Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold133
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: 2564099
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 17052 characters in sequence are not A, C, G, or T
File 10 of 17
Found at i:1212362 original size:33 final size:33
Alignment explanation
Indices: 1212307--1212371 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1212297 TACCACTGTT
*
1212307 TGTATCGATACATGGCACATTGTATTGATACAA
1 TGTATCGATACATGGCACATTGTATCGATACAA
1212340 TGTATCGATACATGATG-A-ATTGTATCGATACA
1 TGTATCGATACATG--GCACATTGTATCGATACA
1212372 TTGATTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGGCACATTGTATCGATACAA
Found at i:1218688 original size:20 final size:20
Alignment explanation
Indices: 1218650--1218688 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1218640 TTTCAAATTT
1218650 CTTTATTTTCACTTCAAAAAA
1 CTTTATTTTCAC-TCAAAAAA
1218671 CTTTATTTTTCA-TCAAAA
1 CTTTA-TTTTCACTCAAAA
1218689 TTATCAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 5 0.29
22 6 0.35
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.46
Consensus pattern (20 bp):
CTTTATTTTCACTCAAAAAA
Found at i:1220451 original size:20 final size:22
Alignment explanation
Indices: 1220409--1220454 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1220399 TTTTAAATGA
*
1220409 TTATCAAGAGGGAGAAAATTTT
1 TTATCAAGAGAGAGAAAATTTT
*
1220431 TTATTAAGAGAGAG-AAATTTT
1 TTATCAAGAGAGAGAAAATTTT
1220452 TTA
1 TTA
1220455 AACGAAAGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (22 bp):
TTATCAAGAGAGAGAAAATTTT
Found at i:1221049 original size:13 final size:13
Alignment explanation
Indices: 1221031--1221057 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1221021 ACATTATGCT
1221031 TTGTATCGATACA
1 TTGTATCGATACA
1221044 TTGTATCGATACA
1 TTGTATCGATACA
1221057 T
1 T
1221058 GCATAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1221145 original size:33 final size:32
Alignment explanation
Indices: 1221108--1221172 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
1221098 TACCATTGTT
1221108 TGTATCAAAACATG-GCACATTGTATCGATACAA
1 TGTATCAAAACATGAG-A-ATTGTATCGATACAA
* *
1221141 TGTATCGATACATGATGAATTGTATCGATACA
1 TGTATCAAAACATGA-GAATTGTATCGATACA
1221173 TTGCTTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (32 bp):
TGTATCAAAACATGAGAATTGTATCGATACAA
Found at i:1221146 original size:13 final size:13
Alignment explanation
Indices: 1221128--1221152 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1221118 CATGGCACAT
1221128 TGTATCGATACAA
1 TGTATCGATACAA
1221141 TGTATCGATACA
1 TGTATCGATACA
1221153 TGATGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1225393 original size:17 final size:17
Alignment explanation
Indices: 1225371--1225407 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1225361 TATCGATACA
1225371 TCACTGTTCCTAACTGT
1 TCACTGTTCCTAACTGT
*
1225388 TCACTGTTCTTAACTGT
1 TCACTGTTCCTAACTGT
1225405 TCA
1 TCA
1225408 TGTATCACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.27, G:0.11, T:0.43
Consensus pattern (17 bp):
TCACTGTTCCTAACTGT
Found at i:1227436 original size:21 final size:21
Alignment explanation
Indices: 1227412--1227469 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
1227402 AATATTCTTA
* *
1227412 AAAAGAAATTAAGTGAATTAG
1 AAAAGAAAATAAATGAATTAG
1227433 AAAAGAAAATAAATGAATTAG
1 AAAAGAAAATAAATGAATTAG
** *
1227454 AGGAGAAAAGAAATGA
1 AAAAGAAAATAAATGA
1227470 GTTGCAAGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (21 bp):
AAAAGAAAATAAATGAATTAG
Found at i:1230928 original size:24 final size:24
Alignment explanation
Indices: 1230900--1230950 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1230890 GTATCGATAC
*
1230900 ATCACTGTTCATAAATGTTCACGT
1 ATCACTATTCATAAATGTTCACGT
* * *
1230924 ATCACTATTCATCACTGTTCATGT
1 ATCACTATTCATAAATGTTCACGT
1230948 ATC
1 ATC
1230951 GATACATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (24 bp):
ATCACTATTCATAAATGTTCACGT
Found at i:1231060 original size:20 final size:20
Alignment explanation
Indices: 1231014--1231060 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1231004 AATTTTAAAT
1231014 GCATGTATCGATACATTATA
1 GCATGTATCGATACATTATA
*
1231034 -AATTGTATCGATACA-TATGA
1 GCA-TGTATCGATACATTAT-A
1231054 GCATGTA
1 GCATGTA
1231061 AGTGCGGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
19 4 0.18
20 17 0.77
21 1 0.05
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (20 bp):
GCATGTATCGATACATTATA
Found at i:1232883 original size:363 final size:363
Alignment explanation
Indices: 1232304--1233735 Score: 2641
Period size: 363 Copynumber: 4.0 Consensus size: 363
1232294 AACTTTTCTC
*
1232304 TAAAATATTTTAAGCTAAG-TATGCAATAAGAACATATTTTTTAGTATCAAGGAATTTAAGACAA
1 TAAAATATTTTAAGCTAAGATATGCAATAAGAACATATTTTTTAATATCAAGGAATTTAAGACAA
1232368 TTTAATATCTTTCAAAATATTTTTAAAATAATTTAAGGAAAAAATACTAAGATTGATAATTTTTA
66 TTTAATATCTTTCAAAATATTTTTAAAATAATTTAAGGAAAAAATACTAAGATTGATAATTTTTA
* * *
1232433 AATAAAAGCTATTTATGCTTACATTATTGTTATATCAAAACCAAAATAAATTCAAAGCTAATAAA
131 AATAAAAGCTATTTAAGCTTACGTTATTGTTATATCAAAACCGAAATAAATTCAAAGCTAATAAA
1232498 AGCTAACAAAATATCTAATTCAAACACATTTTTTATTTTGGTATGACATGGTACGAACGATGTAA
196 AGCTAACAAAATATCTAATTCAAACACATTTTTTATTTTGGTATGACATGGTACGAACGATGTAA
1232563 AATCTTATAAGGTAAATGACAAAAAATCTTTGTGATTTAGGAGAAATAATACTTAGCTTCTTGTG
261 AATCTTATAAGGTAAATGACAAAAAATCTTTGTGATTTAGGAGAAATAATACTTAGCTTCTTGTG
*
1232628 TTTTAAAAATTGACACTTGCATTCTTTCAAAATATTTT
326 TTTTAAAAATTGACACTTGCATTCCTTCAAAATATTTT
*
1232666 TAAAATATTTTAAGCTAAGATATACAATAAGAACATATTTTTTAATATCAAGGAATTTAAGACAA
1 TAAAATATTTTAAGCTAAGATATGCAATAAGAACATATTTTTTAATATCAAGGAATTTAAGACAA
1232731 TTTAATATCTTTCAAAATATTTTTAAAATAATTTAAGGAAAAAATACTAAGATTGATAATTTTTA
66 TTTAATATCTTTCAAAATATTTTTAAAATAATTTAAGGAAAAAATACTAAGATTGATAATTTTTA
*
1232796 AATAAAAGCTATTTAAGCTTACGTTATTGTTATATCAAAACCGAAATAAATTTAAAGCTAATAAA
131 AATAAAAGCTATTTAAGCTTACGTTATTGTTATATCAAAACCGAAATAAATTCAAAGCTAATAAA
1232861 AGCTAACAAAATATCTAATTCAAACACATTTTTTATTTTGGTATGACATGGTACGAACGATGTAA
196 AGCTAACAAAATATCTAATTCAAACACATTTTTTATTTTGGTATGACATGGTACGAACGATGTAA
1232926 AATCTTATAAGGTAAATGACAAAAAATCTTTGTGATTTAGGAGAAATAATACTTAGCTTCTTGTG
261 AATCTTATAAGGTAAATGACAAAAAATCTTTGTGATTTAGGAGAAATAATACTTAGCTTCTTGTG
1232991 TTTTAAAAATTGACACTTGCATTCCTTCAAAATATTTT
326 TTTTAAAAATTGACACTTGCATTCCTTCAAAATATTTT
*
1233029 TAAAATATTTTAAGCTAAGATATGCAATAAGAACATATTTTTTAATATCAAGGAATTTAATACAA
1 TAAAATATTTTAAGCTAAGATATGCAATAAGAACATATTTTTTAATATCAAGGAATTTAAGACAA
*
1233094 TTTAATATCTTTCAAAATATTTTTAAAATAATTTAAGAAAAAAATACTAAGATTGATAATTTTTA
66 TTTAATATCTTTCAAAATATTTTTAAAATAATTTAAGGAAAAAATACTAAGATTGATAATTTTTA
* *
1233159 AATAAAAGCTATTTAAACTTACGTTATTGTTATATCAAAACTGAAATAAATT-----C--ATAAA
131 AATAAAAGCTATTTAAGCTTACGTTATTGTTATATCAAAACCGAAATAAATTCAAAGCTAATAAA
1233217 AGCTAACAAAATATCTAATTCAAACACATTTTTTATTTTGGTATGACATGGTACGAACGATGTAA
196 AGCTAACAAAATATCTAATTCAAACACATTTTTTATTTTGGTATGACATGGTACGAACGATGTAA
1233282 AATCTTATAAGGTAAATGACAAAAAATCTTTGTGATTTAGGAGAAATAATACTTAGCTTCTTGTG
261 AATCTTATAAGGTAAATGACAAAAAATCTTTGTGATTTAGGAGAAATAATACTTAGCTTCTTGTG
1233347 TTTTAAAAATTGACACTTGCATTCCTTCAAAATATTTT
326 TTTTAAAAATTGACACTTGCATTCCTTCAAAATATTTT
* *
1233385 TAAAATATTTTAAGCTAAGATATGTAATAAGAACATATTTTTTAATATCAAGTAATTTAAGACAA
1 TAAAATATTTTAAGCTAAGATATGCAATAAGAACATATTTTTTAATATCAAGGAATTTAAGACAA
*
1233450 TTTAATATCTTTCAAAATATTTTT--AATAATTTAAGGAAAAAATACTAAGATTGATAATTTTTT
66 TTTAATATCTTTCAAAATATTTTTAAAATAATTTAAGGAAAAAATACTAAGATTGATAATTTTTA
*
1233513 AATAAAAGCTATTTAAGCTTACGTTATTGTTATATCAAAATCGAAATAAATTCAAAGCTAATAAA
131 AATAAAAGCTATTTAAGCTTACGTTATTGTTATATCAAAACCGAAATAAATTCAAAGCTAATAAA
* *
1233578 AGCTAACAAAATATCTAATTCAAACACATTTTTGATTTTGGTATGACATGGTACGAATGATGTAA
196 AGCTAACAAAATATCTAATTCAAACACATTTTTTATTTTGGTATGACATGGTACGAACGATGTAA
1233643 AATCTTATAAGGTAAATGACAAAAAATCTTTGTGATTTAGGAGAAATAATACTTAGCTTCTTGTG
261 AATCTTATAAGGTAAATGACAAAAAATCTTTGTGATTTAGGAGAAATAATACTTAGCTTCTTGTG
1233708 TTTTAAAAATTGACACTTGCATTCCTTC
326 TTTTAAAAATTGACACTTGCATTCCTTC
1233736 TGCTTTCATT
Statistics
Matches: 1040, Mismatches: 22, Indels: 17
0.96 0.02 0.02
Matches are distributed among these distances:
354 86 0.08
356 259 0.25
358 1 0.00
359 1 0.00
361 161 0.15
362 19 0.02
363 513 0.49
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (363 bp):
TAAAATATTTTAAGCTAAGATATGCAATAAGAACATATTTTTTAATATCAAGGAATTTAAGACAA
TTTAATATCTTTCAAAATATTTTTAAAATAATTTAAGGAAAAAATACTAAGATTGATAATTTTTA
AATAAAAGCTATTTAAGCTTACGTTATTGTTATATCAAAACCGAAATAAATTCAAAGCTAATAAA
AGCTAACAAAATATCTAATTCAAACACATTTTTTATTTTGGTATGACATGGTACGAACGATGTAA
AATCTTATAAGGTAAATGACAAAAAATCTTTGTGATTTAGGAGAAATAATACTTAGCTTCTTGTG
TTTTAAAAATTGACACTTGCATTCCTTCAAAATATTTT
Found at i:1234996 original size:2 final size:2
Alignment explanation
Indices: 1234989--1235028 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1234979 AGCTCATGAG
1234989 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
1235029 TAATTTAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1235796 original size:22 final size:20
Alignment explanation
Indices: 1235736--1235806 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 20
1235726 CTAAAAATGT
1235736 TATAATAAAATTTTATAAAA-A
1 TATAA-AAAA-TTTATAAAATA
1235757 T-TAAAAAATTTAATTAAAATA
1 TATAAAAAATTT-A-TAAAATA
1235778 TATAAAAAATAATTATAAAAT-
1 TATAAAAAAT--TTATAAAATA
1235799 T-TAAAAAA
1 TATAAAAAA
1235807 AGATATTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
18 3 0.07
19 5 0.11
20 15 0.34
21 4 0.09
22 14 0.32
23 1 0.02
24 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TATAAAAAATTTATAAAATA
Found at i:1235807 original size:22 final size:22
Alignment explanation
Indices: 1235748--1235807 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 22
1235738 TAATAAAATT
* **
1235748 TTATAAAAATTAAAAAATTTAA
1 TTATAAAATTTAAAAAAAATAA
* *
1235770 -T-TAAAATATATAAAAAATAA
1 TTATAAAATTTAAAAAAAATAA
1235790 TTATAAAATTTAAAAAAA
1 TTATAAAATTTAAAAAAA
1235808 GATATTTTAA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 14 0.48
21 2 0.07
22 13 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TTATAAAATTTAAAAAAAATAA
Found at i:1237166 original size:22 final size:22
Alignment explanation
Indices: 1237134--1237181 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1237124 TTATAAATAA
*
1237134 TATTTTTATTAAAATAATAAAT
1 TATTTTAATTAAAATAATAAAT
* * *
1237156 TATTTTAATTATATTAATAATT
1 TATTTTAATTAAAATAATAAAT
1237178 TATT
1 TATT
1237182 ATTTATTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTTTAATTAAAATAATAAAT
Found at i:1237338 original size:3 final size:3
Alignment explanation
Indices: 1237330--1237361 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1237320 TAAATATTTT
1237330 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1237362 TTTAGCTCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1239177 original size:12 final size:12
Alignment explanation
Indices: 1239162--1239188 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1239152 TATATATATA
1239162 TATATATTCAGG
1 TATATATTCAGG
1239174 TATATATTCAGG
1 TATATATTCAGG
1239186 TAT
1 TAT
1239189 GCTCCTACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (12 bp):
TATATATTCAGG
Found at i:1239442 original size:27 final size:26
Alignment explanation
Indices: 1239389--1239442 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
1239379 ATGAATACTA
*
1239389 AACAAAAAATTTAAACAAATTTTAATT
1 AACAAAAAA-TTAAACAAATTTCAATT
1239416 AACAAAAAA-TAAACAAATAATTCAATT
1 AACAAAAAATTAAACAAAT--TTCAATT
1239443 TTAAATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 9 0.38
27 15 0.62
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (26 bp):
AACAAAAAATTAAACAAATTTCAATT
Found at i:1239951 original size:24 final size:23
Alignment explanation
Indices: 1239911--1239959 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
1239901 GAACGAAAAA
*
1239911 AAGGAAGAAATAAGAGGAGGAGAG
1 AAGGAAGAAATAAGAGG-GAAGAG
*
1239935 AAGGAAGGAAA-AGGAGGGAAGAG
1 AAGGAA-GAAATAAGAGGGAAGAG
1239958 AA
1 AA
1239960 AAAGTTAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 7 0.32
24 11 0.50
25 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.43, T:0.02
Consensus pattern (23 bp):
AAGGAAGAAATAAGAGGGAAGAG
Found at i:1240883 original size:17 final size:16
Alignment explanation
Indices: 1240842--1240885 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1240832 TGTATATACC
* *
1240842 TTAATAAATTTTAATT
1 TTAATTAATTTTAATA
1240858 TTAACTTAATTTTAATAA
1 TTAA-TTAATTTTAAT-A
1240876 TTAATTAATT
1 TTAATTAATT
1240886 ATGAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATTAATTTTAATA
Found at i:1243655 original size:3 final size:3
Alignment explanation
Indices: 1243635--1243677 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
1243625 TTGATGCATC
* * *
1243635 ATA AAA ATA ATG ATA ATA ATA ATA ATA ATA ATG ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1243678 AGCTCAATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1246381 original size:13 final size:13
Alignment explanation
Indices: 1246363--1246388 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1246353 TACACAAAGT
1246363 ATGTATCGATACA
1 ATGTATCGATACA
1246376 ATGTATCGATACA
1 ATGTATCGATACA
1246389 CAAAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1246386 original size:32 final size:33
Alignment explanation
Indices: 1246345--1246408 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1246335 TAGCCAAACT
**
1246345 TGTATCGATACAC-AAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAATGTATCGATACAA
1246377 TGTATCGATACACAAAAAAATGTATCGATACA
1 TGTATCGATACACAAAAAAATGTATCGATACA
1246409 TTGGTTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTATCGATACACAAAAAAATGTATCGATACAA
Found at i:1250079 original size:19 final size:19
Alignment explanation
Indices: 1250052--1250107 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
1250042 GGTATTGATA
*
1250052 CATTATATCGATACATGCT
1 CATTGTATCGATACATGCT
*
1250071 CATTGTATCGATACATACT
1 CATTGTATCGATACATGCT
1250090 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
1250108 AAACTGGCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:1250161 original size:20 final size:20
Alignment explanation
Indices: 1250131--1250184 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1250121 CTATCCTAAG
*
1250131 AGAAATGTATCGATACATG-
1 AGAATTGTATCGATACATGA
*
1250150 GGACATTGTATCGATACATGA
1 AGA-ATTGTATCGATACATGA
1250171 AGAATTGTATCGAT
1 AGAATTGTATCGAT
1250185 GCATTATGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.07
20 26 0.87
21 2 0.07
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (20 bp):
AGAATTGTATCGATACATGA
Found at i:1254730 original size:20 final size:20
Alignment explanation
Indices: 1254705--1254749 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1254695 GAAAATATTG
1254705 ATACAAATCCA-AATGTATCA
1 ATACAAA-CCATAATGTATCA
* *
1254725 ATACAAAGCATAATGTATCG
1 ATACAAACCATAATGTATCA
1254745 ATACA
1 ATACA
1254750 TTGTATAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.49, C:0.18, G:0.09, T:0.24
Consensus pattern (20 bp):
ATACAAACCATAATGTATCA
Found at i:1254773 original size:19 final size:19
Alignment explanation
Indices: 1254748--1254838 Score: 113
Period size: 19 Copynumber: 5.1 Consensus size: 19
1254738 TGTATCGATA
*
1254748 CATTGTATAGATACATGTT
1 CATTGTATCGATACATGTT
*
1254767 TATTGTATCGATACATGTT
1 CATTGTATCGATACATGTT
1254786 CATTGTATCGAT--A----
1 CATTGTATCGATACATGTT
1254799 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGTT
*
1254818 CATTGTATCGATACATATT
1 CATTGTATCGATACATGTT
1254837 CA
1 CA
1254839 ATCGTATTGA
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
13 12 0.19
15 1 0.02
17 1 0.02
19 48 0.77
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (19 bp):
CATTGTATCGATACATGTT
Found at i:1254799 original size:51 final size:51
Alignment explanation
Indices: 1254738--1254838 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
1254728 CAAAGCATAA
* *
1254738 TGTATCGATACATTGTATAGATACATGTTTATTGTATCGATACATGTTCAT
1 TGTATCGATACATTGTATAGATACATGTTCATTGTATCGATACATATTCAT
*
1254789 TGTATCGATACATTGTATCGATACATGTTCATTGTATCGATACATATTCA
1 TGTATCGATACATTGTATAGATACATGTTCATTGTATCGATACATATTCA
1254839 ATCGTATTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.42
Consensus pattern (51 bp):
TGTATCGATACATTGTATAGATACATGTTCATTGTATCGATACATATTCAT
Found at i:1254804 original size:13 final size:13
Alignment explanation
Indices: 1254786--1254814 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1254776 GATACATGTT
1254786 CATTGTATCGATA
1 CATTGTATCGATA
1254799 CATTGTATCGATA
1 CATTGTATCGATA
1254812 CAT
1 CAT
1254815 GTTCATTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1254804 original size:32 final size:32
Alignment explanation
Indices: 1254768--1254833 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
1254758 ATACATGTTT
1254768 ATTGTATCGATACATGTTCATTGTATCGATAC
1 ATTGTATCGATACATGTTCATTGTATCGATAC
1254800 ATTGTATCGATACATGTTCATTGTATCGATAC
1 ATTGTATCGATACATGTTCATTGTATCGATAC
1254832 AT
1 AT
1254834 ATTCAATCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (32 bp):
ATTGTATCGATACATGTTCATTGTATCGATAC
Found at i:1254920 original size:13 final size:13
Alignment explanation
Indices: 1254899--1254928 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1254889 TGATACATGG
1254899 TACACTGTATCGA
1 TACACTGTATCGA
*
1254912 TACAGTGTATCGA
1 TACACTGTATCGA
1254925 TACA
1 TACA
1254929 TAGTGAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (13 bp):
TACACTGTATCGA
Found at i:1263510 original size:20 final size:19
Alignment explanation
Indices: 1263467--1263519 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
1263457 ACATTATGGT
* * *
1263467 TTGTATTGATACATGTTCA
1 TTGTATCGATACATCTTAA
1263486 TTGTATCGATACATACTTAA
1 TTGTATCGATACAT-CTTAA
*
1263506 TTGTATCGGTACAT
1 TTGTATCGATACAT
1263520 GAAAATAGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (19 bp):
TTGTATCGATACATCTTAA
Found at i:1263583 original size:13 final size:13
Alignment explanation
Indices: 1263565--1263595 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1263555 TGATACATGG
*
1263565 TACATTGTATTGA
1 TACATTGTATCGA
1263578 TACATTGTATCGA
1 TACATTGTATCGA
1263591 TACAT
1 TACAT
1263596 AGTGAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1280869 original size:28 final size:26
Alignment explanation
Indices: 1280838--1280975 Score: 136
Period size: 28 Copynumber: 5.1 Consensus size: 26
1280828 ATCCTCCGCA
*
1280838 AAAAAAATAAAGAAGAAGAGAAAAAAAC
1 AAAAAAATAAACAA-AAGA-AAAAAAAC
*
1280866 AAAAAAA-ACAACAAAAAAATAAAAAAC
1 AAAAAAATA-AACAAAAGAA-AAAAAAC
* *
1280893 AGAAAAAAAAAACAACAACAAAAAAAAC
1 A-AAAAAATAAACAA-AAGAAAAAAAAC
* *
1280921 AAAAAAACAAA-AAGAGAAAAAAAAC
1 AAAAAAATAAACAAAAGAAAAAAAAC
1280946 AAAAAAATAAACAAACAGACAAAAAAAC
1 AAAAAAATAAACAAA-AGA-AAAAAAAC
1280974 AA
1 AA
1280976 CAACAAAAAG
Statistics
Matches: 94, Mismatches: 8, Indels: 16
0.80 0.07 0.14
Matches are distributed among these distances:
25 20 0.21
26 5 0.05
27 24 0.26
28 40 0.43
29 5 0.05
ACGTcount: A:0.82, C:0.10, G:0.06, T:0.02
Consensus pattern (26 bp):
AAAAAAATAAACAAAAGAAAAAAAAC
Found at i:1280872 original size:9 final size:9
Alignment explanation
Indices: 1280858--1280952 Score: 99
Period size: 9 Copynumber: 10.7 Consensus size: 9
1280848 AGAAGAAGAG
1280858 AAAAAAACA
1 AAAAAAACA
1280867 AAAAAAACA
1 AAAAAAACA
1280876 ACAAAAAA-A
1 A-AAAAAACA
*
1280885 TAAAAAACA
1 AAAAAAACA
1280894 GAAAAAAA-A
1 -AAAAAAACA
*
1280903 AACAACAACA
1 AA-AAAAACA
1280913 AAAAAAAC-
1 AAAAAAACA
1280921 AAAAAAAC-
1 AAAAAAACA
* *
1280929 AAAAAGAGA
1 AAAAAAACA
1280938 AAAAAAACA
1 AAAAAAACA
1280947 AAAAAA
1 AAAAAA
1280953 TAAACAAACA
Statistics
Matches: 72, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
8 22 0.31
9 35 0.49
10 15 0.21
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (9 bp):
AAAAAAACA
Found at i:1280882 original size:40 final size:37
Alignment explanation
Indices: 1280838--1280960 Score: 131
Period size: 43 Copynumber: 3.1 Consensus size: 37
1280828 ATCCTCCGCA
1280838 AAAAAAATAAAGAAGAAGAGAAAAAAACAAAAAAAACAAC
1 AAAAAAATAAA-AAGAAGA-AAAAAAACAAAAAAAA-AAC
*
1280878 AAAAAAATAAAAAACAGAAAAAAAAAACAACAACAAAAAAAAC
1 AAAAAAAT--AAAA-AG-AAGAAAAAA-AACAA-AAAAAAAAC
*
1280921 AAAAAAACAAAAAG-AGAAAAAAAACAAAAAAATAAAC
1 AAAAAAATAAAAAGAAGAAAAAAAACAAAAAAA-AAAC
1280958 AAA
1 AAA
1280961 CAGACAAAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 17
0.78 0.03 0.18
Matches are distributed among these distances:
36 5 0.07
37 12 0.16
38 7 0.10
40 10 0.14
41 5 0.07
42 10 0.14
43 18 0.25
44 6 0.08
ACGTcount: A:0.83, C:0.09, G:0.06, T:0.02
Consensus pattern (37 bp):
AAAAAAATAAAAAGAAGAAAAAAAACAAAAAAAAAAC
Found at i:1280897 original size:37 final size:36
Alignment explanation
Indices: 1280838--1280981 Score: 120
Period size: 34 Copynumber: 4.0 Consensus size: 36
1280828 ATCCTCCGCA
*
1280838 AAAAAAATAAAGAAGAAGAGAAAAAAACAAAAAAAACAAC
1 AAAAAAAT-AA-AA-AACAGAAAAAAA-AAAAAAAACAAC
*
1280878 AAAAAAATAAAAAACAG--AAAAAAAAAACAACAAC
1 AAAAAAATAAAAAACAGAAAAAAAAAAAAAAACAAC
* *
1280912 AAAAAAA-ACAAAAA-A-ACAAAAAGAGAAAAAA-AAC
1 AAAAAAATA-AAAAACAGA-AAAAAAAAAAAAAACAAC
* * *
1280946 AAAAAAATAAACAAACAGACAAAAAAACAACAACAA
1 AAAAAAATAAA-AAACAGAAAAAAAAAAAAAAACAA
1280982 AAAGGGTCAG
Statistics
Matches: 85, Mismatches: 10, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
33 2 0.02
34 35 0.41
35 19 0.22
36 10 0.12
37 7 0.08
38 2 0.02
39 2 0.02
40 8 0.09
ACGTcount: A:0.81, C:0.11, G:0.06, T:0.02
Consensus pattern (36 bp):
AAAAAAATAAAAAACAGAAAAAAAAAAAAAAACAAC
Found at i:1280910 original size:34 final size:34
Alignment explanation
Indices: 1280860--1280984 Score: 141
Period size: 34 Copynumber: 3.6 Consensus size: 34
1280850 AAGAAGAGAA
*
1280860 AAAAACAAAAAAAACAACAAAAAAATAAAAAACAG
1 AAAAA-AAAAACAACAACAAAAAAATAAAAAACAG
*
1280895 AAAAAAAAAACAACAACAAAAAAAACAAAAAAACA-
1 AAAAAAAAAACAACAAC-AAAAAAA-TAAAAAACAG
*
1280930 AAAAGAGAAAA-AA-AACAAAAAAATAAACAAACAG
1 AAAA-AAAAAACAACAACAAAAAAATAAA-AAACAG
*
1280964 -ACAAAAAAACAACAACAAAAA
1 AAAAAAAAAACAACAACAAAAA
1280985 GGGTCAGGAT
Statistics
Matches: 77, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
32 8 0.10
33 16 0.21
34 22 0.29
35 18 0.23
36 13 0.17
ACGTcount: A:0.82, C:0.13, G:0.03, T:0.02
Consensus pattern (34 bp):
AAAAAAAAAACAACAACAAAAAAATAAAAAACAG
Found at i:1280916 original size:43 final size:41
Alignment explanation
Indices: 1280836--1280977 Score: 126
Period size: 42 Copynumber: 3.4 Consensus size: 41
1280826 GCATCCTCCG
* * * *
1280836 CAAAAAAAATAAAGA-AGAAGAGAAAAAAACAAAAAAAACAA
1 CAAAAAAAA-AAAAACAGAAAAAAAAAAAACAAAAAAAAAAA
*
1280877 CAAAAAAATAAAAAACAGAAAAAAAAAACAACAACAAAAAAAA
1 CAAAAAAA-AAAAAACAGAAAAAAAAAA-AACAAAAAAAAAAA
* * * *
1280920 CAAAAAAACAAAAAGAGAAAAAAAACAAAA-AAATAAACAAA
1 CAAAAAAAAAAAAACAGAAAAAAAA-AAAACAAAAAAAAAAA
* *
1280961 CAGACAAAAAAACAACA
1 CA-AAAAAAAAAAAACA
1280978 ACAAAAAGGG
Statistics
Matches: 82, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
41 22 0.27
42 38 0.46
43 22 0.27
ACGTcount: A:0.81, C:0.11, G:0.06, T:0.02
Consensus pattern (41 bp):
CAAAAAAAAAAAAACAGAAAAAAAAAAAACAAAAAAAAAAA
Found at i:1280972 original size:1 final size:1
Alignment explanation
Indices: 1280858--1280952 Score: 64
Period size: 1 Copynumber: 95.0 Consensus size: 1
1280848 AGAAGAAGAG
* * * * * * * * * *
1280858 AAAAAAACAAAAAAAACAACAAAAAAATAAAAAACAGAAAAAAAAAACAACAACAAAAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
1280923 AAAAACAAAAAGAGAAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1280953 TAAACAAACA
Statistics
Matches: 66, Mismatches: 28, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (1 bp):
A
Found at i:1282555 original size:58 final size:58
Alignment explanation
Indices: 1282408--1282729 Score: 472
Period size: 58 Copynumber: 5.6 Consensus size: 58
1282398 CATTCCTCAC
* * *
1282408 CCTTCAAAAGCCCACAAGTCAGTGGCA-TCTTTTTCAAAGCCCACAAGTTAGTAGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAGTCAGTGGCAA
* *
1282465 CCTTC-AAAGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAGTCAGTGGCAA
* *
1282522 CCTTCAAAAGCCCACAAGTCAGTGGCACTCTTTTTCAAAGCCCACAAGTCAGTGACAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAGTCAGTGGCAA
* * *
1282580 CCTTC-AAAGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCACAAATCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAGTCAGTGGCAA
* * *
1282637 CCTTCAAAAGCCCACAAGTTAGTGGCACCCTTTTTCAAAACCCACAAATCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAGTCAGTGGCAA
* * *
1282695 CCTTTAAAAGCCCACAAGTCGGTGGCA-TCTTTTTC
1 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTTC
1282730 CTTTTAAGCC
Statistics
Matches: 240, Mismatches: 22, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
56 20 0.08
57 95 0.40
58 125 0.52
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.21
Consensus pattern (58 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAGTCAGTGGCAA
Found at i:1282609 original size:115 final size:115
Alignment explanation
Indices: 1282408--1282730 Score: 506
Period size: 115 Copynumber: 2.8 Consensus size: 115
1282398 CATTCCTCAC
*
1282408 CCTTCAAAAGCCCACAAGTCAGTGGCA-TCTTTTTCAAAGCCCACAAGTTAGT-AGCAACCTTCA
1 CCTTCAAAAGCCCACAAGTCAGTGGCACTCTTTTTCAAAGCCCACAAGTCAGTGA-CAACCTTCA
*
1282471 AAGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCAA
65 AAGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCACAAATCAGTGGCAA
1282522 CCTTCAAAAGCCCACAAGTCAGTGGCACTCTTTTTCAAAGCCCACAAGTCAGTGACAACCTTCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCACTCTTTTTCAAAGCCCACAAGTCAGTGACAACCTTCAA
1282587 AGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCACAAATCAGTGGCAA
66 AGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCACAAATCAGTGGCAA
* * * * * *
1282637 CCTTCAAAAGCCCACAAGTTAGTGGCACCCTTTTTCAAAACCCACAAATCAGTGGCAACCTTTAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCACTCTTTTTCAAAGCCCACAAGTCAGTGACAACC-TTCA
* * * *
1282702 AAGCCCACAAGTCGGTGGCATCTTTTTCC
65 AAGCCCACAAATCAGTGGCACCCTTTTCC
1282731 TTTTAAGCCC
Statistics
Matches: 194, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
114 27 0.14
115 138 0.71
116 29 0.15
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.21
Consensus pattern (115 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCACTCTTTTTCAAAGCCCACAAGTCAGTGACAACCTTCAA
AGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCACAAATCAGTGGCAA
Found at i:1282767 original size:32 final size:32
Alignment explanation
Indices: 1282702--1282791 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
1282692 CAACCTTTAA
* * *
1282702 AAGCCCACAAGTCGGTGGCATCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCA-CCTTTTCCTTTT
* *
1282735 AAGCCCACAACTCCGTGGCGCCTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTCCTTTT
* *
1282767 AAGTCCACAACTTCGTGGCACCTTT
1 AAGCCCACAACTCCGTGGCACCTTT
1282792 AAAACCAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 32 0.65
33 17 0.35
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (32 bp):
AAGCCCACAACTCCGTGGCACCTTTTCCTTTT
Found at i:1282897 original size:43 final size:43
Alignment explanation
Indices: 1282836--1283388 Score: 385
Period size: 49 Copynumber: 11.8 Consensus size: 43
1282826 GGCACCTTGT
*
1282836 CTTTAAGACCAATGTCGCTGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
* * * *
1282879 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGTATATTGGCACCTTTGTC
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-------C
*
1282929 ATCTTTAAGACCAATGTTGCTGGCCTTGAATCAGCACATTGGCA-
1 --CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
* *
1282973 C---AAGACCAATGTCGCTGGCCATGAATCAGCATATTGGCGCCTTCATC
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATT-G-G----CA-C
* *
1283020 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCGCCTTCAT
1 --CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATT-G-G----CAC
* *
1283071 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCAC
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG------CAC
* * *
1283120 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1283163 CTTTATCTTTAGGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTC
1 CTTTA-----A-GACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C
1283216 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
* * * * * *
1283261 CTTTAAGTCCAATATCGCTGGCCTTGAATCAATATATTGGCGCTTTTGTCAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATC-----A---GCAC-ATTGGCAC
** *
1283313 CTTTAAGACCAATGTCGCTGGCCTTGTCTCAGCACATTGTCAC
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
* *
1283356 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGC
1283389 CTATTGACAT
Statistics
Matches: 424, Mismatches: 41, Indels: 90
0.76 0.07 0.16
Matches are distributed among these distances:
39 31 0.07
40 1 0.00
41 1 0.00
42 1 0.00
43 108 0.25
44 3 0.01
45 3 0.01
47 2 0.00
48 3 0.01
49 151 0.36
50 2 0.00
51 3 0.01
52 109 0.26
53 1 0.00
55 5 0.01
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (43 bp):
CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:1282990 original size:39 final size:39
Alignment explanation
Indices: 1282935--1283010 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
1282925 TGTCATCTTT
* *
1282935 AAGACCAATGTTGCTGGCCTTGAATCAGCACATTGGCAC
1 AAGACCAATGTCGCTGGCCATGAATCAGCACATTGGCAC
*
1282974 AAGACCAATGTCGCTGGCCATGAATCAGCATATTGGC
1 AAGACCAATGTCGCTGGCCATGAATCAGCACATTGGC
1283011 GCCTTCATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (39 bp):
AAGACCAATGTCGCTGGCCATGAATCAGCACATTGGCAC
Found at i:1283090 original size:49 final size:49
Alignment explanation
Indices: 1282978--1283502 Score: 464
Period size: 49 Copynumber: 10.6 Consensus size: 49
1282968 TGGCACAAGA
* *
1282978 CCAATGTCGCTGGCCATGAATCAGCATATTGGCGCCTTCATCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCGCC-T--TCATCTTTAAGT
1283030 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCGCCTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCGCCTTCATCTTTAAGT
* ** *
1283079 CCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCACCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCGCCTTCATCTTTAAGT
* * * * * *
1283128 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAGGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCGCCTTCATCTTTAAGT
* * *
1283177 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCGCCTTCATCTTTAAGT
*
1283226 CCAATGTCGCTGGCCTTGAATCAGCACATT-G-G----CACCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCGCCTTCATCTTTAAGT
* ** * * *
1283269 CCAATATCGCTGGCCTTGAATCAATATATTGGCGCTTTTGTCATCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCGC--CT-TCATCTTTAAGT
** *
1283321 CCAATGTCGCTGGCCTTGTCTCAGCACATT---G---TCACCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCGCCTTCATCTTTAAGT
* * * * **
1283364 CCAATATCGCTGGCCTTGAATCAGC-CTATTGACATCTTTTTTCTCATCTTTAAAAC
1 CCAATGTCGCTGGCCTTGAATCAGCAC-ATTGGC-GC----CT-TCATCTTT-AAGT
* * * *
1283420 CCAATGTCGCTGGCCTTGAATCAGCACATTGACATTCTTCTCATCTTCAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGC--GCCT-TCATCTTTAAGT
* * *
1283472 CTAATGTCGCTGACCGTGAATCAGCACATTG
1 CCAATGTCGCTGGCCTTGAATCAGCACATTG
1283503 ACATCCTTTT
Statistics
Matches: 399, Mismatches: 49, Indels: 50
0.80 0.10 0.10
Matches are distributed among these distances:
42 1 0.00
43 70 0.18
44 1 0.00
45 1 0.00
48 1 0.00
49 175 0.44
51 1 0.00
52 97 0.24
53 10 0.03
55 7 0.02
56 32 0.08
57 3 0.01
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (49 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCGCCTTCATCTTTAAGT
Found at i:1283159 original size:98 final size:93
Alignment explanation
Indices: 1282785--1283450 Score: 654
Period size: 98 Copynumber: 7.0 Consensus size: 93
1282775 AACTTCGTGG
** * * **
1282785 CACCTTTAAAACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAAT
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCACCTTTAAGACCAAT
*
1282849 GTCGCTGACCTTGAATCAGCACATTGG-
66 GTCGCTGGCCTTGAATCAGCACATTGGT
* * * *
1282876 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGTATATTGGCACCTTTGTCATCTTTAAGACC
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--TCT-TCACCTTTAAGACC
*
1282941 AATGTTGCTGGCCTTGAATCAGCACATTGG-
63 AATGTCGCTGGCCTTGAATCAGCACATTGGT
* * * * ** *
1282971 CA-C---AAGACCAATGTCGCTGGCCATGAATCAGCATATTGGCGCCTTCATCATCTTTAAGTCC
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCA-C--CTTTAAGACC
1283032 AATGTCGCTGGCCTTGAATCAGCACATTGGCGCCTT
63 AATGTCGCTGGCCTTGAATCAGCACATT-G-G---T
* *
1283068 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCACCTTTAAGTCCAAT
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCACCTTTAAGACCAAT
* *
1283133 ATCGCTGGCCTTGAATCAGCATATTGG-
66 GTCGCTGGCCTTGAATCAGCACATTGGT
* * *
1283160 CACCTTTATCTTTAGGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTTCATCTTTAA
1 CACCTTTA-----A-GTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATC-TTCACCTTTAA
1283224 GACCAATGTCGCTGGCCTTGAATCAGCACATTGG-
59 GACCAATGTCGCTGGCCTTGAATCAGCACATTGGT
** * * * *
1283258 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAATATATTGGCGCTTTTGTCATCTTTAAGACC
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT-G-GCATCT-TCACCTTTAAGACC
**
1283323 AATGTCGCTGGCCTTGTCTCAGCACATT-GT
63 AATGTCGCTGGCCTTGAATCAGCACATTGGT
* *
1283353 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC-CTATTGACATCTTTTTTCTCATCTTTAA
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCAC-ATTGGCATC-----T-TCACCTTTAA
*
1283417 AACCCAATGTCGCTGGCCTTGAATCAGCACATTG
59 GA-CCAATGTCGCTGGCCTTGAATCAGCACATTG
1283451 ACATTCTTCT
Statistics
Matches: 486, Mismatches: 52, Indels: 65
0.81 0.09 0.11
Matches are distributed among these distances:
88 3 0.01
89 1 0.00
91 111 0.23
92 35 0.07
93 6 0.01
94 7 0.01
95 118 0.24
96 1 0.00
97 5 0.01
98 132 0.27
99 28 0.06
100 1 0.00
101 38 0.08
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.31
Consensus pattern (93 bp):
CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCACCTTTAAGACCAAT
GTCGCTGGCCTTGAATCAGCACATTGGT
Found at i:1283441 original size:56 final size:54
Alignment explanation
Indices: 1283364--1283548 Score: 207
Period size: 52 Copynumber: 3.4 Consensus size: 54
1283354 ACCTTTAAGT
1283364 CCAATATCGCTGGCCTTGAATCAGC-CTATTGACATCTTTTTTCTCATCTTTAAAA
1 CCAATATCGCTGGCCTTGAATCAGCAC-ATTGACATCTTTTTTCTCATCTTT-AAA
* * * *
1283419 CCCAATGTCGCTGGCCTTGAATCAGCACATTGACA---TTCTTCTCATCTTCAAGT
1 -CCAATATCGCTGGCCTTGAATCAGCACATTGACATCTTTTTTCTCATCTTTAA-A
* * * * *
1283472 CTAATGTCGCTGACCGTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGACATCTTTTTTCTCATCTTTAAA
* *
1283526 CCAATATCGTTGGCCATGAATCA
1 CCAATATCGCTGGCCTTGAATCA
1283549 ACGTATTGAT
Statistics
Matches: 109, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
52 33 0.30
53 12 0.11
54 18 0.17
55 14 0.13
56 31 0.28
57 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (54 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGACATCTTTTTTCTCATCTTTAAA
Found at i:1288015 original size:18 final size:18
Alignment explanation
Indices: 1287992--1288026 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1287982 ATTAAATTTA
*
1287992 ATAATTTTAAAACACAAC
1 ATAATTATAAAACACAAC
*
1288010 ATAATTATATAACACAA
1 ATAATTATAAAACACAA
1288027 ATGCAATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAATTATAAAACACAAC
Found at i:1288209 original size:36 final size:36
Alignment explanation
Indices: 1288169--1288248 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
1288159 CAAATATATT
*
1288169 AAATAAAAAAGTAAAGGCATAAAATTAAAAAA-AAAC
1 AAATAAAAAAGTAAA-GCATAAAAGTAAAAAATAAAC
** ** *
1288205 AAATAAAAATTTAAAGTTTAAAAGTAAAAAATAAAT
1 AAATAAAAAAGTAAAGCATAAAAGTAAAAAATAAAC
1288241 AAATAAAA
1 AAATAAAA
1288249 TGAGTGCGGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
35 13 0.35
36 24 0.65
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (36 bp):
AAATAAAAAAGTAAAGCATAAAAGTAAAAAATAAAC
Found at i:1290216 original size:27 final size:28
Alignment explanation
Indices: 1290163--1290233 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
1290153 CGTAAAAAAT
1290163 ATAATATGAAAAATAATTAAAATATG-AC
1 ATAATAT-AAAAATAATTAAAATATGAAC
*
1290191 ATAATATAAAAATAATATGAAA-ATGAAAC
1 ATAATATAAAAATAAT-TAAAATATG-AAC
*
1290220 A-AATAAAAAAATAA
1 ATAATATAAAAATAA
1290234 CGTGTCAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 12 0.32
28 23 0.61
29 3 0.08
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.24
Consensus pattern (28 bp):
ATAATATAAAAATAATTAAAATATGAAC
Found at i:1290355 original size:18 final size:18
Alignment explanation
Indices: 1290332--1290379 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1290322 ATTAAATTTA
*
1290332 ATAATTTTAAAACACAAC
1 ATAATTATAAAACACAAC
*
1290350 ATAATTATATAACACAA-
1 ATAATTATAAAACACAAC
*
1290367 ATACAATATAAAA
1 ATA-ATTATAAAA
1290380 ATAATTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.27
Consensus pattern (18 bp):
ATAATTATAAAACACAAC
Found at i:1290421 original size:40 final size:40
Alignment explanation
Indices: 1290376--1290451 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
1290366 AATACAATAT
1290376 AAAAATAATTAAAAATTAAACAAAA-AAAGTATTAATACAC
1 AAAAAT-ATTAAAAATTAAACAAAATAAAGTATTAATACAC
* * * *
1290416 AAAAATATTAAAATTTATATAAAATAAATTATTAAT
1 AAAAATATTAAAAATTAAACAAAATAAAGTATTAAT
1290452 TTTTCAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 15 0.48
40 16 0.52
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.30
Consensus pattern (40 bp):
AAAAATATTAAAAATTAAACAAAATAAAGTATTAATACAC
Found at i:1292291 original size:14 final size:14
Alignment explanation
Indices: 1292250--1292294 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1292240 TTCATGTAGT
*
1292250 TTTATTAATTAATA
1 TTTATTACTTAATA
*
1292264 ATT-TTAC-T-ATA
1 TTTATTACTTAATA
1292275 TTTATTACTTAATA
1 TTTATTACTTAATA
1292289 TTTATT
1 TTTATT
1292295 TTTAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
11 5 0.20
12 5 0.20
13 4 0.16
14 11 0.44
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTATTACTTAATA
Found at i:1292439 original size:11 final size:11
Alignment explanation
Indices: 1292395--1292439 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
1292385 TTATATGATA
1292395 AAAATATAATAT
1 AAAATATAA-AT
* *
1292407 AAAAAATAATT
1 AAAATATAAAT
1292418 AAAATAT-AAT
1 AAAATATAAAT
1292428 AAAATATAAAT
1 AAAATATAAAT
1292439 A
1 A
1292440 GTAATATGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
10 9 0.32
11 11 0.39
12 8 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAATATAAAT
Found at i:1296218 original size:2 final size:2
Alignment explanation
Indices: 1296211--1296248 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1296201 CTTTATATGC
1296211 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1296249 GAGTCATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1297448 original size:20 final size:19
Alignment explanation
Indices: 1297423--1297461 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1297413 CCACGACTTT
*
1297423 GTATCGATACCTTGCCTTAA
1 GTATCGATACATTG-CTTAA
1297443 GTATCGATACATTGCTTAA
1 GTATCGATACATTGCTTAA
1297462 AAAACTAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (19 bp):
GTATCGATACATTGCTTAA
Found at i:1300389 original size:49 final size:48
Alignment explanation
Indices: 1300244--1300392 Score: 135
Period size: 48 Copynumber: 3.1 Consensus size: 48
1300234 TTTTAGTGAG
* * * * *
1300244 TGTATCAATACAATCT-GGAAACCTAGATGTACCGATACATTTTGCAT
1 TGTATCCATACATTCTCGAAAACCTAGATGTATCGATACATTTTACAT
* * * * *
1300291 TGTTTCGATACATTCTCGAAAACCCA-AAGATATTGATACATTTTACAT
1 TGTATCCATACATTCTCGAAAACCTAGATG-TATCGATACATTTTACAT
*
1300339 TGTATCCATACATTCT-GAAAAAACCTAGATGTATCGATACGTTGTT-CAT
1 TGTATCCATACATTCTCG--AAAACCTAGATGTATCGATACATT-TTACAT
1300388 TGTAT
1 TGTAT
1300393 TGATACAAAA
Statistics
Matches: 81, Mismatches: 15, Indels: 10
0.76 0.14 0.09
Matches are distributed among these distances:
47 16 0.20
48 36 0.44
49 25 0.31
50 4 0.05
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (48 bp):
TGTATCCATACATTCTCGAAAACCTAGATGTATCGATACATTTTACAT
Found at i:1303832 original size:52 final size:52
Alignment explanation
Indices: 1303687--1303812 Score: 234
Period size: 52 Copynumber: 2.4 Consensus size: 52
1303677 AATATGAAAT
*
1303687 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATTTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
*
1303739 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGTAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
1303791 TTTGCCTGCATGTATCGATACA
1 TTTGCCTGCATGTATCGATACA
1303813 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
Found at i:1303897 original size:30 final size:30
Alignment explanation
Indices: 1303863--1303960 Score: 76
Period size: 30 Copynumber: 3.2 Consensus size: 30
1303853 AATGTATCGA
1303863 TACATTTTCTTGGCAGTAGCTTCGTAACTG
1 TACATTTTCTTGGCAGTAGCTTCGTAACTG
* * * * * *
1303893 TACATTGTATCGAT-ACA-AAACTTATGTATC-G
1 TACATT-T-TC-TTGGCAGTAGCTT-CGTAACTG
1303924 ATACATTTTCTTGGCAGTAGCTTCGTAACTG
1 -TACATTTTCTTGGCAGTAGCTTCGTAACTG
1303955 TACATT
1 TACATT
1303961 GTATCGATAC
Statistics
Matches: 48, Mismatches: 12, Indels: 16
0.63 0.16 0.21
Matches are distributed among these distances:
29 1 0.02
30 20 0.42
31 12 0.25
32 14 0.29
33 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (30 bp):
TACATTTTCTTGGCAGTAGCTTCGTAACTG
Found at i:1303935 original size:62 final size:62
Alignment explanation
Indices: 1303854--1303992 Score: 278
Period size: 62 Copynumber: 2.2 Consensus size: 62
1303844 CATTTGAGTA
1303854 ATGTATCGATACATTTTCTTGGCAGTAGCTTCGTAACTGTACATTGTATCGATACAAAACTT
1 ATGTATCGATACATTTTCTTGGCAGTAGCTTCGTAACTGTACATTGTATCGATACAAAACTT
1303916 ATGTATCGATACATTTTCTTGGCAGTAGCTTCGTAACTGTACATTGTATCGATACAAAACTT
1 ATGTATCGATACATTTTCTTGGCAGTAGCTTCGTAACTGTACATTGTATCGATACAAAACTT
1303978 ATGTATCGATACATT
1 ATGTATCGATACATT
1303993 GTATCGATAC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 77 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.37
Consensus pattern (62 bp):
ATGTATCGATACATTTTCTTGGCAGTAGCTTCGTAACTGTACATTGTATCGATACAAAACTT
Found at i:1303997 original size:13 final size:13
Alignment explanation
Indices: 1303978--1304043 Score: 114
Period size: 13 Copynumber: 5.1 Consensus size: 13
1303968 TACAAAACTT
1303978 ATGTATCGATACA
1 ATGTATCGATACA
*
1303991 TTGTATCGATACA
1 ATGTATCGATACA
1304004 ATGTATCGATACA
1 ATGTATCGATACA
*
1304017 TTGTATCGATACA
1 ATGTATCGATACA
1304030 ATGTATCGATACA
1 ATGTATCGATACA
1304043 A
1 A
1304044 CACTTATGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1304007 original size:26 final size:26
Alignment explanation
Indices: 1303978--1304042 Score: 130
Period size: 26 Copynumber: 2.5 Consensus size: 26
1303968 TACAAAACTT
1303978 ATGTATCGATACATTGTATCGATACA
1 ATGTATCGATACATTGTATCGATACA
1304004 ATGTATCGATACATTGTATCGATACA
1 ATGTATCGATACATTGTATCGATACA
1304030 ATGTATCGATACA
1 ATGTATCGATACA
1304043 ACACTTATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (26 bp):
ATGTATCGATACATTGTATCGATACA
Found at i:1308357 original size:3 final size:3
Alignment explanation
Indices: 1308349--1308381 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1308339 TTCCTTAACC
1308349 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1308382 CTTTGAGTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:1309858 original size:38 final size:38
Alignment explanation
Indices: 1309761--1309858 Score: 108
Period size: 38 Copynumber: 2.6 Consensus size: 38
1309751 AGCTTAAGTA
* * ** *
1309761 GTTTTTGTTTCTAACTATACCATTGGTTTAGAATAATG
1 GTTTTTGTTTCTAACTATGCCACTAATTAAGAATAATG
* *
1309799 ATTTTTGTTT-TGAACTGTGCCACTAATTAAGAATAATG
1 GTTTTTGTTTCT-AACTATGCCACTAATTAAGAATAATG
*
1309837 GTTTTTGTTTCTAACCATGCCA
1 GTTTTTGTTTCTAACTATGCCA
1309859 TCAATTGATA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
37 1 0.02
38 46 0.96
39 1 0.02
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (38 bp):
GTTTTTGTTTCTAACTATGCCACTAATTAAGAATAATG
Found at i:1311750 original size:79 final size:79
Alignment explanation
Indices: 1311649--1312007 Score: 340
Period size: 79 Copynumber: 4.6 Consensus size: 79
1311639 CTCGAGACAA
*
1311649 AAAATT-TAATATTTTTG-AAATAAAAACGGGGTTGGAGTATCCCCTCAAAAATAATGAGGTTTG
1 AAAATTCT-ATATTTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCAAAAATAATGAGGTTGG
1311712 AGTATCCCCGAAATG
65 AGTATCCCCGAAATG
* * * ** * ** *
1311727 AAAATTCGATATTTTTGGAAATAAAAACAGGGGTTGCAGTATTTCCTCGAAAATAACAAAGTTGG
1 AAAATTCTATATTTTTGAAAATAAAAAC-GGGGTTGGAGTATCCCCTCAAAAATAATGAGGTTGG
* *
1311792 AGTATCTCCGAGATG
65 AGTATCCCCGAAATG
* * * *
1311807 -AAATTCTA-ATATTTTGAAAATAAAAA-TGGGTTAGAGTATCCCCTCAAAATTAATGGGGTTGG
1 AAAATTCTATAT-TTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCAAAAATAATGAGGTTGG
* * **
1311869 AATACCCCCGTGATGG
65 AGTATCCCCGAAAT-G
* * * * *
1311885 AGAATT-TA-ATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCGAAATTGATGTGGTTGG
1 AAAATTCTATAT-TTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCAAAAATAATGAGGTTGG
*
1311948 AGTATCTCC-AAGATG
65 AGTATCCCCGAA-ATG
* *
1311963 AAAATTTTA-ATATTTTGAAAATAAAAATGGGGTTGGAGTATCCCC
1 AAAATTCTATAT-TTTTGAAAATAAAAACGGGGTTGGAGTATCCCC
1312008 GATAAAGAAT
Statistics
Matches: 231, Mismatches: 41, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
77 35 0.15
78 44 0.19
79 111 0.48
80 41 0.18
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (79 bp):
AAAATTCTATATTTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCAAAAATAATGAGGTTGGA
GTATCCCCGAAATG
Found at i:1311900 original size:157 final size:156
Alignment explanation
Indices: 1311649--1312007 Score: 427
Period size: 157 Copynumber: 2.3 Consensus size: 156
1311639 CTCGAGACAA
* *
1311649 AAAATTTAATATTTTTG-AAATAAAAACGGGGTTGGAGTATCCCCTCAAAAATAATGAGGTTTGA
1 AAAATTTAATA-TTTTGAAAATAAAAA-TGGGTTGGAGTATCCCCTCAAAAATAATGAGGTTGGA
* * * * **
1311713 GTATCCCCGAAATGAAAATTCGATATTTTTGGAAATAAAAACAGGGGTTGCAGTATTTCCTCGAA
64 ATACCCCCGAAATGAAAATTCAATATTTTTGAAAATAAAAAC-GGGGTTGCAGTATCCCCTCGAA
*
1311778 AATAACAAAGTTGGAGTATCTCCGAGATG
128 AATAACAAAGTTGGAGTATCTCCAAGATG
* * *
1311807 -AAATTCTAATATTTTGAAAATAAAAATGGGTTAGAGTATCCCCTCAAAATTAATGGGGTTGGAA
1 AAAATT-TAATATTTTGAAAATAAAAATGGGTTGGAGTATCCCCTCAAAAATAATGAGGTTGGAA
** * * *
1311871 TACCCCCGTGATGGAGAATTTAATA-TTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCGAAA
65 TACCCCCGAAAT-GAAAATTCAATATTTTTGAAAATAAAAACGGGGTTGCAGTATCCCCTCGAAA
* * ****
1311935 TTGATGTGGTTGGAGTATCTCCAAGATG
129 ATAACAAAGTTGGAGTATCTCCAAGATG
1311963 AAAATTTTAATATTTTGAAAATAAAAATGGGGTTGGAGTATCCCC
1 AAAA-TTTAATATTTTGAAAATAAAAAT-GGGTTGGAGTATCCCC
1312008 GATAAAGAAT
Statistics
Matches: 171, Mismatches: 24, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
156 41 0.24
157 90 0.53
158 40 0.23
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (156 bp):
AAAATTTAATATTTTGAAAATAAAAATGGGTTGGAGTATCCCCTCAAAAATAATGAGGTTGGAAT
ACCCCCGAAATGAAAATTCAATATTTTTGAAAATAAAAACGGGGTTGCAGTATCCCCTCGAAAAT
AACAAAGTTGGAGTATCTCCAAGATG
Found at i:1312028 original size:49 final size:49
Alignment explanation
Indices: 1311942--1312083 Score: 169
Period size: 49 Copynumber: 2.8 Consensus size: 49
1311932 AAATTGATGT
*
1311942 GGTTGGAGTATCTCCAAGATGAAAATTTTAATATTTTGAAAATAAAAATGG
1 GGTTGGAGTATCTCC-AGAT-AAAAATTTAATATTTTGAAAATAAAAATGG
* *
1311993 GGTTGGAGTATC-CCCGATAAAGAATTTAATATTTTGGAAATAAAAATGG
1 GGTTGGAGTATCTCCAGATAAA-AATTTAATATTTTGAAAATAAAAATGG
* * *
1312042 GGTTAGAGTGTTCTCGAGATAAAAAATTTAATATTTTTGAAA
1 GGTTGGAGT-ATCTCCAGAT-AAAAATTTAATA-TTTTGAAA
1312084 GGAAAAATTT
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
48 3 0.04
49 36 0.46
50 4 0.05
51 25 0.32
52 10 0.13
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.34
Consensus pattern (49 bp):
GGTTGGAGTATCTCCAGATAAAAATTTAATATTTTGAAAATAAAAATGG
Found at i:1314496 original size:20 final size:21
Alignment explanation
Indices: 1314471--1314520 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
1314461 TTAGGCATGC
1314471 ATCGATACATTCACT-TATGT
1 ATCGATACATTCACTGTATGT
* *
1314491 ATCGATACATTTACTGTTTGT
1 ATCGATACATTCACTGTATGT
1314512 ATCGATACA
1 ATCGATACA
1314521 AACTGTAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (21 bp):
ATCGATACATTCACTGTATGT
Found at i:1316962 original size:15 final size:16
Alignment explanation
Indices: 1316932--1316962 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1316922 ATAATTAATT
1316932 CAAAATGACACAAACC
1 CAAAATGACACAAACC
1316948 CAAAATGAC-CAAACC
1 CAAAATGACACAAACC
1316963 TAAGAAACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.55, C:0.32, G:0.06, T:0.06
Consensus pattern (16 bp):
CAAAATGACACAAACC
Found at i:1319151 original size:13 final size:13
Alignment explanation
Indices: 1319133--1319157 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1319123 CATAAAATGT
1319133 TGTATCGATACAA
1 TGTATCGATACAA
1319146 TGTATCGATACA
1 TGTATCGATACA
1319158 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1319155 original size:33 final size:33
Alignment explanation
Indices: 1319113--1319179 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1319103 TTCAACGATT
1319113 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1319146 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1319179 T
1 T
1319180 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1319386 original size:52 final size:52
Alignment explanation
Indices: 1319258--1319378 Score: 217
Period size: 52 Copynumber: 2.3 Consensus size: 52
1319248 CACTGATCTT
*
1319258 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTTTATAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATATTATAA
1319310 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTA-AA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACA-TATTATAA
1319362 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1319379 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
52 63 0.94
53 4 0.06
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATATTATAA
Found at i:1324197 original size:56 final size:56
Alignment explanation
Indices: 1324107--1324218 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 56
1324097 TTATATTGAT
* *
1324107 AGACTAGTTACAAAAAGATTTCTTCAAGTTATCATTAACTCTTCAACATTTGGGTG
1 AGACTAGTTACAAAAAGATTTCTTCAAGTCATCATTAACTCTTCAACATTTAGGTG
* *
1324163 AGACTGGTTACAGAAAGATTTCTTCAAGTCATCATTAACTCTTCAACATTTAGGTG
1 AGACTAGTTACAAAAAGATTTCTTCAAGTCATCATTAACTCTTCAACATTTAGGTG
1324219 GTCATGATGG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (56 bp):
AGACTAGTTACAAAAAGATTTCTTCAAGTCATCATTAACTCTTCAACATTTAGGTG
Found at i:1326003 original size:2 final size:2
Alignment explanation
Indices: 1325996--1326026 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1325986 CTGTTTTGCT
1325996 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1326027 TTATGATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1335205 original size:52 final size:52
Alignment explanation
Indices: 1335064--1335212 Score: 203
Period size: 52 Copynumber: 2.9 Consensus size: 52
1335054 CGAAATATGA
* *
1335064 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATATGATAGTGTATCGATACATCTGGGC
* * * *
1335116 AAATTTGCCTGTATGTATCGATACATTATGA-AATGTATCAATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACA-TATGATAGTGTATCGATACATCTGGGC
*
1335168 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATATGAT-AGTGTATCGATACA
1335213 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
50 3 0.04
52 78 0.93
53 3 0.04
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATATGATAGTGTATCGATACATCTGGGC
Found at i:1335219 original size:13 final size:13
Alignment explanation
Indices: 1335201--1335225 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1335191 CAAAGATCAG
1335201 TGTATCGATACAA
1 TGTATCGATACAA
1335214 TGTATCGATACA
1 TGTATCGATACA
1335226 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1335302 original size:19 final size:19
Alignment explanation
Indices: 1335278--1335392 Score: 110
Period size: 19 Copynumber: 6.7 Consensus size: 19
1335268 AGCGATACAT
*
1335278 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
1335297 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1335316 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
1335329 TGTATCGATACAACACTAA
1 TGTATCGATACAACACTTA
1335348 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
* *
1335361 TGTATCAATACAACACTAA
1 TGTATCGATACAACACTTA
1335380 TGTATCGATACAA
1 TGTATCGATACAA
1335393 ATCATTGAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 24
0.72 0.06 0.22
Matches are distributed among these distances:
13 17 0.22
14 1 0.01
16 12 0.15
19 48 0.62
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1335333 original size:32 final size:32
Alignment explanation
Indices: 1335297--1335391 Score: 172
Period size: 32 Copynumber: 3.0 Consensus size: 32
1335287 ACAAAACTTA
*
1335297 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCGATACAACACTAATGTATCGATACAT
1335329 TGTATCGATACAACACTAATGTATCGATACAT
1 TGTATCGATACAACACTAATGTATCGATACAT
*
1335361 TGTATCAATACAACACTAATGTATCGATACA
1 TGTATCGATACAACACTAATGTATCGATACA
1335392 AATCATTGAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.32
Consensus pattern (32 bp):
TGTATCGATACAACACTAATGTATCGATACAT
Found at i:1335334 original size:13 final size:13
Alignment explanation
Indices: 1335316--1335372 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
1335306 ACAACACTTA
1335316 TGTATCGATACAT
1 TGTATCGATACAT
1335329 TGTATCGATACAACACT
1 TGTATCGAT---ACA-T
1335346 AATGTATCGATACAT
1 --TGTATCGATACAT
*
1335361 TGTATCAATACA
1 TGTATCGATACA
1335373 ACACTAATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 20 0.54
15 1 0.03
16 6 0.16
17 1 0.03
19 9 0.24
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1336907 original size:14 final size:13
Alignment explanation
Indices: 1336872--1336913 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1336862 TCACAATAAA
*
1336872 CTTTCTTTTATTT
1 CTTTCTTTTTTTT
1336885 CTTTCTTTTTTTT
1 CTTTCTTTTTTTT
1336898 C--TCTTGTTTTTT
1 CTTTCTT-TTTTTT
1336910 CTTT
1 CTTT
1336914 TCATTGAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 4 0.16
12 7 0.28
13 13 0.52
14 1 0.04
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (13 bp):
CTTTCTTTTTTTT
Found at i:1339665 original size:36 final size:36
Alignment explanation
Indices: 1339594--1339665 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
1339584 ACTGTTAGAT
**
1339594 AATTAAAATTCATAAATATTTTATATTTTTATATAA
1 AATTAAAATTCATAAATATTTTATATTACTATATAA
1339630 AATTAAAATTGCATAAATATTTT-TA-TACTAGTATAA
1 AATTAAAATT-CATAAATATTTTATATTACTA-TATAA
1339666 TTTTTTTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 3 0.09
36 17 0.53
37 12 0.38
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (36 bp):
AATTAAAATTCATAAATATTTTATATTACTATATAA
Found at i:1339996 original size:19 final size:20
Alignment explanation
Indices: 1339972--1340025 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
1339962 TATTTTAAAA
*
1339972 TATATTAAAATT-TTAATTT
1 TATATTAAAATTAATAATTT
* *
1339991 TATATTAATATTAATATTTT
1 TATATTAAAATTAATAATTT
1340011 TATAATTAAAATTAA
1 TAT-ATTAAAATTAA
1340026 ATAAATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 11 0.38
20 8 0.28
21 10 0.34
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATTAAAATTAATAATTT
Found at i:1340508 original size:24 final size:24
Alignment explanation
Indices: 1340481--1340528 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1340471 ACAATTAGAT
1340481 ATTTAAATACAATATA-ATATTAAA
1 ATTTAAATA-AATATATATATTAAA
* *
1340505 ATTTATATATATATATATATTAAA
1 ATTTAAATAAATATATATATTAAA
1340529 TATCATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTTAAATAAATATATATATTAAA
Found at i:1340536 original size:24 final size:23
Alignment explanation
Indices: 1340492--1340545 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
1340482 TTTAAATACA
*
1340492 ATATAATATTAAAATTTATATAT
1 ATATAATATTAAAATTCATATAT
*
1340515 ATATATATATT-AAATATCATATTT
1 ATATA-ATATTAAAAT-TCATATAT
*
1340539 TTATAAT
1 ATATAAT
1340546 TGAAAAGTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATAATATTAAAATTCATATAT
Found at i:1342470 original size:2 final size:2
Alignment explanation
Indices: 1342463--1342506 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
1342453 CTCACAAGAA
* *
1342463 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT -T 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
1342504 AT A
1 AT A
1342507 AAAGAGTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1342872 original size:22 final size:22
Alignment explanation
Indices: 1342837--1342879 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1342827 TATTTTTATT
1342837 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
1342859 TAAATATTAA-TATAAAAATAT
1 TAAAT-TTAATTATAAAAATAT
1342880 TATTATGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:1344693 original size:65 final size:65
Alignment explanation
Indices: 1344589--1344712 Score: 221
Period size: 65 Copynumber: 1.9 Consensus size: 65
1344579 TAACCACCTA
* *
1344589 GCAATTAGCATGCAGAATCCAGATCTTAAAATTGGATTGCATTTTGTTGCCATATCCAGTATGTT
1 GCAATTAGCATACAGAATCCAGATCTTAAAATTGGATTGCATTTTGTTGACATATCCAGTATGTT
*
1344654 GCAATTAGCTTACAGAATCCAGATCTTAAAATTGGATTGCATTTTGTTGACATATCCAG
1 GCAATTAGCATACAGAATCCAGATCTTAAAATTGGATTGCATTTTGTTGACATATCCAG
1344713 CATGATGAAC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (65 bp):
GCAATTAGCATACAGAATCCAGATCTTAAAATTGGATTGCATTTTGTTGACATATCCAGTATGTT
Found at i:1345623 original size:4 final size:4
Alignment explanation
Indices: 1345614--1345692 Score: 50
Period size: 4 Copynumber: 19.5 Consensus size: 4
1345604 TTTGGGTCTC
* * * * * *
1345614 TATG TATG TATG TATG CATG TATG GATG GATG GATG TATG CATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* ** * *
1345662 CATG TATG CGTG CATA TATG TATG TACTG TA
1 TATG TATG TATG TATG TATG TATG TA-TG TA
1345693 GGCATTAGGT
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
4 58 0.94
5 4 0.06
ACGTcount: A:0.25, C:0.09, G:0.28, T:0.38
Consensus pattern (4 bp):
TATG
Found at i:1345627 original size:8 final size:8
Alignment explanation
Indices: 1345615--1345670 Score: 67
Period size: 8 Copynumber: 7.0 Consensus size: 8
1345605 TTGGGTCTCT
*
1345615 ATGTATGT
1 ATGTATGC
1345623 ATGTATGC
1 ATGTATGC
*
1345631 ATGTATGG
1 ATGTATGC
* *
1345639 ATGGATGG
1 ATGTATGC
1345647 ATGTATGC
1 ATGTATGC
*
1345655 ATGCATGC
1 ATGTATGC
1345663 ATGTATGC
1 ATGTATGC
1345671 GTGCATATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 41 1.00
ACGTcount: A:0.25, C:0.09, G:0.30, T:0.36
Consensus pattern (8 bp):
ATGTATGC
Found at i:1351644 original size:37 final size:37
Alignment explanation
Indices: 1351603--1352050 Score: 283
Period size: 37 Copynumber: 12.3 Consensus size: 37
1351593 TACCAATGAT
*
1351603 AAAGGCTTGAGACTTTCAAATATATCTAGCCTTTAGC
1 AAAGGCTTGAGACTTTCAAATATATCTAGCCTTCAGC
* * * ** * *
1351640 AAAGGCTTAAGATTTTTAAATCCATCTTGCCTTCAAC
1 AAAGGCTTGAGACTTTCAAATATATCTAGCCTTCAGC
* ** **
1351677 AAAGGCTTGAGACTTTCATATATATCTCA-TTTTCAAT
1 AAAGGCTTGAGACTTTCAAATATATCT-AGCCTTCAGC
** * * *
1351714 AAAGGCTTCCGACTTT----TAAATC--GCTTTTAGC
1 AAAGGCTTGAGACTTTCAAATATATCTAGCCTTCAGC
* * * * * * *
1351745 AAAGGCGTGAGACCTTCAAATACATCTCGCCAATGA-T
1 AAAGGCTTGAGACTTTCAAATATATCTAGCC-TTCAGC
* * * *
1351782 AAAGACTTGAGATTTTCAAATACATCTTGCCTTCAGC
1 AAAGGCTTGAGACTTTCAAATATATCTAGCCTTCAGC
* * * *
1351819 AAAGTCTTAAGACTTTTAAATATATCTAGTCTTCAGC
1 AAAGGCTTGAGACTTTCAAATATATCTAGCCTTCAGC
* * * *
1351856 AAAGGTTTGAGACTTTCAAATATATCTTGCCGATGA-C
1 AAAGGCTTGAGACTTTCAAATATATCTAGCC-TTCAGC
* * * *
1351893 AAAGGTTTGAGACTTTCAAATACACCTCA-CCTTCAAC
1 AAAGGCTTGAGACTTTCAAATATATCT-AGCCTTCAGC
1351930 AAAGGCTTGAGACTTTCAAATATATCTCA-CCTTCAGC
1 AAAGGCTTGAGACTTTCAAATATATCT-AGCCTTCAGC
* * * *
1351967 AAAAGCTTGAGACTTTCAAACATATCT--CATTGATGAC
1 AAAGGCTTGAGACTTTCAAATATATCTAGCCTTCA-G-C
* * * * * *
1352004 AAAGACTGGAGACTTTTAAATATATTTGGCCTTCAAC
1 AAAGGCTTGAGACTTTCAAATATATCTAGCCTTCAGC
1352041 AAAGGCTTGA
1 AAAGGCTTGA
1352051 AATTATTATT
Statistics
Matches: 313, Mismatches: 81, Indels: 34
0.73 0.19 0.08
Matches are distributed among these distances:
31 16 0.05
33 5 0.02
35 9 0.03
36 5 0.02
37 270 0.86
38 4 0.01
39 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (37 bp):
AAAGGCTTGAGACTTTCAAATATATCTAGCCTTCAGC
Found at i:1351943 original size:111 final size:109
Alignment explanation
Indices: 1351603--1352050 Score: 363
Period size: 111 Copynumber: 4.1 Consensus size: 109
1351593 TACCAATGAT
* * * * *
1351603 AAAGGCTTGAGACTTTCAAATATATCTAGCCTTTAGCAAAGGCTTAAGATTTTTAAATCCATCTT
1 AAAGGCTTGAGACTTTCAAATATATCTA-CCTTCAGCAAAGGCTTGAGACTTTCAAATACATCTT
* * * * ** *
1351668 GCCTTCAACAAAGGCTTGAGACTTTCATATATATCTCATTTTCAAT
65 GCCAT-GACAAAGGCTTGAGACTTTCAAATACATCTCACCTTCAAC
** * * * * * * *
1351714 AAAGGCTTCCGACTTT----TAAATC-GCTTTTAGCAAAGGCGTGAGACCTTCAAATACATCTCG
1 AAAGGCTTGAGACTTTCAAATATATCTACCTTCAGCAAAGGCTTGAGACTTTCAAATACATCTTG
* * * ** *
1351774 CCAATGATAAAGACTTGAGATTTTCAAATACATCTTGCCTTCAGC
66 CC-ATGACAAAGGCTTGAGACTTTCAAATACATCTCACCTTCAAC
* * * * * *
1351819 AAAGTCTTAAGACTTTTAAATATATCTAGTCTTCAGCAAAGGTTTGAGACTTTCAAATATATCTT
1 AAAGGCTTGAGACTTTCAAATATATCTA-CCTTCAGCAAAGGCTTGAGACTTTCAAATACATCTT
* *
1351884 GCCGATGACAAAGGTTTGAGACTTTCAAATACACCTCACCTTCAAC
65 GCC-ATGACAAAGGCTTGAGACTTTCAAATACATCTCACCTTCAAC
*
1351930 AAAGGCTTGAGACTTTCAAATATATCTCACCTTCAGCAAAAGCTTGAGACTTTCAAACATATC-T
1 AAAGGCTTGAGACTTTCAAATATATCT-ACCTTCAGCAAAGGCTTGAGACTTTC-AA-ATA-CAT
* * * * * **
1351994 CATTG--ATGACAAAGACTGGAGACTTTTAAATATATTTGGCCTTCAAC
62 C-TTGCCATGACAAAGGCTTGAGACTTTCAAATACATCTCACCTTCAAC
1352041 AAAGGCTTGA
1 AAAGGCTTGA
1352051 AATTATTATT
Statistics
Matches: 262, Mismatches: 63, Indels: 24
0.75 0.18 0.07
Matches are distributed among these distances:
105 72 0.27
106 1 0.00
107 5 0.02
109 5 0.02
111 168 0.64
112 3 0.01
113 5 0.02
114 3 0.01
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (109 bp):
AAAGGCTTGAGACTTTCAAATATATCTACCTTCAGCAAAGGCTTGAGACTTTCAAATACATCTTG
CCATGACAAAGGCTTGAGACTTTCAAATACATCTCACCTTCAAC
Found at i:1352067 original size:31 final size:31
Alignment explanation
Indices: 1352032--1352091 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1352022 AATATATTTG
* * *
1352032 GCCTTCAACAAAGGCTTGAAATTATTATTGC
1 GCCTTCAAAAAAAGCTTGAAACTATTATTGC
1352063 GCCTTCAAAAAAAGCTTGAAACTATTATT
1 GCCTTCAAAAAAAGCTTGAAACTATTATT
1352092 ACTCTTTCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (31 bp):
GCCTTCAAAAAAAGCTTGAAACTATTATTGC
Found at i:1354039 original size:16 final size:16
Alignment explanation
Indices: 1354003--1354039 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1353993 TAAATTAAAT
*
1354003 AATTAATTTTATAAAA
1 AATTAATTTTACAAAA
*
1354019 TATTAATTTTACAAAA
1 AATTAATTTTACAAAA
1354035 AATTA
1 AATTA
1354040 TATGTTAGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTAATTTTACAAAA
Found at i:1354267 original size:13 final size:13
Alignment explanation
Indices: 1354249--1354273 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1354239 ATATAAAATA
1354249 ATATAAATATATG
1 ATATAAATATATG
1354262 ATATAAATATAT
1 ATATAAATATAT
1354274 AAATATTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
ATATAAATATATG
Found at i:1354299 original size:33 final size:33
Alignment explanation
Indices: 1354256--1354335 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 33
1354246 ATAATATAAA
* *
1354256 TATATGATATAAATATATAAATATTTTAAAATT
1 TATATAATATAAATATATAAATATATTAAAATT
*
1354289 TATATAATATAAAT-TATTAATATATTAAAATT
1 TATATAATATAAATATATAAATATATTAAAATT
*
1354321 T-T-TAATTTAAATATA
1 TATATAATATAAATATA
1354336 ATTATAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 9 0.21
31 3 0.07
32 17 0.40
33 13 0.31
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (33 bp):
TATATAATATAAATATATAAATATATTAAAATT
Found at i:1355760 original size:14 final size:14
Alignment explanation
Indices: 1355743--1355786 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
1355733 TAATAATTGT
1355743 AAAATATTTATTAA
1 AAAATATTTATTAA
1355757 AAAATATTTAATATTAA
1 AAAATA-TT--TATTAA
*
1355774 TAAATATTTATTA
1 AAAATATTTATTA
1355787 TTCATAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 11 0.42
15 2 0.08
16 2 0.08
17 11 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAAATATTTATTAA
Found at i:1355793 original size:17 final size:17
Alignment explanation
Indices: 1355751--1355793 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1355741 GTAAAATATT
*
1355751 TATTAAAAAATATTTAA
1 TATTAATAAATATTTAA
*
1355768 TATTAATAAATATTTAT
1 TATTAATAAATATTTAA
*
1355785 TATTCATAA
1 TATTAATAA
1355794 TATAACTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTAATAAATATTTAA
Found at i:1357519 original size:103 final size:103
Alignment explanation
Indices: 1357303--1357520 Score: 246
Period size: 103 Copynumber: 2.1 Consensus size: 103
1357293 TTGAAAGGCA
* * *
1357303 GAGTTGGAGTATCTCCTCGGAAAGATGGGGTTGGAGTATCCTCGTGAATGACAAATAGTTTTGAC
1 GAGTTGGAGTATCCCCTCGGAAAGATGAGGTTGGAGTATCCTCATGAATGACAAATAGTTTTGAC
* * * * *
1357368 AATGAAAAAGTTCAAGTCTTTACAAATTTTGAAGAGCG
66 AAGGAAAAAGTTCAAATCTTAACAAATTTCGAAAAGCG
* * * *
1357406 GGGTTGGAGTATCCCCTC-GAAAGGTTGAGGTTGGAGTATTCCT-ATGGATGACCAAT-GATTTT
1 GAGTTGGAGTATCCCCTCGGAAA-GATGAGGTTGGAGTA-TCCTCATGAATGACAAATAG-TTTT
*
1357468 GACAAAGGAAAAA-TTCAAATCTTAACAAATTTCGAAAATCG
63 GAC-AAGGAAAAAGTTCAAATCTTAACAAATTTCGAAAAGCG
*
1357509 GAGTTAGAGTAT
1 GAGTTGGAGTAT
1357521 TTCTGATGAT
Statistics
Matches: 96, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
102 5 0.05
103 79 0.82
104 12 0.12
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (103 bp):
GAGTTGGAGTATCCCCTCGGAAAGATGAGGTTGGAGTATCCTCATGAATGACAAATAGTTTTGAC
AAGGAAAAAGTTCAAATCTTAACAAATTTCGAAAAGCG
Found at i:1359183 original size:20 final size:20
Alignment explanation
Indices: 1359160--1359209 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1359150 ACCCTGAAAA
*
1359160 GTATCGATATACATTGAATT
1 GTATCGATACACATTGAATT
** *
1359180 GTATCGATACATGTTGCATT
1 GTATCGATACACATTGAATT
1359200 GTATCGATAC
1 GTATCGATAC
1359210 TTGAAAAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (20 bp):
GTATCGATACACATTGAATT
Found at i:1359301 original size:13 final size:13
Alignment explanation
Indices: 1359283--1359307 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1359273 ACACATAGTA
1359283 TGTATCGATACAT
1 TGTATCGATACAT
1359296 TGTATCGATACA
1 TGTATCGATACA
1359308 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1359304 original size:32 final size:33
Alignment explanation
Indices: 1359263--1359330 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
1359253 GTAGTTAAAC
**
1359263 TTGTATCGATACA-CATAGTATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
1359295 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
1359328 TTG
1 TTG
1359331 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:1360927 original size:9 final size:9
Alignment explanation
Indices: 1360913--1360955 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
1360903 AACCATCAAG
1360913 GATGATGAA
1 GATGATGAA
1360922 GATGATGAA
1 GATGATGAA
1360931 GATGATGAA
1 GATGATGAA
* *
1360940 GAAGATGAT
1 GATGATGAA
1360949 GATGATG
1 GATGATG
1360956 GTGACTCAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (9 bp):
GATGATGAA
Found at i:1360928 original size:3 final size:3
Alignment explanation
Indices: 1360913--1360955 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
1360903 AACCATCAAG
* * * *
1360913 GAT GAT GAA GAT GAT GAA GAT GAT GAA GAA GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1360956 GTGACTCAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:1365513 original size:13 final size:13
Alignment explanation
Indices: 1365495--1365533 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1365485 ACAGCATTCT
1365495 TTGTATCGATACA
1 TTGTATCGATACA
*
1365508 TTGTATCGATATA
1 TTGTATCGATACA
*
1365521 CTGTATCGATACA
1 TTGTATCGATACA
1365534 GGGGGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1365700 original size:20 final size:20
Alignment explanation
Indices: 1365665--1365705 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
1365655 CAAAATTCTT
1365665 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
1365687 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
1365706 TTCAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:1367173 original size:20 final size:22
Alignment explanation
Indices: 1367148--1367187 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1367138 TATCTAGTAA
1367148 TTTATTTGC-TTG-ACTTTGTG
1 TTTATTTGCATTGTACTTTGTG
1367168 TTTATTTGCATTGTACTTTG
1 TTTATTTGCATTGTACTTTG
1367188 ACTTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 3 0.17
22 6 0.33
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.60
Consensus pattern (22 bp):
TTTATTTGCATTGTACTTTGTG
Found at i:1367976 original size:20 final size:20
Alignment explanation
Indices: 1367953--1368002 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1367943 ACCCTGAAAA
1367953 GTATCGATACACATTGAATT
1 GTATCGATACACATTGAATT
** *
1367973 GTATCGATACATGTTGCATT
1 GTATCGATACACATTGAATT
*
1367993 GTAACGATAC
1 GTATCGATAC
1368003 TTGAAAAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (20 bp):
GTATCGATACACATTGAATT
Found at i:1368094 original size:13 final size:13
Alignment explanation
Indices: 1368076--1368100 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1368066 ACACATAGTA
1368076 TGTATCGATACAT
1 TGTATCGATACAT
1368089 TGTATCGATACA
1 TGTATCGATACA
1368101 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1368097 original size:32 final size:33
Alignment explanation
Indices: 1368056--1368123 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
1368046 GTAGCTAAAC
**
1368056 TTGTATCGATACA-CATAGTATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
1368088 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
1368121 TTG
1 TTG
1368124 GCTTGTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:1373917 original size:10 final size:10
Alignment explanation
Indices: 1373904--1373928 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1373894 ACTTAGATAC
1373904 TTCTAGATTT
1 TTCTAGATTT
1373914 TTCTAGATTT
1 TTCTAGATTT
1373924 TTCTA
1 TTCTA
1373929 ACATGTATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.60
Consensus pattern (10 bp):
TTCTAGATTT
Found at i:1374023 original size:19 final size:19
Alignment explanation
Indices: 1373978--1374032 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1373968 GGTTTTCCAG
**
1373978 ATTGTATCGATACAATGCAA
1 ATTGTATCGATAC-ATTAAA
*
1373998 TTTGTATCGATACATTAAA
1 ATTGTATCGATACATTAAA
*
1374017 ATTGTATCAATACATT
1 ATTGTATCGATACATT
1374033 TTGCTTATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (19 bp):
ATTGTATCGATACATTAAA
Found at i:1374146 original size:20 final size:21
Alignment explanation
Indices: 1374118--1374156 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1374108 CACTCACTAA
*
1374118 TCTTTAAAA-TCTTCAAATAC
1 TCTTCAAAATTCTTCAAATAC
1374138 TCTTCAAAATTCTTCAAAT
1 TCTTCAAAATTCTTCAAAT
1374157 TAGCATCACA
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:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (21 bp):
TCTTCAAAATTCTTCAAATAC
Found at i:1376516 original size:33 final size:33
Alignment explanation
Indices: 1376458--1376522 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
1376448 CATATGCATA
* *
1376458 TGTATCGATATAAATTGCTAAGTATCGCTACAT
1 TGTATCGATACAAATTGCTAAGTATCGATACAT
**
1376491 TGTATCGATACAAATTGCTTTGTATCGATACA
1 TGTATCGATACAAATTGCTAAGTATCGATACA
1376523 CTTGAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAAATTGCTAAGTATCGATACAT
Found at i:1376613 original size:21 final size:21
Alignment explanation
Indices: 1376567--1376646 Score: 85
Period size: 21 Copynumber: 3.9 Consensus size: 21
1376557 GCTAACCCTT
* *
1376567 GATTGTATTGATACATGTTGAA
1 GATTGTATCGATACAT-TTCAA
*
1376589 -ATTGTATCGATACATTTTAA
1 GATTGTATCGATACATTTCAA
*
1376609 GATTGAATCGATACA--TCAA
1 GATTGTATCGATACATTTCAA
1376628 GAATTGTATCGATACATTT
1 G-ATTGTATCGATACATTT
1376647 GGCCCAATGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 4 0.08
20 17 0.35
21 27 0.55
22 1 0.02
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (21 bp):
GATTGTATCGATACATTTCAA
Found at i:1376638 original size:20 final size:20
Alignment explanation
Indices: 1376588--1376644 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
1376578 TACATGTTGA
*
1376588 AATTGTATCGATACATTTTAAG
1 AATTGTATCGATACA--TCAAG
*
1376610 -ATTGAATCGATACATCAAG
1 AATTGTATCGATACATCAAG
1376629 AATTGTATCGATACAT
1 AATTGTATCGATACAT
1376645 TTGGCCCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 4 0.13
20 14 0.45
21 13 0.42
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (20 bp):
AATTGTATCGATACATCAAG
Found at i:1382594 original size:17 final size:15
Alignment explanation
Indices: 1382552--1382652 Score: 80
Period size: 15 Copynumber: 6.4 Consensus size: 15
1382542 ATTTAACATG
1382552 AATAATAAAAAATAA
1 AATAATAAAAAATAA
*
1382567 AAAAATAAAAAATAA
1 AATAATAAAAAATAA
*
1382582 AATAATCATAAAAATAT
1 AATAAT-A-AAAAATAA
*
1382599 AATAATAAAATAGTAA
1 AATAATAAAA-AATAA
*
1382615 TAATTAATTAATTAAATAA
1 -AA-TAA-TAA-AAAATAA
*
1382634 AA-AAT-AAACATAA
1 AATAATAAAAAATAA
1382647 AATAAT
1 AATAAT
1382653 GACAATAATT
Statistics
Matches: 69, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
13 7 0.10
14 4 0.06
15 23 0.33
16 7 0.10
17 15 0.22
18 5 0.07
19 7 0.10
20 1 0.01
ACGTcount: A:0.71, C:0.02, G:0.01, T:0.26
Consensus pattern (15 bp):
AATAATAAAAAATAA
Found at i:1382610 original size:8 final size:8
Alignment explanation
Indices: 1382552--1382640 Score: 64
Period size: 8 Copynumber: 11.6 Consensus size: 8
1382542 ATTTAACATG
1382552 AATAATAA
1 AATAATAA
1382560 AA-AATAA
1 AATAATAA
*
1382567 AAAAATAA
1 AATAATAA
1382575 AA-AATAA
1 AATAATAA
1382582 AATAATCATA
1 AATAAT-A-A
*
1382592 AA-AATAT
1 AATAATAA
1382599 AATAATAA
1 AATAATAA
*
1382607 AATAGT--
1 AATAATAA
*
1382613 AATAATTA
1 AATAATAA
* *
1382621 ATTAATTA
1 AATAATAA
1382629 AATAA-AA
1 AATAATAA
1382636 AATAA
1 AATAA
1382641 ACATAAAATA
Statistics
Matches: 67, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
6 5 0.07
7 22 0.33
8 33 0.49
9 4 0.06
10 3 0.04
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.26
Consensus pattern (8 bp):
AATAATAA
Found at i:1382617 original size:25 final size:24
Alignment explanation
Indices: 1382552--1382617 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 24
1382542 ATTTAACATG
1382552 AATAATAAAA-AATAA-AAAAATA
1 AATAATAAAATAATAATAAAAATA
* *
1382574 AAAAATAAAATAATCATAAAAATA
1 AATAATAAAATAATAATAAAAATA
*
1382598 TAATAATAAAATAGTAATAA
1 -AATAATAAAATAATAATAA
1382618 TTAATTAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 9 0.25
23 4 0.11
24 7 0.19
25 16 0.44
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (24 bp):
AATAATAAAATAATAATAAAAATA
Found at i:1383015 original size:17 final size:17
Alignment explanation
Indices: 1382995--1383030 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1382985 TATACTTTCT
1382995 TTTAACTTCATTTTTGC
1 TTTAACTTCATTTTTGC
1383012 TTTAACTTCATTTTTGC
1 TTTAACTTCATTTTTGC
1383029 TT
1 TT
1383031 GATTTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTAACTTCATTTTTGC
Done.