indices: 35219082--35219166 Score: 134
Period size: 36 Copynumber: 2.4 Consensus size: 36
35219072 GGTTAGCCAT
* *
35219082 ATATACCATCAACCATGTATAACAATATAAGCAACA
1 ATATACCAACAACCATGTATAACAACATAAGCAACA
*
35219118 ATATACCAACACCCATGTATAACAACATAAGCAACA
1 ATATACCAACAACCATGTATAACAACATAAGCAACA
*
35219154 ATATACCAGCAAC
1 ATATACCAACAAC
35219167 AATATTACAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.49, C:0.26, G:0.06, T:0.19
Consensus pattern (36 bp):
ATATACCAACAACCATGTATAACAACATAAGCAACA
Found at i:35219181 original size:36 final size:36
Alignment explanation
Indices: 35219082--35219185 Score: 102
Period size: 36 Copynumber: 2.9 Consensus size: 36
35219072 GGTTAGCCAT
* * * * *
35219082 ATATACCATCAACCATGTATAACAATATAAGCAACA
1 ATATACCAACAACAATATATAAAAACATAAGCAACA
* * * *
35219118 ATATACCAACACCCATGTATAACAACATAAGCAACA
1 ATATACCAACAACAATATATAAAAACATAAGCAACA
*
35219154 ATATACCAGCAACAATAT-TACAAAACATAAGC
1 ATATACCAACAACAATATATA-AAAACATAAGC
35219186 TGGTTTTTAG
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
35 2 0.03
36 57 0.97
ACGTcount: A:0.51, C:0.24, G:0.06, T:0.19
Consensus pattern (36 bp):
ATATACCAACAACAATATATAAAAACATAAGCAACA
Found at i:35219527 original size:3 final size:3
Alignment explanation
Indices: 35219513--35219554 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
35219503 TGCTTCAGCA
*
35219513 TCT TCAT TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT TC
1 TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
35219555 ACTAACCCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:35221872 original size:3 final size:3
Alignment explanation
Indices: 35221864--35221900 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
35221854 TCCATGATCC
35221864 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
35221901 CAAAACAGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:35224405 original size:14 final size:14
Alignment explanation
Indices: 35224386--35224426 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
35224376 ATAAAATTAT
35224386 TAAATATTAAATAC
1 TAAATATTAAATAC
35224400 TAAATATTAAAATAC
1 TAAATATT-AAATAC
35224415 TATAATA-TAAAT
1 TA-AATATTAAAT
35224427 GTTTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 12 0.48
15 9 0.36
16 4 0.16
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (14 bp):
TAAATATTAAATAC
Found at i:35224425 original size:15 final size:14
Alignment explanation
Indices: 35224375--35224425 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
35224365 ATAAAAAATG
*
35224375 TATAAAATTATTAAA
1 TATAAAA-TACTAAA
*
35224390 TATTAAATACTAAA
1 TATAAAATACTAAA
35224404 TATTAAAATACTATAA
1 TA-TAAAATACTA-AA
35224420 TATAAA
1 TATAAA
35224426 TGTTTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 8 0.26
15 19 0.61
16 4 0.13
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (14 bp):
TATAAAATACTAAA
Found at i:35224583 original size:17 final size:17
Alignment explanation
Indices: 35224558--35224591 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35224548 CAAACATAAA
35224558 ATATGTTAATATCATCT
1 ATATGTTAATATCATCT
* *
35224575 ATATTTTAATATTATCT
1 ATATGTTAATATCATCT
35224592 TTAAATAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (17 bp):
ATATGTTAATATCATCT
Found at i:35225291 original size:3 final size:3
Alignment explanation
Indices: 35225283--35225308 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35225273 CACATGACAA
35225283 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
35225309 ATAGTAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:35227554 original size:24 final size:24
Alignment explanation
Indices: 35227527--35227585 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
35227517 GCAAGCTGTG
35227527 GCTGCTGCTGCAACTGGG-GCA-TCT
1 GCTGCTGCTGCAACTGGGAG-AGT-T
* * *
35227551 GCTGTTGTTGCAGCTGGGAGAGTT
1 GCTGCTGCTGCAACTGGGAGAGTT
35227575 GCTGCTGCTGC
1 GCTGCTGCTGC
35227586 TGCTGCTGCT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.10, C:0.24, G:0.37, T:0.29
Consensus pattern (24 bp):
GCTGCTGCTGCAACTGGGAGAGTT
Found at i:35227582 original size:3 final size:3
Alignment explanation
Indices: 35227574--35227605 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
35227564 CTGGGAGAGT
35227574 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
35227606 TTGTTGTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:35227590 original size:54 final size:54
Alignment explanation
Indices: 35227527--35227635 Score: 132
Period size: 54 Copynumber: 2.0 Consensus size: 54
35227517 GCAAGCTGTG
* *
35227527 GCTGCTGCTGCAACTGGGGCAT-CTGCTGTTGTTGCAGCTG-GGAGAGTTGCTGCT
1 GCTGCTGCTGCAACTGCGGC-TGCTGCTGTTGTTGCAGCTGTGG-GAGCTGCTGCT
** * *
35227581 GCTGCTGCTGCTGCTGCTGCTGCTGTTGTTGTTGCAGCTGTGGGAGCTGCTGCT
1 GCTGCTGCTGCAACTGCGGCTGCTGCTGTTGTTGCAGCTGTGGGAGCTGCTGCT
35227635 G
1 G
35227636 TGGCATCTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 1 0.02
54 44 0.94
55 2 0.04
ACGTcount: A:0.07, C:0.23, G:0.38, T:0.32
Consensus pattern (54 bp):
GCTGCTGCTGCAACTGCGGCTGCTGCTGTTGTTGCAGCTGTGGGAGCTGCTGCT
Found at i:35227630 original size:39 final size:39
Alignment explanation
Indices: 35227587--35227686 Score: 98
Period size: 39 Copynumber: 2.6 Consensus size: 39
35227577 TGCTGCTGCT
* * *
35227587 GCTGCTGCTGCTGCTGCTGTTGTTGTTGCAGCTGTGGGA
1 GCTGCTGCTGCTGCTGCTGTTGCTGTTGCAGCAGTGGCA
* *
35227626 GCTGCTGCTG-TGGCAT-CTGTTGCTGTTGTAGCAGTGGCT
1 GCTGCTGCTGCT-GC-TGCTGTTGCTGTTGCAGCAGTGGCA
*
35227665 GCAT-CTGTTGCTGCTGCTGTTG
1 GC-TGCTGCTGCTGCTGCTGTTG
35227687 ATGCTGGCTT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
38 2 0.04
39 45 0.90
40 3 0.06
ACGTcount: A:0.06, C:0.21, G:0.36, T:0.37
Consensus pattern (39 bp):
GCTGCTGCTGCTGCTGCTGTTGCTGTTGCAGCAGTGGCA
Found at i:35231736 original size:15 final size:15
Alignment explanation
Indices: 35231716--35231747 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
35231706 TATTTGCTAA
35231716 TGTGCTTAAGAGAGC
1 TGTGCTTAAGAGAGC
35231731 TGTGCTTAAGAGAGC
1 TGTGCTTAAGAGAGC
35231746 TG
1 TG
35231748 AGCTACGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.34, T:0.28
Consensus pattern (15 bp):
TGTGCTTAAGAGAGC
Found at i:35242406 original size:15 final size:15
Alignment explanation
Indices: 35242386--35242418 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
35242376 GTGAGCGCTC
35242386 AATTGAATCGAATCG
1 AATTGAATCGAATCG
*
35242401 AATTGAATTGAATCG
1 AATTGAATCGAATCG
35242416 AAT
1 AAT
35242419 GAAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.30
Consensus pattern (15 bp):
AATTGAATCGAATCG
Found at i:35242998 original size:29 final size:29
Alignment explanation
Indices: 35242943--35243002 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
35242933 GGGAGGAAGT
35242943 AAAAGTTTTGGGGAAAAGCAAAAGGAAAA
1 AAAAGTTTTGGGGAAAAGCAAAAGGAAAA
* * *
35242972 AAAAGTTTTGGGG-GAAGTAAAAGGGAAA
1 AAAAGTTTTGGGGAAAAGCAAAAGGAAAA
35243000 AAA
1 AAA
35243003 TTTAGCGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.15
Consensus pattern (29 bp):
AAAAGTTTTGGGGAAAAGCAAAAGGAAAA
Found at i:35243060 original size:19 final size:20
Alignment explanation
Indices: 35243015--35243052 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35243005 TAGCGGTTCG
*
35243015 GGGGGAAGTAAAATTTTTTA
1 GGGGGAAGTAAAATGTTTTA
35243035 GGGGGAAGT-AAATGTTTT
1 GGGGGAAGTAAAATGTTTT
35243053 GGGAGGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (20 bp):
GGGGGAAGTAAAATGTTTTA
Found at i:35253435 original size:10 final size:10
Alignment explanation
Indices: 35253400--35253445 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
35253390 CATATTCCGA
35253400 CACATATCAAT
1 CACATAT-AAT
*
35253411 CACATATAAG
1 CACATATAAT
35253421 CACATATAAT
1 CACATATAAT
* *
35253431 TACATACAAT
1 CACATATAAT
35253441 CACAT
1 CACAT
35253446 TTAGTCATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 23 0.77
11 7 0.23
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.26
Consensus pattern (10 bp):
CACATATAAT
Found at i:35265464 original size:28 final size:28
Alignment explanation
Indices: 35265423--35265479 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
35265413 AAAAAAGTGA
35265423 AAAAAACAACAAAATAACAACAAAATAGT
1 AAAAAACAACAAAATAACAA-AAAATAGT
* *
35265452 AAAAAA-AAGAAAATAATAAAAAATAGT
1 AAAAAACAACAAAATAACAAAAAATAGT
35265479 A
1 A
35265480 GTTTTTTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 9 0.35
28 11 0.42
29 6 0.23
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.12
Consensus pattern (28 bp):
AAAAAACAACAAAATAACAAAAAATAGT
Found at i:35267152 original size:25 final size:25
Alignment explanation
Indices: 35267124--35267235 Score: 138
Period size: 25 Copynumber: 4.5 Consensus size: 25
35267114 TAAGTAATAC
* *
35267124 GCCAC-AAGGACTCTTTAGATCATCT
1 GCCACAAAGG-CTCTTCAGATAATCT
**
35267149 GCCATTAAGGCTCTTCAGATAATCT
1 GCCACAAAGGCTCTTCAGATAATCT
* *
35267174 GCCACAAAGGCTCTTTAGATAATTT
1 GCCACAAAGGCTCTTCAGATAATCT
35267199 GCCACAAAGGCTCTTCAGATAAT-T
1 GCCACAAAGGCTCTTCAGATAATCT
35267223 GGCCACAAAGGCT
1 -GCCACAAAGGCT
35267236 TGGTTTGGTT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
24 1 0.01
25 72 0.94
26 4 0.05
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (25 bp):
GCCACAAAGGCTCTTCAGATAATCT
Found at i:35267202 original size:50 final size:50
Alignment explanation
Indices: 35267124--35267235 Score: 156
Period size: 50 Copynumber: 2.2 Consensus size: 50
35267114 TAAGTAATAC
* **
35267124 GCCAC-AAGGACTCTTTAGATCATCTGCCATTAAGGCTCTTCAGATAATCT-
1 GCCACAAAGG-CTCTTTAGATAATCTGCCACAAAGGCTCTTCAGATAAT-TG
*
35267174 GCCACAAAGGCTCTTTAGATAATTTGCCACAAAGGCTCTTCAGATAATTG
1 GCCACAAAGGCTCTTTAGATAATCTGCCACAAAGGCTCTTCAGATAATTG
35267224 GCCACAAAGGCT
1 GCCACAAAGGCT
35267236 TGGTTTGGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
49 1 0.02
50 51 0.91
51 4 0.07
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (50 bp):
GCCACAAAGGCTCTTTAGATAATCTGCCACAAAGGCTCTTCAGATAATTG
Found at i:35273935 original size:13 final size:13
Alignment explanation
Indices: 35273917--35273948 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
35273907 TTTCCAGCAA
35273917 TTATGAATTTATT
1 TTATGAATTTATT
35273930 TTATGAATTTATT
1 TTATGAATTTATT
*
35273943 TGATGA
1 TTATGA
35273949 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:35274163 original size:50 final size:51
Alignment explanation
Indices: 35274043--35274285 Score: 294
Period size: 50 Copynumber: 4.7 Consensus size: 51
35274033 ATTTGGGTAA
* *
35274043 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTATGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC-GATGA-C--G
*
35274099 AGAGATCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGATGACG
* * * *
35274149 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA-GATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGATGACG
* * * *
35274199 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCAACC-ATCACG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGC-ACCGATGACG
*
35274250 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGC
35274286 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
50 84 0.51
51 7 0.04
52 30 0.18
53 2 0.01
54 1 0.01
55 2 0.01
56 40 0.24
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (51 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGATGACG
Found at i:35276285 original size:3 final size:3
Alignment explanation
Indices: 35276279--35276304 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35276269 TGATACAATT
35276279 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
35276305 TTTTGAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:35279655 original size:29 final size:29
Alignment explanation
Indices: 35279628--35279798 Score: 106
Period size: 29 Copynumber: 6.0 Consensus size: 29
35279618 TTTTCTTTTC
35279628 CAAAGATAGCCACAAAGGGTTTCCTTT--
1 CAAAGATAGCCACAAAGGGTTTCCTTTAG
* * *
35279655 TAAAGTCTCA-TCACAAAGGTGTTT--TTT-G
1 CAAAG-AT-AGCCACAAAGG-GTTTCCTTTAG
* *
35279683 ACAGAGATAGCCACAAAGGTTTTCCTTTAG
1 -CAAAGATAGCCACAAAGGGTTTCCTTTAG
* * * *
35279713 TAGAGATTAGCCACAAAGGCTATCCTTTAG
1 CAAAGA-TAGCCACAAAGGGTTTCCTTTAG
* *
35279743 CAAAGATAGCCACAAA-GGCTTCCTTTAA
1 CAAAGATAGCCACAAAGGGTTTCCTTTAG
** *
35279771 CTGAGAGTAGCCACAAA-GGCTTCCTTTA
1 CAAAGA-TAGCCACAAAGGGTTTCCTTTA
35279799 ACATTCAGTA
Statistics
Matches: 114, Mismatches: 19, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
27 11 0.10
28 30 0.26
29 47 0.41
30 26 0.23
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (29 bp):
CAAAGATAGCCACAAAGGGTTTCCTTTAG
Found at i:35279726 original size:30 final size:28
Alignment explanation
Indices: 35279685--35279936 Score: 149
Period size: 29 Copynumber: 8.7 Consensus size: 28
35279675 GTTTTTTGAC
*
35279685 AGAGATAGCCACAAAGGTTTTCCTTTAGT
1 AGAGATAGCCACAAAGG-CTTCCTTTAGT
*
35279714 AGAGATTAGCCACAAAGGCTATCCTTTAGC
1 AGAGA-TAGCCACAAAGGCT-TCCTTTAGT
* *
35279744 AAAGATAGCCACAAAGGCTTCCTTTAACT
1 AGAGATAGCCACAAAGGCTTCCTTT-AGT
*
35279773 -GAGAGTAGCCACAAAGGCTTCCTTTAACAT
1 AGAGA-TAGCCACAAAGGCTTCCTTT-A-GT
** * *
35279803 TCAGTACTCA-CCACAAAGGCTTTCTTT-TT
1 AGAG-A-T-AGCCACAAAGGCTTCCTTTAGT
**
35279832 AGAGTATTTCCACAAAGGCATTCCTTTCAG-
1 AGAG-ATAGCCACAAAGGC-TTCCTTT-AGT
* * **
35279862 AG-G-TAGCCACAAAGACATTCTTTTAAC
1 AGAGATAGCCACAAAGGC-TTCCTTTAGT
* * *
35279889 AGAGATAGCCACAAAGACTTTCTTATAAT
1 AGAGATAGCCACAAAGGCTTCCTT-TAGT
35279918 AGATG-TAGCCACAAAGGCT
1 AGA-GATAGCCACAAAGGCT
35279937 CACTTATATA
Statistics
Matches: 181, Mismatches: 25, Indels: 34
0.75 0.10 0.14
Matches are distributed among these distances:
26 1 0.01
27 19 0.10
28 25 0.14
29 87 0.48
30 28 0.15
31 2 0.01
32 18 0.10
33 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (28 bp):
AGAGATAGCCACAAAGGCTTCCTTTAGT
Found at i:35279768 original size:58 final size:58
Alignment explanation
Indices: 35279687--35279798 Score: 165
Period size: 58 Copynumber: 1.9 Consensus size: 58
35279677 TTTTTGACAG
* * *
35279687 AGATAGCCACAAAGGTTTTCCTTT-AGTAGAGATTAGCCACAAAGGCTATCCTTTAGCAA
1 AGATAGCCACAAAGGTCTTCCTTTAACT-GAGAGTAGCCACAAAGGCT-TCCTTTAGCAA
35279746 AGATAGCCACAAAGG-CTTCCTTTAACTGAGAGTAGCCACAAAGGCTTCCTTTA
1 AGATAGCCACAAAGGTCTTCCTTTAACTGAGAGTAGCCACAAAGGCTTCCTTTA
35279799 ACATTCAGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
57 7 0.14
58 25 0.51
59 17 0.35
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (58 bp):
AGATAGCCACAAAGGTCTTCCTTTAACTGAGAGTAGCCACAAAGGCTTCCTTTAGCAA
Found at i:35282058 original size:9 final size:9
Alignment explanation
Indices: 35282044--35282069 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
35282034 AGAGTCATGT
35282044 TCACATATA
1 TCACATATA
35282053 TCACATATA
1 TCACATATA
35282062 TCACATAT
1 TCACATAT
35282070 TGTGTGCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (9 bp):
TCACATATA
Found at i:35283430 original size:26 final size:26
Alignment explanation
Indices: 35283392--35283441 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
35283382 GGATCACTTA
* *
35283392 TTTTAATTCTTTTCTTTTTCTTTTTG
1 TTTTAATTCTTTTATTTTTATTTTTG
* *
35283418 TTTTAGTTGTTTTATTTTTATTTT
1 TTTTAATTCTTTTATTTTTATTTT
35283442 CTTAAACTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.10, C:0.06, G:0.06, T:0.78
Consensus pattern (26 bp):
TTTTAATTCTTTTATTTTTATTTTTG
Found at i:35291154 original size:21 final size:20
Alignment explanation
Indices: 35291130--35291176 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
35291120 ATTATAAAAT
35291130 ATTTTAAAAAATATTTTTAT-A
1 ATTTTAAAAAAT-TTTTT-TGA
* *
35291151 ATTTTTAATAATTTTTTTGA
1 ATTTTAAAAAATTTTTTTGA
35291171 ATTTTA
1 ATTTTA
35291177 CTCTTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 11 0.50
21 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTTTAAAAAATTTTTTTGA
Found at i:35299802 original size:48 final size:48
Alignment explanation
Indices: 35299603--35299799 Score: 225
Period size: 48 Copynumber: 4.1 Consensus size: 48
35299593 TACTATGCGT
35299603 ACCGATAATCTGTTATGACACAAAGGTGGCACGGACTGTGTGCAGGCC
1 ACCGATAATCTGTTATGACACAAAGGTGGCACGGACTGTGTGCAGGCC
* * * * * *
35299651 ACCGATATTCTATTGTAACACAAGGGTGGCACAGACTGTGTGCAGGCC
1 ACCGATAATCTGTTATGACACAAAGGTGGCACGGACTGTGTGCAGGCC
* * * * * *
35299699 ACCAATAA-CTTGTTAAGATACAAGGGTGGTACGGACTATGTGCAGGCC
1 ACCGATAATC-TGTTATGACACAAAGGTGGCACGGACTGTGTGCAGGCC
* * * * *
35299747 ATCGAGAATCTGTTATTACACAAAGGTGGTATGGACTGTGTGCAGGCC
1 ACCGATAATCTGTTATGACACAAAGGTGGCACGGACTGTGTGCAGGCC
35299795 ACCGA
1 ACCGA
35299800 GAAATTTGTT
Statistics
Matches: 121, Mismatches: 26, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
47 1 0.01
48 119 0.98
49 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (48 bp):
ACCGATAATCTGTTATGACACAAAGGTGGCACGGACTGTGTGCAGGCC
Done.