Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 51 of 198
Found at i:15272814 original size:49 final size:50
Alignment explanation
Indices: 15272695--15272828 Score: 234
Period size: 50 Copynumber: 2.7 Consensus size: 50
15272685 AAAGCTTTGG
* **
15272695 TCACGTATGTAGTACTATGTGAAGGCTACTACGTGAGTTGTAAAACTTGA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTGTAAAACTTGA
15272745 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTGTAAAAC-TGA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTGTAAAACTTGA
15272794 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
15272829 TATCGAATGA
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
49 38 0.47
50 43 0.53
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTGTAAAACTTGA
Found at i:15281176 original size:23 final size:23
Alignment explanation
Indices: 15281146--15281192 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
15281136 ACTTTATGTA
15281146 ATATTAATCAGCTCAGGAATTGG
1 ATATTAATCAGCTCAGGAATTGG
*
15281169 ATATTAATCAGCTCGGGAATTGG
1 ATATTAATCAGCTCAGGAATTGG
15281192 A
1 A
15281193 CGGAGTCAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (23 bp):
ATATTAATCAGCTCAGGAATTGG
Found at i:15290441 original size:138 final size:138
Alignment explanation
Indices: 15290193--15290756 Score: 821
Period size: 138 Copynumber: 4.1 Consensus size: 138
15290183 TAGATAAAAG
* * *
15290193 AATTATATTATTTCCAAAAGAATATTAATGTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACTGAAATTAATTAA
* * * *
15290258 TATAATTATTTATATTAATAAATTTCG-TAAAATATATACAATTAATATTTTTTATGAATTAAAT
66 TATAACTATTTATAGTAATAAA-TTCGATAAAATATATACAATTAATATTTTGTATGAATCAAAT
15290322 TCATATATT
130 TCATATATT
15290331 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGA-TCGAAATTAATTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACT-GAAATTAATTA
* *
15290395 ATATAACTATTTATAGTACTAAATTCGATAAAATATATACGATTAATATTTTGTATGAATCAAAT
65 ATATAACTATTTATAGTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAAT
15290460 TCATATATT
130 TCATATATT
* * * *
15290469 AACTATATT-TTTCCAAAAGAATATTAATTTCCATGTCATTTATATTTTCACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACTGAAATTAATTAA
* * * * *
15290533 TATAAGTGTTTATATTAATAAATTCGGTAAAATATATA-AATTACTATTTTGTATGAATCAAATT
66 TATAACTATTTATAGTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
*
15290597 CAGATATT
131 CATATATT
* * * * *
15290605 AATTATATTCTTTCTAAAATAATATTAATTTTCATGTATTTTATAGTTTGACTGGAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACTGAAATTAATTAA
* * * *
15290670 CATCACTGTTTATAGTAATAAATTCAATAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTATTTATAGTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
*
15290735 CATATACT
131 CATATATT
15290743 AATTATATTCTTTC
1 AATTATATTCTTTC
15290757 TTCTCTATTT
Statistics
Matches: 382, Mismatches: 39, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
136 39 0.10
137 166 0.43
138 177 0.46
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.45
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACTGAAATTAATTAA
TATAACTATTTATAGTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:15290694 original size:274 final size:276
Alignment explanation
Indices: 15290196--15290756 Score: 853
Period size: 274 Copynumber: 2.0 Consensus size: 276
15290186 ATAAAAGAAT
* *
15290196 TATATTATTTCCAAAAGAATATTAATGTTCATGTCTTTTATATTTTGACCGAAATTAATTAATAT
1 TATATTATTTCCAAAAGAATATTAATGTTCATGTCATTTATATTTTCACCGAAATTAATTAATAT
* * * *
15290261 AATTATTTATATTAATAAATTTCGTAAAATATATACAATTAATATTTTTTATGAATTAAATTCAT
66 AAGTATTTATATTAATAAATTTCGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCAG
* *
15290326 ATATTAATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGATCGAAATTA
131 ATATTAATTATATTCTTTCCAAAAGAATATTAATTTTCATGTATTTTATAGTTTGATCGAAATTA
* * * *
15290391 ATTAATATAACTATTTATAGTACTAAATTCGATAAAATATATACGATTAATATTTTGTATGAATC
196 ATTAACATAACTATTTATAGTAATAAATTCAATAAAATATATACAATTAATATTTTGTATGAATC
*
15290456 AAATTCATATATTAAC
261 AAATTCATATACTAAC
*
15290472 TATATT-TTTCCAAAAGAATATTAAT-TTCCATGTCATTTATATTTTCACTGAAATTAATTAATA
1 TATATTATTTCCAAAAGAATATTAATGTT-CATGTCATTTATATTTTCACCGAAATTAATTAATA
* *
15290535 TAAGTGTTTATATTAATAAA-TTCGGTAAAATATATA-AATTACTATTTTGTATGAATCAAATTC
65 TAAGTATTTATATTAATAAATTTC-GTAAAATATATACAATTAATATTTTGTATGAATCAAATTC
* * *
15290598 AGATATTAATTATATTCTTTCTAAAATAATATTAATTTTCATGTATTTTATAGTTTGA-CTGGAA
129 AGATATTAATTATATTCTTTCCAAAAGAATATTAATTTTCATGTATTTTATAGTTTGATC-GAAA
* *
15290662 TTAATTAACATCACTGTTTATAGTAATAAATTCAATAAAATATATACAATTAATATTTTGTATGA
193 TTAATTAACATAACTATTTATAGTAATAAATTCAATAAAATATATACAATTAATATTTTGTATGA
*
15290727 ATCAAATTCATATACTAAT
258 ATCAAATTCATATACTAAC
*
15290746 TATATTCTTTC
1 TATATTATTTC
15290757 TTCTCTATTT
Statistics
Matches: 259, Mismatches: 22, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
273 1 0.00
274 167 0.64
275 85 0.33
276 6 0.02
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.45
Consensus pattern (276 bp):
TATATTATTTCCAAAAGAATATTAATGTTCATGTCATTTATATTTTCACCGAAATTAATTAATAT
AAGTATTTATATTAATAAATTTCGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCAG
ATATTAATTATATTCTTTCCAAAAGAATATTAATTTTCATGTATTTTATAGTTTGATCGAAATTA
ATTAACATAACTATTTATAGTAATAAATTCAATAAAATATATACAATTAATATTTTGTATGAATC
AAATTCATATACTAAC
Found at i:15307512 original size:27 final size:26
Alignment explanation
Indices: 15307471--15307523 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
15307461 AATGAAAAGG
*
15307471 GGGGTTGCTATGTGCTGATTCCTCCGA
1 GGGGTTGCTAAGTGCTGATTCC-CCGA
15307498 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
15307524 TTCATTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.13, C:0.23, G:0.34, T:0.30
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:15307756 original size:102 final size:102
Alignment explanation
Indices: 15307431--15307748 Score: 575
Period size: 101 Copynumber: 3.1 Consensus size: 102
15307421 CCCGAGGGGT
* *
15307431 TGCTAAGTGCGATATCCACCATATCTTTGAAATGAAAAGGGGGGTTGCTATGTGCTGATTCCTCC
1 TGCTAAGTGCGATATCCA-CATATCTTTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
15307496 GAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGG
64 GAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGG
15307535 TGCTAAGTGCGATATCCACATATCTTTG-AATAAAAAGGGGGTTGCTATGTGCTGATTCCCCCGA
1 TGCTAAGTGCGATATCCACATATCTTTGAAATAAAAAGGGGGTTGCTATGTGCTGATTCCCCCGA
15307599 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGG
66 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGG
15307636 TGCTAAGTGCGATATCCACATATCTTTGAAATAAAAAGGGGGTTGCTATGTGCTGATTCCCCCGA
1 TGCTAAGTGCGATATCCACATATCTTTGAAATAAAAAGGGGGTTGCTATGTGCTGATTCCCCCGA
* *
15307701 GGGGTTGCTAAGTGCTGATTCTCCGATTCAGTGGTGG
66 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGG
15307738 TGCTAAGTGCG
1 TGCTAAGTGCG
15307749 GGATCCACCA
Statistics
Matches: 209, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
101 96 0.46
102 85 0.41
103 10 0.05
104 18 0.09
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.31
Consensus pattern (102 bp):
TGCTAAGTGCGATATCCACATATCTTTGAAATAAAAAGGGGGTTGCTATGTGCTGATTCCCCCGA
GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGG
Found at i:15313571 original size:26 final size:26
Alignment explanation
Indices: 15313535--15313586 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
15313525 AAAACAAGAA
*
15313535 TGAACCCGTAACAAAGGTTAAGGACC
1 TGAACCAGTAACAAAGGTTAAGGACC
*
15313561 TGAACCAGTAACAAATGTTAAGGACC
1 TGAACCAGTAACAAAGGTTAAGGACC
15313587 CGATTCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (26 bp):
TGAACCAGTAACAAAGGTTAAGGACC
Found at i:15342638 original size:24 final size:24
Alignment explanation
Indices: 15342591--15342639 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
15342581 TACATTAATA
* *
15342591 AGAGTTTGACTAGGAAAAATAATC
1 AGAGTTTAACTAGGAAAAAAAATC
15342615 AGAGTTTAACTA-GAAGAAAAAATC
1 AGAGTTTAACTAGGAA-AAAAAATC
15342639 A
1 A
15342640 AGAAAATTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.51, C:0.08, G:0.18, T:0.22
Consensus pattern (24 bp):
AGAGTTTAACTAGGAAAAAAAATC
Found at i:15343634 original size:86 final size:86
Alignment explanation
Indices: 15343527--15343701 Score: 341
Period size: 86 Copynumber: 2.0 Consensus size: 86
15343517 ATAATAACAA
15343527 ATTGAAGATTTTTATAAAATTATAATCATAATACTAATTAGAAAATTAGTTAAAATTAATAACAA
1 ATTGAAGATTTTTATAAAATTATAATCATAATACTAATTAGAAAATTAGTTAAAATTAATAACAA
15343592 CATACAAATAGAAAGTGAAGC
66 CATACAAATAGAAAGTGAAGC
*
15343613 ATTGAAGATTTTTATAAAATTATAATCATAATACTAATTAGAAAATTAGTTAAAATTAATAATAA
1 ATTGAAGATTTTTATAAAATTATAATCATAATACTAATTAGAAAATTAGTTAAAATTAATAACAA
15343678 CATACAAATAGAAAGTGAAGC
66 CATACAAATAGAAAGTGAAGC
15343699 ATT
1 ATT
15343702 CATATTAGAC
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 88 1.00
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (86 bp):
ATTGAAGATTTTTATAAAATTATAATCATAATACTAATTAGAAAATTAGTTAAAATTAATAACAA
CATACAAATAGAAAGTGAAGC
Found at i:15343863 original size:16 final size:18
Alignment explanation
Indices: 15343842--15343880 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
15343832 TAGCTCAAAC
*
15343842 TATAAAAACT-TTATT-A
1 TATAAAAAATATTATTGA
15343858 TATAAAAAATATTATTGA
1 TATAAAAAATATTATTGA
15343876 TATAA
1 TATAA
15343881 TTTTATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 5 0.25
18 6 0.30
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (18 bp):
TATAAAAAATATTATTGA
Found at i:15344169 original size:24 final size:24
Alignment explanation
Indices: 15344130--15344176 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
15344120 TTCTAATAAG
* *
15344130 TAATAACCTCCCTTTGTTGAATGC
1 TAATAACCTCCATTTGTCGAATGC
*
15344154 TAATAACTTCCATTTGTCGAATG
1 TAATAACCTCCATTTGTCGAATG
15344177 TTATTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (24 bp):
TAATAACCTCCATTTGTCGAATGC
Found at i:15345494 original size:56 final size:56
Alignment explanation
Indices: 15345408--15345522 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
15345398 AACTCTATTT
15345408 TGATTTGCTAAATTTCAGATTCTAAGGCCACCAAAGTCTGTTGGCTTACAACGATC
1 TGATTTGCTAAATTTCAGATTCTAAGGCCACCAAAGTCTGTTGGCTTACAACGATC
15345464 TGATTTGCTAAATTTCAGATTCTAAGGCCACCAAAGTCTGTTGGCTTACAACGATC
1 TGATTTGCTAAATTTCAGATTCTAAGGCCACCAAAGTCTGTTGGCTTACAACGATC
15345520 TGA
1 TGA
15345523 CCAATTCAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (56 bp):
TGATTTGCTAAATTTCAGATTCTAAGGCCACCAAAGTCTGTTGGCTTACAACGATC
Found at i:15349725 original size:25 final size:25
Alignment explanation
Indices: 15349697--15349745 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
15349687 ATATAGTTTT
*
15349697 TATATTAT-TTATAAATGTTATAATA
1 TATATTATATTAT-AATATTATAATA
15349722 TATATTATATTATAATATTATAAT
1 TATATTATATTATAATATTATAAT
15349746 TAAATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TATATTATATTATAATATTATAATA
Found at i:15350205 original size:41 final size:41
Alignment explanation
Indices: 15350142--15350240 Score: 128
Period size: 41 Copynumber: 2.4 Consensus size: 41
15350132 ATATGATTTT
* * * *
15350142 AGCACTAAATGTGAG-AATTAAATGATGAGGTTGAATAACA
1 AGCACTAAGTGTGCGAAATTAAATAATGAGGTTAAATAACA
* *
15350182 AGCACTAAGTGTGCGAAATTAAATAATGATGTTAAATAACG
1 AGCACTAAGTGTGCGAAATTAAATAATGAGGTTAAATAACA
*
15350223 GGCACTAAGTGTGCGAAA
1 AGCACTAAGTGTGCGAAA
15350241 CTGAGATTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 13 0.25
41 38 0.75
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.24
Consensus pattern (41 bp):
AGCACTAAGTGTGCGAAATTAAATAATGAGGTTAAATAACA
Found at i:15353324 original size:44 final size:43
Alignment explanation
Indices: 15353224--15353325 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 43
15353214 GTTAGTTCAT
* * **
15353224 TTAAATATGATTCATATGAATTTGACATGGATAACCATTATAC
1 TTAAACATGATTCATAGGAATTAAACATGGATAACCATTATAC
* * * *
15353267 TTGAGCATAATTCATAGGCAATTAAACATGGATAGCCATTATAC
1 TTAAACATGATTCATAGG-AATTAAACATGGATAACCATTATAC
15353311 TTAAACATGATTCAT
1 TTAAACATGATTCAT
15353326 TTGGATTTGT
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
43 13 0.28
44 34 0.72
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (43 bp):
TTAAACATGATTCATAGGAATTAAACATGGATAACCATTATAC
Found at i:15363368 original size:22 final size:21
Alignment explanation
Indices: 15363340--15363397 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
15363330 ATGCAATCGC
* *
15363340 AGATATGATATGTAATCTTAG
1 AGATATGATTTGTAATCATAG
15363361 AAGATATGATTTTGTAATCATAG
1 -AGATATGA-TTTGTAATCATAG
*
15363384 AGATTTGATTTGTA
1 AGATATGATTTGTA
15363398 GATACCTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.19
22 15 0.47
23 11 0.34
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.41
Consensus pattern (21 bp):
AGATATGATTTGTAATCATAG
Found at i:15373463 original size:2 final size:2
Alignment explanation
Indices: 15373458--15373542 Score: 161
Period size: 2 Copynumber: 42.5 Consensus size: 2
15373448 AAAGTAAAAG
15373458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
15373500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15373542 A
1 A
15373543 CCAGCAATAT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15374320 original size:21 final size:20
Alignment explanation
Indices: 15374294--15374350 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 20
15374284 TATTATAGAA
15374294 ATATATATAAAATATAAGTAT
1 ATATATATAAAATATAAG-AT
* * *
15374315 ATATATATATATTATCAGAT
1 ATATATATAAAATATAAGAT
*
15374335 ATA-ATAAAAAATATAA
1 ATATATATAAAATATAA
15374351 ACATGTATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
19 9 0.31
20 5 0.17
21 15 0.52
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (20 bp):
ATATATATAAAATATAAGAT
Found at i:15374460 original size:2 final size:2
Alignment explanation
Indices: 15374243--15374441 Score: 135
Period size: 2 Copynumber: 102.0 Consensus size: 2
15374233 AGGTGTATTG
** *
15374243 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GG AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
15374285 AT -T AT AG AA AT AT AT AT A- AA AT AT A- AGT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * * * * * *
15374325 AT -T AT CAG AT AT A- AT A- AA AA AT AT AA AC AT GT AT TT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
15374365 AT TT AT GA- AA AT -T AA AG AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
15374406 AT AT AT AT AT AT AT AT AT AG AT AT AT GT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15374442 GTGTAAGTTA
Statistics
Matches: 154, Mismatches: 32, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
1 8 0.05
2 143 0.93
3 3 0.02
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.43
Consensus pattern (2 bp):
AT
Found at i:15374696 original size:3 final size:3
Alignment explanation
Indices: 15374682--15374762 Score: 60
Period size: 3 Copynumber: 27.3 Consensus size: 3
15374672 GAATGAGTAG
* *
15374682 ATA ATT ATA ATA ATA ATA A-A GTA AGTA ATA ATA ATA A-A TATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA -ATA ATA
* * * * *
15374727 CTA ATA ATA GTA ATA GTA GTA GTA ATA AT- ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
15374763 ATAGAAGGGA
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
2 4 0.06
3 55 0.87
4 4 0.06
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:15374712 original size:18 final size:17
Alignment explanation
Indices: 15374688--15374741 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
15374678 GTAGATAATT
15374688 ATAATAATAATAAAGTA
1 ATAATAATAATAAAGTA
15374705 AGTAATAATAATAAA-T-
1 A-TAATAATAATAAAGTA
*
15374721 ATAATACTAATAATAGTA
1 ATAATAATAATAA-AGTA
15374739 ATA
1 ATA
15374742 GTAGTAGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 11 0.34
16 2 0.06
17 3 0.09
18 16 0.50
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (17 bp):
ATAATAATAATAAAGTA
Found at i:15375281 original size:9 final size:8
Alignment explanation
Indices: 15375242--15375277 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
15375232 ATGCAGCCGC
15375242 AAAAAATA
1 AAAAAATA
15375250 AAAAAATA
1 AAAAAATA
15375258 AAAAAATA
1 AAAAAATA
15375266 AAAGAAATA
1 AAA-AAATA
15375275 AAA
1 AAA
15375278 GAAAGAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (8 bp):
AAAAAATA
Found at i:15375565 original size:2 final size:2
Alignment explanation
Indices: 15375560--15375592 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15375550 ATATTCTTAT
15375560 AC AC AC 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 AC AC AC A
15375593 TATATATATG
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:15376442 original size:41 final size:41
Alignment explanation
Indices: 15376388--15376488 Score: 141
Period size: 41 Copynumber: 2.5 Consensus size: 41
15376378 GTTCCACTGT
* * *
15376388 AACTTCGGGGAGATAAGGTTTGATATGATCTACTCTACTA-C
1 AACTTCAGAGAGATAAGATTTGATATGATCTACTCTAC-AGC
* *
15376429 AACTTCAGAGAGATAAGATTTGATATGATCTGCTCTACAGT
1 AACTTCAGAGAGATAAGATTTGATATGATCTACTCTACAGC
15376470 AACTTCAGAGAGATAAGAT
1 AACTTCAGAGAGATAAGAT
15376489 CTGTGGCTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 1 0.02
41 53 0.98
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.30
Consensus pattern (41 bp):
AACTTCAGAGAGATAAGATTTGATATGATCTACTCTACAGC
Found at i:15377096 original size:89 final size:89
Alignment explanation
Indices: 15377003--15377299 Score: 264
Period size: 89 Copynumber: 3.4 Consensus size: 89
15376993 ATTTTTTATT
* * * *
15377003 TGCTTCACTACCAGTATAGGAAGACAATATCTGTTATTTTCAGTCTGCTCTACTGCAAACTCAGG
1 TGCTTCACTGCCAGTATAGGAAGACAAGATCTGTAATTTTCAGTCTGCTCCACTGCAAACTCAGG
**
15377068 GAGGCGAGGCTTGTGTCTTCGATC
66 GAGGTAAGGCTTGTGTCTTCGATC
* ** ** ** * *
15377092 TGCTTCACTGCC-GATACAGGAAGACAAGATCTACAATTTTCAACCTATTCCACTG-ATACTGAG
1 TGCTTCACTGCCAG-TATAGGAAGACAAGATCTGTAATTTTCAGTCTGCTCCACTGCAAACTCAG
* ** *
15377155 GGAGATAAGGC-T-ACTCTTTGATC
65 GGAGGTAAGGCTTGTGTCTTCGATC
* ** * *
15377178 TGCTTCACTGCCAGTATAGGAAGACAAGATCCGCTGCTTTT-AGTCTGCTCCGCTGCAAACTCAA
1 TGCTTCACTGCCAGTATAGGAAGACAAGATCTG-TAATTTTCAGTCTGCTCCACTGCAAACTCAG
* *
15377242 GGAAGTTAGGCTTGTGTCTTCGATC
65 GGAGGTAAGGCTTGTGTCTTCGATC
* * *
15377267 TGTTTCACCGTC-GATATAGGAAGACAAGATCTG
1 TGCTTCACTGCCAG-TATAGGAAGACAAGATCTG
15377300 CTGCTTTTAG
Statistics
Matches: 158, Mismatches: 43, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
86 45 0.28
87 19 0.12
88 17 0.11
89 77 0.49
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (89 bp):
TGCTTCACTGCCAGTATAGGAAGACAAGATCTGTAATTTTCAGTCTGCTCCACTGCAAACTCAGG
GAGGTAAGGCTTGTGTCTTCGATC
Found at i:15377547 original size:15 final size:15
Alignment explanation
Indices: 15377507--15377547 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
15377497 TAACTAGGTG
15377507 TGTATGAATGATATT
1 TGTATGAATGATATT
*
15377522 TGCATTGAATGATATT
1 TGTA-TGAATGATATT
15377538 TGTATGAATG
1 TGTATGAATG
15377548 TAGAATGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.44
Consensus pattern (15 bp):
TGTATGAATGATATT
Found at i:15378744 original size:60 final size:60
Alignment explanation
Indices: 15378610--15378812 Score: 243
Period size: 59 Copynumber: 3.4 Consensus size: 60
15378600 GTCTCAAGGT
* * * ** *
15378610 GCCCTTTGCGGGTTTTCACCTTGGCCTCTCCTT-TTTT-TTTTCTTTTTTTGACTCAAAGC
1 GCCCTTTGCAGGTTTTCACCTTGGTCTTTTTTTCTTTTCTTTTC-TTTTTTGACCCAAAGC
* * *
15378669 GCTCTTTGCAAGTTTTCACCTTGGTCTTTTTTTCTTTTCTTTTCTTTTTTGACCCAATGC
1 GCCCTTTGCAGGTTTTCACCTTGGTCTTTTTTTCTTTTCTTTTCTTTTTTGACCCAAAGC
* * *
15378729 GCCCTTTGTAGGTTTTCACCTTGGT-TTTTTTTCTTTTCTTTTTTTTTTTGACCCAAGGC
1 GCCCTTTGCAGGTTTTCACCTTGGTCTTTTTTTCTTTTCTTTTCTTTTTTGACCCAAAGC
*
15378788 GCCCTTTG-TGGATTTTCACCTTGGT
1 GCCCTTTGCAGG-TTTTCACCTTGGT
15378813 TTCTTCCTTT
Statistics
Matches: 126, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
58 2 0.02
59 79 0.63
60 40 0.32
61 5 0.04
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (60 bp):
GCCCTTTGCAGGTTTTCACCTTGGTCTTTTTTTCTTTTCTTTTCTTTTTTGACCCAAAGC
Found at i:15383370 original size:23 final size:23
Alignment explanation
Indices: 15383342--15383389 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
15383332 AAAGAAAGAA
*
15383342 ATAAAAAAATG-AATAAGAT-TAT
1 ATAAAAAAAAGTAA-AAGATATAT
15383364 ATAAAAAAAAGTAAAAGATATAT
1 ATAAAAAAAAGTAAAAGATATAT
15383387 ATA
1 ATA
15383390 TATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (23 bp):
ATAAAAAAAAGTAAAAGATATAT
Found at i:15383386 original size:2 final size:2
Alignment explanation
Indices: 15383381--15383412 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
15383371 AAAGTAAAAG
15383381 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
15383413 GCATATAAAA
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:15383824 original size:3 final size:3
Alignment explanation
Indices: 15383810--15383887 Score: 54
Period size: 3 Copynumber: 26.3 Consensus size: 3
15383800 GAATGAGTAG
* * *
15383810 ATA ATT ATA ATA ATA ATA A-A GTA AGTA ATA ATA A-A TATA ATA CTA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA -ATA ATA ATA
* * * *
15383855 ATA ATA GTA ATA GTA GTA GTA ATA AT- ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
15383888 ATAAAAGGGA
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
2 4 0.07
3 52 0.87
4 4 0.07
ACGTcount: A:0.58, C:0.01, G:0.08, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:15384352 original size:8 final size:8
Alignment explanation
Indices: 15384307--15384345 Score: 78
Period size: 8 Copynumber: 4.9 Consensus size: 8
15384297 TATGCAGCTG
15384307 AAAAAAAT
1 AAAAAAAT
15384315 AAAAAAAT
1 AAAAAAAT
15384323 AAAAAAAT
1 AAAAAAAT
15384331 AAAAAAAT
1 AAAAAAAT
15384339 AAAAAAA
1 AAAAAAA
15384346 AATAAAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:15384366 original size:24 final size:22
Alignment explanation
Indices: 15384306--15384366 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
15384296 ATATGCAGCT
*
15384306 GAAAAAAATAAAAAAATAAAAAAA
1 GAAAAAAA-AAAAAAA-AATAAAA
*
15384330 TAAAAAAATAAAAAAAAATAAAA
1 GAAAAAAA-AAAAAAAAATAAAA
* *
15384353 GAAAGAAAGAAAAA
1 GAAAAAAAAAAAAA
15384367 GAGACCCCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 5 0.16
23 12 0.38
24 15 0.47
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.08
Consensus pattern (22 bp):
GAAAAAAAAAAAAAAAATAAAA
Found at i:15388445 original size:21 final size:21
Alignment explanation
Indices: 15388419--15388465 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
15388409 GTGGCTTAAA
15388419 CGTAAAGGAATG-TCTTTGTGG
1 CGTAAAGGAATGCT-TTTGTGG
**
15388440 CGTAAAGGGGTGCTTTTGTGG
1 CGTAAAGGAATGCTTTTGTGG
15388461 CGTAA
1 CGTAA
15388466 TCGTAAAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.21, C:0.11, G:0.36, T:0.32
Consensus pattern (21 bp):
CGTAAAGGAATGCTTTTGTGG
Found at i:15388486 original size:27 final size:27
Alignment explanation
Indices: 15388456--15388518 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
15388446 GGGGTGCTTT
*
15388456 TGTGGCGTAATCGTAAAGG-AATGCCTC
1 TGTGGCATAATCGT-AAGGAAATGCCTC
*
15388483 TGTGGCATAATTGTAAGGAAATGCCT-
1 TGTGGCATAATCGTAAGGAAATGCCTC
15388509 TAGTGGCATA
1 T-GTGGCATA
15388519 GTATGAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 5 0.16
27 27 0.84
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (27 bp):
TGTGGCATAATCGTAAGGAAATGCCTC
Found at i:15390275 original size:32 final size:31
Alignment explanation
Indices: 15390234--15390302 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
15390224 TTTTTTAGAA
15390234 TTTAAAAAATTA-AAAAAATAAATAAAAATATT
1 TTTAAAAAA-TAGAAAAAATAAA-AAAAATATT
**
15390266 TTTAAAAAATAGAAATTATAAAAAAAATATT
1 TTTAAAAAATAGAAAAAATAAAAAAAATATT
15390297 TTTAAA
1 TTTAAA
15390303 TTTTTTTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 17 0.50
32 17 0.50
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (31 bp):
TTTAAAAAATAGAAAAAATAAAAAAAATATT
Found at i:15392436 original size:79 final size:79
Alignment explanation
Indices: 15392305--15392460 Score: 312
Period size: 79 Copynumber: 2.0 Consensus size: 79
15392295 CCTCTTCTCT
15392305 AATGTGGACTGATGTCGAAGGAAAAACGATCTCATGTAGACTAGTCGATGATTGAACTATACCTG
1 AATGTGGACTGATGTCGAAGGAAAAACGATCTCATGTAGACTAGTCGATGATTGAACTATACCTG
15392370 CATAAAACAATGTG
66 CATAAAACAATGTG
15392384 AATGTGGACTGATGTCGAAGGAAAAACGATCTCATGTAGACTAGTCGATGATTGAACTATACCTG
1 AATGTGGACTGATGTCGAAGGAAAAACGATCTCATGTAGACTAGTCGATGATTGAACTATACCTG
15392449 CATAAAACAATG
66 CATAAAACAATG
15392461 ATCAACTTCT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.25
Consensus pattern (79 bp):
AATGTGGACTGATGTCGAAGGAAAAACGATCTCATGTAGACTAGTCGATGATTGAACTATACCTG
CATAAAACAATGTG
Found at i:15394745 original size:3 final size:3
Alignment explanation
Indices: 15394730--15394831 Score: 123
Period size: 3 Copynumber: 33.7 Consensus size: 3
15394720 AAAAGGTATT
* * **
15394730 TAA TAA TAT TAA TAA TGA TGC TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* **
15394778 TAA TAA TAA TAA TAA TAA TAA TAG TTT TAA TAA TAA TATA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
*
15394824 AAA TAA TA
1 TAA TAA TA
15394832 GCATATATTA
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
3 82 0.96
4 3 0.04
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:15394888 original size:10 final size:9
Alignment explanation
Indices: 15394869--15394938 Score: 50
Period size: 10 Copynumber: 6.9 Consensus size: 9
15394859 ATATATAAAG
15394869 ATAAATAAAA
1 ATAAA-AAAA
15394879 ATATAAAAAA
1 ATA-AAAAAA
*
15394889 ATAAAAATTA
1 ATAAAAA-AA
*
15394899 ATAGTTAAAAA
1 ATA--AAAAAA
15394910 ATAAAATAAA
1 ATAAAA-AAA
15394920 ATAAAATAAA
1 ATAAAA-AAA
15394930 ATAACAAAA
1 ATAA-AAAA
15394939 GGGATTAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
9 6 0.12
10 33 0.66
11 8 0.16
12 3 0.06
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:15394892 original size:20 final size:19
Alignment explanation
Indices: 15394859--15394938 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 19
15394849 GTACACACAT
* *
15394859 ATATATAAAGATAAATAAAA
1 ATATAAAAAAATAAA-AAAA
*
15394879 ATATAAAAAAATAAAAATTA
1 ATATAAAAAAATAAAAA-AA
*
15394899 ATAGTTAAAAAATAAAATAAA
1 ATA-TAAAAAAATAAAA-AAA
15394920 ATA-AAATAAAATAACAAAA
1 ATATAAA-AAAATAA-AAAA
15394939 GGGATTAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
19 4 0.08
20 26 0.53
21 18 0.37
22 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.23
Consensus pattern (19 bp):
ATATAAAAAAATAAAAAAA
Found at i:15394917 original size:5 final size:5
Alignment explanation
Indices: 15394907--15394933 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
15394897 TAATAGTTAA
15394907 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
15394934 CAAAAGGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:15394922 original size:21 final size:20
Alignment explanation
Indices: 15394871--15394933 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
15394861 ATATAAAGAT
15394871 AAATAAAAATATAAAAAAATA
1 AAAT-AAAATATAAAAAAATA
* *
15394892 AAA-ATTAATAGTTAAAAAATA
1 AAATA-AAATA-TAAAAAAATA
15394913 AAATAAAATA-AAATAAAATA
1 AAATAAAATATAAA-AAAATA
15394933 A
1 A
15394934 CAAAAGGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
19 3 0.09
20 11 0.32
21 19 0.56
22 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (20 bp):
AAATAAAATATAAAAAAATA
Found at i:15396154 original size:9 final size:9
Alignment explanation
Indices: 15396137--15396173 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
15396127 TGAGTTTTCG
15396137 AATTCGAAT
1 AATTCGAAT
*
15396146 AACTCGAAT
1 AATTCGAAT
15396155 AATTCGAAT
1 AATTCGAAT
15396164 AATTCGAAT
1 AATTCGAAT
15396173 A
1 A
15396174 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:15396435 original size:30 final size:31
Alignment explanation
Indices: 15396387--15396446 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
15396377 AAACCTTTTA
*
15396387 TTTTCTCCCAAAATTTTTACT-CCTTTCCAC
1 TTTTCTCCCAAAACTTTTACTCCCTTTCCAC
*
15396417 TTTTC-CCCTAAAACTTTTATTCCCTTTCCA
1 TTTTCTCCC-AAAACTTTTACTCCCTTTCCA
15396447 TCTCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 15 0.58
31 8 0.31
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (31 bp):
TTTTCTCCCAAAACTTTTACTCCCTTTCCAC
Found at i:15396599 original size:20 final size:20
Alignment explanation
Indices: 15396563--15396600 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
15396553 TTATTCTCCA
*
15396563 AAACTTTTTATTTTCGCCCT
1 AAACTTTTTATTCTCGCCCT
15396583 AAAC-TTTTACTTCTCGCC
1 AAACTTTTTA-TTCTCGCC
15396601 GTTTACTGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.21, C:0.29, G:0.05, T:0.45
Consensus pattern (20 bp):
AAACTTTTTATTCTCGCCCT
Found at i:15397843 original size:89 final size:89
Alignment explanation
Indices: 15397667--15398365 Score: 998
Period size: 89 Copynumber: 7.9 Consensus size: 89
15397657 ATTGTTTTTT
* * * *
15397667 GATCTGCTTCGCTGCCAGTACAGGGAGGCATGATCTGGTATCTTCAGTGTGCTCCGCTG-CA-AA
1 GATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGCCAGTA
* *
15397730 CTCAGAAAGGCAAGGCTGGTGTCTTC
66 C-AAG-GAGGCAAGGCTGGTGTCTTC
* * **
15397756 GATCT-CTTTGCTGCCAGTATAGGAAGGCATGATCTGCTATCTTCAGTCTAGCTCCGCTGTTAGT
1 GATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCT-GCTCCGCTGCCAGT
15397820 ACAAGGAGGCAAGGCTGGTGTCTTC
65 ACAAGGAGGCAAGGCTGGTGTCTTC
** * * * *
15397845 GATCTGCTTTACTGCCAGTACAGGAAGGCAAGATATGCTATCTTTAGTTTGCTCCGCTGCCAGTA
1 GATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGCCAGTA
*
15397910 TAA-GAGGGCAAGGCTGGTGTCTTC
66 CAAGGA-GGCAAGGCTGGTGTCTTC
* *
15397934 GATCTGCTTCACTGCCAGTACAAGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGCCAGTA
1 GATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGCCAGTA
* *
15397999 CAGGGAGGCAAGGCTAGTGTCTTC
66 CAAGGAGGCAAGGCTGGTGTCTTC
* *
15398023 GATCTGCTTCGCTGCCAGTACAGGAAGGCGTGACCTGCTATCTTCAGTCTGCTCCGCTGCCAGTA
1 GATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGCCAGTA
*
15398088 CAGGGAGGCAAGGCTGGTGTCTTC
66 CAAGGAGGCAAGGCTGGTGTCTTC
* * * *
15398112 GATCTGCTTCGCTACCAGTACAGGGAGGCATGATCTGGTATCTTCAGTGTGCTCCGCTGCCAGTA
1 GATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGCCAGTA
15398177 C-AGGAGGCAAGGCTGGTG-CTTC
66 CAAGGAGGCAAGGCTGGTGTCTTC
* * *
15398199 GATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGTTCTGCTGTCAGTA
1 GATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGCCAGTA
15398264 C-AGAGAGGCAAGGCTGGTGTCTTC
66 CAAG-GAGGCAAGGCTGGTGTCTTC
* *
15398288 GATCTGCTTCGCTGCCAGTACAGGAAGGTAAGATCTGCTATCTTCAGTCTGCTCCGCTGCCAGTA
1 GATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGCCAGTA
*
15398353 CAGGGAGGCAAGG
66 CAAGGAGGCAAGG
15398366 TTGAAATCTT
Statistics
Matches: 549, Mismatches: 52, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
87 65 0.12
88 72 0.13
89 366 0.67
90 44 0.08
91 2 0.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (89 bp):
GATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGCCAGTA
CAAGGAGGCAAGGCTGGTGTCTTC
Found at i:15397865 original size:44 final size:44
Alignment explanation
Indices: 15397667--15398365 Score: 450
Period size: 45 Copynumber: 15.8 Consensus size: 44
15397657 ATTGTTTTTT
* * * *
15397667 GATCTGCTTCGCTGCCAGTACAGGGAGGCATGATCTGGTATCTTC
1 GATCTGCTTCGCTGCCAGTACAAGGAGGCAAG-GCTGGTGTCTTC
* * * * *
15397712 -AGTGTGCTCCGCTG-CA-AACTCAGAAAGGCAAGGCTGGTGTCTTC
1 GA-TCTGCTTCGCTGCCAGTAC-AAG-GAGGCAAGGCTGGTGTCTTC
* * * * * *
15397756 GATCT-CTTTGCTGCCAGTA-TAGGAAGGCATGATCTGCTATCTTC
1 GATCTGCTTCGCTGCCAGTACAAGG-AGGCAAG-GCTGGTGTCTTC
* **
15397800 -AGTCTAGCTCCGCTGTTAGTACAAGGAGGCAAGGCTGGTGTCTTC
1 GA-TCT-GCTTCGCTGCCAGTACAAGGAGGCAAGGCTGGTGTCTTC
** ** * *
15397845 GATCTGCTTTACTGCCAGTAC-AGGAAGGCAAGATATGCTATCTT-
1 GATCTGCTTCGCTGCCAGTACAAGG-AGGCAAG-GCTGGTGTCTTC
* * * *
15397889 TAGTTTGCTCCGCTGCCAGTATAA-GAGGGCAAGGCTGGTGTCTTC
1 GA-TCTGCTTCGCTGCCAGTACAAGGA-GGCAAGGCTGGTGTCTTC
* * * * * *
15397934 GATCTGCTTCACTGCCAGTACAAGAAGGCATGATCTGCTATCTTC
1 GATCTGCTTCGCTGCCAGTACAAGGAGGCAAG-GCTGGTGTCTTC
* * *
15397979 -AGTCTGCTCCGCTGCCAGTACAGGGAGGCAAGGCTAGTGTCTTC
1 GA-TCTGCTTCGCTGCCAGTACAAGGAGGCAAGGCTGGTGTCTTC
** * * *
15398023 GATCTGCTTCGCTGCCAGTAC-AGGAAGGCGTGACCTGCTATCTTC
1 GATCTGCTTCGCTGCCAGTACAAGG-AGGCAAG-GCTGGTGTCTTC
* *
15398068 -AGTCTGCTCCGCTGCCAGTACAGGGAGGCAAGGCTGGTGTCTTC
1 GA-TCTGCTTCGCTGCCAGTACAAGGAGGCAAGGCTGGTGTCTTC
* * * * *
15398112 GATCTGCTTCGCTACCAGTACAGGGAGGCATGATCTGGTATCTTC
1 GATCTGCTTCGCTGCCAGTACAAGGAGGCAAG-GCTGGTGTCTTC
* *
15398157 -AGTGTGCTCCGCTGCCAGTAC-AGGAGGCAAGGCTGGTG-CTTC
1 GA-TCTGCTTCGCTGCCAGTACAAGGAGGCAAGGCTGGTGTCTTC
* * * *
15398199 GATCTGCTTCGCTGCCAGTAC-AGGAAGGCATGATCTGCTATCTTC
1 GATCTGCTTCGCTGCCAGTACAAGG-AGGCAAG-GCTGGTGTCTTC
*
15398244 -AGTCTG-TTCTGCTGTCAGTAC-AGAGAGGCAAGGCTGGTGTCTTC
1 GA-TCTGCTTC-GCTGCCAGTACAAG-GAGGCAAGGCTGGTGTCTTC
* * * *
15398288 GATCTGCTTCGCTGCCAGTAC-AGGAAGGTAAGATCTGCTATCTTC
1 GATCTGCTTCGCTGCCAGTACAAGG-AGGCAAG-GCTGGTGTCTTC
* *
15398333 -AGTCTGCTCCGCTGCCAGTACAGGGAGGCAAGG
1 GA-TCTGCTTCGCTGCCAGTACAAGGAGGCAAGG
15398366 TTGAAATCTT
Statistics
Matches: 498, Mismatches: 113, Indels: 87
0.71 0.16 0.12
Matches are distributed among these distances:
42 24 0.05
43 35 0.07
44 197 0.40
45 216 0.43
46 23 0.05
47 3 0.01
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (44 bp):
GATCTGCTTCGCTGCCAGTACAAGGAGGCAAGGCTGGTGTCTTC
Found at i:15398469 original size:45 final size:45
Alignment explanation
Indices: 15398419--15398510 Score: 85
Period size: 45 Copynumber: 2.0 Consensus size: 45
15398409 CTAGTGCTTC
* * *
15398419 CGATCTGCTTCACTGCCAGTACAAGAAGGTAAGATCTGCTATCTT
1 CGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTT
* * * * * ** *
15398464 CGATCTACTTCACTACTAATACAGGAAGATAAGATCTGCTATATT
1 CGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTT
15398509 CG
1 CG
15398511 CCGATTTGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (45 bp):
CGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTT
Found at i:15403243 original size:15 final size:15
Alignment explanation
Indices: 15403223--15403251 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
15403213 TGTGGAGATA
15403223 TAAAAATTTAAAATT
1 TAAAAATTTAAAATT
15403238 TAAAAATTTAAAAT
1 TAAAAATTTAAAAT
15403252 ACAAAACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAAATTTAAAATT
Found at i:15403257 original size:15 final size:15
Alignment explanation
Indices: 15403224--15403257 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
15403214 GTGGAGATAT
**
15403224 AAAAATTTAAAATTT
1 AAAAATTTAAAATAC
15403239 AAAAATTTAAAATAC
1 AAAAATTTAAAATAC
15403254 AAAA
1 AAAA
15403258 CATGATGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATTTAAAATAC
Found at i:15404558 original size:3 final size:3
Alignment explanation
Indices: 15404543--15404618 Score: 66
Period size: 3 Copynumber: 25.7 Consensus size: 3
15404533 AAAAGGTATT
* ** * **
15404543 TAA TAA TAT TAA TAA TAA TGC TAA TAA TAA TAA TAA TAA TAG TTT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
15404591 TAA TAA TATA TAA GAA TAA -AA -AA TAA TA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA
15404619 GCACATATTA
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
2 4 0.07
3 51 0.88
4 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:15404682 original size:16 final size:17
Alignment explanation
Indices: 15404648--15404715 Score: 56
Period size: 16 Copynumber: 4.2 Consensus size: 17
15404638 ACACACATAT
*
15404648 ATATAAAGATAAATGAAA
1 ATATAAATATAAAT-AAA
15404666 ATATAAATA-AAATAAA
1 ATATAAATATAAATAAA
* *
15404682 A-ATTAATAGTTAA-AAA
1 ATATAAATA-TAAATAAA
15404698 A-ATAAATA-AAATAAA
1 ATATAAATATAAATAAA
15404713 ATA
1 ATA
15404716 AAAAAATGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 2 0.05
15 10 0.24
16 15 0.37
17 6 0.15
18 8 0.20
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (17 bp):
ATATAAATATAAATAAA
Found at i:15407091 original size:39 final size:40
Alignment explanation
Indices: 15407047--15407143 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 40
15407037 CACTTTTAAA
*
15407047 CATATATCACAATACTCATATAATCACAT-AACATTCAAG
1 CATATATCACAATACTCAGATAATCACATAAACATTCAAG
*
15407086 CATATATCACTAGT-CTCAGATAATCACATAAACATTCAAG
1 CATATATCAC-AATACTCAGATAATCACATAAACATTCAAG
15407126 CATATATCACAATACTCA
1 CATATATCACAATACTCA
15407144 AAAACATGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
39 26 0.50
40 26 0.50
ACGTcount: A:0.44, C:0.24, G:0.04, T:0.28
Consensus pattern (40 bp):
CATATATCACAATACTCAGATAATCACATAAACATTCAAG
Found at i:15415535 original size:18 final size:17
Alignment explanation
Indices: 15415512--15415564 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
15415502 ATATATTATG
*
15415512 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATT-ATAT
15415530 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
15415547 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
15415565 TTGATAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:15415756 original size:39 final size:43
Alignment explanation
Indices: 15415711--15415816 Score: 139
Period size: 46 Copynumber: 2.5 Consensus size: 43
15415701 TTTCCTTATG
* *
15415711 CTATTACACCTCTATTCCATTCA-A-CCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCATAGCCAAACAAAAGAATTAC
15415751 C-ATTACGCCTCTATTCCATTTCATTCAGCCAAACAAAAGAATTAC
1 CTATTACGCCTCTATTCCA-TTCA-T-AGCCAAACAAAAGAATTAC
15415796 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
15415817 ACGCATCTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
39 16 0.28
40 5 0.09
43 1 0.02
44 12 0.21
45 6 0.11
46 17 0.30
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.30
Consensus pattern (43 bp):
CTATTACGCCTCTATTCCATTCATAGCCAAACAAAAGAATTAC
Found at i:15415791 original size:44 final size:46
Alignment explanation
Indices: 15415728--15415816 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
15415718 ACCTCTATTC
*
15415728 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTT
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTT
*
15415772 CATTCAGCCAAACAAAAGAATTACCTATTACGCCTCTATTCCATT
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATT
15415817 ACGCATCTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 18 0.44
45 4 0.10
46 19 0.46
ACGTcount: A:0.36, C:0.30, G:0.06, T:0.28
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTT
Found at i:15415819 original size:16 final size:16
Alignment explanation
Indices: 15415798--15415850 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
15415788 AGAATTACCT
15415798 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
15415814 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
*
15415830 ATTACACCTCTATTCC
1 ATTACGCCTCTATTCC
15415846 ATTAC
1 ATTAC
15415851 AGCGAACCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.25, C:0.34, G:0.04, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:15418899 original size:39 final size:39
Alignment explanation
Indices: 15418848--15419061 Score: 270
Period size: 39 Copynumber: 5.5 Consensus size: 39
15418838 ATTCACTTTT
* * * * *
15418848 AAGCATATATCACATTACACATTTAATCACATAAAATTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
15418887 AAGCATATATCACAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
15418926 AAGCATATATCACAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
*
15418965 AAGCATATATCACAACACTC--ATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* * * * * * * * *
15419002 TAGCATACATCAAAATGCTTAAATAACCACATAACGTTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
*
15419041 AAGCATATATCATAATACTCA
1 AAGCATATATCACAATACTCA
15419062 AAAACATGTT
Statistics
Matches: 153, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
37 31 0.20
39 122 0.80
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.29
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:15418917 original size:17 final size:17
Alignment explanation
Indices: 15418890--15418956 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 17
15418880 AAAATTTAAG
15418890 CATAT-ATCACAATACT
1 CATATAATCACAATACT
15418906 CATATAATCAC-ATAACATT
1 CATATAATCACAAT-AC--T
*
15418925 CAAGCATATATCACAATACT
1 C-A-TATA-ATCACAATACT
15418945 CATATAATCACA
1 CATATAATCACA
15418957 TAACATTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 15
0.71 0.03 0.26
Matches are distributed among these distances:
16 7 0.17
17 13 0.32
18 3 0.07
19 3 0.07
20 3 0.07
21 3 0.07
22 7 0.17
23 2 0.05
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.28
Consensus pattern (17 bp):
CATATAATCACAATACT
Found at i:15419035 original size:76 final size:76
Alignment explanation
Indices: 15418875--15419061 Score: 248
Period size: 76 Copynumber: 2.4 Consensus size: 76
15418865 CACATTTAAT
* * *
15418875 CACATAAAATTTAAGCATATATCACAATACTCATATAATCACATAACATTCAAGCATATATCACA
1 CACATAACATTTAAGCATATATCACAATACTC--ATAATCACATAACATTCAAGCATACATCAAA
* *
15418940 ATACTCATATAAT
64 ATACTCAAATAAC
* * *
15418953 CACATAACATTCAAGCATATATCACAACACTCATAATCACATAACATTCTAGCATACATCAAAAT
1 CACATAACATTTAAGCATATATCACAATACTCATAATCACATAACATTCAAGCATACATCAAAAT
* *
15419018 GCTTAAATAAC
66 ACTCAAATAAC
* *
15419029 CACATAACGTTTAAGCATATATCATAATACTCA
1 CACATAACATTTAAGCATATATCACAATACTCA
15419062 AAAACATGTT
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
76 66 0.69
78 29 0.31
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (76 bp):
CACATAACATTTAAGCATATATCACAATACTCATAATCACATAACATTCAAGCATACATCAAAAT
ACTCAAATAAC
Found at i:15419052 original size:115 final size:116
Alignment explanation
Indices: 15418848--15419061 Score: 281
Period size: 115 Copynumber: 1.8 Consensus size: 116
15418838 ATTCACTTTT
* * * *
15418848 AAGCATATATCACATTACACATTTAATCACATAAAATTTAAGCATATATCACAATACTCATATAA
1 AAGCATATATCACA-TACACATATAATCACATAAAATTTAAGCATACATCAAAATACTCAAATAA
*
15418913 TCACATAACATTCAAGCATATATCACAATACTCATATAATCACATAACATTC
65 CCACATAACATTCAAGCATATATCACAATACTCATATAATCACATAACATTC
* * *
15418965 AAGCATATATCACA-ACAC-TCATAATCACATAACATTCT-AGCATACATCAAAATGCTTAAATA
1 AAGCATATATCACATACACAT-ATAATCACATAAAATT-TAAGCATACATCAAAATACTCAAATA
* * *
15419027 ACCACATAACGTTTAAGCATATATCATAATACTCA
64 ACCACATAACATTCAAGCATATATCACAATACTCA
15419062 AAAACATGTT
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
114 1 0.01
115 68 0.81
116 1 0.01
117 14 0.17
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.29
Consensus pattern (116 bp):
AAGCATATATCACATACACATATAATCACATAAAATTTAAGCATACATCAAAATACTCAAATAAC
CACATAACATTCAAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:15421256 original size:30 final size:30
Alignment explanation
Indices: 15421190--15421351 Score: 159
Period size: 30 Copynumber: 5.4 Consensus size: 30
15421180 ACCATCGAAC
15421190 TATGAAAAGGGATAGCTTCGGCTATC-AAT
1 TATGAAAAGGGATAGCTTCGGCTATCAAAT
* *
15421219 CATGAAAAGGGATGGCTTCGGCTATCAAAT
1 TATGAAAAGGGATAGCTTCGGCTATCAAAT
* * * * * *
15421249 TATGAAAAGTGA-GGGTGAT-GACTATCGAAC
1 TATGAAAAGGGATAGCT--TCGGCTATCAAAT
* * *
15421279 TATGAAATGTGATAGCTACGGCTATCAAAT
1 TATGAAAAGGGATAGCTTCGGCTATCAAAT
*
15421309 TATGAAAAGGGATAGCTTCGACTATCAAAT
1 TATGAAAAGGGATAGCTTCGGCTATCAAAT
* *
15421339 TACGAAAAAGGAT
1 TATGAAAAGGGAT
15421352 GTGTCAACCA
Statistics
Matches: 107, Mismatches: 21, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
29 27 0.25
30 77 0.72
31 3 0.03
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (30 bp):
TATGAAAAGGGATAGCTTCGGCTATCAAAT
Found at i:15421294 original size:89 final size:89
Alignment explanation
Indices: 15421098--15421346 Score: 324
Period size: 89 Copynumber: 2.8 Consensus size: 89
15421088 CCATCATCAA
* * * * *
15421098 CGAA-TATGAAAAGGGATAGCTTCGGCTATCAGTTATGAAAAAGGATGG-TGACGACCATC-GAT
1 CGAACTATGAAAAGGGATAGCTTCGGCTATCAATTATGAAAAGGGATGGCT-TCGACTATCAAAT
* *
15421160 AATGAAAAGTGATGGTGATGACCAT
65 TATGAAAAGTGAGGGTGATGACCAT
* *
15421185 CGAACTATGAAAAGGGATAGCTTCGGCTATCAATCATGAAAAGGGATGGCTTCGGCTATCAAATT
1 CGAACTATGAAAAGGGATAGCTTCGGCTATCAATTATGAAAAGGGATGGCTTCGACTATCAAATT
*
15421250 ATGAAAAGTGAGGGTGATGACTAT
66 ATGAAAAGTGAGGGTGATGACCAT
* * * *
15421274 CGAACTATGAAATGTGATAGCTACGGCTATCAAATTATGAAAAGGGATAGCTTCGACTATCAAAT
1 CGAACTATGAAAAGGGATAGCTTCGGCTATC-AATTATGAAAAGGGATGGCTTCGACTATCAAAT
*
15421339 TACGAAAA
65 TATGAAAA
15421347 AGGATGTGTC
Statistics
Matches: 141, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
87 4 0.03
88 47 0.33
89 53 0.38
90 37 0.26
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (89 bp):
CGAACTATGAAAAGGGATAGCTTCGGCTATCAATTATGAAAAGGGATGGCTTCGACTATCAAATT
ATGAAAAGTGAGGGTGATGACCAT
Found at i:15421332 original size:60 final size:59
Alignment explanation
Indices: 15421103--15421336 Score: 165
Period size: 59 Copynumber: 4.0 Consensus size: 59
15421093 ATCAACGAAT
* * * * * * * *
15421103 ATGAAAAGGGATAGCTTCGGCTATC-AGTTATGAAAAAGGAT-GGTGACGACCATCGATA
1 ATGAAAAGGGATAGCTACGGCTATCAAATTATGAAAAGGGATAGCT-TCGACTATCAATC
* * * * * * * *
15421161 ATGAAAAGTGAT-GGTGATGACCATCGAACTATGAAAAGGGATAGCTTCGGCTATCAATC
1 ATGAAAAGGGATAGCT-ACGGCTATCAAATTATGAAAAGGGATAGCTTCGACTATCAATC
* * * * *
15421220 ATGAAAAGGGATGGCTTCGGCTATCAAATTATGAAAAGTGA-GGGTGAT-GACTATCGAA-C
1 ATGAAAAGGGATAGCTACGGCTATCAAATTATGAAAAGGGATAGCT--TCGACTATC-AATC
* *
15421279 TATGAAATGTGATAGCTACGGCTATCAAATTATGAAAAGGGATAGCTTCGACTATCAA
1 -ATGAAAAGGGATAGCTACGGCTATCAAATTATGAAAAGGGATAGCTTCGACTATCAA
15421337 ATTACGAAAA
Statistics
Matches: 132, Mismatches: 34, Indels: 19
0.71 0.18 0.10
Matches are distributed among these distances:
57 2 0.02
58 18 0.14
59 60 0.45
60 50 0.38
61 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (59 bp):
ATGAAAAGGGATAGCTACGGCTATCAAATTATGAAAAGGGATAGCTTCGACTATCAATC
Found at i:15425297 original size:17 final size:18
Alignment explanation
Indices: 15425264--15425299 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
15425254 CATGTTTTCA
15425264 GCCCGTGTGGATCCACAC
1 GCCCGTGTGGATCCACAC
15425282 GCCCGTGTGG-TCCACAC
1 GCCCGTGTGGATCCACAC
15425299 G
1 G
15425300 ACCCAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.14, C:0.39, G:0.31, T:0.17
Consensus pattern (18 bp):
GCCCGTGTGGATCCACAC
Found at i:15431073 original size:7 final size:7
Alignment explanation
Indices: 15431061--15431087 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
15431051 TAATTTGAAA
15431061 AGAAAAG
1 AGAAAAG
15431068 AGAAAAG
1 AGAAAAG
15431075 AGAAAAG
1 AGAAAAG
15431082 AGAAAA
1 AGAAAA
15431088 AGTAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (7 bp):
AGAAAAG
Found at i:15431265 original size:15 final size:16
Alignment explanation
Indices: 15431217--15431266 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
15431207 AAATCAAAAT
*
15431217 AAGAGAAAAGAAATGA
1 AAGAGAAAAGAAAGGA
15431233 AA-AGAAAA-AAAGGAA
1 AAGAGAAAAGAAAGG-A
15431248 AAGAGAAAAGAAA-GA
1 AAGAGAAAAGAAAGGA
15431263 AAGA
1 AAGA
15431267 ATAGATAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.13
15 14 0.47
16 9 0.30
17 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (16 bp):
AAGAGAAAAGAAAGGA
Found at i:15437496 original size:32 final size:32
Alignment explanation
Indices: 15437459--15437540 Score: 101
Period size: 32 Copynumber: 2.6 Consensus size: 32
15437449 TTGAAATTAG
* *
15437459 TTTGTTGGATTTTGAAATTATTATGTCTTAAA
1 TTTGTTGGATATTGAAATTATCATGTCTTAAA
* * * *
15437491 TTTGTTAGATATTGAATTTATCATGTTTTAAG
1 TTTGTTGGATATTGAAATTATCATGTCTTAAA
*
15437523 CTTGTTGGATATTGAAAT
1 TTTGTTGGATATTGAAAT
15437541 GATTGACAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.51
Consensus pattern (32 bp):
TTTGTTGGATATTGAAATTATCATGTCTTAAA
Found at i:15440018 original size:25 final size:25
Alignment explanation
Indices: 15439990--15440039 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
15439980 ATGTTGAAGA
* * *
15439990 ATATGAGCATTAAAGCTAGTCCATC
1 ATATGAGAAGTAAAACTAGTCCATC
*
15440015 ATATTAGAAGTAAAACTAGTCCATC
1 ATATGAGAAGTAAAACTAGTCCATC
15440040 CAATCAGGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (25 bp):
ATATGAGAAGTAAAACTAGTCCATC
Found at i:15441321 original size:46 final size:46
Alignment explanation
Indices: 15441177--15441324 Score: 163
Period size: 46 Copynumber: 3.2 Consensus size: 46
15441167 TTTGGTCTGA
* * * * **
15441177 AACATATGCAGGAACTCAGAACCTAATCACGTATTCTTGAGTTCAT
1 AACATATGCAAGAGCTCAGAACCTAATCATGTATTCTTGAGTCCGC
* * * * *
15441223 AACATAAGAAAGAGCTCAGAACCTAATCCTGTATTCTCGAGTCTGC
1 AACATATGCAAGAGCTCAGAACCTAATCATGTATTCTTGAGTCCGC
* *
15441269 AACATATGCAAGAGCT-AGAAATCTATTCATGTATTCTTGAGTCCGC
1 AACATATGCAAGAGCTCAG-AACCTAATCATGTATTCTTGAGTCCGC
15441315 AACATATGCA
1 AACATATGCA
15441325 GGAATTCAAA
Statistics
Matches: 83, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
45 2 0.02
46 81 0.98
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (46 bp):
AACATATGCAAGAGCTCAGAACCTAATCATGTATTCTTGAGTCCGC
Found at i:15447812 original size:30 final size:30
Alignment explanation
Indices: 15447776--15447835 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
15447766 TAGTCAGATG
15447776 AATGGAGTATGTGCTACTATGGGCTTCCGA
1 AATGGAGTATGTGCTACTATGGGCTTCCGA
15447806 AATGGAGTATGTGCTACTATGGGCTTCCGA
1 AATGGAGTATGTGCTACTATGGGCTTCCGA
15447836 TAAAATATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (30 bp):
AATGGAGTATGTGCTACTATGGGCTTCCGA
Found at i:15454829 original size:45 final size:45
Alignment explanation
Indices: 15454756--15454890 Score: 184
Period size: 45 Copynumber: 3.0 Consensus size: 45
15454746 CCGTTACACG
* * * ***
15454756 GTGG-ATCAGCACATAAC-ACCACCCTTATAATCAATTATATTTA
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACCCA
15454799 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACCCA
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACCCA
* *
15454844 GTGGAATCAGCACATAGCAACCAACTTTATAATCAATGATACTCA
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACCCA
15454889 GT
1 GT
15454891 ACATGTAGTA
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
43 4 0.05
44 12 0.15
45 66 0.80
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.26
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACCCA
Found at i:15460575 original size:31 final size:30
Alignment explanation
Indices: 15460521--15460578 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
15460511 TAAATACTCG
* *
15460521 AAATTTGAGGGATTAAAGTGTAAATATGAA
1 AAATTTGAAGGACTAAAGTGTAAATATGAA
15460551 AAATTTGAAGGACTAATAGTGTAAATAT
1 AAATTTGAAGGACTAA-AGTGTAAATAT
15460579 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.47, C:0.02, G:0.21, T:0.31
Consensus pattern (30 bp):
AAATTTGAAGGACTAAAGTGTAAATATGAA
Found at i:15464275 original size:28 final size:28
Alignment explanation
Indices: 15464217--15464287 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
15464207 AAGACGCCTC
15464217 TGTGGCAATCTCT-ATAAAGGACATCTA
1 TGTGGCAATCTCTGATAAAGGACATCTA
* * ** *
15464244 TGTGACAATCTCTGTTAAAGGATGTCTT
1 TGTGGCAATCTCTGATAAAGGACATCTA
15464272 TGTGGCGAATCTCTGA
1 TGTGGC-AATCTCTGA
15464288 AAGGAAAACT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
27 12 0.34
28 15 0.43
29 8 0.23
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (28 bp):
TGTGGCAATCTCTGATAAAGGACATCTA
Found at i:15464388 original size:28 final size:28
Alignment explanation
Indices: 15464322--15464422 Score: 73
Period size: 28 Copynumber: 3.6 Consensus size: 28
15464312 TGAATAAGAA
*
15464322 TTGTGGCTATCTCTGTTAAAGAAAGTCT
1 TTGTGGCTATCTATGTTAAAGAAAGTCT
* *
15464350 TTATGG-AATCTATGTTAAAGGAAA-TGC-
1 TTGTGGCTATCTATGTTAAA-GAAAGT-CT
* * * *
15464377 TTGTGGCTATCTCTGTGAATGGAAAGCCT
1 TTGTGGCTATCTATGTTAA-AGAAAGTCT
* *
15464406 TTGTTGCTATCTCTGTT
1 TTGTGGCTATCTATGTT
15464423 CTAGGAAAAC
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
27 17 0.30
28 24 0.43
29 15 0.27
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.40
Consensus pattern (28 bp):
TTGTGGCTATCTATGTTAAAGAAAGTCT
Found at i:15466988 original size:50 final size:50
Alignment explanation
Indices: 15466882--15467072 Score: 168
Period size: 50 Copynumber: 3.7 Consensus size: 50
15466872 GAGGACGAGA
* *
15466882 TCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAGA-TA--AGAGG
*
15466938 TCCCATGTAAGACCATGTCTAGGG-CATGGCGTTGGCACCGAGATAAGAGG
1 TCCCATGTAAGACCATGTCT-GGGACATGGCATTGGCACCGAGATAAGAGG
*** * * * * **
15466988 TCCCCCATAAGACCATGTCTGGGACATGGCATGGGCACCTATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGG
* * * *
15467038 TCCCATGTAAGACCATATTTGGGATATGGTATTGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGG
15467073 AAGTACAGGA
Statistics
Matches: 112, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
49 3 0.03
50 68 0.61
52 2 0.02
53 4 0.04
55 1 0.01
56 31 0.28
57 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGG
Found at i:15468277 original size:29 final size:29
Alignment explanation
Indices: 15468244--15468303 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
15468234 TAGGGAAAAT
15468244 TTACAGATCTAAATTTTGAGTTTCTTAGC
1 TTACAGATCTAAATTTTGAGTTTCTTAGC
15468273 TTACAGATCTAAATTTTGAGTTTCTTAGC
1 TTACAGATCTAAATTTTGAGTTTCTTAGC
15468302 TT
1 TT
15468304 GAGTTATAAT
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:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (29 bp):
TTACAGATCTAAATTTTGAGTTTCTTAGC
Found at i:15478543 original size:15 final size:14
Alignment explanation
Indices: 15478517--15478556 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 14
15478507 AAATTGTCAC
*
15478517 ATATCTTTTTTTTA
1 ATATTTTTTTTTTA
15478531 ATATTTATTTTTTTA
1 ATATTT-TTTTTTTA
15478546 ATATTTTTTTT
1 ATATTTTTTTT
15478557 ACTTTATAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (14 bp):
ATATTTTTTTTTTA
Found at i:15478978 original size:2 final size:2
Alignment explanation
Indices: 15478971--15478997 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15478961 AAAAGTAAAA
15478971 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 A
15478998 AACTCATTAA
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15479508 original size:17 final size:17
Alignment explanation
Indices: 15479474--15479520 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
15479464 ATTTTGAATT
15479474 AAATTTATTCAAAA-TTTA
1 AAATTT-TT-AAAATTTTA
15479492 AAATTTTTAAAATTTTA
1 AAATTTTTAAAATTTTA
15479509 AAA-TTTTAAAAT
1 AAATTTTTAAAAT
15479521 GTATTCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 13 0.46
17 9 0.32
18 6 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTTTTAAAATTTTA
Found at i:15479509 original size:8 final size:8
Alignment explanation
Indices: 15479484--15479520 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
15479474 AAATTTATTC
15479484 AAAA-TTT
1 AAAATTTT
15479491 AAAATTTTT
1 AAAA-TTTT
15479500 AAAATTTT
1 AAAATTTT
15479508 AAAATTTT
1 AAAATTTT
15479516 AAAAT
1 AAAAT
15479521 GTATTCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 4 0.14
8 17 0.61
9 7 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAAATTTT
Found at i:15483508 original size:2 final size:2
Alignment explanation
Indices: 15483501--15483541 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
15483491 TCAATGAATC
*
15483501 TA TA TA TA TA TA TA TA TA TG 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 TA TA TA T
15483542 CCATGCCATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15486340 original size:32 final size:32
Alignment explanation
Indices: 15486304--15486682 Score: 501
Period size: 32 Copynumber: 11.8 Consensus size: 32
15486294 ATATATTATG
* ***
15486304 TATTGTCGAATTGAATTGTATAGGTATACACC
1 TATTGTCGAATTGAATTGTATATGTATACTTA
*
15486336 TATTGTCGAATTGAATTGTATATGTATACGTA
1 TATTGTCGAATTGAATTGTATATGTATACTTA
*
15486368 TATTGCCGAATTGAATTGTATATGTATACTTA
1 TATTGTCGAATTGAATTGTATATGTATACTTA
* * ***
15486400 TATTGTCGAATTGAATTGTATAGGTGTACACC
1 TATTGTCGAATTGAATTGTATATGTATACTTA
15486432 TATTGTCGAATTGAATTGTATATGTATACTTA
1 TATTGTCGAATTGAATTGTATATGTATACTTA
* ***
15486464 TATTG-CTGAATTGAATTGTATAGGTATACACC
1 TATTGTC-GAATTGAATTGTATATGTATACTTA
15486496 TATTGTCGAATTGAATTGTATATGTATACTTA
1 TATTGTCGAATTGAATTGTATATGTATACTTA
15486528 TATTGTCGAATTGAATTGTATATGTATACTTA
1 TATTGTCGAATTGAATTGTATATGTATACTTA
* * ***
15486560 TATTGTCGAATTGAATTGAATAGGTATACACC
1 TATTGTCGAATTGAATTGTATATGTATACTTA
15486592 TATTGTCGAATTGAATTGTATATGTATACTTA
1 TATTGTCGAATTGAATTGTATATGTATACTTA
* *
15486624 TAATGCCGAATTGAATTGTATATGTATACTTA
1 TATTGTCGAATTGAATTGTATATGTATACTTA
* * *
15486656 TGTT-TCCAAATTGATTTGTATATGTAT
1 TATTGT-CGAATTGAATTGTATATGTAT
15486683 TTATATATTG
Statistics
Matches: 302, Mismatches: 42, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
31 1 0.00
32 300 0.99
33 1 0.00
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (32 bp):
TATTGTCGAATTGAATTGTATATGTATACTTA
Found at i:15486932 original size:41 final size:43
Alignment explanation
Indices: 15486826--15486944 Score: 145
Period size: 43 Copynumber: 2.8 Consensus size: 43
15486816 GAGTTGTAAT
15486826 TTCGTGTAAGACCATGTTTGGGACATTGGCATCGAAGTGAGAA
1 TTCGTGTAAGACCATGTTTGGGACATTGGCATCGAAGTGAGAA
** *
15486869 AACGTGTAAGACCATGTTTGGGACATTGGCATCG-TGT-ATG-A
1 TTCGTGTAAGACCATGTTTGGGACATTGGCATCGAAGTGA-GAA
* * * *
15486910 TTCGTATAAGACCCTGTCTGGGACAGTGGCATCGA
1 TTCGTGTAAGACCATGTTTGGGACATTGGCATCGA
15486945 TATATGTTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
41 30 0.46
42 3 0.05
43 32 0.49
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (43 bp):
TTCGTGTAAGACCATGTTTGGGACATTGGCATCGAAGTGAGAA
Found at i:15496718 original size:86 final size:86
Alignment explanation
Indices: 15496549--15496710 Score: 252
Period size: 86 Copynumber: 1.9 Consensus size: 86
15496539 CCAACAAGTG
* **
15496549 GTGGCTCGTCCACAAAACCCAGTGGCAATTTGTTTAATCTACAAATATGTTGTGCACTCACAATG
1 GTGGCTCGTCCACAAAACCCAGTGACAATTTGTTTAATCTACAAATATGTTGTGCACTCACAACA
15496614 AGTGGCAGTAACTACAAATAT
66 AGTGGCAGTAACTACAAATAT
* * ***
15496635 GTGGCTCGTCCACAAAACCCAGTGATAGTTTGTTTAATCTGTGAATATGTTGTGCACTCACAACA
1 GTGGCTCGTCCACAAAACCCAGTGACAATTTGTTTAATCTACAAATATGTTGTGCACTCACAACA
15496700 AGTGGCAGTAA
66 AGTGGCAGTAA
15496711 TTGCAAATGT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 68 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (86 bp):
GTGGCTCGTCCACAAAACCCAGTGACAATTTGTTTAATCTACAAATATGTTGTGCACTCACAACA
AGTGGCAGTAACTACAAATAT
Found at i:15497848 original size:15 final size:15
Alignment explanation
Indices: 15497823--15497857 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
15497813 AACTCTATTT
*
15497823 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
15497837 TAATTAATATTAAGA
1 TAATTAATATTAAGA
15497852 TAATTA
1 TAATTA
15497858 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:15504247 original size:5 final size:5
Alignment explanation
Indices: 15504233--15504315 Score: 55
Period size: 5 Copynumber: 16.4 Consensus size: 5
15504223 GCAACCTAAT
* * *
15504233 TTTTA TTTTTA TTTT- TGTT- TTTTG TTTTT TTATTA TTTTA TTTTA TTTT-
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA
* * *
15504282 CTTTA CTTTA TTTATTA CTTTA TTTTA TTTTA TT
1 TTTTA TTTTA -TT-TTA TTTTA TTTTA TTTTA TT
15504316 ATTTATTACT
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
4 9 0.14
5 41 0.64
6 11 0.17
7 3 0.05
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:15504276 original size:21 final size:21
Alignment explanation
Indices: 15504238--15504286 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
15504228 CTAATTTTTA
* *
15504238 TTTTTATTTTTGTTTTTTGTT
1 TTTTTATTTTTGTATTTTATT
15504259 TTTTTATTATTT-TATTTTATT
1 TTTTTATT-TTTGTATTTTATT
15504280 TTCTTTA
1 TT-TTTA
15504287 CTTTATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.82
Consensus pattern (21 bp):
TTTTTATTTTTGTATTTTATT
Found at i:15504301 original size:12 final size:12
Alignment explanation
Indices: 15504284--15504330 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
15504274 TTTATTTTCT
15504284 TTACTTTATTTA
1 TTACTTTATTTA
15504296 TTACTTTATTTTA
1 TTACTTTA-TTTA
*
15504309 TT-TTATTATTTA
1 TTACT-TTATTTA
15504321 TTAC-TTATTT
1 TTACTTTATTT
15504331 GGATATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
11 6 0.20
12 15 0.50
13 9 0.30
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (12 bp):
TTACTTTATTTA
Found at i:15504505 original size:22 final size:23
Alignment explanation
Indices: 15504477--15504540 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
15504467 GCCCAGAATG
* *
15504477 CCTGCAGCCAAACTACCC-TATT
1 CCTGCAGCCAAACCACCCTTATC
15504499 CCTGCAGCC-AACCACCCTTATC
1 CCTGCAGCCAAACCACCCTTATC
*
15504521 CCTGCACCCAAGCACCACCC
1 CCTGCAGCCAA--ACCACCC
15504541 CTTAGCACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 7 0.20
22 20 0.57
23 1 0.03
25 7 0.20
ACGTcount: A:0.25, C:0.50, G:0.09, T:0.16
Consensus pattern (23 bp):
CCTGCAGCCAAACCACCCTTATC
Found at i:15512216 original size:12 final size:12
Alignment explanation
Indices: 15512199--15512233 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
15512189 TTTTATATAC
15512199 TGGTTAGCTTAT
1 TGGTTAGCTTAT
15512211 TGGTTAGCTTAT
1 TGGTTAGCTTAT
* *
15512223 TTGTTTGCTTA
1 TGGTTAGCTTA
15512234 GTTGTTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.09, G:0.23, T:0.54
Consensus pattern (12 bp):
TGGTTAGCTTAT
Found at i:15513828 original size:19 final size:19
Alignment explanation
Indices: 15513804--15513840 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
15513794 AATTTTATTT
15513804 TTTAAAAAAATATTAAAAA
1 TTTAAAAAAATATTAAAAA
* *
15513823 TTTAAAACATTATTAAAA
1 TTTAAAAAAATATTAAAA
15513841 TCATTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
TTTAAAAAAATATTAAAAA
Found at i:15513947 original size:7 final size:7
Alignment explanation
Indices: 15513946--15513990 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
15513936 TTAAATTATA
15513946 AAAAATT
1 AAAAATT
15513953 AAAAATT
1 AAAAATT
15513960 AAAAATT
1 AAAAATT
15513967 AAAAA-T
1 AAAAATT
* *
15513973 ATATATT
1 AAAAATT
15513980 AAAAATT
1 AAAAATT
15513987 AAAA
1 AAAA
15513991 GAAAGCCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 4 0.12
7 29 0.88
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAAATT
Found at i:15514422 original size:7 final size:7
Alignment explanation
Indices: 15514410--15514443 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
15514400 TTTTTAAAAT
15514410 AATTTTA
1 AATTTTA
15514417 AATTTTA
1 AATTTTA
15514424 AATTTTA
1 AATTTTA
15514431 AATTTTA
1 AATTTTA
15514438 AATTTT
1 AATTTT
15514444 TTATATGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:15514943 original size:6 final size:6
Alignment explanation
Indices: 15514932--15514960 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
15514922 AGGAAAGGGC
15514932 AGGGAG AGGGAG AGGGAG AGGGAG AGGGA
1 AGGGAG AGGGAG AGGGAG AGGGAG AGGGA
15514961 AAGAGAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
AGGGAG
Found at i:15525777 original size:98 final size:97
Alignment explanation
Indices: 15525606--15525894 Score: 431
Period size: 98 Copynumber: 3.0 Consensus size: 97
15525596 AAATAAAGGT
* * *
15525606 TTAGGGTTTAGGGTTTCTTAATTAAATTAATTATAAA--TTTAAAAAATTAGATTAGGGTTTAGT
1 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAGT
* *
15525669 GTTTATGGTTTCTAAGGAAAAAATCAAATAAA
66 GTTTAGGGTTTTTAAGGAAAAAATCAAATAAA
*
15525701 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTAAAAAATTTAGATTAAGGTTTAG
1 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTAAAAAA-TTAGATTAGGGTTTAG
* * *
15525766 GGTTTAGGGTTTTTAAGTAAAAAATAAAATAAA
65 TGTTTAGGGTTTTTAAGGAAAAAATCAAATAAA
* *
15525799 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTAAAAAATTAGATTGGGGTTTTGT
1 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAGT
* *
15525864 ATTTAGGATTTTTAAGG-AAAAATCAAATAAA
66 GTTTAGGGTTTTTAAGGAAAAAATCAAATAAA
15525895 GCTAGTTGTT
Statistics
Matches: 174, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
95 34 0.20
96 13 0.07
97 36 0.21
98 91 0.52
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (97 bp):
TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAGT
GTTTAGGGTTTTTAAGGAAAAAATCAAATAAA
Found at i:15526066 original size:21 final size:21
Alignment explanation
Indices: 15526042--15526083 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
15526032 TATTTTTAAA
15526042 TTTTA-AAATAGAAAAAGAGTT
1 TTTTATAAA-AGAAAAAGAGTT
*
15526063 TTTTATGAAAGAAAAAGAGTT
1 TTTTATAAAAGAAAAAGAGTT
15526084 AAAATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (21 bp):
TTTTATAAAAGAAAAAGAGTT
Found at i:15526466 original size:11 final size:11
Alignment explanation
Indices: 15526450--15526500 Score: 67
Period size: 11 Copynumber: 5.1 Consensus size: 11
15526440 GTTAGACTTC
15526450 ATAATTAATTT
1 ATAATTAATTT
15526461 ATAATTAATTT
1 ATAATTAATTT
15526472 ATAATT--TTT
1 ATAATTAATTT
15526481 -TAA--AATTT
1 ATAATTAATTT
15526489 ATAATTAATTT
1 ATAATTAATTT
15526500 A
1 A
15526501 ATTAAGAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
8 6 0.17
9 6 0.17
11 23 0.66
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATAATTAATTT
Found at i:15533530 original size:17 final size:17
Alignment explanation
Indices: 15533508--15533540 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
15533498 GCCCGGCCCG
*
15533508 TAAACCAAATCAAAATA
1 TAAACCAAATAAAAATA
15533525 TAAACCAAATAAAAAT
1 TAAACCAAATAAAAAT
15533541 TAATAACAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.18
Consensus pattern (17 bp):
TAAACCAAATAAAAATA
Found at i:15541321 original size:19 final size:19
Alignment explanation
Indices: 15541299--15541349 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
15541289 TCATATATTA
* *
15541299 AAAATTTATATAAACTGAT
1 AAAATTTATAAAAACTCAT
* *
15541318 AAAATTCATAAAAATTCAT
1 AAAATTTATAAAAACTCAT
15541337 AAAGATTTATAAA
1 AAA-ATTTATAAA
15541350 TATTATAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (19 bp):
AAAATTTATAAAAACTCAT
Found at i:15542258 original size:9 final size:9
Alignment explanation
Indices: 15542240--15542320 Score: 56
Period size: 10 Copynumber: 8.6 Consensus size: 9
15542230 TTTAAATGAC
15542240 TTTTTATATA
1 TTTTT-TATA
15542250 TTTTTTATA
1 TTTTTTATA
15542259 -TTTTTATAA
1 TTTTTTAT-A
* *
15542268 TTTATTAGAA
1 TTTTTTA-TA
15542278 TTTTTTATA
1 TTTTTTATA
**
15542287 TTGCTTATAA
1 TTTTTTAT-A
*
15542297 GTTTTTATGA
1 TTTTTTAT-A
*
15542307 ATTTTTATA
1 TTTTTTATA
15542316 TTTTT
1 TTTTT
15542321 GATAAAATTT
Statistics
Matches: 55, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
8 7 0.13
9 17 0.31
10 31 0.56
ACGTcount: A:0.27, C:0.01, G:0.05, T:0.67
Consensus pattern (9 bp):
TTTTTTATA
Found at i:15542262 original size:19 final size:18
Alignment explanation
Indices: 15542240--15542325 Score: 59
Period size: 19 Copynumber: 4.5 Consensus size: 18
15542230 TTTAAATGAC
15542240 TTTTTATATATTTTTTATA
1 TTTTTATA-ATTTTTTATA
* *
15542259 TTTTTATAATTTATTAGAA
1 TTTTTATAATTTTTTA-TA
**
15542278 TTTTT-TATATTGCTTATAA
1 TTTTTATA-ATTTTTTAT-A
15542297 GTTTTTATGAA-TTTTTATA
1 -TTTTTAT-AATTTTTTATA
15542316 TTTTTGATAA
1 TTTTT-ATAA
15542326 AATTTTAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
18 16 0.30
19 24 0.45
20 10 0.19
21 2 0.04
22 1 0.02
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.64
Consensus pattern (18 bp):
TTTTTATAATTTTTTATA
Found at i:15542294 original size:29 final size:29
Alignment explanation
Indices: 15542240--15542317 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 29
15542230 TTTAAATGAC
*
15542240 TTTTTAT-ATATTTTTTATATTTTTATAA-
1 TTTTTATGA-ATTTTTTATATTCTTATAAG
15542268 TTTATTA-GAATTTTTTATATTGCTTATAAG
1 TTT-TTATGAATTTTTTATATT-CTTATAAG
15542298 TTTTTATGAA-TTTTTATATT
1 TTTTTATGAATTTTTTATATT
15542318 TTTGATAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
28 15 0.34
29 23 0.52
30 6 0.14
ACGTcount: A:0.28, C:0.01, G:0.05, T:0.65
Consensus pattern (29 bp):
TTTTTATGAATTTTTTATATTCTTATAAG
Found at i:15542325 original size:29 final size:28
Alignment explanation
Indices: 15542249--15542325 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 28
15542239 CTTTTTATAT
15542249 ATTTTTTATATTTTTATAATTTATTAGA
1 ATTTTTTATATTTTTATAATTTATTAGA
*
15542277 ATTTTTTATATTGCTTATAAGTTT-TTATGA
1 ATTTTTTATATT-TTTATAA-TTTATTA-GA
15542307 A-TTTTTATATTTTTGATAA
1 ATTTTTTATATTTTT-ATAA
15542326 AATTTTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
28 14 0.33
29 23 0.53
30 6 0.14
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.62
Consensus pattern (28 bp):
ATTTTTTATATTTTTATAATTTATTAGA
Found at i:15542331 original size:29 final size:28
Alignment explanation
Indices: 15542240--15542340 Score: 91
Period size: 29 Copynumber: 3.5 Consensus size: 28
15542230 TTTAAATGAC
*
15542240 TTTTTATATATTTTTTATATTTTTAT-AA
1 TTTTTAGA-ATTTTTTATATTTTTATAAA
* *
15542268 TTTATTAGAATTTTTTATATTGCTTATAAG
1 TTT-TTAGAATTTTTTATATT-TTTATAAA
15542298 TTTTTATGAA-TTTTTATATTTTTGATAAA
1 TTTTTA-GAATTTTTTATATTTTT-ATAAA
* *
15542327 ATTTTA-AATATTTT
1 TTTTTAGAATTTTTT
15542341 GAATTTGTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
27 2 0.03
28 21 0.35
29 30 0.50
30 7 0.12
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (28 bp):
TTTTTAGAATTTTTTATATTTTTATAAA
Found at i:15542405 original size:31 final size:31
Alignment explanation
Indices: 15542370--15542441 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
15542360 ATAAAGAAAT
* *
15542370 TATAATTTTTTTTATAATTTTTGTAAGTTTA
1 TATAATTTTTTTTATAATTTTTATAAGTATA
*
15542401 TATAAATTTTTTTATAATTTTTATAAGTATA
1 TATAATTTTTTTTATAATTTTTATAAGTATA
15542432 TATCAATTTT
1 TAT-AATTTT
15542442 AATAATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 31 0.86
32 5 0.14
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (31 bp):
TATAATTTTTTTTATAATTTTTATAAGTATA
Found at i:15542446 original size:29 final size:30
Alignment explanation
Indices: 15542377--15542450 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 30
15542367 AATTATAATT
* *
15542377 TTTTTTATAATTTTTGTAAGTTTATATAAA
1 TTTTTTATAATTTTTATAAGTATATATAAA
*
15542407 TTTTTTTATAATTTTTATAAGTATATATCAA
1 -TTTTTTATAATTTTTATAAGTATATATAAA
*
15542438 -TTTTAATAATTTT
1 TTTTTTATAATTTT
15542451 ATGAGAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 12 0.31
31 27 0.69
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (30 bp):
TTTTTTATAATTTTTATAAGTATATATAAA
Found at i:15546352 original size:21 final size:21
Alignment explanation
Indices: 15546326--15546369 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
15546316 TATTTAAGAA
15546326 ATTTTTATTA-AATTATATATT
1 ATTTTTA-TAGAATTATATATT
*
15546347 ATTTTTATAGTATTATATATT
1 ATTTTTATAGAATTATATATT
15546368 AT
1 AT
15546370 GATTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTTTATAGAATTATATATT
Found at i:15546431 original size:20 final size:20
Alignment explanation
Indices: 15546328--15546442 Score: 80
Period size: 20 Copynumber: 5.8 Consensus size: 20
15546318 TTTAAGAAAT
15546328 TTTTATTAAATTATATATTA
1 TTTTATTAAATTATATATTA
*
15546348 TTTT-TATAGTATTATATATTA
1 TTTTAT-TA-AATTATATATTA
* *
15546369 TGATTT-TTTAATTCATATAATA
1 T--TTTATTAAATT-ATATATTA
* * * *
15546391 -ATAATTATATTA-AGA--A
1 TTTTATTAAATTATATATTA
15546407 TTTTATTAAATTATATATTA
1 TTTTATTAAATTATATATTA
15546427 TTTTATTAAATTATAT
1 TTTTATTAAATTATAT
15546443 TTAATAATAA
Statistics
Matches: 72, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
16 1 0.01
17 9 0.12
18 4 0.06
19 3 0.04
20 28 0.39
21 15 0.21
22 8 0.11
23 4 0.06
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTATTAAATTATATATTA
Found at i:15546448 original size:55 final size:56
Alignment explanation
Indices: 15546358--15546520 Score: 136
Period size: 56 Copynumber: 2.9 Consensus size: 56
15546348 TTTTTATAGT
* * * *
15546358 ATTATATATTATGATTT-TTTAATTCATATAATAATAATTA-TATTAAGAATTTTATTAA
1 ATTATATATTAT--TTTATTAAATT-ATATAATAATAATAATTATTAA-AATATGATTAA
* * * *
15546416 ATTATATATTATTTTATTAAATTATAT-TTAATAATAATTGTTAATATATGGTTAA
1 ATTATATATTATTTTATTAAATTATATAATAATAATAATTATTAAAATATGATTAA
* * *
15546471 ATTATTTATTATTTATATTAAATTAT-TTATATTAATAACCTTATTAAAAT
1 ATTATATATTATTT-TATTAAATTATATAATAATAATAA--TTATTAAAAT
15546521 TTAATAACAA
Statistics
Matches: 86, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
55 29 0.34
56 31 0.36
57 6 0.07
58 20 0.23
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (56 bp):
ATTATATATTATTTTATTAAATTATATAATAATAATAATTATTAAAATATGATTAA
Found at i:15546497 original size:14 final size:14
Alignment explanation
Indices: 15546478--15546505 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15546468 TAAATTATTT
15546478 ATTATTTATATTAA
1 ATTATTTATATTAA
15546492 ATTATTTATATTAA
1 ATTATTTATATTAA
15546506 TAACCTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTATTTATATTAA
Found at i:15546696 original size:45 final size:44
Alignment explanation
Indices: 15546608--15546700 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 44
15546598 ATTACAACAT
15546608 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
*
15546652 CATTCCATTCAACCAAACA-ATTGAATTACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAGTTCTATTC
15546697 CATT
1 CATT
15546701 ACAGCTTTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.48
45 23 0.50
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
Found at i:15546703 original size:16 final size:16
Alignment explanation
Indices: 15546682--15546753 Score: 108
Period size: 16 Copynumber: 4.5 Consensus size: 16
15546672 TTGAATTACT
*
15546682 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
* *
15546698 ATTACAGCTTTATTCT
1 ATTACAGCTCTATTCC
*
15546714 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
15546730 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
15546746 ATTACAGC
1 ATTACAGC
15546754 GAACCAAACG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:15547100 original size:28 final size:27
Alignment explanation
Indices: 15546993--15547125 Score: 83
Period size: 28 Copynumber: 4.7 Consensus size: 27
15546983 GCTTAATTGA
15546993 TTAT-AATTTTATATTATTTATAAGTTT
1 TTATGAATTTTATATTATTTATAA-TTT
* *
15547020 TTATAAAATTTTA-AATATTT-TGAATATGTT
1 TTAT-GAATTTTATATTATTTAT--A-AT-TT
* ** **
15547050 TTATTAATTTTATAAAAAATATAATTT
1 TTATGAATTTTATATTATTTATAATTT
15547077 ATTATGAATTTTATATTATTTATAACTTT
1 -TTATGAATTTTATATTATTTATAA-TTT
* * *
15547106 TTATGATTTTTTTATAATTT
1 TTATGAATTTTATATTATTT
15547126 TCAAAAGTTT
Statistics
Matches: 83, Mismatches: 13, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
27 7 0.08
28 44 0.53
29 20 0.24
30 11 0.13
31 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.59
Consensus pattern (27 bp):
TTATGAATTTTATATTATTTATAATTT
Found at i:15547695 original size:19 final size:18
Alignment explanation
Indices: 15547671--15547706 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
15547661 TAATAAATTA
*
15547671 TTTAATATTACAATTTTAT
1 TTTAATAATA-AATTTTAT
15547690 TTTAATAATAAATTTTA
1 TTTAATAATAAATTTTA
15547707 AAAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAATAATAAATTTTAT
Found at i:15548057 original size:32 final size:33
Alignment explanation
Indices: 15548006--15548072 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
15547996 AAATTTTTAG
* *
15548006 AAAATGATTTTAAAGAAATTA-CTAAACAACAA
1 AAAATGATTTTAAAAAAATTATCCAAACAACAA
*
15548038 AAAAT-ATTTTAAACAAAATTATCCAAACACCAA
1 AAAATGATTTTAAA-AAAATTATCCAAACAACAA
15548071 AA
1 AA
15548073 GAAAATTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 8 0.27
32 11 0.37
33 11 0.37
ACGTcount: A:0.60, C:0.13, G:0.03, T:0.24
Consensus pattern (33 bp):
AAAATGATTTTAAAAAAATTATCCAAACAACAA
Found at i:15548422 original size:16 final size:17
Alignment explanation
Indices: 15548393--15548447 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
15548383 TTTTTAATTT
15548393 AAATAATTTATAAA-AA
1 AAATAATTTATAAATAA
* *
15548409 AAATATTTTTTAAATAA
1 AAATAATTTATAAATAA
15548426 AAA-AA-TTATTAAATAA
1 AAATAATTTA-TAAATAA
*
15548442 ATATAA
1 AAATAA
15548448 ACAACATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 2 0.06
16 22 0.71
17 7 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATAATTTATAAATAA
Found at i:15549943 original size:21 final size:21
Alignment explanation
Indices: 15549918--15549957 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
15549908 TGCCAAGTTC
*
15549918 AAAAACTA-AAGTAGACAAAAA
1 AAAAAATACAAGTA-ACAAAAA
15549939 AAAAAATACAAGTAACAAA
1 AAAAAATACAAGTAACAAA
15549958 GTAGACCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.72, C:0.10, G:0.07, T:0.10
Consensus pattern (21 bp):
AAAAAATACAAGTAACAAAAA
Found at i:15551248 original size:99 final size:98
Alignment explanation
Indices: 15550969--15551459 Score: 739
Period size: 98 Copynumber: 5.0 Consensus size: 98
15550959 AAAAGAAAAG
* **
15550969 AAACTATTTTAACTTCCAAGTATTTCAAGTTCCAAACCGAGGAATGATGTTCCATATACCAATAT
1 AAACTATTTTAACTT-CAAGTATTTCAAGTTCAAAACCGAGGAATGATGTTCCATATGTCAATAT
* * *
15551034 GGAGGTGCTACTATAAATTTCAGTTGAAGCTAGC
65 GGAGCTGCTACTGTAAATTTCAGTTGAAGCTAGT
* **
15551068 AAACTATTTTAACTTCAAGTATTTCAAGTTCAAAACCGAGGACTGATACTCCATATGTCAATATG
1 AAACTATTTTAACTTCAAGTATTTCAAGTTCAAAACCGAGGAATGATGTTCCATATGTCAATATG
*
15551133 GAGCTGCTACTGTAAATTTCTGTTGAAGCTAGT
66 GAGCTGCTACTGTAAATTTCAGTTGAAGCTAGT
* *
15551166 AAACTATTTTAACTTCAAGTATTTCAAAATTCAAAACCGAGGAATGATGTTCCATATGTCAATGT
1 AAACTATTTTAACTTCAAGTATTTC-AAGTTCAAAACCGAGGAATGATGTTCCATATGTCAATAT
*
15551231 GGAGCTGCTACTGTAAATTTCAGTAGAAGCTAGT
65 GGAGCTGCTACTGTAAATTTCAGTTGAAGCTAGT
15551265 AAACTATTTTTAACTTCAAGTATTTCAAGTTCAAAACCGAGGAATGATGTTCCATATGTCAATAT
1 AAACTA-TTTTAACTTCAAGTATTTCAAGTTCAAAACCGAGGAATGATGTTCCATATGTCAATAT
* *
15551330 GGAGCAGCTACTGTAAATTTCAGTTGAAGCTCGT
65 GGAGCTGCTACTGTAAATTTCAGTTGAAGCTAGT
* * * * *
15551364 AAACAATTTTAACTTCAAGTATTTCAAGTTCAAAACCGAGAAATAATGCTCCATATGTAAATATG
1 AAACTATTTTAACTTCAAGTATTTCAAGTTCAAAACCGAGGAATGATGTTCCATATGTCAATATG
* * * *
15551429 GACCTGATACTGTAAATCTCAGATGAAGCTA
66 GAGCTGCTACTGTAAATTTCAGTTGAAGCTA
15551460 ACAAAGTATT
Statistics
Matches: 357, Mismatches: 33, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
98 178 0.50
99 160 0.45
100 19 0.05
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (98 bp):
AAACTATTTTAACTTCAAGTATTTCAAGTTCAAAACCGAGGAATGATGTTCCATATGTCAATATG
GAGCTGCTACTGTAAATTTCAGTTGAAGCTAGT
Found at i:15551516 original size:29 final size:29
Alignment explanation
Indices: 15551472--15551533 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
15551462 AAAGTATTTC
* *
15551472 AAGTTCAAAACTAAGGACTGATGTTCCAT
1 AAGTTCAAAACCAAGGACTGATATTCCAT
*
15551501 AAGTTCAAAACCAAGGAGTGATATTCCAT
1 AAGTTCAAAACCAAGGACTGATATTCCAT
15551530 AAGT
1 AAGT
15551534 CAATATGGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (29 bp):
AAGTTCAAAACCAAGGACTGATATTCCAT
Found at i:15553673 original size:27 final size:27
Alignment explanation
Indices: 15553635--15553711 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
15553625 TAGTATTGGC
15553635 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
15553662 GCCTACCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
15553689 GCC-ATTCTGAGAGGCGCCAATGG
1 GCCTA-TCTGGGAGGCGCCAATGG
15553712 GTCGGGCCGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.17, C:0.25, G:0.39, T:0.19
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Done.