Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 4 of 438
Found at i:1131250 original size:34 final size:35
Alignment explanation
Indices: 1131211--1131277 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 35
1131201 TAAAATTACA
1131211 ATTTAA-CCTTCAAAAAAAATATATAT-ATATATAT
1 ATTTAACCCTTCAAAAAAAATATA-ATCATATATAT
* *
1131245 ATTTAATCCCTTTAAAAACAATATAATCATATA
1 ATTTAA-CCCTTCAAAAAAAATATAATCATATA
1131278 CTAATATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 6 0.21
35 2 0.07
36 20 0.71
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (35 bp):
ATTTAACCCTTCAAAAAAAATATAATCATATATAT
Found at i:1133849 original size:17 final size:19
Alignment explanation
Indices: 1133817--1133853 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
1133807 TTGACTTGTT
1133817 TTAAAAATATTTTAAAATA
1 TTAAAAATATTTTAAAATA
1133836 TTAAAAA-A-TTTAAAATA
1 TTAAAAATATTTTAAAATA
1133853 T
1 T
1133854 AATTTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 1 0.06
19 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TTAAAAATATTTTAAAATA
Found at i:1136260 original size:17 final size:18
Alignment explanation
Indices: 1136240--1136287 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
1136230 AATTGAATTG
1136240 ATTTATTAATTTTTTAA-
1 ATTTATTAATTTTTTAAT
* *
1136257 ATTTTTTAAATTTTTAATT
1 ATTTATTAATTTTTTAA-T
1136276 ATTTATTTAATT
1 ATTTA-TTAATT
1136288 ATTGTTGATC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 15 0.62
19 4 0.17
20 5 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTATTAATTTTTTAAT
Found at i:1136261 original size:9 final size:9
Alignment explanation
Indices: 1136247--1136271 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1136237 TTGATTTATT
1136247 AATTTTTTA
1 AATTTTTTA
1136256 AATTTTTTA
1 AATTTTTTA
1136265 AATTTTT
1 AATTTTT
1136272 AATTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
AATTTTTTA
Found at i:1140267 original size:41 final size:41
Alignment explanation
Indices: 1140205--1140282 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
1140195 ACCTGGGTCC
*
1140205 TTTAGTTCAATTTAAGTTAAAAACTAGTGTAACTAGGCCCT
1 TTTAGTTCAATGTAAGTTAAAAACTAGTGTAACTAGGCCCT
1140246 TTTAGTTCAATGTAA-TGTAAAAACTAGTGTAACTAGG
1 TTTAGTTCAATGTAAGT-TAAAAACTAGTGTAACTAGG
1140283 GATGGCAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 1 0.03
41 34 0.97
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (41 bp):
TTTAGTTCAATGTAAGTTAAAAACTAGTGTAACTAGGCCCT
Found at i:1141163 original size:335 final size:335
Alignment explanation
Indices: 1140553--1141209 Score: 1224
Period size: 335 Copynumber: 2.0 Consensus size: 335
1140543 TTAATAATTA
1140553 TATATAAAGATAAAATGATAATTTTATATAGTGGAGCAGAGTGCAGTAAGACAAGCAATTATTAT
1 TATATAAAGATAAAATGATAATTTTATATAGTGGAGCAGAGTGCAGTAAGACAAGCAATTATTAT
*
1140618 AACCACTCAGCCTCCAATTTCCAAGAGAAAAAACTCACTTTCTTAAAGAATCGGTTTGAAATCCA
66 AACCACTCAGCCTCCAATTTCCAAAAGAAAAAACTCACTTTCTTAAAGAATCGGTTTGAAATCCA
* *
1140683 TTTTCAGACTTTGCACCATAGAAACCACTACATGCAAACTAATTGATTACAAGCAACTACACTTG
131 TTTTCAGACTTTGAACCATAGAAACCACTACATGCAAACTAATTCATTACAAGCAACTACACTTG
*
1140748 CAATAAGTGGATCGACTAGTTAATTTAACATGGCAATAACAGGTACTAAACTAGAGCTTTATTAC
196 CAATAAGTGGATCGACTAGTTAATTTAACATGGCAATAACAGGTACTAAACTAGAGCTCTATTAC
1140813 CAGAAATCACTATCTCAACGATTTTCGAATCGGTATGCACGATCCCAGTTAACGAATGCTAGTGG
261 CAGAAATCACTATCTCAACGATTTTCGAATCGGTATGCACGATCCCAGTTAACGAATGCTAGTGG
1140878 AGCAGAGCTC
326 AGCAGAGCTC
* *
1140888 TATATAAAGATAAAATGATAATTTTATATAGTGGAGCAGAGTGCGGTGAGACAAGCAATTATTAT
1 TATATAAAGATAAAATGATAATTTTATATAGTGGAGCAGAGTGCAGTAAGACAAGCAATTATTAT
*
1140953 AACCACTCGGCCTCCAATTTCCAAAAGAAAAAACTCACTTTCTTAAAGAATCGGTTTGAAATCCA
66 AACCACTCAGCCTCCAATTTCCAAAAGAAAAAACTCACTTTCTTAAAGAATCGGTTTGAAATCCA
1141018 TTTTCAGACTTTGAACCATAGAAACCACTACATGCAAACTAATTCATTACAAGCAACTACACTTG
131 TTTTCAGACTTTGAACCATAGAAACCACTACATGCAAACTAATTCATTACAAGCAACTACACTTG
* *
1141083 CAATCAGTGGATCGACTAGTTTATTTAACATGGCAATAACAGGTACTAAACTAGAGCTCTATTAC
196 CAATAAGTGGATCGACTAGTTAATTTAACATGGCAATAACAGGTACTAAACTAGAGCTCTATTAC
*
1141148 CAGAAATCACTATCTCAACGATTTTCGAATCGGTATGCACGATCCCAGTTAAGGAATGCTAG
261 CAGAAATCACTATCTCAACGATTTTCGAATCGGTATGCACGATCCCAGTTAACGAATGCTAG
1141210 AGGTTCAATT
Statistics
Matches: 312, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
335 312 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (335 bp):
TATATAAAGATAAAATGATAATTTTATATAGTGGAGCAGAGTGCAGTAAGACAAGCAATTATTAT
AACCACTCAGCCTCCAATTTCCAAAAGAAAAAACTCACTTTCTTAAAGAATCGGTTTGAAATCCA
TTTTCAGACTTTGAACCATAGAAACCACTACATGCAAACTAATTCATTACAAGCAACTACACTTG
CAATAAGTGGATCGACTAGTTAATTTAACATGGCAATAACAGGTACTAAACTAGAGCTCTATTAC
CAGAAATCACTATCTCAACGATTTTCGAATCGGTATGCACGATCCCAGTTAACGAATGCTAGTGG
AGCAGAGCTC
Found at i:1143865 original size:14 final size:14
Alignment explanation
Indices: 1143848--1143875 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1143838 GGGAAAGATG
1143848 AAGTTACATATTTT
1 AAGTTACATATTTT
1143862 AAGTTACATATTTT
1 AAGTTACATATTTT
1143876 TATGACGGTT
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:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (14 bp):
AAGTTACATATTTT
Found at i:1147918 original size:89 final size:89
Alignment explanation
Indices: 1147676--1147931 Score: 363
Period size: 88 Copynumber: 2.9 Consensus size: 89
1147666 CATATACACA
*
1147676 TCAAATATGTGAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAACTAAAACTC
1 TCAAATATGTGAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATTAAAACTC
*
1147741 TATAATTCAAAAAAAAAAATTAAT
66 TATAATTCAAACAAAAAAATTAAT
*
1147765 TCAAATATGTGAAC-GATATCACTTAC-AAACTCATCTGCAAAATTACAAAGCCAAATAAAAACT
1 TCAAATATGTGAACTGA-ATCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATTAAAACT
* * *******
1147828 CTAGAATACAAACTTTTTTTTTAAT
65 CTATAATTCAAACAAAAAAATTAAT
* *
1147853 TGAAATATGTGAACTGAATCACTTACAAAACTTATCTGCAAAATTACAAAGCCAAATTAAAACTC
1 TCAAATATGTGAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATTAAAACTC
1147918 TATAATTCAAACAA
66 TATAATTCAAACAA
1147932 GAAAGAGAAA
Statistics
Matches: 145, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
88 74 0.51
89 71 0.49
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.27
Consensus pattern (89 bp):
TCAAATATGTGAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATTAAAACTC
TATAATTCAAACAAAAAAATTAAT
Found at i:1153107 original size:91 final size:88
Alignment explanation
Indices: 1152893--1153137 Score: 267
Period size: 89 Copynumber: 2.7 Consensus size: 88
1152883 GGTGTGTACA
* * * *
1152893 TTTGTATTCTAGAGTTTTTATTTGGCTTTGTAATTTTGCAGATGAGTATTGTTAATGACTCACTT
1 TTTGAATTCTAGAGTTTTTATTTGGCTTTGTAATTTTGCAGATGAGTTTTG-TAATGATTCAGTT
* * *
1152958 CACATATTTGATTTTTTTTAAATG
65 AAAATATTTGATTTTTTTTAAAAG
* * * * * *
1152982 TTTAAATTATAGAGTTTTAATTTGGCTTTGTAATTATGTAGATGAATTTTGTAAGTGATTCAGTT
1 TTTGAATTCTAGAGTTTTTATTTGGCTTTGTAATTTTGCAGATGAGTTTTGTAA-TGATTCAGTT
1153047 AAAATATTTGAATTTTTTTTAAAAAAG
65 AAAATATTTG-ATTTTTTTT--AAAAG
* * * * *
1153074 TTTGAATTCTAG-TTTTTTTTTTGGCTCTGTAATTTTGGAGATGAGTTTTGTAACTGATTTAGTT
1 TTTGAATTCTAGAGTTTTTATTTGGCTTTGTAATTTTGCAGATGAGTTTTGTAA-TGATTCAGTT
1153138 CTAGTATTTT
Statistics
Matches: 128, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
88 3 0.02
89 59 0.46
90 9 0.07
91 43 0.34
92 14 0.11
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.51
Consensus pattern (88 bp):
TTTGAATTCTAGAGTTTTTATTTGGCTTTGTAATTTTGCAGATGAGTTTTGTAATGATTCAGTTA
AAATATTTGATTTTTTTTAAAAG
Found at i:1153695 original size:25 final size:25
Alignment explanation
Indices: 1153667--1153717 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1153657 TATGGTACCC
1153667 GACTTTTACTTCAATATTCAAAATG
1 GACTTTTACTTCAATATTCAAAATG
1153692 GACTTTTACTTCAATATTCAAAATG
1 GACTTTTACTTCAATATTCAAAATG
1153717 G
1 G
1153718 CATGCAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (25 bp):
GACTTTTACTTCAATATTCAAAATG
Found at i:1157554 original size:31 final size:31
Alignment explanation
Indices: 1157519--1157583 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
1157509 AAATTAAACT
1157519 TAACTTCTAGATAGTTTGCAATTTATGTACG
1 TAACTTCTAGATAGTTTGCAATTTATGTACG
1157550 TAACTTCTAGATAGTTTGCAATTTATGTACG
1 TAACTTCTAGATAGTTTGCAATTTATGTACG
1157581 TAA
1 TAA
1157584 ACTTTTTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (31 bp):
TAACTTCTAGATAGTTTGCAATTTATGTACG
Found at i:1159437 original size:89 final size:90
Alignment explanation
Indices: 1159109--1159470 Score: 402
Period size: 93 Copynumber: 4.0 Consensus size: 90
1159099 AAACTCTTTT
* ** * * * *
1159109 TTTTTTTTAAAACTCAAATATTTGAACTGAATCACTGAAAAAAATCATCTGCATAATTACAAAGC
1 TTTTTTTTAAAATTCAAATATGCGAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGC
* *
1159174 CAAATTAAAACTCCATAATTTAAACA
66 CAAATTAAAACTCTATAATTCAAA-A
***** * * * * **
1159200 TTTAAAAAAAAAATCAAATATGTGAAGTGAATCAATTACAGGACTCATCTGCAAAATTACAAAGC
1 TTTTTTTTAAAATTCAAATATGCGAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGC
* *
1159265 TAAATTAAAACTCTATAATTCAAAC
66 CAAATTAAAACTCTATAATTCAAAA
* *
1159290 TTTTTTTTACAAAAATTCAAATATGCGAACGGAACCACTTACAAAACTCATCTGCAAAATTACAA
1 TTTTTTTT---AAAATTCAAATATGCGAACTGAATCACTTACAAAACTCATCTGCAAAATTACAA
* * *
1159355 AGCCAAATAAAAACTCTAGAATACAAAA
63 AGCCAAATTAAAACTCTATAATTCAAAA
* * *
1159383 TTTTTTTT-TAATTCAAATATGCGAACTGAATCACTTACAAAACTTATCTGCAAAATTACGAAGC
1 TTTTTTTTAAAATTCAAATATGCGAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGC
*
1159447 CAAATTAAACCTCTATAATTCAAA
66 CAAATTAAAACTCTATAATTCAAA
1159471 CATGAAAGAG
Statistics
Matches: 222, Mismatches: 46, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
89 71 0.32
90 3 0.01
91 71 0.32
93 77 0.35
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.29
Consensus pattern (90 bp):
TTTTTTTTAAAATTCAAATATGCGAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGC
CAAATTAAAACTCTATAATTCAAAA
Found at i:1167077 original size:16 final size:16
Alignment explanation
Indices: 1167056--1167087 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1167046 TGATTAAGAC
1167056 ACGAATTTCGATTCAA
1 ACGAATTTCGATTCAA
*
1167072 ACGAATTTCGGTTCAA
1 ACGAATTTCGATTCAA
1167088 CTCTGCCTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (16 bp):
ACGAATTTCGATTCAA
Found at i:1167278 original size:24 final size:24
Alignment explanation
Indices: 1167251--1167300 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1167241 CTTAATAAGT
1167251 TTAAACTTAAAAATATTCATCTTA
1 TTAAACTTAAAAATATTCATCTTA
*
1167275 TTAAACTTAAAAATATTCATTTTA
1 TTAAACTTAAAAATATTCATCTTA
1167299 TT
1 TT
1167301 TGTTTCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (24 bp):
TTAAACTTAAAAATATTCATCTTA
Found at i:1167453 original size:19 final size:20
Alignment explanation
Indices: 1167406--1167453 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1167396 ACGAATTAAA
*
1167406 TTATATTATTTTTAATTATT
1 TTATAATATTTTTAATTATT
* *
1167426 TAAATAATATTTTTTA-TATT
1 T-TATAATATTTTTAATTATT
1167446 TTATAATA
1 TTATAATA
1167454 AAAATAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 6 0.26
20 6 0.26
21 11 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATAATATTTTTAATTATT
Found at i:1167480 original size:13 final size:13
Alignment explanation
Indices: 1167447--1167481 Score: 56
Period size: 11 Copynumber: 2.8 Consensus size: 13
1167437 TTTTATATTT
1167447 TATAATAAAAATA
1 TATAATAAAAATA
1167460 -AT-ATAAAAATA
1 TATAATAAAAATA
1167471 TATAATAAAAA
1 TATAATAAAAA
1167482 ATTAAATCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 9 0.45
12 4 0.20
13 7 0.35
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
TATAATAAAAATA
Found at i:1170969 original size:22 final size:23
Alignment explanation
Indices: 1170939--1170992 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1170929 ATGATACATA
* *
1170939 TGTAAATA-TTTTCTAAATTTAT
1 TGTATATATTTTTCTAAAATTAT
*
1170961 TGTATATATTTTTTTAAAATTAT
1 TGTATATATTTTTCTAAAATTAT
1170984 TCGTATATA
1 T-GTATATA
1170993 GCTTGGCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 7 0.26
23 13 0.48
24 7 0.26
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (23 bp):
TGTATATATTTTTCTAAAATTAT
Found at i:1171597 original size:9 final size:8
Alignment explanation
Indices: 1171575--1171599 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1171565 TGTTGGGTTT
1171575 CGTTTTTC
1 CGTTTTTC
1171583 CGTTTTTC
1 CGTTTTTC
1171591 CGTTTTTC
1 CGTTTTTC
1171599 C
1 C
1171600 AAATAACGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.28, G:0.12, T:0.60
Consensus pattern (8 bp):
CGTTTTTC
Found at i:1173163 original size:20 final size:20
Alignment explanation
Indices: 1173129--1173187 Score: 55
Period size: 24 Copynumber: 2.8 Consensus size: 20
1173119 TAATATTAGA
* *
1173129 ATTAATTATGTTAATTAGTT
1 ATTAATTAGGATAATTAGTT
1173149 ATTAATTAGGATAATGTTTTAGTT
1 ATTAATTAGGATAA----TTAGTT
*
1173173 ATTAATTTGGATAAT
1 ATTAATTAGGATAAT
1173188 GTTGTTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 13 0.41
24 19 0.59
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.51
Consensus pattern (20 bp):
ATTAATTAGGATAATTAGTT
Found at i:1173170 original size:24 final size:24
Alignment explanation
Indices: 1173143--1173190 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1173133 ATTATGTTAA
1173143 TTAGTTATTAATTAGGATAATGTT
1 TTAGTTATTAATTAGGATAATGTT
*
1173167 TTAGTTATTAATTTGGATAATGTT
1 TTAGTTATTAATTAGGATAATGTT
1173191 GTTTTACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (24 bp):
TTAGTTATTAATTAGGATAATGTT
Found at i:1173351 original size:23 final size:25
Alignment explanation
Indices: 1173296--1173351 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
1173286 TTACATATAA
*
1173296 ATATATTTATATCGATGTAATTTTG
1 ATATATTTATATCGATGTAATATTG
1173321 ATATATTTATAT-GTATGT-ATATT-
1 ATATATTTATATCG-ATGTAATATTG
1173344 ATATATTT
1 ATATATTT
1173352 TTAAAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 8 0.28
24 5 0.17
25 16 0.55
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (25 bp):
ATATATTTATATCGATGTAATATTG
Found at i:1173405 original size:2 final size:2
Alignment explanation
Indices: 1173398--1173426 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1173388 TAGGTTGTTA
1173398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1173427 AGAAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1173636 original size:13 final size:14
Alignment explanation
Indices: 1173613--1173653 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
1173603 AATTATTATT
*
1173613 TTAAGTATAAAATA
1 TTAATTATAAAATA
*
1173627 TT-TTTATAAAAT-
1 TTAATTATAAAATA
1173639 TTAATTATAAAATA
1 TTAATTATAAAATA
1173653 T
1 T
1173654 ATAAAATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
12 2 0.09
13 17 0.77
14 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
TTAATTATAAAATA
Found at i:1173656 original size:22 final size:22
Alignment explanation
Indices: 1173631--1173678 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1173621 AAAATATTTT
*
1173631 TATAAAATTTAAT-TATAAAATA
1 TATAAAATTCAATGTA-AAAATA
*
1173653 TATAAAATTCAATGTAAAATTA
1 TATAAAATTCAATGTAAAAATA
1173675 TATA
1 TATA
1173679 TTTTTAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
TATAAAATTCAATGTAAAAATA
Found at i:1176759 original size:28 final size:29
Alignment explanation
Indices: 1176701--1176759 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
1176691 GATAGGGTCA
* * * *
1176701 AAGTGTGAATATTTAAAAATTAAGGGGTT
1 AAGTGTAAATATTTAAAAAATAAAGGATT
1176730 AAGTGTAAAT-TTTAAAAAATAAAGGATT
1 AAGTGTAAATATTTAAAAAATAAAGGATT
1176758 AA
1 AA
1176760 AAGTGAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.32
Consensus pattern (29 bp):
AAGTGTAAATATTTAAAAAATAAAGGATT
Found at i:1179135 original size:17 final size:17
Alignment explanation
Indices: 1179115--1179165 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
1179105 TTAAAAATAG
*
1179115 TTAAATTGTTATTTTTA
1 TTAAATTATTATTTTTA
1179132 TTAAATTATTATTTTTA
1 TTAAATTATTATTTTTA
* *
1179149 ATAAAATATTATATTTT
1 TTAAATTATTAT-TTTT
1179166 TAATACCTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 26 0.87
18 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TTAAATTATTATTTTTA
Found at i:1179165 original size:19 final size:17
Alignment explanation
Indices: 1179123--1179170 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
1179113 AGTTAAATTG
* *
1179123 TTATTTTTATTAAATTA
1 TTATTTTTAATAAAATA
1179140 TTATTTTTAATAAAATA
1 TTATTTTTAATAAAATA
1179157 TTATATTTTTAATA
1 -T-TATTTTTAATA
1179171 CCTAAATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 15 0.56
18 1 0.04
19 11 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTTTTAATAAAATA
Found at i:1186461 original size:50 final size:51
Alignment explanation
Indices: 1186356--1186468 Score: 117
Period size: 50 Copynumber: 2.2 Consensus size: 51
1186346 GGGTGTTGAT
* * *
1186356 TAAATTTGTT-TAATCAAGACCAATTTGACATAATGTATAAATATTATGGAT
1 TAAATTTGTTATAATCAAGACCAATTTGACATAATG-ATAAATACTAAGGAC
* *
1186407 TAAATTTGTTAT-ATCAAGATCAA-TTGACAATATATG-TAAATACTAAGGGC
1 TAAATTTGTTATAATCAAGACCAATTTGAC-ATA-ATGATAAATACTAAGGAC
*
1186457 TAAATTTATTAT
1 TAAATTTGTTAT
1186469 TATAGTAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
50 26 0.49
51 23 0.43
52 4 0.08
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.39
Consensus pattern (51 bp):
TAAATTTGTTATAATCAAGACCAATTTGACATAATGATAAATACTAAGGAC
Found at i:1189456 original size:20 final size:20
Alignment explanation
Indices: 1189431--1189472 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1189421 TATTGTTCTC
*
1189431 GATTCACGTGTGTCGAATAT
1 GATTCACGTGTGCCGAATAT
*
1189451 GATTCATGTGTGCCGAATAT
1 GATTCACGTGTGCCGAATAT
1189471 GA
1 GA
1189473 GTATGTGTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (20 bp):
GATTCACGTGTGCCGAATAT
Found at i:1192777 original size:48 final size:48
Alignment explanation
Indices: 1192706--1192802 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
1192696 AAAGCAGAAC
1192706 AGTAAGAAATATCAGCCTAATTCTTTCAAACCAAAAATGGAGGGTAAT
1 AGTAAGAAATATCAGCCTAATTCTTTCAAACCAAAAATGGAGGGTAAT
1192754 AGTAAGAAATATCAGCCTAATTCTTTCAAACCAAAAATGGAGGGTAAT
1 AGTAAGAAATATCAGCCTAATTCTTTCAAACCAAAAATGGAGGGTAAT
1192802 A
1 A
1192803 ACTTACAGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.25
Consensus pattern (48 bp):
AGTAAGAAATATCAGCCTAATTCTTTCAAACCAAAAATGGAGGGTAAT
Found at i:1194180 original size:247 final size:244
Alignment explanation
Indices: 1193724--1194194 Score: 565
Period size: 247 Copynumber: 1.9 Consensus size: 244
1193714 TTAATGCTTA
* * ***
1193724 TAGAAACACCCACAAATAGTAGTGTAAGTGAGACAATGCTTTTGACTCGAAAAAAAGCTCTGGTT
1 TAGAAACACCCACAAATACTAG-GT-AGTGAGACAATGCTTTTGACTCGAAAAAAAGATCAAATT
* * * * *
1193789 CAATTCAGTCATTCTCGAGCTGAGTCGAGTTCAAGCTATTGAACGAGCGAAGTTTCTTAACACTC
64 CAATTCAGTCATTCTCGAGCTGAGTCGAGCTCAAGCTATCGAACGAGCAAAGTATCTCAACACTC
*
1193854 AATTTGAGCAACTCACAAACTTAATCAAGCTCGAGCTTTTACTACTTAATCCAAAAAAATTGTAT
129 AATCTGAGCAACTCACAAACTTAATCAAGCTCGAGCTTTTACTACTTAATCCAAAAAAATTGTAT
* * *
1193919 ATGTAACAGACTCAAGCTCGAACTTGAGTCAAACTGAGTCAAACTCGAGCT
194 ATGCAACAGACTCAAGCTCAAACTCGAGTCAAACTGAGTCAAACTCGAGCT
* *
1193970 TAGATACACCCACAAATACTA-GT-GTGAGACAATGCTTTTGACTTG-AAAAAAGATCAAATTCA
1 TAGAAACACCCACAAATACTAGGTAGTGAGACAATGCTTTTGACTCGAAAAAAAGATCAAATTCA
* * * *
1194032 ATTCAGTCATTCTCGAGCTGGGTCGAGCTCGAGCTATCGAGCGAGCCAACTTTGAGTATCTCAAT
66 ATTCAGTCATTCTCGAGCTGAGTCGAGCTCAAGCTATCGAACGAG-CAA-----AGTATCTCAAC
** *** * * *
1194097 ACTTGATCTGAGCAACTCGTTAACTTAATCAAGCTTGAGCTTTTACTACTTTATCC-AAAAATTT
125 ACTCAATCTGAGCAACTCACAAACTTAATCAAGCTCGAGCTTTTACTACTTAATCCAAAAAAATT
1194161 GTATATGCAA-ATGGACTCAAGCTCAAACTCGAGT
190 GTATATGCAACA--GACTCAAGCTCAAACTCGAGT
1194195 TTGAGGATAT
Statistics
Matches: 189, Mismatches: 28, Indels: 15
0.81 0.12 0.06
Matches are distributed among these distances:
241 53 0.28
242 23 0.12
244 2 0.01
245 1 0.01
246 35 0.19
247 75 0.40
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (244 bp):
TAGAAACACCCACAAATACTAGGTAGTGAGACAATGCTTTTGACTCGAAAAAAAGATCAAATTCA
ATTCAGTCATTCTCGAGCTGAGTCGAGCTCAAGCTATCGAACGAGCAAAGTATCTCAACACTCAA
TCTGAGCAACTCACAAACTTAATCAAGCTCGAGCTTTTACTACTTAATCCAAAAAAATTGTATAT
GCAACAGACTCAAGCTCAAACTCGAGTCAAACTGAGTCAAACTCGAGCT
Found at i:1198021 original size:28 final size:28
Alignment explanation
Indices: 1197981--1198048 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
1197971 GCAATCAAAT
* * *
1197981 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTACGAAATATTGAAA
* *
1198009 ATGGCACTTAGTGTGCGAGATATTGAAA
1 ATGGCACTTAGTGTACGAAATATTGAAA
*
1198037 ATGACACTTAGT
1 ATGGCACTTAGT
1198049 CTGCAAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTACGAAATATTGAAA
Found at i:1198059 original size:28 final size:28
Alignment explanation
Indices: 1197998--1198059 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1197988 TCAGTGTACG
* * * *
1197998 AAATATTGAGAATGGCACTTAGTGTGCG
1 AAATATTGAAAATGACACTTAGTCTGCA
*
1198026 AGATATTGAAAATGACACTTAGTCTGCA
1 AAATATTGAAAATGACACTTAGTCTGCA
1198054 AAATAT
1 AAATAT
1198060 CGAATGATTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (28 bp):
AAATATTGAAAATGACACTTAGTCTGCA
Found at i:1211428 original size:51 final size:54
Alignment explanation
Indices: 1211338--1211474 Score: 160
Period size: 51 Copynumber: 2.6 Consensus size: 54
1211328 TTATTATTTT
* * *
1211338 CAATAGAAGATCATTATAAATCTCAACCCTTC--AT-CTCCTCCATTGGAGCTC
1 CAATTGAAGATCATTACAAATCTCAACCCTTCATATCCTCCTCTATTGGAGCTC
* *
1211389 CAATTGAAGTTCATTACAAATCTCAACCTTTCATATCCTCCTTCTATTGGAGCTC
1 CAATTGAAGATCATTACAAATCTCAACCCTTCATATCCTCC-TCTATTGGAGCTC
* *
1211444 TAA-T--AGGTCATTACAAATCTCAACCCTTCAT
1 CAATTGAAGATCATTACAAATCTCAACCCTTCAT
1211475 CTCTACTTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
51 28 0.38
52 25 0.34
53 2 0.03
54 5 0.07
55 14 0.19
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.33
Consensus pattern (54 bp):
CAATTGAAGATCATTACAAATCTCAACCCTTCATATCCTCCTCTATTGGAGCTC
Found at i:1211467 original size:52 final size:52
Alignment explanation
Indices: 1211348--1211474 Score: 154
Period size: 52 Copynumber: 2.5 Consensus size: 52
1211338 CAATAGAAGA
* *
1211348 TCATTATAAATCTCAACCCTTC--ATCTCCTCCATTGGAGCTCCAATTGAAGT
1 TCATTACAAATCTCAACCCTTCATATCTCCTCCATTGGAGCTCCAATT-AAGG
* * *
1211399 TCATTACAAATCTCAACCTTTCATATCCTCCTTCTATTGGAGCTCTAA-T-AGG
1 TCATTACAAATCTCAACCCTTCATAT-CTCC-TCCATTGGAGCTCCAATTAAGG
1211451 TCATTACAAATCTCAACCCTTCAT
1 TCATTACAAATCTCAACCCTTCAT
1211475 CTCTACTTTA
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
51 20 0.30
52 25 0.38
53 2 0.03
54 5 0.08
55 14 0.21
ACGTcount: A:0.28, C:0.29, G:0.08, T:0.35
Consensus pattern (52 bp):
TCATTACAAATCTCAACCCTTCATATCTCCTCCATTGGAGCTCCAATTAAGG
Found at i:1211738 original size:61 final size:58
Alignment explanation
Indices: 1211643--1211776 Score: 178
Period size: 61 Copynumber: 2.3 Consensus size: 58
1211633 ATGTTAGAGA
*
1211643 AAGGAGGAGATGAAGGGCTAAAATTTGTAATGACCTTCTATTGGAGCAGGAGCTCCAATAG
1 AAGGAGGAGATGAAGGGCTAAAATTTGTAATGACCTTCTATTGGAGC--G-CCTCCAATAG
* * * *
1211704 AAGGAGGAGATGAAGGGCTGAGATTTGTATTGACCTTTTATTGGAGCGCCTCCAATAG
1 AAGGAGGAGATGAAGGGCTAAAATTTGTAATGACCTTCTATTGGAGCGCCTCCAATAG
* *
1211762 AAAGATGAGATGAAG
1 AAGGAGGAGATGAAG
1211777 AGATGAAGGT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
58 22 0.33
59 1 0.02
61 43 0.65
ACGTcount: A:0.34, C:0.12, G:0.31, T:0.24
Consensus pattern (58 bp):
AAGGAGGAGATGAAGGGCTAAAATTTGTAATGACCTTCTATTGGAGCGCCTCCAATAG
Found at i:1211968 original size:55 final size:55
Alignment explanation
Indices: 1211880--1212006 Score: 200
Period size: 55 Copynumber: 2.3 Consensus size: 55
1211870 CATATGTTAG
* * *
1211880 AGAAAGTAGGAGATGAAGGGCTGAGATTTGTAATGATCTTCTATTAGAGCTCCAAT
1 AGAAAG-AGGAGATGAAGGACTGAGATTTGTAATGACCTTATATTAGAGCTCCAAT
* *
1211936 AGAAGGAGGAGATGAAGGACTGAGATTTGTAATGACCTTATATTGGAGCTCCAAT
1 AGAAAGAGGAGATGAAGGACTGAGATTTGTAATGACCTTATATTAGAGCTCCAAT
1211991 AGAAAGAGGAGATGAA
1 AGAAAGAGGAGATGAA
1212007 TAGATGAAAG
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
55 60 0.92
56 5 0.08
ACGTcount: A:0.37, C:0.09, G:0.29, T:0.24
Consensus pattern (55 bp):
AGAAAGAGGAGATGAAGGACTGAGATTTGTAATGACCTTATATTAGAGCTCCAAT
Found at i:1213293 original size:63 final size:60
Alignment explanation
Indices: 1213194--1213317 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 60
1213184 GAGAAAGGAG
1213194 GAGATGAAGGGCTGAGATTTGTAATGACCTTCTATTGGAGCTCCAATAGAAAGTGGAGATGAA
1 GAGATGAAGGGCTGAGATTTGTAATGACCTTCTATTGGAGCTCCAATA-AAA--GGAGATGAA
* *
1213257 GAGATGAAGGGTTGAGATTTGTAATGACCTTCTATTGGAGCTCTAATAAAAGGAGATGAA
1 GAGATGAAGGGCTGAGATTTGTAATGACCTTCTATTGGAGCTCCAATAAAAGGAGATGAA
1213317 G
1 G
1213318 GGTTGAGATT
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
60 10 0.17
62 3 0.05
63 46 0.78
ACGTcount: A:0.34, C:0.10, G:0.30, T:0.27
Consensus pattern (60 bp):
GAGATGAAGGGCTGAGATTTGTAATGACCTTCTATTGGAGCTCCAATAAAAGGAGATGAA
Found at i:1213585 original size:55 final size:55
Alignment explanation
Indices: 1213437--1213680 Score: 224
Period size: 55 Copynumber: 4.3 Consensus size: 55
1213427 CTTTTTTGAC
* * *
1213437 CTTCATTTTCTCCTTCTATTGGAGCTCCAATAGAAAGTCATTACAAATCT--T-A
1 CTTCATCTTCTCTTTCTATTGGAGCTCCAATAAAAAGTCATTACAAATCTCATCA
* * * * *
1213489 GTCTCATCTCCTTTTTCTATTGGAGCTCCAATAGAAGGTCATTACAAATCTCATCA
1 CT-TCATCTTCTCTTTCTATTGGAGCTCCAATAAAAAGTCATTACAAATCTCATCA
* * * *
1213545 CTTCATCTTCTCTTTCTATTGGAGTTCTAATAAAAAGTCATTACAAATCTCAACC
1 CTTCATCTTCTCTTTCTATTGGAGCTCCAATAAAAAGTCATTACAAATCTCATCA
* * * *
1213600 CTTCATCTCTTCATCTCCATTTTCTATTGGAGCTCCAATAAAATGTCAATACAAATCTCAGCC
1 CTTCA--TC-T--TCT-C--TTTCTATTGGAGCTCCAATAAAAAGTCATTACAAATCTCATCA
*
1213663 CTTCATCTCCTCATTTCT
1 CTTCATCTTCTC-TTTCT
1213681 CTAACATTTG
Statistics
Matches: 158, Mismatches: 22, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
52 1 0.01
53 43 0.27
55 51 0.32
56 7 0.04
57 3 0.02
58 3 0.02
60 4 0.03
61 3 0.02
63 43 0.27
ACGTcount: A:0.27, C:0.26, G:0.09, T:0.38
Consensus pattern (55 bp):
CTTCATCTTCTCTTTCTATTGGAGCTCCAATAAAAAGTCATTACAAATCTCATCA
Found at i:1213612 original size:63 final size:63
Alignment explanation
Indices: 1213539--1213682 Score: 193
Period size: 63 Copynumber: 2.3 Consensus size: 63
1213529 ATTACAAATC
* * * *
1213539 TCATCACTTCATCTTCTCTTTCTATTGGAGTTCTAATAAAAAGTCATTACAAATCTCAACCCT
1 TCATCTCTTCATCTTCTCTTTCTATTGGAGCTCCAATAAAAAGTCAATACAAATCTCAACCCT
* * *
1213602 TCATCTCTTCATCTCCAT-TTTCTATTGGAGCTCCAATAAAATGTCAATACAAATCTCAGCCCT
1 TCATCTCTTCATCTTC-TCTTTCTATTGGAGCTCCAATAAAAAGTCAATACAAATCTCAACCCT
*
1213665 TCATCTCCTCAT-TTCTCT
1 TCATCTCTTCATCTTCTCT
1213683 AACATTTGTC
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
61 1 0.01
62 3 0.04
63 65 0.93
64 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.06, T:0.38
Consensus pattern (63 bp):
TCATCTCTTCATCTTCTCTTTCTATTGGAGCTCCAATAAAAAGTCAATACAAATCTCAACCCT
Found at i:1217278 original size:137 final size:137
Alignment explanation
Indices: 1217032--1217318 Score: 529
Period size: 137 Copynumber: 2.1 Consensus size: 137
1217022 CATTGGGCCT
**
1217032 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
1217097 AGCCCCTTATTCAGATAACAGTATGACCCATAGGCCTATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGACCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
1217162 CATATGC
131 CATATGC
1217169 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
* *
1217234 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAGCATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGACCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
1217299 CATATGC
131 CATATGC
1217306 AAGCCCATTTGGG
1 AAGCCCATTTGGG
1217319 GAGACTACTC
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 145 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGACCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:1219135 original size:26 final size:26
Alignment explanation
Indices: 1219104--1219211 Score: 155
Period size: 26 Copynumber: 4.2 Consensus size: 26
1219094 TGAAATTCCC
1219104 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
1219130 ATCATGAAACATTTACCT-AACTCATT
1 ATCATGGAACATTTACCTAAAC-CATT
* *
1219156 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
1219182 GTCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
1219208 ATCA
1 ATCA
1219212 ATTTGTATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
25 3 0.04
26 67 0.93
27 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:1219187 original size:52 final size:52
Alignment explanation
Indices: 1219104--1219211 Score: 171
Period size: 52 Copynumber: 2.1 Consensus size: 52
1219094 TGAAATTCCC
*
1219104 ATCATGGAACATTTACCTAAACCATTATCATGAAACATTTACCTAACTCATT
1 ATCATGGAACATTTACCTAAACCATTATCATGAAACATTTACCTAACCCATT
* * * *
1219156 ATCATGGAATATTTACCTAATCCATTGTCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATTATCATGAAACATTTACCTAACCCATT
1219208 ATCA
1 ATCA
1219212 ATTTGTATCA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (52 bp):
ATCATGGAACATTTACCTAAACCATTATCATGAAACATTTACCTAACCCATT
Found at i:1220784 original size:15 final size:15
Alignment explanation
Indices: 1220735--1220799 Score: 51
Period size: 15 Copynumber: 4.0 Consensus size: 15
1220725 ATGAACGACC
1220735 AAATAAGAAGTAACTAA
1 AAATAAGAA-TAAC-AA
1220752 AAA-AAGATAATGACACAA
1 AAATAAG--AAT-A-ACAA
*
1220770 AAATAATAATAACAA
1 AAATAAGAATAACAA
*
1220785 TAATAAGAATAACAA
1 AAATAAGAATAACAA
1220800 TGATAACAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
15 17 0.43
16 4 0.10
17 7 0.17
18 8 0.20
19 4 0.10
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.17
Consensus pattern (15 bp):
AAATAAGAATAACAA
Found at i:1220800 original size:15 final size:15
Alignment explanation
Indices: 1220766--1220805 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1220756 AGATAATGAC
* *
1220766 ACAAAAATAATAATA
1 ACAATAATAAGAATA
1220781 ACAATAATAAGAATA
1 ACAATAATAAGAATA
*
1220796 ACAATGATAA
1 ACAATAATAA
1220806 CAATGATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (15 bp):
ACAATAATAAGAATA
Found at i:1222284 original size:22 final size:20
Alignment explanation
Indices: 1222237--1222284 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
1222227 AAAAAGATTT
*
1222237 ATAAAATAAATAAAACAAAA
1 ATAAAATAAAAAAAACAAAA
*
1222257 ACAAAATAGAAAAAAATCAAAA
1 ATAAAATA-AAAAAAA-CAAAA
1222279 ATAAAA
1 ATAAAA
1222285 AATAAGAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 7 0.30
21 6 0.26
22 10 0.43
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.12
Consensus pattern (20 bp):
ATAAAATAAAAAAAACAAAA
Found at i:1222285 original size:16 final size:15
Alignment explanation
Indices: 1222244--1222286 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1222234 TTTATAAAAT
1222244 AAATAAAACAAAAACA
1 AAATAAAA-AAAAACA
*
1222260 AAATAGAAAAAAATCAA
1 AAATA-AAAAAAAAC-A
1222277 AAATAAAAAA
1 AAATAAAAAA
1222287 TAAGAGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.81, C:0.07, G:0.02, T:0.09
Consensus pattern (15 bp):
AAATAAAAAAAAACA
Found at i:1222955 original size:43 final size:43
Alignment explanation
Indices: 1222907--1223005 Score: 180
Period size: 43 Copynumber: 2.3 Consensus size: 43
1222897 AAAAAAAGTT
*
1222907 GCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCTCACAAATGCC
1 GCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCACAAATGCC
1222950 GCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCACAAATGCC
1 GCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCACAAATGCC
*
1222993 GCTAAAAGTCATG
1 GCTAAAGGTCATG
1223006 AAATTTAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (43 bp):
GCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCACAAATGCC
Found at i:1223188 original size:19 final size:18
Alignment explanation
Indices: 1223136--1223188 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
1223126 ATTCATTATC
1223136 AAATAAAAATAAAAACAA
1 AAATAAAAATAAAAACAA
* * *
1223154 AAATATACAATCAAAACTA
1 AAATA-AAAATAAAAACAA
1223173 AAATAAATAATAAAAA
1 AAATAAA-AATAAAAA
1223189 TTAGATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATAAAAATAAAAACAA
Found at i:1227842 original size:46 final size:46
Alignment explanation
Indices: 1227790--1228272 Score: 580
Period size: 46 Copynumber: 10.5 Consensus size: 46
1227780 ATAATCCACA
*
1227790 ACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAC
* *
1227836 ACTTCAATTTACAGCATTAAAATACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAC
* * ** * *
1227882 ATTTCAATTAACAATATTTATAGCACTTCAATTTGCAACA-TTTAAGC
1 ACTTCAATTTACAGCATTTA-AACACTTCAATTTGCAGCACTTTAA-C
*
1227929 ACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAC
* * *
1227975 ATTTCAATTAACAACATTTAAACACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAC
* * *
1228021 ATTTCAATTAACAACATTTAAACACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAC
*
1228067 ACTTCAATTTACAGCATTAAAACACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAC
* * * * *
1228113 ATTTCAATTAACAACATTTAAACA-TCTCAATTTCCAGCAAC-TAAAC
1 ACTTCAATTTACAGCATTTAAACACT-TCAATTTGCAGC-ACTTTAAC
* * * * * *
1228159 ACTTCAATTTGCAGTACTTAAACACTCCAATTTACAGCACTCTAAC
1 ACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAC
* * *
1228205 ACTTCAATTTGCAGCACTTT-AACAGTTCAATTTACAGCA-TTTAAAC
1 ACTTCAATTTACAGCA-TTTAAACACTTCAATTTGCAGCACTTT-AAC
*
1228251 ACTTCAATTTGCAGCACTTTAA
1 ACTTCAATTTACAGCA-TTTAA
1228273 CATCTCAATT
Statistics
Matches: 381, Mismatches: 46, Indels: 19
0.85 0.10 0.04
Matches are distributed among these distances:
45 5 0.01
46 333 0.87
47 43 0.11
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (46 bp):
ACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAC
Found at i:1228274 original size:23 final size:23
Alignment explanation
Indices: 1227790--1228282 Score: 445
Period size: 23 Copynumber: 21.4 Consensus size: 23
1227780 ATAATCCACA
*
1227790 ACTTCAATTTACAGCA-TTCAAAC
1 ACTTCAATTTACAGCACTT-TAAC
*
1227813 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTTTAAC
* *
1227836 ACTTCAATTTACAGCA-TTAAAAT
1 ACTTCAATTTACAGCACTT-TAAC
*
1227859 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTTTAAC
* * **
1227882 ATTTCAATTAACAATA-TTTATAGC
1 ACTTCAATTTACAGCACTTTA-A-C
* *
1227906 ACTTCAATTTGCAACA-TTTAAGC
1 ACTTCAATTTACAGCACTTTAA-C
*
1227929 ACTTCAATTTACAGCA-TTCAAAC
1 ACTTCAATTTACAGCACTT-TAAC
*
1227952 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTTTAAC
* * *
1227975 ATTTCAATTAACAACA-TTTAAAC
1 ACTTCAATTTACAGCACTTT-AAC
*
1227998 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTTTAAC
* * *
1228021 ATTTCAATTAACAACA-TTTAAAC
1 ACTTCAATTTACAGCACTTT-AAC
*
1228044 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTTTAAC
*
1228067 ACTTCAATTTACAGCA-TTAAAAC
1 ACTTCAATTTACAGCACTT-TAAC
*
1228090 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTTTAAC
* * *
1228113 ATTTCAATTAACAACA-TTTAA-
1 ACTTCAATTTACAGCACTTTAAC
* *
1228134 ACATCTCAATTTCCAGCAAC-TAAAC
1 AC-T-TCAATTTACAGC-ACTTTAAC
* * *
1228159 ACTTCAATTTGCAGTACTTAAAC
1 ACTTCAATTTACAGCACTTTAAC
* *
1228182 ACTCCAATTTACAGCACTCTAAC
1 ACTTCAATTTACAGCACTTTAAC
*
1228205 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTTTAAC
*
1228228 AGTTCAATTTACAGCA-TTTAAAC
1 ACTTCAATTTACAGCACTTT-AAC
*
1228251 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTTTAAC
1228274 A-TCTCAATT
1 ACT-TCAATT
1228283 AACAACATTT
Statistics
Matches: 383, Mismatches: 65, Indels: 44
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.00
22 26 0.07
23 313 0.82
24 41 0.11
25 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (23 bp):
ACTTCAATTTACAGCACTTTAAC
Found at i:1228678 original size:12 final size:12
Alignment explanation
Indices: 1228663--1228712 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
1228653 ACACACACAT
1228663 ATTAACATCTCA
1 ATTAACATCTCA
*
1228675 ATTAACA--ACA
1 ATTAACATCTCA
* *
1228685 TTTATACACCTCA
1 ATTA-ACATCTCA
1228698 ATTAACATCTCA
1 ATTAACATCTCA
1228710 ATT
1 ATT
1228713 TCTAGCAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
10 5 0.17
11 3 0.10
12 17 0.57
13 5 0.17
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.34
Consensus pattern (12 bp):
ATTAACATCTCA
Found at i:1229928 original size:15 final size:15
Alignment explanation
Indices: 1229908--1229938 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1229898 CCTTGAATTA
1229908 GAAGAAAACCAGTAG
1 GAAGAAAACCAGTAG
1229923 GAAGAAAACCAGTAG
1 GAAGAAAACCAGTAG
1229938 G
1 G
1229939 TTACCTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.13, G:0.29, T:0.06
Consensus pattern (15 bp):
GAAGAAAACCAGTAG
Found at i:1231585 original size:46 final size:46
Alignment explanation
Indices: 1231518--1231609 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
1231508 CACTATTCAC
* * *
1231518 TGATCAGGTAGTCGGAGCTACCATTTTTCACTAATCAAGTAGCCGA
1 TGATCAGGTAGCCGAAGCTACCACTTTTCACTAATCAAGTAGCCGA
* * *
1231564 TGATCAGGTAGCCGAAGCTACCACTTTTCATTGATCAGGTAGCCGA
1 TGATCAGGTAGCCGAAGCTACCACTTTTCACTAATCAAGTAGCCGA
1231610 AGCTACCACT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (46 bp):
TGATCAGGTAGCCGAAGCTACCACTTTTCACTAATCAAGTAGCCGA
Found at i:1231602 original size:31 final size:31
Alignment explanation
Indices: 1231564--1231622 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
1231554 AAGTAGCCGA
1231564 TGATCAGGTAGCCGAAGCTACCACTTTTCAT
1 TGATCAGGTAGCCGAAGCTACCACTTTTCAT
1231595 TGATCAGGTAGCCGAAGCTACCACTTTT
1 TGATCAGGTAGCCGAAGCTACCACTTTT
1231623 TACTTGCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (31 bp):
TGATCAGGTAGCCGAAGCTACCACTTTTCAT
Found at i:1231696 original size:50 final size:50
Alignment explanation
Indices: 1231602--1231878 Score: 437
Period size: 50 Copynumber: 5.5 Consensus size: 50
1231592 CATTGATCAG
* * * *
1231602 GTAGCCGAAGCTACCACTTTTTACTTGCCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
*
1231653 GTAGCTGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* * *
1231703 GTAGCCGAAGCTATCACTTATCACTTTCACTTATCCTTGATCAAATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1231753 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* * *
1231803 GTAGCCGAAGCTATCACTTATCACTTTGACTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
1231853 GTAGCTGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
1231879 GTTGCCATGG
Statistics
Matches: 210, Mismatches: 16, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
50 188 0.90
51 22 0.10
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:1234573 original size:7 final size:7
Alignment explanation
Indices: 1234561--1234689 Score: 73
Period size: 7 Copynumber: 18.1 Consensus size: 7
1234551 ACTAATTAAT
1234561 CTAAACC
1 CTAAACC
1234568 CTAAACC
1 CTAAACC
*
1234575 TCTTAACC
1 -CTAAACC
*
1234583 C-ATATCC
1 CTA-AACC
*
1234590 CATAAACA
1 C-TAAACC
*
1234598 CTAAACT
1 CTAAACC
1234605 CTAAACC
1 CTAAACC
*
1234612 CTTAACC
1 CTAAACC
*
1234619 CTTAACC
1 CTAAACC
*
1234626 CCAAACC
1 CTAAACC
*
1234633 CTTACACC
1 C-TAAACC
* *
1234641 TTAAACT
1 CTAAACC
*
1234648 CT-AACA
1 CTAAACC
*
1234654 CTAACCC
1 CTAAACC
1234661 CTAAACC
1 CTAAACC
*
1234668 CTAAATC
1 CTAAACC
* *
1234675 ATAATCC
1 CTAAACC
1234682 CTAAACC
1 CTAAACC
1234689 C
1 C
1234690 ATAATTCATC
Statistics
Matches: 90, Mismatches: 26, Indels: 12
0.70 0.20 0.09
Matches are distributed among these distances:
6 5 0.06
7 71 0.79
8 13 0.14
9 1 0.01
ACGTcount: A:0.39, C:0.40, G:0.00, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:1234646 original size:43 final size:44
Alignment explanation
Indices: 1234560--1234651 Score: 109
Period size: 43 Copynumber: 2.1 Consensus size: 44
1234550 TACTAATTAA
*
1234560 TCTAAACCCTAAACCTCTTAACCCATATCCCATAAACACTAAAC
1 TCTAAACCCTAAACCTCTTAACCCATAACCCATAAACACTAAAC
* * *
1234604 TCTAAACCCTTAACC-CTTAACCCCA-AACCCTTACAC-CTTAAAC
1 TCTAAACCCTAAACCTCTTAA-CCCATAACCCATAAACAC-TAAAC
1234647 TCTAA
1 TCTAA
1234652 CACTAACCCC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
42 1 0.02
43 23 0.55
44 18 0.43
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.24
Consensus pattern (44 bp):
TCTAAACCCTAAACCTCTTAACCCATAACCCATAAACACTAAAC
Found at i:1234758 original size:21 final size:21
Alignment explanation
Indices: 1234730--1234816 Score: 84
Period size: 21 Copynumber: 4.0 Consensus size: 21
1234720 TAACACCTAA
*
1234730 ACCTTAAACCCTAAACCATAT
1 ACCTTAAACCATAAACCATAT
* * *
1234751 ATCTTAAACTATAGTTAACTCATAA
1 ACCTTAAACCATA---AAC-CATAT
*
1234776 ACCTTAAACCCTAAACCATAT
1 ACCTTAAACCATAAACCATAT
*
1234797 ACCTTAAACCAAAAACCATA
1 ACCTTAAACCATAAACCATA
1234817 AACTATAATG
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
21 32 0.62
22 3 0.06
24 3 0.06
25 14 0.27
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (21 bp):
ACCTTAAACCATAAACCATAT
Found at i:1234769 original size:46 final size:46
Alignment explanation
Indices: 1234699--1234805 Score: 153
Period size: 46 Copynumber: 2.3 Consensus size: 46
1234689 CATAATTCAT
* *
1234699 CATAAACCTTCAAA-TACTAGTTAACACCTAAACCTTAAACCCTAAAC
1 CATATACCTT-AAACTA-TAGTTAACACATAAACCTTAAACCCTAAAC
* *
1234746 CATATATCTTAAACTATAGTTAACTCATAAACCTTAAACCCTAAAC
1 CATATACCTTAAACTATAGTTAACACATAAACCTTAAACCCTAAAC
1234792 CATATACCTTAAAC
1 CATATACCTTAAAC
1234806 CAAAAACCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
46 44 0.81
47 10 0.19
ACGTcount: A:0.44, C:0.27, G:0.02, T:0.27
Consensus pattern (46 bp):
CATATACCTTAAACTATAGTTAACACATAAACCTTAAACCCTAAAC
Found at i:1234824 original size:7 final size:7
Alignment explanation
Indices: 1234771--1234824 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
1234761 ATAGTTAACT
1234771 CATAAAC
1 CATAAAC
*
1234778 CTTAAAC
1 CATAAAC
*
1234785 CCTAAAC
1 CATAAAC
*
1234792 CATATAC
1 CATAAAC
*
1234799 CTTAAAC
1 CATAAAC
*
1234806 CAAAAAC
1 CATAAAC
1234813 CATAAAC
1 CATAAAC
*
1234820 TATAA
1 CATAA
1234825 TGATAATTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (7 bp):
CATAAAC
Found at i:1235037 original size:41 final size:41
Alignment explanation
Indices: 1234980--1235197 Score: 237
Period size: 41 Copynumber: 5.4 Consensus size: 41
1234970 GTTATATGAC
* *
1234980 TTTTAGCGACGTTTTACCAAAAGCGCCGCTAATGTTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
1235021 TTTTAGCGGTGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* *
1235062 TTTTAGGGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*** * *
1235103 TTTTAGCGGCGTTTTTGGAAAAACGCCGCTAATGCTAT--T
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* * * * *
1235142 TTTTTGCGGCTTTTTTTACTAAAA-CTCCGCTATTGCTCT-GT
1 TTTTAGCGGC--GTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* *
1235183 TTTTAGTGGCATTTT
1 TTTTAGCGGCGTTTT
1235198 TGGTAAAACG
Statistics
Matches: 152, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
39 14 0.09
40 12 0.08
41 126 0.83
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
Found at i:1235198 original size:41 final size:40
Alignment explanation
Indices: 1234991--1235228 Score: 203
Period size: 41 Copynumber: 5.8 Consensus size: 40
1234981 TTTAGCGACG
* *
1234991 TTTTACCAAAAGCGCCGCTAATGTTCTGGTTTTTAGCGG-TG
1 TTTTACCAAAA-CGCCGCTAATGCTCT-GTTTTTAGCGGCTT
* *
1235032 TTTTACCAAAAGCGCCGCTAATGCTCTGGTTTTTAGGGGCGT
1 TTTTACCAAAA-CGCCGCTAATGCTCT-GTTTTTAGCGGCTT
*
1235074 TTTT-CCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGT
1 TTTTACCAAAA-CGCCGCTAATGCTCT-GTTTTTAGCGGCTT
*** * *
1235115 TTTTGGAAAAACGCCGCTAATGCTAT-TTTTTTGCGGCTTT
1 TTTTACCAAAACGCCGCTAATGCTCTGTTTTTAGCGGC-TT
* * * * *
1235155 TTTTACTAAAACTCCGCTATTGCTCTGTTTTTAGTGGCAT
1 TTTTACCAAAACGCCGCTAATGCTCTGTTTTTAGCGGCTT
*** * *
1235195 TTTTGGTAAAACGCCGCTATTGCTATGTGTTTTA
1 TTTTACCAAAACGCCGCTAATGCTCTGT-TTTTA
1235229 CAATTTTTGC
Statistics
Matches: 169, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
39 10 0.06
40 46 0.27
41 105 0.62
42 8 0.05
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (40 bp):
TTTTACCAAAACGCCGCTAATGCTCTGTTTTTAGCGGCTT
Found at i:1235236 original size:80 final size:81
Alignment explanation
Indices: 1235087--1235236 Score: 196
Period size: 80 Copynumber: 1.9 Consensus size: 81
1235077 TCCAAAAGCG
* * * **
1235087 CCGCTAATGCTCTGGTTTTTAGCGGCGTTTTTGGAAAAACGCCGCTAATGCTATTTTTTTGCGGC
1 CCGCTAATGCTCTGGTTTTTAGCGGCATTTTTGGAAAAACGCCGCTAATGCTATTGTTTTACGAA
1235152 TTTTTTTACTAAAACT
66 TTTTTTTACTAAAACT
* * * *
1235168 CCGCTATTGCTCT-GTTTTTAGTGGCATTTTTGGTAAAACGCCGCTATTGCTATGTGTTTTAC-A
1 CCGCTAATGCTCTGGTTTTTAGCGGCATTTTTGGAAAAACGCCGCTAATGCTAT-TGTTTTACGA
1235231 ATTTTT
65 ATTTTT
1235237 GCGGTGTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
80 41 0.69
81 18 0.31
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (81 bp):
CCGCTAATGCTCTGGTTTTTAGCGGCATTTTTGGAAAAACGCCGCTAATGCTATTGTTTTACGAA
TTTTTTTACTAAAACT
Found at i:1239907 original size:25 final size:25
Alignment explanation
Indices: 1239876--1239923 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1239866 TCTTTACTTA
1239876 TTGTCGTATAACGAGAACAGAGTTG
1 TTGTCGTATAACGAGAACAGAGTTG
* *
1239901 TTGTCGTGTAACGAGAATAGAGT
1 TTGTCGTATAACGAGAACAGAGT
1239924 AAAGACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.29
Consensus pattern (25 bp):
TTGTCGTATAACGAGAACAGAGTTG
Found at i:1240694 original size:14 final size:14
Alignment explanation
Indices: 1240675--1240710 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1240665 AGTTGATTTT
1240675 TTTGAAAAGCAGAA
1 TTTGAAAAGCAGAA
1240689 TTTGAAAAGCAGAA
1 TTTGAAAAGCAGAA
*
1240703 ATTGAAAA
1 TTTGAAAA
1240711 TACCTCAGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.22
Consensus pattern (14 bp):
TTTGAAAAGCAGAA
Found at i:1240734 original size:89 final size:88
Alignment explanation
Indices: 1240466--1241123 Score: 776
Period size: 89 Copynumber: 7.4 Consensus size: 88
1240456 GTGAGCCAAT
* * * * * **
1240466 GCTCAACTCACCTCTCGCAATATGAGTTG--GTTTTTG-AAA-CTTAATTTGGAAAGCAGATTTT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCATAAATTGAAAAACAGAAATT
* **
1240527 GAAAATACCTTGACA-TGTGACCCAAG
66 GAAAATACC-T--CAGCGTG-CCTGAG
**
1240553 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAATATAAATTGAAAAAACAGAAAT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCATAAATTG-AAAAACAGAAAT
* *
1240616 TAAAAATACCTCAGCGTGTCCTAAG
65 TGAAAATACCTCAGCGTG-CCTGAG
* * *
1240641 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAATTTGAAAAGCAGAAATT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCATAAATTGAAAAACAGAAATT
1240706 GAAAATACCTCAGCGTGCCTTGAG
66 GAAAATACCTCAGCGTGCC-TGAG
* * * *
1240730 GCTCAACTCACCTTTCACAATATGAGTTGATTTTTTTTTTGAAAAGTAAAAATTGAAAAACAGAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTTGAAAAGCATAAATTGAAAAACAGAA
* *
1240795 ATTGAAAATACCTCGGCGTGTGACTTGAG
63 ATTGAAAATACCTCAGC--GTG-CCTGAG
* * *
1240824 GCTCAACTCACCTCTAGCAATATGAATTGA--TTTTTGAAAAGCATAAATTGAATAACAGAAATT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCATAAATTGAAAAACAGAAATT
1240887 GAAAATACCTCAGCGTGTCCTGAG
66 GAAAATACCTCAGCGTG-CCTGAG
* * *
1240911 GCTCAACTCACCTATCGCAATATGAGTTGATTTTTTTGAAAAGCACAAATTAAAAAACAGAAATT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCATAAATTGAAAAACAGAAATT
* *
1240976 GAAAATACCTCAGCATATCCTGAG
66 GAAAATACCTCAGCGT-GCCTGAG
* * * *
1241000 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTGGAAAGCATAAATT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCATAAATTGAAAAACAGAAATT
*
1241065 AAAAATACCTCAGCGTGCCCTGAG
66 GAAAATACCTCAGCGTG-CCTGAG
*
1241089 GCTCAACTCACCTCTCGCAACATGAGTTGATTTTT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1241124 GACAAACAGA
Statistics
Matches: 499, Mismatches: 54, Indels: 34
0.85 0.09 0.06
Matches are distributed among these distances:
87 72 0.14
88 43 0.09
89 273 0.55
90 33 0.07
92 44 0.09
94 33 0.07
95 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (88 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCATAAATTGAAAAACAGAAATT
GAAAATACCTCAGCGTGCCTGAG
Found at i:1240941 original size:270 final size:263
Alignment explanation
Indices: 1240372--1241217 Score: 894
Period size: 270 Copynumber: 3.2 Consensus size: 263
1240362 CGGCATGTGA
** * * * * * * *
1240372 TCCTGA-GCTCAACTCATTTCTCGTAATATGAATTGA-CTCTTT-AAAAACAGACATT-AAAAAT
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAAAC
* * * * *
1240433 AGAAATTGAAAATAGCTTAGCACGTGAGCC-AATGCTCAACTCACCTCTCGCAATATGAGTTG--
66 AGAAATTGAAAATACCTCAGCA--T-AGCCTGAGGCTCAACTCACCTCTCACAATATGAGTTGAT
* ** * * * ** * * **
1240495 GTTTTTG-AAA-CTTAATTTGGAAAGCAGATTTTGAAAATACCTTGACA-TGTGACCCAAGGCTC
128 TTTTTTGAAAAGCAAAAATTGAAAAACAGAAATTAAAAATACC-T--CAGCGTGACCTGAGGCTC
* *
1240557 AACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAACAGAAATTAAAAA
190 AACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACATAAATTG--AAAACAGAAATTGAAAA
1240622 TACCTCAGCGTG
252 TACCTCAGCGTG
* * *
1240634 TCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAATTTGAAAAGC
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAAAC
* *
1240699 AGAAATTGAAAATACCTCAGCGT-GCCTTGAGGCTCAACTCACCTTTCACAATATGAGTTGATTT
66 AGAAATTGAAAATACCTCAGCATAGCC-TGAGGCTCAACTCACCTCTCACAATATGAGTTGA---
* * * *
1240763 TTTTTTTGAAAAGTAAAAATTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGACTTGAGGCTC
127 TTTTTTTGAAAAGCAAAAATTGAAAAACAGAAATTAAAAATACCTCAGC--GTGACCTGAGGCTC
* *
1240828 AACTCACCTCTAGCAATATGAATTGATTTTTGAAAAGCATAAATTGAATAACAGAAATTGAAAAT
190 AACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-CATAAATTGAA-AACAGAAATTGAAAAT
1240893 ACCTCAGCGTG
253 ACCTCAGCGTG
* * *
1240904 TCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTTTTGAAAAGCACAAATTAAAAAAC
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAAAC
* *
1240969 AGAAATTGAAAATACCTCAGCATATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
66 AGAAATTGAAAATACCTCAGCATAGCCTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTT
* * * * *
1241034 TTTGAAAAGCAGAAATTGGAAAGCATAAATTAAAAATACCTCAGCGTGCCCTGAGGCTCAACTCA
131 TTTGAAAAGCAAAAATTGAAAAACAGAAATTAAAAATACCTCAGCGTGACCTGAGGCTCAACTCA
* *
1241099 CCTCTCGCAACATGAGTTGATTTTTG---AC---------AAACAGAAATTGAAATTACCTCAGC
196 CCTCTCGCAATATGAGTTGATTTTTGAAAACATAAATTGAAAACAGAAATTGAAAATACCTCAGC
1241152 GTG
261 GTG
*
1241155 TCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTTG-AAAGACAGAAATTGAAAA
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAG-CAGAAATTGAAAA
1241218 TTACCTCAGC
Statistics
Matches: 500, Mismatches: 64, Indels: 51
0.81 0.10 0.08
Matches are distributed among these distances:
250 4 0.01
251 80 0.16
252 1 0.00
261 1 0.00
262 9 0.02
263 26 0.05
264 33 0.07
265 51 0.10
266 23 0.05
267 42 0.08
268 1 0.00
269 8 0.02
270 147 0.29
271 74 0.15
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (263 bp):
TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAAAC
AGAAATTGAAAATACCTCAGCATAGCCTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTT
TTTGAAAAGCAAAAATTGAAAAACAGAAATTAAAAATACCTCAGCGTGACCTGAGGCTCAACTCA
CCTCTCGCAATATGAGTTGATTTTTGAAAACATAAATTGAAAACAGAAATTGAAAATACCTCAGC
GTG
Found at i:1241249 original size:76 final size:75
Alignment explanation
Indices: 1241060--1241286 Score: 354
Period size: 76 Copynumber: 3.1 Consensus size: 75
1241050 TGGAAAGCAT
* * *
1241060 AAATT-AAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAACATGAGTTGA--TTT
1 AAATTGAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1241122 TTGACAAACAG
66 TTGA-AAACAG
*
1241133 AAATTG-AAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTT
1 AAATTGAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1241197 TTGAAAGACAG
66 TTGAAA-ACAG
* *
1241208 AAATTGAAAATTACCTCAGCATGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1241273 TTGAAAACAG
66 TTGAAAACAG
1241283 AAAT
1 AAAT
1241287 AAAAACATCA
Statistics
Matches: 142, Mismatches: 7, Indels: 8
0.90 0.04 0.05
Matches are distributed among these distances:
73 54 0.38
74 2 0.01
75 25 0.18
76 61 0.43
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (75 bp):
AAATTGAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
TTGAAAACAG
Found at i:1242857 original size:49 final size:49
Alignment explanation
Indices: 1242797--1243109 Score: 545
Period size: 49 Copynumber: 6.4 Consensus size: 49
1242787 TACATATATG
* * * * * *
1242797 TGTGATAAGGCCGAATGGCCAATGCGATGAATGTGAAAGTGGATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1242846 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1242895 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
*
1242944 TGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1242993 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
*
1243042 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
*
1243091 TGTGATAAGGCCTAATGGC
1 TGTGATGAGGCCTAATGGC
1243110 TAATGTAAAA
Statistics
Matches: 255, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 255 1.00
ACGTcount: A:0.28, C:0.09, G:0.34, T:0.29
Consensus pattern (49 bp):
TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
Found at i:1243260 original size:37 final size:37
Alignment explanation
Indices: 1243210--1243331 Score: 226
Period size: 37 Copynumber: 3.3 Consensus size: 37
1243200 GGAATATGTT
*
1243210 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
1243247 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
*
1243284 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
1243321 CCGGGTAAGAC
1 CCGGGTAAGAC
1243332 TTCTTTTATA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 83 1.00
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
Found at i:1245445 original size:29 final size:29
Alignment explanation
Indices: 1245400--1245851 Score: 805
Period size: 29 Copynumber: 15.6 Consensus size: 29
1245390 AATGAATATG
*
1245400 GGCACTATGTGTGCGAGATCAGTAATCGA
1 GGCACTACGTGTGCGAGATCAGTAATCGA
* *
1245429 GGCACTATGTGTTCGAGATCAGTAATCGA
1 GGCACTACGTGTGCGAGATCAGTAATCGA
1245458 GGCACTACGTGTGCGAGATCAGTAATCGA
1 GGCACTACGTGTGCGAGATCAGTAATCGA
1245487 GGCACTACGTGTGCGAGATCAGTAATCGA
1 GGCACTACGTGTGCGAGATCAGTAATCGA
1245516 GGCACTACGTGTGCGAGATCAGTAATCGA
1 GGCACTACGTGTGCGAGATCAGTAATCGA
1245545 GGCACTACGTGTGCGAGATCAGTAATCGA
1 GGCACTACGTGTGCGAGATCAGTAATCGA
1245574 GGCACTACGTGTGCGAGATCAGTAATCGA
1 GGCACTACGTGTGCGAGATCAGTAATCGA
1245603 GGCACTACGTGTGCGAGATCAGTAATCGA
1 GGCACTACGTGTGCGAGATCAGTAATCGA
1245632 GGCACTACGTGTGCGAGATCAGTAATCGA
1 GGCACTACGTGTGCGAGATCAGTAATCGA
1245661 GGCACTACGTGTGCGAGATCAGTAATCGA
1 GGCACTACGTGTGCGAGATCAGTAATCGA
1245690 GGCACTACGTGTGCGAGATCAGTAATCGA
1 GGCACTACGTGTGCGAGATCAGTAATCGA
1245719 GGCACTACGTGTGCGAGATCAGTAATCGA
1 GGCACTACGTGTGCGAGATCAGTAATCGA
* *
1245748 GGCACCATGTGTGCGAGATCAGTAATCGA
1 GGCACTACGTGTGCGAGATCAGTAATCGA
* *
1245777 GGCACTATGTGTGCGAGATCAGTAATTGA
1 GGCACTACGTGTGCGAGATCAGTAATCGA
* *
1245806 GGCACTATGTGTGCGAGATCAGTAATTGA
1 GGCACTACGTGTGCGAGATCAGTAATCGA
**
1245835 GGCACTGTGTGTGCGAG
1 GGCACTACGTGTGCGAG
1245852 TTTTTCAACA
Statistics
Matches: 415, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 415 1.00
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.22
Consensus pattern (29 bp):
GGCACTACGTGTGCGAGATCAGTAATCGA
Found at i:1246433 original size:40 final size:41
Alignment explanation
Indices: 1246335--1246433 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 41
1246325 TTCGAATGGT
* ** * *
1246335 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTTACTAA
1 ATCCGGGCTATGTCCCGAAGGCAATTGTGCGAAGTAACTAA
1246376 ATCCGGGCTAAT-TCCCGAAGGCAATTGTGCGAA-TAACTATA
1 ATCCGGGCT-ATGTCCCGAAGGCAATTGTGCGAAGTAACTA-A
1246417 A-CCGGGCTATGTCCCGA
1 ATCCGGGCTATGTCCCGA
1246434 GGACAATCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
39 2 0.04
40 18 0.36
41 29 0.58
42 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.25
Consensus pattern (41 bp):
ATCCGGGCTATGTCCCGAAGGCAATTGTGCGAAGTAACTAA
Found at i:1248539 original size:49 final size:49
Alignment explanation
Indices: 1248479--1248791 Score: 581
Period size: 49 Copynumber: 6.4 Consensus size: 49
1248469 TACATATATG
* * *
1248479 TGTGATAAGGCCTAATGGCCGATGCGATGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
*
1248528 TGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1248577 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1248626 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1248675 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1248724 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
*
1248773 TGTGATAAGGCCTAATGGC
1 TGTGATGAGGCCTAATGGC
1248792 TAATGTAAAA
Statistics
Matches: 260, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 260 1.00
ACGTcount: A:0.27, C:0.09, G:0.34, T:0.30
Consensus pattern (49 bp):
TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
Found at i:1248942 original size:37 final size:37
Alignment explanation
Indices: 1248892--1249013 Score: 226
Period size: 37 Copynumber: 3.3 Consensus size: 37
1248882 GGAATATGTT
*
1248892 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
1248929 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
*
1248966 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
1249003 CCGGGTAAGAC
1 CCGGGTAAGAC
1249014 TTCTTTTATA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 83 1.00
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
Found at i:1259844 original size:19 final size:17
Alignment explanation
Indices: 1259805--1259838 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1259795 TTCTTCTTTT
1259805 CTTTCCTCTCATTTTCC
1 CTTTCCTCTCATTTTCC
1259822 CTTTCCTCTC-TTTTCC
1 CTTTCCTCTCATTTTCC
1259838 C
1 C
1259839 ACCTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.03, C:0.44, G:0.00, T:0.53
Consensus pattern (17 bp):
CTTTCCTCTCATTTTCC
Found at i:1266717 original size:40 final size:40
Alignment explanation
Indices: 1266670--1266745 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
1266660 GAGGCCGATA
*
1266670 CATGTCCCAGATATATCTTACACTAGCACTCATCTTGATT
1 CATGTCCCAGACATATCTTACACTAGCACTCATCTTGATT
* *
1266710 CATGTCCCAGACATGTCTTACACTAGCACTCGTCTT
1 CATGTCCCAGACATATCTTACACTAGCACTCATCTT
1266746 AATGCCGATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.33
Consensus pattern (40 bp):
CATGTCCCAGACATATCTTACACTAGCACTCATCTTGATT
Found at i:1266763 original size:47 final size:47
Alignment explanation
Indices: 1266710--1266830 Score: 133
Period size: 47 Copynumber: 2.6 Consensus size: 47
1266700 CATCTTGATT
*
1266710 CATGTCCCAGACATGTCTTACACTAGCACTCGTCTTAA-T-GCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCACTC-TCATAAGTGGCCGATG
* * *
1266756 CCATGTCCTAGACATGGTCTTACA-TTG-GCTCTCATAATGTGGCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCACTCTCATAA-GTGGCCGATG
*
1266804 AATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
1266831 TCACTTACAT
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
45 5 0.08
46 11 0.18
47 30 0.49
48 15 0.25
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTAGCACTCTCATAAGTGGCCGATG
Found at i:1267509 original size:19 final size:19
Alignment explanation
Indices: 1267464--1267510 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1267454 AGATATTTAT
*
1267464 TTATA-TATTAAATTATTG
1 TTATATTATTAAATTATTA
1267482 TTATAATTATT-AATTATTA
1 TTAT-ATTATTAAATTATTA
1267501 TTAATATTAT
1 TT-ATATTAT
1267511 ATTATATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 4 0.16
19 15 0.60
20 6 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TTATATTATTAAATTATTA
Found at i:1268381 original size:3 final size:3
Alignment explanation
Indices: 1268368--1268496 Score: 74
Period size: 3 Copynumber: 42.0 Consensus size: 3
1268358 AAAAGCAAAT
* * *
1268368 ATA AT- ATA ATA ATA ATA TTA A-A ATA AT- GTA ATTA AAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
*
1268411 CT- ATA TATA A-A TATA TATA TATA CATA CATA ATA A-A A-A CATA CATTA
1 ATA ATA -ATA ATA -ATA -ATA -ATA -ATA -ATA ATA ATA ATA -ATA -A-TA
*
1268458 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1268497 TGTATTAAAT
Statistics
Matches: 104, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
2 10 0.10
3 66 0.63
4 26 0.25
5 2 0.02
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1268522 original size:34 final size:34
Alignment explanation
Indices: 1268481--1268564 Score: 159
Period size: 34 Copynumber: 2.5 Consensus size: 34
1268471 TAATAATAAT
1268481 AATAATAGTAATAATATGTATTAAATGGTAAAAC
1 AATAATAGTAATAATATGTATTAAATGGTAAAAC
1268515 AATAATAGTAATAATATGTATTAAATGGTAAAAC
1 AATAATAGTAATAATATGTATTAAATGGTAAAAC
*
1268549 AATAATAGTAACAATA
1 AATAATAGTAATAATA
1268565 ATAGTAATAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.55, C:0.04, G:0.11, T:0.31
Consensus pattern (34 bp):
AATAATAGTAATAATATGTATTAAATGGTAAAAC
Found at i:1268574 original size:18 final size:18
Alignment explanation
Indices: 1268549--1268601 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
1268539 ATGGTAAAAC
1268549 AATAATAGTAACAATAAT
1 AATAATAGTAACAATAAT
* *
1268567 AGTAATAGTAA-AAGGAAT
1 AATAATAGTAACAA-TAAT
1268585 AATAATAGTAACAATAA
1 AATAATAGTAACAATAA
1268602 GAGCGTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.07
18 25 0.86
19 2 0.07
ACGTcount: A:0.60, C:0.04, G:0.11, T:0.25
Consensus pattern (18 bp):
AATAATAGTAACAATAAT
Found at i:1268623 original size:12 final size:12
Alignment explanation
Indices: 1268456--1268678 Score: 99
Period size: 12 Copynumber: 18.6 Consensus size: 12
1268446 AAACATACAT
*
1268456 TAATAATAATAA
1 TAATAATAGTAA
*
1268468 TAATAATAATAA
1 TAATAATAGTAA
1268480 TAATAATAGTAA
1 TAATAATAGTAA
1268492 TAAT-AT-GT-A
1 TAATAATAGTAA
* *
1268501 TTA-AATGGTAAAA
1 TAATAATAGT--AA
*
1268514 CAATAATAGTAA
1 TAATAATAGTAA
1268526 TAAT-AT-GT-A
1 TAATAATAGTAA
* *
1268535 TTA-AATGGTAAAA
1 TAATAATAGT--AA
*
1268548 CAATAATAGTAA
1 TAATAATAGTAA
*
1268560 CAATAATAGTAA
1 TAATAATAGTAA
* * *
1268572 TAGTAAAAGGAA
1 TAATAATAGTAA
1268584 TAATAATAGTAA
1 TAATAATAGTAA
* * ***
1268596 CAATAAGAGCGT
1 TAATAATAGTAA
1268608 TAATAATAGTAA
1 TAATAATAGTAA
*
1268620 TAAT-ATAAATAA
1 TAATAAT-AGTAA
1268632 TAATATATATGT-A
1 TAATA-ATA-GTAA
*
1268645 TGAA-AATAATAA
1 T-AATAATAGTAA
1268657 TAATAGAAGTAGTAA
1 TAAT--AA-TAGTAA
1268672 TAATAAT
1 TAATAAT
1268679 GGTATTAGAA
Statistics
Matches: 158, Mismatches: 31, Indels: 44
0.68 0.13 0.19
Matches are distributed among these distances:
9 10 0.06
10 8 0.05
11 9 0.06
12 95 0.60
13 10 0.06
14 17 0.11
15 9 0.06
ACGTcount: A:0.57, C:0.02, G:0.10, T:0.31
Consensus pattern (12 bp):
TAATAATAGTAA
Found at i:1272229 original size:20 final size:20
Alignment explanation
Indices: 1272186--1272231 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1272176 ACTATTTTAT
1272186 TATGGG-CCAACTGTATTAA
1 TATGGGCCCAACTGTATTAA
* * *
1272205 AATGGGCCCAACTGTGTTGA
1 TATGGGCCCAACTGTATTAA
1272225 TATGGGC
1 TATGGGC
1272232 AAGGCCCAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TATGGGCCCAACTGTATTAA
Found at i:1272358 original size:28 final size:28
Alignment explanation
Indices: 1272260--1272372 Score: 88
Period size: 28 Copynumber: 3.9 Consensus size: 28
1272250 ACTTGTAATA
*
1272260 GGGCTACGGCCCAGATTAATACTGATAT
1 GGGCTAAGGCCCAGATTAATACTGATAT
** *
1272288 GGGCT-AGGCCCAGTATACTCTGTTACTG-TAAG
1 GGGCTAAGGCCCAG---A-T-TAATACTGAT-AT
* *
1272320 GGGTTATGGCCCAGATTAATACTGATAT
1 GGGCTAAGGCCCAGATTAATACTGATAT
*
1272348 GGGCTAAGGCCCAG-TTAACACTGAT
1 GGGCTAAGGCCCAGATTAATACTGAT
1272373 TTCTAAATAG
Statistics
Matches: 65, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
27 17 0.26
28 24 0.37
29 2 0.03
30 2 0.03
31 2 0.03
32 11 0.17
33 7 0.11
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (28 bp):
GGGCTAAGGCCCAGATTAATACTGATAT
Found at i:1274290 original size:41 final size:37
Alignment explanation
Indices: 1274244--1274353 Score: 94
Period size: 37 Copynumber: 2.8 Consensus size: 37
1274234 TCGACCTCGA
1274244 GTCGATGAGACACTGGGTGTCATTATATTTCTTCGGATAG
1 GTCGATGAGACACTGGGTGTCA--A-ATTTCTTCGGATAG
* * * ** * *
1274284 ATTCGATGAGGCATTGGGTACCAACTTTCTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCAAATTTCTTCGGATAG
* *
1274322 GCCGATGAGACACTGGGTGTCAACTTTGCTTC
1 GTCGATGAGACACTGGGTGTCAAATTT-CTTC
1274354 TAACTATCCG
Statistics
Matches: 55, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
37 21 0.38
38 16 0.29
39 1 0.02
41 17 0.31
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (37 bp):
GTCGATGAGACACTGGGTGTCAAATTTCTTCGGATAG
Found at i:1280030 original size:36 final size:36
Alignment explanation
Indices: 1279983--1280055 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1279973 ATATTGAAAA
1279983 ATAGGGTTTGATCTTTATCTTGTTATCTGTGATATT
1 ATAGGGTTTGATCTTTATCTTGTTATCTGTGATATT
*
1280019 ATAGGGTTTGATCTTTATCTTGTTATTTGTGATATT
1 ATAGGGTTTGATCTTTATCTTGTTATCTGTGATATT
1280055 A
1 A
1280056 GTTGTTGTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.21, C:0.07, G:0.19, T:0.53
Consensus pattern (36 bp):
ATAGGGTTTGATCTTTATCTTGTTATCTGTGATATT
Found at i:1281207 original size:18 final size:20
Alignment explanation
Indices: 1281186--1281223 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
1281176 TTTTTGAACA
1281186 ATTTATTT-TTT-TCTTTTT
1 ATTTATTTATTTCTCTTTTT
*
1281204 ATTTCTTTATTTCTCTTTTT
1 ATTTATTTATTTCTCTTTTT
1281224 TTCTTCCCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 3 0.18
20 7 0.41
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (20 bp):
ATTTATTTATTTCTCTTTTT
Found at i:1282217 original size:48 final size:48
Alignment explanation
Indices: 1282158--1282255 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
1282148 AATATAAAAG
1282158 AAAAAACTTTAAATTGCTCAAAATGAAAAAATATGGGACCAATTTTAT
1 AAAAAACTTTAAATTGCTCAAAATGAAAAAATATGGGACCAATTTTAT
1282206 AAAAAACTTTAAATTGCTCAAAATGAAAAAATATGGGACCAATTTTAT
1 AAAAAACTTTAAATTGCTCAAAATGAAAAAATATGGGACCAATTTTAT
1282254 AA
1 AA
1282256 TTTAACCTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (48 bp):
AAAAAACTTTAAATTGCTCAAAATGAAAAAATATGGGACCAATTTTAT
Found at i:1288872 original size:18 final size:18
Alignment explanation
Indices: 1288839--1288930 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
1288829 CCCAACTACT
*
1288839 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* *
1288857 GTATTCGTAAATAGTACC
1 GTATACGTGAATAGTACC
*
1288875 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
* *
1288893 GTATACGT-AATAGTGCT
1 GTATACGTGAATAGTACC
1288910 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
1288928 GTA
1 GTA
1288931 AACGGTCGTA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
17 16 0.25
18 48 0.75
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:1288914 original size:35 final size:36
Alignment explanation
Indices: 1288835--1288930 Score: 140
Period size: 35 Copynumber: 2.7 Consensus size: 36
1288825 CAATCCCAAC
* *
1288835 TACTGTATACGTGAACAGTACCGTATTCGTAAATAG
1 TACTGTATACGTGAATAGTACCGTATACGTAAATAG
* *
1288871 TACCGTATACGTGAATAGTACTGTATACGT-AATAG
1 TACTGTATACGTGAATAGTACCGTATACGTAAATAG
*
1288906 TGCTGTATACGTGAATAGTACCGTA
1 TACTGTATACGTGAATAGTACCGTA
1288931 AACGGTCGTA
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 27 0.51
36 26 0.49
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (36 bp):
TACTGTATACGTGAATAGTACCGTATACGTAAATAG
Found at i:1299715 original size:68 final size:67
Alignment explanation
Indices: 1299635--1299772 Score: 258
Period size: 68 Copynumber: 2.0 Consensus size: 67
1299625 TTAATATTTC
*
1299635 AATTATAATTTATTTTAATGTTAGAATTCATACTAGAAATAAAAAAATTAAACTTTTTGTATATT
1 AATTATAATTTATTTTAATGTTAGAATTCATACTAGAAAT-AAAAAATTAAACTTTTTATATATT
1299700 AAA
65 AAA
1299703 AATTATAATTTATTTTAATGTTAGAATTCATACTAGAAATAAAAAATTAAACTTTTTATATATTA
1 AATTATAATTTATTTTAATGTTAGAATTCATACTAGAAATAAAAAATTAAACTTTTTATATATTA
1299768 AA
66 AA
1299770 AAT
1 AAT
1299773 GTAAAGAACT
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
67 29 0.42
68 40 0.58
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (67 bp):
AATTATAATTTATTTTAATGTTAGAATTCATACTAGAAATAAAAAATTAAACTTTTTATATATTA
AA
Found at i:1300303 original size:2 final size:2
Alignment explanation
Indices: 1300291--1300331 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1300281 AAGATTGAAT
* *
1300291 TA TA AA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1300332 GAAAATGGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1303645 original size:15 final size:16
Alignment explanation
Indices: 1303625--1303657 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1303615 TCATTTCTCA
1303625 TAAATAGAAA-ACATT
1 TAAATAGAAATACATT
*
1303640 TAAATATAAATACATT
1 TAAATAGAAATACATT
1303656 TA
1 TA
1303658 GTTATTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (16 bp):
TAAATAGAAATACATT
Found at i:1305809 original size:2 final size:2
Alignment explanation
Indices: 1305804--1305834 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1305794 ATATATACAT
*
1305804 AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1305835 CCTGCAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1322372 original size:19 final size:20
Alignment explanation
Indices: 1322340--1322377 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1322330 ATCGGTCAAA
*
1322340 TTAAAAAATTATTAAAAATT
1 TTAAAAAATAATTAAAAATT
1322360 TTAAAAAA-AATTAAAAAT
1 TTAAAAAATAATTAAAAAT
1322378 CTCAATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAAAAAATAATTAAAAATT
Found at i:1322829 original size:129 final size:127
Alignment explanation
Indices: 1322589--1322861 Score: 316
Period size: 129 Copynumber: 2.1 Consensus size: 127
1322579 CCGGTAAGAA
* * * * * *
1322589 AACCCGACTCGGTAGGAAATTAGTGATGATATTTATAACCGAGTCCGAATATCATATGGGTTGTC
1 AACCCGACCCGGTAAGAAACTAGTGACGATATTTATAACCGAGTCCGAATATCATACGGGTTATC
* * *
1322654 CACTCCTCTAGAAACATAACTAGTGACGATATCACAATAGAGTCCGAGTCACATATGAGCTATC
66 CACTCATCCAGAAACATAACTAGTGACGATAT--CAATAGAATCCGAGTCACATATGAGCTATC
* *
1322718 AACCCGACCCGGTAAGAAACTAGTGACGATGTTTATAACCGGGTCCGAATATCATACGGGTTATC
1 AACCCGACCCGGTAAGAAACTAGTGACGATATTTATAACCGAGTCCGAATATCATACGGGTTATC
* * ** * *
1322783 CACTTGATCCAGTAGGA-AACTAGTGAAACGATAGT-AGTAGAATCCGAGTCACATATGGGCTAT
66 CAC-TCATCCAGAAACATAACTAGTG--ACGATA-TCAATAGAATCCGAGTCACATATGAGCTAT
1322846 C
127 C
*
1322847 AACCCGACCCAGTAA
1 AACCCGACCCGGTAA
1322862 CATCCGAGAA
Statistics
Matches: 122, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
129 108 0.89
130 7 0.06
131 6 0.05
132 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (127 bp):
AACCCGACCCGGTAAGAAACTAGTGACGATATTTATAACCGAGTCCGAATATCATACGGGTTATC
CACTCATCCAGAAACATAACTAGTGACGATATCAATAGAATCCGAGTCACATATGAGCTATC
Found at i:1326319 original size:23 final size:23
Alignment explanation
Indices: 1326270--1326319 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1326260 CCCAATTTGG
* * *
1326270 AATTTTTTTCACATTGGTTTTTG
1 AATTTTTTTCACATTAGTTTATA
1326293 AATTTTTTT-ACATTAGTTCTATA
1 AATTTTTTTCACATTAGTT-TATA
1326316 AATT
1 AATT
1326320 GACAGTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.58
Consensus pattern (23 bp):
AATTTTTTTCACATTAGTTTATA
Found at i:1329689 original size:13 final size:13
Alignment explanation
Indices: 1329673--1329705 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1329663 CTAAAATTTT
1329673 AAAAGCACTTCTC
1 AAAAGCACTTCTC
*
1329686 AAAAGCACTTTTC
1 AAAAGCACTTCTC
1329699 AAAAGCA
1 AAAAGCA
1329706 TTGCCAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.21
Consensus pattern (13 bp):
AAAAGCACTTCTC
Found at i:1335038 original size:46 final size:45
Alignment explanation
Indices: 1334945--1335030 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 45
1334935 TACATCTCAC
* *
1334945 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCG-ACATGCGCAACCATAAGT
* *
1334991 GAACTCGGACTCAACTCAACGAGTTCG-GATGCTCAACCAT
1 GAACTCGGACTCAACTCAACGAGTTCGACATGCGCAACCAT
1335031 CCTAGTGACA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 9 0.25
46 27 0.75
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGACATGCGCAACCATAAGT
Found at i:1337478 original size:75 final size:75
Alignment explanation
Indices: 1337388--1337567 Score: 220
Period size: 75 Copynumber: 2.4 Consensus size: 75
1337378 CGATAGTGAA
*** * *
1337388 TGTGAGCCCAGCTCTAGTTGGATAAACCATCTATATTTG-AGCCCAAC-ACTAGTTGGATATACT
1 TGTGAGCCCAGCTCTAGTTGGATAAACCAAAGATATTTGCA--CCAACTACTAGTCGGATATACC
*
1337451 GACGATAATAAT
64 AACGATAATAAT
* * *
1337463 TGTGAGCCCAACTCTAGTTGGATAAACCAAAGATATTTGCACCTACTGCTAGTCGGATATACCAA
1 TGTGAGCCCAGCTCTAGTTGGATAAACCAAAGATATTTGCACCAACTACTAGTCGGATATACCAA
1337528 CGATAATAAT
66 CGATAATAAT
* * *
1337538 TTTGAGCCCAGCTCTAGTCGGATATACCAA
1 TGTGAGCCCAGCTCTAGTTGGATAAACCAA
1337568 CAATAATAAT
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
74 4 0.04
75 85 0.94
76 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (75 bp):
TGTGAGCCCAGCTCTAGTTGGATAAACCAAAGATATTTGCACCAACTACTAGTCGGATATACCAA
CGATAATAAT
Found at i:1337480 original size:40 final size:40
Alignment explanation
Indices: 1337388--1337786 Score: 244
Period size: 40 Copynumber: 10.6 Consensus size: 40
1337378 CGATAGTGAA
* * *
1337388 TGTGAGCCCAGCTCTAGTTGGATAAACCATC--T-AT-AT
1 TGTGAGCCCAACTCTAGTTGGATATACCAACGATAATAAT
* **
1337424 T-TGAGCCCAACACTAGTTGGATATACTGACGATAATAAT
1 TGTGAGCCCAACTCTAGTTGGATATACCAACGATAATAAT
* *
1337463 TGTGAGCCCAACTCTAGTTGGATAAACCAAAGAT-AT--T
1 TGTGAGCCCAACTCTAGTTGGATATACCAACGATAATAAT
* * *
1337500 TG-CA--CCTACTGCTAGTCGGATATACCAACGATAATAAT
1 TGTGAGCCCAACT-CTAGTTGGATATACCAACGATAATAAT
* * * *
1337538 TTTGAGCCCAGCTCTAGTCGGATATACCAACAATAATAAT
1 TGTGAGCCCAACTCTAGTTGGATATACCAACGATAATAAT
* * *
1337578 TTTGAGCCCAGCTCTAGTTGGATAAACCAACGAT-AT--T
1 TGTGAGCCCAACTCTAGTTGGATATACCAACGATAATAAT
* * *
1337615 TG-CA-CCC-AGTGCTAGTCGGATATACCGAA-GATAATAAT
1 TGTGAGCCCAACT-CTAGTTGGATATACC-AACGATAATAAT
* * *
1337653 TGTGAGCCCAACTCTAGTTGGATAAACCAATGGT-AT--T
1 TGTGAGCCCAACTCTAGTTGGATATACCAACGATAATAAT
* * * * * * *
1337690 TG-CA-CCC-AGTGCTAGTCGGATATATCAGCAATAATAAC
1 TGTGAGCCCAACT-CTAGTTGGATATACCAACGATAATAAT
* * *
1337728 TGTGAACCCAGCTCTAGTTGGATAAACCAAC---AATAA-
1 TGTGAGCCCAACTCTAGTTGGATATACCAACGATAATAAT
*
1337764 T-TGCGCCCAACTCTAGTTGGATA
1 TGTGAGCCCAACTCTAGTTGGATA
1337787 AACTAACAAT
Statistics
Matches: 280, Mismatches: 55, Indels: 57
0.71 0.14 0.15
Matches are distributed among these distances:
34 8 0.03
35 96 0.34
36 13 0.05
37 14 0.05
38 9 0.03
39 14 0.05
40 119 0.43
41 7 0.03
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (40 bp):
TGTGAGCCCAACTCTAGTTGGATATACCAACGATAATAAT
Found at i:1337562 original size:115 final size:115
Alignment explanation
Indices: 1337423--1337682 Score: 387
Period size: 115 Copynumber: 2.3 Consensus size: 115
1337413 ACCATCTATA
* ** *
1337423 TTTGAGCCCAACACTAGTTGGATATACTGACGATAATAATTGTGAGCCCAACTCTAGTTGGATAA
1 TTTGAGCCCAACTCTAGTTGGATATACCAACAATAATAATTGTGAGCCCAACTCTAGTTGGATAA
*
1337488 ACCAAAGATATTTGCACCTACTGCTAGTCGGATATACC-AACGATAATAAT
66 ACCAAAGATATTTGCACCCACTGCTAGTCGGATATACCGAA-GATAATAAT
* * * *
1337538 TTTGAGCCCAGCTCTAGTCGGATATACCAACAATAATAATTTTGAGCCCAGCTCTAGTTGGATAA
1 TTTGAGCCCAACTCTAGTTGGATATACCAACAATAATAATTGTGAGCCCAACTCTAGTTGGATAA
* *
1337603 ACCAACGATATTTGCACCCAGTGCTAGTCGGATATACCGAAGATAATAAT
66 ACCAAAGATATTTGCACCCACTGCTAGTCGGATATACCGAAGATAATAAT
* *
1337653 TGTGAGCCCAACTCTAGTTGGATAAACCAA
1 TTTGAGCCCAACTCTAGTTGGATATACCAA
1337683 TGGTATTTGC
Statistics
Matches: 129, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
115 127 0.98
116 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (115 bp):
TTTGAGCCCAACTCTAGTTGGATATACCAACAATAATAATTGTGAGCCCAACTCTAGTTGGATAA
ACCAAAGATATTTGCACCCACTGCTAGTCGGATATACCGAAGATAATAAT
Found at i:1337623 original size:75 final size:75
Alignment explanation
Indices: 1337551--1337799 Score: 322
Period size: 75 Copynumber: 3.3 Consensus size: 75
1337541 GAGCCCAGCT
*
1337551 CTAGTCGGATATACCAACAATAATAATTTTGAGCCCAGCTCTAGTTGGATAAACCAACGATATTT
1 CTAGTCGGATATACCAACAATAATAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACGATATTT
1337616 GCACCCAGTG
66 GCACCCAGTG
* * * *
1337626 CTAGTCGGATATACCGAA-GATAATAATTGTGAGCCCAACTCTAGTTGGATAAACCAATGGTATT
1 CTAGTCGGATATACC-AACAATAATAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACGATATT
1337690 TGCACCCAGTG
65 TGCACCCAGTG
* * * * * *
1337701 CTAGTCGGATATATCAGCAATAATAACTGTGAACCCAGCTCTAGTTGGATAAACCAACAATAATT
1 CTAGTCGGATATACCAACAATAATAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACGATATTT
* *
1337766 GCGCCCAACT-
66 GCACCC-AGTG
* * *
1337776 CTAGTTGGATAAACTAACAATAAT
1 CTAGTCGGATATACCAACAATAAT
1337800 TGCGTCCAGC
Statistics
Matches: 149, Mismatches: 22, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
74 1 0.01
75 144 0.97
76 4 0.03
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (75 bp):
CTAGTCGGATATACCAACAATAATAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACGATATTT
GCACCCAGTG
Found at i:1337676 original size:190 final size:185
Alignment explanation
Indices: 1337390--1337821 Score: 560
Period size: 190 Copynumber: 2.3 Consensus size: 185
1337380 ATAGTGAATG
* * * * * * *
1337390 TGAGCCCAGCTCTAGTTGGATAAACCATCTATATTTG-AGCCCAACACTAGTTGGATATACTGAC
1 TGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGCA-CCCAGCGCTAGTCGGATATACCGAA
*
1337454 GATAATAATTGTGAGCCCAACTCTAGTTGGATAAACCAAAGATATTTGCACCTACTGCTAGTCGG
65 GATAATAATTGTGAGCCCAACTCTAGTTGGATAAACCAAAGATATTTGCACCCACTGCTAGTCGG
* * * * *
1337519 ATATACCAACGATAATAATTTTGAGCCCAGCTCTAGTCGGATATACCAACAATAATAATTT
130 ATATACCAACAATAATAACTGTGAACCCAGCTCTAGTCGGATAAACCAAC---AATAA--T
* *
1337580 TGAGCCCAGCTCTAGTTGGATAAACCAACGATATTTGCACCCAGTGCTAGTCGGATATACCGAAG
1 TGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGCACCCAGCGCTAGTCGGATATACCGAAG
* * *
1337645 ATAATAATTGTGAGCCCAACTCTAGTTGGATAAACCAATGGTATTTGCACCCAGTGCTAGTCGGA
66 ATAATAATTGTGAGCCCAACTCTAGTTGGATAAACCAAAGATATTTGCACCCACTGCTAGTCGGA
* * *
1337710 TATATCAGCAATAATAACTGTGAACCCAGCTCTAGTTGGATAAACCAACAATAAT
131 TATACCAACAATAATAACTGTGAACCCAGCTCTAGTCGGATAAACCAACAATAAT
* * * * **
1337765 TGCGCCCAACTCTAGTTGGATAAACTAACAATAATTGCGTCCAGCGCTAGTCGGATA
1 TGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGCACCCAGCGCTAGTCGGATA
1337822 AACCAACGAT
Statistics
Matches: 213, Mismatches: 28, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
185 50 0.23
187 5 0.02
190 157 0.74
191 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (185 bp):
TGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGCACCCAGCGCTAGTCGGATATACCGAAG
ATAATAATTGTGAGCCCAACTCTAGTTGGATAAACCAAAGATATTTGCACCCACTGCTAGTCGGA
TATACCAACAATAATAACTGTGAACCCAGCTCTAGTCGGATAAACCAACAATAAT
Found at i:1337795 original size:35 final size:35
Alignment explanation
Indices: 1337393--1337828 Score: 196
Period size: 35 Copynumber: 11.7 Consensus size: 35
1337383 GTGAATGTGA
* * * *
1337393 GCCCAGCTCTAGTTGGATAAACCATCTATATTTGA
1 GCCCAGCTCTAGTTGGATAAACCAACAATAATTGC
* * * * * *
1337428 GCCCAACACTAGTTGGATATACTGACGATAATAATTGTGA
1 GCCCAGCTCTAGTTGGATAAAC---CAACAATAA-T-TGC
* *
1337468 GCCCAACTCTAGTTGGATAAACCAA-AGATATTTGC
1 GCCCAGCTCTAGTTGGATAAACCAACA-ATAATTGC
* * * * *
1337503 ACCTA-CTGCTAGTCGGATATACCAACGATAATAATTTTGA
1 GCCCAGCT-CTAGTTGGATAAACCAAC---AATAA--TTGC
* * *
1337543 GCCCAGCTCTAGTCGGATATACCAACAATAATAATTTTGA
1 GCCCAGCTCTAGTTGGATAAACCAAC---AATAA--TTGC
* *
1337583 GCCCAGCTCTAGTTGGATAAACCAACGATATTTGC
1 GCCCAGCTCTAGTTGGATAAACCAACAATAATTGC
* * * * *
1337618 ACCCAG-TGCTAGTCGGATATACCGAAGATAATAATTGTGA
1 GCCCAGCT-CTAGTTGGATAAACC--A-ACAATAA-T-TGC
* *** *
1337658 GCCCAACTCTAGTTGGATAAACCAATGGTATTTGC
1 GCCCAGCTCTAGTTGGATAAACCAACAATAATTGC
* * * * *
1337693 ACCCAG-TGCTAGTCGGATATATCAGCAATAATAACTGTGA
1 GCCCAGCT-CTAGTTGGATA-A--ACCAACAATAA-T-TGC
*
1337733 ACCCAGCTCTAGTTGGATAAACCAACAATAATTGC
1 GCCCAGCTCTAGTTGGATAAACCAACAATAATTGC
* *
1337768 GCCCAACTCTAGTTGGATAAACTAACAATAATTGC
1 GCCCAGCTCTAGTTGGATAAACCAACAATAATTGC
* * *
1337803 GTCCAGCGCTAGTCGGATAAACCAAC
1 GCCCAGCTCTAGTTGGATAAACCAAC
1337829 GATATTGATT
Statistics
Matches: 311, Mismatches: 62, Indels: 56
0.72 0.14 0.13
Matches are distributed among these distances:
34 4 0.01
35 131 0.42
36 5 0.02
37 22 0.07
38 19 0.06
39 5 0.02
40 121 0.39
41 4 0.01
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (35 bp):
GCCCAGCTCTAGTTGGATAAACCAACAATAATTGC
Found at i:1341717 original size:58 final size:57
Alignment explanation
Indices: 1341630--1341751 Score: 165
Period size: 58 Copynumber: 2.1 Consensus size: 57
1341620 AAATGAATAG
* *
1341630 AAATGAAGAAATATGAAACATTTGGAAATGATTATGGTTTTCTCTAAAAATGAAAATGA
1 AAATGAAGAAATA-GAAACATTTGGAAATGAATATGGCTTTCTC-AAAAATGAAAATGA
* * *
1341689 AAATGGAGAAATA-AAATCATTTGGAAATGAATGTGGCTTTCTCCAAAATGAAAATGA
1 AAATGAAGAAATAGAAA-CATTTGGAAATGAATATGGCTTTCTCAAAAATGAAAATGA
1341746 AAATGA
1 AAATGA
1341752 CTTGAAAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
57 21 0.38
58 23 0.41
59 12 0.21
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.28
Consensus pattern (57 bp):
AAATGAAGAAATAGAAACATTTGGAAATGAATATGGCTTTCTCAAAAATGAAAATGA
Found at i:1351537 original size:2 final size:2
Alignment explanation
Indices: 1351530--1351554 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1351520 CCAAACTCAT
1351530 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1351555 TAAAGTAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1357120 original size:14 final size:14
Alignment explanation
Indices: 1357101--1357133 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1357091 AGAGGAAGGC
1357101 AAGAAAA-AGAAAGA
1 AAGAAAATAGAAA-A
1357115 AAGAAAATAGAAAA
1 AAGAAAATAGAAAA
1357129 AAGAA
1 AAGAA
1357134 GAAAAAGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (14 bp):
AAGAAAATAGAAAA
Found at i:1357911 original size:6 final size:6
Alignment explanation
Indices: 1357900--1357927 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1357890 TTAGAATTGA
1357900 GAAATT GAAATT GAAATT GAAATT GAAA
1 GAAATT GAAATT GAAATT GAAATT GAAA
1357928 ATCCTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.18, T:0.29
Consensus pattern (6 bp):
GAAATT
Found at i:1357923 original size:26 final size:25
Alignment explanation
Indices: 1357881--1357929 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
1357871 ATTTTGATTA
*
1357881 AAATTGAATTTAGAATTGAGAAATTG
1 AAATTGAATTGAGAATTGA-AAATTG
1357907 AAATTGAAATTGA-AATTGAAAAT
1 AAATTG-AATTGAGAATTGAAAAT
1357930 CCTATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 12 0.57
27 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (25 bp):
AAATTGAATTGAGAATTGAAAATTG
Found at i:1358468 original size:52 final size:52
Alignment explanation
Indices: 1358411--1358578 Score: 121
Period size: 52 Copynumber: 3.1 Consensus size: 52
1358401 GGATTTGGAA
1358411 ATTATATGAATTAAATGTGCATGTTTAATTATTTTGTTTTAAAAGTATTCGG
1 ATTATATGAATTAAATGTGCATGTTTAATTATTTTGTTTTAAAAGTATTCGG
* ** * * * *
1358463 ATTATA-GAAAT-ACCGCTG-AGTATTTATATGTGA-ATTGATTAATTGAATAG-ATTTGG
1 ATTATATGAATTAAATG-TGCA-TGTTTA-AT-T-ATTTTG-TT--TT-AAAAGTATTCGG
* *
1358519 AAATTATATGAATTAAATTTGCATGTTTAATTATTTTGTTTTAAAAGTATTCAG
1 --ATTATATGAATTAAATGTGCATGTTTAATTATTTTGTTTTAAAAGTATTCGG
1358573 ATTATA
1 ATTATA
1358579 GAAATACCGC
Statistics
Matches: 84, Mismatches: 16, Indels: 32
0.64 0.12 0.24
Matches are distributed among these distances:
50 3 0.04
51 11 0.13
52 14 0.17
53 8 0.10
54 9 0.11
56 10 0.12
57 8 0.10
58 8 0.10
59 11 0.13
60 2 0.02
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (52 bp):
ATTATATGAATTAAATGTGCATGTTTAATTATTTTGTTTTAAAAGTATTCGG
Found at i:1358505 original size:110 final size:110
Alignment explanation
Indices: 1358374--1358593 Score: 413
Period size: 110 Copynumber: 2.0 Consensus size: 110
1358364 GTGATAAATG
*
1358374 ATTTATATGTGAATTGATTAATTGAATGGATTTGGAAATTATATGAATTAAATGTGCATGTTTAA
1 ATTTATATGTGAATTGATTAATTGAATAGATTTGGAAATTATATGAATTAAATGTGCATGTTTAA
*
1358439 TTATTTTGTTTTAAAAGTATTCGGATTATAGAAATACCGCTGAGT
66 TTATTTTGTTTTAAAAGTATTCAGATTATAGAAATACCGCTGAGT
*
1358484 ATTTATATGTGAATTGATTAATTGAATAGATTTGGAAATTATATGAATTAAATTTGCATGTTTAA
1 ATTTATATGTGAATTGATTAATTGAATAGATTTGGAAATTATATGAATTAAATGTGCATGTTTAA
1358549 TTATTTTGTTTTAAAAGTATTCAGATTATAGAAATACCGCTGAGT
66 TTATTTTGTTTTAAAAGTATTCAGATTATAGAAATACCGCTGAGT
1358594 TTATACTTAG
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 107 1.00
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (110 bp):
ATTTATATGTGAATTGATTAATTGAATAGATTTGGAAATTATATGAATTAAATGTGCATGTTTAA
TTATTTTGTTTTAAAAGTATTCAGATTATAGAAATACCGCTGAGT
Found at i:1369149 original size:2 final size:2
Alignment explanation
Indices: 1369142--1369175 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1369132 TGTAATTTGG
1369142 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1369176 GTAACATCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1372464 original size:13 final size:13
Alignment explanation
Indices: 1372446--1372470 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1372436 CCAAAATTTC
1372446 AAAAAATAAAAAT
1 AAAAAATAAAAAT
1372459 AAAAAATAAAAA
1 AAAAAATAAAAA
1372471 AATTTCAAAA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:1372544 original size:29 final size:31
Alignment explanation
Indices: 1372479--1372551 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
1372469 AAAATTTCAA
*
1372479 AAAAATTACATCTTAGACCCATAAACTTTTT
1 AAAAATTACATTTTAGACCCATAAACTTTTT
**
1372510 TTAAATTACATTTTA-A-CCATAAA-TTTTCT
1 AAAAATTACATTTTAGACCCATAAACTTTT-T
1372539 AAAAATTACATTT
1 AAAAATTACATTT
1372552 AGCCCCAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 4 0.11
29 19 0.53
30 1 0.03
31 12 0.33
ACGTcount: A:0.42, C:0.15, G:0.01, T:0.41
Consensus pattern (31 bp):
AAAAATTACATTTTAGACCCATAAACTTTTT
Found at i:1372783 original size:14 final size:15
Alignment explanation
Indices: 1372766--1372815 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 15
1372756 AAAAAAGAGC
1372766 AAAAAATTCCAGCAAAA
1 AAAAAATTCCAGC--AA
1372783 AAAAAATTCCAGCAA
1 AAAAAATTCCAGCAA
1372798 AAAAAA-TCCA--AA
1 AAAAAATTCCAGCAA
1372810 AAAAAA
1 AAAAAA
1372816 AACATTAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.24
14 4 0.12
15 8 0.24
17 13 0.39
ACGTcount: A:0.70, C:0.16, G:0.04, T:0.10
Consensus pattern (15 bp):
AAAAAATTCCAGCAA
Found at i:1372788 original size:17 final size:17
Alignment explanation
Indices: 1372766--1372803 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1372756 AAAAAAGAGC
1372766 AAAAAATTCCAGCAAAA
1 AAAAAATTCCAGCAAAA
1372783 AAAAAATTCCAGCAAAA
1 AAAAAATTCCAGCAAAA
1372800 AAAA
1 AAAA
1372804 TCCAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.68, C:0.16, G:0.05, T:0.11
Consensus pattern (17 bp):
AAAAAATTCCAGCAAAA
Found at i:1372816 original size:14 final size:14
Alignment explanation
Indices: 1372778--1372817 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1372768 AAAATTCCAG
*
1372778 CAAAAAAAAAATTC
1 CAAAAAAAAAAATC
**
1372792 CAGCAAAAAAAATC
1 CAAAAAAAAAAATC
1372806 CAAAAAAAAAAA
1 CAAAAAAAAAAA
1372818 CATTAGCAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.75, C:0.15, G:0.03, T:0.07
Consensus pattern (14 bp):
CAAAAAAAAAAATC
Found at i:1373048 original size:19 final size:20
Alignment explanation
Indices: 1373024--1373065 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1373014 TGTTTTCATA
*
1373024 TTTTCTTTCCTT-GGTTTTT
1 TTTTCTTTCCTTAGATTTTT
*
1373043 TTTTCTTTCTTTAGATTTTT
1 TTTTCTTTCCTTAGATTTTT
1373063 TTT
1 TTT
1373066 ATTTTCTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.76
Consensus pattern (20 bp):
TTTTCTTTCCTTAGATTTTT
Done.