Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 42
Found at i:2962268 original size:54 final size:54
Alignment explanation
Indices: 2962069--2962367 Score: 175
Period size: 55 Copynumber: 5.5 Consensus size: 54
2962059 CACGATTGTT
* * * * * **
2962069 GAAGATTGTTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGC-AGACACGATTGTT
1 GAAGA-TGTTCGAGTTCT-ATACTCCCTGAAAAAAGAGGGAGCGA-ACCCGTTTGAA
* * * * * * **
2962124 GAAGATTATTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGC-AGACACGATTGTT
1 GAAGA-TGTTCGAGTTCT-ATACTCCCTGAAAAAAGAGGGAGCGA-ACCCGTTTGAA
* * * *
2962179 GAAGATTGTTCGAGTTTTACACTCCCT-AGAGAAAGAGGGAGCAAACCCGTTTGAA
1 GAAGA-TGTTCGAGTTCTATACTCCCTGA-AAAAAGAGGGAGCGAACCCGTTTGAA
* * *
2962234 GAAGATATTCGAGTTCTATTCTCCCTGAAAAAAGAGGGAGTGAACCCGTTT--A
1 GAAGATGTTCGAGTTCTATACTCCCTGAAAAAAGAGGGAGCGAACCCGTTTGAA
* * * * **
2962286 -AAGACGTTCGAGTTCCATACTCCCT-AGATAAAGAGGGAACGAACCCGTAAGAA
1 GAAGATGTTCGAGTTCTATACTCCCTGA-AAAAAGAGGGAGCGAACCCGTTTGAA
* * *
2962339 GAATATGTTCAAGTTCTATACTCTCTGAA
1 GAAGATGTTCGAGTTCTATACTCCCTGAA
2962368 GGACTGGGGT
Statistics
Matches: 204, Mismatches: 31, Indels: 19
0.80 0.12 0.07
Matches are distributed among these distances:
50 1 0.00
51 39 0.19
52 1 0.00
53 1 0.00
54 59 0.29
55 100 0.49
56 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (54 bp):
GAAGATGTTCGAGTTCTATACTCCCTGAAAAAAGAGGGAGCGAACCCGTTTGAA
Found at i:2962319 original size:51 final size:53
Alignment explanation
Indices: 2962199--2962340 Score: 150
Period size: 51 Copynumber: 2.7 Consensus size: 53
2962189 CGAGTTTTAC
* * * *
2962199 ACTCCCTAGAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATATTCGAGTTCTAT
1 ACTCCCTAGAAAAAGAGGGAGCGAACCCGTTT-AAGAAGACATTCGAGTTCCAT
* * *
2962253 TCTCCCT-GAAAAAAGAGGGAGTGAACCCGTTT-A-AAGACGTTCGAGTTCCAT
1 ACTCCCTAG-AAAAAGAGGGAGCGAACCCGTTTAAGAAGACATTCGAGTTCCAT
* *
2962304 ACTCCCTAGATAAAGAGGGAACGAACCCG--TAAGAAGA
1 ACTCCCTAGAAAAAGAGGGAGCGAACCCGTTTAAGAAGA
2962341 ATATGTTCAA
Statistics
Matches: 73, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
49 1 0.01
50 1 0.01
51 42 0.58
52 2 0.03
53 1 0.01
54 26 0.36
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (53 bp):
ACTCCCTAGAAAAAGAGGGAGCGAACCCGTTTAAGAAGACATTCGAGTTCCAT
Found at i:2970418 original size:21 final size:21
Alignment explanation
Indices: 2970381--2970420 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2970371 TCTGCTGAAA
**
2970381 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGTTGCGGAGTATG
2970402 CTCCACCTGTTGCGGAGTA
1 CTCCACCTGTTGCGGAGTA
2970421 CTACTTGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.33
Consensus pattern (21 bp):
CTCCACCTGTTGCGGAGTATG
Found at i:2975547 original size:19 final size:21
Alignment explanation
Indices: 2975525--2975571 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
2975515 ATAAGGTAAA
2975525 ATTATTTTTATTATAT-TAT-
1 ATTATTTTTATTATATATATG
* *
2975544 ATTATATTTATTTTATATATG
1 ATTATTTTTATTATATATATG
2975565 ATTATTT
1 ATTATTT
2975572 GAAAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 14 0.61
20 3 0.13
21 6 0.26
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
ATTATTTTTATTATATATATG
Found at i:2976537 original size:15 final size:15
Alignment explanation
Indices: 2976514--2976552 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2976504 TTATAACTGC
*
2976514 AAAAATTAATATAAT
1 AAAAATTAATAAAAT
*
2976529 AAAATTTAATAAAAT
1 AAAAATTAATAAAAT
2976544 AATAAATTA
1 AA-AAATTA
2976553 TTAATTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAATTAATAAAAT
Found at i:2981830 original size:184 final size:185
Alignment explanation
Indices: 2981399--2981774 Score: 531
Period size: 185 Copynumber: 2.0 Consensus size: 185
2981389 AACCGAAATT
* * *** * ** * *
2981399 AAATTTTAAATATATTATATATAACATAT-AGGCTCAGCCCAAACCATTTAAAACCCAATTAATA
1 AAATATTATATATATTATATATAACATATGA-GAAAAGCCAAAAAAATTTAAAATCAAATTAATA
2981463 ATTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATT
65 ATTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATT
*
2981528 TTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTAATTAAA
* ** * ** *
2981584 AAATATTATATATATTATATATAACATATGGGTTAAGCCCAAACCATTTAAAATCCAATTAATAA
1 AAATATTATATATATTATATATAACATATGAGAAAAGCCAAAAAAATTTAAAATCAAATTAATAA
* * *
2981649 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAA-TT
66 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
*
2981713 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTAATTAAA
2981768 AAATATT
1 AAATATT
2981775 TAATTTTTAT
Statistics
Matches: 179, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
184 62 0.35
185 117 0.65
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (185 bp):
AAATATTATATATATTATATATAACATATGAGAAAAGCCAAAAAAATTTAAAATCAAATTAATAA
TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTAATTAAA
Found at i:2982968 original size:15 final size:16
Alignment explanation
Indices: 2982945--2982975 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2982935 GTTTCAAAAT
2982945 AATTCATTTTATTTTA
1 AATTCATTTTATTTTA
2982961 AATT-ATTTTATTTTA
1 AATTCATTTTATTTTA
2982976 TAACTGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTCATTTTATTTTA
Found at i:2987178 original size:23 final size:23
Alignment explanation
Indices: 2987152--2987221 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
2987142 CTATTACAAC
*
2987152 TGTTAGGTTTTGAGTTTGTTTGA
1 TGTTATGTTTTGAGTTTGTTTGA
* *
2987175 TGTTATGTTTTGAGTTTGTCTGG
1 TGTTATGTTTTGAGTTTGTTTGA
*
2987198 TGTTATATTTTGAGTTTGTTTGA
1 TGTTATGTTTTGAGTTTGTTTGA
2987221 T
1 T
2987222 TATAAAAACT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.13, C:0.01, G:0.27, T:0.59
Consensus pattern (23 bp):
TGTTATGTTTTGAGTTTGTTTGA
Found at i:2988537 original size:3 final size:3
Alignment explanation
Indices: 2988529--2988566 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
2988519 GCATGTAAAT
*
2988529 TAA TAA TAA TAA TTAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TA
2988567 TTATTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 27 0.87
4 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2988544 original size:13 final size:13
Alignment explanation
Indices: 2988526--2988575 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
2988516 CCTGCATGTA
2988526 AATTAATAATAAT
1 AATTAATAATAAT
2988539 AATTAATAATAAT
1 AATTAATAATAAT
2988552 AA-TAATTTAATAAT
1 AATTAA--TAATAAT
*
2988566 -ATTATTAATA
1 AATTAATAATA
2988576 TTTTTGACCC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
12 8 0.24
13 16 0.48
14 9 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AATTAATAATAAT
Found at i:2988574 original size:9 final size:9
Alignment explanation
Indices: 2988532--2988577 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
2988522 TGTAAATTAA
2988532 TAATAATAAT
1 TAATAAT-AT
*
2988542 TAATAATAA
1 TAATAATAT
2988551 TAATAAT-T
1 TAATAATAT
2988559 TAATAATAT
1 TAATAATAT
*
2988568 TATTAATAT
1 TAATAATAT
2988577 T
1 T
2988578 TTTGACCCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.22
9 18 0.56
10 7 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TAATAATAT
Found at i:2988574 original size:17 final size:17
Alignment explanation
Indices: 2988529--2988566 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
2988519 GCATGTAAAT
2988529 TAATAATAATAA-TTAA
1 TAATAATAATAATTTAA
2988545 TAATAATAATAATTTAA
1 TAATAATAATAATTTAA
2988562 TAATA
1 TAATA
2988567 TTATTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATAATAATAATTTAA
Found at i:2989976 original size:10 final size:10
Alignment explanation
Indices: 2989961--2990041 Score: 61
Period size: 10 Copynumber: 8.7 Consensus size: 10
2989951 GGGTCTCCAA
2989961 CGTTTATGTT
1 CGTTTATGTT
2989971 CGTTTATGTT
1 CGTTTATGTT
*
2989981 CATGTTCATGTT
1 C--GTTTATGTT
*
2989993 CATTTATGTT
1 CGTTTATGTT
2990003 CG----TGTT
1 CGTTTATGTT
2990009 CGTTTATGTT
1 CGTTTATGTT
2990019 C---T-TGTT
1 CGTTTATGTT
*
2990025 TGTTTATGTT
1 CGTTTATGTT
2990035 CGTTTAT
1 CGTTTAT
2990042 TTATTAAATG
Statistics
Matches: 55, Mismatches: 6, Indels: 20
0.68 0.07 0.25
Matches are distributed among these distances:
6 10 0.18
7 1 0.02
9 1 0.02
10 34 0.62
12 9 0.16
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:2989987 original size:16 final size:16
Alignment explanation
Indices: 2989982--2990035 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
2989972 GTTTATGTTC
*
2989982 ATGTTCATGTTCATTT
1 ATGTTCATGTTCGTTT
*
2989998 ATGTTCGTGTTCGTTT
1 ATGTTCATGTTCGTTT
* *
2990014 ATGTTCTTGTTTGTTT
1 ATGTTCATGTTCGTTT
2990030 ATGTTC
1 ATGTTC
2990036 GTTTATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (16 bp):
ATGTTCATGTTCGTTT
Found at i:2990004 original size:32 final size:32
Alignment explanation
Indices: 2989963--2990041 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
2989953 GTCTCCAACG
2989963 TTTATGTTCGTTTATGTTCATGTTCATGTTCA
1 TTTATGTTCGTTTATGTTCATGTTCATGTTCA
* * * **
2989995 TTTATGTTCGTGTT-CGTTTATGTTCTTGTTTG
1 TTTATGTTCGT-TTATGTTCATGTTCATGTTCA
2990027 TTTATGTTCGTTTAT
1 TTTATGTTCGTTTAT
2990042 TTATTAAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 2 0.05
32 35 0.90
33 2 0.05
ACGTcount: A:0.11, C:0.10, G:0.18, T:0.61
Consensus pattern (32 bp):
TTTATGTTCGTTTATGTTCATGTTCATGTTCA
Found at i:2990024 original size:22 final size:22
Alignment explanation
Indices: 2989966--2990009 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2989956 TCCAACGTTT
*
2989966 ATGTTCGTTTATGTTCATGTTC
1 ATGTTCATTTATGTTCATGTTC
*
2989988 ATGTTCATTTATGTTCGTGTTC
1 ATGTTCATTTATGTTCATGTTC
2990010 GTTTATGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (22 bp):
ATGTTCATTTATGTTCATGTTC
Found at i:2993673 original size:25 final size:25
Alignment explanation
Indices: 2993645--2993703 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
2993635 TTCTTATTGC
* *
2993645 ATTAATCGATACTTACAAAATGTAA
1 ATTAATCAAGACTTACAAAATGTAA
* * *
2993670 ATTAGTCAAGACTTACAAATTTTAA
1 ATTAATCAAGACTTACAAAATGTAA
2993695 ATTAATCAA
1 ATTAATCAA
2993704 AATTTATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (25 bp):
ATTAATCAAGACTTACAAAATGTAA
Found at i:2994333 original size:3 final size:3
Alignment explanation
Indices: 2994327--2994380 Score: 56
Period size: 3 Copynumber: 17.3 Consensus size: 3
2994317 CTTTTTTTAT
* *
2994327 TTA TTA TTA TTA TTA TTTA TTA TTA TTA TT- TTGT TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
2994373 TTAA TTA T
1 TT-A TTA T
2994381 GTTACATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
2 2 0.05
3 34 0.77
4 8 0.18
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2994339 original size:13 final size:13
Alignment explanation
Indices: 2994330--2994357 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2994320 TTTTTATTTA
2994330 TTATTATTATTAT
1 TTATTATTATTAT
2994343 TTATTATTATTAT
1 TTATTATTATTAT
2994356 TT
1 TT
2994358 TGTTTATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:2997973 original size:30 final size:30
Alignment explanation
Indices: 2997937--2997996 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
2997927 ATTATCTTAC
* *
2997937 TTGTACTAACTAATTTCTTTTCTTTTGTTT
1 TTGTACTAACTAATTTCTTCTCTCTTGTTT
* *
2997967 TTGTACTAATTTATTTCTTCTCTCTTGTTT
1 TTGTACTAACTAATTTCTTCTCTCTTGTTT
2997997 GTGTCATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (30 bp):
TTGTACTAACTAATTTCTTCTCTCTTGTTT
Found at i:3002116 original size:35 final size:36
Alignment explanation
Indices: 3002070--3002166 Score: 133
Period size: 35 Copynumber: 2.7 Consensus size: 36
3002060 TTTCTTTGGT
* *
3002070 AAAACAAATTTTGTCTCGCTTAAGACAGTTT-TCTA
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTA
* * *
3002105 AAAACAAATTTTGTCTCGCTTGAGATAATTTCTTTC
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTA
*
3002141 AAAACAAATTTCGTCTCGCTTGAGAC
1 AAAACAAATTTTGTCTCGCTTGAGAC
3002167 CTTTTCCCTT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 28 0.52
36 26 0.48
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTA
Found at i:3002325 original size:105 final size:105
Alignment explanation
Indices: 3002133--3002478 Score: 461
Period size: 105 Copynumber: 3.3 Consensus size: 105
3002123 CTTGAGATAA
* * *
3002133 TTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTGGATATACAAATTTCGAATTT
1 TTTCTTTCAAAACAAACTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATACAAATTTCGAATTT
* *
3002198 GTTTCACATTAAGCAAAGTTAATATCACTTGAGATTGTTG
66 GTTTCACATTAAACAAAGTTAATCTCACTTGAGATTGTTG
* ** * * *
3002238 TTTCTTTTAAAACAAACTTCGTCTCGCTTGAGATATTTTTCCTTTAAGATACAAATTTCAAATTT
1 TTTCTTTCAAAACAAACTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATACAAATTTCGAATTT
* *
3002303 GATTCAC-TTAAAACAAAATTAATCTCACCTT-AGATTGTTG
66 GTTTCACATT-AAACAAAGTTAATCTCA-CTTGAGATTGTTG
* *
3002343 TTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTT
1 TTTCTTTCAAAACAAACTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATACAAATTTCGAATTT
* *
3002408 GTTTCACATTAAACAAAGTTGATCTCACTTGAGATCG-T-
66 GTTTCACATTAAACAAAGTTAATCTCACTTGAGATTGTTG
*
3002446 TTTC--TCAAAAACAAACTTTGTCTCGCTTGAGAC
1 TTTCTTTC-AAAACAAACTTCGTCTCGCTTGAGAC
3002479 AATTTCTCTA
Statistics
Matches: 209, Mismatches: 27, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
101 2 0.01
102 24 0.11
103 4 0.02
104 6 0.03
105 168 0.80
106 5 0.02
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (105 bp):
TTTCTTTCAAAACAAACTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATACAAATTTCGAATTT
GTTTCACATTAAACAAAGTTAATCTCACTTGAGATTGTTG
Found at i:3002475 original size:36 final size:34
Alignment explanation
Indices: 3002430--3002548 Score: 114
Period size: 36 Copynumber: 3.4 Consensus size: 34
3002420 ACAAAGTTGA
*
3002430 TCTCACTTGAGATCGTTTTCTCAAAAACAAACTTTG
1 TCTCACTTGAGA-C-TTTTCTCAAAAACAAATTTTG
* *
3002466 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGAC-TTTTCTC-AAAAACAAATTTTG
* * * *
3002502 TCTCATTTGAGACTATATCT-TAAAGCAAATTTTG
1 TCTCACTTGAGACT-TTTCTCAAAAACAAATTTTG
*
3002536 TCTCGCTTGAGAC
1 TCTCACTTGAGAC
3002549 ATCATTTTCT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 23 0.33
35 7 0.10
36 39 0.57
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (34 bp):
TCTCACTTGAGACTTTTCTCAAAAACAAATTTTG
Found at i:3002536 original size:34 final size:36
Alignment explanation
Indices: 3002448--3002549 Score: 129
Period size: 36 Copynumber: 2.9 Consensus size: 36
3002438 GAGATCGTTT
* *
3002448 TCTC-AAAAACAAACTTTGTCTCGCTTGAGACAATT
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
** *
3002483 TCTCTAAAAACAAATTTTGTCTCATTTGAGACTATA
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
*
3002519 TCT-T-AAAGCAAATTTTGTCTCGCTTGAGACA
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
3002550 TCATTTTCTC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 23 0.40
35 5 0.09
36 29 0.51
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (36 bp):
TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
Found at i:3002833 original size:28 final size:28
Alignment explanation
Indices: 3002795--3002855 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
3002785 GACAATTTTG
*
3002795 TGAAAAAAATCTTTGAGAT-TGTTTCTTT
1 TGAAAAAAATCTTTGAG-TCTATTTCTTT
3002823 TGAAAAAAATCTTTGAGTCTATTTCTTT
1 TGAAAAAAATCTTTGAGTCTATTTCTTT
3002851 TGAAA
1 TGAAA
3002856 CAAAGTTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.44
Consensus pattern (28 bp):
TGAAAAAAATCTTTGAGTCTATTTCTTT
Found at i:3002919 original size:143 final size:144
Alignment explanation
Indices: 3002762--3003030 Score: 445
Period size: 146 Copynumber: 1.9 Consensus size: 144
3002752 GAATCTTTTA
3002762 AAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTG-AAAAAAATCTTTGAGATTGTTTCTTTTG-
1 AAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAAATCTTTGAGA--GTTTCTTTTGA
* *
3002825 AA-AAAAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTTAAGACAATTTCGTGA
64 AACAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGACAATTTCGTGA
3002889 AAAATCTTTGAGTCTG
129 AAAATCTTTGAGTCTG
3002905 AAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAAAAATCTTTGAGAGTTTCTTTTGA
1 AAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTG--AAAAAAAATCTTTGAGAGTTTCTTTTGA
* *
3002970 AACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTC
64 AACAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGACAATTTC
3003031 TTTTGAAACA
Statistics
Matches: 117, Mismatches: 4, Indels: 7
0.91 0.03 0.05
Matches are distributed among these distances:
143 35 0.30
144 10 0.09
145 2 0.02
146 70 0.60
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.41
Consensus pattern (144 bp):
AAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAAATCTTTGAGAGTTTCTTTTGAAA
CAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGACAATTTCGTGAAA
AATCTTTGAGTCTG
Found at i:3002993 original size:30 final size:30
Alignment explanation
Indices: 3002945--3003073 Score: 95
Period size: 30 Copynumber: 4.1 Consensus size: 30
3002935 TTGTGAAAAA
* *
3002945 AAAAATCTTTGAG--AGTTTCTTTTGAAAC
1 AAAAATCTTTGAGTCTGTTTCTTTGGAAAC
3002973 AAAAATCTTTGAGTCTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGTCTGTTTCTTTGGAAAC
** *
3003003 -AAAAT-TTTGTCTCTCTTAAGATAATTTCTTTTGAAAC
1 AAAAATCTTTG--AGTC-T--G----TTTCTTTGGAAAC
*
3003040 AAAAATCTTTGGGTCTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGTCTGTTTCTTTGGAAAC
3003070 AAAA
1 AAAA
3003074 TTTTGTCTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 24
0.71 0.07 0.21
Matches are distributed among these distances:
28 17 0.21
29 5 0.06
30 31 0.39
31 1 0.01
33 1 0.01
34 1 0.01
36 1 0.01
37 14 0.17
38 5 0.06
39 4 0.05
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (30 bp):
AAAAATCTTTGAGTCTGTTTCTTTGGAAAC
Found at i:3003040 original size:37 final size:37
Alignment explanation
Indices: 3002990--3003115 Score: 103
Period size: 37 Copynumber: 3.6 Consensus size: 37
3002980 TTTGAGTCTG
3002990 TTTCTTTGGAAACAAAAT-TTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAACAAAATCTTTGTCTCTCTTAAGAT-A
* **
3003027 TTTCTTTTGAAACAAAAATCTTTG--GGTC-T--G---
1 TTTCTTTGGAAAC-AAAATCTTTGTCTCTCTTAAGATA
*
3003057 TTTCTTTGGAAACAAAAT-TTTGTCTTTCTTAAGATA
1 TTTCTTTGGAAACAAAATCTTTGTCTCTCTTAAGATA
*
3003093 TTTTCTTTTGAAA-AAAATCTTTG
1 -TTTCTTTGGAAACAAAATCTTTG
3003116 AATATGTTTC
Statistics
Matches: 70, Mismatches: 7, Indels: 24
0.69 0.07 0.24
Matches are distributed among these distances:
28 4 0.06
29 5 0.07
30 14 0.20
31 1 0.01
33 1 0.01
34 1 0.01
36 6 0.09
37 29 0.41
38 5 0.07
39 4 0.06
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (37 bp):
TTTCTTTGGAAACAAAATCTTTGTCTCTCTTAAGATA
Found at i:3003068 original size:67 final size:67
Alignment explanation
Indices: 3002960--3003126 Score: 275
Period size: 67 Copynumber: 2.5 Consensus size: 67
3002950 TCTTTGAGAG
3002960 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
3003025 AA
66 AA
* *
3003027 TTTCTTTTGAAACAAAAATCTTTGGGTCTGTTTCTTTGGAAACAAAATTTTGTCTTTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
*
3003092 AT
66 AA
* *
3003094 TTTCTTTTG-AA-AAAAATCTTTGAATATGTTTCT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCT
3003127 CTTAAAATGA
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
65 19 0.20
66 2 0.02
67 73 0.78
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
AA
Found at i:3003162 original size:64 final size:66
Alignment explanation
Indices: 3002958--3003168 Score: 241
Period size: 67 Copynumber: 3.2 Consensus size: 66
3002948 AATCTTTGAG
* *
3002958 AGTTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAG
1 AGTTTCTTTTGAAACAAAAATCTTTGAATATGTTTCTTT-GAAACAAAATTTTGTCTCTCTTAAG
3003023 AT
65 AT
* ** * *
3003025 AATTTCTTTTGAAACAAAAATCTTTGGGTCTGTTTCTTTGGAAACAAAATTTTGTCTTTCTTAAG
1 AGTTTCTTTTGAAACAAAAATCTTTGAATATGTTTCTTT-GAAACAAAATTTTGTCTCTCTTAAG
3003090 AT
65 AT
* * * *
3003092 ATTTTCTTTTG-AA-AAAAATCTTTGAATATGTTTCTCTT-AAA-ATGAATTTTGTATCTCTTGA
1 AGTTTCTTTTGAAACAAAAATCTTTGAATATGTTTCT-TTGAAACA-AAATTTTGTCTCTCTTAA
*
3003153 GAC
64 GAT
*
3003156 AGTTTCTCTTGAA
1 AGTTTCTTTTGAA
3003169 GTAGATCTTT
Statistics
Matches: 127, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
63 1 0.01
64 28 0.22
65 20 0.16
66 4 0.03
67 74 0.58
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (66 bp):
AGTTTCTTTTGAAACAAAAATCTTTGAATATGTTTCTTTGAAACAAAATTTTGTCTCTCTTAAGA
T
Found at i:3003218 original size:25 final size:27
Alignment explanation
Indices: 3003157--3003218 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 27
3003147 TCTTGAGACA
3003157 GTTTCTCTTGAAGTAGATCTTTGAATAT
1 GTTTCTCTTGAAG-AGATCTTTGAATAT
* *
3003185 G-TTCATCTTGAA-A-ATCTTTGAGTTT
1 GTTTC-TCTTGAAGAGATCTTTGAATAT
3003210 GTTTCTCTT
1 GTTTCTCTT
3003219 AACAAAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 15 0.50
26 4 0.13
27 3 0.10
28 8 0.27
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.50
Consensus pattern (27 bp):
GTTTCTCTTGAAGAGATCTTTGAATAT
Found at i:3003978 original size:30 final size:29
Alignment explanation
Indices: 3003944--3004006 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
3003934 ATTTTGTCTC
*
3003944 ATTTGAG-ACAGTTTCCCATGAAACACAAAT
1 ATTTGAGAAC-GTTTCCC-TGAAAAACAAAT
*
3003974 ATTTGAGAACGTTTCCCTTAAAAACAAAT
1 ATTTGAGAACGTTTCCCTGAAAAACAAAT
3004003 -TTTG
1 ATTTG
3004007 TCTCGCTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 4 0.13
29 10 0.33
30 14 0.47
31 2 0.07
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (29 bp):
ATTTGAGAACGTTTCCCTGAAAAACAAAT
Found at i:3004127 original size:31 final size:28
Alignment explanation
Indices: 3004089--3004185 Score: 101
Period size: 28 Copynumber: 3.4 Consensus size: 28
3004079 GAGACAGTTG
3004089 CTTTTGAAACACATTATCTTTGAG-CTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGTC-TGTTT
3004120 -TTCTTGAAACAAATCTTTGAGTCTGTTT
1 CTT-TTGAAACAAATCTTTGAGTCTGTTT
*
3004148 CTTTTGAAACAAATCTTTGAAT-TGGTTT
1 CTTTTGAAACAAATCTTTGAGTCT-GTTT
*
3004176 CTCTTGAAAC
1 CTTTTGAAAC
3004186 CATAACTCCT
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
27 1 0.02
28 45 0.75
29 3 0.05
30 3 0.05
31 8 0.13
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTCTGTTT
Found at i:3004135 original size:28 final size:27
Alignment explanation
Indices: 3004104--3004185 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 27
3004094 GAAACACATT
3004104 ATCTTTGAGCTTGTTTTTCTTGAAACAA
1 ATCTTTGAG-TTGTTTTTCTTGAAACAA
3004132 ATCTTTGAGTCTGTTTCTT-TTGAAACAA
1 ATCTTTGAGT-TGTTT-TTCTTGAAACAA
* *
3004160 ATCTTTGAATTGGTTTCTCTTGAAAC
1 ATCTTTGAGTT-GTTTTTCTTGAAAC
3004186 CATAACTCCT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
27 3 0.06
28 43 0.90
29 2 0.04
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (27 bp):
ATCTTTGAGTTGTTTTTCTTGAAACAA
Found at i:3004304 original size:43 final size:44
Alignment explanation
Indices: 3004251--3004494 Score: 189
Period size: 46 Copynumber: 5.6 Consensus size: 44
3004241 AGACCAGATT
*
3004251 TCCTTATCACGTAGGAGCCGTGTCA-ACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
* * * ** *
3004293 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCAT-ACC-ATAGATAACCAGACC
* * * * *
3004340 TCTTCATCACGTATGAGCCGTGTCATTCC-CAG---ACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
*
3004380 TCCTTATCACGTAGGAGCCGTGTCA-ACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
* * * ** *
3004422 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCAT-ACC-ATAGATAACCAGACC
* *
3004469 TCTTCATCACGTATGAGCCGTGTCAT
1 TCCTCATCACGTAGGAGCCGTGTCAT
3004495 TCCCCGACCA
Statistics
Matches: 156, Mismatches: 32, Indels: 23
0.74 0.15 0.11
Matches are distributed among these distances:
39 2 0.01
40 30 0.19
42 1 0.01
43 51 0.33
45 8 0.05
46 62 0.40
47 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (44 bp):
TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
Found at i:3004428 original size:129 final size:129
Alignment explanation
Indices: 3004231--3004524 Score: 552
Period size: 129 Copynumber: 2.3 Consensus size: 129
3004221 GTAGGAACCA
*
3004231 TGTCATCCCCAGACCAGATTTCCTTATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTC
1 TGTCATTCCCAGACCAGATTTCCTTATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTC
3004296 CTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCG
66 CTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCG
*
3004360 TGTCATTCCCAGACCAGATCTCCTTATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTC
1 TGTCATTCCCAGACCAGATTTCCTTATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTC
3004425 CTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCG
66 CTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCG
* *
3004489 TGTCATTCCCCGACCAGATTTCCTCATCACGTAGGA
1 TGTCATTCCCAGACCAGATTTCCTTATCACGTAGGA
3004525 ACCGCGTTAA
Statistics
Matches: 160, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 160 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (129 bp):
TGTCATTCCCAGACCAGATTTCCTTATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTC
CTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCG
Found at i:3004732 original size:3 final size:3
Alignment explanation
Indices: 3004726--3004782 Score: 62
Period size: 3 Copynumber: 18.3 Consensus size: 3
3004716 CTTTTTTTAT
* *
3004726 TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TT- TTGT TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A TTA TTA TTA
3004772 TTA TTAA TTA T
1 TTA TT-A TTA T
3004783 GTTACATATA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.04
3 37 0.79
4 8 0.17
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3004738 original size:13 final size:13
Alignment explanation
Indices: 3004722--3004782 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
3004712 GGGTCTTTTT
3004722 TTATTTATTATTA
1 TTATTTATTATTA
3004735 TTA-TTATTATTTA
1 TTATTTATTA-TTA
3004748 TTA-TTATTATT-
1 TTATTTATTATTA
* *
3004759 TTGTTTATTGTTA
1 TTATTTATTATTA
*
3004772 TTATTAATTAT
1 TTATTTATTAT
3004783 GTTACATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 2 0.05
12 15 0.38
13 23 0.57
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:3007711 original size:42 final size:42
Alignment explanation
Indices: 3007664--3008082 Score: 297
Period size: 42 Copynumber: 9.4 Consensus size: 42
3007654 TAGGCCTTAG
3007664 TTATAAAGGTAAAAATTGAGATTAAAAAACTTAGGGCCTCAA
1 TTATAAAGGTAAAAATTGAGATTAAAAAACTTAGGGCCTCAA
* * * *
3007706 CTATAAAAGTAGAAATTGAGACTGAAAAAACTTAGGAGCCTCAA
1 TTATAAAGGTAAAAATTGAGA-TTAAAAAACTTAGG-GCCTCAA
* * **
3007750 TTAGAAAGGTAGAAAGAGAGATTAAAAAAACTTAAGGGCCTCAA
1 TTATAAAGGTAAAAATTGAGATT-AAAAAACTT-AGGGCCTCAA
* * * *
3007794 TTATAAAGTTAAAAAGTGGGATTAAAAAA-TTAGGGGTCTCAA
1 TTATAAAGGTAAAAATTGAGATTAAAAAACTTA-GGGCCTCAA
* * *
3007836 -TATAAAGGTATAAATTGAGATCGAAAAAACTTAGGGGCTTCAA
1 TTATAAAGGTAAAAATTGAGAT-TAAAAAACTTA-GGGCCTCAA
* * * *
3007879 ATGTAAAGGTAGAAAAGATAGGAAGTGAGATTGAAAAGACTTAAGGACCTCAA
1 TTATAAAGGT--AAAA-AT------TGAGATT-AAAAAACTT-AGGGCCTCAA
* *
3007932 TTATAAAGTTAAAAAGTGAGATTAAAAAA-TTAGGGGCCTCAA
1 TTATAAAGGTAAAAATTGAGATTAAAAAACTTA-GGGCCTCAA
* *
3007974 TTATAAATGTAGAAAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGCCTCAA
1 TTATAAAGGTA-AAAA--T------TGAGATT-AAAAAACTTAGGGCCTCAA
* * * *
3008026 TTATAAAGTTCAAAATTGTGTTTAAAAAA-TTAGGGGCCTCAA
1 TTATAAAGGTAAAAATTGAGATTAAAAAACTTA-GGGCCTCAA
3008068 TTATAAAGGTAAAAA
1 TTATAAAGGTAAAAA
3008083 AAATGATTGA
Statistics
Matches: 298, Mismatches: 47, Indels: 64
0.73 0.11 0.16
Matches are distributed among these distances:
41 22 0.07
42 80 0.27
43 45 0.15
44 72 0.24
45 3 0.01
46 3 0.01
47 2 0.01
49 1 0.00
50 1 0.00
51 15 0.05
52 22 0.07
53 31 0.10
54 1 0.00
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.24
Consensus pattern (42 bp):
TTATAAAGGTAAAAATTGAGATTAAAAAACTTAGGGCCTCAA
Found at i:3007762 original size:44 final size:42
Alignment explanation
Indices: 3007664--3008078 Score: 246
Period size: 44 Copynumber: 9.3 Consensus size: 42
3007654 TAGGCCTTAG
* *
3007664 TTATAAAGGTAAAAATTGAGATTAAAAAACTTAGGGCCTCAA
1 TTATAAAGGTAGAAATTGAGATGAAAAAACTTAGGGCCTCAA
* *
3007706 CTATAAAAGTAGAAATTGAGACTGAAAAAACTTAGGAGCCTCAA
1 TTATAAAGGTAGAAATTGAGA-TGAAAAAACTTAGG-GCCTCAA
* ** *
3007750 TTAGAAAGGTAGAAAGAGAGATTAAAAAAACTTAAGGGCCTCAA
1 TTATAAAGGTAGAAATTGAGA-TGAAAAAACTT-AGGGCCTCAA
* * * * * *
3007794 TTATAAAGTTAAAAAGTGGGATTAAAAAA-TTAGGGGTCTCAA
1 TTATAAAGGTAGAAATTGAGATGAAAAAACTTA-GGGCCTCAA
* *
3007836 -TATAAAGGTATAAATTGAGATCGAAAAAACTTAGGGGCTTCAA
1 TTATAAAGGTAGAAATTGAGAT-GAAAAAACTTA-GGGCCTCAA
* * * *
3007879 ATGTAAAGGTAGAAAAGATAGGAAGTGAGATTGAAAAGACTTAAGGACCTCAA
1 TTATAAAGGTAG--AA-AT------TGAGA-TGAAAAAACTT-AGGGCCTCAA
* * * *
3007932 TTATAAAGTTAAAAAGTGAGATTAAAAAA-TTAGGGGCCTCAA
1 TTATAAAGGTAGAAATTGAGATGAAAAAACTTA-GGGCCTCAA
* *
3007974 TTATAAATGTAGAAAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGCCTCAA
1 -T-T--A--T---AAAGGTAGAAATTGAGA-TGAAAAAACTTAGGGCCTCAA
* * * *
3008026 TTATAAAGTTCA-AAATTGTGTTTAAAAAA-TTAGGGGCCTCAA
1 TTATAAAGGT-AGAAATTGAGATGAAAAAACTTA-GGGCCTCAA
3008068 TTATAAAGGTA
1 TTATAAAGGTA
3008079 AAAAAAATGA
Statistics
Matches: 292, Mismatches: 49, Indels: 65
0.72 0.12 0.16
Matches are distributed among these distances:
41 23 0.08
42 68 0.23
43 49 0.17
44 72 0.25
45 3 0.01
46 4 0.01
47 2 0.01
48 2 0.01
50 2 0.01
51 18 0.06
52 15 0.05
53 32 0.11
54 2 0.01
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.25
Consensus pattern (42 bp):
TTATAAAGGTAGAAATTGAGATGAAAAAACTTAGGGCCTCAA
Found at i:3008000 original size:95 final size:94
Alignment explanation
Indices: 3007806--3008083 Score: 337
Period size: 94 Copynumber: 2.9 Consensus size: 94
3007796 ATAAAGTTAA
* * * * * *
3007806 AAAGTGGGATT-AAAAAA-TTAGGGGTCTCAA-TATAAAGGTATAAATTGAGATCGAAAAAACTT
1 AAAGTGAGATTGAAAAAACTTA-AGGCCTCAATTATAAAGTTAAAAATTGAGAT-TAAAAAA-TT
* * *
3007868 AGGGGCTTCAAATGTAAAGGTAGAAAAGATAG
63 AGGGGCCTCAATTATAAAGGTAGAAAAGATAG
* * *
3007900 GAAGTGAGATTGAAAAGACTTAAGGACCTCAATTATAAAGTTAAAAAGTGAGATTAAAAAATTAG
1 AAAGTGAGATTGAAAAAACTTAAGG-CCTCAATTATAAAGTTAAAAATTGAGATTAAAAAATTAG
* *
3007965 GGGCCTCAATTATAAATGTAGAAAAGGTAG
65 GGGCCTCAATTATAAAGGTAGAAAAGATAG
* * *
3007995 AAAGTGAGATTGAAAAAACTTAAGGCCTCAATTATAAAGTTCAAAATTGTGTTTAAAAAATTAGG
1 AAAGTGAGATTGAAAAAACTTAAGGCCTCAATTATAAAGTTAAAAATTGAGATTAAAAAATTAGG
*
3008060 GGCCTCAATTATAAAGGTAAAAAA
66 GGCCTCAATTATAAAGGTAGAAAA
3008084 AATGATTGAA
Statistics
Matches: 158, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
94 67 0.42
95 59 0.37
96 14 0.09
97 18 0.11
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25
Consensus pattern (94 bp):
AAAGTGAGATTGAAAAAACTTAAGGCCTCAATTATAAAGTTAAAAATTGAGATTAAAAAATTAGG
GGCCTCAATTATAAAGGTAGAAAAGATAG
Found at i:3008608 original size:2 final size:2
Alignment explanation
Indices: 3008601--3008635 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3008591 AGCATTTATT
3008601 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3008636 TTTGATCAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3009236 original size:6 final size:6
Alignment explanation
Indices: 3009218--3009295 Score: 147
Period size: 6 Copynumber: 12.8 Consensus size: 6
3009208 CTTTGTGGTT
3009218 TTGCCC TTTGCCC TTGCCC TTGCCC TTGCCC TTGCCC TTGCCC TTGCCC
1 TTGCCC -TTGCCC TTGCCC TTGCCC TTGCCC TTGCCC TTGCCC TTGCCC
3009267 TTGCCC TTGCCC TTGCCC TTGCCC TTGCC
1 TTGCCC TTGCCC TTGCCC TTGCCC TTGCC
3009296 TTCACCTAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
6 65 0.92
7 6 0.08
ACGTcount: A:0.00, C:0.49, G:0.17, T:0.35
Consensus pattern (6 bp):
TTGCCC
Found at i:3009648 original size:10 final size:10
Alignment explanation
Indices: 3009633--3009661 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3009623 TAAATCACTT
3009633 ATTTAAAAAA
1 ATTTAAAAAA
3009643 ATTTAAAAAA
1 ATTTAAAAAA
3009653 ATTTAAAAA
1 ATTTAAAAA
3009662 TATAATTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
ATTTAAAAAA
Found at i:3011870 original size:50 final size:51
Alignment explanation
Indices: 3011764--3011947 Score: 235
Period size: 51 Copynumber: 3.6 Consensus size: 51
3011754 TTCATACTAC
* * * * *
3011764 AAAAGAATGTAGCACTTAACGCATACTTACTCCGGTGTAAGTGGATAAAAC
1 AAAAAAATGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* * * *
3011815 AAAAAAATGTAACACTTAACACATGC-TACACCGATGTAAGTGAATATAAT
1 AAAAAAATGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* * *
3011865 AAAAAAATATAGCACTTAACACATACTTACAACGGTGTAAGTAAATAAAAT
1 AAAAAAATGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* *
3011916 AAAAAATTGTAGCACTTAACACACACTTACAC
1 AAAAAAATGTAGCACTTAACACATACTTACAC
3011948 TGATATAAGT
Statistics
Matches: 112, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
50 42 0.38
51 70 0.62
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.23
Consensus pattern (51 bp):
AAAAAAATGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
Found at i:3011975 original size:101 final size:100
Alignment explanation
Indices: 3011764--3011958 Score: 246
Period size: 101 Copynumber: 1.9 Consensus size: 100
3011754 TTCATACTAC
* * * ** **
3011764 AAAAGAATGTAGCACTTAACGCATACTTACTCCGGTGTAAGTGGATAAAACAAAAAAATGTAACA
1 AAAAAAATATAGCACTTAACACATACTTACAACGGTGTAAGTAAATAAAACAAAAAAATGTAACA
** *
3011829 CTTAACACATGCTACACCGATGTAAGTGAATATAAT
66 CTTAACACACACTACACCGATATAAGT-AATATAAT
* * *
3011865 AAAAAAATATAGCACTTAACACATACTTACAACGGTGTAAGTAAATAAAATAAAAAATTGTAGCA
1 AAAAAAATATAGCACTTAACACATACTTACAACGGTGTAAGTAAATAAAACAAAAAAATGTAACA
*
3011930 CTTAACACACACTTACACTGATATAAGTA
66 CTTAACACACAC-TACACCGATATAAGTA
3011959 TGTACATTTC
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
101 66 0.84
102 13 0.16
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (100 bp):
AAAAAAATATAGCACTTAACACATACTTACAACGGTGTAAGTAAATAAAACAAAAAAATGTAACA
CTTAACACACACTACACCGATATAAGTAATATAAT
Found at i:3012083 original size:35 final size:36
Alignment explanation
Indices: 3012037--3012105 Score: 106
Period size: 38 Copynumber: 1.9 Consensus size: 36
3012027 TAAAAATATA
3012037 TATACAAA-TTT-TAAAAATATATATTAAATTATTTG
1 TATACAAATTTTATAAAAATATATA-TAAATTATTTG
3012072 TATACAAATTTTATTAAAAATATATATAAATTAT
1 TATACAAATTTTA-TAAAAATATATATAAATTAT
3012106 AAATAATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 8 0.26
36 3 0.10
37 8 0.26
38 12 0.39
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (36 bp):
TATACAAATTTTATAAAAATATATATAAATTATTTG
Found at i:3012105 original size:20 final size:20
Alignment explanation
Indices: 3012022--3012115 Score: 58
Period size: 20 Copynumber: 4.7 Consensus size: 20
3012012 GTAAGTATGC
3012022 TTATGTAAAAATATATATACAAA
1 TTAT-TAAAAATATATAT--AAA
3012045 TT-TTAAAAATATATATTAAA
1 TTATTAAAAATATATA-TAAA
* *
3012065 TTATT-----TGTATACAAA
1 TTATTAAAAATATATATAAA
3012080 TTTTATTAAAAATATATATAAA
1 --TTATTAAAAATATATATAAA
3012102 TTA-TAAATAATATA
1 TTATTAAA-AATATA
3012116 AATTTATATT
Statistics
Matches: 57, Mismatches: 4, Indels: 23
0.68 0.05 0.27
Matches are distributed among these distances:
15 3 0.05
16 5 0.09
17 5 0.09
19 4 0.07
20 14 0.25
21 14 0.25
22 10 0.18
23 2 0.04
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
TTATTAAAAATATATATAAA
Found at i:3012119 original size:38 final size:39
Alignment explanation
Indices: 3012047--3012127 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 39
3012037 TATACAAATT
***
3012047 TTAAAAATATATATTAAATTATTTGTATACAAATTT-TA
1 TTAAAAATATATATTAAATTATAAATATACAAATTTATA
*
3012085 TTAAAAATATATA-TAAATTATAAATAATATAAATTTATA
1 TTAAAAATATATATTAAATTATAAAT-ATACAAATTTATA
3012124 TTAA
1 TTAA
3012128 GTTATTTATG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 9 0.24
38 22 0.59
39 6 0.16
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (39 bp):
TTAAAAATATATATTAAATTATAAATATACAAATTTATA
Found at i:3012123 original size:17 final size:17
Alignment explanation
Indices: 3012084--3012119 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
3012074 TACAAATTTT
*
3012084 ATTAAAAATATATATAA
1 ATTATAAATATATATAA
3012101 ATTATAAATA-ATATAA
1 ATTATAAATATATATAA
3012117 ATT
1 ATT
3012120 TATATTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTATAAATATATATAA
Found at i:3012521 original size:22 final size:22
Alignment explanation
Indices: 3012496--3012551 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
3012486 ATAATCACTT
3012496 TTATTTTGTTTTAATTAAGATA
1 TTATTTTGTTTTAATTAAGATA
3012518 TTATTTTGTTTTAATTAAGATA
1 TTATTTTGTTTTAATTAAGATA
3012540 TTAACTTTTGTT
1 TT-A-TTTTGTT
3012552 AGCATCGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 24 0.75
23 1 0.03
24 7 0.22
ACGTcount: A:0.29, C:0.02, G:0.09, T:0.61
Consensus pattern (22 bp):
TTATTTTGTTTTAATTAAGATA
Found at i:3014409 original size:2 final size:2
Alignment explanation
Indices: 3014402--3014429 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3014392 AACAATTGTC
3014402 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3014430 TATTAAGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3024796 original size:19 final size:18
Alignment explanation
Indices: 3024774--3024856 Score: 55
Period size: 18 Copynumber: 4.3 Consensus size: 18
3024764 TTCATAATAA
3024774 TTTAATATATTTTTAAAAT
1 TTTAA-ATATTTTTAAAAT
*
3024793 TTTATTATATCTTTAATAAAAT
1 TTTA-AATAT-TTT--TAAAAT
3024815 TTATAAAT-TTTTTAACAA-
1 TT-TAAATATTTTTAA-AAT
*
3024833 TTTAAA-AGTTTTAAAAT
1 TTTAAATATTTTTAAAAT
3024850 GTTTAAA
1 -TTTAAA
3024857 ATTCATAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 19
0.70 0.04 0.26
Matches are distributed among these distances:
16 2 0.04
17 10 0.19
18 11 0.21
19 10 0.19
20 6 0.12
21 1 0.02
22 10 0.19
23 2 0.04
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTAAATATTTTTAAAAT
Found at i:3024817 original size:21 final size:19
Alignment explanation
Indices: 3024767--3024836 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 19
3024757 TATTGAGTTC
*
3024767 ATAATAATTTAATATATTTT
1 ATAA-AATTTATTATATTTT
3024787 -TAAAATTTTATTATATCTTT
1 ATAAAA-TTTATTATAT-TTT
*
3024807 AATAAAATTTA-TAAATTTT
1 -ATAAAATTTATTATATTTT
*
3024826 TTAACAATTTA
1 ATAA-AATTTA
3024837 AAAGTTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
18 5 0.12
19 21 0.50
20 7 0.17
21 4 0.10
22 5 0.12
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
ATAAAATTTATTATATTTT
Found at i:3025628 original size:28 final size:28
Alignment explanation
Indices: 3025596--3025652 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
3025586 ATGTATGATC
3025596 ATATGTTAGAAGTGAACTTGGATTTATA
1 ATATGTTAGAAGTGAACTTGGATTTATA
3025624 ATATGTTAGAAGTGAACTTGGATTTATA
1 ATATGTTAGAAGTGAACTTGGATTTATA
3025652 A
1 A
3025653 AATTTTAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.39
Consensus pattern (28 bp):
ATATGTTAGAAGTGAACTTGGATTTATA
Found at i:3025660 original size:28 final size:28
Alignment explanation
Indices: 3025598--3025660 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
3025588 GTATGATCAT
*
3025598 ATGTTAGAAGTGAACTTGGATTTATAAT
1 ATGTTAGAAGTGAACTTGGATTTATAAA
3025626 ATGTTAGAAGTGAACTTGGATTTATAAA
1 ATGTTAGAAGTGAACTTGGATTTATAAA
*
3025654 ATTTTAG
1 ATGTTAG
3025661 GGGAGCGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.40
Consensus pattern (28 bp):
ATGTTAGAAGTGAACTTGGATTTATAAA
Found at i:3025673 original size:30 final size:30
Alignment explanation
Indices: 3025609--3025693 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 30
3025599 TGTTAGAAGT
* * * *
3025609 GAACTTGGATTTATAATATGTTA--GAAGT
1 GAACTTGGATTTATAAAATTTTAGGGGAGC
3025637 GAACTTGGATTTATAAAATTTTAGGGGAGC
1 GAACTTGGATTTATAAAATTTTAGGGGAGC
* * *
3025667 GAACTTGAACTTGTAAAATTTTAGGGG
1 GAACTTGGATTTATAAAATTTTAGGGG
3025694 GCTACCCATG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 21 0.44
30 27 0.56
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (30 bp):
GAACTTGGATTTATAAAATTTTAGGGGAGC
Found at i:3026779 original size:21 final size:21
Alignment explanation
Indices: 3026755--3026806 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
3026745 TAGATTAGAG
3026755 TATATCAATGAGATACTGATA
1 TATATCAATGAGATACTGATA
3026776 TATATCAATGAGATACTGATA
1 TATATCAATGAGATACTGATA
*
3026797 TGTATCAATG
1 TATATCAATG
3026807 TATGATTATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
TATATCAATGAGATACTGATA
Found at i:3028350 original size:23 final size:23
Alignment explanation
Indices: 3028317--3028379 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
3028307 AACCTTATAT
*
3028317 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACAC
* * *
3028340 GGCACTACGGTGCAATTCTACAT
1 GGCACTTCGGTGCATTTCTACAC
*
3028363 GGCACTTCAGTGCATTT
1 GGCACTTCGGTGCATTT
3028380 ATATGAGCTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACAC
Found at i:3032733 original size:2 final size:2
Alignment explanation
Indices: 3032686--3032719 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3032676 ATTTAGGTAA
3032686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3032720 TTGTGTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3039116 original size:20 final size:20
Alignment explanation
Indices: 3039087--3039125 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3039077 AGAGCTCATA
*
3039087 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
3039107 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
3039126 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:3042591 original size:3 final size:3
Alignment explanation
Indices: 3042583--3042619 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
3042573 ACTCCACCTT
* *
3042583 TTC TTC TTC TTC TTC TTA TTC TTC TTC TTT TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
3042620 GACGTTTTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:3047580 original size:13 final size:13
Alignment explanation
Indices: 3047562--3047605 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
3047552 TGATAAATAA
*
3047562 AAAAAATTACAAT
1 AAAAAACTACAAT
* *
3047575 AAAAAAGTCCAAT
1 AAAAAACTACAAT
*
3047588 AAACAACTACAAT
1 AAAAAACTACAAT
3047601 AAAAA
1 AAAAA
3047606 GTACTAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.68, C:0.14, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAACTACAAT
Found at i:3049737 original size:21 final size:21
Alignment explanation
Indices: 3049708--3049769 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
3049698 CATCTGCAAA
*
3049708 AAATTAATTAAATAAAATATT
1 AAATAAATTAAATAAAATATT
3049729 AAATAAATTAAATACAAAATATT
1 AAATAAATTAAAT--AAAATATT
3049752 -AA-AAA-TATAATAAAATAT
1 AAATAAATTA-AATAAAATAT
3049770 ACCTTAGATA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
19 7 0.19
20 2 0.05
21 18 0.49
22 2 0.05
23 8 0.22
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATAAATTAAATAAAATATT
Found at i:3050740 original size:20 final size:23
Alignment explanation
Indices: 3050695--3050751 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 23
3050685 GCATGGGTAG
3050695 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCACATGTT-AAGAA
3050719 TGCATCGATGCA-ATG-T-AGAA
1 TGCATCGATGCACATGTTAAGAA
*
3050739 TGTATCGATGCAC
1 TGCATCGATGCAC
3050752 TTCAAAGGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (23 bp):
TGCATCGATGCACATGTTAAGAA
Found at i:3056383 original size:22 final size:24
Alignment explanation
Indices: 3056331--3056385 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
3056321 TTTAATACTA
* *
3056331 ATAATGAAAAATATAATTTTTTAAT
1 ATAAT-AATAATATAATTTTATAAT
3056356 ACTAATAATAATAT-ATTTTATAAT
1 A-TAATAATAATATAATTTTATAAT
3056380 -TAATAA
1 ATAATAA
3056386 ATTAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 6 0.22
24 9 0.33
25 8 0.30
26 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
ATAATAATAATATAATTTTATAAT
Found at i:3059867 original size:21 final size:21
Alignment explanation
Indices: 3059835--3059874 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3059825 AACGGATATA
3059835 TATTTATTTATATTAGTTCGAT
1 TATTTATTTATATTA-TTCGAT
3059857 TATTT-TTTATATTATTCG
1 TATTTATTTATATTATTCG
3059875 TGTTTGGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (21 bp):
TATTTATTTATATTATTCGAT
Found at i:3061529 original size:9 final size:9
Alignment explanation
Indices: 3061469--3061534 Score: 55
Period size: 9 Copynumber: 7.3 Consensus size: 9
3061459 TTTATTTATG
3061469 TATTTTTAA
1 TATTTTTAA
*
3061478 TA-TTATAA
1 TATTTTTAA
*
3061486 TATTTTAAA
1 TATTTTTAA
* *
3061495 AATATTTAA
1 TATTTTTAA
*
3061504 GT-TTTTAAA
1 -TATTTTTAA
3061513 TGATTTTTAA
1 T-ATTTTTAA
3061523 TATTTTTAA
1 TATTTTTAA
3061532 TAT
1 TAT
3061535 CATCTTAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
8 8 0.19
9 28 0.65
10 7 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (9 bp):
TATTTTTAA
Found at i:3067820 original size:2 final size:2
Alignment explanation
Indices: 3067813--3067849 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3067803 CCATATAAAT
3067813 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3067850 ATTAAAGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3068171 original size:13 final size:14
Alignment explanation
Indices: 3068134--3068176 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3068124 TAATCTGTTT
3068134 ATTTATATTCATTC
1 ATTTATATTCATTC
*
3068148 ATTTATGTTCATT-
1 ATTTATATTCATTC
*
3068161 GTTTATATTCAATTC
1 ATTTATATTC-ATTC
3068176 A
1 A
3068177 ATCTCCACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (14 bp):
ATTTATATTCATTC
Found at i:3070262 original size:8 final size:10
Alignment explanation
Indices: 3070227--3070274 Score: 87
Period size: 10 Copynumber: 4.8 Consensus size: 10
3070217 ATCACACCAT
3070227 ATTCTCTCAA
1 ATTCTCTCAA
3070237 ATTCTCTCAA
1 ATTCTCTCAA
*
3070247 GTTCTCTCAA
1 ATTCTCTCAA
3070257 ATTCTCTCAA
1 ATTCTCTCAA
3070267 ATTCTCTC
1 ATTCTCTC
3070275 TCTATTTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.25, C:0.31, G:0.02, T:0.42
Consensus pattern (10 bp):
ATTCTCTCAA
Found at i:3071993 original size:18 final size:18
Alignment explanation
Indices: 3071962--3071996 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3071952 CAATAGCCAC
* *
3071962 CGCAGTCATTTATGATGT
1 CGCAGCCATATATGATGT
3071980 CGCAGCCATATATGATG
1 CGCAGCCATATATGATG
3071997 CTGCCGCCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (18 bp):
CGCAGCCATATATGATGT
Found at i:3072559 original size:26 final size:24
Alignment explanation
Indices: 3072488--3072559 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
3072478 TTATATTTGT
3072488 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
3072513 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
3072535 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
3072560 GTTGGATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:3076001 original size:12 final size:12
Alignment explanation
Indices: 3075984--3076010 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3075974 GTATAATAAA
3075984 AAATTTATAACG
1 AAATTTATAACG
3075996 AAATTTATAACG
1 AAATTTATAACG
3076008 AAA
1 AAA
3076011 AATCGCACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (12 bp):
AAATTTATAACG
Found at i:3079564 original size:24 final size:24
Alignment explanation
Indices: 3079532--3079577 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3079522 CCTAAAGTAT
3079532 TAGAAAACAGTAACCTTAGACTAC
1 TAGAAAACAGTAACCTTAGACTAC
*
3079556 TAGAAAACAGTAGCCTTAGACT
1 TAGAAAACAGTAACCTTAGACT
3079578 TTACATTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
TAGAAAACAGTAACCTTAGACTAC
Found at i:3090854 original size:11 final size:11
Alignment explanation
Indices: 3090838--3090863 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3090828 TATAGAAAAC
3090838 GAAGGAAGAGT
1 GAAGGAAGAGT
3090849 GAAGGAAGAGT
1 GAAGGAAGAGT
3090860 GAAG
1 GAAG
3090864 AAATATATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.46, T:0.08
Consensus pattern (11 bp):
GAAGGAAGAGT
Found at i:3091977 original size:2 final size:2
Alignment explanation
Indices: 3091970--3092033 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
3091960 TTTTAAATTA
3091970 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3092012 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
3092034 CAACAACATA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3095621 original size:25 final size:26
Alignment explanation
Indices: 3095582--3095630 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
3095572 CTTAATTAGA
3095582 TTTTTATTATATTTT-TTCTTTTTCT
1 TTTTTATTATATTTTATTCTTTTTCT
* * *
3095607 TTTTTATTTTCTTTTATTTTTTTT
1 TTTTTATTATATTTTATTCTTTTT
3095631 TGAATCGGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (26 bp):
TTTTTATTATATTTTATTCTTTTTCT
Found at i:3097164 original size:43 final size:42
Alignment explanation
Indices: 3097108--3097242 Score: 173
Period size: 43 Copynumber: 3.1 Consensus size: 42
3097098 AAAATGTCTC
*
3097108 TAGGTTTAAACATTTAGCGGCGTTTTTCTCACAAACGCCGCAA
1 TAGG-TTAAACATTTAGCGACGTTTTTCTCACAAACGCCGCAA
**
3097151 TAGGTTAAGACATTTAGCGACGTTTTTC-CTACAAACGTTAGCAA
1 TAGGTTAA-ACATTTAGCGACGTTTTTCTC-ACAAACG-CCGCAA
* *
3097195 TAGGTTCAAACATTTAGCGACATTTTTCTTACAAACGCCGCAA
1 TAGGTT-AAACATTTAGCGACGTTTTTCTCACAAACGCCGCAA
3097238 TAGGT
1 TAGGT
3097243 AGGTAATTTA
Statistics
Matches: 80, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
42 5 0.06
43 38 0.47
44 35 0.44
45 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (42 bp):
TAGGTTAAACATTTAGCGACGTTTTTCTCACAAACGCCGCAA
Found at i:3097210 original size:44 final size:42
Alignment explanation
Indices: 3097108--3097242 Score: 164
Period size: 44 Copynumber: 3.1 Consensus size: 42
3097098 AAAATGTCTC
* *
3097108 TAGGTTTAAACATTTAGCGGCGTTTTT-CTCACAAACGCCGCAA
1 TAGG-TTAAACATTTAGCGACGTTTTTCCT-ACAAACGCAGCAA
*
3097151 TAGGTTAAGACATTTAGCGACGTTTTTCCTACAAACGTTAGCAA
1 TAGGTTAA-ACATTTAGCGACGTTTTTCCTACAAACG-CAGCAA
* * *
3097195 TAGGTTCAAACATTTAGCGACATTTTTCTTACAAACGCCGCAA
1 TAGGTT-AAACATTTAGCGACGTTTTTCCTACAAACGCAGCAA
3097238 TAGGT
1 TAGGT
3097243 AGGTAATTTA
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
42 4 0.05
43 37 0.46
44 38 0.47
45 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (42 bp):
TAGGTTAAACATTTAGCGACGTTTTTCCTACAAACGCAGCAA
Found at i:3099157 original size:23 final size:22
Alignment explanation
Indices: 3099119--3099161 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3099109 CAATTCCTTT
3099119 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTTCTTTATCTTGTTTTA
*
3099141 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
3099162 CCAGCACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTA
Found at i:3099532 original size:25 final size:25
Alignment explanation
Indices: 3099487--3099541 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
3099477 CTATTTTTTT
*
3099487 CAAAAAAAAAAACAAACAAAAAAGG
1 CAAAAAAAAAAACAAACAAAAAAGC
*
3099512 CAAAAAAAACAA-AAACAAAAAAAGC
1 CAAAAAAAAAAACAAAC-AAAAAAGC
3099537 CAAAA
1 CAAAA
3099542 TATCAAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.80, C:0.15, G:0.05, T:0.00
Consensus pattern (25 bp):
CAAAAAAAAAAACAAACAAAAAAGC
Found at i:3099541 original size:16 final size:15
Alignment explanation
Indices: 3099487--3099534 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 15
3099477 CTATTTTTTT
*
3099487 CAAAAAAAAAAACAAA
1 CAAAAACAAAAA-AAA
3099503 CAAAAAAGGCAAAAAAAA
1 C-AAAAA--CAAAAAAAA
3099521 CAAAAACAAAAAAA
1 CAAAAACAAAAAAA
3099535 GCCAAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 8 0.29
16 1 0.04
17 10 0.36
18 4 0.14
19 5 0.18
ACGTcount: A:0.83, C:0.12, G:0.04, T:0.00
Consensus pattern (15 bp):
CAAAAACAAAAAAAA
Found at i:3099541 original size:24 final size:24
Alignment explanation
Indices: 3099487--3099554 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
3099477 CTATTTTTTT
* *
3099487 CAAAAAAAAAAACAAACAAAAAAGG
1 CAAAAAAAACAA-AAACAAAAAAAG
3099512 CAAAAAAAACAAAAACAAAAAAAG
1 CAAAAAAAACAAAAACAAAAAAAG
* * *
3099536 CCAAAATATC-AAAACAAAA
1 CAAAAAAAACAAAAACAAAA
3099555 TTTGCAAACA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
23 9 0.24
24 18 0.47
25 11 0.29
ACGTcount: A:0.78, C:0.15, G:0.04, T:0.03
Consensus pattern (24 bp):
CAAAAAAAACAAAAACAAAAAAAG
Found at i:3103867 original size:23 final size:22
Alignment explanation
Indices: 3103829--3103871 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3103819 CAATTCCTTT
3103829 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTTCTTTATCTTGTTTTA
*
3103851 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
3103872 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTA
Found at i:3104739 original size:15 final size:15
Alignment explanation
Indices: 3104721--3104751 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3104711 GATATTCGAG
*
3104721 TATGTGTTATTCAGA
1 TATGAGTTATTCAGA
3104736 TATGAGTTATTCAGA
1 TATGAGTTATTCAGA
3104751 T
1 T
3104752 TGGATTGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.45
Consensus pattern (15 bp):
TATGAGTTATTCAGA
Found at i:3108270 original size:20 final size:22
Alignment explanation
Indices: 3108240--3108282 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
3108230 TAAAATATTT
3108240 TATATTTTTAATAAT-TAAAAA
1 TATATTTTTAATAATATAAAAA
3108261 TATA-TTTTAATAATATAAAAA
1 TATATTTTTAATAATATAAAAA
3108282 T
1 T
3108283 CACTATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TATATTTTTAATAATATAAAAA
Found at i:3117054 original size:37 final size:36
Alignment explanation
Indices: 3116995--3117115 Score: 147
Period size: 36 Copynumber: 3.3 Consensus size: 36
3116985 ATCCCATTAT
* *
3116995 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
3117030 CTATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
* * *
3117067 CA-TTTTCAAAAAAAACATTTACTAAACTTTGAAAAT
1 CATTTTTC-AAAGAAACATTTACCAAACTTTGAAAAA
3117103 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
3117116 TTGGTTGTCA
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
35 6 0.08
36 35 0.47
37 28 0.38
38 5 0.07
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
Found at i:3121140 original size:16 final size:17
Alignment explanation
Indices: 3121109--3121143 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3121099 CGCATCGCCG
3121109 ACAAAATTTCACTATTC
1 ACAAAATTTCACTATTC
*
3121126 ACAAAA-TTCATTATTC
1 ACAAAATTTCACTATTC
3121142 AC
1 AC
3121144 GTAAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:3121600 original size:37 final size:36
Alignment explanation
Indices: 3121550--3121667 Score: 148
Period size: 37 Copynumber: 3.2 Consensus size: 36
3121540 CCCATTATCA
* * *
3121550 TTTTTCAACAAACATCTACCAAACTTTGAAAAACTAT
1 TTTTTAAAGAAACATTTACCAAACTTTGAAAAAC-AT
*
3121587 TTTTTAAAGAAACATTTACCAAACTTTGAAAACCA-
1 TTTTTAAAGAAACATTTACCAAACTTTGAAAAACAT
* * *
3121622 TTTTCAAAAAAACATTTACCAAACTTTGAAAATCAT
1 TTTTTAAAGAAACATTTACCAAACTTTGAAAAACAT
3121658 TTTTTCAAAG
1 TTTTT-AAAG
3121668 TTGGTTACCA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
35 32 0.46
36 5 0.07
37 33 0.47
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.34
Consensus pattern (36 bp):
TTTTTAAAGAAACATTTACCAAACTTTGAAAAACAT
Found at i:3121623 original size:21 final size:20
Alignment explanation
Indices: 3121596--3121659 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
3121586 TTTTTTAAAG
3121596 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
3121616 AAACCATTT-TCAAA-----A
1 AAA-CATTTACCAAACTTTGA
3121631 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
3121651 AAATCATTT
1 AAA-CATTT
3121660 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 8 0.24
20 11 0.32
21 10 0.29
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:3121642 original size:35 final size:35
Alignment explanation
Indices: 3121551--3121660 Score: 141
Period size: 35 Copynumber: 3.1 Consensus size: 35
3121541 CCATTATCAT
* * *
3121551 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTA
1 TTTTCAAAAAAACATTTACCAAACTTTG-AAAACCA
* *
3121586 TTTTTTAAAGAAACATTTACCAAACTTTGAAAACCA
1 -TTTTCAAAAAAACATTTACCAAACTTTGAAAACCA
*
3121622 TTTTCAAAAAAACATTTACCAAACTTTGAAAATCA
1 TTTTCAAAAAAACATTTACCAAACTTTGAAAACCA
3121657 TTTT
1 TTTT
3121661 TTCAAAGTTG
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
35 36 0.55
36 10 0.15
37 20 0.30
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.34
Consensus pattern (35 bp):
TTTTCAAAAAAACATTTACCAAACTTTGAAAACCA
Found at i:3128112 original size:15 final size:15
Alignment explanation
Indices: 3128092--3128127 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3128082 GAATATATTA
*
3128092 ATATTTTAAAATACT
1 ATATTTTAAAATAAT
*
3128107 ATATTTTATAATAAT
1 ATATTTTAAAATAAT
3128122 ATATTT
1 ATATTT
3128128 ATAATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTTAAAATAAT
Found at i:3128156 original size:15 final size:15
Alignment explanation
Indices: 3128087--3128156 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 15
3128077 TCTTTGAATA
*
3128087 TATTAATATTTTAAAA
1 TATT-ATATTTTAAAT
*
3128103 TACTATATTTTATAA-
1 TATTATATTTTA-AAT
*
3128118 TAATATATTTATAATTATT
1 TATTATATTT-TAA--A-T
3128137 TATTATATTTTAAAT
1 TATTATATTTTAAAT
3128152 TATTA
1 TATTA
3128157 AAATAATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
15 24 0.53
16 8 0.18
17 1 0.02
18 3 0.07
19 9 0.20
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTATATTTTAAAT
Found at i:3128163 original size:42 final size:39
Alignment explanation
Indices: 3128116--3128213 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 39
3128106 TATATTTTAT
* *
3128116 AATAATATATTTATAATTATTTATTATATTTTAAATTATTAA
1 AATAATATATTTATAATGATTT-TTATATTTT-AATAATT-A
*
3128158 AATAATATATTATATAATGATTTTTATATTTTTATAATTA
1 AATAATATATT-TATAATGATTTTTATATTTTAATAATTA
3128198 AATAATATATTT-TAAT
1 AATAATATATTTATAAT
3128214 AATATAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
38 4 0.08
39 1 0.02
40 12 0.23
41 5 0.10
42 20 0.38
43 10 0.19
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (39 bp):
AATAATATATTTATAATGATTTTTATATTTTAATAATTA
Found at i:3128185 original size:55 final size:55
Alignment explanation
Indices: 3128084--3128192 Score: 134
Period size: 57 Copynumber: 2.0 Consensus size: 55
3128074 ATTTCTTTGA
* *
3128084 ATATATTAATATTTTAAAATACTATATTTTATAATAATATATTTATAATTATTTATT
1 ATATATTAATATTTTAAAATAATATATTATATAATAATATATTTAT-ATT-TTTATT
* *
3128141 ATATTTTAA-ATTATTAAAATAATATATTATATAATGAT-T-TTTATATTTTTAT
1 ATATATTAATATT-TTAAAATAATATATTATATAATAATATATTTATATTTTTAT
3128193 AATTAAATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
53 5 0.11
54 3 0.06
55 5 0.11
56 4 0.09
57 30 0.64
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (55 bp):
ATATATTAATATTTTAAAATAATATATTATATAATAATATATTTATATTTTTATT
Found at i:3128206 original size:21 final size:21
Alignment explanation
Indices: 3128182--3128225 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3128172 TAATGATTTT
*
3128182 TATATTTTTATAAT-TAAATAA
1 TATATTTTAATAATATAAA-AA
3128203 TATATTTTAATAATATAAAAA
1 TATATTTTAATAATATAAAAA
3128224 TA
1 TA
3128226 AAAATCCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TATATTTTAATAATATAAAAA
Found at i:3131477 original size:14 final size:14
Alignment explanation
Indices: 3131460--3131486 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3131450 GAAACATCTT
3131460 AAAAATCATTTTTA
1 AAAAATCATTTTTA
3131474 AAAAATCATTTTT
1 AAAAATCATTTTT
3131487 CAAACAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAAATCATTTTTA
Found at i:3133599 original size:3 final size:3
Alignment explanation
Indices: 3133591--3133626 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3133581 AATTTTCTGT
3133591 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3133627 CAAATGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3134181 original size:31 final size:31
Alignment explanation
Indices: 3134143--3134214 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
3134133 AGTTTCAAAA
* * *
3134143 GTAACAAATTAGTCACCAATGATATCTATTT
1 GTAACAAAATAGTCACCAACGATATCAATTT
* * *
3134174 GTAACAAAATGGTCACTAACGTTATCAATTT
1 GTAACAAAATAGTCACCAACGATATCAATTT
3134205 GTAACAAAAT
1 GTAACAAAAT
3134215 GATTACGCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (31 bp):
GTAACAAAATAGTCACCAACGATATCAATTT
Found at i:3135859 original size:23 final size:23
Alignment explanation
Indices: 3135833--3135901 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
3135823 CACCACAGCT
*
3135833 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
3135856 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* * *
3135879 CATAGAATAGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
3135902 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:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:3138912 original size:12 final size:11
Alignment explanation
Indices: 3138870--3138921 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
3138860 CCCCCCCCTT
*
3138870 CTTTTCCCTTC
1 CTTTTCCTTTC
3138881 CATTTTCCTTTC
1 C-TTTTCCTTTC
3138893 AC-TTTCCTTTAC
1 -CTTTTCCTTT-C
3138905 CTTTTCCTTT-
1 CTTTTCCTTTC
3138915 CTTTTCC
1 CTTTTCC
3138922 AATAGCACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
10 7 0.19
11 10 0.28
12 18 0.50
13 1 0.03
ACGTcount: A:0.06, C:0.37, G:0.00, T:0.58
Consensus pattern (11 bp):
CTTTTCCTTTC
Found at i:3140792 original size:14 final size:14
Alignment explanation
Indices: 3140773--3140812 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 14
3140763 TGATACTATT
3140773 AAAATAATTTAATA
1 AAAATAATTTAATA
3140787 AAAATAATTTTTAATA
1 AAAATAA--TTTAATA
3140803 AAAATAATTT
1 AAAATAATTT
3140813 TTTATAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 10 0.42
16 14 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAATAATTTAATA
Found at i:3140801 original size:16 final size:16
Alignment explanation
Indices: 3140780--3140819 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
3140770 ATTAAAATAA
3140780 TTTAATAAAAATAATT
1 TTTAATAAAAATAATT
3140796 TTTAATAAAAATAATT
1 TTTAATAAAAATAATT
*
3140812 TTTTATAA
1 TTTAATAA
3140820 TGTTTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAATAAAAATAATT
Found at i:3143291 original size:58 final size:57
Alignment explanation
Indices: 3143229--3143397 Score: 196
Period size: 58 Copynumber: 2.9 Consensus size: 57
3143219 ATCACCTTTA
* * *
3143229 TTAAAAATAATTACCAAAATATCATTATTTTACAAATAATTCCCAAAATGTCATCGTT
1 TTAAAAATAATTACCAAAATGTCACTATTTT-CAAATAATTCCCAAAATGTCATAGTT
* * * * *
3143287 TTAAAAATAATTACCAGAATGTCACTATTTTTTAAAAAATTCCCAAAATATCATATTT
1 TTAAAAATAATTACCAAAATGTCACTA-TTTTCAAATAATTCCCAAAATGTCATAGTT
* * *
3143345 TTCAAAATAATTCCCAAAATGTCACCT-TTTTCAAAATAATTCCTAAAATGTCA
1 TTAAAAATAATTACCAAAATGTCA-CTATTTTC-AAATAATTCCCAAAATGTCA
3143398 CCGGGTCGGG
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
57 4 0.04
58 83 0.89
59 6 0.06
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.36
Consensus pattern (57 bp):
TTAAAAATAATTACCAAAATGTCACTATTTTCAAATAATTCCCAAAATGTCATAGTT
Found at i:3143353 original size:87 final size:88
Alignment explanation
Indices: 3143232--3143398 Score: 241
Period size: 87 Copynumber: 1.9 Consensus size: 88
3143222 ACCTTTATTA
*
3143232 AAAATAATTACCAAAATATCATTATTTTACAAATAATTCCCAAAATGTCATCGTTTTAAAAATAA
1 AAAATAATTACCAAAATATCATTATTTTACAAATAATTCCCAAAATGTCACCGTTTTAAAAATAA
*
3143297 TTACC-AGAATGTCACTATTTTTT
66 TT-CCTAAAATGTCACTATTTTTT
* * * *
3143320 AAAA-AATTCCCAAAATATCA-TATTTTTCAAAATAATTCCCAAAATGTCACCTTTTTCAAAATA
1 AAAATAATTACCAAAATATCATTATTTTAC-AAATAATTCCCAAAATGTCACCGTTTTAAAAATA
3143383 ATTCCTAAAATGTCAC
65 ATTCCTAAAATGTCAC
3143399 CGGGTCGGGT
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
86 9 0.13
87 58 0.82
88 4 0.06
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.35
Consensus pattern (88 bp):
AAAATAATTACCAAAATATCATTATTTTACAAATAATTCCCAAAATGTCACCGTTTTAAAAATAA
TTCCTAAAATGTCACTATTTTTT
Found at i:3143374 original size:29 final size:29
Alignment explanation
Indices: 3143214--3143399 Score: 178
Period size: 29 Copynumber: 6.4 Consensus size: 29
3143204 GAAAATTACA
* *
3143214 AAAATATCACCTTTATTAAAAATAATTACC
1 AAAATGTCACCTTT-TTAAAAATAATTCCC
* * *
3143244 AAAATATCA-TTATTTTACAAATAATTCCC
1 AAAATGTCACCT-TTTTAAAAATAATTCCC
* * *
3143273 AAAATGTCATCGTTTTAAAAATAATTACC
1 AAAATGTCACCTTTTTAAAAATAATTCCC
* * *
3143302 AGAATGTCACTATTTTTTAAAA-AATTCCC
1 AAAATGTCAC-CTTTTTAAAAATAATTCCC
* ** *
3143331 AAAATATCATATTTTTCAAAATAATTCCC
1 AAAATGTCACCTTTTTAAAAATAATTCCC
* *
3143360 AAAATGTCACCTTTTTCAAAATAATTCCT
1 AAAATGTCACCTTTTTAAAAATAATTCCC
3143389 AAAATGTCACC
1 AAAATGTCACC
3143400 GGGTCGGGTC
Statistics
Matches: 130, Mismatches: 22, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
28 10 0.08
29 101 0.78
30 19 0.15
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATGTCACCTTTTTAAAAATAATTCCC
Found at i:3143425 original size:18 final size:18
Alignment explanation
Indices: 3143394--3143445 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
3143384 TTCCTAAAAT
* *
3143394 GTCACCGGGTCGGGTCGG
1 GTCAACGGGCCGGGTCGG
*
3143412 GTCAATGGGCCGGGTCGG
1 GTCAACGGGCCGGGTCGG
*
3143430 GTCAACGGGTCGGGTC
1 GTCAACGGGCCGGGTC
3143446 AGACCGGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.10, C:0.25, G:0.48, T:0.17
Consensus pattern (18 bp):
GTCAACGGGCCGGGTCGG
Found at i:3143438 original size:13 final size:13
Alignment explanation
Indices: 3143422--3143446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3143412 GTCAATGGGC
3143422 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
3143435 CGGGTCGGGTCA
1 CGGGTCGGGTCA
3143447 GACCGGTTTG
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:0.12, C:0.24, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:3150829 original size:60 final size:59
Alignment explanation
Indices: 3150759--3150888 Score: 156
Period size: 60 Copynumber: 2.2 Consensus size: 59
3150749 AAAAGTTACA
* *
3150759 AAAATATCACCTTTATTAAAAATAATT-ACAAGAATGTCACTATTTTTTAAAA-AATATCCC
1 AAAATATCACCTTTATTAAAAATAATTCACAA-AATATCAC-ATTTTTCAAAATAAT-TCCC
* * * * *
3150819 AAAATGTCACCTTTTTTCAAAATAATTCCCAAAATATCACATTTTTCAAAATAATTTCC
1 AAAATATCACCTTTATTAAAAATAATTCACAAAATATCACATTTTTCAAAATAATTCCC
3150878 AAAATATCACC
1 AAAATATCACC
3150889 GGGTCGGGCC
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
59 23 0.38
60 34 0.57
61 3 0.05
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (59 bp):
AAAATATCACCTTTATTAAAAATAATTCACAAAATATCACATTTTTCAAAATAATTCCC
Found at i:3150863 original size:29 final size:29
Alignment explanation
Indices: 3150759--3150887 Score: 127
Period size: 30 Copynumber: 4.3 Consensus size: 29
3150749 AAAAGTTACA
* * *
3150759 AAAATATCACCTTTATTAAAAATAATT-AC
1 AAAATATCACATTT-TTCAAAATAATTCCC
* *
3150788 AAGAATGTCACTATTTTTTAAAA-AATATCCC
1 AA-AATATCAC-ATTTTTCAAAATAAT-TCCC
* *
3150819 AAAATGTCACCTTTTTTCAAAATAATTCCC
1 AAAATATCA-CATTTTTCAAAATAATTCCC
*
3150849 AAAATATCACATTTTTCAAAATAATTTCC
1 AAAATATCACATTTTTCAAAATAATTCCC
3150878 AAAATATCAC
1 AAAATATCAC
3150888 CGGGTCGGGC
Statistics
Matches: 85, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
29 33 0.39
30 42 0.49
31 10 0.12
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAATATCACATTTTTCAAAATAATTCCC
Found at i:3155342 original size:15 final size:16
Alignment explanation
Indices: 3155324--3155356 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3155314 GTGGCAGATC
3155324 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
3155339 AAAATCCAGAACGGGA
1 AAAATCCAGAACGGGA
3155355 AA
1 AA
3155357 GAAAGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.52, C:0.18, G:0.24, T:0.06
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:3159137 original size:26 final size:26
Alignment explanation
Indices: 3159101--3159161 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
3159091 AATTGAAGCT
*
3159101 TCGAGCAATATTATTTCTCCTACCAG
1 TCGAGCAATATTATTTCTCCCACCAG
*
3159127 TCGAGCAATATTATTTCTCCCATCAG
1 TCGAGCAATATTATTTCTCCCACCAG
3159153 TCGAGCAAT
1 TCGAGCAAT
3159162 TTCTGGAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (26 bp):
TCGAGCAATATTATTTCTCCCACCAG
Found at i:3164255 original size:180 final size:176
Alignment explanation
Indices: 3163929--3164261 Score: 461
Period size: 176 Copynumber: 1.9 Consensus size: 176
3163919 GACTCGTAGA
* * * * *
3163929 GCATTTGCAGGTCATCACAATCAATCTAATAGCTTTGGAAAGAATTTTCATGTGAATCGTATATC
1 GCATTTGCAAGTCATCACAATCAATCTAATAGCTCTAGAAAGAATTTTCATATGAATCATATATC
* * *
3163994 TGCTCTTAGAAAAACAGTTTTTCATTTGAATCAATGACAACTATAACCAATGGCCAAACTTCTAC
66 TGCTCTTAGAAAAACAATTTTTCATTTCAATCAATGACAACTATAACCAATGGCAAAACTTCTAC
3164059 AATGCAGAAATGGAAAACATGTGAATCATAGTGCATGCAGGTGTTG
131 AATGCAGAAATGGAAAACATGTGAATCATAGTGCATGCAGGTGTTG
* * * *
3164105 GCATTTTCAAGTCATCATAATCGATCTAATAGCTCTAGAAAGAATTTTCATATGAATCATATATT
1 GCATTTGCAAGTCATCACAATCAATCTAATAGCTCTAGAAAGAATTTTCATATGAATCATATATC
* * * * *
3164170 TGGTCTTAGCAAAGCAATTTTTCATGTGAATCAATCAATGATAACTATAACCAATGGGAAAACTT
66 TGCTCTTAGAAAAACAATTTTTCAT-T---TCAATCAATGACAACTATAACCAATGGCAAAACTT
3164235 CTACAATGC-GTAAATGGAAAACATGTG
127 CTACAATGCAG-AAATGGAAAACATGTG
3164262 CGAAACCTAG
Statistics
Matches: 135, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
176 77 0.57
177 1 0.01
179 1 0.01
180 56 0.41
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (176 bp):
GCATTTGCAAGTCATCACAATCAATCTAATAGCTCTAGAAAGAATTTTCATATGAATCATATATC
TGCTCTTAGAAAAACAATTTTTCATTTCAATCAATGACAACTATAACCAATGGCAAAACTTCTAC
AATGCAGAAATGGAAAACATGTGAATCATAGTGCATGCAGGTGTTG
Found at i:3171670 original size:2 final size:2
Alignment explanation
Indices: 3171663--3171712 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
3171653 CCTCAAAAAT
3171663 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3171705 -A TA TA TA T
1 TA TA TA TA T
3171713 TAAGATGACC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3173887 original size:36 final size:35
Alignment explanation
Indices: 3173776--3174125 Score: 306
Period size: 36 Copynumber: 9.2 Consensus size: 35
3173766 TTTCGTCTAC
** **
3173776 ATTATATATATATATAGTTTGCAAATGATTTTTGAAA
1 ATTATATA-ATATATAGTTTTTAAAACA-TTTTGAAA
3173813 ATACGTATATAATATATAGTTTTT-AAACATTTTTGAAA
1 AT---TATATAATATATAGTTTTTAAAACA-TTTTGAAA
*
3173851 ATTATATAATATATAATTTTTAAAACATTTTAGAAA
1 ATTATATAATATATAGTTTTTAAAACATTTT-GAAA
*
3173887 ATTATATAATATATAGTTTTTGAAAACATTTTTAAA
1 ATTATATAATATATAGTTTTT-AAAACATTTTGAAA
* * *
3173923 ATATATATAATATACAGTTTTGAAAATATTTTGAAAA
1 AT-TATATAATATATAGTTTTTAAAACATTTTG-AAA
* *
3173960 CATTTATATATTATATAGTTTTTAAAAAAATCATTTTAAAA
1 -A-TTATATAATATATAGTTTTT---AAAA-CATTTTGAAA
* *
3174001 ATATATATAATATATGGTTTTTTAAATCATTTTGAAA
1 AT-TATATAATATATAG-TTTTTAAAACATTTTGAAA
*
3174038 ATTTATATAATATATAGTTTTAAAAACATTTTGAAA
1 A-TTATATAATATATAGTTTTTAAAACATTTTGAAA
*
3174074 ATAAGTATATATTATATAGTTTTTTTTAAAAACATGTTTGAAA
1 AT---TATATAATATATAG---TTTTT-AAAACAT-TTTGAAA
3174117 ATATATATA
1 AT-TATATA
3174126 GTTTTAAATT
Statistics
Matches: 262, Mismatches: 26, Indels: 46
0.78 0.08 0.14
Matches are distributed among these distances:
35 23 0.09
36 61 0.23
37 55 0.21
38 48 0.18
39 13 0.05
40 19 0.07
41 22 0.08
42 12 0.05
43 9 0.03
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (35 bp):
ATTATATAATATATAGTTTTTAAAACATTTTGAAA
Found at i:3174039 original size:115 final size:110
Alignment explanation
Indices: 3173805--3174125 Score: 362
Period size: 115 Copynumber: 2.8 Consensus size: 110
3173795 TGCAAATGAT
* * *
3173805 TTTTGAAAATACGTATATAATATATAGTTTTTAAACAT-TTTTG-AAAATTATATAATATATAAT
1 TTTTGAAAATA--TATATAATATATAG-TTTTAAAAATATTTTGAAAAATTATATATTATATAGT
3173868 TTTT-AAAACATTTTAGAAAAT-TATATAATATATAGTTTTTGAAAACA
63 TTTTAAAAACATTTTA-AAAATATATATAATATATAGTTTTTGAAAACA
* * *
3173915 TTTTTAAAATATATATAATATACAGTTTTGAAAATATTTTGAAAACATTTATATATTATATAGTT
1 TTTTGAAAATATATATAATATATAGTTTTAAAAATATTTTGAAAA-A-TTATATATTATATAGTT
* * *
3173980 TTTAAAAAAATCATTTTAAAAATATATATAATATATGGTTTTTTAAATCA
64 TTT--AAAAA-CATTTTAAAAATATATATAATATATAGTTTTTGAAAACA
* * *
3174030 TTTTGAAAATTTATATAATATATAGTTTTAAAAACATTTTGAAAATAAGTATATATTATATAGTT
1 TTTTGAAAATATATATAATATATAGTTTTAAAAATATTTTG-AAA-AATTATATATTATATAG--
*
3174095 TTTTTTAAAAACATGTTTGAAAATATATATA
62 -TTTTTAAAAACAT-TTTAAAAATATATATA
3174126 GTTTTAAATT
Statistics
Matches: 180, Mismatches: 16, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
107 8 0.04
108 18 0.10
109 3 0.02
110 11 0.06
111 18 0.10
114 9 0.05
115 83 0.46
116 24 0.13
117 1 0.01
118 5 0.03
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (110 bp):
TTTTGAAAATATATATAATATATAGTTTTAAAAATATTTTGAAAAATTATATATTATATAGTTTT
TAAAAACATTTTAAAAATATATATAATATATAGTTTTTGAAAACA
Found at i:3174236 original size:13 final size:13
Alignment explanation
Indices: 3174220--3174254 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
3174210 AAAAATAATT
3174220 TTTTATTTATTAA
1 TTTTATTTATTAA
*
3174233 TTTTATTTATTAT
1 TTTTATTTATTAA
3174246 TTGTTATTT
1 TT-TTATTT
3174255 TATTTATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTTATTTATTAA
Found at i:3174256 original size:19 final size:20
Alignment explanation
Indices: 3174217--3174262 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
3174207 TTAAAAAATA
*
3174217 ATTTTTTATTTATTAATTTT
1 ATTTATTATTTATTAATTTT
*
3174237 ATTTATTATTTGTT-ATTTT
1 ATTTATTATTTATTAATTTT
3174256 ATTTATT
1 ATTTATT
3174263 GTTTTTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (20 bp):
ATTTATTATTTATTAATTTT
Found at i:3175552 original size:20 final size:20
Alignment explanation
Indices: 3175483--3175584 Score: 57
Period size: 20 Copynumber: 4.8 Consensus size: 20
3175473 CCTGGTTTGC
*
3175483 TATTATTTCATTTTAGTCCTTT
1 TATTATTT-ATTTTA-TTCTTT
* *
3175505 T-TGT-TTTGTTTTATT-TTA
1 TAT-TATTTATTTTATTCTTT
3175523 TATTATTTTATTTTATTCTTT
1 TATTA-TTTATTTTATTCTTT
**
3175544 TATTATTTAATCGATATTACTTT
1 TATTATTT-AT-TTTATT-CTTT
3175567 TATTATATATATTTTATT
1 TATTAT-T-TATTTTATT
3175585 TATTTCATTT
Statistics
Matches: 61, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
18 4 0.07
19 2 0.03
20 18 0.30
21 13 0.21
22 6 0.10
23 14 0.23
24 3 0.05
25 1 0.02
ACGTcount: A:0.23, C:0.06, G:0.04, T:0.68
Consensus pattern (20 bp):
TATTATTTATTTTATTCTTT
Done.