Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 13 of 27
Found at i:1667401 original size:28 final size:27
Alignment explanation
Indices: 1667356--1667408 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
1667346 ATTTATTTTT
*
1667356 AAAATAATAATAAATTTATCTTAAATA
1 AAAATAATAATAAATTTACCTTAAATA
* *
1667383 AAAATAAATAGTATATTTACCTTAAA
1 AAAAT-AATAATAAATTTACCTTAAA
1667409 ATTAATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36
Consensus pattern (27 bp):
AAAATAATAATAAATTTACCTTAAATA
Found at i:1667711 original size:16 final size:17
Alignment explanation
Indices: 1667690--1667725 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1667680 AGAAAGCAAA
*
1667690 TTTAAAATAAT-AATAT
1 TTTAAAAAAATAAATAT
1667706 TTTAAAAAAATAAATAT
1 TTTAAAAAAATAAATAT
1667723 TTT
1 TTT
1667726 TTGATATACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAAAAAATAAATAT
Found at i:1668125 original size:12 final size:12
Alignment explanation
Indices: 1668089--1668176 Score: 63
Period size: 12 Copynumber: 7.3 Consensus size: 12
1668079 CATTAATTTT
1668089 TAATAAAATTAA
1 TAATAAAATTAA
* **
1668101 AAATAATTTTAA
1 TAATAAAATTAA
1668113 TAATAAAATTAA
1 TAATAAAATTAA
* * * *
1668125 TGATTATATTTTA
1 T-AATAAAATTAA
*
1668138 TAATAAAAAT-A
1 TAATAAAATTAA
*
1668149 TTATAAAATTAA
1 TAATAAAATTAA
1668161 -AATTAAAATTAA
1 TAA-TAAAATTAA
1668173 TAAT
1 TAAT
1668177 TTAATATTTT
Statistics
Matches: 55, Mismatches: 17, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
11 10 0.18
12 35 0.64
13 10 0.18
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (12 bp):
TAATAAAATTAA
Found at i:1668667 original size:29 final size:29
Alignment explanation
Indices: 1668639--1668696 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 29
1668629 AAGTCTTTTA
*
1668639 TAAATGTTTTTTGA-ATTTAAATA-AATT
1 TAAAAGTTTTTTGATATTTAAATATAATT
*
1668666 TAAAAGTTTTTTTATTATTTAAATATAATT
1 TAAAAGTTTTTTGA-TATTTAAATATAATT
1668696 T
1 T
1668697 TTATATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 12 0.46
29 9 0.35
30 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (29 bp):
TAAAAGTTTTTTGATATTTAAATATAATT
Found at i:1669724 original size:5 final size:5
Alignment explanation
Indices: 1669716--1669783 Score: 50
Period size: 5 Copynumber: 13.4 Consensus size: 5
1669706 AAATATATTT
* * * *
1669716 TTATA TTATA TAATTA TTTTA TTATA TTTATG TTATA TAATA TT-T- TTATA
1 TTATA TTATA TTA-TA TTATA TTATA -TTATA TTATA TTATA TTATA TTATA
*
1669766 TTATA TTTTAA TTATA TT
1 TTATA TTAT-A TTATA TT
1669784 TCAAAGTTAT
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 33 0.69
6 11 0.23
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:1669741 original size:29 final size:30
Alignment explanation
Indices: 1669709--1669782 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 30
1669699 TTAATTTAAA
1669709 TATATTTTTATATTATATAAT-TATTT-TAT
1 TATA-TTTTATATTATATAATATATTTATAT
* *
1669738 TATA-TTTATGTTATATAATATTTTTATAT
1 TATATTTTATATTATATAATATATTTATAT
1669767 TATATTTTA-ATTATAT
1 TATATTTTATATTATAT
1669783 TTCAAAGTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 14 0.36
28 4 0.10
29 17 0.44
30 4 0.10
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (30 bp):
TATATTTTATATTATATAATATATTTATAT
Found at i:1669765 original size:40 final size:40
Alignment explanation
Indices: 1669721--1669802 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 40
1669711 TATTTTTATA
*
1669721 TTATATAATTATTTT-ATTATATTT-ATGTTATATAATATTT
1 TTATATAA-TATTTTAATTATATTTAAAGTTATAT-ATATTT
*
1669761 TTATATTATATTTTAATTATATTTCAAAGTTATATATATTT
1 TTATATAATATTTTAATTATATTT-AAAGTTATATATATTT
1669802 T
1 T
1669803 AGTAGCAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
39 6 0.16
40 16 0.43
41 7 0.19
42 8 0.22
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.61
Consensus pattern (40 bp):
TTATATAATATTTTAATTATATTTAAAGTTATATATATTT
Found at i:1669780 original size:16 final size:14
Alignment explanation
Indices: 1669709--1669783 Score: 64
Period size: 16 Copynumber: 5.1 Consensus size: 14
1669699 TTAATTTAAA
1669709 TATATTT-TTATAT
1 TATATTTATTATAT
*
1669722 TATATAATTATTTTAT
1 TATAT--TTATTATAT
1669738 TATATTTATGTTATAT
1 TATATTTA--TTATAT
*
1669754 AATATTT-TTATAT
1 TATATTTATTATAT
1669767 TATATTTTAATTATAT
1 TATA-TTT-ATTATAT
1669783 T
1 T
1669784 TCAAAGTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
13 14 0.28
14 6 0.12
15 2 0.04
16 28 0.56
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (14 bp):
TATATTTATTATAT
Found at i:1670756 original size:363 final size:368
Alignment explanation
Indices: 1670254--1670943 Score: 957
Period size: 363 Copynumber: 1.9 Consensus size: 368
1670244 ATTTTTATTT
* * * *
1670254 TTTGTAATTACAAAAGTTACATAAGTGAAAATTGTAGTTCCTCAATGCGTTTTAGGTGATGAGAG
1 TTTGTAATTACAAAAGTTACATAAATGAAAACTGTAGTTCCTCAATGCATTTTAGGAGATGAGAG
* * *
1670319 TTGCCGTTTTCACGTTATTGAGATATTTAGGCTTTTAAAATACGAACTGAATTGAACTTAAGTTG
66 TTGCCATTTTCACCTTATTGAGATATTTAGGCTTTTAAAATACGAACTAAATTGAACTTAAGTTG
* * * *
1670384 ATTAACTAAAATTCCTATTACTTGAGTAGGGCTATAAATTATAATAAAAATGTTTGTAATAATAT
131 ATTAACTAAAATTCCTATTACTTGAGTAGAGCTATAAATTACAAGAAAAATGTTTATAATAATAT
* * * *
1670449 TATCA-T-TTTTTTAAATCGCTTTAGCATCTACGTGTGAT-GGAGTGGTGAAGAATGAT-ATTAT
196 TACCATTATTTTTTAAATCGCCTTAGCATCTACGTATGATCCG-GTGGTGAAGAATGATGATTAT
* *
1670510 TGGAATTAACATGCCCAAAA-TCTCTG-TTTTTTCTTTTTTTAATTAGTTGAT-TTGAGGCCAAG
260 TGGAATTAACATGCCCAAAATTCTCTGTTTTTTTC-TTTTTTAATAAGTAGATATTGAGGCCAAG
1670572 ATCTGTCCAAAATTTCACTTATTTTTATATGATTTATATATTTTG
324 ATCTGTCCAAAATTTCACTTATTTTTATATGATTTATATATTTTG
** *
1670617 TTTGTAATTACAATAA-TTTTATAAATGAAAACTGTAGTTCCTCAATGCATTTTAGGAGATGCGA
1 TTTGTAATTACAA-AAGTTACATAAATGAAAACTGTAGTTCCTCAATGCATTTTAGGAGATGAGA
* *
1670681 GTTGCCATTTTCACCTTATTGAGATATTTAGGCTTTCT-AAATATGAACTAAATTGAACTTGAGT
65 GTTGCCATTTTCACCTTATTGAGATATTTAGGCTTT-TAAAATACGAACTAAATTGAACTTAAGT
* **
1670745 TGATTAACTAAAATTCCTATTAGTTGAGTAGAGCTATAAATTACAAGAAATTTGTTTATAATAAT
129 TGATTAACTAAAATTCCTATTACTTGAGTAGAGCTATAAATTACAAGAAAAATGTTTATAATAAT
* * ** * *
1670810 ATTACCATTATTTTTTAACTCGCCTTAGCATCTATGTATTCTCCGGTGGTGAAGATTGATGGTTA
194 ATTACCATTATTTTTTAAATCGCCTTAGCATCTACGTATGATCCGGTGGTGAAGAATGATGATTA
* * * *
1670875 TTGGAATTAACGTGTCCAAAATTTCTCTGTTTTTTTCTTTTTTGATAAGTAGATATTGAGGCCGA
259 TTGGAATTAACATGCCCAAAA-TTCTCTGTTTTTTTCTTTTTTAATAAGTAGATATTGAGGCCAA
1670940 GATC
323 GATC
1670944 CGTGCATTGC
Statistics
Matches: 282, Mismatches: 35, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
363 175 0.62
364 4 0.01
365 40 0.14
366 23 0.08
368 20 0.07
369 20 0.07
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (368 bp):
TTTGTAATTACAAAAGTTACATAAATGAAAACTGTAGTTCCTCAATGCATTTTAGGAGATGAGAG
TTGCCATTTTCACCTTATTGAGATATTTAGGCTTTTAAAATACGAACTAAATTGAACTTAAGTTG
ATTAACTAAAATTCCTATTACTTGAGTAGAGCTATAAATTACAAGAAAAATGTTTATAATAATAT
TACCATTATTTTTTAAATCGCCTTAGCATCTACGTATGATCCGGTGGTGAAGAATGATGATTATT
GGAATTAACATGCCCAAAATTCTCTGTTTTTTTCTTTTTTAATAAGTAGATATTGAGGCCAAGAT
CTGTCCAAAATTTCACTTATTTTTATATGATTTATATATTTTG
Found at i:1673974 original size:2 final size:2
Alignment explanation
Indices: 1673969--1673995 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1673959 ACACACGTGT
1673969 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1673996 TTCCACTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1684022 original size:433 final size:434
Alignment explanation
Indices: 1682642--1684894 Score: 2250
Period size: 440 Copynumber: 5.1 Consensus size: 434
1682632 TACCTGAAGT
* * * *
1682642 CTCATACTTGAATGTATAGATTGACTACTGAAGTAGAGAGGCAG-TGGGAGATGTAGTGCCCAGA
1 CTCATACTTTAATGTATAGATTGACTACTGAAGTAGAGAGG-TGTTGAGAGATGTAGTGTCCAGA
* * *
1682706 TGTAGCTCAAGTAATAACGAAACACATACTACCGGGCAACGATGGGCTCCTTCAAGGGATGGCTA
65 TGTAGCTCAAGTAATAACTAAACACATAGTACCGGGCAACGATGGACTCCTTCAAGGGA-GGCTA
* * * *
1682771 ATAAATAGATTGGAAACCCAAACCTTCAATCCCTTCCCTATCTTTTTATTTTCCAGACATGTAGC
129 ATAGATAGATTGGAAACCCAAACCATCAATTCCTTCCCTATC--TTTATTTTCCAGACATGTAAC
* * * * * * *
1682836 AGTCCCTACCATCATATCAAAGGCAGAAACCTGACTACGTCTGGCTAGACACAGGGGAGGCAAAC
192 AGTCCCTACCATCATATCAAAGGTAGACACCTGACTACATCTGGTTAGACTCATGGGACGC--A-
* * * *
1682901 AACTAAATATTAAATAATAATTCACAGACAAAAATC-TAAAAATGTATCTACTTTTAAAAGGTAT
254 AACT-AA-ATTAAATAATAGTTCACAGACAAACA-CATAAAAATGTATCTACATTCAAAAGGTAT
*
1682965 ATAAGCATAGAAAGTATTT-CAAAGTGCATATATTAAGTGTTATTATCATTCGCTTCACTATCTC
316 ATAAGCATAGAAAGTATTTCCAAA-TGCATATATTAAGTGTTATTATCATTTGCTTCACTATCTC
* * * *
1683029 TTCAAAAAAGAACAGATTCACAGCAGTGGTCCACTGGTCCACTATATCTAAATTAAGAATGGC
380 TTTAAAAAAGAACAGATTCACAGCA---GT----T-GTTCACTATATCAAAAATAAGAATGGC
* * *
1683092 CTCATA---T--CG-AGAGA-TGTACTTACT-AATATAGAGAGGTGTTGAGAGATGTAGTGTCCA
1 CTCATACTTTAATGTATAGATTG-AC-TACTGAA-GTAGAGAGGTGTTGAGAGATGTAGTGTCCA
* * ** * *
1683149 GATGTAGCTCAAGTAATAAGTAAGCACATAGTACCAAGCAATGATGGATTCCTTCAAGGGATGGC
63 GATGTAGCTCAAGTAATAACTAAACACATAGTACCGGGCAACGATGGACTCCTTCAAGGGA-GGC
* * * * **
1683214 TAATAGATAGACTGG-GACCCAAACCATCAATTACTTCCCAATCTTTAATTTTTTAGACATGTAA
127 TAATAGATAGATTGGAAACCCAAACCATCAATTCCTTCCCTATCTTT-ATTTTCCAGACATGTAA
* * * * *
1683278 CAGTCCCTACCAACATATCAAAGGTAGACACCTGACAACATCTAGTTACACTCGTGGGACGCGAA
191 CAGTCCCTACCATCATATCAAAGGTAGACACCTGACTACATCTGGTTAGACTCATGGGACGC--A
* * * * *
1683343 CAACTAAATATTAAATAATAGTTCATA-ACCAAA-ACCTAAAAATGCATCTATATTCAAAATAAG
254 -AACT-AA-ATTAAATAATAGTTCACAGA-CAAACACATAAAAATGTATCTACATTC-AAA-AGG
* * *
1683406 T-TGATAGATGCATAAAAAGCATTTCCAAATGCATATATTAAGCGTTATTATCATTTGCTTCACT
313 TAT-ATA-A-GCATAGAAAGTATTTCCAAATGCATATATTAAGTGTTATTATCATTTGCTTCACT
* * * * *
1683470 A--TCTTTAAAAACAGAACTGATTCACAGTAGTGGTCCA-TATATCAAAAATATGAATGGC
375 ATCTCTTTAAAAA-AGAACAGATTCACAGCAGTTGTTCACTATATCAAAAATAAGAATGGC
* * *
1683528 CTCATACTTTAATGTATTGATTGACTACTGAAGTAGAAAGGTGTTGAGAGATGTTGTGTCCAGAT
1 CTCATACTTTAATGTATAGATTGACTACTGAAGTAGAGAGGTGTTGAGAGATGTAGTGTCCAGAT
* ** * * * *
1683593 GCAGCTCAAGTAATAACTAAATGCATAGTACTGGGCAACGAAGGACTCCTTGAAGGG-GCGCTAC
66 GTAGCTCAAGTAATAACTAAACACATAGTACCGGGCAACGATGGACTCCTTCAAGGGAG-GCTAA
* * * *
1683657 TAGATAGATTGGAAACCCAAACCACCAATTCCTTCCCTATCTTTATATTCCAGAAATGCAACAGT
130 TAGATAGATTGGAAACCCAAACCATCAATTCCTTCCCTATCTTTATTTTCCAGACATGTAACAGT
* * * *
1683722 CCCTACCATCATATCAAAGGTAGTCACCTGACCACATCTGGTTATACTCATAGGACGCAAAC-AA
195 CCCTACCATCATATCAAAGGTAGACACCTGACTACATCTGGTTAGACTCATGGGACGCAAACTAA
** * * *
1683786 ATT-AATTCT-GATCCACAGACAAACACATAAAAATGTATGTACATTCAAAAGGTATATAAGAAT
260 ATTAAATAATAG-TTCACAGACAAACACATAAAAATGTATCTACATTCAAAAGGTATATAAGCAT
* * * *
1683849 AGCAAGTATTTCCAAATGCATATATCAATTGTTATTATCATTTGCTTCATTATCTCTTTAAAAAA
324 AGAAAGTATTTCCAAATGCATATATTAAGTGTTATTATCATTTGCTTCACTATCTCTTTAAAAAA
*
1683914 GGAACAGATTCACAGCAGTTGTTCACCATATCAAAAATAAGAATGGC
389 -GAACAGATTCACAGCAGTTGTTCACTATATCAAAAATAAGAATGGC
* **
1683961 CTCATGCTTTAATGTATAGATTGACTACTGACCTAGAGAGGTGTTGAGAGATGTAGTGTCCAGAT
1 CTCATACTTTAATGTATAGATTGACTACTGAAGTAGAGAGGTGTTGAGAGATGTAGTGTCCAGAT
* * * * * *
1684026 GTAGTTCATGTTATAACTAAACACATAGTACTGGGCAATGATGGCCTCCTTCAAGGGAGGCCTAA
66 GTAGCTCAAGTAATAACTAAACACATAGTACCGGGCAACGATGGACTCCTTCAAGGGAGG-CTAA
* * * *
1684091 TAGATAGATTGAAAACCCAAACCATCAATTCCTTCCCTCTC-TTGTTTTCCAGACATGTAACAAT
130 TAGATAGATTGGAAACCCAAACCATCAATTCCTTCCCTATCTTTATTTTCCAGACATGTAACAGT
* * * * * **
1684155 CCCTACCATCACATCAAAAGTAAGACATCTAACTACATCTGGTTAGAC-CAT-GCA-AAAAACTA
195 CCCTACCATCATATCAAAGGT-AGACACCTGACTACATCTGGTTAGACTCATGGGACGCAAACTA
* * * * * *
1684217 AATACTAAATAATAGTTCACAGACAAAGACATAAAAA-GCATCTATAGTCAAAGGGTATACAAGC
259 AAT--TAAATAATAGTTCACAGACAAACACATAAAAATGTATCTACATTCAAAAGGTATATAAGC
* * * * * *
1684281 ATAGAAAGTAATTCCAAAAGCATATATTAAGTGTTATAATCATTTGTTTCACTATCTATTGAAAA
322 ATAGAAAGTATTTCCAAATGCATATATTAAGTGTTATTATCATTTGCTTCACTATCTCTTTAAAA
* *
1684346 AAGAACAGATTCACAGCAGTT-ATCACTGTAT-AGAAAATAAGAATGGC
387 AAGAACAGATTCACAGCAGTTGTTCACTATATCA-AAAATAAGAATGGC
** *
1684393 CTCATACAGTCATTCTTGAATGTATAGATTGACTACCAAAGTAGAGAGGTGTTAAGAGATGTAGT
1 CTCAT--A--C--T-TT-AATGTATAGATTGACTACTGAAGTAGAGAGGTGTTGAGAGATGTAGT
* *
1684458 GTCCAGATGTAGCTCAAGTAATAACTAAACACCTACTACCGGGCAACGATGGACTCCTTCAAGGG
58 GTCCAGATGTAGCTCAAGTAATAACTAAACACATAGTACCGGGCAACGATGGACTCCTTCAAGGG
* * *
1684523 AGGGCTAATTGATAGATTGGGAACCCAAACCATCAATTCCTTCCCTATCTTTTATTTTCCAGACG
123 A-GGCTAATAGATAGATTGGAAACCCAAACCATCAATTCCTTCCCTATC-TTTATTTTCCAGACA
** * *
1684588 TGTAACAGTCCCTACCATCATATCAAAGGTAGACACCTGACTATGTCTGGTTATACTCACGGGAC
186 TGTAACAGTCCCTACCATCATATCAAAGGTAGACACCTGACTACATCTGGTTAGACTCATGGGAC
* * * * **
1684653 GGAAACAACTAAATATTAGATAATAGTTCAAAGACAAACACCA-AAAAATGTAGCTGTATTCCTA
251 -G-CA-AACT-AA-ATTAAATAATAGTTCACAGACAAACA-CATAAAAATGTATCTACATT-C-A
* * * * * *
1684717 ATAAGGTAAATAAGCATATAAAGTATTTCCAAATGCTTATATTAAGCGCTATTATCA-TTGTTTC
308 A-AAGGTATATAAGCATAGAAAGTATTTCCAAATGCATATATTAAGTGTTATTATCATTTGCTTC
** ** * * *
1684781 AGAATCTCTTTAAAAAAAAGAACAGACACACAGCAG-TGGTCAACCATATCCAAAATAAGAATGG
372 ACTATCTCTTT--AAAAAAGAACAGATTCACAGCAGTTGTTC-ACTATATCAAAAATAAGAATGG
1684845 C
434 C
* * * * *
1684846 CTCATACTTAAATGTATGGCTTGACT-CTTGAGGTAGAGAAGTGTTGAGA
1 CTCATACTTTAATGTATAGATTGACTAC-TGAAGTAGAGAGGTGTTGAGA
1684895 AACGATGGAC
Statistics
Matches: 1491, Mismatches: 241, Indels: 147
0.79 0.13 0.08
Matches are distributed among these distances:
430 48 0.03
431 7 0.00
432 69 0.05
433 201 0.13
434 163 0.11
435 26 0.02
436 26 0.02
437 8 0.01
438 2 0.00
439 4 0.00
440 223 0.15
441 131 0.09
442 70 0.05
443 105 0.07
444 48 0.03
445 144 0.10
446 50 0.03
447 35 0.02
448 11 0.01
449 4 0.00
450 22 0.01
451 47 0.03
452 23 0.02
453 24 0.02
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (434 bp):
CTCATACTTTAATGTATAGATTGACTACTGAAGTAGAGAGGTGTTGAGAGATGTAGTGTCCAGAT
GTAGCTCAAGTAATAACTAAACACATAGTACCGGGCAACGATGGACTCCTTCAAGGGAGGCTAAT
AGATAGATTGGAAACCCAAACCATCAATTCCTTCCCTATCTTTATTTTCCAGACATGTAACAGTC
CCTACCATCATATCAAAGGTAGACACCTGACTACATCTGGTTAGACTCATGGGACGCAAACTAAA
TTAAATAATAGTTCACAGACAAACACATAAAAATGTATCTACATTCAAAAGGTATATAAGCATAG
AAAGTATTTCCAAATGCATATATTAAGTGTTATTATCATTTGCTTCACTATCTCTTTAAAAAAGA
ACAGATTCACAGCAGTTGTTCACTATATCAAAAATAAGAATGGC
Found at i:1687648 original size:18 final size:18
Alignment explanation
Indices: 1687612--1687645 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1687602 AATATATAAT
*
1687612 TTAATATAATATAAATTA
1 TTAATATATTATAAATTA
1687630 TTAATATATTA-AAATT
1 TTAATATATTATAAATT
1687646 TATATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATATATTATAAATTA
Found at i:1687654 original size:27 final size:27
Alignment explanation
Indices: 1687614--1687688 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
1687604 TATATAATTT
*
1687614 AATATAATATAAATTATTAATATATTAA
1 AATATTATATAAATTATTAATAT-TTAA
*
1687642 AAT-TTATATAAA-TATATAATATTTCA
1 AATATTATATAAATTAT-TAATATTTAA
* *
1687668 AATATTATTTAAATAATTAAT
1 AATATTATATAAATTATTAAT
1687689 TATAATAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 9 0.22
27 26 0.65
28 5 0.12
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (27 bp):
AATATTATATAAATTATTAATATTTAA
Found at i:1687803 original size:12 final size:12
Alignment explanation
Indices: 1687786--1687815 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1687776 ATTAAATAAA
1687786 ATAAATTATTTT
1 ATAAATTATTTT
1687798 ATAAATTATTTT
1 ATAAATTATTTT
*
1687810 TTAAAT
1 ATAAAT
1687816 AAAAATATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATAAATTATTTT
Found at i:1688000 original size:31 final size:32
Alignment explanation
Indices: 1687965--1688039 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
1687955 AATTAACTAA
*
1687965 TTAAAAATAA-TTATTATTTT-CATCATTAAAT
1 TTAAAAATAATTTA-TATTTTAAATCATTAAAT
*
1687996 TT-AAAATAATTTATATTTTAAATTATTAAAT
1 TTAAAAATAATTTATATTTTAAATCATTAAAT
*
1688027 TTAATAATAATTT
1 TTAAAAATAATTT
1688040 TGTTAAAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
30 13 0.34
31 16 0.42
32 9 0.24
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (32 bp):
TTAAAAATAATTTATATTTTAAATCATTAAAT
Found at i:1688003 original size:30 final size:31
Alignment explanation
Indices: 1687963--1688039 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 31
1687953 GAAATTAACT
* *
1687963 AATTAAAAATAA-TTATTATTTT-CATCATTA
1 AATTTAAAATAATTTA-TATTTTAAATCATTA
*
1687993 AATTTAAAATAATTTATATTTTAAATTATTA
1 AATTTAAAATAATTTATATTTTAAATCATTA
1688024 AATTTAATAATAATTT
1 AATTTAA-AATAATTT
1688040 TGTTAAAAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
30 17 0.41
31 16 0.39
32 8 0.20
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (31 bp):
AATTTAAAATAATTTATATTTTAAATCATTA
Found at i:1688304 original size:22 final size:22
Alignment explanation
Indices: 1688262--1688304 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1688252 TGAAATTAGT
* *
1688262 ATAAATAATTTATTTTTTAATA
1 ATAAATAATTTATTATATAATA
1688284 ATAAA-AATTTATTAATATAAT
1 ATAAATAATTTATT-ATATAAT
1688305 TTGATGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAAATAATTTATTATATAATA
Found at i:1689679 original size:19 final size:21
Alignment explanation
Indices: 1689635--1689679 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
1689625 TATTATAATG
1689635 AATAATAAATATAAATATTTT
1 AATAATAAATATAAATATTTT
*
1689656 -A-AATAAATA-AACT-TTTT
1 AATAATAAATATAAATATTTT
1689673 AATAATA
1 AATAATA
1689680 TAACTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
17 4 0.19
18 4 0.19
19 12 0.57
20 1 0.05
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AATAATAAATATAAATATTTT
Found at i:1689682 original size:17 final size:17
Alignment explanation
Indices: 1689637--1689682 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
1689627 TTATAATGAA
1689637 TAATAAATATAAATATTT
1 TAAT-AATATAAATATTT
1689655 TAAATAA-ATAAACT-TTT
1 T-AATAATATAAA-TATTT
1689672 TAATAATATAA
1 TAATAATATAA
1689683 CTAAAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 5 0.20
17 13 0.52
18 4 0.16
19 3 0.12
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATAATATAAATATTT
Found at i:1690664 original size:22 final size:21
Alignment explanation
Indices: 1690595--1690666 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 21
1690585 AATAAAAATG
*
1690595 ATATTTAATAAATTTGAATTTTA
1 ATATTAAATAAATTT--ATTTTA
*
1690618 ATATT-TATAAATTT-TTTT-
1 ATATTAAATAAATTTATTTTA
*
1690636 ATTTTAAATAAATTTATTTTA
1 ATATTAAATAAATTTATTTTA
1690657 ATGATTAAAT
1 AT-ATTAAAT
1690667 TTAAACATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.10
19 12 0.29
20 4 0.10
21 2 0.05
22 14 0.34
23 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
ATATTAAATAAATTTATTTTA
Found at i:1691122 original size:16 final size:16
Alignment explanation
Indices: 1691082--1691123 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
1691072 ATAATATAAA
*
1691082 TATATATTTAAA-TTT
1 TATATATTAAAATTTT
1691097 TA-AT-TTAAAATTTT
1 TATATATTAAAATTTT
1691111 TATATATTAAAAT
1 TATATATTAAAAT
1691124 AATTATATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 5 0.22
14 7 0.30
15 4 0.17
16 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATATTAAAATTTT
Found at i:1692129 original size:20 final size:19
Alignment explanation
Indices: 1692093--1692132 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1692083 ATATTTTATT
1692093 TAAATTTAATTACAAAATA
1 TAAATTTAATTACAAAATA
1692112 TAAATATTAATATA-AAAATA
1 TAAAT-TTAAT-TACAAAATA
1692132 T
1 T
1692133 TTTTGTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 12 0.63
21 2 0.11
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATTTAATTACAAAATA
Found at i:1692898 original size:21 final size:21
Alignment explanation
Indices: 1692849--1692898 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
1692839 GTTAATTTGG
* *
1692849 TAATA-AAAAAATTATTTAAA
1 TAATATAAAAAATAATATAAA
*
1692869 -AATTTTAAAAAATAATATAAA
1 TAA-TATAAAAAATAATATAAA
1692890 TAATATAAA
1 TAATATAAA
1692899 TTTAAAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
19 2 0.09
20 1 0.04
21 18 0.78
22 2 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
TAATATAAAAAATAATATAAA
Found at i:1693102 original size:13 final size:13
Alignment explanation
Indices: 1693084--1693108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1693074 ATATTAATCA
1693084 TATTTATATATTT
1 TATTTATATATTT
1693097 TATTTATATATT
1 TATTTATATATT
1693109 AATAATTTAA
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:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTATATATTT
Found at i:1693108 original size:30 final size:28
Alignment explanation
Indices: 1693074--1693165 Score: 84
Period size: 30 Copynumber: 3.3 Consensus size: 28
1693064 AAAAATTGAA
1693074 ATATTAATCATATTTATATATTTTATTTAT
1 ATATTAAT-ATATTTATATA-TTTATTTAT
* *
1693104 ATATTAATA-ATTTA-A-A-TTATATAA
1 ATATTAATATATTTATATATTTATTTAT
*
1693128 ATTTTAATATATTTATATATATTATATTAT
1 ATATTAATATATTTATATAT-TTAT-TTAT
*
1693158 ATTTTAAT
1 ATATTAAT
1693166 TAAGTTTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
24 14 0.27
25 5 0.10
26 2 0.04
27 2 0.04
28 5 0.10
29 5 0.10
30 18 0.35
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (28 bp):
ATATTAATATATTTATATATTTATTTAT
Found at i:1693143 original size:20 final size:20
Alignment explanation
Indices: 1693120--1693161 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1693110 ATAATTTAAA
*
1693120 TTATATAAATTTTAATATAT
1 TTATATAAATTATAATATAT
* *
1693140 TTATATATATTATATTATAT
1 TTATATAAATTATAATATAT
1693160 TT
1 TT
1693162 TAATTAAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATATAAATTATAATATAT
Found at i:1694126 original size:22 final size:21
Alignment explanation
Indices: 1694082--1694122 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1694072 AAATAAAATT
1694082 AAAAATTATTTTTTAAATTTA
1 AAAAATTATTTTTTAAATTTA
1694103 AAAAATTATTTTTTAAATTT
1 AAAAATTATTTTTTAAATTT
1694123 TAAATTAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AAAAATTATTTTTTAAATTTA
Found at i:1694890 original size:3 final size:3
Alignment explanation
Indices: 1694882--1694917 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1694872 CATGTTGCAA
1694882 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1694918 TTTTATTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1697294 original size:10 final size:10
Alignment explanation
Indices: 1697271--1697368 Score: 54
Period size: 9 Copynumber: 10.7 Consensus size: 10
1697261 AATATTAATC
*
1697271 ATATTTAAATT
1 ATATTTATA-T
1697282 ATATTTATAT
1 ATATTTATAT
1697292 ATA-TT-TAT
1 ATATTTATAT
1697300 ATATTTATA-
1 ATATTTATAT
*
1697309 ATATTTTTAT
1 ATATTTATAT
* * *
1697319 TTATATAAAT
1 ATATTTATAT
1697329 A-ATTTA-A-
1 ATATTTATAT
*
1697336 AT-TATATA-
1 ATATTTATAT
*
1697344 AAATTTA-AT
1 ATATTTATAT
1697353 ATATTTATAT
1 ATATTTATAT
1697363 AT-TTTA
1 ATATTTA
1697369 ATTTTTTTAT
Statistics
Matches: 67, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
7 4 0.06
8 10 0.15
9 29 0.43
10 16 0.24
11 8 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATATTTATAT
Found at i:1697369 original size:18 final size:18
Alignment explanation
Indices: 1697271--1697380 Score: 73
Period size: 18 Copynumber: 6.1 Consensus size: 18
1697261 AATATTAATC
*
1697271 ATATTTAAATTATATTTAT
1 ATATTTTAA-TATATTTAT
1697290 ATATATTT-ATATATTTAT
1 ATAT-TTTAATATATTTAT
* * * *
1697308 AATATTTTTATTTATATAA
1 -ATATTTTAATATATTTAT
* *
1697327 ATAATTTAA-AT-TATAT
1 ATATTTTAATATATTTAT
* *
1697343 AAAATTTAATATATTTAT
1 ATATTTTAATATATTTAT
* *
1697361 ATATTTTAATTTTTTTAT
1 ATATTTTAATATATTTAT
1697379 AT
1 AT
1697381 CAAATGAAAT
Statistics
Matches: 72, Mismatches: 14, Indels: 11
0.74 0.14 0.11
Matches are distributed among these distances:
16 12 0.17
17 3 0.04
18 39 0.54
19 16 0.22
20 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATATTTTAATATATTTAT
Found at i:1697391 original size:53 final size:51
Alignment explanation
Indices: 1697286--1697392 Score: 117
Period size: 52 Copynumber: 2.1 Consensus size: 51
1697276 TAAATTATAT
* * * *
1697286 TTATATATATTTATATATTTATAATATTTTTATTTATATAAATAATTTAAA
1 TTATATAAATTTATATATTTATAATATTTTAATTTATATAAATAAATGAAA
* * *
1697337 TTATATAAAATTTAATATATTTAT-ATATTTTAATTTTTTTATATCAAATGAAA
1 TTATAT-AAATTT-ATATATTTATAATATTTTAATTTATATAAAT-AAATGAAA
1697390 TTA
1 TTA
1697393 AAAAAAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
51 6 0.13
52 21 0.46
53 19 0.41
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (51 bp):
TTATATAAATTTATATATTTATAATATTTTAATTTATATAAATAAATGAAA
Found at i:1697640 original size:2 final size:2
Alignment explanation
Indices: 1697628--1697661 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1697618 TTCGTTCTTT
1697628 TA TA T- TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1697662 AATTGCTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1699028 original size:15 final size:15
Alignment explanation
Indices: 1699005--1699052 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1698995 GATATCCGAA
*
1699005 TTATTTTTTAATATT
1 TTATATTTTAATATT
*
1699020 TTATATTTTAAAATT
1 TTATATTTTAATATT
* *
1699035 TTATAATTAAATATT
1 TTATATTTTAATATT
1699050 TTA
1 TTA
1699053 AAATTATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATATTTTAATATT
Found at i:1705135 original size:3 final size:3
Alignment explanation
Indices: 1705127--1705169 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1705117 CTGGCACCTT
1705127 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1705170 CTGATTGCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1715013 original size:2 final size:2
Alignment explanation
Indices: 1715008--1715032 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1714998 ATATATACAT
1715008 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1715033 TATGATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1715573 original size:26 final size:25
Alignment explanation
Indices: 1715506--1715579 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 25
1715496 GTTTGAAAGT
1715506 TAATTTTATTA-TTAAAAATAAAAA
1 TAATTTTATTATTTAAAAATAAAAA
* *
1715530 TATTTTTAATT-TAATAAAAATAAAAA
1 TAATTTT-ATTAT-TTAAAAATAAAAA
1715556 TAAATTTTATTATTTAAATAATAA
1 T-AATTTTATTATTTAAA-AATAA
1715580 TTGATAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
24 6 0.15
25 3 0.08
26 20 0.50
27 11 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TAATTTTATTATTTAAAAATAAAAA
Found at i:1718570 original size:14 final size:14
Alignment explanation
Indices: 1718551--1718592 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1718541 TTACATTAAG
1718551 TAAATTTATTTATA
1 TAAATTTATTTATA
**
1718565 TAAATTTATAAATAA
1 TAAATTTATTTAT-A
1718580 TAAATTT-TTTATA
1 TAAATTTATTTATA
1718593 CAAACTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 1 0.04
14 14 0.61
15 8 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAAATTTATTTATA
Found at i:1718969 original size:30 final size:30
Alignment explanation
Indices: 1718902--1718970 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
1718892 ATTATTTTAA
* *
1718902 ATATACTAATATTTTTAAAATATTTTTATAC
1 ATATA-TAATATTTTTAAAATATTCTAATAC
1718933 ATATATAATATATTTTAAAAT-TTACTAATAC
1 ATATATAATAT-TTTTAAAATATT-CTAATAC
1718964 A-ATATAA
1 ATATATAA
1718971 ATTATAGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 14 0.41
31 20 0.59
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (30 bp):
ATATATAATATTTTTAAAATATTCTAATAC
Found at i:1719064 original size:25 final size:25
Alignment explanation
Indices: 1719035--1719090 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
1719025 TTTAAACTTA
* * *
1719035 TAAATATTTAATGAATTACAAT-TTT
1 TAAATATTAAAT-AAATAAAATATTT
1719060 TAAATATTAAATAAATAAAATATTT
1 TAAATATTAAATAAATAAAATATTT
1719085 TAAATA
1 TAAATA
1719091 AATAATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
TAAATATTAAATAAATAAAATATTT
Found at i:1719329 original size:17 final size:19
Alignment explanation
Indices: 1719307--1719345 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
1719297 TTAAATAAAT
*
1719307 AAAATTTT-TATTT-TTAA
1 AAAATTTTAAATTTATTAA
1719324 AAAATTTTAAATTTATTAA
1 AAAATTTTAAATTTATTAA
1719343 AAA
1 AAA
1719346 GAACTCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAAATTTTAAATTTATTAA
Found at i:1720110 original size:19 final size:19
Alignment explanation
Indices: 1720062--1720112 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
1720052 TATTATCAAA
*
1720062 TTAATTAATTTTATATATTT
1 TTAA-TAATTTTATATATGT
*
1720082 TTTATAATTTTATATATAGT
1 TTAATAATTTTATATAT-GT
1720102 TTAAT-ATTTTA
1 TTAATAATTTTA
1720113 ATAAATTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTAATAATTTTATATATGT
Found at i:1721045 original size:21 final size:21
Alignment explanation
Indices: 1721021--1721060 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1721011 TCTAAATTTA
1721021 TTTTTATTAATTTAATAAATT
1 TTTTTATTAATTTAATAAATT
* *
1721042 TTTTTATTGATTTGATAAA
1 TTTTTATTAATTTAATAAA
1721061 ATGTTAATTT
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:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTTTATTAATTTAATAAATT
Found at i:1721632 original size:18 final size:17
Alignment explanation
Indices: 1721609--1721657 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
1721599 TATTTATTTA
1721609 AATTAAAAATTAAATATT
1 AATTAAAAATTAAATA-T
*
1721627 AATTAAAAA-T-GATAT
1 AATTAAAAATTAAATAT
1721642 AATATAAAAATTAAAT
1 AAT-TAAAAATTAAAT
1721658 TTTTAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.15
16 9 0.35
17 2 0.08
18 11 0.42
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AATTAAAAATTAAATAT
Found at i:1721844 original size:17 final size:17
Alignment explanation
Indices: 1721812--1721845 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1721802 TAAGTTATTA
*
1721812 TTTAAAAATATGATTTT
1 TTTAAAAATATAATTTT
*
1721829 TTTAAAAATTTAATTTT
1 TTTAAAAATATAATTTT
1721846 AATTTTTAAT
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:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAAAAATATAATTTT
Found at i:1723980 original size:29 final size:29
Alignment explanation
Indices: 1723938--1723997 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1723928 AAGTTTGTTT
1723938 TGTCTTCATATGTTTGATTGGATTCAGAC
1 TGTCTTCATATGTTTGATTGGATTCAGAC
1723967 TGTCTTCATATGTTTGATTGGATTCAGAC
1 TGTCTTCATATGTTTGATTGGATTCAGAC
1723996 TG
1 TG
1723998 ATAATTCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.20, C:0.13, G:0.22, T:0.45
Consensus pattern (29 bp):
TGTCTTCATATGTTTGATTGGATTCAGAC
Found at i:1731369 original size:10 final size:10
Alignment explanation
Indices: 1731354--1731427 Score: 58
Period size: 10 Copynumber: 7.0 Consensus size: 10
1731344 TAAAAAATTA
1731354 TAATTTAAAT
1 TAATTTAAAT
1731364 TAATTTAAAT
1 TAATTTAAAT
* *
1731374 TGATATAAAT
1 TAATTTAAAT
*
1731384 TATTTTTAAAT
1 TA-ATTTAAAT
***
1731395 AATAATTTTTTT
1 --TAATTTAAAT
1731407 TAATTTAAAT
1 TAATTTAAAT
1731417 TAATTATAAAT
1 TAATT-TAAAT
1731428 ATTAATATAA
Statistics
Matches: 48, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
10 31 0.65
11 11 0.23
12 4 0.08
13 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (10 bp):
TAATTTAAAT
Found at i:1740192 original size:16 final size:16
Alignment explanation
Indices: 1740171--1740216 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
1740161 TGAATATTTT
1740171 TAAAATAATTTAAACG
1 TAAAATAATTTAAACG
* *
1740187 TAAAATATTTTAAACT
1 TAAAATAATTTAAACG
* *
1740203 TAACATAATCTAAA
1 TAAAATAATTTAAA
1740217 TTTGAATACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.35
Consensus pattern (16 bp):
TAAAATAATTTAAACG
Found at i:1740689 original size:18 final size:16
Alignment explanation
Indices: 1740646--1740689 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1740636 TTTCAAATAC
1740646 AATAAAAATATAAAAA
1 AATAAAAATATAAAAA
*
1740662 AATTAAAATATAATATAA
1 AATAAAAATATAA-A-AA
*
1740680 CATAAAAATA
1 AATAAAAATA
1740690 ATATTAATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 12 0.52
17 1 0.04
18 10 0.43
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
AATAAAAATATAAAAA
Found at i:1748549 original size:2 final size:2
Alignment explanation
Indices: 1748542--1748584 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1748532 AAATTTCTTT
1748542 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1748583 TA
1 TA
1748585 ACAGGTTGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1749992 original size:3 final size:3
Alignment explanation
Indices: 1749978--1750015 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1749968 GCAATACCTG
*
1749978 CTT CTG CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1750016 AGTGTTTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:1750712 original size:14 final size:14
Alignment explanation
Indices: 1750676--1750716 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 14
1750666 TATATTTGAT
1750676 ATATATTTAAATATA
1 ATAT-TTTAAATATA
*
1750691 A-A-TATAAATATA
1 ATATTTTAAATATA
1750703 ATATTTTAAATATA
1 ATATTTTAAATATA
1750717 TATAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 10 0.45
13 1 0.05
14 10 0.45
15 1 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATTTTAAATATA
Found at i:1750728 original size:18 final size:18
Alignment explanation
Indices: 1750674--1750730 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
1750664 TTTATATTTG
** *
1750674 ATATATATTTAAATATAA
1 ATATATATAAAAATTTAA
* *
1750692 ATATAAATATAATATTTTAA
1 ATAT--ATATAAAAATTTAA
1750712 ATATATATAAAAATTTAA
1 ATATATATAAAAATTTAA
1750730 A
1 A
1750731 AAAATTAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
18 17 0.57
20 13 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATATATAAAAATTTAA
Found at i:1757805 original size:14 final size:16
Alignment explanation
Indices: 1757786--1757819 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
1757776 TTTTTACATC
1757786 ATAATTATAT-TTAA-
1 ATAATTATATATTAAT
1757800 ATAATTATATATTAAT
1 ATAATTATATATTAAT
1757816 ATAA
1 ATAA
1757820 AATTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 4 0.22
16 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATTATATATTAAT
Found at i:1757897 original size:5 final size:5
Alignment explanation
Indices: 1757851--1757922 Score: 50
Period size: 5 Copynumber: 15.4 Consensus size: 5
1757841 TATATCGAAT
* * *
1757851 TTATA TTAT- TT-T- TTATA TTA-A -TATA TTTTAA TTTTT TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA TTATA TTATA
1757897 TTAATA TTATA -TA-A TTATA TTATA TT
1 TT-ATA TTATA TTATA TTATA TTATA TT
1757923 TAAAATTATG
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
3 6 0.11
4 9 0.16
5 30 0.55
6 10 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTATA
Found at i:1757911 original size:29 final size:29
Alignment explanation
Indices: 1757863--1757922 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
1757853 ATATTATTTT
* * *
1757863 TTATATTAATATATTTTAATTTTTTTATA
1 TTATATTAATATATTATAATTATATTATA
1757892 TTATATTAATAT-TATATAATTATATTATA
1 TTATATTAATATAT-TATAATTATATTATA
1757921 TT
1 TT
1757923 TAAAATTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
TTATATTAATATATTATAATTATATTATA
Found at i:1757913 original size:19 final size:17
Alignment explanation
Indices: 1757891--1757931 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
1757881 ATTTTTTTAT
*
1757891 ATTATATTAATATTATATA
1 ATTATATT-ATATT-TAAA
1757910 ATTATATTATATTTAAA
1 ATTATATTATATTTAAA
1757927 ATTAT
1 ATTAT
1757932 GAATTATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 5 0.24
19 8 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTATATTATATTTAAA
Found at i:1757916 original size:13 final size:11
Alignment explanation
Indices: 1757835--1757924 Score: 58
Period size: 11 Copynumber: 7.7 Consensus size: 11
1757825 AATATATTTA
1757835 TATATTTATAT
1 TATATTTATAT
*
1757846 CGA-ATTTATAT
1 -TATATTTATAT
*
1757857 TATTTTTTATAT
1 TA-TATTTATAT
*
1757869 TAATATATTTTAAT
1 T-ATAT-TTAT-AT
*
1757883 T-TTTTTATAT
1 TATATTTATAT
*
1757893 TATATTAATAT
1 TATATTTATAT
1757904 TATATAATTATAT
1 TATAT--TTATAT
1757917 TATATTTA
1 TATATTTA
1757925 AAATTATGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
10 4 0.07
11 26 0.43
12 13 0.22
13 14 0.23
14 3 0.05
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1757936 original size:24 final size:24
Alignment explanation
Indices: 1757887--1757938 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1757877 TTTAATTTTT
* *
1757887 TTATATTATATTAATATTATATAA
1 TTATATTATATTAAAATTATAGAA
1757911 TTATATTATATTTAAAATTAT-GAA
1 TTATATTATA-TTAAAATTATAGAA
1757935 TTAT
1 TTAT
1757939 CTTAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TTATATTATATTAAAATTATAGAA
Found at i:1758204 original size:15 final size:15
Alignment explanation
Indices: 1758184--1758214 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1758174 TATTCAAATA
1758184 ATCAAAATATATATT
1 ATCAAAATATATATT
*
1758199 ATCAAAATTTATATT
1 ATCAAAATATATATT
1758214 A
1 A
1758215 ATATATAAAC
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:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
ATCAAAATATATATT
Found at i:1758256 original size:26 final size:24
Alignment explanation
Indices: 1758202--1758257 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 24
1758192 ATATATTATC
* *
1758202 AAAATTTATATTAATATATAAACT
1 AAAATTTATATTAATAAATAAAAT
* *
1758226 TAAATTTATGTATTCATAAATAAAAT
1 AAAATTTA--TATTAATAAATAAAAT
1758252 AAAATT
1 AAAATT
1758258 CACGTCCAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 7 0.28
26 18 0.72
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (24 bp):
AAAATTTATATTAATAAATAAAAT
Found at i:1759204 original size:7 final size:8
Alignment explanation
Indices: 1759165--1759289 Score: 59
Period size: 7 Copynumber: 15.6 Consensus size: 8
1759155 ATAATTCAAG
1759165 TATTTATA
1 TATTTATA
1759173 TTATTT-TA
1 -TATTTATA
*
1759181 T-TATATAA
1 TATTTAT-A
*
1759189 TAATTATA
1 TATTTATA
1759197 T-TTTATA
1 TATTTATA
1759204 TATTT-TA
1 TATTTATA
1759211 TATTTATA
1 TATTTATA
*
1759219 TTATGTA-A
1 -TATTTATA
1759227 -ATTTATA
1 TATTTATA
1759234 TAAATTTAATA
1 T--ATTT-ATA
*
1759245 TATTAATA
1 TATTTATA
1759253 -ATTTATA
1 TATTTATA
*
1759260 T-TATATA
1 TATTTATA
* *
1759267 AAGTTTAAAA
1 TA-TTT-ATA
1759277 TATTTATA
1 TATTTATA
1759285 TATTT
1 TATTT
1759290 TTAACATATT
Statistics
Matches: 87, Mismatches: 14, Indels: 31
0.66 0.11 0.23
Matches are distributed among these distances:
6 6 0.07
7 27 0.31
8 22 0.25
9 21 0.24
10 7 0.08
11 4 0.05
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (8 bp):
TATTTATA
Found at i:1759257 original size:41 final size:44
Alignment explanation
Indices: 1759210--1759307 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 44
1759200 TATATATTTT
* *
1759210 ATATTTATATTATGTAAA-TTTATATAA-ATTTA-ATA-TATTAAT
1 ATATTTATATTATATAAAGTTTA-A-AATATTTATATATTATTAAC
*
1759252 A-ATTTATATTATATAAAGTTTAAAATATTTATATATTTTTAAC
1 ATATTTATATTATATAAAGTTTAAAATATTTATATATTATTAAC
1759295 ATATTTATATTAT
1 ATATTTATATTAT
1759308 TTTTCGAATC
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
40 2 0.04
41 21 0.44
42 8 0.17
43 6 0.12
44 11 0.23
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (44 bp):
ATATTTATATTATATAAAGTTTAAAATATTTATATATTATTAAC
Found at i:1759280 original size:32 final size:32
Alignment explanation
Indices: 1759229--1759289 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1759219 TTATGTAAAT
*
1759229 TTATATAAATTTAATATATTAATA-ATTTATA
1 TTATATAAATTTAAAATATTAATATATTTATA
*
1759260 TTATATAAAGTTTAAAATATTTATATATTT
1 TTATATAAA-TTTAAAATATTAATATATTT
1759290 TTAACATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 9 0.35
32 13 0.50
33 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (32 bp):
TTATATAAATTTAAAATATTAATATATTTATA
Found at i:1759292 original size:19 final size:20
Alignment explanation
Indices: 1759270--1759311 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
1759260 TTATATAAAG
1759270 TTTAAAATATTTATA-TATT
1 TTTAAAATATTTATATTATT
*
1759289 TTTAACATATTTATATTATT
1 TTTAAAATATTTATATTATT
1759309 TTT
1 TTT
1759312 CGAATCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTAAAATATTTATATTATT
Found at i:1761073 original size:16 final size:15
Alignment explanation
Indices: 1761043--1761094 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 15
1761033 TTAAATATAA
1761043 ATTATAAATTATTAATAT
1 ATTA-AAATT-TTAA-AT
*
1761061 ATTAAAATTTTAAAAA
1 ATTAAAATTTT-AAAT
1761077 ATATAAAATTTTAAAT
1 AT-TAAAATTTTAAAT
1761093 AT
1 AT
1761095 AATTATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 10 0.33
17 16 0.53
18 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAAAATTTTAAAT
Found at i:1761325 original size:10 final size:10
Alignment explanation
Indices: 1761310--1761380 Score: 51
Period size: 10 Copynumber: 7.1 Consensus size: 10
1761300 TATTATTTTA
1761310 TAAATTTAAT
1 TAAATTTAAT
*
1761320 TAAATTAAAT
1 TAAATTTAAT
1761330 TAAATTTAAATT
1 TAAATTT-AA-T
1761342 TAAA--TAA-
1 TAAATTTAAT
*
1761349 AAAATTTAA-
1 TAAATTTAAT
*
1761358 AAAATTTTAAT
1 TAAA-TTTAAT
1761369 TATAATTTAAT
1 TA-AATTTAAT
1761380 T
1 T
1761381 CAACTTATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
7 3 0.06
9 9 0.18
10 21 0.42
11 10 0.20
12 7 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TAAATTTAAT
Found at i:1762222 original size:26 final size:26
Alignment explanation
Indices: 1762191--1762250 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
1762181 AAAATTTAAA
**
1762191 AATTAAATATT-TTTTAATACCAAATT
1 AATTAAATATTATTTT-ATAAAAAATT
*
1762217 TATTAAATATTATTTTATAAAAAATT
1 AATTAAATATTATTTTATAAAAAATT
1762243 AATTAAAT
1 AATTAAAT
1762251 TAAACTCCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (26 bp):
AATTAAATATTATTTTATAAAAAATT
Found at i:1762908 original size:29 final size:28
Alignment explanation
Indices: 1762848--1762902 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
1762838 ATAGTTGTTG
*
1762848 TATTTATTATTAAAACTAATTGTTTAAAT
1 TATTTATTATTAAAAC-AATTATTTAAAT
*
1762877 TATTTTTTATTAAAAC-ATTATTTAAA
1 TATTTATTATTAAAACAATTATTTAAA
1762903 AATTATGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.38
29 15 0.62
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (28 bp):
TATTTATTATTAAAACAATTATTTAAAT
Found at i:1764099 original size:121 final size:122
Alignment explanation
Indices: 1763893--1764137 Score: 393
Period size: 121 Copynumber: 2.0 Consensus size: 122
1763883 AAAAATCAAA
* * *
1763893 TATAAGAGAGTCCTCCCTATCTCTGTTCTTCCTTAAAAGTGATAAAAATGGCTTACTCAACTGAA
1 TATAAGAGAGTCCTCCCTATCCCTGTCCTGCCTTAAAAGTGATAAAAATGGCTTACTCAACTGAA
1763958 TTAATTAATAACCAACTGTGATCTCCACCCAACATTTTCTATTGGCTCAAAATGATT
66 TTAATTAATAACCAACTGTGATCTCCACCCAACATTTTCTATTGGCTCAAAATGATT
* * * *
1764015 TATAAGAGAGTCCTCCCTATCCCTGTCCTGCCTT-ACAGTGATAGAGATGGTTTACTCAACTGAA
1 TATAAGAGAGTCCTCCCTATCCCTGTCCTGCCTTAAAAGTGATAAAAATGGCTTACTCAACTGAA
* **
1764079 TTAATTAATAACCAATTGTGATCTTTACCCAACATTTTCTATTGGCTCAAAATGATT
66 TTAATTAATAACCAACTGTGATCTCCACCCAACATTTTCTATTGGCTCAAAATGATT
1764136 TA
1 TA
1764138 GTTATTTCTT
Statistics
Matches: 113, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
121 82 0.73
122 31 0.27
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (122 bp):
TATAAGAGAGTCCTCCCTATCCCTGTCCTGCCTTAAAAGTGATAAAAATGGCTTACTCAACTGAA
TTAATTAATAACCAACTGTGATCTCCACCCAACATTTTCTATTGGCTCAAAATGATT
Found at i:1769287 original size:6 final size:6
Alignment explanation
Indices: 1769271--1769305 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1769261 ACAATACCTG
* *
1769271 TGCTTT GGCTTT TGCTTT TGCTTT TACTTT TGCTT
1 TGCTTT TGCTTT TGCTTT TGCTTT TGCTTT TGCTT
1769306 GAAATCTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.17, G:0.17, T:0.63
Consensus pattern (6 bp):
TGCTTT
Found at i:1777845 original size:25 final size:25
Alignment explanation
Indices: 1777817--1777867 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1777807 TAACGCGCTT
1777817 TTGACCCTAAGGCTGGCTTGCATTG
1 TTGACCCTAAGGCTGGCTTGCATTG
1777842 TTGACCCTAAGGCTGGCTTGCATTG
1 TTGACCCTAAGGCTGGCTTGCATTG
1777867 T
1 T
1777868 CTATCGGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (25 bp):
TTGACCCTAAGGCTGGCTTGCATTG
Found at i:1781650 original size:11 final size:11
Alignment explanation
Indices: 1781634--1781769 Score: 54
Period size: 11 Copynumber: 12.3 Consensus size: 11
1781624 TATATATTTT
1781634 ATTATATTATA
1 ATTATATTATA
1781645 ATTATATT-TAA
1 ATTATATTAT-A
* *
1781656 AATATTTTATA
1 ATTATATTATA
* *
1781667 TTTAAATATTTTA
1 ATT--ATATTATA
1781680 TATT-TATTAATA
1 -ATTATATT-ATA
1781692 ATTTATATTAT-
1 A-TTATATTATA
* *
1781703 A-TAAATTTTA
1 ATTATATTATA
1781713 A-TATATT-TA
1 ATTATATTATA
1781722 TATATATATTAT-
1 -AT-TATATTATA
*
1781734 ATTAATATTATT
1 ATT-ATATTATA
*
1781746 TTTATATTAT-
1 ATTATATTATA
*
1781756 ATTATATTTTA
1 ATTATATTATA
1781767 ATT
1 ATT
1781770 TTTATATCAT
Statistics
Matches: 95, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
9 8 0.08
10 17 0.18
11 42 0.44
12 15 0.16
13 11 0.12
14 2 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTATATTATA
Found at i:1781702 original size:22 final size:24
Alignment explanation
Indices: 1781614--1781763 Score: 98
Period size: 24 Copynumber: 6.2 Consensus size: 24
1781604 ATAATTTATG
* * *
1781614 TATTTATATATATATATTTTATTA
1 TATTAATATATTTATATTATATTA
**
1781638 TATT-ATA-A-TTATATT-TAAAA
1 TATTAATATATTTATATTATATTA
*
1781658 TATT-TTATATTTAAATATTTTATATT-
1 TATTAATATATTT--ATA--TTATATTA
*
1781684 TATTAATA-ATTTATATTATATAAA
1 TATTAATATATTTATATTATAT-TA
*
1781708 TTTTAATATATTTATATATATATTA
1 TATTAATATATTTATAT-TATATTA
1781733 TATTAATATTATTTTTATATTATATTA
1 TATTAATA-TA--TTTATATTATATTA
1781760 TATT
1 TATT
1781764 TTAATTTTTA
Statistics
Matches: 100, Mismatches: 11, Indels: 27
0.72 0.08 0.20
Matches are distributed among these distances:
20 9 0.09
21 7 0.07
22 9 0.09
23 3 0.03
24 17 0.17
25 16 0.16
26 17 0.17
27 15 0.15
28 7 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTAATATATTTATATTATATTA
Found at i:1781770 original size:24 final size:22
Alignment explanation
Indices: 1781726--1781776 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 22
1781716 TATTTATATA
1781726 TATATTATATTAATATTATTTT
1 TATATTATATTAATATTATTTT
*
1781748 TATATTATATTATATTTTAATTTT
1 TATATTATATTA-ATATT-ATTTT
1781772 TATAT
1 TATAT
1781777 CATAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 12 0.46
23 4 0.15
24 10 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TATATTATATTAATATTATTTT
Found at i:1782592 original size:33 final size:30
Alignment explanation
Indices: 1782545--1782678 Score: 93
Period size: 31 Copynumber: 4.4 Consensus size: 30
1782535 GATATTCTTA
1782545 TATAATATAATATAAAATAATTAAAATATAATAT
1 TATAATA-AATATAAAAT-A-TAAAATAT-ATAT
1782579 TATAATAAATAT-AAATATATAAATAT-T-T
1 TATAATAAATATAAAATATA-AAATATATAT
** *
1782607 TA-AAT-TTTATAAAATATAAATTAT-TAAT
1 TATAATAAATATAAAATATAAAATATAT-AT
*
1782635 ATATTATAAATATAAAATATTTAAAATATA-AT
1 -TATAATAAATATAAAATA--TAAAATATATAT
1782667 TATAATATAATA
1 TATAATA-AATA
1782679 ATATATCTAT
Statistics
Matches: 81, Mismatches: 8, Indels: 24
0.72 0.07 0.21
Matches are distributed among these distances:
26 9 0.11
27 10 0.12
28 4 0.05
29 3 0.04
30 4 0.05
31 22 0.27
32 10 0.12
33 12 0.15
34 7 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
TATAATAAATATAAAATATAAAATATATAT
Found at i:1782622 original size:50 final size:52
Alignment explanation
Indices: 1782562--1782714 Score: 172
Period size: 50 Copynumber: 3.0 Consensus size: 52
1782552 TAATATAAAA
1782562 TAATTAAAATATAATATTATAATA-AATATAAATATATAAATATTTTAAATT
1 TAATTAAAATATAATATTATAATATAATATAAATATATAAATATTTTAAATT
* * * *
1782613 TTA-TAAAATATAA-ATTATTAATATATTATAAATATA-AAATATTTAAAATA
1 TAATTAAAATATAATATTA-TAATATAATATAAATATATAAATATTTTAAATT
* * * * *
1782663 TAATTATAATATAATAATATATCTATAATATTAATATATAAAT-GTTTAAATT
1 TAATTAAAATATAATATTATA-ATATAATATAAATATATAAATATTTTAAATT
1782715 AATACTTCCA
Statistics
Matches: 83, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
49 4 0.05
50 29 0.35
51 24 0.29
52 22 0.27
53 4 0.05
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.44
Consensus pattern (52 bp):
TAATTAAAATATAATATTATAATATAATATAAATATATAAATATTTTAAATT
Found at i:1782623 original size:25 final size:25
Alignment explanation
Indices: 1782566--1782663 Score: 87
Period size: 25 Copynumber: 3.9 Consensus size: 25
1782556 ATAAAATAAT
* *
1782566 TAAAATAT-AATATTAT-AATAAATA
1 TAAAATATAAATATTTTAAAT-ATTA
*
1782590 TAAATATATAAATATTTTAAATTTTA
1 TAAA-ATATAAATATTTTAAATATTA
*
1782616 TAAAATATAAAT-TATTAATATATTA
1 TAAAATATAAATATTTTAA-ATATTA
*
1782641 T-AAATATAAAATATTTAAAATAT
1 TAAAATAT-AAATATTTTAAATAT
1782664 AATTATAATA
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
24 15 0.25
25 26 0.43
26 17 0.28
27 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TAAAATATAAATATTTTAAATATTA
Found at i:1782661 original size:16 final size:18
Alignment explanation
Indices: 1782632--1782665 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1782622 ATAAATTATT
1782632 AATATATTATAAATATAA
1 AATATATTATAAATATAA
1782650 AATAT-TTA-AAATATAA
1 AATATATTATAAATATAA
1782666 TTATAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATATATTATAAATATAA
Found at i:1782683 original size:19 final size:21
Alignment explanation
Indices: 1782650--1782703 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
1782640 ATAAATATAA
1782650 AATATTTAA-AATATAAT-TAT
1 AATA-TTAATAATATAATCTAT
1782670 AATA-TAATAATAT-ATCTAT
1 AATATTAATAATATAATCTAT
1782689 AATATTAAT-ATATAA
1 AATATTAATAATATAA
1782704 ATGTTTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
18 5 0.17
19 16 0.53
20 9 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AATATTAATAATATAATCTAT
Found at i:1782700 original size:11 final size:12
Alignment explanation
Indices: 1782543--1782703 Score: 81
Period size: 11 Copynumber: 13.6 Consensus size: 12
1782533 AGGATATTCT
1782543 TATATAATATAA
1 TATATAATATAA
1782555 TATA-AA-ATAA
1 TATATAATATAA
*
1782565 T-TAAAATATAA
1 TATATAATATAA
1782576 TATTATAATA-AA
1 TA-TATAATATAA
1782588 TATA-AATAT-A
1 TATATAATATAA
* * *
1782598 TAAATATTTTAA
1 TATATAATATAA
* * *
1782610 -ATTTTATAAAA
1 TATATAATATAA
1782621 TATA-AATTATTAA
1 TATATAA-TA-TAA
*
1782634 TATATTATA-AA
1 TATATAATATAA
*
1782645 TATAAAATATTTAA
1 TATATAATA--TAA
*
1782659 AATATAATTATAA
1 TATATAA-TATAA
1782672 TATAATAATAT-A
1 TAT-ATAATATAA
*
1782684 TCTATAATATTAA
1 TATATAATA-TAA
1782697 TATATAA
1 TATATAA
1782704 ATGTTTAAAT
Statistics
Matches: 110, Mismatches: 21, Indels: 35
0.66 0.13 0.21
Matches are distributed among these distances:
9 2 0.02
10 15 0.14
11 33 0.30
12 17 0.15
13 29 0.26
14 12 0.11
15 2 0.02
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATAATATAA
Found at i:1782957 original size:17 final size:16
Alignment explanation
Indices: 1782900--1782959 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
1782890 TCACATTATA
*
1782900 AATTT-TTATTATTTAA
1 AATTTATTATTATTT-T
* *
1782916 AATTCATT-TAATTTT
1 AATTTATTATTATTTT
*
1782931 AATTTTTTATTATTTT
1 AATTTATTATTATTTT
1782947 ATATTTATTATTA
1 A-ATTTATTATTA
1782960 ATAAAAAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
15 6 0.18
16 16 0.47
17 12 0.35
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTTATTATTATTTT
Found at i:1783174 original size:29 final size:30
Alignment explanation
Indices: 1783137--1783194 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
1783127 AAATATATAA
*
1783137 ATTTTAAATAA-T-ATTTAAATTTTTTTAT
1 ATTTTAAATAAGTAATTAAAATTTTTTTAT
1783165 ATTTATAAATAAGTAATTAAAATTTTTTTA
1 ATTT-TAAATAAGTAATTAAAATTTTTTTA
1783195 AGTTTGTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 4 0.15
29 7 0.27
30 1 0.04
31 14 0.54
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
ATTTTAAATAAGTAATTAAAATTTTTTTAT
Found at i:1783191 original size:30 final size:28
Alignment explanation
Indices: 1783137--1783192 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
1783127 AAATATATAA
* *
1783137 ATTTTAAATAATATTTAAATTTTTTTAT
1 ATTTTAAATAATAATTAAAATTTTTTAT
1783165 ATTTATAAATAAGTAATTAAAATTTTTT
1 ATTT-TAAATAA-TAATTAAAATTTTTT
1783193 TAAGTTTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 7 0.29
30 13 0.54
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
ATTTTAAATAATAATTAAAATTTTTTAT
Found at i:1784533 original size:15 final size:16
Alignment explanation
Indices: 1784510--1784543 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1784500 AAACCCTTCT
1784510 ATTACTATTTTTT-TA
1 ATTACTATTTTTTGTA
*
1784525 ATTATTATTTTTTGTA
1 ATTACTATTTTTTGTA
1784541 ATT
1 ATT
1784544 TTTAATTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (16 bp):
ATTACTATTTTTTGTA
Found at i:1785622 original size:4 final size:4
Alignment explanation
Indices: 1785615--1785641 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1785605 AAAAGAGGGA
1785615 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1785642 TACTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1789661 original size:40 final size:40
Alignment explanation
Indices: 1789601--1789677 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
1789591 TCCATATCAT
1789601 ATTCATCCATTGATGAGGGTAGATGAGCTACTGGTAGTGA
1 ATTCATCCATTGATGAGGGTAGATGAGCTACTGGTAGTGA
* *
1789641 ATTCTTCCATTGTTGAGGGTAGATGAGCTACTGGTAG
1 ATTCATCCATTGATGAGGGTAGATGAGCTACTGGTAG
1789678 CTCACGTCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.32
Consensus pattern (40 bp):
ATTCATCCATTGATGAGGGTAGATGAGCTACTGGTAGTGA
Found at i:1790388 original size:2 final size:2
Alignment explanation
Indices: 1790381--1790411 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1790371 AATTTTACAC
1790381 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1790412 GACGAGAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1792924 original size:17 final size:16
Alignment explanation
Indices: 1792899--1792933 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1792889 GTTTTAGGAG
1792899 AAAACAGAAAAAAGAAA
1 AAAACAG-AAAAAGAAA
*
1792916 AAAATAGAAAAAGAAA
1 AAAACAGAAAAAGAAA
1792932 AA
1 AA
1792934 CGAAGAGAAA
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:0.83, C:0.03, G:0.11, T:0.03
Consensus pattern (16 bp):
AAAACAGAAAAAGAAA
Found at i:1793402 original size:45 final size:45
Alignment explanation
Indices: 1793342--1793438 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
1793332 CTTATTTTTA
1793342 ATAATATTATATATAACATAA-ACAAAATATATTTTATATAATAAT
1 ATAATATTATATATAACATAATACAAAATATATTTTATATAAT-AT
* ** *
1793387 ATAATATTATATATAATATAATACATTATTTATTTTATATAATAT
1 ATAATATTATATATAACATAATACAAAATATATTTTATATAATAT
1793432 ATAATAT
1 ATAATAT
1793439 ATAAATTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
45 29 0.62
46 18 0.38
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (45 bp):
ATAATATTATATATAACATAATACAAAATATATTTTATATAATAT
Found at i:1793405 original size:7 final size:7
Alignment explanation
Indices: 1793376--1793442 Score: 53
Period size: 7 Copynumber: 9.0 Consensus size: 7
1793366 AAATATATTT
1793376 TATATAA
1 TATATAA
1793383 TAATATAA
1 T-ATATAA
1793391 TATTATATA
1 TA-TATA-A
1793400 TAATATAA
1 T-ATATAA
* *
1793408 TACATTA
1 TATATAA
* **
1793415 TTTATTT
1 TATATAA
1793422 TATATAA
1 TATATAA
1793429 TATATAA
1 TATATAA
1793436 TATATAA
1 TATATAA
1793443 ATTTTTATAA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
7 28 0.58
8 13 0.27
9 6 0.12
10 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (7 bp):
TATATAA
Found at i:1793407 original size:17 final size:18
Alignment explanation
Indices: 1793375--1793409 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1793365 AAAATATATT
1793375 TTATATAATAATATAATA
1 TTATATAATAATATAATA
1793393 TTATAT-ATAATATAATA
1 TTATATAATAATATAATA
1793410 CATTATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTATATAATAATATAATA
Found at i:1793572 original size:32 final size:33
Alignment explanation
Indices: 1793509--1793573 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
1793499 ATTAATTATT
* *
1793509 TTTATTTTTAATTTATTTATTTAATAGTTTTAA
1 TTTATTTTTAATTTATTCATTCAATAGTTTTAA
*
1793542 TTTA-TTTTATTTTATTCATTCAATTA-TTTTAA
1 TTTATTTTTAATTTATTCATTCAA-TAGTTTTAA
1793574 ATAAAATTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 22 0.79
33 6 0.21
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (33 bp):
TTTATTTTTAATTTATTCATTCAATAGTTTTAA
Found at i:1795322 original size:80 final size:82
Alignment explanation
Indices: 1795237--1795388 Score: 188
Period size: 82 Copynumber: 1.9 Consensus size: 82
1795227 TAGTCGTATC
*
1795237 ATATTTATGTAATT-TTTTATATTAT-TATTA-TTATTATAT-TTATAATATACGTTAATAA-TT
1 ATATTTAT-TAATTATTTTAT-TTATATATTATTTATTATATCATATAATATA-GTTAATAATTT
1795297 TTTATTATATAAATTTTAAA
63 TTTATTATATAAATTTTAAA
* * * * *
1795317 ATATTTATTATTTATTTTATTTTTATATTATTTTTTATATCATATTATATATTTAATAATTTTTT
1 ATATTTATTAATTATTTTATTTATATATTATTTATTATATCATATAATATAGTTAATAATTTTTT
1795382 ATTATAT
66 ATTATAT
1795389 TTATATTATA
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
79 7 0.11
80 19 0.31
81 15 0.25
82 20 0.33
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (82 bp):
ATATTTATTAATTATTTTATTTATATATTATTTATTATATCATATAATATAGTTAATAATTTTTT
ATTATATAAATTTTAAA
Found at i:1795337 original size:16 final size:16
Alignment explanation
Indices: 1795318--1795350 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1795308 AATTTTAAAA
1795318 TATTTATTAT-TTATTT
1 TATTT-TTATATTATTT
1795334 TATTTTTATATTATTT
1 TATTTTTATATTATTT
1795350 T
1 T
1795351 TTATATCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TATTTTTATATTATTT
Found at i:1795354 original size:30 final size:30
Alignment explanation
Indices: 1795320--1795394 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
1795310 TTTTAAAATA
* * * *
1795320 TTTATTAT-TTATTTTATTTTTATATTATTT
1 TTTATTATCATATTATATATTTA-ATAATTT
1795350 TTTA-TATCATATTATATATTTAATAATTT
1 TTTATTATCATATTATATATTTAATAATTT
1795379 TTTATTAT-AT-TTATAT
1 TTTATTATCATATTATAT
1795395 TATATAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 6 0.15
29 15 0.38
30 18 0.46
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (30 bp):
TTTATTATCATATTATATATTTAATAATTT
Found at i:1795405 original size:13 final size:11
Alignment explanation
Indices: 1795325--1795422 Score: 52
Period size: 11 Copynumber: 8.1 Consensus size: 11
1795315 AAATATTTAT
*
1795325 TATTTATTTTA
1 TATTTATATTA
*
1795336 TTTTTATATTA
1 TATTTATATTA
* *
1795347 TTTTTTATATCA
1 -TATTTATATTA
1795359 TATTATATATTTAA
1 TATT-TATA-TT-A
*
1795373 TAATTTTTTATTA
1 T-A-TTTATATTA
1795386 TATTTATATTA
1 TATTTATATTA
**
1795397 TATAATTATATCG
1 TAT--TTATATTA
1795410 TATTTAATATTA
1 TATTT-ATATTA
1795422 T
1 T
1795423 TGATTTATCG
Statistics
Matches: 67, Mismatches: 11, Indels: 17
0.71 0.12 0.18
Matches are distributed among these distances:
11 25 0.37
12 20 0.30
13 12 0.18
14 4 0.06
15 4 0.06
16 2 0.03
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (11 bp):
TATTTATATTA
Found at i:1795644 original size:6 final size:6
Alignment explanation
Indices: 1795633--1795659 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1795623 GCACACGACT
1795633 TTAAAA TTAAAA TTAAAA TTAAAA TTA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTA
1795660 GGACACCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TTAAAA
Found at i:1795955 original size:33 final size:33
Alignment explanation
Indices: 1795883--1795955 Score: 80
Period size: 35 Copynumber: 2.2 Consensus size: 33
1795873 TATTATATTA
*
1795883 TTAAA-ATATTATTTTTATATTTATAATTAAAT
1 TTAAATATATTATTTTTATATTAATAATTAAAT
1795915 TAATAAATATATTATTTTTATTATTAAATAA-T-AAT
1 T--TAAATATATTATTTTTA-TATT-AATAATTAAAT
1795950 TTAAAT
1 TTAAAT
1795956 TGAATCGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
32 1 0.03
33 5 0.14
34 4 0.11
35 16 0.46
36 5 0.14
37 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TTAAATATATTATTTTTATATTAATAATTAAAT
Found at i:1797891 original size:32 final size:33
Alignment explanation
Indices: 1797827--1797908 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
1797817 TTTGGTTGAA
1797827 TAAAATATTAAAAAATAATATTATTTTATAATT
1 TAAAATATTAAAAAATAATATTATTTTATAATT
*
1797860 TAAAA-ATTAAAAAAATAATTTTATTTT-TAATT
1 TAAAATATT-AAAAAATAATATTATTTTATAATT
* *
1797892 TAATATAATAAACAAAT
1 TAAAATATTAAA-AAAT
1797909 TGAATGAGAC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
32 15 0.35
33 28 0.65
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (33 bp):
TAAAATATTAAAAAATAATATTATTTTATAATT
Found at i:1798101 original size:51 final size:51
Alignment explanation
Indices: 1798045--1798157 Score: 121
Period size: 49 Copynumber: 2.2 Consensus size: 51
1798035 AAATTAATTT
1798045 TTAATAATTAAAAAT-ATTTTT---ATTTAAATTTAATTATAAAATATATAAATA
1 TTAATAATTAAAAATAATTTTTAAAATTT-AA-TTAATTAT-AAATA-ATAAATA
*
1798096 TTAAT-A-TAAAAATAATTTTTAAAATTTTATTAATTATAAATAATAAATA
1 TTAATAATTAAAAATAATTTTTAAAATTTAATTAATTATAAATAATAAATA
*
1798145 TAAATAATATAAA
1 TTAATAAT-TAAA
1798158 TAAATTAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
49 18 0.34
50 13 0.25
51 13 0.25
52 5 0.09
53 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (51 bp):
TTAATAATTAAAAATAATTTTTAAAATTTAATTAATTATAAATAATAAATA
Found at i:1798148 original size:13 final size:13
Alignment explanation
Indices: 1798130--1798175 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
1798120 TTTTATTAAT
1798130 TATAAATAATAAA
1 TATAAATAATAAA
1798143 TATAAATAATATAA
1 TATAAATAATA-AA
1798157 -ATAAAT--TAAA
1 TATAAATAATAAA
*
1798167 TAAAAATAA
1 TATAAATAA
1798176 ACTTAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
10 2 0.07
11 7 0.25
13 17 0.61
14 2 0.07
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TATAAATAATAAA
Found at i:1798909 original size:2 final size:2
Alignment explanation
Indices: 1798902--1798936 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1798892 GAAAGGTAAG
1798902 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
1798937 GTATGTATGT
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:1800074 original size:2 final size:2
Alignment explanation
Indices: 1800067--1800095 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1800057 TTACAAATCT
1800067 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 T
1800096 TTATTTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1800667 original size:21 final size:23
Alignment explanation
Indices: 1800641--1800690 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1800631 TTATTTAAAA
1800641 ATATTATAAAATT-TAT-TTTTT
1 ATATTATAAAATTATATATTTTT
*
1800662 ATATTA-ATAATTATATATTTTT
1 ATATTATAAAATTATATATTTTT
*
1800684 TTATTAT
1 ATATTAT
1800691 TATTTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 5 0.21
21 9 0.38
22 10 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATATTATAAAATTATATATTTTT
Found at i:1800671 original size:22 final size:23
Alignment explanation
Indices: 1800641--1800689 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
1800631 TTATTTAAAA
*
1800641 ATATT-ATAA-AATTTATTTTTT
1 ATATTAATAATAATATATTTTTT
*
1800662 ATATTAATAATTATATATTTTTT
1 ATATTAATAATAATATATTTTTT
1800685 -TATTA
1 ATATTA
1800690 TTATTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.21
22 9 0.38
23 10 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATATTAATAATAATATATTTTTT
Found at i:1801457 original size:26 final size:27
Alignment explanation
Indices: 1801418--1801496 Score: 94
Period size: 26 Copynumber: 3.0 Consensus size: 27
1801408 TTGACTCATA
*
1801418 TAAT-TAAATTTTAAATAAATTTA-AT
1 TAATATAAATTTTAAATTAATTTATAT
* *
1801443 TAATATAAATATTAATTTAA-TTATAT
1 TAATATAAATTTTAAATTAATTTATAT
1801469 T-ATATAAATTTTTAAATTAATTTATAT
1 TAATATAAA-TTTTAAATTAATTTATAT
1801496 T
1 T
1801497 TAATTCAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
25 14 0.31
26 24 0.53
27 7 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TAATATAAATTTTAAATTAATTTATAT
Found at i:1802972 original size:33 final size:33
Alignment explanation
Indices: 1802935--1802999 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1802925 ATATCATAAA
1802935 ATATTATATTTATATTTATATT-T-TTTATATTAT
1 ATATTATA-TTAT-TTTATATTATATTTATATTAT
*
1802968 ATATTATATTATTTTTTATTATATTTATATTA
1 ATATTATATTATTTTATATTATATTTATATTA
1803000 CATCAATCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 7 0.24
32 5 0.17
33 17 0.59
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (33 bp):
ATATTATATTATTTTATATTATATTTATATTAT
Found at i:1802989 original size:10 final size:11
Alignment explanation
Indices: 1802938--1802999 Score: 76
Period size: 12 Copynumber: 5.7 Consensus size: 11
1802928 TCATAAAATA
1802938 TTATATTTATAT
1 TTATA-TTATAT
1802950 TTATATT-T-T
1 TTATATTATAT
1802959 TTATATTATAT
1 TTATATTATAT
1802970 ATTATATTAT-T
1 -TTATATTATAT
*
1802981 TTTTATTATAT
1 TTATATTATAT
1802992 TTATATTA
1 TTATATTA
1803000 CATCAATCAC
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
9 8 0.18
10 10 0.23
11 12 0.27
12 14 0.32
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATATTATAT
Found at i:1803559 original size:2 final size:2
Alignment explanation
Indices: 1803552--1803582 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1803542 TAAAATCGAC
1803552 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1803583 ATGAAACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1805539 original size:2 final size:2
Alignment explanation
Indices: 1805532--1805563 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1805522 CTTTCCCGAA
1805532 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
1805564 TTACAAGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1806074 original size:2 final size:2
Alignment explanation
Indices: 1806067--1806095 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1806057 TAAGCTCTAA
1806067 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1806096 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1806100 original size:2 final size:2
Alignment explanation
Indices: 1806095--1806119 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1806085 TCTCTCTCTC
1806095 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 T
1806120 TCACACCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1807285 original size:18 final size:18
Alignment explanation
Indices: 1807259--1807295 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1807249 AGACTGGTTA
*
1807259 TTAAGTAGGGCTCATTAT
1 TTAAATAGGGCTCATTAT
*
1807277 TTAAATAGGGCTTATTAT
1 TTAAATAGGGCTCATTAT
1807295 T
1 T
1807296 ATTGTGGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.43
Consensus pattern (18 bp):
TTAAATAGGGCTCATTAT
Found at i:1807656 original size:14 final size:16
Alignment explanation
Indices: 1807637--1807668 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1807627 TTTATTTTTT
1807637 AATATTT-TT-TTAAA
1 AATATTTATTATTAAA
1807651 AATATTTATTATTAAA
1 AATATTTATTATTAAA
1807667 AA
1 AA
1807669 ATTAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATATTTATTATTAAA
Found at i:1810725 original size:3 final size:3
Alignment explanation
Indices: 1810711--1810741 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1810701 GTTTCCTAAG
*
1810711 GAA GAG GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1810742 CAAAATATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1812751 original size:2 final size:2
Alignment explanation
Indices: 1812744--1812772 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1812734 TTATACATAC
1812744 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1812773 CCCAATGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1815076 original size:16 final size:15
Alignment explanation
Indices: 1815050--1815088 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
1815040 ATGATTTAAA
1815050 TTTTAAA-TTTTGAT
1 TTTTAAATTTTTGAT
*
1815064 TTTTATAATTTTTTAT
1 TTTTA-AATTTTTGAT
1815080 TTTTAAATT
1 TTTTAAATT
1815089 ATAATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 6 0.27
16 11 0.50
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTTAAATTTTTGAT
Found at i:1815097 original size:14 final size:14
Alignment explanation
Indices: 1815044--1815097 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
1815034 TATTAAATGA
*
1815044 TTTAAATTTTAAAT
1 TTTAATTTTTAAAT
*
1815058 TTTGATTTTTATAATT
1 TTTAATTTTTA-AA-T
*
1815074 TTTTATTTTTAAAT
1 TTTAATTTTTAAAT
*
1815088 TATAATTTTT
1 TTTAATTTTT
1815098 TTATATCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
14 18 0.55
15 4 0.12
16 11 0.33
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTAATTTTTAAAT
Found at i:1819770 original size:15 final size:16
Alignment explanation
Indices: 1819750--1819783 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1819740 GGCAACAATC
1819750 TTATCACT-TAGTATT
1 TTATCACTCTAGTATT
1819765 TTATCACTCTAGTATT
1 TTATCACTCTAGTATT
1819781 TTA
1 TTA
1819784 ATATTTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (16 bp):
TTATCACTCTAGTATT
Found at i:1822466 original size:20 final size:21
Alignment explanation
Indices: 1822431--1822473 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
1822421 GATCTTACCA
1822431 TTTATATATTTATAATAATAT
1 TTTATATATTTATAATAATAT
1822452 TTTATATATTT-TAATAATAT
1 TTTATATATTTATAATAATAT
1822472 TT
1 TT
1822474 AAAATATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTATATATTTATAATAATAT
Done.