Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 144 of 204
Found at i:43419213 original size:102 final size:102
Alignment explanation
Indices: 43419042--43419241 Score: 357
Period size: 102 Copynumber: 2.0 Consensus size: 102
43419032 TGTTGTTGAT
43419042 AATGGGAATGGGAATGGGAAATGGGAATGGGTATTGCATGGGAATGGGAAATGGGAGGAGGGCAC
1 AATGGGAATGGGAATGGGAAATGGGAATGGGTATTGCATGGGAATGGGAAATGGGAGGAGGGCAC
*
43419107 GGTGGAAGAGAGGAATCGATGGAAGAGGGGAGATGGG
66 GGTGGAAAAGAGGAATCGATGGAAGAGGGGAGATGGG
*
43419144 AATGGGAAATGGGAATGGG-AATGGGAATGGGTATTGCATGGGGATGGGAAATGGGAGGAGGGCA
1 AATGGG-AATGGGAATGGGAAATGGGAATGGGTATTGCATGGGAATGGGAAATGGGAGGAGGGCA
*
43419208 CGGTGGAAAAGGGGAATCGATGGAAGAGGGGAGA
65 CGGTGGAAAAGAGGAATCGATGGAAGAGGGGAGA
43419242 NNNNNNNNNN
Statistics
Matches: 94, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
102 82 0.87
103 12 0.13
ACGTcount: A:0.33, C:0.04, G:0.49, T:0.14
Consensus pattern (102 bp):
AATGGGAATGGGAATGGGAAATGGGAATGGGTATTGCATGGGAATGGGAAATGGGAGGAGGGCAC
GGTGGAAAAGAGGAATCGATGGAAGAGGGGAGATGGG
Found at i:43419384 original size:29 final size:29
Alignment explanation
Indices: 43419342--43419778 Score: 498
Period size: 29 Copynumber: 14.5 Consensus size: 29
43419332 NNNNNNNNNN
* *
43419342 TTTAAAAATAAAAAATATATGTATTATAT
1 TTTAAAAATAAAAAATATATGTAGTGTAT
*
43419371 TTTAAAAATAAAAAATAAATGTAGTGTAT
1 TTTAAAAATAAAAAATATATGTAGTGTAT
43419400 TTTAAAAATAAAAAATATATGTAGTGTAT
1 TTTAAAAATAAAAAATATATGTAGTGTAT
*
43419429 TTTAAAAATAAAAAAGATATATGTAGTGTAA
1 TTTAAAAAT-AAAAA-ATATATGTAGTGTAT
* *
43419460 TTAAAAAATAAAAAAATAAATGTAGTGTAT
1 TTTAAAAAT-AAAAAATATATGTAGTGTAT
*
43419490 TTTAAAAATAAAAAATATATGTAATGTAT
1 TTTAAAAATAAAAAATATATGTAGTGTAT
* *
43419519 TTTAAAAATAAAAAAAATATGCAGTGTAT
1 TTTAAAAATAAAAAATATATGTAGTGTAT
* *
43419548 TTTAATATATATATATATATATATGTAGTGTAT
1 TTTAA-A-A-ATA-AAAAATATATGTAGTGTAT
* *
43419581 TTTAAAAGTAAAAAAAAAAATATGTATGTGTAT
1 TTT-AAA--AATAAAAAATATATGTA-GTGTAT
43419614 TTTAAAAATAAAAAAGATATATGTAGTGTAT
1 TTTAAAAAT-AAAAA-ATATATGTAGTGTAT
* * * **
43419645 TTAAAAAATAAAAAAATAAATATAGCATAT
1 TTTAAAAAT-AAAAAATATATGTAGTGTAT
*
43419675 TTTAAAAATAAAAAATATATGTAGCGTAT
1 TTTAAAAATAAAAAATATATGTAGTGTAT
43419704 TTTAAAAATAAAAAAAATATATGTAGTGTAT
1 TTTAAAAAT--AAAAAATATATGTAGTGTAT
* * * *
43419735 TTT-AATATATATATATATATGTAGTATAT
1 TTTAAAAATA-AAAAATATATGTAGTGTAT
*
43419764 TTTAAAAGTAAAAAA
1 TTTAAAAATAAAAAA
43419779 ATACATAAAT
Statistics
Matches: 351, Mismatches: 42, Indels: 30
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.00
29 160 0.46
30 56 0.16
31 76 0.22
32 24 0.07
33 30 0.09
34 4 0.01
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (29 bp):
TTTAAAAATAAAAAATATATGTAGTGTAT
Found at i:43419503 original size:60 final size:59
Alignment explanation
Indices: 43419342--43419781 Score: 528
Period size: 60 Copynumber: 7.3 Consensus size: 59
43419332 NNNNNNNNNN
* * *
43419342 TTTAAAAAT-AAAAAATATATGTATTATATTTTAAAAATAAAAAATAAATGTAGTGTAT
1 TTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAATATATGTAGTGTAT
*
43419400 TTTAAAAAT-AAAAAATATATGTAGTGTATTTTAAAAATAAAAAAGATATATGTAGTGTAA
1 TTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAAT-AAAAA-ATATATGTAGTGTAT
* * *
43419460 TTAAAAAATAAAAAAATAAATGTAGTGTATTTTAAAAATAAAAAATATATGTAATGTAT
1 TTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAATATATGTAGTGTAT
* * *
43419519 TTTAAAAATAAAAAAA-ATATGCAGTGTATTTTAATATATATATATATATATATGTAGTGTAT
1 TTTAAAAATAAAAAAATATATGTAGTGTATTTTAA-A-A-ATA-AAAAATATATGTAGTGTAT
* *
43419581 TTTAAAAGTAAAAAAAAAAATATGTATGTGTATTTTAAAAATAAAAAAGATATATGTAGTGTAT
1 TTTAAAA--ATAAAAAAATATATGTA-GTGTATTTTAAAAAT-AAAAA-ATATATGTAGTGTAT
* * * ** *
43419645 TTAAAAAATAAAAAAATAAATATAGCATATTTTAAAAATAAAAAATATATGTAGCGTAT
1 TTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAATATATGTAGTGTAT
* * * *
43419704 TTTAAAAATAAAAAAAATATATGTAGTGTATTTT-AATATATATATATATATGTAGTATAT
1 TTTAAAAAT-AAAAAAATATATGTAGTGTATTTTAAAAATA-AAAAATATATGTAGTGTAT
*
43419764 TTTAAAAGTAAAAAAATA
1 TTTAAAAATAAAAAAATA
43419782 CATAAATAAA
Statistics
Matches: 330, Mismatches: 37, Indels: 29
0.83 0.09 0.07
Matches are distributed among these distances:
58 52 0.16
59 70 0.21
60 75 0.23
61 44 0.13
62 36 0.11
63 4 0.01
64 31 0.09
65 7 0.02
66 11 0.03
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (59 bp):
TTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAATATATGTAGTGTAT
Found at i:43419651 original size:185 final size:183
Alignment explanation
Indices: 43419342--43419779 Score: 633
Period size: 185 Copynumber: 2.4 Consensus size: 183
43419332 NNNNNNNNNN
* * * * * *
43419342 TTTAAAAATAAAAAATATATGTATTATATTTTAA-AA-ATA-AAAAATAAATGTAGTGTATTTT-
1 TTTAAAAATAAAAAAAATATGTAGTGTATTTTAATAATATATATATATATATGTAGTGTATTTTA
* *
43419403 AAA--AATAAAAAATATATGTAGTGTATTTTAAAAATAAAAAAGATATATGTAGTGTAATTAAAA
66 AAAGTAAAAAAAAAAATATGTAGTGTATTTTAAAAATAAAAAAGATATATGTAGTGTAATTAAAA
* ** *
43419466 AATAAAAAAATAAATGTAGTGTATTTTAAAAATAAAAAATATATGTAATGTAT
131 AATAAAAAAATAAATATAGCATATTTTAAAAATAAAAAATATATGTAACGTAT
*
43419519 TTTAAAAATAAAAAAAATATGCAGTGTATTTTAATATATATATATATATATATGTAGTGTATTTT
1 TTTAAAAATAAAAAAAATATGTAGTGTATTTTAATA-ATATATATATATATATGTAGTGTATTTT
*
43419584 AAAAGTAAAAAAAAAAATATGTATGTGTATTTTAAAAATAAAAAAGATATATGTAGTGTATTTAA
65 AAAAGTAAAAAAAAAAATATGTA-GTGTATTTTAAAAATAAAAAAGATATATGTAGTGTAATTAA
*
43419649 AAAATAAAAAAATAAATATAGCATATTTTAAAAATAAAAAATATATGTAGCGTAT
129 AAAATAAAAAAATAAATATAGCATATTTTAAAAATAAAAAATATATGTAACGTAT
*
43419704 TTTAAAAATAAAAAAAATATATGTAGTGTA-TTT--TAATATATATATATATATGTAGTATATTT
1 TTTAAAAAT-AAAAAAA-ATATGTAGTGTATTTTAATAATATATATATATATATGTAGTGTATTT
43419766 TAAAAGTAAAAAAA
64 TAAAAGTAAAAAAA
43419780 TACATAAATA
Statistics
Matches: 234, Mismatches: 17, Indels: 14
0.88 0.06 0.05
Matches are distributed among these distances:
177 30 0.13
178 1 0.00
179 1 0.00
180 3 0.01
181 19 0.08
182 3 0.01
183 40 0.17
184 17 0.07
185 99 0.42
186 10 0.04
187 11 0.05
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (183 bp):
TTTAAAAATAAAAAAAATATGTAGTGTATTTTAATAATATATATATATATATGTAGTGTATTTTA
AAAGTAAAAAAAAAAATATGTAGTGTATTTTAAAAATAAAAAAGATATATGTAGTGTAATTAAAA
AATAAAAAAATAAATATAGCATATTTTAAAAATAAAAAATATATGTAACGTAT
Found at i:43423437 original size:21 final size:21
Alignment explanation
Indices: 43423413--43423467 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
43423403 ACCATTGTTT
*
43423413 CTAAGCTCACCGCTACAGTAC
1 CTAATCTCACCGCTACAGTAC
43423434 CTAATCTCACCGCTACAGTAC
1 CTAATCTCACCGCTACAGTAC
43423455 CTAATCTCACCGC
1 CTAATCTCACCGC
43423468 GGTTAGTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.27, C:0.40, G:0.11, T:0.22
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAC
Found at i:43427212 original size:17 final size:18
Alignment explanation
Indices: 43427185--43427220 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
43427175 GTTAGTACTC
*
43427185 AATATTTAATTAAATAAA
1 AATATTTAATTAAAGAAA
43427203 AATA-TTAATTAAAGAAA
1 AATATTTAATTAAAGAAA
43427220 A
1 A
43427221 TTTATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
AATATTTAATTAAAGAAA
Found at i:43428773 original size:21 final size:21
Alignment explanation
Indices: 43428732--43428774 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
43428722 ATGATCTAAA
* *
43428732 TCTCAAATGTTGTTCTAGGTG
1 TCTCAAATGTTATTATAGGTG
*
43428753 TCTCAAATGTTATTATGGGTG
1 TCTCAAATGTTATTATAGGTG
43428774 T
1 T
43428775 ACAACATTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.23, T:0.44
Consensus pattern (21 bp):
TCTCAAATGTTATTATAGGTG
Found at i:43430955 original size:15 final size:15
Alignment explanation
Indices: 43430935--43430975 Score: 61
Period size: 13 Copynumber: 2.9 Consensus size: 15
43430925 TTTTTATCAA
43430935 ATATATATATT--TT
1 ATATATATATTAATT
43430948 ATATATATATTAATT
1 ATATATATATTAATT
43430963 ATATATAT-TTAAT
1 ATATATATATTAAT
43430976 ATGGGCCGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.42
14 5 0.19
15 10 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATATATATTAATT
Found at i:43432376 original size:33 final size:34
Alignment explanation
Indices: 43432333--43432476 Score: 155
Period size: 31 Copynumber: 4.5 Consensus size: 34
43432323 TAGATTAATT
43432333 TATATTTTATATATCATTATATTAAATTATTTAAA
1 TATA-TTTATATATCATTATATTAAATTATTTAAA
*
43432368 TA-ATTTATATATCATTATGTTAAATTATTTAAA
1 TATATTTATATATCATTATATTAAATTATTTAAA
* *
43432401 TATAATT-TAT-T-ATTATATTAAATCATTTAAA
1 TATATTTATATATCATTATATTAAATTATTTAAA
* *
43432432 TCT-TATT-TAT-T-ATTATATTTAATT-TTTAAA
1 TATAT-TTATATATCATTATATTAAATTATTTAAA
43432462 -ATATTTATATATCAT
1 TATATTTATATATCAT
43432477 CCATTTTACA
Statistics
Matches: 94, Mismatches: 9, Indels: 15
0.80 0.08 0.13
Matches are distributed among these distances:
29 3 0.03
30 10 0.11
31 38 0.40
32 3 0.03
33 34 0.36
34 4 0.04
35 2 0.02
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (34 bp):
TATATTTATATATCATTATATTAAATTATTTAAA
Found at i:43432397 original size:24 final size:23
Alignment explanation
Indices: 43432358--43432403 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
43432348 ATTATATTAA
*
43432358 ATTATTTAAATAATTTATATATC
1 ATTATTTAAATAATTTAAATATC
*
43432381 ATTATGTTAAATTATTTAAATAT
1 ATTAT-TTAAATAATTTAAATAT
43432404 AATTTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTATTTAAATAATTTAAATATC
Found at i:43447517 original size:231 final size:231
Alignment explanation
Indices: 43447241--43447714 Score: 648
Period size: 231 Copynumber: 2.1 Consensus size: 231
43447231 TGCTCATACA
* ** **
43447241 GTTTTACATTAACTTCAAGATCTCTACAACGTTCTTTGAAAGCCTTCTCTTCCCTCTCAAACTCC
1 GTTTTACACTAACTTCAAGATCTCTACAACGTTCTTCCAAAGCCTTCTCTTCCAACTCAAACTCC
* * * * * * *
43447306 ATATAACGCTTCACAAAACTCTTCTCTTTCAACTCAAATTGTACTTCTTTCAACTCATACTCGCT
66 ATACAACGCTTCACAAAACTCTTCTCTTTCAACCCAAATTGTACTTCTCTCAACACAAAATCACT
* * * *
43447371 CAAGC-ACTTCTCCAAAT-ATTTCTCTTTCACCCCAACTTCCTCCAACTTATCTTTTACTGA-TT
131 CAAGCGA-TTCTCCAAATCA-TTCTCTTTCAACCCAACTTCCCCCAACTTATCATTTAC-CACTT
43447433 TCTCCATCAACTTAAACTCTTCACATTGCCGCTCACATT
193 TCTCCATCAACTTAAACTCTTCACATTGCCGCTCACATT
* * *
43447472 GTTTTACACTAACTTCAAGATCTCTGCGACGTTCTTCCAAAGCCTTTTCTTCCAACTCAAACTCC
1 GTTTTACACTAACTTCAAGATCTCTACAACGTTCTTCCAAAGCCTTCTCTTCCAACTCAAACTCC
* * **
43447537 ATACACCGCTTCTCAAAACTCTTCTCTTTCAACCCAAATTGTTGTTCTCTCAACACAAAATCACT
66 ATACAACGCTTCACAAAACTCTTCTCTTTCAACCCAAATTGTACTTCTCTCAACACAAAATCACT
* *
43447602 CAAGCGATTCTCCAAATCATTCTCTTTTAACCCAATTTCCCCCAACTTATCATTTACCACTTTCT
131 CAAGCGATTCTCCAAATCATTCTCTTTCAACCCAACTTCCCCCAACTTATCATTTACCACTTTCT
* *
43447667 CCATCAACTTAAACTCTTTACATTGCTGCTCACATT
196 CCATCAACTTAAACTCTTCACATTGCCGCTCACATT
*
43447703 GTTCTACACTAA
1 GTTTTACACTAA
43447715 ATTGGAGATC
Statistics
Matches: 212, Mismatches: 28, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
230 1 0.00
231 209 0.99
232 2 0.01
ACGTcount: A:0.27, C:0.32, G:0.05, T:0.36
Consensus pattern (231 bp):
GTTTTACACTAACTTCAAGATCTCTACAACGTTCTTCCAAAGCCTTCTCTTCCAACTCAAACTCC
ATACAACGCTTCACAAAACTCTTCTCTTTCAACCCAAATTGTACTTCTCTCAACACAAAATCACT
CAAGCGATTCTCCAAATCATTCTCTTTCAACCCAACTTCCCCCAACTTATCATTTACCACTTTCT
CCATCAACTTAAACTCTTCACATTGCCGCTCACATT
Found at i:43447762 original size:231 final size:231
Alignment explanation
Indices: 43447245--43447774 Score: 613
Period size: 231 Copynumber: 2.3 Consensus size: 231
43447235 CATACAGTTT
* * * * ** * ** *
43447245 TACATTAACTTCAAGATCTCTACAACGTTCTTTGAAAGCCTTCTCTTCCCTCTCAAACTCCATAT
1 TACACTAAATTCAAGATCTCTACGACGTGCTTCCAAAGCCTTTTCTTCCAACTCAAACTCCATAC
* * * * * *
43447310 AACGCTTCACAAAACTCTTCTCTTTCAACTCAAATTGTACTTCTTTCAACTCATACTCGCTCAAG
66 AACGCTTCACAAAACTCTTCTCTTTCAACCCAAATTGTACTTCTCTCAACACAAAATCACTCAAG
* * * *
43447375 CACTTCTCCAAATATTTCTCTTTCACCCCAACTTCCTCCAACTTATCTTTTACTGATTTCTCCAT
131 CACTTCTCCAAATATTTCTCTTTCAACCCAACTTCCCCCAACTTATCATTTACTCATTTCTCCAT
*
43447440 CAACTTAAACTCTTCACATTGCCGCTCACATTGTTT
196 CAACTTAAACTCTTCACATTGCCGCTCACATTGTTC
* * *
43447476 TACACTAACTTCAAGATCTCTGCGACGTTCTTCCAAAGCCTTTTCTTCCAACTCAAACTCCATAC
1 TACACTAAATTCAAGATCTCTACGACGTGCTTCCAAAGCCTTTTCTTCCAACTCAAACTCCATAC
* * **
43447541 ACCGCTTCTCAAAACTCTTCTCTTTCAACCCAAATTGTTGTTCTCTCAACACAAAATCACTCAAG
66 AACGCTTCACAAAACTCTTCTCTTTCAACCCAAATTGTACTTCTCTCAACACAAAATCACTCAAG
* *
43447606 CGA-TTCTCCAAATCA-TTCTCTTTTAACCCAATTTCCCCCAACTTATCATTTAC-CACTTTCTC
131 C-ACTTCTCCAAAT-ATTTCTCTTTCAACCCAACTTCCCCCAACTTATCATTTACTCA-TTTCTC
* *
43447668 CATCAACTTAAACTCTTTACATTGCTGCTCACATTGTTC
193 CATCAACTTAAACTCTTCACATTGCCGCTCACATTGTTC
** * * * * *
43447707 TACACTAAATTGGAGATCTTTACGAC-TGCGTT-CAAGATCCTTCTTC-TCTAACTCAAAATCCC
1 TACACTAAATTCAAGATCTCTACGACGTGC-TTCCAA-AGCCTT-TTCTTCCAACTCAAACTCCA
43447769 TACAAC
63 TACAAC
43447775 ACTTGTCAAA
Statistics
Matches: 254, Mismatches: 39, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
230 6 0.02
231 243 0.96
232 5 0.02
ACGTcount: A:0.27, C:0.32, G:0.06, T:0.35
Consensus pattern (231 bp):
TACACTAAATTCAAGATCTCTACGACGTGCTTCCAAAGCCTTTTCTTCCAACTCAAACTCCATAC
AACGCTTCACAAAACTCTTCTCTTTCAACCCAAATTGTACTTCTCTCAACACAAAATCACTCAAG
CACTTCTCCAAATATTTCTCTTTCAACCCAACTTCCCCCAACTTATCATTTACTCATTTCTCCAT
CAACTTAAACTCTTCACATTGCCGCTCACATTGTTC
Found at i:43448294 original size:7 final size:7
Alignment explanation
Indices: 43448282--43448317 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
43448272 AAAAGGAAAG
43448282 AAAATTA
1 AAAATTA
43448289 AAAATTA
1 AAAATTA
43448296 AAAATTA
1 AAAATTA
*
43448303 GAAATTA
1 AAAATTA
43448310 AAAATTA
1 AAAATTA
43448317 A
1 A
43448318 TTTTTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (7 bp):
AAAATTA
Found at i:43451512 original size:24 final size:24
Alignment explanation
Indices: 43451485--43451536 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
43451475 ATGTCTGCAT
43451485 GTCTAAAAC-TTAAAAATTTGCAAA
1 GTCTAAAACATT-AAAATTTGCAAA
* *
43451509 GTCTTAAACATTAAATTTTGCAAA
1 GTCTAAAACATTAAAATTTGCAAA
43451533 GTCT
1 GTCT
43451537 TATAATAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (24 bp):
GTCTAAAACATTAAAATTTGCAAA
Found at i:43458705 original size:40 final size:40
Alignment explanation
Indices: 43458670--43458745 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
43458660 GATTCAAGAT
*
43458670 TACCAAAGTACAAACAGGGGCACGTATGTGCATTCAAAGG
1 TACCAAAGTACAAACAGGGGCACATATGTGCATTCAAAGG
* * *
43458710 TACCGAATTACAAACATGGGCACATATGTGCATTCA
1 TACCAAAGTACAAACAGGGGCACATATGTGCATTCA
43458746 GGCAATAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (40 bp):
TACCAAAGTACAAACAGGGGCACATATGTGCATTCAAAGG
Found at i:43463845 original size:2 final size:2
Alignment explanation
Indices: 43463838--43463870 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
43463828 ATTTGGCCGA
43463838 AT 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 AT A
43463871 ATGTCATTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43464564 original size:45 final size:44
Alignment explanation
Indices: 43464413--43464608 Score: 185
Period size: 45 Copynumber: 4.5 Consensus size: 44
43464403 ATATTGAACA
* * *
43464413 ATGCCAACGTCTCAGACGTGGTCTTACATGCT-ATCTC-ATATCG
1 ATGCCATCGTCCCAGACGTGGTCTTACAT-CTAATCACAATATCG
*
43464456 ATGCCA-CTGTCCCAGACAG-GGTCTTACA-CGAATCA-AATA-CG
1 ATGCCATC-GTCCCAGAC-GTGGTCTTACATCTAATCACAATATCG
* * *
43464497 ATGCCAAT-GTCCTAGACATGGTCTTACATATAATCACATATATCG
1 ATGCC-ATCGTCCCAGACGTGGTCTTACATCTAATCACA-ATATCG
*
43464542 ATGCCATCGTCCCAGACGTGGTCTTACA-CGTAATCACATAAATCG
1 ATGCCATCGTCCCAGACGTGGTCTTACATC-TAATCACA-ATATCG
*
43464587 ATGCCATTGTCCCAGACGTGGT
1 ATGCCATCGTCCCAGACGTGGT
43464609 TTTGCACGAG
Statistics
Matches: 128, Mismatches: 12, Indels: 24
0.78 0.07 0.15
Matches are distributed among these distances:
41 25 0.20
42 13 0.10
43 24 0.19
44 6 0.05
45 60 0.47
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (44 bp):
ATGCCATCGTCCCAGACGTGGTCTTACATCTAATCACAATATCG
Found at i:43467062 original size:44 final size:47
Alignment explanation
Indices: 43466955--43467062 Score: 123
Period size: 49 Copynumber: 2.3 Consensus size: 47
43466945 ACCATATTCT
* * *
43466955 AATAGAAGTAGTGTAGTAAGGTTGAAACACCTAATTCTAATCAATATCA
1 AATAGAAGAAGTGTAATAAGGTTGAAAAACCTAATTCTAA-CAATA-CA
* *
43467004 AATAGAGGAAGTGTAATAAGGTTGAAAAACCTTATTCTAA-AATA-A
1 AATAGAAGAAGTGTAATAAGGTTGAAAAACCTAATTCTAACAATACA
*
43467049 AATA-AATAAGTGTA
1 AATAGAAGAAGTGTA
43467063 GTTCTATATG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
44 8 0.15
45 5 0.10
47 4 0.08
49 35 0.67
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.28
Consensus pattern (47 bp):
AATAGAAGAAGTGTAATAAGGTTGAAAAACCTAATTCTAACAATACA
Found at i:43476684 original size:25 final size:26
Alignment explanation
Indices: 43476638--43476688 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
43476628 GTTAGTATGA
43476638 ATGTAACACCCTTAAATTTCTTAACT
1 ATGTAACACCCTTAAATTTCTTAACT
43476664 ATGTAACACCC-TAAATTTCTTAACT
1 ATGTAACACCCTTAAATTTCTTAACT
43476689 TTCTTTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (26 bp):
ATGTAACACCCTTAAATTTCTTAACT
Found at i:43479220 original size:24 final size:24
Alignment explanation
Indices: 43479182--43479233 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
43479172 AGGACCTAAG
*
43479182 TATGTATTTGCATCTAATTATGAA
1 TATGTATCTGCATCTAATTATGAA
*
43479206 TATGTATCTGTATCTAATTATGAA
1 TATGTATCTGCATCTAATTATGAA
43479230 TATG
1 TATG
43479234 ATTTTGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (24 bp):
TATGTATCTGCATCTAATTATGAA
Found at i:43481618 original size:20 final size:20
Alignment explanation
Indices: 43481593--43481632 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43481583 GATTAATTAT
43481593 TATAATTTTACAATTATATA
1 TATAATTTTACAATTATATA
* *
43481613 TATAATTTTATAATTTTATA
1 TATAATTTTACAATTATATA
43481633 ATTTTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TATAATTTTACAATTATATA
Found at i:43481646 original size:8 final size:8
Alignment explanation
Indices: 43481613--43481644 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
43481603 CAATTATATA
43481613 TATAATTT
1 TATAATTT
43481621 TATAATTT
1 TATAATTT
43481629 TATAATTT
1 TATAATTT
43481637 T-TAATTT
1 TATAATTT
43481644 T
1 T
43481645 TTTTAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TATAATTT
Found at i:43481665 original size:27 final size:27
Alignment explanation
Indices: 43481618--43481674 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
43481608 ATATATATAA
* *
43481618 TTTTATAATTTTATAATTTTTAATTTT
1 TTTTAAAATTTTATAAATTTTAATTTT
*
43481645 TTTTAAAATTTGTA-AAATTTTGATTTT
1 TTTTAAAATTT-TATAAATTTTAATTTT
43481672 TTT
1 TTT
43481675 AATACATGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (27 bp):
TTTTAAAATTTTATAAATTTTAATTTT
Found at i:43481884 original size:5 final size:5
Alignment explanation
Indices: 43481874--43481901 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
43481864 AAGGGCTTAA
43481874 TTATT TTATT TTATT TTATT TTATT TTA
1 TTATT TTATT TTATT TTATT TTATT TTA
43481902 ATAAGGACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:43484843 original size:27 final size:27
Alignment explanation
Indices: 43484807--43485134 Score: 335
Period size: 27 Copynumber: 12.2 Consensus size: 27
43484797 AGAGGTCAAT
* * *
43484807 AAATGATCGAATTACCCCCACATGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
*
43484834 AAATGATCGAATTACCCCACA-A-GGTA
1 AAATGATCGAAATACCCC-CATAGGGTA
* *
43484860 AAATGA-CTGAAATACCCTCATAGGGCA
1 AAATGATC-GAAATACCCCCATAGGGTA
* * *
43484887 AAATGATCGAAATATCCCTATAGGTTA
1 AAATGATCGAAATACCCCCATAGGGTA
43484914 AAATGA-CTGAAATACCCCCATAGGGTA
1 AAATGATC-GAAATACCCCCATAGGGTA
* *
43484941 AAATGACCGAAATACCCTCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* * * *
43484968 AAAT-AACTAAAATACCCTCATAGGATA
1 AAATGATC-GAAATACCCCCATAGGGTA
* * *
43484995 AAATGACCGAAATACCCCTATAGGGTC
1 AAATGATCGAAATACCCCCATAGGGTA
*
43485022 AAATGATCGAAATACTCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
43485049 AAATGACCG-AATACCCACATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* * *
43485075 AAATAACCGAAATACCCCTATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
***
43485102 AAATGATCGAAATACCTTTATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
43485129 AAATGA
1 AAATGA
43485135 CTGTTATACC
Statistics
Matches: 256, Mismatches: 35, Indels: 20
0.82 0.11 0.06
Matches are distributed among these distances:
25 3 0.01
26 45 0.18
27 202 0.79
28 6 0.02
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.21
Consensus pattern (27 bp):
AAATGATCGAAATACCCCCATAGGGTA
Found at i:43485404 original size:26 final size:26
Alignment explanation
Indices: 43485368--43485444 Score: 111
Period size: 26 Copynumber: 3.0 Consensus size: 26
43485358 TTTGCCACAT
* *
43485368 ATACTGTTACTGGCAGCTTTGTTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
43485394 ATACTGATACTGGCAGCTTTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
*
43485420 ATGCT-ATTACTGGCAGCTTTGCTGC
1 ATACTGA-TACTGGCAGCTTTGCTGC
43485445 AATATTGGTG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
25 1 0.02
26 46 0.98
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTGCTGCG
Found at i:43485593 original size:28 final size:28
Alignment explanation
Indices: 43485550--43485667 Score: 130
Period size: 28 Copynumber: 4.2 Consensus size: 28
43485540 TATTGCACTG
* * *
43485550 CACTATTACTGTATTGGGCTAAGGCCTA
1 CACTGTTATTGTATTGGGCTAAGGCCCA
* * *
43485578 CACTGATT-CTATATTGGGATAAGGCCCA
1 CACTG-TTATTGTATTGGGCTAAGGCCCA
* * *
43485606 CACTGTTATTGTATTAGGCTAAGGTCTA
1 CACTGTTATTGTATTGGGCTAAGGCCCA
*
43485634 CGCTGTTATTGTATTGGGCTAAGGCCCA
1 CACTGTTATTGTATTGGGCTAAGGCCCA
43485662 CACTGT
1 CACTGT
43485668 ACTGTCACTG
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
27 2 0.03
28 69 0.95
29 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (28 bp):
CACTGTTATTGTATTGGGCTAAGGCCCA
Found at i:43492182 original size:3 final size:3
Alignment explanation
Indices: 43492176--43492228 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
43492166 TGTTTTTTTC
*
43492176 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43492224 TTA TT
1 TTA TT
43492229 TCCATGTACA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:43492376 original size:16 final size:16
Alignment explanation
Indices: 43492355--43492388 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
43492345 CATAATTTTT
43492355 ATATACATGTATATAC
1 ATATACATGTATATAC
*
43492371 ATATACATTTATATAC
1 ATATACATGTATATAC
43492387 AT
1 AT
43492389 TTTCCTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (16 bp):
ATATACATGTATATAC
Found at i:43496750 original size:14 final size:13
Alignment explanation
Indices: 43496731--43496769 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
43496721 TCATATGCTC
43496731 AAGAAAAAAAGGAA
1 AAGAAAAAAAGG-A
*
43496745 AAGAAAAGAAAAGA
1 AAGAAAA-AAAGGA
43496759 AAGAAAAAAAG
1 AAGAAAAAAAG
43496770 AGAGCATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 3 0.14
14 15 0.68
15 4 0.18
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAGGA
Found at i:43497379 original size:27 final size:26
Alignment explanation
Indices: 43497319--43497379 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
43497309 TCGAAATTCA
*
43497319 TAATTTAATTATAAAATAATTAATTT
1 TAATTAAATTATAAAATAATTAATTT
* *
43497345 GAACTTAAATTATTAAAA-ATTTGAATTT
1 TAA-TTAAATTA-TAAAATAATT-AATTT
43497373 TAATTAA
1 TAATTAA
43497380 TTTTATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
26 2 0.07
27 14 0.50
28 12 0.43
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (26 bp):
TAATTAAATTATAAAATAATTAATTT
Found at i:43500522 original size:24 final size:22
Alignment explanation
Indices: 43500479--43500521 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
43500469 CACCTATGCG
*
43500479 AAGGAGACACACGCTCGTGTGA
1 AAGGAGACACACGCCCGTGTGA
*
43500501 AAGGAGGCACACGCCCGTGTG
1 AAGGAGACACACGCCCGTGTG
43500522 TCCGGGGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.26, G:0.35, T:0.12
Consensus pattern (22 bp):
AAGGAGACACACGCCCGTGTGA
Found at i:43501232 original size:13 final size:13
Alignment explanation
Indices: 43501214--43501239 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43501204 GAGAAAAAAA
43501214 CATGAAAATTATT
1 CATGAAAATTATT
43501227 CATGAAAATTATT
1 CATGAAAATTATT
43501240 TTGGCCCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
CATGAAAATTATT
Found at i:43503573 original size:68 final size:69
Alignment explanation
Indices: 43503462--43503644 Score: 199
Period size: 68 Copynumber: 2.7 Consensus size: 69
43503452 ATAAAAATCG
* * * * * * *
43503462 TATTAAGGCTCGCAGGATAAAAACCACAGCCTCGAACATAGTTAGTGAAAGCAAAGC-CCTAGTT
1 TATTAAGGCTCACAGGATAAAAATCGCAGCCTCGAACACAGTTAGCGAAAGCAAAGCTCCCAGCT
43503526 GTCA
66 GTCA
* * *
43503530 TATTAAGGCTCACAGGATAAAAGTCGCAGCCTTC-AACACAGTTAGCGAGAGCTAAGCTCCCAGC
1 TATTAAGGCTCACAGGATAAAAATCGCAGCC-TCGAACACAGTTAGCGAAAGCAAAGCTCCCAGC
43503594 TGTCA
65 TGTCA
** * * * *
43503599 TATTAAGGCTCTTAGGATAAAAATCGCAACATCCAACATAGTTAGC
1 TATTAAGGCTCACAGGATAAAAATCGCAGCCTCGAACACAGTTAGC
43503645 CAAAATTGAA
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
68 48 0.50
69 48 0.50
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.22
Consensus pattern (69 bp):
TATTAAGGCTCACAGGATAAAAATCGCAGCCTCGAACACAGTTAGCGAAAGCAAAGCTCCCAGCT
GTCA
Found at i:43503617 original size:69 final size:68
Alignment explanation
Indices: 43503462--43503644 Score: 206
Period size: 69 Copynumber: 2.7 Consensus size: 68
43503452 ATAAAAATCG
* * * * * *
43503462 TATTAAGGCTCGCAGGATAAAAACCACAGCC-TCGAACATAGTTAGTGAAAGCAAAGCCCTAGTT
1 TATTAAGGCTCACAGGATAAAAATCGCAGCCTTC-AACATAGTTAGCGAAAGCAAAGCCCCAGCT
43503526 GTCA
65 GTCA
* * * *
43503530 TATTAAGGCTCACAGGATAAAAGTCGCAGCCTTCAACACAGTTAGCGAGAGCTAAGCTCCCAGCT
1 TATTAAGGCTCACAGGATAAAAATCGCAGCCTTCAACATAGTTAGCGAAAGCAAAGC-CCCAGCT
43503595 GTCA
65 GTCA
** * * *
43503599 TATTAAGGCTCTTAGGATAAAAATCGCAACATCCAACATAGTTAGC
1 TATTAAGGCTCACAGGATAAAAATCGCAGCCTTCAACATAGTTAGC
43503645 CAAAATTGAA
Statistics
Matches: 96, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
68 46 0.48
69 50 0.52
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.22
Consensus pattern (68 bp):
TATTAAGGCTCACAGGATAAAAATCGCAGCCTTCAACATAGTTAGCGAAAGCAAAGCCCCAGCTG
TCA
Found at i:43503760 original size:58 final size:57
Alignment explanation
Indices: 43503665--43503876 Score: 191
Period size: 58 Copynumber: 3.7 Consensus size: 57
43503655 CTCCCAGTAT
** *
43503665 GTTATCTTTCAAAAGTTTCTCAAGTATAAAACAGCTCGCGGATTCACATCCTCAGCTG
1 GTTATCTTTCAAATTTTTCTCAAGTATAAAACTGCTCGCGGATTCACATCC-CAGCTG
* * * *
43503723 GTTATCCTTCAAATTTTTCTTAAGTATAAAACTGCTCGTGGA-TCTACATCCCTAGCTA
1 GTTATCTTTCAAATTTTTCTCAAGTATAAAACTGCTCGCGGATTC-ACATCCC-AGCTG
* * * * * *
43503781 GTTATCTTTCAAATTTCTCTTAAGTATGAAA-TAGCTCGTGGACTT--TATCCCCAGTTG
1 GTTATCTTTCAAATTTTTCTCAAGTATAAAACT-GCTCGCGGA-TTCACAT-CCCAGCTG
* * *
43503838 GTTATCTTTGAAA-TTTTCTCAAGTATAAATCTACTCGCG
1 GTTATCTTTCAAATTTTTCTCAAGTATAAAACTGCTCGCG
43503877 AATTAATATT
Statistics
Matches: 127, Mismatches: 20, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
56 18 0.14
57 22 0.17
58 86 0.68
60 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.37
Consensus pattern (57 bp):
GTTATCTTTCAAATTTTTCTCAAGTATAAAACTGCTCGCGGATTCACATCCCAGCTG
Found at i:43506872 original size:22 final size:22
Alignment explanation
Indices: 43506844--43506915 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
43506834 AACATACGAG
43506844 AAAATATTACTCAATAAAATAA
1 AAAATATTACTCAATAAAATAA
43506866 AAAATATTA--C-ATACAAAT--
1 AAAATATTACTCAATA-AAATAA
**
43506884 TGAATATTACTCAATAAAATAA
1 AAAATATTACTCAATAAAATAA
43506906 AAAATATTAC
1 AAAATATTAC
43506916 ATACAAATTG
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
18 7 0.17
19 3 0.08
20 10 0.25
21 3 0.08
22 17 0.43
ACGTcount: A:0.60, C:0.10, G:0.01, T:0.29
Consensus pattern (22 bp):
AAAATATTACTCAATAAAATAA
Found at i:43506883 original size:20 final size:20
Alignment explanation
Indices: 43506860--43506923 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
43506850 TTACTCAATA
43506860 AAATAAAAAATATTACATAC
1 AAATAAAAAATATTACATAC
**
43506880 AAAT--TGAATATTACTCAATA-
1 AAATAAAAAATATTA--C-ATAC
43506900 AAATAAAAAATATTACATAC
1 AAATAAAAAATATTACATAC
43506920 AAAT
1 AAAT
43506924 TGATATACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
18 7 0.21
19 3 0.09
20 14 0.41
21 3 0.09
22 7 0.21
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.28
Consensus pattern (20 bp):
AAATAAAAAATATTACATAC
Found at i:43506891 original size:40 final size:40
Alignment explanation
Indices: 43506846--43506926 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
43506836 CATACGAGAA
43506846 AATATTACTCAATAAAATAAAAAATATTACATACAAATTG
1 AATATTACTCAATAAAATAAAAAATATTACATACAAATTG
43506886 AATATTACTCAATAAAATAAAAAATATTACATACAAATTG
1 AATATTACTCAATAAAATAAAAAATATTACATACAAATTG
43506926 A
1 A
43506927 TATACATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (40 bp):
AATATTACTCAATAAAATAAAAAATATTACATACAAATTG
Found at i:43509950 original size:43 final size:43
Alignment explanation
Indices: 43509889--43509975 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
43509879 ATTCTCACAT
43509889 TGATATGGAAATCAAAGAAGAAAGCAGAGAGGTCGAATGGAGG
1 TGATATGGAAATCAAAGAAGAAAGCAGAGAGGTCGAATGGAGG
43509932 TGATATGGAAATCAAAGAAGAAAGCAGAGAGGTCGAATGGAGG
1 TGATATGGAAATCAAAGAAGAAAGCAGAGAGGTCGAATGGAGG
43509975 T
1 T
43509976 TTACCAGTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.44, C:0.07, G:0.34, T:0.15
Consensus pattern (43 bp):
TGATATGGAAATCAAAGAAGAAAGCAGAGAGGTCGAATGGAGG
Found at i:43510158 original size:27 final size:26
Alignment explanation
Indices: 43510110--43510161 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
43510100 TTCATTCGAG
* *
43510110 AAAAAAATGGGAAGGTTGAGAGAAGA
1 AAAAAAATGGCAACGTTGAGAGAAGA
*
43510136 AAAACAAATGGCAACGTTTAGAGAAG
1 AAAA-AAATGGCAACGTTGAGAGAAG
43510162 TTCTGGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.52, C:0.06, G:0.29, T:0.13
Consensus pattern (26 bp):
AAAAAAATGGCAACGTTGAGAGAAGA
Found at i:43512045 original size:17 final size:17
Alignment explanation
Indices: 43512023--43512056 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
43512013 GAAAAATTGG
43512023 AGTATTTGTAATCTTTC
1 AGTATTTGTAATCTTTC
43512040 AGTATTTGTAATCTTTC
1 AGTATTTGTAATCTTTC
43512057 TACAGGAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (17 bp):
AGTATTTGTAATCTTTC
Found at i:43515859 original size:25 final size:28
Alignment explanation
Indices: 43515814--43515868 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
43515804 TTAAGAACAC
*
43515814 ATATATATTATATAAAGAAAT-ATGTAT
1 ATATATACTATATAAAGAAATCATGTAT
43515841 ATATATACTATAT-AA-AAATGCATGTAT
1 ATATATACTATATAAAGAAAT-CATGTAT
43515868 A
1 A
43515869 AGTTTAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 4 0.16
26 2 0.08
27 19 0.76
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (28 bp):
ATATATACTATATAAAGAAATCATGTAT
Found at i:43517140 original size:21 final size:21
Alignment explanation
Indices: 43517094--43517140 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
43517084 GTTTTTATTT
*
43517094 TAAAAAATAATTCATAATAAA
1 TAAAAAATAATTAATAATAAA
* *
43517115 CAAAAAATAAATTAAT-ATTAA
1 TAAAAAAT-AATTAATAATAAA
43517136 TAAAA
1 TAAAA
43517141 TGTTATTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAAAATAATTAATAATAAA
Found at i:43523407 original size:29 final size:28
Alignment explanation
Indices: 43523350--43523404 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
43523340 CTCAAAAAGG
* * *
43523350 TATTTAAATTTCAACTTTTTTTTACAAT
1 TATTTAAATTTCAAATTTTTTTAAAAAT
43523378 TATTTGAAATTT-AAATTTTTTTAAAAA
1 TATTT-AAATTTCAAATTTTTTTAAAAA
43523405 ATTTATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (28 bp):
TATTTAAATTTCAAATTTTTTTAAAAAT
Found at i:43523473 original size:23 final size:23
Alignment explanation
Indices: 43523447--43523500 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
43523437 ATTATTTTGA
** *
43523447 ATTTTTAAAATTTATAATGATAT
1 ATTTTTAAAATTTATAAAAAAAT
*
43523470 A-TTTTATAATTTTATAAAAAAAT
1 ATTTTTA-AAATTTATAAAAAAAT
43523493 ATTTTTAA
1 ATTTTTAA
43523501 GCCTTTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 5 0.20
23 15 0.60
24 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTTTTAAAATTTATAAAAAAAT
Found at i:43523691 original size:7 final size:7
Alignment explanation
Indices: 43523681--43523706 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43523671 TAATATTATA
43523681 ATTTTCT
1 ATTTTCT
43523688 ATTTTCT
1 ATTTTCT
43523695 ATTTTCT
1 ATTTTCT
43523702 ATTTT
1 ATTTT
43523707 TAAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTCT
Found at i:43524190 original size:13 final size:13
Alignment explanation
Indices: 43524174--43524207 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
43524164 TATCTCTAAA
43524174 AATTTTCTAAAAG
1 AATTTTCTAAAAG
* *
43524187 AATTTTTTTAAAG
1 AATTTTCTAAAAG
43524200 AATTTTCT
1 AATTTTCT
43524208 CTCTACAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (13 bp):
AATTTTCTAAAAG
Found at i:43524466 original size:20 final size:19
Alignment explanation
Indices: 43524416--43524468 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
43524406 CTACAATATA
43524416 AATATTAAATT-A-AATTT
1 AATATTAAATTAATAATTT
43524433 AATATTAAGA-TAATAACTTT
1 AATATTAA-ATTAATAA-TTT
*
43524453 GATATTAAATTAATAA
1 AATATTAAATTAATAA
43524469 AATACTATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 9 0.30
18 2 0.07
19 3 0.10
20 16 0.53
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (19 bp):
AATATTAAATTAATAATTT
Found at i:43527556 original size:25 final size:25
Alignment explanation
Indices: 43527537--43527614 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 25
43527527 GAATCGAAAT
*
43527537 GCTCTCACGAGCTAGAAATCGGTAA
1 GCTCTCACGAGCTAGAAATCAGTAA
43527562 GCTCAT-ACGAGCT-GAGAATCAGTAA
1 GCTC-TCACGAGCTAGA-AATCAGTAA
*
43527587 GCTCTCACGAGC-AGAAATCGGTAA
1 GCTCTCACGAGCTAGAAATCAGTAA
43527611 GCTC
1 GCTC
43527615 ATACAAGCTG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
24 15 0.32
25 31 0.66
26 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (25 bp):
GCTCTCACGAGCTAGAAATCAGTAA
Found at i:43527591 original size:50 final size:50
Alignment explanation
Indices: 43527516--43527624 Score: 161
Period size: 50 Copynumber: 2.2 Consensus size: 50
43527506 ATGTGTGCTA
43527516 ATACGAGCT-ATGAATCGAAATGCTCTCACGAGCTAGAAATCGGTAAGCTC
1 ATACGAGCTGATGAATCGAAATGCTCTCACGAGC-AGAAATCGGTAAGCTC
*
43527566 ATACGAGCTGA-GAATCAGTAA-GCTCTCACGAGCAGAAATCGGTAAGCTC
1 ATACGAGCTGATGAATC-GAAATGCTCTCACGAGCAGAAATCGGTAAGCTC
*
43527615 ATACAAGCTG
1 ATACGAGCTG
43527625 TGGTGTGTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
49 25 0.45
50 26 0.47
51 4 0.07
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (50 bp):
ATACGAGCTGATGAATCGAAATGCTCTCACGAGCAGAAATCGGTAAGCTC
Found at i:43530205 original size:16 final size:16
Alignment explanation
Indices: 43530184--43530214 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
43530174 ATTAAGAAAA
43530184 TGTTACAAAAATGTGG
1 TGTTACAAAAATGTGG
43530200 TGTTACAAAAATGTG
1 TGTTACAAAAATGTG
43530215 AAAATAGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (16 bp):
TGTTACAAAAATGTGG
Found at i:43530613 original size:20 final size:21
Alignment explanation
Indices: 43530577--43530615 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43530567 CATCCATACC
*
43530577 ATTTGAACATACATTCAAAAG
1 ATTTAAACATACATTCAAAAG
43530598 ATTTAAACAT-CATTCAAA
1 ATTTAAACATACATTCAAA
43530616 CACACATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (21 bp):
ATTTAAACATACATTCAAAAG
Found at i:43538484 original size:26 final size:26
Alignment explanation
Indices: 43538412--43538484 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 26
43538402 TCATCCATAA
* *
43538412 TTTA-CCCTCAGTAAAATTTTGATGAT
1 TTTACCCCT-AGTAAAATTTTAAAGAT
*
43538438 TTTACCCC-CGATAAAATTTTTAAAGAT
1 TTTACCCCTAG-TAAAA-TTTTAAAGAT
*
43538465 TTTACCCCTAGTGAAATTTT
1 TTTACCCCTAGTAAAATTTT
43538485 GAAAAAATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
25 1 0.03
26 13 0.34
27 23 0.61
28 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.41
Consensus pattern (26 bp):
TTTACCCCTAGTAAAATTTTAAAGAT
Found at i:43542408 original size:13 final size:14
Alignment explanation
Indices: 43542385--43542416 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
43542375 TCCGCCATAG
43542385 AAATACATCCAACA
1 AAATACATCCAACA
43542399 AAAT-CATCCAACA
1 AAATACATCCAACA
43542412 AAATA
1 AAATA
43542417 AAAACATCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.59, C:0.25, G:0.00, T:0.16
Consensus pattern (14 bp):
AAATACATCCAACA
Found at i:43544502 original size:20 final size:20
Alignment explanation
Indices: 43544477--43544514 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
43544467 CCATTTTCTA
*
43544477 GCTCTGCTGCATGTACCCTT
1 GCTCTGCTGCAAGTACCCTT
43544497 GCTCTGCTGCAAGTACCC
1 GCTCTGCTGCAAGTACCC
43544515 CTAACCCGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.37, G:0.21, T:0.29
Consensus pattern (20 bp):
GCTCTGCTGCAAGTACCCTT
Found at i:43545672 original size:41 final size:41
Alignment explanation
Indices: 43545613--43545724 Score: 118
Period size: 41 Copynumber: 2.8 Consensus size: 41
43545603 CGGAAGTGTT
** * * *
43545613 ATTC-GGGGTACCGTAGTACAAACAGGGGTATATATATGCA
1 ATTCAGGGGTACCAAAGTACAAATAGGGGCATACATATGCA
* * * * *
43545653 ATTTAGTGGTACCAAAGTACAAATAGGGCCATGCATGTGCA
1 ATTCAGGGGTACCAAAGTACAAATAGGGGCATACATATGCA
*
43545694 ATTCAGGGGTACGAAAGTACAAATAGGGGCA
1 ATTCAGGGGTACCAAAGTACAAATAGGGGCA
43545725 CGTATGTGCA
Statistics
Matches: 57, Mismatches: 14, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
40 3 0.05
41 54 0.95
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (41 bp):
ATTCAGGGGTACCAAAGTACAAATAGGGGCATACATATGCA
Found at i:43545732 original size:41 final size:41
Alignment explanation
Indices: 43545649--43545739 Score: 128
Period size: 41 Copynumber: 2.2 Consensus size: 41
43545639 GGTATATATA
* * *
43545649 TGCAATTTAGTGGTACCAAAGTACAAATAGGGCCATGCATG
1 TGCAATTCAGGGGTACCAAAGTACAAATAGGGCCACGCATG
* * *
43545690 TGCAATTCAGGGGTACGAAAGTACAAATAGGGGCACGTATG
1 TGCAATTCAGGGGTACCAAAGTACAAATAGGGCCACGCATG
43545731 TGCAATTCA
1 TGCAATTCA
43545740 AATATAATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.23
Consensus pattern (41 bp):
TGCAATTCAGGGGTACCAAAGTACAAATAGGGCCACGCATG
Found at i:43548033 original size:10 final size:9
Alignment explanation
Indices: 43547988--43548029 Score: 59
Period size: 9 Copynumber: 4.6 Consensus size: 9
43547978 CAACAAATAT
43547988 ACATACATA
1 ACATACATA
43547997 ACATACATA
1 ACATACATA
43548006 ACAGTACATA
1 ACA-TACATA
43548016 ACATAACAT-
1 ACAT-ACATA
43548025 ACATA
1 ACATA
43548030 AACAGTAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 1 0.03
9 17 0.55
10 13 0.42
ACGTcount: A:0.55, C:0.21, G:0.02, T:0.21
Consensus pattern (9 bp):
ACATACATA
Found at i:43548033 original size:15 final size:15
Alignment explanation
Indices: 43547997--43548030 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
43547987 TACATACATA
43547997 ACAT-ACATAACAGT
1 ACATAACATAACAGT
43548011 ACATAACATAACA-T
1 ACATAACATAACAGT
43548025 ACATAA
1 ACATAA
43548031 ACAGTAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.56, C:0.21, G:0.03, T:0.21
Consensus pattern (15 bp):
ACATAACATAACAGT
Found at i:43551714 original size:25 final size:24
Alignment explanation
Indices: 43551684--43551760 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 24
43551674 ATAGCAAAAA
43551684 AAATTAAGATAATCACTTTAATATT
1 AAATTAA-ATAATCACTTTAATATT
* *
43551709 AAATTAATAAAAT-ACTATTAATATA
1 AAATTAA-ATAATCACT-TTAATATT
*
43551734 AATATTAAAT--TCAATTTAATATT
1 AA-ATTAAATAATCACTTTAATATT
43551757 AAAT
1 AAAT
43551761 CTATTAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
22 2 0.05
23 10 0.23
24 5 0.12
25 21 0.49
26 5 0.12
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.40
Consensus pattern (24 bp):
AAATTAAATAATCACTTTAATATT
Found at i:43551771 original size:17 final size:17
Alignment explanation
Indices: 43551703--43551760 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
43551693 TAATCACTTT
*
43551703 AATATTAAATT-AATAA
1 AATATTAAATTCAATTA
*
43551719 AATACT--ATT-AATATA
1 AATATTAAATTCAAT-TA
*
43551734 AATATTAAATTCAATTT
1 AATATTAAATTCAATTA
43551751 AATATTAAAT
1 AATATTAAAT
43551761 CTATTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
14 6 0.18
15 6 0.18
16 5 0.15
17 14 0.41
18 3 0.09
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATTAAATTCAATTA
Found at i:43553364 original size:15 final size:15
Alignment explanation
Indices: 43553344--43553375 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
43553334 TATTCATGCA
*
43553344 AAATATGAAAGACAG
1 AAATATAAAAGACAG
43553359 AAATATAAAAGACAG
1 AAATATAAAAGACAG
43553374 AA
1 AA
43553376 TAGTGACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.16, T:0.12
Consensus pattern (15 bp):
AAATATAAAAGACAG
Found at i:43553799 original size:29 final size:27
Alignment explanation
Indices: 43553762--43553952 Score: 118
Period size: 28 Copynumber: 6.7 Consensus size: 27
43553752 GTTATTCCTA
43553762 TATATGTGAGCCTTTGTGGCGTAACTTG
1 TATATGTGAGCCTTTGTGGCG-AACTTG
* *
43553790 TTGTATGTGAGTCTTTGTGGCAGAA-TATG
1 -TATATGTGAGCCTTTGTGGC-GAACT-TG
** * *
43553819 -ATATACGAGCCCTTGTGGTAGTAACTTGG
1 TATATGTGAGCCTTTGTGG-CG-AACTT-G
* *
43553848 TATATGTGAGCCTTGGTGGCCGATC-TG
1 TATATGTGAGCCTTTGTGG-CGAACTTG
*
43553875 TTATATGTGAGCCCTTGTGGCGGGAACTTG
1 -TATATGTGAGCCTTTGTGGC--GAACTTG
* ** *
43553905 TGATATGTGAGCCTTTGTGACTGTTCTTT
1 T-ATATGTGAGCCTTTGTGGC-GAACTTG
*
43553934 TATATGTGAGCCATTGTGG
1 TATATGTGAGCCTTTGTGG
43553953 AAAAAATCGT
Statistics
Matches: 124, Mismatches: 26, Indels: 25
0.71 0.15 0.14
Matches are distributed among these distances:
27 16 0.13
28 38 0.31
29 35 0.28
30 35 0.28
ACGTcount: A:0.18, C:0.14, G:0.30, T:0.38
Consensus pattern (27 bp):
TATATGTGAGCCTTTGTGGCGAACTTG
Found at i:43553903 original size:58 final size:57
Alignment explanation
Indices: 43553762--43553952 Score: 181
Period size: 58 Copynumber: 3.3 Consensus size: 57
43553752 GTTATTCCTA
* * * * *
43553762 TATATGTGAGCCTTTGTGGCGTAACTTGTTGTATGTGAGTCTTTGTGGCAGAATATG-
1 TATATGTGAGCCCTTGTGGCGTAACTTGGTATATGTGAGCCTTTGTGGCAG-ATCTGT
** * * *
43553819 -ATATACGAGCCCTTGTGGTAGTAACTTGGTATATGTGAGCCTTGGTGGCCGATCTGT
1 TATATGTGAGCCCTTGTGG-CGTAACTTGGTATATGTGAGCCTTTGTGGCAGATCTGT
* * * * *
43553876 TATATGTGAGCCCTTGTGGCGGGAACTT-GTGATATGTGAGCCTTTGTGACTGTTCTTT
1 TATATGTGAGCCCTTGTGGC-GTAACTTGGT-ATATGTGAGCCTTTGTGGCAGATCTGT
*
43553934 TATATGTGAGCCATTGTGG
1 TATATGTGAGCCCTTGTGG
43553953 AAAAAATCGT
Statistics
Matches: 109, Mismatches: 20, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
56 19 0.17
57 28 0.26
58 62 0.57
ACGTcount: A:0.18, C:0.14, G:0.30, T:0.38
Consensus pattern (57 bp):
TATATGTGAGCCCTTGTGGCGTAACTTGGTATATGTGAGCCTTTGTGGCAGATCTGT
Found at i:43553913 original size:30 final size:29
Alignment explanation
Indices: 43553763--43553923 Score: 109
Period size: 29 Copynumber: 5.6 Consensus size: 29
43553753 TTATTCCTAT
* *
43553763 ATATGTGAGCCTTTGTGGCGTAACTTGTTG
1 ATATGTGAGCCCTTGTGGCGGAACTTG-TG
* * * *
43553793 -TATGTGAGTCTTTGTGGCAGAA--TATG
1 ATATGTGAGCCCTTGTGGCGGAACTTGTG
** * *
43553819 ATATACGAGCCCTTGTGGTAGTAACTTG-G
1 ATATGTGAGCCCTTGTGG-CGGAACTTGTG
* * *
43553848 TATATGTGAG-CCTTGGTGGCCGATC-TGTT
1 -ATATGTGAGCCCTT-GTGGCGGAACTTGTG
43553877 ATATGTGAGCCCTTGTGGCGGGAACTTGTG
1 ATATGTGAGCCCTTGTGGC-GGAACTTGTG
*
43553907 ATATGTGAGCCTTTGTG
1 ATATGTGAGCCCTTGTG
43553924 ACTGTTCTTT
Statistics
Matches: 98, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
26 2 0.02
27 14 0.14
28 18 0.18
29 33 0.34
30 31 0.32
ACGTcount: A:0.19, C:0.14, G:0.31, T:0.36
Consensus pattern (29 bp):
ATATGTGAGCCCTTGTGGCGGAACTTGTG
Found at i:43557163 original size:21 final size:21
Alignment explanation
Indices: 43557139--43557180 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
43557129 TTTTTTCATT
43557139 AATTGATTAACTA-AATGTTAA
1 AATTGATTAACTATAAT-TTAA
**
43557160 AATTTCTTAACTATAATTTAA
1 AATTGATTAACTATAATTTAA
43557181 TACGACTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (21 bp):
AATTGATTAACTATAATTTAA
Found at i:43563891 original size:16 final size:15
Alignment explanation
Indices: 43563870--43563899 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
43563860 GTTACCTCTC
43563870 ATTGAAATTAGTTAGG
1 ATTGAAATTA-TTAGG
43563886 ATTGAAATTATTAG
1 ATTGAAATTATTAG
43563900 TGTTTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (15 bp):
ATTGAAATTATTAGG
Found at i:43567424 original size:10 final size:11
Alignment explanation
Indices: 43567402--43567430 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
43567392 AAATTTTGTT
43567402 TTTTTAAAGAA
1 TTTTTAAAGAA
43567413 TTTTTAAA-AA
1 TTTTTAAAGAA
43567423 TTTTTAAA
1 TTTTTAAA
43567431 TAGTTATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (11 bp):
TTTTTAAAGAA
Found at i:43578767 original size:21 final size:21
Alignment explanation
Indices: 43578743--43578784 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
43578733 TTCTTTAGTG
43578743 TTACTATTTGACTTTGGATCA
1 TTACTATTTGACTTTGGATCA
*
43578764 TTACTGTTTGACTTTGGATCA
1 TTACTATTTGACTTTGGATCA
43578785 ATGCATCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (21 bp):
TTACTATTTGACTTTGGATCA
Found at i:43600218 original size:26 final size:26
Alignment explanation
Indices: 43600156--43600225 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 26
43600146 AAGATTTAAT
*
43600156 ATTAAATTTAATCTAATATTTATCAAG
1 ATTAAATTTAATTTAATATTTA-CAAG
*
43600183 ATTATA-TTAATTTAATA-TTA-AAGTG
1 ATTAAATTTAATTTAATATTTACAA--G
43600208 ATTAAATTTAATTATAAT
1 ATTAAATTTAATT-TAAT
43600226 TGAACTCCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 2 0.06
25 9 0.25
26 16 0.44
27 9 0.25
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (26 bp):
ATTAAATTTAATTTAATATTTACAAG
Found at i:43601886 original size:16 final size:17
Alignment explanation
Indices: 43601860--43601895 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
43601850 ATATCTTTCT
43601860 TTAATAATAAATTAAAA
1 TTAATAATAAATTAAAA
*
43601877 TTAA-AATAAATTAAGA
1 TTAATAATAAATTAAAA
43601893 TTA
1 TTA
43601896 TTTTTTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TTAATAATAAATTAAAA
Found at i:43613044 original size:15 final size:16
Alignment explanation
Indices: 43613024--43613056 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43613014 TGTAATTTTT
43613024 TTATAAA-ATTATATA
1 TTATAAACATTATATA
*
43613039 TTATAAACTTTATATA
1 TTATAAACATTATATA
43613055 TT
1 TT
43613057 TGGTGCAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATAAACATTATATA
Found at i:43618687 original size:25 final size:24
Alignment explanation
Indices: 43618659--43618755 Score: 83
Period size: 25 Copynumber: 3.9 Consensus size: 24
43618649 CAACTCGTAT
43618659 GAGCTTACCGATTTGCAGCTCGTGA
1 GAGCTTACCGATTT-CAGCTCGTGA
* *
43618684 GAGCTTATCGATTCTCAGCTTGT-A
1 GAGCTTACCGATT-TCAGCTCGTGA
* *
43618708 TGAGCTTACCGTTATTT-AGCTCGGGG
1 -GAGCTTACCG--ATTTCAGCTCGTGA
43618734 GAGCTTACC-ATTTACAGCTCGT
1 GAGCTTACCGATTT-CAGCTCGT
43618756 ATGAGCATAC
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
22 4 0.07
24 7 0.12
25 42 0.72
26 2 0.03
27 3 0.05
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.33
Consensus pattern (24 bp):
GAGCTTACCGATTTCAGCTCGTGA
Found at i:43618730 original size:50 final size:48
Alignment explanation
Indices: 43618647--43618761 Score: 126
Period size: 50 Copynumber: 2.3 Consensus size: 48
43618637 GCGGACATGC
* * *
43618647 TACAACTCGTATGAGCTTACCGATTTGCAGCTCGTGAGAGCTTATCGATT
1 TACAGCTCGTATGAGCTTACCGATTT-CAGCTCGGGAGAGCTTA-CCATT
* *
43618697 CT-CAGCTTGTATGAGCTTACCGTTATTT-AGCTCGGGGGAGCTTACCATT
1 -TACAGCTCGTATGAGCTTACCG--ATTTCAGCTCGGGAGAGCTTACCATT
43618746 TACAGCTCGTATGAGC
1 TACAGCTCGTATGAGC
43618762 ATACACGTAC
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
48 1 0.02
49 17 0.31
50 32 0.58
51 1 0.02
52 4 0.07
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (48 bp):
TACAGCTCGTATGAGCTTACCGATTTCAGCTCGGGAGAGCTTACCATT
Found at i:43619878 original size:12 final size:12
Alignment explanation
Indices: 43619861--43619891 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
43619851 CTCTAGTTTT
43619861 CACACGGCCTAG
1 CACACGGCCTAG
*
43619873 CACACGGCCTGG
1 CACACGGCCTAG
43619885 CACACGG
1 CACACGG
43619892 GCGTGTGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.42, G:0.29, T:0.06
Consensus pattern (12 bp):
CACACGGCCTAG
Found at i:43622834 original size:20 final size:20
Alignment explanation
Indices: 43622800--43622859 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
43622790 ATAATCAAGT
*
43622800 AAATTAAAA-ATTAAATTAA
1 AAATAAAAATATTAAATTAA
*
43622819 AAATAAAAATATTAAAATAA
1 AAATAAAAATATTAAATTAA
*
43622839 AAATAAAAATGACTAAATTAA
1 AAATAAAAAT-ATTAAATTAA
43622860 TAGAAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.23
20 19 0.54
21 8 0.23
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (20 bp):
AAATAAAAATATTAAATTAA
Found at i:43622867 original size:6 final size:6
Alignment explanation
Indices: 43622804--43622848 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
43622794 TCAAGTAAAT
* *
43622804 TAAAAA TTAAAT TAAAAA TAAAAA TATTAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA TA--AAAA TAAAAA TAAAAA T
43622849 GACTAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 27 0.82
8 6 0.18
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (6 bp):
TAAAAA
Found at i:43632563 original size:27 final size:27
Alignment explanation
Indices: 43632530--43632587 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
43632520 CCTTGGTCAC
*
43632530 GCCAATGGCATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
43632557 GCCAATGCCATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
43632584 GCCA
1 GCCA
43632588 TACTGATTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.22, C:0.29, G:0.31, T:0.17
Consensus pattern (27 bp):
GCCAATGCCATTGGCGGCACCAATGGT
Found at i:43632768 original size:19 final size:21
Alignment explanation
Indices: 43632730--43632768 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
43632720 AATAATTGAT
*
43632730 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
43632751 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
43632769 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:43632820 original size:3 final size:3
Alignment explanation
Indices: 43632814--43632880 Score: 107
Period size: 3 Copynumber: 22.3 Consensus size: 3
43632804 AAAATAATAG
* *
43632814 TAT TAT TAT TAT TAT TAC TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
43632862 TAT CAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
43632881 GTTGTTGTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:43632885 original size:3 final size:3
Alignment explanation
Indices: 43632879--43632925 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
43632869 ATTATTATTA
* *
43632879 TTG TTG TTG TTG TTG TTG TTG TTG TTG ATG CTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
43632926 AGTATTAAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.02, C:0.02, G:0.32, T:0.64
Consensus pattern (3 bp):
TTG
Found at i:43636042 original size:34 final size:34
Alignment explanation
Indices: 43636004--43636073 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
43635994 TATAAAAGGT
43636004 AATTGTATCCAAATTGTATACAGATTAAGTTATA
1 AATTGTATCCAAATTGTATACAGATTAAGTTATA
* *
43636038 AATTGTATCCAAATTGTTTCCAGATTAAGTTATA
1 AATTGTATCCAAATTGTATACAGATTAAGTTATA
43636072 AA
1 AA
43636074 ATACTATGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (34 bp):
AATTGTATCCAAATTGTATACAGATTAAGTTATA
Found at i:43638963 original size:27 final size:27
Alignment explanation
Indices: 43638888--43638955 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
43638878 TATTATCAAC
43638888 TGGTGCCGCCAATGGTATTGGCACCAT
1 TGGTGCCGCCAATGGTATTGGCACCAT
* *
43638915 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGTATTGGCACCAT
43638942 TGGTGCCGCCAATG
1 TGGTGCCGCCAATG
43638956 CCATTGGCGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.15, C:0.26, G:0.31, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAATGGTATTGGCACCAT
Found at i:43639045 original size:27 final size:28
Alignment explanation
Indices: 43639015--43639070 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
43639005 GTTTTTTTTG
43639015 ATATATTTTAGTAAAT-AAAAAAATTAT
1 ATATATTTTAGTAAATAAAAAAAATTAT
* *
43639042 ATATTTTTTGGTAAATAAAAAAAATTAT
1 ATATATTTTAGTAAATAAAAAAAATTAT
43639070 A
1 A
43639071 ACATTTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (28 bp):
ATATATTTTAGTAAATAAAAAAAATTAT
Found at i:43639077 original size:27 final size:27
Alignment explanation
Indices: 43639019--43639082 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
43639009 TTTTTGATAT
* *
43639019 ATTTTAGTAAATAAAAAAATTATATAT
1 ATTTTGGTAAATAAAAAAATTATATAC
*
43639046 TTTTTGGTAAATAAAAAAAATTATA-AC
1 ATTTTGGTAAAT-AAAAAAATTATATAC
43639073 ATTTTGGTAA
1 ATTTTGGTAA
43639083 TTTTTTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 20 0.62
28 12 0.38
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.41
Consensus pattern (27 bp):
ATTTTGGTAAATAAAAAAATTATATAC
Found at i:43642556 original size:23 final size:22
Alignment explanation
Indices: 43642513--43642570 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
43642503 AAAGGGTATC
* *
43642513 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
43642534 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
43642557 TGCATATCATATCT
1 TACAAATCATATCT
43642571 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:43644230 original size:17 final size:17
Alignment explanation
Indices: 43644189--43644243 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
43644179 ATTTAGGGTT
* * *
43644189 AAAGAAAAAGAAAAGAA
1 AAAGAAGAAGAAGAGGA
*
43644206 AGAAGAAGAAGATGAGGA
1 A-AAGAAGAAGAAGAGGA
*
43644224 AAAGAAGGAGAAGAGGA
1 AAAGAAGAAGAAGAGGA
43644241 AAA
1 AAA
43644244 TGAATACGCC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 18 0.58
18 13 0.42
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (17 bp):
AAAGAAGAAGAAGAGGA
Found at i:43644888 original size:23 final size:24
Alignment explanation
Indices: 43644849--43644894 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
43644839 AAAGAAAGAA
*
43644849 ACATTTGTATTTCTCAATTCTCAC
1 ACATTTGTATTTCTCAATACTCAC
43644873 ACATTTGT-TTTCTCAATACTCA
1 ACATTTGTATTTCTCAATACTCA
43644895 TATGTTAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.26, C:0.24, G:0.04, T:0.46
Consensus pattern (24 bp):
ACATTTGTATTTCTCAATACTCAC
Found at i:43646127 original size:28 final size:28
Alignment explanation
Indices: 43646087--43646140 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
43646077 CACACACACC
*
43646087 TAAAAAACGGTCACTACATGCATATTAT
1 TAAAAAACAGTCACTACATGCATATTAT
* * *
43646115 TAAAAAATAGTCATTGCATGCATATT
1 TAAAAAACAGTCACTACATGCATATT
43646141 CAAAAATAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (28 bp):
TAAAAAACAGTCACTACATGCATATTAT
Found at i:43646159 original size:26 final size:25
Alignment explanation
Indices: 43646112--43646160 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
43646102 ACATGCATAT
**
43646112 TATTAAAAAATAGTCATTGCATGCA
1 TATTAAAAAATAGTCACAGCATGCA
*
43646137 TATTCAAAAATAGTCAACAGCATG
1 TATTAAAAAATAGTC-ACAGCATG
43646161 TGACCATCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (25 bp):
TATTAAAAAATAGTCACAGCATGCA
Found at i:43646335 original size:78 final size:77
Alignment explanation
Indices: 43646131--43646380 Score: 315
Period size: 80 Copynumber: 3.2 Consensus size: 77
43646121 ATAGTCATTG
* * **
43646131 CATGCATATTCAAAAATAGTCAACAGCATGTGACCATCCCCACCAACAATCATACACACACACCT
1 CATGCATATTAAAAAATAGTCAACAGCATGTGACCATCCCCACCAACAATCATACACAGACAAAT
* *
43646196 AAAAAATAGTCACTG
66 TAAAAA-A--CACTA
* * *
43646211 CATGCATATTAAAAAATAGTCAATAGCATATGACCATCCCCTCCAACAATCAT-CAACAGACAAA
1 CATGCATATTAAAAAATAGTCAACAGCATGTGACCATCCCCACCAACAATCATAC-ACAGACAAA
43646275 TTAAAAAACACTA
65 TTAAAAAACACTA
* * * * *
43646288 CATGCATATTAAAAAAATAGTCAACAACATGTAACCAACCCCACCAACAATCATACATAGACAGA
1 CATGCATATT-AAAAAATAGTCAACAGCATGTGACCATCCCCACCAACAATCATACACAGACAAA
43646353 TTAAAAAA-ACTA
65 TTAAAAAACACTA
43646365 CATGCATATTAAAAAA
1 CATGCATATTAAAAAA
43646381 CATTCACTAA
Statistics
Matches: 150, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
76 6 0.04
77 28 0.19
78 52 0.35
79 3 0.02
80 61 0.41
ACGTcount: A:0.48, C:0.25, G:0.07, T:0.20
Consensus pattern (77 bp):
CATGCATATTAAAAAATAGTCAACAGCATGTGACCATCCCCACCAACAATCATACACAGACAAAT
TAAAAAACACTA
Found at i:43648428 original size:41 final size:41
Alignment explanation
Indices: 43648383--43648521 Score: 233
Period size: 41 Copynumber: 3.4 Consensus size: 41
43648373 GGCTATGTGC
*
43648383 CTAGCAGGCTTAATGCCGATGAAATATTTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTACGT
* *
43648424 CTAGCAGGCTTAATACCGGTGAAATATTTCAGAATTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTACGT
* *
43648465 CTAGCAGGCTTAATGCAGGTGAAATATTTCAGACTTTATGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTACGT
43648506 CTAGCAGGCTTAATGC
1 CTAGCAGGCTTAATGC
43648522 TTACATCTAG
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 91 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTACGT
Found at i:43648563 original size:63 final size:63
Alignment explanation
Indices: 43648459--43648584 Score: 216
Period size: 63 Copynumber: 2.0 Consensus size: 63
43648449 ATTTCAGAAT
*
43648459 TTACGTCTAGCAGGCTTAATGCAGGTGAAATATTTCAGACTTTATGTCTAGCAGGCTTAATGC
1 TTACATCTAGCAGGCTTAATGCAGGTGAAATATTTCAGACTTTATGTCTAGCAGGCTTAATGC
** *
43648522 TTACATCTAGCAGGCTTAATGCCTGTGAAATATTTCAGACTTTATGTCTAGTAGGCTTAATGC
1 TTACATCTAGCAGGCTTAATGCAGGTGAAATATTTCAGACTTTATGTCTAGCAGGCTTAATGC
43648585 CGATATTCTG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (63 bp):
TTACATCTAGCAGGCTTAATGCAGGTGAAATATTTCAGACTTTATGTCTAGCAGGCTTAATGC
Found at i:43648614 original size:104 final size:104
Alignment explanation
Indices: 43648418--43648619 Score: 237
Period size: 104 Copynumber: 1.9 Consensus size: 104
43648408 ATTTCAGACT
*
43648418 TTACGTCTAGCAGGCTTAATACCGGTGAAATATTTCAGAATTTACGTCTAGCAGGCTTAATGCAG
1 TTACATCTAGCAGGCTTAATACCGGTGAAATATTTCAGAATTTACGTCTAGCAGGCTTAATGCAG
* * * * *
43648483 GTGAAATATTTCAGACTTTATGTCTAGCAGGCTTAATGC
66 ATGAAATATATCAGACTTCAAGCCTAGCAGGCTTAATGC
* * * * * *
43648522 TTACATCTAGCAGGCTTAATGCCTGTGAAATATTTCAGACTTTATGTCTAGTAGGCTTAATGCCG
1 TTACATCTAGCAGGCTTAATACCGGTGAAATATTTCAGAATTTACGTCTAGCAGGCTTAATGCAG
* * *
43648587 AT--ATTCTGAATCAGTCTTCAAGCCTAGCAGGCT
66 ATGAAATAT--ATCAGACTTCAAGCCTAGCAGGCT
43648620 ACATGCCGGT
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
102 3 0.04
104 78 0.96
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (104 bp):
TTACATCTAGCAGGCTTAATACCGGTGAAATATTTCAGAATTTACGTCTAGCAGGCTTAATGCAG
ATGAAATATATCAGACTTCAAGCCTAGCAGGCTTAATGC
Found at i:43648791 original size:2 final size:2
Alignment explanation
Indices: 43648784--43648812 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43648774 GATATTGATG
43648784 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
43648813 GTATTCGATG
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:43652649 original size:28 final size:27
Alignment explanation
Indices: 43652590--43652647 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
43652580 ACATTAATAA
43652590 TAAATAAAACCAAAATCGAAAAAACAC
1 TAAATAAAACCAAAATCGAAAAAACAC
* *
43652617 TAAATCAAAATCAAAATCGAAATAAC-C
1 TAAAT-AAAACCAAAATCGAAAAAACAC
43652644 TAAA
1 TAAA
43652648 ATAACCCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 10 0.36
28 18 0.64
ACGTcount: A:0.64, C:0.17, G:0.03, T:0.16
Consensus pattern (27 bp):
TAAATAAAACCAAAATCGAAAAAACAC
Found at i:43652664 original size:16 final size:17
Alignment explanation
Indices: 43652645--43652681 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
43652635 GAAATAACCT
43652645 AAAATAACCCTAAAT-C
1 AAAATAACCCTAAATCC
43652661 AAAATAACCCTAAATCC
1 AAAATAACCCTAAATCC
43652678 AAAA
1 AAAA
43652682 AATAAAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.59, C:0.24, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAATAACCCTAAATCC
Found at i:43653078 original size:21 final size:21
Alignment explanation
Indices: 43653052--43653092 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
43653042 CAACGTGACA
43653052 AGTTAACTGGCCACAGCAGCT
1 AGTTAACTGGCCACAGCAGCT
* *
43653073 AGTTAACTTGCCACATCAGC
1 AGTTAACTGGCCACAGCAGC
43653093 GGTCCCGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (21 bp):
AGTTAACTGGCCACAGCAGCT
Found at i:43664179 original size:22 final size:20
Alignment explanation
Indices: 43664145--43664187 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
43664135 TAAACGCAAA
43664145 ATTAAACAAATTCATAATTAAC
1 ATTAAACAAATTC-T-ATTAAC
**
43664167 ATTAAACTTATTCTATTAAC
1 ATTAAACAAATTCTATTAAC
43664187 A
1 A
43664188 AAATCATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 1 0.05
22 11 0.58
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (20 bp):
ATTAAACAAATTCTATTAAC
Found at i:43675292 original size:25 final size:26
Alignment explanation
Indices: 43675239--43675297 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
43675229 AAAAATAATT
43675239 AAAATATTATAATTTTTTTATTTACC
1 AAAATATTATAATTTTTTTATTTACC
*
43675265 AAAATATTATAATTTTTTTATTTACA
1 AAAATATTATAATTTTTTTATTTACC
43675291 AAAATAT
1 AAAATAT
43675298 ACCAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (26 bp):
AAAATATTATAATTTTTTTATTTACC
Found at i:43675385 original size:27 final size:27
Alignment explanation
Indices: 43675355--43675454 Score: 119
Period size: 27 Copynumber: 3.7 Consensus size: 27
43675345 CCTGGTCGTA
* *
43675355 CCAAGGTGATTGGCGGCACCAAAGTTG
1 CCAAAGTGATTGGCGGCACCAAAGGTG
43675382 CCAAAGTGATTGGCGGCACCAAAGGTG
1 CCAAAGTGATTGGCGGCACCAAAGGTG
** * * *
43675409 CCAAAGACATTGGAGACACCAATGGTG
1 CCAAAGTGATTGGCGGCACCAAAGGTG
* *
43675436 CCATACTGATTGGCGGCAC
1 CCAAAGTGATTGGCGGCAC
43675455 TACTCGTGTT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.29, C:0.24, G:0.30, T:0.17
Consensus pattern (27 bp):
CCAAAGTGATTGGCGGCACCAAAGGTG
Found at i:43675629 original size:19 final size:21
Alignment explanation
Indices: 43675591--43675629 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
43675581 AATAATTGAT
*
43675591 TATATTGTTGTTATTGTTTTG
1 TATATTGTTGTTATTATTTTG
43675612 TATATT-TTG-TATTATTTT
1 TATATTGTTGTTATTATTTT
43675630 TTGTTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.69
Consensus pattern (21 bp):
TATATTGTTGTTATTATTTTG
Found at i:43675683 original size:3 final size:3
Alignment explanation
Indices: 43675675--43675731 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
43675665 ATAGTTTTAG
43675675 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43675723 TTA TTA TTA
1 TTA TTA TTA
43675732 AGGTATTAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:43681684 original size:37 final size:37
Alignment explanation
Indices: 43681633--43681779 Score: 163
Period size: 37 Copynumber: 3.9 Consensus size: 37
43681623 TTTTTTTTCT
*
43681633 TCCTTCCCTCTTCTTCTTCTTCTTTTTTTTTCTCTTC
1 TCCTTTCCTCTTCTTCTTCTTCTTTTTTTTTCTCTTC
* * *
43681670 TCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTTTTCTTC
1 TCCTTTCCTCTTC-TT-CTTCTTCTT-TTT-TTTTCTCTTC
*
43681711 TCCTTTCCTCTTCTTCTTCTT-TCTTTTTTTTCCCTTC
1 TCCTTTCCTCTTCTTCTTCTTCT-TTTTTTTTCTCTTC
* * *
43681748 TCCTTTCCTTTTCTT-TCCTTCTTTTTCTTTCT
1 TCCTTTCCTCTTCTTCTTCTTCTTTTTTTTTCT
43681780 TTCCTCTCCT
Statistics
Matches: 93, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
36 12 0.13
37 34 0.37
38 6 0.06
39 15 0.16
40 5 0.05
41 21 0.23
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (37 bp):
TCCTTTCCTCTTCTTCTTCTTCTTTTTTTTTCTCTTC
Found at i:43681691 original size:36 final size:37
Alignment explanation
Indices: 43681613--43681807 Score: 161
Period size: 37 Copynumber: 5.2 Consensus size: 37
43681603 ATAAAATTTA
* * *
43681613 CCTT-TTTTTCTTTT-TTTTCTTCCTTCCCTCTTCTTCT
1 CCTTCTTTTTCTTTTCTCTTC-TCCTTTCCTTTTCTT-T
*
43681650 TCTTCTTTTT-TTTTCTCTTCTCCTTTCCTTTTCTTT
1 CCTTCTTTTTCTTTTCTCTTCTCCTTTCCTTTTCTTT
* *
43681686 CCTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTC-TT
1 CCTTC---TT-TTTCTTTTCTCTTCTCCTTTCCTTTTCTTT
* *
43681726 -CTTCTTTCTTTTTTTTCCCTTCTCCTTTCCTTTTCTTT
1 CCTTC-TT-TTTCTTTTCTCTTCTCCTTTCCTTTTCTTT
* *
43681764 CCTTCTTTTTCTTTCTTTCCTCTCCTTT-C-TTTCTTT
1 CCTTCTTTTTCTTT-TCTCTTCTCCTTTCCTTTTCTTT
*
43681800 CTTTCTTT
1 CCTTCTTT
43681808 CTTTCCCCCA
Statistics
Matches: 132, Mismatches: 16, Indels: 21
0.78 0.09 0.12
Matches are distributed among these distances:
36 19 0.14
37 54 0.41
38 23 0.17
39 10 0.08
40 5 0.04
41 21 0.16
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (37 bp):
CCTTCTTTTTCTTTTCTCTTCTCCTTTCCTTTTCTTT
Found at i:43681700 original size:4 final size:4
Alignment explanation
Indices: 43681679--43681812 Score: 72
Period size: 4 Copynumber: 34.0 Consensus size: 4
43681669 CTCCTTTCCT
*
43681679 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC TTCTCC TTTCC TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C T-TTC
* * * *
43681724 -TTC -TTC TTTC TTT- TTT- TTCC CTTC -TCC TTTCC TTTTC TTTC CTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C -TTTC TTTC TTTC
*
43681769 -TT- TTTC TTTC TTTCC TCTCC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC TTTC
43681813 CCCCAACAAC
Statistics
Matches: 106, Mismatches: 9, Indels: 30
0.73 0.06 0.21
Matches are distributed among these distances:
3 24 0.23
4 61 0.58
5 12 0.11
6 9 0.08
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:43681741 original size:78 final size:78
Alignment explanation
Indices: 43681615--43681781 Score: 277
Period size: 78 Copynumber: 2.2 Consensus size: 78
43681605 AAAATTTACC
*
43681615 TTTT-TTTCTTTTTTTTCTTCCTTCCCTCTTCTTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCCT
1 TTTTCTTTCTTTTTTTTCTTCCTTCCCTCTTCTTCTTCTTCTTTTTTTTTCCCTTCTCCTTTCCT
43681679 TTTCTTTCCTTCT
66 TTTCTTTCCTTCT
*
43681692 TTTTCTTTCTTTTTTCTTC-TCCTTTCCTCTTCTTCTTCTT-TCTTTTTTTTCCCTTCTCCTTTC
1 TTTTCTTTCTTTTTT-TTCTTCCTTCCCTCTTCTTCTTCTTCT-TTTTTTTTCCCTTCTCCTTTC
43681755 CTTTTCTTTCCTTCT
64 CTTTTCTTTCCTTCT
43681770 TTTTCTTTCTTT
1 TTTTCTTTCTTT
43681782 CCTCTCCTTT
Statistics
Matches: 85, Mismatches: 2, Indels: 5
0.92 0.02 0.05
Matches are distributed among these distances:
77 5 0.06
78 77 0.91
79 3 0.04
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (78 bp):
TTTTCTTTCTTTTTTTTCTTCCTTCCCTCTTCTTCTTCTTCTTTTTTTTTCCCTTCTCCTTTCCT
TTTCTTTCCTTCT
Found at i:43681765 original size:10 final size:10
Alignment explanation
Indices: 43681672--43681808 Score: 61
Period size: 10 Copynumber: 14.5 Consensus size: 10
43681662 TTCTCTTCTC
43681672 CTTTCCTTTT
1 CTTTCCTTTT
43681682 CTTTCCTTCTT
1 CTTTCCTT-TT
43681693 -TTT-C-TTT
1 CTTTCCTTTT
43681700 C-TT--TTTT
1 CTTTCCTTTT
*
43681707 CTTCTCCTTTC
1 CTT-TCCTTTT
43681718 CTCTT-CTTCTT
1 CT-TTCCTT-TT
43681729 CTTT-CTTTT
1 CTTTCCTTTT
* *
43681738 TTTTCCCTTCTC
1 CTTT-CCTT-TT
43681750 CTTTCCTTTT
1 CTTTCCTTTT
43681760 CTTTCCTTCTT
1 CTTTCCTT-TT
43681771 -TTT-C-TTT
1 CTTTCCTTTT
* *
43681778 CTTTCCTCTC
1 CTTTCCTTTT
43681788 CTTT-C-TTT
1 CTTTCCTTTT
43681796 CTTT-C-TTT
1 CTTTCCTTTT
43681804 CTTTC
1 CTTTC
43681809 TTTCCCCCAA
Statistics
Matches: 100, Mismatches: 10, Indels: 35
0.69 0.07 0.24
Matches are distributed among these distances:
7 10 0.10
8 19 0.19
9 10 0.10
10 36 0.36
11 20 0.20
12 5 0.05
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:43681806 original size:78 final size:77
Alignment explanation
Indices: 43681613--43681811 Score: 270
Period size: 78 Copynumber: 2.6 Consensus size: 77
43681603 ATAAAATTTA
* * *
43681613 CCTT-TTTTTCTTT-TTTTTCT-TCCTTCCCTCTTCTTCTTC-TTCTTTTTTTTTCTCTTCTCCT
1 CCTTCTTTTTCTTTCTTTTCCTCTCCTTTCCTCTTCTTCTTCTTTCTTTTTTTTTCCCTTCTCCT
43681674 TTCCTTTTCTTT
66 TTCCTTTTCTTT
*
43681686 CCTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTCTTCTTCTTTC-TTTTTTTTCCCTTCTC
1 CCTTCTTTTTCTTTC--TTTTCCTCTCCTTTCCTCTTCTTCTTCTTTCTTTTTTTTTCCCTTCTC
43681750 CTTTCCTTTTCTTT
64 CTTTCCTTTTCTTT
43681764 CCTTCTTTTTCTTTC-TTTCCTCTCCTTT-CT-TTCTTTCTTTCTTTCTTT
1 CCTTCTTTTTCTTTCTTTTCCTCTCCTTTCCTCTTC-TTC-TTCTTTCTTT
43681812 CCCCCAACAA
Statistics
Matches: 112, Mismatches: 5, Indels: 15
0.85 0.04 0.11
Matches are distributed among these distances:
73 7 0.06
74 14 0.12
75 19 0.17
76 2 0.02
77 5 0.04
78 62 0.55
79 3 0.03
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (77 bp):
CCTTCTTTTTCTTTCTTTTCCTCTCCTTTCCTCTTCTTCTTCTTTCTTTTTTTTTCCCTTCTCCT
TTCCTTTTCTTT
Found at i:43681881 original size:27 final size:27
Alignment explanation
Indices: 43681843--43681921 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
43681833 TATTATAACA
*
43681843 TTGGTGCCGCCAATGTCTTTGGCACCT
1 TTGGTGCCGCCAATGACTTTGGCACCT
43681870 TTGGTGCCGCCAATGACTTTGGCACCT
1 TTGGTGCCGCCAATGACTTTGGCACCT
* *
43681897 TTGGTGCCGCCAATCACCTTGGCAC
1 TTGGTGCCGCCAATGACTTTGGCAC
43681922 GACCAGTGTG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.14, C:0.32, G:0.25, T:0.29
Consensus pattern (27 bp):
TTGGTGCCGCCAATGACTTTGGCACCT
Found at i:43682009 original size:27 final size:27
Alignment explanation
Indices: 43681978--43682038 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
43681968 TGTTTCTGGT
43681978 ATATTTTGGTAAATAAAAAAAATTATA
1 ATATTTTGGTAAATAAAAAAAATTATA
* *
43682005 TTATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAATTATA
43682032 ATATTTT
1 ATATTTT
43682039 AGTTATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAATTATA
Found at i:43685741 original size:160 final size:158
Alignment explanation
Indices: 43685434--43685757 Score: 490
Period size: 161 Copynumber: 2.0 Consensus size: 158
43685424 TGGGTGGCCA
* *
43685434 AAATGAAAGTGTAATTATACTGTGGAGTGTATAATTAACCTTCGTTAGAGATATAATAGTTGAAT
1 AAATGAAAGTGTAAATATACTGTGGAGTGTACAATTAACCTTCGTTAGAGATATAATAGTTGAAT
** * *
43685499 GATTAAAATGAAAGCGCCTTAAAAGTTGGGTGACGAAATTACAAGAATTTTATTTTGAGTGGCCA
66 GATTAAAATGAAA-CGAATTAAAAGTTGGGTGACGAAATTACAAGAATTTCATTTTGAGTGACCA
43685564 AAATGAAAGTACACTAAAAGTGATGTGACC
130 AAATGAAAGTACACTAAAAGTGAT-TGACC
* * *
43685594 ACAATGAAAGTGTAAATATGA-TGTGGAGTGTACAGTTAACTTTTGTTAGAGATATAATAGTTGA
1 A-AATGAAAGTGTAAATAT-ACTGTGGAGTGTACAATTAACCTTCGTTAGAGATATAATAGTTGA
*
43685658 ATGATTAAAATGAAA-GAATGTAAAAGTTGGGTGACGAAATTGCAAGAATTTCATTTTGAGTGAC
64 ATGATTAAAATGAAACGAAT-TAAAAGTTGGGTGACGAAATTACAAGAATTTCATTTTGAGTGAC
*
43685722 CAAAATGAAAGTGCACTAAAAGTGATTGACC
128 CAAAATGAAAGTACACTAAAAGTGATTGACC
43685753 AAATG
1 AAATG
43685758 GGTAGTTTAC
Statistics
Matches: 150, Mismatches: 11, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
158 4 0.03
159 8 0.05
160 67 0.45
161 70 0.47
162 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (158 bp):
AAATGAAAGTGTAAATATACTGTGGAGTGTACAATTAACCTTCGTTAGAGATATAATAGTTGAAT
GATTAAAATGAAACGAATTAAAAGTTGGGTGACGAAATTACAAGAATTTCATTTTGAGTGACCAA
AATGAAAGTACACTAAAAGTGATTGACC
Found at i:43696545 original size:2 final size:2
Alignment explanation
Indices: 43696538--43696567 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
43696528 CTCACTTGTG
*
43696538 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43696568 ATCTTGTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43700286 original size:14 final size:14
Alignment explanation
Indices: 43700263--43700296 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
43700253 TGGTATGGGT
43700263 TTAT-GGGTTTTAG
1 TTATAGGGTTTTAG
*
43700276 TTATAGGGTTTTGG
1 TTATAGGGTTTTAG
43700290 TTATAGG
1 TTATAGG
43700297 CAAATGATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTAG
Found at i:43700872 original size:13 final size:14
Alignment explanation
Indices: 43700848--43700876 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
43700838 GTCACTAAAC
43700848 TATTTAAAATTATT
1 TATTTAAAATTATT
43700862 TATTT-AAATTATT
1 TATTTAAAATTATT
43700875 TA
1 TA
43700877 CTGGGTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTAAAATTATT
Found at i:43702328 original size:13 final size:13
Alignment explanation
Indices: 43702308--43702346 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
43702298 ATCTTTTTAA
43702308 TATTATTTAATTT
1 TATTATTTAATTT
*
43702321 TTTTATTTTAATTT
1 TATTA-TTTAATTT
*
43702335 TATAATTTAATT
1 TATTATTTAATT
43702347 AAACCCTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTATTTAATTT
Found at i:43702455 original size:365 final size:364
Alignment explanation
Indices: 43701779--43702471 Score: 954
Period size: 365 Copynumber: 1.9 Consensus size: 364
43701769 CAAAAAAACT
*
43701779 CTCAAAGCTCTCTAAATTTTTTATTTGTCTAAATTATTAATATTTTTTTATAATTTCTAAGAAAT
1 CTCAAAGCTCTCTAAATTTTTTATTTGTCTAAATTATTAATATTTTTTTATAATTTCTAAAAAAT
** * * * * *
43701844 TTGATCGTGTTAGCAATGGCCTAACAATTAATTCATTTTGATAATAAACATATCTCCATCGACAA
66 TAAATCGTGTTAACAATAGCCCAACAATTAATTCATCTTGATAATAAACATATCTCCATCAACAA
* * *
43701909 AATGAAAATGATAAGAGTTAATTTTATTTTTTAACATTATTTAATTTTTTTATTTTATTTTTATA
131 AATGAAAATGATAAGAGTTAAATTCATTTTTTAACATTATTTAATTTTTTTATTTTAATTTTATA
* *
43701974 ACTTAATTAAATCTTAAACCCTAATCAAACCCAAAAACCCTAAACCTAGACCCTAATTACCAAAT
196 ACTTAATTAAACCCTAAACCCTAATCAAACCCAAAAACCCTAAACCTAGACCCTAATTACCAAAT
* * * * * *
43702039 AATCCACTGGAGATTACACAGCTAAAAGCGCATCCACATTAGAATGCTTTTGCCTGACACAAGGA
261 AATCCACTGAAGATTACACAGCCAAAAACACATCCACATCAGAACGCTTTTGCCTGACACAA-GA
43702104 AAAAAAATGTTGACTTGAAAGCATTTTTCTAAGTTATCCC
325 AAAAAAATGTTGACTTGAAAGCATTTTTCTAAGTTATCCC
* *
43702144 CTCAAAGCTCTCTAAAATTTTTT-TTTGTTTGAATTATT-AT-TTTCTTTTATAATTT-TAAAAA
1 CTCAAAGCTCTCT-AAATTTTTTATTTGTCTAAATTATTAATATTT-TTTTATAATTTCT-AAAA
* * * **
43702205 AATTAAATTGTGTTAACAATAGCCCAACAATTAATTCATCTTGATGATAAACATATTTCTGTCAA
63 AATTAAATCGTGTTAACAATAGCCCAACAATTAATTCATCTTGATAATAAACATATCTCCATCAA
* *
43702270 CCAAATGAAAATGATAA-AGGTTAAATTCATCTTTTTAATATTATTTAATTTTTTTATTTTAATT
128 CAAAATGAAAATGATAAGA-GTTAAATTCAT-TTTTTAACATTATTTAATTTTTTTATTTTAATT
* *
43702334 TTATAATTTAATTAAACCCTGAACCC-ATATCAAACCCAAAAACCCTAAACCTA-AGCCCTAATT
191 TTATAACTTAATTAAACCCTAAACCCTA-ATCAAACCCAAAAACCCTAAACCTAGA-CCCTAATT
*
43702397 AGCAAATAATCCACTGAAGATTACAC-GACCAAAAACACATCCACATCA-AAGCGCTTTTGCCTG
254 ACCAAATAATCCACTGAAGATTACACAG-CCAAAAACACATCCACATCAGAA-CGCTTTTGCCTG
43702460 ACACAAGAAAAA
317 ACACAAGAAAAA
43702472 GTACTGACAT
Statistics
Matches: 288, Mismatches: 31, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
363 5 0.02
364 105 0.36
365 169 0.59
366 9 0.03
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.36
Consensus pattern (364 bp):
CTCAAAGCTCTCTAAATTTTTTATTTGTCTAAATTATTAATATTTTTTTATAATTTCTAAAAAAT
TAAATCGTGTTAACAATAGCCCAACAATTAATTCATCTTGATAATAAACATATCTCCATCAACAA
AATGAAAATGATAAGAGTTAAATTCATTTTTTAACATTATTTAATTTTTTTATTTTAATTTTATA
ACTTAATTAAACCCTAAACCCTAATCAAACCCAAAAACCCTAAACCTAGACCCTAATTACCAAAT
AATCCACTGAAGATTACACAGCCAAAAACACATCCACATCAGAACGCTTTTGCCTGACACAAGAA
AAAAAATGTTGACTTGAAAGCATTTTTCTAAGTTATCCC
Found at i:43702689 original size:57 final size:57
Alignment explanation
Indices: 43702579--43702754 Score: 322
Period size: 57 Copynumber: 3.1 Consensus size: 57
43702569 AAACGGCCCA
*
43702579 CTTCCATAAATAATTTCAAAAATGAG---CCTTTATTGATACTAAACCCTATTTAAG
1 CTTCCATAAATAATTTCAGAAATGAGCCTCCTTTATTGATACTAAACCCTATTTAAG
43702633 CTTCCATAAATAATTTCAGAAATGAGCCTCCTTTATTGATACTAAACCCTATTTAAG
1 CTTCCATAAATAATTTCAGAAATGAGCCTCCTTTATTGATACTAAACCCTATTTAAG
43702690 CTTCCATAAATAATTTCAGAAATGAGCCTCCTTTATTGATACTAAACCCTATTTAAG
1 CTTCCATAAATAATTTCAGAAATGAGCCTCCTTTATTGATACTAAACCCTATTTAAG
43702747 CTTCCATA
1 CTTCCATA
43702755 CATGTAATTC
Statistics
Matches: 118, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
54 25 0.21
57 93 0.79
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (57 bp):
CTTCCATAAATAATTTCAGAAATGAGCCTCCTTTATTGATACTAAACCCTATTTAAG
Found at i:43709312 original size:56 final size:53
Alignment explanation
Indices: 43709181--43709322 Score: 144
Period size: 57 Copynumber: 2.5 Consensus size: 53
43709171 ATATTTTTTG
*
43709181 GGGTGCTGGGACACTAATGGTCGGCA-CCTCTATACCCGATTTAAAAAAAAATT
1 GGGTGCT-GGACACTAATGGTCGGCACCCTCTATACCAGATTTAAAAAAAAATT
*
43709234 GTTTGAGTGCTGTGACACTAATGGTCGGCACCCTC-GTACCAGATTTGGAAAAAAAAACTT
1 G---G-GTGCTG-GACACTAATGGTCGGCACCCTCTATACCAGATTT--AAAAAAAAA-TT
* *
43709294 GGGTGCTAGGACACTAATGGCCGACACCC
1 GGGTGCT-GGACACTAATGGTCGGCACCC
43709323 CTTCAATATA
Statistics
Matches: 75, Mismatches: 4, Indels: 17
0.78 0.04 0.18
Matches are distributed among these distances:
53 1 0.01
56 25 0.33
57 33 0.44
58 4 0.05
59 9 0.12
60 3 0.04
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (53 bp):
GGGTGCTGGACACTAATGGTCGGCACCCTCTATACCAGATTTAAAAAAAAATT
Done.