Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 58 of 91
Found at i:13257294 original size:36 final size:36
Alignment explanation
Indices: 13257126--13257303 Score: 200
Period size: 36 Copynumber: 4.9 Consensus size: 36
13257116 ATCTTGTTTA
* *
13257126 GCTTCACTACTCTTTTTGTGAAGGCTTG-AATTAATTT
1 GCTTCACTACTC-TTCTGTGAAGGC-TGAAATTGATTT
* *
13257163 GCTTCACTACTCTTCTGTGAATGATGAAATTGATTT
1 GCTTCACTACTCTTCTGTGAAGGCTGAAATTGATTT
* *
13257199 GCTTCACTACTCTT-TAGTGAAGACTGAAATTGGTTT
1 GCTTCACTACTCTTCT-GTGAAGGCTGAAATTGATTT
* * * *
13257235 GCTTCACTACCCTTCTGTGAAGGCTTATATTGATTA
1 GCTTCACTACTCTTCTGTGAAGGCTGAAATTGATTT
*
13257271 GCTTCACTACTCTTCTTTGAAGGCT-AATATTGA
1 GCTTCACTACTCTTCTGTGAAGGCTGAA-ATTGA
13257304 GGTTGATTTG
Statistics
Matches: 120, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
35 4 0.03
36 103 0.86
37 13 0.11
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.41
Consensus pattern (36 bp):
GCTTCACTACTCTTCTGTGAAGGCTGAAATTGATTT
Found at i:13258699 original size:36 final size:36
Alignment explanation
Indices: 13258619--13258796 Score: 191
Period size: 36 Copynumber: 4.9 Consensus size: 36
13258609 ATCTTGTTTA
* * *
13258619 GCTTCACTACTCTTTTAGTGAAGGCTTG-GATTAATTT
1 GCTTCACTACTCTTCTA-TGAAGGC-TGAAATTGATTT
* *
13258656 GCTTCACTACTCTTCTATGAATGATGAAATTGATTT
1 GCTTCACTACTCTTCTATGAAGGCTGAAATTGATTT
*
13258692 GCTTCACTACTCTTC-AGTGAAGGCTGAAATTGGTTT
1 GCTTCACTACTCTTCTA-TGAAGGCTGAAATTGATTT
* * * *
13258728 TCTTCACTACTCTTCTATGAAGGCTTATATTGATTA
1 GCTTCACTACTCTTCTATGAAGGCTGAAATTGATTT
* *
13258764 ACTTCACTACTCTTCTGTGAAGGCT-AAGATTGA
1 GCTTCACTACTCTTCTATGAAGGCTGAA-ATTGA
13258797 GGTTGATTTA
Statistics
Matches: 121, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
35 4 0.03
36 100 0.83
37 17 0.14
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.40
Consensus pattern (36 bp):
GCTTCACTACTCTTCTATGAAGGCTGAAATTGATTT
Found at i:13258737 original size:72 final size:71
Alignment explanation
Indices: 13258616--13258788 Score: 211
Period size: 72 Copynumber: 2.4 Consensus size: 71
13258606 TTGATCTTGT
* * *
13258616 TTAGCTTCACTACTCTTTTAGTGAAGGCTTGGATTAATTTGCTTCACTACTCTTCTATGAATGAT
1 TTAGCTTCACTACTC-TTCAGTGAAGGC-TGAATTAATTTGCTTCACTACTCTTCTATGAAGGAT
13258681 GAAATTGA
64 GAAATTGA
* ** * * *
13258689 TTTGCTTCACTACTCTTCAGTGAAGGCTGAAATTGGTTTTCTTCACTACTCTTCTATGAAGGCTT
1 TTAGCTTCACTACTCTTCAGTGAAGGCTG-AATTAATTTGCTTCACTACTCTTCTATGAAGGATG
*
13258754 ATATTGA
65 AAATTGA
* *
13258761 TTAACTTCACTACTCTTCTGTGAAGGCT
1 TTAGCTTCACTACTCTTCAGTGAAGGCT
13258789 AAGATTGAGG
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
71 2 0.02
72 70 0.81
73 14 0.16
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (71 bp):
TTAGCTTCACTACTCTTCAGTGAAGGCTGAATTAATTTGCTTCACTACTCTTCTATGAAGGATGA
AATTGA
Found at i:13260198 original size:36 final size:36
Alignment explanation
Indices: 13260118--13260295 Score: 200
Period size: 36 Copynumber: 4.9 Consensus size: 36
13260108 ATCTTGTTTA
* * * *
13260118 GCTTCACTACTCTTTTTGTGAAGGCTTG-GATTAATTT
1 GCTTCACTACTC-TTCTATGAAGGC-TGAAATTGATTT
* *
13260155 GCTTCACTACTCTTCTATGAATGATGAAATTGATTT
1 GCTTCACTACTCTTCTATGAAGGCTGAAATTGATTT
*
13260191 GCTTCACTACTCTTC-AGTGAAGGCTGAAATTGGTTT
1 GCTTCACTACTCTTCTA-TGAAGGCTGAAATTGATTT
* * * *
13260227 GCTTCACTACTCTTCTGTGAAGGCTTATATTGATTA
1 GCTTCACTACTCTTCTATGAAGGCTGAAATTGATTT
13260263 GCTTCACTACTCTTCTATGAAGGCT-AAGATTGA
1 GCTTCACTACTCTTCTATGAAGGCTGAA-ATTGA
13260296 GGTTGATTTA
Statistics
Matches: 121, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
35 4 0.03
36 105 0.87
37 12 0.10
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.40
Consensus pattern (36 bp):
GCTTCACTACTCTTCTATGAAGGCTGAAATTGATTT
Found at i:13261698 original size:36 final size:36
Alignment explanation
Indices: 13261618--13261795 Score: 175
Period size: 36 Copynumber: 4.9 Consensus size: 36
13261608 ATCTTGTTTA
* * * *
13261618 GCTTCACTACTCTTTTTGTGAAGGCTTG-GATTAATTT
1 GCTTCACTACTC-TTCTATGAAGGC-TGAAATTGATTT
*
13261655 GCTTCACTACTCTTCTATG-AGTGATGAAATTGATTT
1 GCTTCACTACTCTTCTATGAAG-GCTGAAATTGATTT
*
13261691 GCTTCACTACTCTTC-AGTGAAGGCTGAAATTGGTTT
1 GCTTCACTACTCTTCTA-TGAAGGCTGAAATTGATTT
* * * * *
13261727 TCTTCACTACTCTTCTGTGAAGGCTTATATTGATTA
1 GCTTCACTACTCTTCTATGAAGGCTGAAATTGATTT
*
13261763 GCTTCACTACTCTTCTGTGAAGGCT-AAGATTGA
1 GCTTCACTACTCTTCTATGAAGGCTGAA-ATTGA
13261796 GGTTGATTTA
Statistics
Matches: 120, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
35 6 0.05
36 100 0.83
37 14 0.12
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (36 bp):
GCTTCACTACTCTTCTATGAAGGCTGAAATTGATTT
Found at i:13263195 original size:36 final size:36
Alignment explanation
Indices: 13263146--13263290 Score: 186
Period size: 36 Copynumber: 4.0 Consensus size: 36
13263136 GATTGGATTA
* * *
13263146 ATTTACTTCACTACTCTTCTATGAATGATGAAATTG
1 ATTTGCTTCACTACTCTTCTATGAAGGCTGAAATTG
13263182 ATTTGCTTCACTACTCTTC-AGTGAAGGCTGAAATTG
1 ATTTGCTTCACTACTCTTCTA-TGAAGGCTGAAATTG
* * * *
13263218 GTTTGCTTCACTACTCTTCTGTGAAGGCTTATATTG
1 ATTTGCTTCACTACTCTTCTATGAAGGCTGAAATTG
*
13263254 ATTAGCTTCACTACTCTTCTATGAAGGCT-AAGATTG
1 ATTTGCTTCACTACTCTTCTATGAAGGCTGAA-ATTG
13263290 A
1 A
13263291 GGTTGATTTA
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
35 2 0.02
36 93 0.98
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.39
Consensus pattern (36 bp):
ATTTGCTTCACTACTCTTCTATGAAGGCTGAAATTG
Found at i:13264696 original size:36 final size:36
Alignment explanation
Indices: 13264647--13264791 Score: 186
Period size: 36 Copynumber: 4.0 Consensus size: 36
13264637 GATTGGATTA
* * *
13264647 ATTTACTTCACTACTCTTCTATGAATGATGAAATTG
1 ATTTGCTTCACTACTCTTCTATGAAGGCTGAAATTG
13264683 ATTTGCTTCACTACTCTTC-AGTGAAGGCTGAAATTG
1 ATTTGCTTCACTACTCTTCTA-TGAAGGCTGAAATTG
* * * *
13264719 GTTTGCTTCACTACTCTTCTGTGAAGGCTTATATTG
1 ATTTGCTTCACTACTCTTCTATGAAGGCTGAAATTG
*
13264755 ATTAGCTTCACTACTCTTCTATGAAGGCT-AAGATTG
1 ATTTGCTTCACTACTCTTCTATGAAGGCTGAA-ATTG
13264791 A
1 A
13264792 GGTTGATTTA
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
35 2 0.02
36 93 0.98
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.39
Consensus pattern (36 bp):
ATTTGCTTCACTACTCTTCTATGAAGGCTGAAATTG
Found at i:13266198 original size:36 final size:36
Alignment explanation
Indices: 13266151--13266290 Score: 176
Period size: 36 Copynumber: 3.9 Consensus size: 36
13266141 GATTAAATTA
* *
13266151 CTTCACTACTCTTCTATGAATGATGAAATTGATTTG
1 CTTCACTACTCTTCTATGAAGGCTGAAATTGATTTG
*
13266187 CTTCACTACTCTTC-AGTGAAGGCTGAAATTGGTTTG
1 CTTCACTACTCTTCTA-TGAAGGCTGAAATTGATTTG
* * * *
13266223 CTTCACTACTCTTCTGTGAAGGCTTATATTGATTAG
1 CTTCACTACTCTTCTATGAAGGCTGAAATTGATTTG
*
13266259 CTTCACTACTCTTCTGTGAAGGCT-AAGATTGA
1 CTTCACTACTCTTCTATGAAGGCTGAA-ATTGA
13266291 GGTTGATTTA
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
35 2 0.02
36 90 0.98
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (36 bp):
CTTCACTACTCTTCTATGAAGGCTGAAATTGATTTG
Found at i:13267736 original size:72 final size:72
Alignment explanation
Indices: 13267647--13267782 Score: 191
Period size: 72 Copynumber: 1.9 Consensus size: 72
13267637 CTTTGATTAA
* * *
13267647 TTTGCTTCACTAGTCTTCTATGAATGATGAAATTGATTTGCTTCACTACTCTTCAGTGAAGGCTG
1 TTTGCTTCACTACTCTTCTATGAAAGATGAAATTGATTAGCTTCACTACTCTTCAGTGAAGGCTG
13267712 AAATTGG
66 AAATTGG
* * * * **
13267719 TTTGCTTCACTACTCTTCTGTGAAAGCTTATATTGATTAGCTTCACTACTCTTTTGTGAAGGCT
1 TTTGCTTCACTACTCTTCTATGAAAGATGAAATTGATTAGCTTCACTACTCTTCAGTGAAGGCT
13267783 AAGATTGAGG
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 55 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (72 bp):
TTTGCTTCACTACTCTTCTATGAAAGATGAAATTGATTAGCTTCACTACTCTTCAGTGAAGGCTG
AAATTGG
Found at i:13267777 original size:36 final size:36
Alignment explanation
Indices: 13267646--13267778 Score: 167
Period size: 36 Copynumber: 3.7 Consensus size: 36
13267636 CCTTTGATTA
* * * *
13267646 ATTTGCTTCACTAGTCTTCTATGAATGATGAAATTG
1 ATTTGCTTCACTACTCTTCTGTGAAAGCTGAAATTG
* *
13267682 ATTTGCTTCACTACTCTTCAGTGAAGGCTGAAATTG
1 ATTTGCTTCACTACTCTTCTGTGAAAGCTGAAATTG
* * *
13267718 GTTTGCTTCACTACTCTTCTGTGAAAGCTTATATTG
1 ATTTGCTTCACTACTCTTCTGTGAAAGCTGAAATTG
* *
13267754 ATTAGCTTCACTACTCTTTTGTGAA
1 ATTTGCTTCACTACTCTTCTGTGAA
13267779 GGCTAAGATT
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 84 1.00
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (36 bp):
ATTTGCTTCACTACTCTTCTGTGAAAGCTGAAATTG
Found at i:13274960 original size:26 final size:26
Alignment explanation
Indices: 13274931--13274991 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
13274921 TAAAAAATGC
*
13274931 ATAAAAAAGGT-AAGAAAACAAAAGAA
1 ATAAAAAAGGTAAAG-AAACAAAACAA
** *
13274957 ATAAAAAAATTAAAGAAACAAATCAA
1 ATAAAAAAGGTAAAGAAACAAAACAA
13274983 ATAAAAAAG
1 ATAAAAAAG
13274992 AAAATAAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 26 0.90
27 3 0.10
ACGTcount: A:0.74, C:0.05, G:0.10, T:0.11
Consensus pattern (26 bp):
ATAAAAAAGGTAAAGAAACAAAACAA
Found at i:13275018 original size:24 final size:24
Alignment explanation
Indices: 13274987--13275057 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 24
13274977 AATCAAATAA
13274987 AAAAGAAAATAAAAGAAATAAA-G
1 AAAAGAAAATAAAAGAAATAAAGG
*
13275010 AAAAGGAAAAATAACAA-AAAAAAAGG
1 AAAA-G-AAAATAA-AAGAAATAAAGG
*
13275036 AAAA-AATAATAATAGAAATAAA
1 AAAAGAA-AATAAAAGAAATAAA
13275058 AATAAAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
23 7 0.18
24 12 0.31
25 13 0.33
26 7 0.18
ACGTcount: A:0.77, C:0.01, G:0.11, T:0.10
Consensus pattern (24 bp):
AAAAGAAAATAAAAGAAATAAAGG
Found at i:13275161 original size:19 final size:19
Alignment explanation
Indices: 13275126--13275183 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
13275116 CACAAAGGAG
*
13275126 AAAAAATA-ATA-AAAAAT
1 AAAAAATATATATATAAAT
13275143 AAAAAATATATATATAAAT
1 AAAAAATATATATATAAAT
*
13275162 -AAATATAT-TATATTAAAT
1 AAAAAATATATATA-TAAAT
13275180 AAAA
1 AAAA
13275184 TAAATAAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 12 0.34
18 15 0.43
19 8 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAAATATATATATAAAT
Found at i:13275184 original size:19 final size:19
Alignment explanation
Indices: 13275139--13275185 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
13275129 AAATAATAAA
*
13275139 AAATAAAAAATATATATAT
1 AAATAAAATATATATATAT
13275158 AAAT-AAATATAT-TATATT
1 AAATAAAATATATATATA-T
13275176 AAATAAAATA
1 AAATAAAATA
13275186 AATAAAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 4 0.16
18 12 0.48
19 9 0.36
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATAAAATATATATATAT
Found at i:13275257 original size:19 final size:17
Alignment explanation
Indices: 13275215--13275258 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
13275205 GATTGTCAAA
*
13275215 TTTAAAAGCAAATTGGG
1 TTTAAAATCAAATTGGG
*
13275232 ATTAAAATCAAATTCGAGG
1 TTTAAAATCAAATT-G-GG
13275251 TTTAAAAT
1 TTTAAAAT
13275259 GAATATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 12 0.55
18 1 0.05
19 9 0.41
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (17 bp):
TTTAAAATCAAATTGGG
Found at i:13276282 original size:2 final size:2
Alignment explanation
Indices: 13276270--13276373 Score: 98
Period size: 2 Copynumber: 55.5 Consensus size: 2
13276260 ATATGTAATA
*
13276270 AT AT AT TT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
13276311 AT AT AT AT AT TT AT GCT AT AT A- AT -T AT A- AT AT AT A- AC AT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
13276350 A- AT AT GT AT AT AT -T AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
13276374 ATGCATATAC
Statistics
Matches: 84, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
1 8 0.10
2 75 0.89
3 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13278205 original size:17 final size:18
Alignment explanation
Indices: 13278185--13278223 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
13278175 CCTAAATGTT
13278185 TTTTCATCTT-TTTTTCC
1 TTTTCATCTTCTTTTTCC
* *
13278202 TTTTCATTTTCTTTTTTC
1 TTTTCATCTTCTTTTTCC
13278220 TTTT
1 TTTT
13278224 TCTTCTTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTCATCTTCTTTTTCC
Found at i:13288716 original size:13 final size:13
Alignment explanation
Indices: 13288698--13288730 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
13288688 GGGGAAAAAC
*
13288698 AATAAAAAGATAA
1 AATAAAAAAATAA
13288711 AATAAAAAAATAA
1 AATAAAAAAATAA
13288724 AATAAAA
1 AATAAAA
13288731 TGAAAAAGAA
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:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (13 bp):
AATAAAAAAATAA
Found at i:13288853 original size:6 final size:6
Alignment explanation
Indices: 13288844--13288878 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
13288834 AAAGGAAAAA
13288844 AAAATT AAAA-T AGAAATT AAAATT AAAATT AAAAT
1 AAAATT AAAATT A-AAATT AAAATT AAAATT AAAAT
13288879 ATATAAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 2 0.07
6 23 0.85
7 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:13288862 original size:12 final size:11
Alignment explanation
Indices: 13288839--13288879 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
13288829 AAAGAAAAGG
*
13288839 AAAAAAAAATT
1 AAAATAAAATT
13288850 AAAATAGAAATT
1 AAAATA-AAATT
13288862 AAAATTAAAATT
1 AAAA-TAAAATT
13288874 AAAATA
1 AAAATA
13288880 TATAAATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 7 0.26
12 18 0.67
13 2 0.07
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (11 bp):
AAAATAAAATT
Found at i:13288958 original size:10 final size:10
Alignment explanation
Indices: 13288943--13288977 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
13288933 AAAGGAGAAA
13288943 AAATAAAAAT
1 AAATAAAAAT
13288953 AAATAAAAAT
1 AAATAAAAAT
13288963 AAAT--AAAT
1 AAATAAAAAT
13288971 AAATAAA
1 AAATAAA
13288978 TTAGATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.35
10 15 0.65
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:13288968 original size:14 final size:14
Alignment explanation
Indices: 13288943--13288977 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
13288933 AAAGGAGAAA
13288943 AAATAAAAATAAAT
1 AAATAAAAATAAAT
13288957 AAA-AATAAATAAAT
1 AAATAA-AAATAAAT
13288971 AAATAAA
1 AAATAAA
13288978 TTAGATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.11
14 15 0.79
15 2 0.11
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:13288970 original size:18 final size:16
Alignment explanation
Indices: 13288941--13288977 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
13288931 ACAAAGGAGA
13288941 AAAAATAAAAATAAAT
1 AAAAATAAAAATAAAT
13288957 AAAAATAAATAAATAAAT
1 AAAAAT-AA-AAATAAAT
13288975 AAA
1 AAA
13288978 TTAGATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 2 0.11
18 11 0.58
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAAATAAAAATAAAT
Found at i:13289232 original size:12 final size:11
Alignment explanation
Indices: 13289213--13289246 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
13289203 TTGGGGTTGG
13289213 ATCGGGTCAAC
1 ATCGGGTCAAC
*
13289224 ATGCGGGTCAAA
1 AT-CGGGTCAAC
13289236 ATCGGGTCAAC
1 ATCGGGTCAAC
13289247 GGGTTACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.18
Consensus pattern (11 bp):
ATCGGGTCAAC
Found at i:13291714 original size:24 final size:24
Alignment explanation
Indices: 13291682--13291742 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
13291672 GAACCTAGAT
13291682 AAAGATAAAAATTGTGAGGAGACC
1 AAAGATAAAAATTGTGAGGAGACC
*
13291706 AAAGATAAAAATTGTTAGGAGACC
1 AAAGATAAAAATTGTGAGGAGACC
*
13291730 AAAGCTAAAAATT
1 AAAGATAAAAATT
13291743 AAATATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.52, C:0.08, G:0.20, T:0.20
Consensus pattern (24 bp):
AAAGATAAAAATTGTGAGGAGACC
Found at i:13291922 original size:14 final size:15
Alignment explanation
Indices: 13291892--13291942 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
13291882 TTATTAGCGT
13291892 TTAATATTTAAATTA
1 TTAATATTTAAATTA
13291907 TTAAT-TTT-AATCTA
1 TTAATATTTAAAT-TA
*
13291921 TTTTAATATTTAAATTT
1 --TTAATATTTAAATTA
13291938 TTAAT
1 TTAAT
13291943 TTTTTCAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
13 3 0.10
14 5 0.17
15 10 0.33
16 5 0.17
17 4 0.13
18 3 0.10
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (15 bp):
TTAATATTTAAATTA
Found at i:13301003 original size:13 final size:13
Alignment explanation
Indices: 13300985--13301010 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13300975 TCAAAACTCT
13300985 CGAAAAGTTTTGA
1 CGAAAAGTTTTGA
13300998 CGAAAAGTTTTGA
1 CGAAAAGTTTTGA
13301011 AACTTTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
CGAAAAGTTTTGA
Found at i:13301381 original size:24 final size:22
Alignment explanation
Indices: 13301354--13301402 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
13301344 CCCCTTTTTG
13301354 TTATATAAAAAAATAATTCAAACT
1 TTATATAAAAAAATAA--CAAACT
* *
13301378 TTATGTTAAAAAATAACAAACT
1 TTATATAAAAAAATAACAAACT
13301400 TTA
1 TTA
13301403 GGTTCAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 9 0.39
24 14 0.61
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (22 bp):
TTATATAAAAAAATAACAAACT
Found at i:13301388 original size:22 final size:23
Alignment explanation
Indices: 13301361--13301418 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 23
13301351 TTGTTATATA
*
13301361 AAAAAATAATTCAAACTTTATGTT-
1 AAAAAATAA--CAAACTTTAGGTTC
13301385 AAAAAATAACAAACTTTAGGTTC
1 AAAAAATAACAAACTTTAGGTTC
13301408 -AAAAATAACAA
1 AAAAAATAACAA
13301419 TGGAGAGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 23 0.72
24 9 0.28
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (23 bp):
AAAAAATAACAAACTTTAGGTTC
Found at i:13304291 original size:21 final size:22
Alignment explanation
Indices: 13304267--13304314 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
13304257 AACTTTTTGG
*
13304267 GAAACTTTCTTGGAG-AGTTTC
1 GAAACTTTCATGGAGAAGTTTC
*
13304288 GAAAC--TCATGTAGAAGTTTC
1 GAAACTTTCATGGAGAAGTTTC
13304308 GAAACTT
1 GAAACTT
13304315 CTGGTCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
19 6 0.27
20 11 0.50
21 5 0.23
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (22 bp):
GAAACTTTCATGGAGAAGTTTC
Found at i:13305268 original size:12 final size:12
Alignment explanation
Indices: 13305251--13305287 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
13305241 TGTAACACCA
*
13305251 ATTTCCGTATAC
1 ATTTCCGTACAC
13305263 ATTTCCGTACAC
1 ATTTCCGTACAC
13305275 ATTTCCGTACAC
1 ATTTCCGTACAC
13305287 A
1 A
13305288 AGTCACAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.27, C:0.30, G:0.08, T:0.35
Consensus pattern (12 bp):
ATTTCCGTACAC
Found at i:13313549 original size:26 final size:27
Alignment explanation
Indices: 13313498--13313550 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
13313488 CAATAATCGA
* *
13313498 CCATATTTAATTAAATCACTTAAAATC
1 CCATATTTAATTAAATCAATAAAAATC
13313525 CCAT-TTTAA-TAAATCAATAATAAATC
1 CCATATTTAATTAAATCAATAA-AAATC
13313551 ACTAATCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 9 0.39
26 10 0.43
27 4 0.17
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (27 bp):
CCATATTTAATTAAATCAATAAAAATC
Found at i:13318957 original size:27 final size:27
Alignment explanation
Indices: 13318927--13319005 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 27
13318917 TTTAGTATGC
13318927 CCAACATACCTATCAATCATTATTTTT
1 CCAACATACCTATCAATCATTATTTTT
* * **
13318954 CCAA-AT---TATC-CT-TTTATTTGC
1 CCAACATACCTATCAATCATTATTTTT
*
13318975 CCTACATACCTATCAATCATTATTTTT
1 CCAACATACCTATCAATCATTATTTTT
13319002 CCAA
1 CCAA
13319006 ACTATGTGTA
Statistics
Matches: 36, Mismatches: 10, Indels: 12
0.62 0.17 0.21
Matches are distributed among these distances:
21 9 0.25
22 3 0.08
23 4 0.11
25 4 0.11
26 3 0.08
27 13 0.36
ACGTcount: A:0.30, C:0.27, G:0.01, T:0.42
Consensus pattern (27 bp):
CCAACATACCTATCAATCATTATTTTT
Found at i:13321537 original size:25 final size:26
Alignment explanation
Indices: 13321509--13321588 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 26
13321499 GCTGGAGTAT
*
13321509 CACTAGGTACCTAGCTAACTAA-CTA
1 CACTAGCTACCTAGCTAACTAAGCTA
* * *
13321534 CACTACCTAGCTAGCTACCTAAGCTA
1 CACTAGCTACCTAGCTAACTAAGCTA
* *
13321560 C-CTAGCTAGCTAACTACACT-AGCTA
1 CACTAGCTACCTAGCTA-ACTAAGCTA
13321585 -ACTA
1 CACTA
13321589 CCCATGACTC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
25 39 0.87
26 6 0.13
ACGTcount: A:0.34, C:0.31, G:0.11, T:0.24
Consensus pattern (26 bp):
CACTAGCTACCTAGCTAACTAAGCTA
Found at i:13321540 original size:21 final size:21
Alignment explanation
Indices: 13321516--13321580 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
13321506 TATCACTAGG
*
13321516 TACCTAGCTAACTAACTACAC
1 TACCTAGCTAGCTAACTACAC
*
13321537 TACCTAGCTAGCTACCTA-AGC
1 TACCTAGCTAGCTAACTACA-C
13321558 TACCTAGCTAGCTAACTACAC
1 TACCTAGCTAGCTAACTACAC
13321579 TA
1 TA
13321581 GCTAACTACC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
20 1 0.03
21 37 0.95
22 1 0.03
ACGTcount: A:0.34, C:0.32, G:0.09, T:0.25
Consensus pattern (21 bp):
TACCTAGCTAGCTAACTACAC
Found at i:13321564 original size:17 final size:17
Alignment explanation
Indices: 13321509--13321584 Score: 59
Period size: 17 Copynumber: 4.5 Consensus size: 17
13321499 GCTGGAGTAT
* *
13321509 CACTAGGTACCTAGCTA
1 CACTAGCTACCTAACTA
* *
13321526 -ACTAACTACACTACCTA
1 CACTAGCTAC-CTAACTA
*
13321543 -GCTAGCTACCTAAGCTA
1 CACTAGCTACCTAA-CTA
*
13321560 C-CTAGCTAGCTAACTA
1 CACTAGCTACCTAACTA
13321576 CACTAGCTA
1 CACTAGCTA
13321585 ACTACCCATG
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
16 14 0.29
17 34 0.71
ACGTcount: A:0.33, C:0.32, G:0.12, T:0.24
Consensus pattern (17 bp):
CACTAGCTACCTAACTA
Found at i:13322387 original size:20 final size:20
Alignment explanation
Indices: 13322361--13322409 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
13322351 TCATTTCTTG
*
13322361 AAAGGGATCAATCCTTTTCA
1 AAAGGGATCAATCCTTTTAA
* *
13322381 CAAGGGATCACTCCTTTTAA
1 AAAGGGATCAATCCTTTTAA
13322401 AAAGGGATC
1 AAAGGGATC
13322410 GATCATTTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (20 bp):
AAAGGGATCAATCCTTTTAA
Found at i:13340559 original size:15 final size:16
Alignment explanation
Indices: 13340534--13340563 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13340524 TCTGTTGAAA
13340534 AAAAAAGGAAAAATAG
1 AAAAAAGGAAAAATAG
13340550 AAAAAA-GAAAAATA
1 AAAAAAGGAAAAATA
13340564 AGTGAAGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (16 bp):
AAAAAAGGAAAAATAG
Found at i:13342252 original size:26 final size:29
Alignment explanation
Indices: 13342220--13342273 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
13342210 TATATAGTTT
13342220 TAAATATAA-TTTT-TT-AATAAATATAG
1 TAAATATAAGTTTTGTTGAATAAATATAG
13342246 TAAATATAAGTTTTGTTGAATAAATATA
1 TAAATATAAGTTTTGTTGAATAAATATA
13342274 TTTCTTAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 9 0.36
27 4 0.16
28 2 0.08
29 10 0.40
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (29 bp):
TAAATATAAGTTTTGTTGAATAAATATAG
Found at i:13342632 original size:20 final size:19
Alignment explanation
Indices: 13342609--13342657 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
13342599 ATCCATTAAT
13342609 AAATAAAATTCCATATTACA
1 AAATAAAATTCCAT-TTACA
* * * *
13342629 AAATAAATTTTCATTTTCG
1 AAATAAAATTCCATTTACA
13342648 AAATAAAATT
1 AAATAAAATT
13342658 AGTCCCAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (19 bp):
AAATAAAATTCCATTTACA
Found at i:13346812 original size:31 final size:31
Alignment explanation
Indices: 13346777--13346835 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
13346767 CTTTTAGGTA
* *
13346777 AAATTACAACTCTAGTTTCTAAACTTTTCCT
1 AAATTACAACTCTAATTACTAAACTTTTCCT
* * *
13346808 AAATTTCTACTTTAATTACTAAACTTTT
1 AAATTACAACTCTAATTACTAAACTTTT
13346836 AAAATTTACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.34, C:0.19, G:0.02, T:0.46
Consensus pattern (31 bp):
AAATTACAACTCTAATTACTAAACTTTTCCT
Found at i:13357336 original size:18 final size:19
Alignment explanation
Indices: 13357302--13357340 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
13357292 TCTCACTAAC
13357302 TTGTTTCCCTTTCATTTTT
1 TTGTTTCCCTTTCATTTTT
*
13357321 TTGTTT-CCTTTTATTTTT
1 TTGTTTCCCTTTCATTTTT
13357339 TT
1 TT
13357341 ATTCACATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.74
Consensus pattern (19 bp):
TTGTTTCCCTTTCATTTTT
Found at i:13360603 original size:20 final size:20
Alignment explanation
Indices: 13360578--13360616 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
13360568 TCTAAACACG
13360578 AGTATATCATAACAATTATA
1 AGTATATCATAACAATTATA
13360598 AGTATATCATAACAATTAT
1 AGTATATCATAACAATTAT
13360617 GATATCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (20 bp):
AGTATATCATAACAATTATA
Found at i:13360744 original size:54 final size:54
Alignment explanation
Indices: 13360671--13360947 Score: 412
Period size: 54 Copynumber: 5.1 Consensus size: 54
13360661 CACATGTAGG
* * * *
13360671 GCCAATATGGAAATTCATAAACTCGTTATGAATATCTTAAGTTGCACACATAGT
1 GCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGT
* *
13360725 GCCAATATGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACATAGT
1 GCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGT
*
13360779 GCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGA
1 GCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGT
* * * *
13360833 GCCAATACAAAAATTCCTAAACTCATTATGAATTTC-AAATGTTGCACACATACT
1 GCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAA-GTTGCACACATAGT
* **
13360887 GCCAATACGGAAATTCATAAACTCATTATGAATTTCTTATTTTGCACACATAGT
1 GCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGT
13360941 GCCAATA
1 GCCAATA
13360948 TGGTAATCAC
Statistics
Matches: 202, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
53 2 0.01
54 199 0.99
55 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (54 bp):
GCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGT
Found at i:13367470 original size:54 final size:54
Alignment explanation
Indices: 13367412--13367635 Score: 326
Period size: 54 Copynumber: 4.1 Consensus size: 54
13367402 CACTTGTAGG
* *
13367412 GCCAATACATAAATTTATAAACTCATTATGAATTTCTTAAGTTGCACACATAGT
1 GCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGT
* *
13367466 GCCAATAC-GAAAATTCATAAACTCATTATGAATTTGTTAAGTTGTACACA-ATGT
1 GCCAATACAG-AAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATA-GT
* * * *
13367520 CCCAATACGGAAATTTATAAATTCATTATGAATTTCTTAAGTTGCACACATAGT
1 GCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGT
* *
13367574 GCCAATACAGAAATTCAAAAACTCATTATAAATTTCTTAAGTTGCACACATAGT
1 GCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGT
13367628 GCCAATAC
1 GCCAATAC
13367636 GGTAATCACA
Statistics
Matches: 151, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
53 1 0.01
54 148 0.98
55 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (54 bp):
GCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGT
Found at i:13368094 original size:22 final size:19
Alignment explanation
Indices: 13368042--13368098 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
13368032 ATTCTGGATC
13368042 CTTGGTATCGATACCTTTTT
1 CTTGGTATCGATA-CTTTTT
*
13368062 CTTAGTATCGATACTTTTAT
1 CTTGGTATCGATACTTTT-T
13368082 ACTATGGTATCGATACT
1 -CT-TGGTATCGATACT
13368099 CTATTATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.16
20 13 0.41
21 2 0.06
22 12 0.38
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.46
Consensus pattern (19 bp):
CTTGGTATCGATACTTTTT
Found at i:13368115 original size:19 final size:19
Alignment explanation
Indices: 13368064--13368135 Score: 90
Period size: 19 Copynumber: 3.6 Consensus size: 19
13368054 ACCTTTTTCT
*
13368064 TAGTATCGATACTTTTATACTA
1 TAGTATCGATAC-TCTAT--TA
*
13368086 TGGTATCGATACTCTATTA
1 TAGTATCGATACTCTATTA
*
13368105 TAGTATAGATACTCTATTA
1 TAGTATCGATACTCTATTA
13368124 TAGTATCGATAC
1 TAGTATCGATAC
13368136 CATTTTTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 30 0.67
21 4 0.09
22 11 0.24
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (19 bp):
TAGTATCGATACTCTATTA
Found at i:13373949 original size:20 final size:21
Alignment explanation
Indices: 13373900--13373954 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
13373890 TACTATAATA
13373900 GGGTATCGATACCATAGTATTG
1 GGGTATCGATACCATAGTA-TG
** *
13373922 TAGTATCGATACCATGGTA-G
1 GGGTATCGATACCATAGTATG
13373942 GGGTATCGATACC
1 GGGTATCGATACC
13373955 GAGGAACCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 12 0.43
22 16 0.57
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (21 bp):
GGGTATCGATACCATAGTATG
Found at i:13374410 original size:27 final size:27
Alignment explanation
Indices: 13374380--13374512 Score: 84
Period size: 27 Copynumber: 5.4 Consensus size: 27
13374370 TGCATTAAGC
*
13374380 CATGAAAGGATGTCCTAATTTAAAATG
1 CATGAAAGGATGTACTAATTTAAAATG
13374407 CATGAAAGGA--TAC--A-TT--AA-G
1 CATGAAAGGATGTACTAATTTAAAATG
*
13374426 CCATGAAAGGATG-CCATAATTTAAAATG
1 -CATGAAAGGATGTAC-TAATTTAAAATG
*
13374454 CATGAAAGGA--TAC--A-TT--AAGG
1 CATGAAAGGATGTACTAATTTAAAATG
*
13374474 CATGAAAGGATATTA-TAATTTAAAATG
1 CATGAAAGGAT-GTACTAATTTAAAATG
13374501 CATGAAAGGATG
1 CATGAAAGGATG
13374513 CATTAAGGCA
Statistics
Matches: 81, Mismatches: 6, Indels: 39
0.64 0.05 0.31
Matches are distributed among these distances:
19 1 0.01
20 25 0.31
21 1 0.01
22 4 0.05
23 4 0.05
24 2 0.02
25 6 0.07
26 1 0.01
27 36 0.44
28 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (27 bp):
CATGAAAGGATGTACTAATTTAAAATG
Found at i:13374423 original size:47 final size:47
Alignment explanation
Indices: 13374349--13374532 Score: 280
Period size: 47 Copynumber: 3.9 Consensus size: 47
13374339 TCGAATTCAA
* *
13374349 AATTTAAAATACATGAAAGGATGCATTAAGCCATGAAAGGATGTCCT
1 AATTTAAAATGCATGAAAGGATACATTAAGCCATGAAAGGATGTCCT
13374396 AATTTAAAATGCATGAAAGGATACATTAAGCCATGAAAGGATG-CCAT
1 AATTTAAAATGCATGAAAGGATACATTAAGCCATGAAAGGATGTCC-T
* * **
13374443 AATTTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATATTAT
1 AATTTAAAATGCATGAAAGGATACATTAAGCCATGAAAGGATGTCCT
* *
13374490 AATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 AATTTAAAATGCATGAAAGGATACATTAAGCCATGAAAGGATG
13374533 CATTAAGGCA
Statistics
Matches: 127, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
46 2 0.02
47 125 0.98
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.25
Consensus pattern (47 bp):
AATTTAAAATGCATGAAAGGATACATTAAGCCATGAAAGGATGTCCT
Found at i:13374560 original size:114 final size:114
Alignment explanation
Indices: 13374406--13374647 Score: 385
Period size: 114 Copynumber: 2.1 Consensus size: 114
13374396 AATTTAAAAT
* * * *
13374406 GCATGAAAGGATACATTAAGCCATGAAAGGATGCCATAATTTAAAATGCATGAAAGGATACATTA
1 GCATGAAAGGATGCATTAAGCCATGAAAGAATGACATAATTTAAAACGCATGAAAGGATACATTA
* *
13374471 AGGCATGAAAGGATATTATAATTTAAAATGCATGAAAGGATGCATTAAG
66 AGGCATGAAAGGATATCATAATTTAAAATGCAGGAAAGGATGCATTAAG
* * *
13374520 GCATGAAAGGATGCATTAAGGCATGAAAGAATGACATAATTTAAAACGCATGAAATGATGCATTA
1 GCATGAAAGGATGCATTAAGCCATGAAAGAATGACATAATTTAAAACGCATGAAAGGATACATTA
*
13374585 AGGCATGAAAGGATGTCATAATTTAAAATGCAGGAAAGGATGCATTAAG
66 AGGCATGAAAGGATATCATAATTTAAAATGCAGGAAAGGATGCATTAAG
*
13374634 GCATGAAAGTATGC
1 GCATGAAAGGATGC
13374648 CATAATTTAA
Statistics
Matches: 117, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 117 1.00
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.24
Consensus pattern (114 bp):
GCATGAAAGGATGCATTAAGCCATGAAAGAATGACATAATTTAAAACGCATGAAAGGATACATTA
AGGCATGAAAGGATATCATAATTTAAAATGCAGGAAAGGATGCATTAAG
Found at i:13374571 original size:47 final size:47
Alignment explanation
Indices: 13374520--13374754 Score: 339
Period size: 47 Copynumber: 5.0 Consensus size: 47
13374510 ATGCATTAAG
* * *
13374520 GCATGAAAGGATGCATTAAGGCATGAAAGAATGACATAATTTAAAAC
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTTAAAAT
* *
13374567 GCATGAAATGATGCATTAAGGCATGAAAGGATGTCATAATTTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTTAAAAT
* *
13374614 GCAGGAAAGGATGCATTAAGGCATGAAAGTATGCCATAATTT-AAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTTAAAAT
* * *
13374660 GCATGAAAGAATGCTTTAAGGCATGAAAGGATGCCAAAATTTTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAA-TTTAAAAT
* *
13374708 GCATGAAAGGATGAATTAAGGCATAAAAGGATGCCATAA-TTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTTAAAAT
13374754 G
1 G
13374755 TATAAATGGA
Statistics
Matches: 168, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
46 46 0.27
47 84 0.50
48 38 0.23
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (47 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTTAAAAT
Found at i:13374574 original size:94 final size:91
Alignment explanation
Indices: 13374360--13374556 Score: 224
Period size: 94 Copynumber: 2.2 Consensus size: 91
13374350 ATTTAAAATA
* * * *
13374360 CATGAAAGGATGCATTAA-GCCATGAAAGGATGTCCTAATTTAAAATGCATGAAAGGATACATTA
1 CATGAAAGAATACATTAACG-CATGAAAGGATATCATAATTTAAAATGCATGAAAGGATACATTA
*
13374424 AGCCATGAAAGGATGCCATAATTTAAAATG
65 AGCCATGAAAGGATGCC--AATTT-AAAGG
* * * *
13374454 CATGAAAGGATACATTAAGGCATGAAAGGATATTATAATTTAAAATGCATGAAAGGATGCATTAA
1 CATGAAAGAATACATTAACGCATGAAAGGATATCATAATTTAAAATGCATGAAAGGATACATTAA
*
13374519 GGCATGAAAGGATG-C-A-TT-AAGG
66 GCCATGAAAGGATGCCAATTTAAAGG
13374541 CATGAAAGAATGACAT
1 CATGAAAGAAT-ACAT
13374557 AATTTAAAAC
Statistics
Matches: 93, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
87 13 0.14
88 4 0.04
89 2 0.02
90 1 0.01
93 1 0.01
94 71 0.76
95 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.24
Consensus pattern (91 bp):
CATGAAAGAATACATTAACGCATGAAAGGATATCATAATTTAAAATGCATGAAAGGATACATTAA
GCCATGAAAGGATGCCAATTTAAAGG
Found at i:13374599 original size:67 final size:67
Alignment explanation
Indices: 13374453--13374599 Score: 233
Period size: 67 Copynumber: 2.2 Consensus size: 67
13374443 AATTTAAAAT
* * * *
13374453 GCATGAAAGGATACATTAAGGCATGAAAGGATATTATAATTTAAAATGCATGAAAGGATGCATTA
1 GCATGAAAGGATGCATTAAGGCATGAAAGAATATCATAATTTAAAACGCATGAAAGGATGCATTA
13374518 AG
66 AG
*
13374520 GCATGAAAGGATGCATTAAGGCATGAAAGAATGA-CATAATTTAAAACGCATGAAATGATGCATT
1 GCATGAAAGGATGCATTAAGGCATGAAAGAAT-ATCATAATTTAAAACGCATGAAAGGATGCATT
13374584 AAG
65 AAG
13374587 GCATGAAAGGATG
1 GCATGAAAGGATG
13374600 TCATAATTTA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
67 73 0.99
68 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.23
Consensus pattern (67 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGAATATCATAATTTAAAACGCATGAAAGGATGCATTA
AG
Found at i:13374647 original size:20 final size:20
Alignment explanation
Indices: 13374360--13374693 Score: 137
Period size: 20 Copynumber: 14.7 Consensus size: 20
13374350 ATTTAAAATA
*
13374360 CATGAAAGGATGCATTAAGC
1 CATGAAAGGATGCATTAAGG
*
13374380 CATGAAAGGATGTCCTAATTTAAAATG
1 CATGAAAGGATG--C--A-TT--AAGG
* *
13374407 CATGAAAGGATACATTAAGC
1 CATGAAAGGATGCATTAAGG
*
13374427 CATGAAAGGATGCCATAATTTAAAATG
1 CATGAAAGGATG-C---A-TT--AAGG
*
13374454 CATGAAAGGATACATTAAGG
1 CATGAAAGGATGCATTAAGG
** *
13374474 CATGAAAGGATATTATAATTTAAAATG
1 CATGAAAGG--A-T-GCA-TT--AAGG
13374501 CATGAAAGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
13374521 CATGAAAGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
* *
13374541 CATGAAAGAATGACATAATTTAAAACG
1 CATGAAAGGATG-C---A-TT--AAGG
*
13374568 CATGAAATGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
*
13374588 CATGAAAGGATGTCATAATTTAAAATG
1 CATGAAAGGATG-C---A-TT--AAGG
*
13374615 CAGGAAAGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
* *
13374635 CATGAAAGTATGCCATAATTTAAATG
1 CATGAAAGGATG-C---A-TT-AAGG
* *
13374661 CATGAAAGAATGCTTTAAGG
1 CATGAAAGGATGCATTAAGG
13374681 CATGAAAGGATGC
1 CATGAAAGGATGC
13374694 CAAAATTTTA
Statistics
Matches: 241, Mismatches: 32, Indels: 82
0.68 0.09 0.23
Matches are distributed among these distances:
20 113 0.47
21 6 0.02
22 12 0.05
23 6 0.02
24 7 0.03
25 15 0.06
26 17 0.07
27 65 0.27
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.24
Consensus pattern (20 bp):
CATGAAAGGATGCATTAAGG
Found at i:13375467 original size:30 final size:31
Alignment explanation
Indices: 13375414--13375487 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
13375404 CAAATATAAC
13375414 TTTTGAAAAC--ATATAGTTTTTTAAAACGAA
1 TTTTGAAAACATATATAGTTTTTTAAAA-GAA
* *
13375444 -TTTGAAAATATATATAG-TTTTTAAAATAA
1 TTTTGAAAACATATATAGTTTTTTAAAAGAA
13375473 TTTTGAAAACATATA
1 TTTTGAAAACATATA
13375488 ATATATAGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 10 0.26
30 22 0.58
31 6 0.16
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (31 bp):
TTTTGAAAACATATATAGTTTTTTAAAAGAA
Found at i:13375496 original size:35 final size:34
Alignment explanation
Indices: 13375451--13375615 Score: 108
Period size: 35 Copynumber: 4.8 Consensus size: 34
13375441 GAATTTGAAA
*
13375451 ATATATATAGTTTTTAAAATAATTTTGAAAACAT
1 ATATATATAGTTTTTAAAATAATTTTAAAAACAT
**
13375485 ATAATATATAGTTTTTAAACAT--TTAAAAAAAACAT
1 AT-ATATATAGTTTTTAAA-ATAATT-TTAAAAACAT
* * *
13375520 ATAATATATGGTTTTTAAAA-CA-TTTAAAAAAAT
1 AT-ATATATAGTTTTTAAAATAATTTTAAAAACAT
* *
13375553 GTATGATATATGATTTTT-AAATAATTTTTTGAAAACAT
1 ATAT-ATATA-G-TTTTTAAAATAA--TTTTAAAAACAT
* * *
13375591 AT-TTTATGGTTTTGAAAATAATTTT
1 ATATATATAGTTTTTAAAATAATTTT
13375616 CGTTTTAAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 27
0.70 0.11 0.19
Matches are distributed among these distances:
32 2 0.02
33 16 0.16
34 14 0.14
35 54 0.53
36 5 0.05
37 1 0.01
38 10 0.10
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.44
Consensus pattern (34 bp):
ATATATATAGTTTTTAAAATAATTTTAAAAACAT
Found at i:13375548 original size:36 final size:35
Alignment explanation
Indices: 13375478--13375573 Score: 131
Period size: 35 Copynumber: 2.7 Consensus size: 35
13375468 AATAATTTTG
*
13375478 AAAACATATAATATATAGTTTTT-AAACATTTAAAA
1 AAAACATATAATATATGGTTTTTAAAACATTT-AAA
13375513 AAAACATATAATATATGGTTTTTAAAACATTTAAA
1 AAAACATATAATATATGGTTTTTAAAACATTTAAA
** * *
13375548 AAAATGTATGATATATGATTTTTAAA
1 AAAACATATAATATATGGTTTTTAAA
13375574 TAATTTTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 47 0.85
36 8 0.15
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (35 bp):
AAAACATATAATATATGGTTTTTAAAACATTTAAA
Found at i:13375729 original size:15 final size:16
Alignment explanation
Indices: 13375696--13375742 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
13375686 TATATATTAT
*
13375696 TTTCAGTTTTTATTCTA
1 TTTCA-TTTTTATTTTA
13375713 -TT-ATTTTTAATTTTA
1 TTTCATTTTT-ATTTTA
13375728 TTTCATTTTTATTTT
1 TTTCATTTTTATTTT
13375743 CCAGGGTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
14 5 0.19
15 6 0.23
16 9 0.35
17 6 0.23
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTCATTTTTATTTTA
Found at i:13381806 original size:24 final size:24
Alignment explanation
Indices: 13381774--13381822 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
13381764 AGTCTTCCTG
13381774 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
13381798 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
13381822 A
1 A
13381823 ATGTCATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:13382019 original size:12 final size:13
Alignment explanation
Indices: 13381996--13382024 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
13381986 GTACTAACAT
13381996 AAATACATTTCCA
1 AAATACATTTCCA
13382009 AAATA-ATTTCCA
1 AAATACATTTCCA
13382021 AAAT
1 AAAT
13382025 CAGACAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATACATTTCCA
Found at i:13388938 original size:24 final size:24
Alignment explanation
Indices: 13388904--13388952 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
13388894 AGTCTTCCTG
*
13388904 ATGATGTATAAAACATCTATGTAC
1 ATGATGCATAAAACATCTATGTAC
13388928 ATGATGCATAAAACATCTATGTAC
1 ATGATGCATAAAACATCTATGTAC
13388952 A
1 A
13388953 ATGTCATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (24 bp):
ATGATGCATAAAACATCTATGTAC
Found at i:13389149 original size:12 final size:13
Alignment explanation
Indices: 13389126--13389154 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
13389116 GTACTAACAT
13389126 AAATACATTTCCA
1 AAATACATTTCCA
13389139 AAATA-ATTTCCA
1 AAATACATTTCCA
13389151 AAAT
1 AAAT
13389155 CAGACAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATACATTTCCA
Found at i:13390350 original size:30 final size:30
Alignment explanation
Indices: 13390314--13390384 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
13390304 TAAAATATAT
13390314 AACTTTTAAAA-ATTATAATTTCAGTCC-CTA
1 AACTTTTAAAAGATTATAATTT-AG-CCACTA
* *
13390344 AACTTTTAAAAGTTTATACTTTAGCCACTA
1 AACTTTTAAAAGATTATAATTTAGCCACTA
*
13390374 AACTTTCAAAA
1 AACTTTTAAAA
13390385 CTTAAACTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 2 0.06
30 26 0.72
31 8 0.22
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.38
Consensus pattern (30 bp):
AACTTTTAAAAGATTATAATTTAGCCACTA
Found at i:13390401 original size:29 final size:30
Alignment explanation
Indices: 13390341--13390402 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
13390331 ATTTCAGTCC
* * * *
13390341 CTAAACTTTTAAAAGTTTATACTTTAGCCA
1 CTAAACTTTCAAAAGCTTAAACTTTAACCA
*
13390371 CTAAACTTTCAAAA-CTTAAACTTTAATCA
1 CTAAACTTTCAAAAGCTTAAACTTTAACCA
13390400 CTA
1 CTA
13390403 GACAAAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.40, C:0.19, G:0.03, T:0.37
Consensus pattern (30 bp):
CTAAACTTTCAAAAGCTTAAACTTTAACCA
Found at i:13392885 original size:10 final size:10
Alignment explanation
Indices: 13392859--13392924 Score: 66
Period size: 10 Copynumber: 6.8 Consensus size: 10
13392849 GCTGGAAAAT
13392859 CGGTTTG-AC
1 CGGTTTGAAC
*
13392868 CAGTTTTGAAC
1 C-GGTTTGAAC
13392879 CGGTTTG-AC
1 CGGTTTGAAC
*
13392888 CGGTTCGAAC
1 CGGTTTGAAC
13392898 CGGTTTG-AC
1 CGGTTTGAAC
*
13392907 CGGTCTGAAC
1 CGGTTTGAAC
*
13392917 CGGGTTGA
1 CGGTTTGA
13392925 CCCGACCCGA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
9 17 0.37
10 26 0.57
11 3 0.07
ACGTcount: A:0.17, C:0.23, G:0.32, T:0.29
Consensus pattern (10 bp):
CGGTTTGAAC
Found at i:13392899 original size:19 final size:19
Alignment explanation
Indices: 13392859--13392926 Score: 84
Period size: 19 Copynumber: 3.5 Consensus size: 19
13392849 GCTGGAAAAT
* *
13392859 CGGTTTGACCAGTTTTGAAC
1 CGGTTTGACC-GGTTCGAAC
13392879 CGGTTTGACCGGTTCGAAC
1 CGGTTTGACCGGTTCGAAC
13392898 CGGTTTGACCGG-TCTGAAC
1 CGGTTTGACCGGTTC-GAAC
*
13392917 CGGGTTGACC
1 CGGTTTGACC
13392927 CGACCCGACT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
18 2 0.05
19 32 0.73
20 10 0.23
ACGTcount: A:0.16, C:0.25, G:0.31, T:0.28
Consensus pattern (19 bp):
CGGTTTGACCGGTTCGAAC
Found at i:13392942 original size:17 final size:17
Alignment explanation
Indices: 13392920--13392977 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
13392910 TCTGAACCGG
13392920 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
13392937 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
13392954 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
13392971 GTTGACC
1 GTTGACC
13392978 GTGACCGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:13392979 original size:7 final size:7
Alignment explanation
Indices: 13392967--13393009 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
13392957 GACCCGACCC
13392967 GACCGTT
1 GACCGTT
13392974 GACCG-T
1 GACCGTT
13392980 GACCGTT
1 GACCGTT
13392987 GACCG-T
1 GACCGTT
13392993 GACCGTT
1 GACCGTT
13393000 GACCGTT
1 GACCGTT
13393007 GAC
1 GAC
13393010 TTTCTTTGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.35
7 22 0.65
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:13392985 original size:13 final size:13
Alignment explanation
Indices: 13392967--13393005 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
13392957 GACCCGACCC
13392967 GACCGTTGACCGT
1 GACCGTTGACCGT
13392980 GACCGTTGACCGT
1 GACCGTTGACCGT
13392993 GACCGTTGACCGT
1 GACCGTTGACCGT
13393006 TGACTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:13392992 original size:20 final size:20
Alignment explanation
Indices: 13392967--13393009 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
13392957 GACCCGACCC
13392967 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCGTGACCGTT
13392987 GACCG-TGACCGTTGACCGTT
1 GACCGTTGACCG-TGACCGTT
13393007 GAC
1 GAC
13393010 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (20 bp):
GACCGTTGACCGTGACCGTT
Found at i:13400194 original size:10 final size:10
Alignment explanation
Indices: 13400165--13400243 Score: 83
Period size: 10 Copynumber: 8.1 Consensus size: 10
13400155 GCTGCTGGAA
13400165 AACCGGTTTG
1 AACCGGTTTG
*
13400175 -ACCAGTTTTG
1 AACC-GGTTTG
13400185 AACCGGTTTG
1 AACCGGTTTG
*
13400195 -ACCGGTTCG
1 AACCGGTTTG
*
13400204 AACCGGTCTG
1 AACCGGTTTG
13400214 AACCGGTTTG
1 AACCGGTTTG
*
13400224 -ACCGGTCTG
1 AACCGGTTTG
*
13400233 AACCGGGTTG
1 AACCGGTTTG
13400243 A
1 A
13400244 CCCGACCTGA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
9 19 0.34
10 34 0.61
11 3 0.05
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:13400215 original size:29 final size:29
Alignment explanation
Indices: 13400183--13400238 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
13400173 TGACCAGTTT
13400183 TGAACCGGTTTGACCGGT-TCGAACCGGTC
1 TGAACCGGTTTGACCGGTCT-GAACCGGTC
13400212 TGAACCGGTTTGACCGGTCTGAACCGG
1 TGAACCGGTTTGACCGGTCTGAACCGG
13400239 GTTGACCCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (29 bp):
TGAACCGGTTTGACCGGTCTGAACCGGTC
Found at i:13400227 original size:19 final size:20
Alignment explanation
Indices: 13400181--13400243 Score: 85
Period size: 19 Copynumber: 3.2 Consensus size: 20
13400171 TTTGACCAGT
*
13400181 TTTGAACCGGTTTG-ACCGG
1 TTTGAACCGGTCTGAACCGG
*
13400200 TTCGAACCGGTCTGAACCGG
1 TTTGAACCGGTCTGAACCGG
13400220 TTTG-ACCGGTCTGAACCGG
1 TTTGAACCGGTCTGAACCGG
*
13400239 GTTGA
1 TTTGA
13400244 CCCGACCTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 30 0.79
20 8 0.21
ACGTcount: A:0.17, C:0.24, G:0.32, T:0.27
Consensus pattern (20 bp):
TTTGAACCGGTCTGAACCGG
Found at i:13400261 original size:17 final size:17
Alignment explanation
Indices: 13400239--13400296 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
13400229 TCTGAACCGG
*
13400239 GTTGACCCGACCTGACT
1 GTTGACCCGACCCGACT
13400256 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
13400273 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
13400290 GTTGACC
1 GTTGACC
13400297 GTGACCGTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.17, C:0.40, G:0.24, T:0.19
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:13400303 original size:6 final size:7
Alignment explanation
Indices: 13400286--13400315 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
13400276 GACCCGACCC
13400286 GACCGTT
1 GACCGTT
13400293 GACCG-T
1 GACCGTT
13400299 GACCGTT
1 GACCGTT
13400306 GACCGTT
1 GACCGTT
13400313 GAC
1 GAC
13400316 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:13400304 original size:13 final size:13
Alignment explanation
Indices: 13400286--13400311 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13400276 GACCCGACCC
13400286 GACCGTTGACCGT
1 GACCGTTGACCGT
13400299 GACCGTTGACCGT
1 GACCGTTGACCGT
13400312 TGACTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:13405278 original size:12 final size:12
Alignment explanation
Indices: 13405261--13405303 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
13405251 ATGTTTACAA
13405261 ATAAATATATTC
1 ATAAATATATTC
*
13405273 ATAAATATA-TA
1 ATAAATATATTC
13405284 ATTAAATATATTC
1 A-TAAATATATTC
*
13405297 ATGAATA
1 ATAAATA
13405304 ATTAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 2 0.08
12 22 0.85
13 2 0.08
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (12 bp):
ATAAATATATTC
Found at i:13405931 original size:30 final size:32
Alignment explanation
Indices: 13405877--13405937 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
13405867 AAGGGATAAC
*
13405877 AAAAAATCAAATCTAGATACTAATA-TATTTG
1 AAAAAATCAAATCTAAATACTAATATTATTTG
* *
13405908 AAAAAAT-AAATTTAAATATTAATATTATTT
1 AAAAAATCAAATCTAAATACTAATATTATTT
13405938 AAGCACAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (32 bp):
AAAAAATCAAATCTAAATACTAATATTATTTG
Found at i:13409140 original size:23 final size:23
Alignment explanation
Indices: 13409093--13409141 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
13409083 AAAAGCAAAA
*
13409093 AAAAATAAAATAAAGAAAAATAG
1 AAAAATAAAATAAAGAAAAAGAG
*
13409116 AAAAATGAAATAAA-AGAAAAGAG
1 AAAAATAAAATAAAGA-AAAAGAG
13409139 AAA
1 AAA
13409142 GAAAAAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (23 bp):
AAAAATAAAATAAAGAAAAAGAG
Found at i:13413528 original size:23 final size:23
Alignment explanation
Indices: 13413498--13413548 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
13413488 TGCTATATCA
13413498 GGGTATCTTAAATATGTTTACTT
1 GGGTATCTTAAATATGTTTACTT
13413521 GGGTATCTTAAATATGTTTACTT
1 GGGTATCTTAAATATGTTTACTT
13413544 GGGTA
1 GGGTA
13413549 GTGATAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.45
Consensus pattern (23 bp):
GGGTATCTTAAATATGTTTACTT
Found at i:13418277 original size:150 final size:150
Alignment explanation
Indices: 13417996--13418303 Score: 411
Period size: 150 Copynumber: 2.1 Consensus size: 150
13417986 ATCTAGAGTA
* * * *
13417996 ATTCGTAGTAGTGTTCATAGAAGATATCTTAGAGTACTCCGAATCAGAGGAGAAGCATGATCGGT
1 ATTCTTAGTAGTGTTCATAGAAGATATATTAGAGTACTCCAAATCAGAGGAGAAGCATGATCGCT
* *
13418061 ATCTCTGTATATTCCTTCAAACACTCTAAGATCATAAGTTGTATGCCAAGTTTAGGGAGTACGAA
66 ATCTCTGTATATTCCTTCAAACACTCTAAGATCATAAGTTGAATGCCAAGTTTAGGAAGTACGAA
13418126 TTTTGGTTACCAGAGGTTTC
131 TTTTGGTTACCAGAGGTTTC
* * * *
13418146 ATTCTTAGTGGTGTTCATAGAAGATATATTAGTGTACTCCAAATTAGAGGATAAGCATGATCGCT
1 ATTCTTAGTAGTGTTCATAGAAGATATATTAGAGTACTCCAAATCAGAGGAGAAGCATGATCGCT
* * * * * * * *
13418211 ATCTCTGTATCGTT-CTTTAGATACTCTGAGATCATCATTTGAATGCCAAGTTTAGGAAGTATGA
66 ATCTCTGTAT-ATTCCTTCAAACACTCTAAGATCATAAGTTGAATGCCAAGTTTAGGAAGTACGA
** *
13418275 ATTTTGGTTATTAGAGGTTTG
130 ATTTTGGTTACCAGAGGTTTC
13418296 ATTCTTAG
1 ATTCTTAG
13418304 GTCATGTCAT
Statistics
Matches: 136, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
150 134 0.99
151 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.35
Consensus pattern (150 bp):
ATTCTTAGTAGTGTTCATAGAAGATATATTAGAGTACTCCAAATCAGAGGAGAAGCATGATCGCT
ATCTCTGTATATTCCTTCAAACACTCTAAGATCATAAGTTGAATGCCAAGTTTAGGAAGTACGAA
TTTTGGTTACCAGAGGTTTC
Found at i:13419986 original size:16 final size:15
Alignment explanation
Indices: 13419961--13419997 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
13419951 AGTTTATATA
*
13419961 TATATAATGGATTATT
1 TATATTATGGATTA-T
13419977 TATATTATGGATTAT
1 TATATTATGGATTAT
13419992 TATATT
1 TATATT
13419998 TTGTATTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (15 bp):
TATATTATGGATTAT
Found at i:13426815 original size:139 final size:139
Alignment explanation
Indices: 13426467--13427530 Score: 1441
Period size: 139 Copynumber: 7.7 Consensus size: 139
13426457 GTAATGGAAA
* *
13426467 CGAGCTAAGGTTGAACAAGTTCTTCTCATTTTGAACTTCTTCTCCTTCATCAGATGAGTTCTTCT
1 CGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTCT
* * ** ** *
13426532 CATTATGAACTCTCC-CAT-GAAATGTTAATCCCTCGAGCAAGGTGTCGTTGATTCGACTCCATA
66 CATTATGAACTCTCCAC-TGGAAATGTTGATCCCTCAAGTGAGGTGTCACTGATTCAACTCCATA
*
13426595 TGTGATGAAT
130 TGCGATGAAT
* *
13426605 CGAG---AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTACTTCT
1 CGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTCT
*
13426667 CATTGTGAACTCTCCACTGGAAATGTTGATCCCTCAAGTGAGGTGTCACTGATTCAACTCCATAT
66 CATTATGAACTCTCCACTGGAAATGTTGATCCCTCAAGTGAGGTGTCACTGATTCAACTCCATAT
13426732 GCGATGAAT
131 GCGATGAAT
* * *
13426741 CGAGCTAAGGTTGAATAAGTTCTTCTCATTATAAACTTCTTCTCCTTCATTGGATGAGTTCTTCT
1 CGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTCT
* **
13426806 CATTATGAACTCTCCACTGGAAATTTTGATCCCTCAAGTGAGGTGTTGCTGATTCAACTCCATAT
66 CATTATGAACTCTCCACTGGAAATGTTGATCCCTCAAGTGAGGTGTCACTGATTCAACTCCATAT
13426871 GCGATGAAT
131 GCGATGAAT
* * * * *
13426880 CAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTT-ATCGAATCAGTTATTC
1 CGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT-CCTTCATCGGATGAGTTCTTC
*
13426944 TCATTATGAACTCTCCACTGAAAATGTTGATCCCTCCAA-TGAGGTGTCACTGATTCAACTCCAT
65 TCATTATGAACTCTCCACTGGAAATGTTGATCCCT-CAAGTGAGGTGTCACTGATTCAACTCCAT
13427008 ATGCGATGAAT
129 ATGCGATGAAT
* * * * * * *
13427019 TGAGGTAAGGCTAAACAAGTTCTTCTCATTATGAGCTTTTTCTCCCTCATCGGATGAGTTCTTCT
1 CGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTCT
* * *
13427084 CATTATGAACTCTCCACTGGAAATGTTGATCCCTCAAGTGAGGTGT-AGTTGATGCAACTCTATA
66 CATTATGAACTCTCCACTGGAAATGTTGATCCCTCAAGTGAGGTGTCA-CTGATTCAACTCCATA
13427148 TGCGATGAAT
130 TGCGATGAAT
* * * *
13427158 CGAGCTAAGGTTGAACAATTTCTTCGT-ATTATAAACTTCTTCTCC-T-ATCGAATGTGTTCTTC
1 CGAGCTAAGGTTGAACAAGTTCTTC-TCATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTC
* * * *
13427220 TCATTATGAACTCTCCACTAGAAATATTGATCCCTCCAGTGAGGTGTCTCTGATTCAACTCCATA
65 TCATTATGAACTCTCCACTGGAAATGTTGATCCCTCAAGTGAGGTGTCACTGATTCAACTCCAT-
13427285 ATGCGATGAAT
129 ATGCGATGAAT
* * * * * *
13427296 CGAGCTAAAGTTGAACAAGTTTTTCTTATTATGAACTTCTTCTCCCTT-ATTGGAAGAGTTCTTT
1 CGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT-CCTTCATCGGATGAGTTCTTC
* ** * * *
13427360 TCATTATGAACTCTCCACTAGAAACATTGATCCCTCGAGTGAGGTGTCATTGATTCAACTTCATA
65 TCATTATGAACTCTCCACTGGAAATGTTGATCCCTCAAGTGAGGTGTCACTGATTCAACTCCATA
* *
13427425 TACAATGAAT
130 TGCGATGAAT
*
13427435 CGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCT
1 CGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTCT
* *
13427500 CATTATGAACTATCCAATGGAAATGTTGATC
66 CATTATGAACTCTCCACTGGAAATGTTGATC
13427531 GGTTTATCCT
Statistics
Matches: 814, Mismatches: 95, Indels: 33
0.86 0.10 0.04
Matches are distributed among these distances:
135 69 0.08
136 52 0.06
137 71 0.09
138 63 0.08
139 480 0.59
140 79 0.10
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (139 bp):
CGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTCT
CATTATGAACTCTCCACTGGAAATGTTGATCCCTCAAGTGAGGTGTCACTGATTCAACTCCATAT
GCGATGAAT
Found at i:13438899 original size:23 final size:23
Alignment explanation
Indices: 13438867--13438918 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
13438857 GTTGTAACAT
* * * *
13438867 GGTTTAGTTTGGGCCTAGTTTAG
1 GGTTTGGTTTAGGCCCAATTTAG
13438890 GGTTTGGTTTAGGCCCAATTTAG
1 GGTTTGGTTTAGGCCCAATTTAG
*
13438913 GATTTG
1 GGTTTG
13438919 TTTTTCTTGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.15, C:0.10, G:0.33, T:0.42
Consensus pattern (23 bp):
GGTTTGGTTTAGGCCCAATTTAG
Found at i:13438954 original size:3 final size:3
Alignment explanation
Indices: 13438946--13439014 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
13438936 ATGGGTGTTG
13438946 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
13438994 TAA TAA TAA TAA TAA GAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
13439015 GGAATATATA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:13445029 original size:35 final size:32
Alignment explanation
Indices: 13444966--13445048 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 32
13444956 AAATTGTTCC
* *
13444966 TAAAAGTAAAAAAAAGGGTTAGAGAATAAAAAA
1 TAAAA-TAAAAAAAAAGGTTAGAAAATAAAAAA
*
13444999 TAAAATAATAAAAAAAGGTTAGTTAAAATAAAATA
1 TAAAATAA-AAAAAAAGGTTAG--AAAATAAAAAA
* *
13445034 TCAAATAGAAAAAAA
1 TAAAATAAAAAAAAA
13445049 TTAAATTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
32 3 0.07
33 17 0.40
34 7 0.17
35 15 0.36
ACGTcount: A:0.67, C:0.01, G:0.12, T:0.19
Consensus pattern (32 bp):
TAAAATAAAAAAAAAGGTTAGAAAATAAAAAA
Found at i:13445063 original size:16 final size:15
Alignment explanation
Indices: 13445024--13445078 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
13445014 AGGTTAGTTA
*
13445024 AAATAAAATATCAAAT
1 AAATAAAA-ATTAAAT
13445040 AGAA-AAAAATTAAATT
1 A-AATAAAAATTAAA-T
*
13445056 AAATAAAAATTGAAT
1 AAATAAAAATTAAAT
13445071 AAATAAAA
1 AAATAAAA
13445079 GAAATAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
15 16 0.47
16 16 0.47
17 2 0.06
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (15 bp):
AAATAAAAATTAAAT
Found at i:13446208 original size:5 final size:5
Alignment explanation
Indices: 13446200--13446349 Score: 75
Period size: 5 Copynumber: 30.2 Consensus size: 5
13446190 AAAATAAAAT
*
13446200 TAATA TAATA TAATA -AAAA TAATACA TAATA -AATA TAAAATA TAATA
1 TAATA TAATA TAATA TAATA TAAT--A TAATA TAATA T--AATA TAATA
* * *
13446247 TTATA -ATATA TAGATA TAATA T-ATA -GATA TAA-A TAATA -ATTTA
1 TAATA TA-ATA TA-ATA TAATA TAATA TAATA TAATA TAATA TA-ATA
* * * *
13446290 TAAAA TAA-A TAATA TTAATA TAATA TAATA TAA-A TTATA TTATA TTATA
1 TAATA TAATA TAATA -TAATA TAATA TAATA TAATA TAATA TAATA TAATA
* *
13446339 TTATA TTATA T
1 TAATA TAATA T
13446350 TTTCAAAAAT
Statistics
Matches: 119, Mismatches: 10, Indels: 32
0.74 0.06 0.20
Matches are distributed among these distances:
4 25 0.21
5 72 0.61
6 12 0.10
7 10 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:13446244 original size:13 final size:13
Alignment explanation
Indices: 13446184--13446317 Score: 55
Period size: 13 Copynumber: 10.1 Consensus size: 13
13446174 AACCTGAACC
*
13446184 AAATA-AAAAATA
1 AAATATAAATATA
13446196 AAAT-T-AATATA
1 AAATATAAATATA
* *
13446207 ATATAATAAAAATA
1 AAAT-ATAAATATA
13446221 ATACATAATAAATATA
1 A-A-AT-ATAAATATA
13446237 AAATATAATATTATA
1 AAATATAA-A-TATA
* *
13446252 ATATATAGATATA
1 AAATATAAATATA
* *
13446265 ATATATAGATAT-
1 AAATATAAATATA
*
13446277 AAATAATAATTTATA
1 AAAT-ATAA-ATATA
*
13446292 AAATAAATAATAT-
1 AAATATA-AATATA
*
13446305 TAATAT-AATATA
1 AAATATAAATATA
13446317 A
1 A
13446318 TATAAATTAT
Statistics
Matches: 94, Mismatches: 15, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
11 13 0.14
12 7 0.07
13 28 0.30
14 18 0.19
15 16 0.17
16 12 0.13
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (13 bp):
AAATATAAATATA
Found at i:13446380 original size:41 final size:40
Alignment explanation
Indices: 13446335--13446423 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 40
13446325 TATATTATAT
* *
13446335 TATATTATATTATATTTTCAAAAATAATATGTTTTAAAAATTA
1 TATATTATA-TATATTTCCAAAAAT-AT-CGTTTTAAAAATTA
*
13446378 TATATTATATATATTTCCAAAAATATCGTTTTAAAAAACTA
1 TATATTATATATATTTCCAAAAATATCGTTTT-AAAAATTA
13446419 TATAT
1 TATAT
13446424 ATGTTTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 5 0.12
41 14 0.33
42 14 0.33
43 9 0.21
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (40 bp):
TATATTATATATATTTCCAAAAATATCGTTTTAAAAATTA
Found at i:13446384 original size:38 final size:36
Alignment explanation
Indices: 13446340--13446635 Score: 150
Period size: 38 Copynumber: 7.9 Consensus size: 36
13446330 TATATTATAT
13446340 TATATTATATTTTCAAAAATAATATGTTTTAAAAATTA
1 TATATTATATTTTCAAAAAT-ATAT-TTTTAAAAATTA
* * *
13446378 TATATTATATATATTTCCAAAAATATCGTTTTAAAAAACTA
1 TATA-T-TATAT-TTT-CAAAAATAT-ATTTTTAAAAATTA
* * *
13446419 TATA-TATGTTTT--TAAATATCATTTTTAAAACTATA
1 TATATTATATTTTCAAAAATAT-ATTTTTAAAAAT-TA
* * ** *
13446454 TATATTATATGTTTTC-AAAAT-GAGTTTCCAAAACTA
1 TATATTATA--TTTTCAAAAATATATTTTTAAAAATTA
* *
13446490 TATAATATATGTTTTCAAAAATATATTTTCAAAACCA-TA
1 TAT-AT-TATATTTTCAAAAATATATTTTTAAAA--ATTA
13446529 T-TA-TATATTTT-AAAAATCGACT-TTTTTAAAAATTA
1 TATATTATATTTTCAAAAAT--A-TATTTTTAAAAATTA
*
13446564 TATATTATATGTTTTCAAAAA-ACATTTTCT-AAAATCTA
1 TATATTATA--TTTTCAAAAATATATTTT-TAAAAAT-TA
*
13446602 TATATTATATGTTTTCAAAAA-ATATTTTCAAAAA
1 TATATTATA--TTTTCAAAAATATATTTTTAAAAA
13446636 CTACATTATA
Statistics
Matches: 203, Mismatches: 26, Indels: 58
0.71 0.09 0.20
Matches are distributed among these distances:
34 22 0.11
35 16 0.08
36 24 0.12
37 33 0.16
38 58 0.29
39 12 0.06
40 11 0.05
41 19 0.09
42 8 0.04
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (36 bp):
TATATTATATTTTCAAAAATATATTTTTAAAAATTA
Found at i:13446424 original size:43 final size:44
Alignment explanation
Indices: 13446330--13446425 Score: 119
Period size: 43 Copynumber: 2.2 Consensus size: 44
13446320 TAAATTATAT
* *
13446330 TATATTATATTATATTATATTTTCAAAAATAATATGTTTTAAAAA
1 TATA-TATATTATATTATATTTCCAAAAATAATACGTTTTAAAAA
13446375 T-TATATATTATA-TATATTTCCAAAAAT-AT-CGTTTTAAAAAA
1 TATATATATTATATTATATTTCCAAAAATAATACGTTTT-AAAAA
13446416 CTATATATAT
1 -TATATATAT
13446426 GTTTTTAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
40 5 0.11
41 7 0.15
42 15 0.33
43 16 0.35
44 2 0.04
45 1 0.02
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (44 bp):
TATATATATTATATTATATTTCCAAAAATAATACGTTTTAAAAA
Found at i:13446509 original size:110 final size:111
Alignment explanation
Indices: 13446378--13446646 Score: 307
Period size: 110 Copynumber: 2.4 Consensus size: 111
13446368 TTAAAAATTA
* * * * * *
13446378 TATATTATATATATTTCCAAAAATATCGTTTTAAAAAACTATA-TATATGTTTTTAAATATC-A-
1 TATATAATATATGTTTTCAAAAATAT-ATTTT-AAAAACTATATTATAT-ATTTTAAAAATCGAC
* **
13446440 TTTTTAAAACTATATATATTATATGTTTTC-AAAATGAGTTTCCAAAA-C
63 TTTTTAAAAAT-TATATATTATATGTTTTCAAAAAACAGTTTCCAAAATC
* *
13446488 TATATAATATATGTTTTCAAAAATATATTTTCAAAACCATATTATATATTTTAAAAATCGACTTT
1 TATATAATATATGTTTTCAAAAATATATTTTAAAAACTATATTATATATTTTAAAAATCGAC-TT
* *
13446553 TTTAAAAATTATATATTATATGTTTTCAAAAAACATTTTCTAAAATC
65 TTTAAAAATTATATATTATATGTTTTCAAAAAACAGTTTCCAAAATC
* *
13446600 TATATATTATATGTTTTCAAAAA-ATATTTTCAAAAACTACATTATAT
1 TATATAATATATGTTTTCAAAAATATATTTT-AAAAACTATATTATAT
13446647 TTTACTAAAT
Statistics
Matches: 135, Mismatches: 17, Indels: 12
0.82 0.10 0.07
Matches are distributed among these distances:
108 18 0.13
109 10 0.07
110 41 0.30
111 30 0.22
112 36 0.27
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (111 bp):
TATATAATATATGTTTTCAAAAATATATTTTAAAAACTATATTATATATTTTAAAAATCGACTTT
TTAAAAATTATATATTATATGTTTTCAAAAAACAGTTTCCAAAATC
Found at i:13455514 original size:29 final size:30
Alignment explanation
Indices: 13455464--13455521 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
13455454 AGAAAAAAAC
* * *
13455464 AATAAAATTAAATTAAATAAAAATTAAATG
1 AATAAAATGAAATAAAAGAAAAATTAAATG
*
13455494 AATAAAA-GAAATAAAAGAAAATTTAAAT
1 AATAAAATGAAATAAAAGAAAAATTAAAT
13455522 TAAATGGGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (30 bp):
AATAAAATGAAATAAAAGAAAAATTAAATG
Found at i:13456626 original size:5 final size:5
Alignment explanation
Indices: 13456611--13456742 Score: 99
Period size: 5 Copynumber: 27.6 Consensus size: 5
13456601 CCAAATAAAA
*
13456611 ATAAT -TAAT ATAAT ATAAT A-AAA ATAAT ACATAAT A-AAT ATAA- A-AAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT --ATAAT ATAAT ATAAT ATAAT
*
13456658 ATAAT AT--T ATAAT ATATGAT ATAAT AT-AT A-GAT ATAA- ATAAT A-ATAT
1 ATAAT ATAAT ATAAT ATA--AT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT
*
13456705 ATAAA ATAA- ATAAT ATTAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATA
13456743 TAATAAAAAC
Statistics
Matches: 105, Mismatches: 4, Indels: 36
0.72 0.03 0.25
Matches are distributed among these distances:
3 5 0.05
4 28 0.27
5 56 0.53
6 6 0.06
7 10 0.10
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:13456659 original size:8 final size:9
Alignment explanation
Indices: 13456604--13456749 Score: 77
Period size: 9 Copynumber: 15.7 Consensus size: 9
13456594 ACATGAACCA
*
13456604 AATAAAAAT
1 AATAAATAT
*
13456613 AATTAATAT
1 AATAAATAT
*
13456622 AATATAATAAA
1 AATA-AAT-AT
*
13456633 AATAATACAT
1 AATAA-ATAT
13456643 AATAAATAT
1 AATAAATAT
13456652 AA-AAATAT
1 AATAAATAT
*
13456660 AAT-ATTAT
1 AATAAATAT
13456668 AATATATGATAT
1 AATA-A--ATAT
* *
13456680 AATATATAG
1 AATAAATAT
13456689 ATATAAATAAT
1 A-ATAAAT-AT
* *
13456700 AATATATAA
1 AATAAATAT
13456709 AATAAATA-
1 AATAAATAT
*
13456717 ATATTAATAT
1 A-ATAAATAT
13456727 AATATAATAT
1 AATA-AATAT
13456737 AAT--ATAT
1 AATAAATAT
13456744 AATAAA
1 AATAAA
13456750 AACTATATAA
Statistics
Matches: 104, Mismatches: 18, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
7 7 0.07
8 16 0.15
9 36 0.35
10 30 0.29
11 8 0.08
12 7 0.07
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (9 bp):
AATAAATAT
Found at i:13456681 original size:20 final size:19
Alignment explanation
Indices: 13456616--13456762 Score: 93
Period size: 20 Copynumber: 7.9 Consensus size: 19
13456606 TAAAAATAAT
*
13456616 TAATATAATATAATAA-AAA
1 TAATATAATAT-ATAATATA
*
13456635 TAATA-CATA-ATAAATATAA
1 TAATATAATATAT-AATAT-A
*
13456654 AAATATAATATTATAATATA
1 TAATATAATA-TATAATATA
*
13456674 TGATATAATATATAGATATA
1 TAATATAATATATA-ATATA
13456694 -AATAATAATATATAA-A-A
1 TAAT-ATAATATATAATATA
13456711 TAA-ATAATAT-T-A-ATA
1 TAATATAATATATAATATA
13456726 TAATAT-A-ATATAATATA
1 TAATATAATATATAATATA
*
13456743 TAATAAAAACTATATAATAT
1 TAAT-ATAA-TATATAATAT
13456763 TATATTTTCA
Statistics
Matches: 102, Mismatches: 8, Indels: 34
0.71 0.06 0.24
Matches are distributed among these distances:
14 4 0.04
15 7 0.07
16 12 0.12
17 10 0.10
18 8 0.08
19 18 0.18
20 27 0.26
21 14 0.14
22 2 0.02
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (19 bp):
TAATATAATATATAATATA
Found at i:13456697 original size:47 final size:47
Alignment explanation
Indices: 13456617--13456766 Score: 102
Period size: 54 Copynumber: 2.9 Consensus size: 47
13456607 AAAAATAATT
* * * * *
13456617 AATATAATATAATAAAAATAATACATAATAAATATAAAAATATAATATTAT
1 AATATAATATAAT-ATAAT-ATAAATAAAAAATATAATATTATAATA-T-T
* * *
13456668 AATATATGATATAATATATAGATATAAATAATAATATATAAAATAAATAATATT
1 AATATA--ATAT-A-ATATA-ATATAAATAA-AAAATATAATAT-TATAATATT
13456722 AATATAATATAATATAATATATAATAAAAACTATATAATATTATA
1 AATATAATATAATATAATATA-AATAAAAA--ATATAATATTATA
13456767 TTTTCAAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
49 7 0.09
50 13 0.16
51 15 0.19
52 4 0.05
53 4 0.05
54 17 0.21
55 14 0.17
56 6 0.08
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (47 bp):
AATATAATATAATATAATATAAATAAAAAATATAATATTATAATATT
Found at i:13456760 original size:42 final size:40
Alignment explanation
Indices: 13456609--13456764 Score: 113
Period size: 41 Copynumber: 3.8 Consensus size: 40
13456599 AACCAAATAA
* * *
13456609 AAATAATTAATATAATATAATAAA-AATAATACATAATAAATAT
1 AAATAA-TAATAT-ATAAAATAAATAATATTA-AT-ATAGATAT
* * * * *
13456652 AAAAATATAATAT-TATAATATATGATATAATATATAGATAT
1 AAATA-ATAATATATAAAATAAATAATATTA-ATATAGATAT
13456693 AAATAATAATATATAAAATAAATAATATTAATATA-ATAT
1 AAATAATAATATATAAAATAAATAATATTAATATAGATAT
*
13456732 AATATAAT-ATATAATAAAAACTATATAATATTA
1 AA-ATAATAATAT-AT-AAAA-TAAATAATATTA
13456765 TATTTTCAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
39 10 0.11
40 19 0.20
41 36 0.39
42 17 0.18
43 10 0.11
44 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (40 bp):
AAATAATAATATATAAAATAAATAATATTAATATAGATAT
Found at i:13456766 original size:10 final size:10
Alignment explanation
Indices: 13456656--13456767 Score: 65
Period size: 10 Copynumber: 11.4 Consensus size: 10
13456646 AAATATAAAA
13456656 ATATAATATT
1 ATATAATATT
*
13456666 ATA-ATATATG
1 ATATA-ATATT
13456676 ATATAATA-T
1 ATATAATATT
*
13456685 ATA-GATA-T
1 ATATAATATT
* *
13456693 AAATAATAAT
1 ATATAATATT
*
13456703 ATATAA-AAT
1 ATATAATATT
*
13456712 AAATAATATT
1 ATATAATATT
*
13456722 AATATAATATA
1 -ATATAATATT
13456733 ATATAATA-T
1 ATATAATATT
* *
13456742 ATAATAAAAACT
1 AT-AT-AATATT
13456754 ATATAATATT
1 ATATAATATT
13456764 ATAT
1 ATAT
13456768 TTTCAAAAAT
Statistics
Matches: 79, Mismatches: 14, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
8 6 0.08
9 17 0.22
10 39 0.49
11 14 0.18
12 3 0.04
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (10 bp):
ATATAATATT
Found at i:13456787 original size:17 final size:17
Alignment explanation
Indices: 13456767--13456799 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13456757 TAATATTATA
13456767 TTTTCAAAAATAATATG
1 TTTTCAAAAATAATATG
*
13456784 TTTTCAAAAATTATAT
1 TTTTCAAAAATAATAT
13456800 ATTATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTTCAAAAATAATATG
Found at i:13456808 original size:41 final size:42
Alignment explanation
Indices: 13456747--13456842 Score: 126
Period size: 41 Copynumber: 2.3 Consensus size: 42
13456737 AATATATAAT
* * *
13456747 AAAAACTATATAATATTATAT-TTT-CAAAAATAATATGTTTTC
1 AAAAATTATATATTATTATATATTTCCAAAAA-AATA-GTTTTA
13456789 AAAAATTATATATTA-TATATATTTCCAAAAAAATAGTTTTA
1 AAAAATTATATATTATTATATATTTCCAAAAAAATAGTTTTA
13456830 AAAAATTATATAT
1 AAAAATTATATAT
13456843 ATGTTTTCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
41 23 0.47
42 20 0.41
43 6 0.12
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (42 bp):
AAAAATTATATATTATTATATATTTCCAAAAAAATAGTTTTA
Found at i:13456859 original size:13 final size:13
Alignment explanation
Indices: 13456841--13456867 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13456831 AAAATTATAT
13456841 ATATGTTTTCAAA
1 ATATGTTTTCAAA
13456854 ATATGTTTTCAAA
1 ATATGTTTTCAAA
13456867 A
1 A
13456868 CTATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
ATATGTTTTCAAA
Found at i:13456960 original size:37 final size:37
Alignment explanation
Indices: 13456748--13456985 Score: 205
Period size: 37 Copynumber: 6.3 Consensus size: 37
13456738 ATATATAATA
*
13456748 AAAACTATATAATATTATATTTTCAAAAATAATATGTTTTC
1 AAAACTATATAATA-TATGTTTTC--AAA-AATATGTTTTC
* * * * *
13456789 AAAAATTATATATTATATATATTTCCAAAAAAATAGTTTTA
1 -AAAACTATATA--ATATATGTTTTCAAAAATAT-GTTTTC
*
13456830 AAAAAT-TAT-ATATATGTTTTC-AAAATATGTTTTC
1 AAAACTATATAATATATGTTTTCAAAAATATGTTTTC
* * * *
13456864 AAAACTATATTATATACGTTTTCAAAAAT-CGTTTTT
1 AAAACTATATAATATATGTTTTCAAAAATATGTTTTC
* * *
13456900 AAAATTATATATATTATACGTTTTCAAAAATGTGTTTTC
1 AAAACTATATA-A-TATATGTTTTCAAAAATATGTTTTC
* *
13456939 AAAACTATATAATATATGTTTTCAAAAACATATTTTC
1 AAAACTATATAATATATGTTTTCAAAAATATGTTTTC
*
13456976 AAAACCATAT
1 AAAACTATAT
13456986 TTAATAACTA
Statistics
Matches: 164, Mismatches: 23, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
34 10 0.06
35 9 0.05
36 35 0.21
37 36 0.22
38 18 0.11
39 18 0.11
40 9 0.05
41 8 0.05
42 10 0.06
43 8 0.05
44 3 0.02
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (37 bp):
AAAACTATATAATATATGTTTTCAAAAATATGTTTTC
Found at i:13456976 original size:14 final size:14
Alignment explanation
Indices: 13456957--13456987 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13456947 ATAATATATG
13456957 TTTTCAAAAACATA
1 TTTTCAAAAACATA
*
13456971 TTTTCAAAACCATA
1 TTTTCAAAAACATA
13456985 TTT
1 TTT
13456988 AATAACTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (14 bp):
TTTTCAAAAACATA
Found at i:13457041 original size:38 final size:37
Alignment explanation
Indices: 13456991--13457070 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 37
13456981 CATATTTAAT
*
13456991 AACTATATATTATATCCTTTCAAAAAATGTTTTCTAAA
1 AACTATATATTATATCCTTTCAAAAAATATTTTC-AAA
**
13457029 AACTATATATTATATGTTTTCAAAAAATATTTTCAAA
1 AACTATATATTATATCCTTTCAAAAAATATTTTCAAA
13457066 AACTA
1 AACTA
13457071 CATTATATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 8 0.21
38 31 0.79
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.41
Consensus pattern (37 bp):
AACTATATATTATATCCTTTCAAAAAATATTTTCAAA
Found at i:13457068 original size:88 final size:87
Alignment explanation
Indices: 13456907--13457066 Score: 245
Period size: 88 Copynumber: 1.8 Consensus size: 87
13456897 TTTAAAATTA
* *
13456907 TATATATTATACGTTTTCAAAAATGTGTTTTCAAAACTATATAATATATGTTTTCAAAAACATAT
1 TATATATTATACGCTTTCAAAAATGTGTTTTAAAAACTATATAATATATGTTTTCAAAAACATAT
13456972 TTTCAAAACCATATTTAATAAC
66 TTTCAAAACCATATTTAATAAC
*
13456994 TATATATTATATC-CTTTCAAAAAATGT-TTTCTAAAAACTATATATTATATGTTTTCAAAAA-A
1 TATATATTATA-CGCTTTC-AAAAATGTGTTT-TAAAAACTATATAATATATGTTTTCAAAAACA
13457056 TATTTTCAAAA
63 TATTTTCAAAA
13457067 ACTACATTAT
Statistics
Matches: 67, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
87 30 0.45
88 37 0.55
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (87 bp):
TATATATTATACGCTTTCAAAAATGTGTTTTAAAAACTATATAATATATGTTTTCAAAAACATAT
TTTCAAAACCATATTTAATAAC
Found at i:13457103 original size:88 final size:88
Alignment explanation
Indices: 13456925--13457104 Score: 199
Period size: 88 Copynumber: 2.0 Consensus size: 88
13456915 ATACGTTTTC
* *
13456925 AAAAATGTGTTTTCAAAACTATATAATATATGTTTTCAAAAACATATTTTCAAAACCATATTTAA
1 AAAAATGTGTTTTAAAAACTATATAATATATGTTTTCAAAAACATATTTTCAAAACCACATTTAA
* * **
13456990 TAACTATATATTATATCCTTTCA
66 TAACTATATATTAAACCCTGACA
* *
13457013 AAAAATGT-TTTCTAAAAACTATATATTATATGTTTTCAAAAA-ATATTTTCAAAAACTACATTA
1 AAAAATGTGTTT-TAAAAACTATATAATATATGTTTTCAAAAACATATTTTC-AAAACCACATT-
*
13457076 TATTATACTA-A-A-TAAACCCTGGACA
63 TAATA-ACTATATATTAAACCCT-GACA
13457101 AAAA
1 AAAA
13457105 TGAGTGACTA
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
87 17 0.22
88 52 0.67
89 5 0.06
90 4 0.05
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (88 bp):
AAAAATGTGTTTTAAAAACTATATAATATATGTTTTCAAAAACATATTTTCAAAACCACATTTAA
TAACTATATATTAAACCCTGACA
Found at i:13458811 original size:20 final size:21
Alignment explanation
Indices: 13458775--13458816 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
13458765 TAATTTTGTA
13458775 AAATTAACTTGTTTCATAATTT
1 AAATTAACTTGTTTCAT-ATTT
13458797 AAATTAA-TT-TTTCATATTT
1 AAATTAACTTGTTTCATATTT
13458816 A
1 A
13458817 TTTATGTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 6 0.30
21 2 0.10
22 7 0.35
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.52
Consensus pattern (21 bp):
AAATTAACTTGTTTCATATTT
Found at i:13462342 original size:30 final size:30
Alignment explanation
Indices: 13462268--13462342 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 30
13462258 ATTCGTTTAA
* * *
13462268 TTTTCTCACTAAATTTTATACATTTAGCAT
1 TTTTATCACTAAACTTAATACATTTAGCAT
* *
13462298 TTTTAGCCACTAAACTTAATACATTTAG-TT
1 TTTTA-TCACTAAACTTAATACATTTAGCAT
13462328 TTTTATCACTTAAAC
1 TTTTATCAC-TAAAC
13462343 GTTACTTTCC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
29 3 0.08
30 15 0.41
31 19 0.51
ACGTcount: A:0.32, C:0.17, G:0.04, T:0.47
Consensus pattern (30 bp):
TTTTATCACTAAACTTAATACATTTAGCAT
Found at i:13463858 original size:2 final size:2
Alignment explanation
Indices: 13463847--13463882 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
13463837 ATCATATCCC
13463847 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13463883 TCCAGAGCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13467475 original size:22 final size:20
Alignment explanation
Indices: 13467424--13467497 Score: 71
Period size: 19 Copynumber: 3.7 Consensus size: 20
13467414 GTGTTGGAAA
*
13467424 CTAGATTTTAGGTTGCAAGC
1 CTAGATTTTAGGTTGCAAAC
* *
13467444 C-AGATGTTAGGTTTCAACAAC
1 CTAGATTTTAGGTTGC-A-AAC
13467465 CTAGATTTTAGGTTG-AAAC
1 CTAGATTTTAGGTTGCAAAC
* *
13467484 CCAGATTTAAGGTT
1 CTAGATTTTAGGTT
13467498 ATAACTGGAT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 27 0.61
20 3 0.07
21 3 0.07
22 11 0.25
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.34
Consensus pattern (20 bp):
CTAGATTTTAGGTTGCAAAC
Found at i:13471369 original size:107 final size:109
Alignment explanation
Indices: 13471164--13471682 Score: 701
Period size: 107 Copynumber: 4.8 Consensus size: 109
13471154 CGGGTTCGCT
* * * *
13471164 CCCTCTTTCTTTAGAGAGTAT-AGAACTCG-GACAATCTTCAATAATCGTGTCTGCTCCCTATTT
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAG-CAATCTTCAA-CATCGTGTCTGCCCCCTATTT
* *
13471227 CTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCC
63 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
13471272 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACATCGTGTCTGCCCCCTA-TTCTT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACATCGTGTCTGCCCCCTATTTCTT
*
13471336 CA-AGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGTC
66 CAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* *
13471379 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCCTATTTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAAC-ATCGTGTCTG-CCCCCTATTTC
* *
13471444 -TCAGAGAGTAT-AGAC-C-CACAATCTTCATA-AATCGCGTATGCC
64 TTCAGAGAGTATAAGACTCGAACAATCTTCA-ACAATCGCGTCTGCC
13471486 CCCTATTTCTTCAGAGAGTAT-AGACTCGAGCAATCTTC-ACAATCGTGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAAC-ATCGTGTCTGCCCCCTATTTCT
*
13471549 TCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCC
65 TCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * * * *
13471594 CCCTATTTCTTCAGAGAG-ATAAGAC-CCA-CAATCTTCATAAATCGCGTATGCCCCATATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCA-ACATCGTGTCTGCCCCCTATTTCT
13471656 TCAGAGAGTATAAGACTCGAACAATCT
65 TCAGAGAGTATAAGACTCGAACAATCT
13471683 CCATCAAACG
Statistics
Matches: 371, Mismatches: 23, Indels: 35
0.86 0.05 0.08
Matches are distributed among these distances:
104 11 0.03
105 34 0.09
106 36 0.10
107 174 0.47
108 89 0.24
109 17 0.05
110 10 0.03
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (109 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACATCGTGTCTGCCCCCTATTTCTT
CAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
Found at i:13471488 original size:160 final size:161
Alignment explanation
Indices: 13471164--13471682 Score: 768
Period size: 160 Copynumber: 3.2 Consensus size: 161
13471154 CGGGTTCGCT
* * * *
13471164 CCCTCTTTCTTTAGAGAGTATAGAACTCGGACAATCTTCAATAATCGTGTCTGCTCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAG-ACTCGAACAATCTTCAACAATCGTGTCTGC-CCCTATTTCT
* * *
13471229 TCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTA
64 TCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTA
* * * *
13471292 TAAGACTCGAGCAATCTTCA-ACATCGTGTCTGCC
129 TAAGAC-CCA-CAATCTTCATAAATCGCGTATGCC
*
13471326 CCCTA-TTCTTCA-AGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGTCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTAT-AGACTCGAACAATCTTCAACAATCGTGTCTG-CCCCTATTTCT
13471389 TCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCCTATTTC-TCAGAGAGT
64 TCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTG-CCCCCTATTTCTTCAGAGAGT
13471453 AT-AGACCCACAATCTTCATAAATCGCGTATGCC
128 ATAAGACCCACAATCTTCATAAATCGCGTATGCC
*
13471486 CCCTATTTCTTCAGAGAGTATAGACTCGAGCAATCTTC-ACAATCGTGTCTGCCCCCTATTTCTT
1 CCCTATTTCTTCAGAGAGTATAGACTCGAACAATCTTCAACAATCGTGTCTG-CCCCTATTTCTT
13471550 CAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAG-AT
65 CAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTAT
13471614 AAGACCCACAATCTTCATAAATCGCGTATGCC
130 AAGACCCACAATCTTCATAAATCGCGTATGCC
*
13471646 CCATATTTCTTCAGAGAGTATAAGACTCGAACAATCT
1 CCCTATTTCTTCAGAGAGTAT-AGACTCGAACAATCT
13471683 CCATCAAACG
Statistics
Matches: 329, Mismatches: 17, Indels: 23
0.89 0.05 0.06
Matches are distributed among these distances:
159 22 0.07
160 202 0.61
161 51 0.16
162 43 0.13
163 11 0.03
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (161 bp):
CCCTATTTCTTCAGAGAGTATAGACTCGAACAATCTTCAACAATCGTGTCTGCCCCTATTTCTTC
AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
AGACCCACAATCTTCATAAATCGCGTATGCC
Found at i:13471669 original size:267 final size:270
Alignment explanation
Indices: 13471176--13471682 Score: 775
Period size: 267 Copynumber: 1.9 Consensus size: 270
13471166 CTCTTTCTTT
* * * *
13471176 AGAGAGTATAGAACTCGGACAATCTTCAATAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATA
1 AGAGAGTATAGAACTCGCACAATCTTCAATAATCGCGTATGCCCCCTATTTCTTCAGAGAGTATA
*
13471241 AGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAGCAA
66 AGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
*
13471306 TCTTCAACATCGTGTCTGCCCCCTATTCTTCAAGAGTATAAGACTCGAACAATCTTCAACAATCG
131 TCTTCAACATCGCGTCTGCCCCCTATTCTTCAAGAGTATAAGACTCGAACAATCTTCAACAATCG
*
13471371 CGTCTGTCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCC
196 CGTATGTCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCC
13471436 CCTATTTCTC
261 CCTATTTCTC
13471446 AGAGAGTATAG-AC-C-CACAATCTTC-ATAAATCGCGTATGCCCCCTATTTCTTCAGAGAGTAT
1 AGAGAGTATAGAACTCGCACAATCTTCAAT-AATCGCGTATGCCCCCTATTTCTTCAGAGAGTAT
* *
13471507 -AGACTCGAGCAATCTTCA-CAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAA
65 AAGAC-CCA-CAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAA
*
13471570 CAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAG-ATAAGAC-C-CACAATCTTCAT
128 CAATCTTCAAC-ATCGCGTCTGCCCCCTA-TTCTTCA-AGAGTATAAGACTCGAACAATCTTCA-
13471632 A-AATCGCGTATG-CCCCATATTTCTTCAGAGAGTATAAGACTCGAACAATCT
189 ACAATCGCGTATGTCCCC-TATTTCTTCAGAGAGTATAAGACTCGAACAATCT
13471683 CCATCAAACG
Statistics
Matches: 219, Mismatches: 10, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
266 10 0.05
267 150 0.68
268 28 0.13
269 16 0.07
270 15 0.07
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (270 bp):
AGAGAGTATAGAACTCGCACAATCTTCAATAATCGCGTATGCCCCCTATTTCTTCAGAGAGTATA
AGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
TCTTCAACATCGCGTCTGCCCCCTATTCTTCAAGAGTATAAGACTCGAACAATCTTCAACAATCG
CGTATGTCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCC
CCTATTTCTC
Found at i:13485539 original size:36 final size:35
Alignment explanation
Indices: 13485499--13485751 Score: 163
Period size: 36 Copynumber: 7.1 Consensus size: 35
13485489 GTTTCTATGT
*
13485499 ATGATATACATGTGTTGGTTACTGATGATTATAAGC
1 ATGATATACATGTGTT-GCTACTGATGATTATAAGC
* * * * *
13485535 ATGATATACACGTGTTTGTTACTGATTATTGTGAGC
1 ATGATATACATGTG-TTGCTACTGATGATTATAAGC
* * * * *
13485571 GTGATATACATGTATTTGCTATTGATTATTATGAGC
1 ATGATATACATGT-GTTGCTACTGATGATTATAAGC
* * * *
13485607 ATGATATGCA---CTTGATAATGATGATTATATA-C
1 ATGATATACATGTGTTGCTACTGATGATTATA-AGC
** * *
13485639 ATGATATACATGCACTTACTACTGATGATTATATGC
1 ATGATATACATG-TGTTGCTACTGATGATTATAAGC
* * * * * *
13485675 ATGATATATATGCGCTCGCTACTAATTATTATAATC
1 ATGATATACATGTG-TTGCTACTGATGATTATAAGC
* * *
13485711 ATGATATACACGTGTTGGTTACTGATGATTATATGC
1 ATGATATACATGTGTT-GCTACTGATGATTATAAGC
13485747 ATGAT
1 ATGAT
13485752 CTTTTAACCA
Statistics
Matches: 167, Mismatches: 40, Indels: 20
0.74 0.18 0.09
Matches are distributed among these distances:
32 24 0.14
33 1 0.01
35 1 0.01
36 139 0.83
37 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (35 bp):
ATGATATACATGTGTTGCTACTGATGATTATAAGC
Found at i:13486446 original size:18 final size:18
Alignment explanation
Indices: 13486425--13486460 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
13486415 ATTTTAATTA
13486425 ATAAATAAATATGATGTG
1 ATAAATAAATATGATGTG
*
13486443 ATAAATAAATGTGATGTG
1 ATAAATAAATATGATGTG
13486461 TACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.33
Consensus pattern (18 bp):
ATAAATAAATATGATGTG
Found at i:13486714 original size:21 final size:21
Alignment explanation
Indices: 13486688--13486729 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
13486678 CAACTAACAA
*
13486688 TATACATTTTCTTTATTTTCT
1 TATACATTTTCTCTATTTTCT
13486709 TATACATTTTCTCTATTTTCT
1 TATACATTTTCTCTATTTTCT
13486730 CGGGAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.17, G:0.00, T:0.64
Consensus pattern (21 bp):
TATACATTTTCTCTATTTTCT
Found at i:13486798 original size:45 final size:45
Alignment explanation
Indices: 13486709--13486798 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
13486699 TTTATTTTCT
** * *
13486709 TATACATTTTCTCTATTTTCTCGGGAAACAAAGAACAACTAACTA
1 TATACATTTTCTCTATTTTCTCAAGAAACAAACAACAACCAACTA
* * * *
13486754 TATACATTTTCTTTATTTTCTTAAGAAATAAACACCAACCAACTA
1 TATACATTTTCTCTATTTTCTCAAGAAACAAACAACAACCAACTA
13486799 GAAATTACAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.36
Consensus pattern (45 bp):
TATACATTTTCTCTATTTTCTCAAGAAACAAACAACAACCAACTA
Done.