Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 5 of 189
Found at i:1658622 original size:31 final size:31
Alignment explanation
Indices: 1658587--1658658 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
1658577 ATACCATTCA
*** **
1658587 TCACTAAATTATAGTTAAGTTTTCATTTTGG
1 TCACTAAATTATACAAAAGTTTTCATTTAAG
** *
1658618 TCACTGCATTATTCAAAAGTTTTCATTTAAG
1 TCACTAAATTATACAAAAGTTTTCATTTAAG
1658649 TCACTAAATT
1 TCACTAAATT
1658659 GTTAAAATTG
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (31 bp):
TCACTAAATTATACAAAAGTTTTCATTTAAG
Found at i:1661156 original size:89 final size:88
Alignment explanation
Indices: 1661001--1661876 Score: 630
Period size: 89 Copynumber: 10.0 Consensus size: 88
1660991 TACTGTCTCT
* * * * * * **
1661001 GGTCGGGGTTTTGT-T-TCGACTCTGCCTAGACTCC-GAT-AGGGTGACACAGTTGAGCATCTTG
1 GGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTCCTG-TCAGGATGACAGAGTTGAGTGTCTTG
* *
1661062 TAGTAACAGGTGAATCTATGTCTTC
65 TAGTAACAGGTGAAACTATGTC-CC
* ** *
1661087 GGTCGAGGTTTTGTCTCCCGCCTCTGTCGAGAATCCTGTCAGGATG-CTAGAGTTGAGTGTCTTG
1 GGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTCCTGTCAGGATGAC-AGAGTTGAGTGTCTTG
* * * *
1661151 TAGTAACAGTTGAATCTATATCCTT
65 TAGTAACAGGTGAAACTATGTCC-C
* * * * * * * *
1661176 GGTGGAGGTTTTGTCTCCCGATTCTGCCGAGAATACTGTCAGGTTGATAGAGTCGAGTGTCTTGT
1 GGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTCCTGTCAGGATGACAGAGTTGAGTGTCTTGT
* *
1661241 AGTAACAGGTGAAACCATGTCGC
66 AGTAACAGGTGAAACTATGTCCC
* * * *
1661264 TGTCTAGGTTTTGTCTCCCGACTCTACCGAGACTCCTGAT-AGGATGACAGAGTTGTGTGTCATG
1 GGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTCCTG-TCAGGATGACAGAGTTGAGTGTCTTG
*
1661328 TAGTAACAGGTGAAACTATATCCCC
65 TAGTAACAGGTGAAACTATGT-CCC
* * * * * * *
1661353 GGTTGAGGTTTTGTCCCCCGGCTCTACAGAGACTCCTGTTAGG-TGGACAAAGTTGAGTGTTTTG
1 GGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTCCTGTCAGGAT-GACAGAGTTGAGTGTCTTG
* * *
1661417 CAGTAACAAGTGAAACTGTGTCCC
65 TAGTAACAGGTGAAACTATGTCCC
** * * * * * * *
1661441 TTTTGAGCTTTTGTCTCCCGACTCTATCGAGACTCCTATTAGGTTTGACAGAGTTGAGTGTCCTG
1 GGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTCCTGTCAGG-ATGACAGAGTTGAGTGTCTTG
** *
1661506 TAGTAACAGGTGAAACCGTGTCCTA
65 TAGTAACAGGTGAAACTATGTCC-C
* * * * ** * *
1661531 GGTTGAGGTTTGGTCTCCTGACTCTACTGAGACTATTGT-AGGTTGACAGCA-TT--GTG--ATG
1 GGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTCCTGTCAGGATGACAG-AGTTGAGTGTCTTG
*
1661590 TAGTAACAGGTGAAACCATGTTCCC
65 TAGTAACAGGTGAAACTATG-TCCC
* * ** * * ** * ** *
1661615 GGTCGAAGTTTTATCTCCTAACTCTACCGAGACTCTTATTGGGTTGTTAGAGTTGAGTTTCTTGT
1 GGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTCCTGTCAGGATGACAGAGTTGAGTGTCTTGT
* *
1661680 AGTAACAAGTGAAACCATGTCTCC
66 AGTAACAGGTGAAACTATGTC-CC
* * * * * * * * * *
1661704 TGTC-AGGGTTTTGTTTCCCTACTTTACCGAGACTCATATTAGGTTGACAGAGTTGAGTGTTTTA
1 GGTCGA-GGTTTTGTCTCCCGACTCTACCGAGACTCCTGTCAGGATGACAGAGTTGAGTGTCTTG
* **
1661768 TACTAACAGGTG-AACCGTGTCCCC
65 TAGTAACAGGTGAAACTATGT-CCC
* * ** * * *
1661792 GGTCAAGGTTCTGTCTCCTAACTCTACCGAGAATCCTATCAGGTTGACAGAGTTGAGTGTCTTGT
1 GGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTCCTGTCAGGATGACAGAGTTGAGTGTCTTGT
*
1661857 AGTAACAGGTGAAACCATGT
66 AGTAACAGGTGAAACTATGT
1661877 GAAACTAAAG
Statistics
Matches: 634, Mismatches: 129, Indels: 51
0.78 0.16 0.06
Matches are distributed among these distances:
84 53 0.08
85 12 0.02
86 16 0.03
87 3 0.00
88 208 0.33
89 312 0.49
90 30 0.05
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (88 bp):
GGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTCCTGTCAGGATGACAGAGTTGAGTGTCTTGT
AGTAACAGGTGAAACTATGTCCC
Found at i:1661318 original size:177 final size:176
Alignment explanation
Indices: 1661057--1661874 Score: 713
Period size: 177 Copynumber: 4.6 Consensus size: 176
1661047 CAGTTGAGCA
* * * * ** *
1661057 TCTTGTAGTAACAGGTGAATCTATGTCTTCGGTCGAGGTTTTGTCTCCCGCCTCTGTCGAGAATC
1 TCTTGTAGTAACAGGTGAAACCATGTC-CCGGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTC
* * * * * * *
1661122 CTGTCAGGATG-CTAGAGTTGAGTGTCTTGTAGTAACAGTTGAATCTATATCCTTGGTGGAGGTT
65 CTAT-AGGTTGAC-AGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCATATCCCTGGTTGAGGTT
* * * * *
1661186 TTGTCTCCCGATTCTGCCGAGAATACTGTCAGGTTGATAGAGTCGAGTG
128 TTGTCTCCCGACTCTACCGAGACTACTGTTAGGTTGACAGAGTCGAGTG
* * *
1661235 TCTTGTAGTAACAGGTGAAACCATGTCGCTGTCTAGGTTTTGTCTCCCGACTCTACCGAGACTCC
1 TCTTGTAGTAACAGGTGAAACCATGTCCCGGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTCC
* * * * *
1661300 TGATAGGATGACAGAGTTGTGTGTCATGTAGTAACAGGTGAAACTATATCCCCGGTTGAGGTTTT
66 T-ATAGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCATATCCCTGGTTGAGGTTTT
* * * * * * *
1661365 GTCCCCCGGCTCTACAGAGACTCCTGTTAGGTGGACAAAGTTGAGTG
130 GTCTCCCGACTCTACCGAGACTACTGTTAGGTTGACAGAGTCGAGTG
* * * ** ** * * *
1661412 TTTTGCAGTAACAAGTGAAACTGTGTCCCTTTTGAGCTTTTGTCTCCCGACTCTATCGAGACTCC
1 TCTTGTAGTAACAGGTGAAACCATGTCCCGGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTCC
* * *
1661477 TATTAGGTTTGACAGAGTTGAGTGTCCTGTAGTAACAGGTGAAACCGTGT-CCTAGGTTGAGGTT
66 TA-TAGG-TTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCATATCCCT-GGTTGAGGTT
* * * * *
1661541 TGGTCTCCTGACTCTACTGAGACTATTG-TAGGTTGAC--AG-C-ATTG
128 TTGTCTCCCGACTCTACCGAGACTACTGTTAGGTTGACAGAGTCGAGTG
** * * **
1661585 TGATGTAGTAACAGGTGAAACCATGTTCCCGGTCGAAGTTTTATCTCCTAACTCTACCGAGACTC
1 TCTTGTAGTAACAGGTGAAACCATG-TCCCGGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTC
* * ** * * * *
1661650 TTATTGGGTTGTTAGAGTTGAGTTTCTTGTAGTAACAAGTGAAACCATGTCTCCT-G-TCAGGGT
65 CTA-TAGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCATATC-CCTGGTTGA-GGT
* * * * *
1661713 TTTGTTTCCCTACTTTACCGAGACT-CATATTAGGTTGACAGAGTTGAGTG
127 TTTGTCTCCCGACTCTACCGAGACTAC-TGTTAGGTTGACAGAGTCGAGTG
* * * * * * ** *
1661763 TTTTATACTAACAGGTG-AACCGTGTCCCCGGTCAAGGTTCTGTCTCCTAACTCTACCGAGAATC
1 TCTTGTAGTAACAGGTGAAACCATGT-CCCGGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTC
1661827 CTATCAGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCAT
65 CTAT-AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCAT
1661875 GTGAAACTAA
Statistics
Matches: 516, Mismatches: 107, Indels: 35
0.78 0.16 0.05
Matches are distributed among these distances:
172 2 0.00
173 82 0.16
174 45 0.09
175 5 0.01
176 5 0.01
177 267 0.52
178 110 0.21
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (176 bp):
TCTTGTAGTAACAGGTGAAACCATGTCCCGGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTCC
TATAGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCATATCCCTGGTTGAGGTTTTG
TCTCCCGACTCTACCGAGACTACTGTTAGGTTGACAGAGTCGAGTG
Found at i:1662183 original size:13 final size:13
Alignment explanation
Indices: 1662144--1662184 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1662134 AGTATGATGA
1662144 TTATGATGTTAGT
1 TTATGATGTTAGT
*
1662157 TTATG-TATTA--
1 TTATGATGTTAGT
1662167 TTATGATGTTAGT
1 TTATGATGTTAGT
1662180 TTATG
1 TTATG
1662185 TTTTAGTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
10 5 0.22
11 4 0.17
12 4 0.17
13 10 0.43
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (13 bp):
TTATGATGTTAGT
Found at i:1670669 original size:69 final size:69
Alignment explanation
Indices: 1670558--1670698 Score: 273
Period size: 69 Copynumber: 2.0 Consensus size: 69
1670548 ATGAAATTGG
1670558 GTTTTGATTAAATTTGTAATCGAGTCGAATTAAACCTCTGAACCGGAGTAATGCTCTTTCAATAT
1 GTTTTGATTAAATTTGTAATCGAGTCGAATTAAACCTCTGAACCGGAGTAATGCTCTTTCAATAT
1670623 TGTT
66 TGTT
*
1670627 GTTTTGATTAAATTTGTAATCGAGTCGAATTAAACCTCTGAACCGGAGTAATGCTCTTTGAATAT
1 GTTTTGATTAAATTTGTAATCGAGTCGAATTAAACCTCTGAACCGGAGTAATGCTCTTTCAATAT
1670692 TGTT
66 TGTT
1670696 GTT
1 GTT
1670699 GTTTTACTCC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (69 bp):
GTTTTGATTAAATTTGTAATCGAGTCGAATTAAACCTCTGAACCGGAGTAATGCTCTTTCAATAT
TGTT
Found at i:1672489 original size:7 final size:7
Alignment explanation
Indices: 1672472--1672501 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
1672462 CCTATATATA
1672472 TATTCAAT
1 TATT-AAT
1672480 TATTAAT
1 TATTAAT
1672487 TATTAAT
1 TATTAAT
1672494 TATTAAT
1 TATTAAT
1672501 T
1 T
1672502 TTTTTATAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (7 bp):
TATTAAT
Found at i:1673836 original size:24 final size:25
Alignment explanation
Indices: 1673794--1673840 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1673784 TTCAAGTTTT
* *
1673794 TTTTTTTTATTCTTCAATTCTTTCA
1 TTTTTATTATTCTTAAATTCTTTCA
1673819 TTTTTATTATT-TTAAATTCTTT
1 TTTTTATTATTCTTAAATTCTTT
1673841 AATATTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTTATTATTCTTAAATTCTTTCA
Found at i:1675016 original size:30 final size:29
Alignment explanation
Indices: 1674941--1675035 Score: 91
Period size: 31 Copynumber: 3.1 Consensus size: 29
1674931 TTTTATTATA
* * *
1674941 CCTTTAAAATTTTAAAAAATTTCAATTAGCT
1 CCTTTGAAATTTTTAAAAATTTC-ATTA-AT
*
1674972 CCCTTGAAATTTTTAAAAATTTCATTAAT
1 CCTTTGAAATTTTTAAAAATTTCATTAAT
* *
1675001 CCTTTCGATATTTTTAAAAATGTTAATTAAAT
1 CCTTT-GAAATTTTTAAAAAT-TTCATT-AAT
1675033 CCT
1 CCT
1675036 AAAAATTTTG
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
29 5 0.09
30 18 0.33
31 25 0.46
32 6 0.11
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.44
Consensus pattern (29 bp):
CCTTTGAAATTTTTAAAAATTTCATTAAT
Found at i:1675123 original size:30 final size:30
Alignment explanation
Indices: 1675089--1675145 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1675079 TTTTTATTAT
* *
1675089 GCCTTTGAAATTTTTAAAAATTCTAATTGA
1 GCCTTTCAAAATTTTAAAAATTCTAATTGA
* *
1675119 GCCTTTCAAAATTTTATAAATTTTAAT
1 GCCTTTCAAAATTTTAAAAATTCTAAT
1675146 AAGACCCTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.46
Consensus pattern (30 bp):
GCCTTTCAAAATTTTAAAAATTCTAATTGA
Found at i:1681243 original size:22 final size:20
Alignment explanation
Indices: 1681217--1681257 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1681207 TGCAATCGTA
1681217 TATTAGACATATTGTATTTTTC
1 TATTA-ACATA-TGTATTTTTC
*
1681239 TATTAATATATGTATTTTT
1 TATTAACATATGTATTTTT
1681258 AAAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 4 0.22
22 5 0.28
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.59
Consensus pattern (20 bp):
TATTAACATATGTATTTTTC
Found at i:1689114 original size:31 final size:31
Alignment explanation
Indices: 1689066--1689146 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
1689056 AAATGATCAC
* *
1689066 TGAATTATTCGAAAGTTTTCACTTAAGTCAT
1 TGAACTATTTGAAAGTTTTCACTTAAGTCAT
* * *
1689097 TGAACTATTTGAAAGTTTTTATTTAAGTTAT
1 TGAACTATTTGAAAGTTTTCACTTAAGTCAT
*
1689128 TGAACTATTTGAAAATTTT
1 TGAACTATTTGAAAGTTTT
1689147 TATTTAAGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.47
Consensus pattern (31 bp):
TGAACTATTTGAAAGTTTTCACTTAAGTCAT
Found at i:1689147 original size:31 final size:31
Alignment explanation
Indices: 1689088--1689160 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
1689078 AAGTTTTCAC
* *
1689088 TTAAGTCATTGAACTATTTGAAAGTTTTTAT
1 TTAAGTTATTGAACTATTTGAAAATTTTTAT
1689119 TTAAGTTATTGAACTATTTGAAAATTTTTAT
1 TTAAGTTATTGAACTATTTGAAAATTTTTAT
*
1689150 TTAAGGTATTG
1 TTAAGTTATTG
1689161 GATTGTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (31 bp):
TTAAGTTATTGAACTATTTGAAAATTTTTAT
Found at i:1694477 original size:24 final size:24
Alignment explanation
Indices: 1694450--1694508 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
1694440 TGCTGCTGCT
*
1694450 GCTGCTGCTGTAGAGGTGGCTGAG
1 GCTGCTGCTGTAGAGGTGACTGAG
* * * *
1694474 GCTGCTGTTGAAGATGTGACTGTG
1 GCTGCTGCTGTAGAGGTGACTGAG
*
1694498 GCTGCAGCTGT
1 GCTGCTGCTGT
1694509 GACTGTCTTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.14, C:0.17, G:0.41, T:0.29
Consensus pattern (24 bp):
GCTGCTGCTGTAGAGGTGACTGAG
Found at i:1730480 original size:16 final size:16
Alignment explanation
Indices: 1730459--1730490 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1730449 GTTTTATGAA
*
1730459 AATTATATAATCAATT
1 AATTATATAAACAATT
1730475 AATTATATAAACAATT
1 AATTATATAAACAATT
1730491 CTAATCAGAA
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:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTATATAAACAATT
Found at i:1739499 original size:3 final size:3
Alignment explanation
Indices: 1739491--1739519 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1739481 TGCAAACTGG
1739491 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1739520 ATGCATAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1741299 original size:12 final size:13
Alignment explanation
Indices: 1741282--1741319 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
1741272 TTGGTGTAAC
1741282 AAATAAAAATA-A
1 AAATAAAAATATA
1741294 AAATAAAAATATA
1 AAATAAAAATATA
*
1741307 TAATAAATAATAT
1 AAATAAA-AATAT
1741320 GCATTTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.48
13 7 0.30
14 5 0.22
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAATAAAAATATA
Found at i:1744397 original size:31 final size:31
Alignment explanation
Indices: 1744362--1744425 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1744352 CAATCCAATA
* *
1744362 ACTTAAATAAAAACTTTCGAATAATTTAGTG
1 ACTTAAATAAAAACTTTAGAATAACTTAGTG
* * *
1744393 ACTTAAATGAGAATTTTAGAATAACTTAGTG
1 ACTTAAATAAAAACTTTAGAATAACTTAGTG
1744424 AC
1 AC
1744426 CATTTTGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTAGAATAACTTAGTG
Found at i:1759251 original size:16 final size:16
Alignment explanation
Indices: 1759227--1759258 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1759217 TGTACTTCAC
*
1759227 TATACTTGATTTTGAT
1 TATAATTGATTTTGAT
1759243 TATAATTGATTTTGAT
1 TATAATTGATTTTGAT
1759259 ATTATTTATT
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:0.28, C:0.03, G:0.12, T:0.56
Consensus pattern (16 bp):
TATAATTGATTTTGAT
Found at i:1766992 original size:12 final size:12
Alignment explanation
Indices: 1766975--1767000 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1766965 AGCTTTTGAT
1766975 TATATATACATA
1 TATATATACATA
1766987 TATATATACATA
1 TATATATACATA
1766999 TA
1 TA
1767001 CTTCAATCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATACATA
Found at i:1767593 original size:21 final size:22
Alignment explanation
Indices: 1767561--1767602 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1767551 ATTTAAGTGG
*
1767561 TTTTAATAT-AAATTTTTTAAC
1 TTTTAATATAAAAATTTTTAAC
1767582 TTTTAA-ACTAAAAATTTTTAA
1 TTTTAATA-TAAAAATTTTTAA
1767603 TCTTCACACC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 1 0.06
21 7 0.39
22 10 0.56
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTAATATAAAAATTTTTAAC
Found at i:1769235 original size:37 final size:38
Alignment explanation
Indices: 1769185--1769270 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
1769175 AAAAATTATA
* * *
1769185 TTTAATACAATAAAACATTTATTATATTTAT-TTGTTT
1 TTTAATATAATAAAACATTTATTATATTTATGGTATTT
*
1769222 TTTAATATAATAAAACATTTATTTTATTTATGGTATTT
1 TTTAATATAATAAAACATTTATTATATTTATGGTATTT
1769260 TTTAAATATAA
1 TTT-AATATAA
1769271 ATATTTTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
37 29 0.67
38 7 0.16
39 7 0.16
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (38 bp):
TTTAATATAATAAAACATTTATTATATTTATGGTATTT
Found at i:1772465 original size:4 final size:4
Alignment explanation
Indices: 1772458--1772491 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
1772448 ATATATATAC
*
1772458 ATGT ATGT ATGT ATGT ATGT ATGT AAGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1772492 ACCTTCCTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:1786366 original size:26 final size:26
Alignment explanation
Indices: 1786311--1786369 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
1786301 GTAAAATTTT
* *
1786311 TTTATATTTTTTAAATAATTATTAGT
1 TTTAAATTTTTTAAATAATTATTAGC
1786337 TTTAAATTTTTT-AATAATTTATTTA-C
1 TTTAAATTTTTTAAATAA-TTA-TTAGC
1786363 TTTAAAT
1 TTTAAAT
1786370 CGATCGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 5 0.17
26 21 0.72
27 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTAAATTTTTTAAATAATTATTAGC
Found at i:1787588 original size:21 final size:21
Alignment explanation
Indices: 1787547--1787588 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1787537 AAATTCATCC
*
1787547 TTAAATTTTAAAACAGTTTAA
1 TTAAATTTTAAAACAGATTAA
*
1787568 TTAAATTCTT-AAACTGATTAA
1 TTAAATT-TTAAAACAGATTAA
1787589 AATATTGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (21 bp):
TTAAATTTTAAAACAGATTAA
Found at i:1792894 original size:35 final size:35
Alignment explanation
Indices: 1792855--1792925 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
1792845 TCCAAATGGA
1792855 TTAATCTATGAATTTTTTGTGGTATATATTTGGTT
1 TTAATCTATGAATTTTTTGTGGTATATATTTGGTT
1792890 TTAATCTATGAATTTTTTGTGGTATATATTTGGTT
1 TTAATCTATGAATTTTTTGTGGTATATATTTGGTT
1792925 T
1 T
1792926 ACTTTGCTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.23, C:0.03, G:0.17, T:0.58
Consensus pattern (35 bp):
TTAATCTATGAATTTTTTGTGGTATATATTTGGTT
Found at i:1812697 original size:23 final size:26
Alignment explanation
Indices: 1812667--1812721 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
1812657 CATGTGACAA
1812667 AAAAAATAAAAA-A-T-AAATTTATT
1 AAAAAATAAAAATACTAAAATTTATT
1812690 AAAAAATAAAAATACTTAAAATTTATT
1 AAAAAATAAAAATAC-TAAAATTTATT
1812717 AAAAA
1 AAAAA
1812722 CTATTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.43
24 1 0.04
26 1 0.04
27 14 0.50
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (26 bp):
AAAAAATAAAAATACTAAAATTTATT
Found at i:1813072 original size:9 final size:9
Alignment explanation
Indices: 1813058--1813181 Score: 63
Period size: 9 Copynumber: 13.4 Consensus size: 9
1813048 TTTTGATACA
*
1813058 TTTTATATT
1 TTTTATAAT
1813067 TTTTATAAT
1 TTTTATAAT
*
1813076 TTTTATAAA
1 TTTTATAAT
** **
1813085 AATTACCAT
1 TTTTATAAT
*
1813094 TTTTCTATAT
1 TTTTATA-AT
* *
1813104 TTTTACGATT
1 TTTTA-TAAT
1813114 TTTTATAAT
1 TTTTATAAT
*
1813123 TTTTAAATAT
1 TTTTATA-AT
*
1813133 TTTTATTAAAA
1 TTTTA-T-AAT
* *
1813144 TATAATAAT
1 TTTTATAAT
1813153 TTTTATAAT
1 TTTTATAAT
*
1813162 TTCTAT--T
1 TTTTATAAT
1813169 TTTTATAAT
1 TTTTATAAT
1813178 TTTT
1 TTTT
1813182 TGTCACATGT
Statistics
Matches: 81, Mismatches: 27, Indels: 14
0.66 0.22 0.11
Matches are distributed among these distances:
7 6 0.07
9 49 0.60
10 20 0.25
11 5 0.06
12 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:1813109 original size:19 final size:19
Alignment explanation
Indices: 1813087--1813127 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1813077 TTTATAAAAA
1813087 TTACCATTTTTCTAT-ATTT
1 TTACCATTTTT-TATAATTT
*
1813106 TTACGATTTTTTATAATTT
1 TTACCATTTTTTATAATTT
1813125 TTA
1 TTA
1813128 AATATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.63
Consensus pattern (19 bp):
TTACCATTTTTTATAATTT
Found at i:1829372 original size:24 final size:26
Alignment explanation
Indices: 1829345--1829400 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
1829335 TTCAATTAAA
1829345 ATCAAATTAAATTT-T-ATTTTTTAT
1 ATCAAATTAAATTTATAATTTTTTAT
**
1829369 ATC-AATTACTTTTATAATTTTTTAT
1 ATCAAATTAAATTTATAATTTTTTAT
*
1829394 ATAAAAT
1 ATCAAAT
1829401 GTTTTCACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 8 0.31
24 4 0.15
25 11 0.42
26 3 0.12
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (26 bp):
ATCAAATTAAATTTATAATTTTTTAT
Found at i:1830090 original size:16 final size:16
Alignment explanation
Indices: 1830069--1830154 Score: 59
Period size: 16 Copynumber: 5.1 Consensus size: 16
1830059 TTATAAAAAT
1830069 ATTATTTAATATATTA
1 ATTATTTAATATATTA
*
1830085 ATTATTTAATGTATT-
1 ATTATTTAATATATTA
1830100 ATTATATTAA-ATTATTTA
1 ATTAT-TTAATA-TA-TTA
** *
1830118 AAAATATAATTATATTGA
1 ATTATTTAA-TATATT-A
1830136 ATTATTTAAATATAGTTA
1 ATTATTT-AATATA-TTA
1830154 A
1 A
1830155 CATTATATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
15 5 0.09
16 20 0.38
17 7 0.13
18 16 0.30
19 5 0.09
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTATTTAATATATTA
Found at i:1830093 original size:8 final size:8
Alignment explanation
Indices: 1830069--1830144 Score: 50
Period size: 8 Copynumber: 9.1 Consensus size: 8
1830059 TTATAAAAAT
1830069 ATTATTTA
1 ATTATTTA
1830077 A-TATATTA
1 ATTAT-TTA
1830085 ATTATTTA
1 ATTATTTA
1830093 ATGTA-TT-
1 AT-TATTTA
1830100 ATTATATTAA
1 ATTAT-TT-A
1830110 ATTATTTA
1 ATTATTTA
** *
1830118 AAAATATA
1 ATTATTTA
1830126 ATTATATTGA
1 ATTAT-TT-A
1830136 ATTATTTA
1 ATTATTTA
1830144 A
1 A
1830145 ATATAGTTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
6 2 0.04
7 5 0.09
8 25 0.47
9 10 0.19
10 11 0.21
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (8 bp):
ATTATTTA
Found at i:1830129 original size:26 final size:25
Alignment explanation
Indices: 1830078--1830145 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 25
1830068 TATTATTTAA
** *
1830078 TATATTAATTATTT-AATGTATTAT
1 TATATTAATTATTTAAAAATATAAT
1830102 TATATTAAATTATTTAAAAATATAAT
1 TATATT-AATTATTTAAAAATATAAT
1830128 TATATTGAATTATTTAAA
1 TATATT-AATTATTTAAA
1830146 TATAGTTAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 6 0.16
25 8 0.21
26 24 0.63
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (25 bp):
TATATTAATTATTTAAAAATATAAT
Found at i:1835050 original size:31 final size:28
Alignment explanation
Indices: 1835004--1835060 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 28
1834994 GGCTTGGACA
1835004 GCTAACCTTTCAAAATAG-TCAAATAAGG
1 GCTAACCTTTCAAAAT-GCTCAAATAAGG
1835032 GCTAAGCCTTTTCGAAAATGCTCAAATAA
1 GCTAA-CC-TTTC-AAAATGCTCAAATAA
1835061 AGGCCAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 5 0.20
29 2 0.08
30 5 0.20
31 13 0.52
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.26
Consensus pattern (28 bp):
GCTAACCTTTCAAAATGCTCAAATAAGG
Found at i:1839380 original size:19 final size:18
Alignment explanation
Indices: 1839342--1839379 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1839332 AAAATTATAA
1839342 TTAAGTTTAATTAAAATT
1 TTAAGTTTAATTAAAATT
*
1839360 TTAAGTATTTATT-AAATT
1 TTAAGT-TTAATTAAAATT
1839378 TT
1 TT
1839380 TTTAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
TTAAGTTTAATTAAAATT
Found at i:1841438 original size:23 final size:23
Alignment explanation
Indices: 1841394--1841440 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1841384 TAATTTATTA
**
1841394 AAAATGTATTATAATATTAAAAT
1 AAAATGTATTATAATAAAAAAAT
1841417 AAAATGTAATTA-AATAAAAAAAT
1 AAAATGT-ATTATAATAAAAAAAT
1841440 A
1 A
1841441 TTTAAAGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (23 bp):
AAAATGTATTATAATAAAAAAAT
Found at i:1842908 original size:16 final size:15
Alignment explanation
Indices: 1842887--1842938 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
1842877 GATAATTACG
1842887 AAAATTAAATTATAT
1 AAAATTAAATTATAT
*
1842902 CAAAATTTAA-TATAT
1 -AAAATTAAATTATAT
* *
1842917 AAAATTACATAATATT
1 AAAATTAAATTATA-T
1842933 AAAATT
1 AAAATT
1842939 TATTTATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 7 0.23
15 8 0.27
16 15 0.50
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATTAAATTATAT
Found at i:1842923 original size:30 final size:30
Alignment explanation
Indices: 1842887--1842990 Score: 84
Period size: 30 Copynumber: 3.3 Consensus size: 30
1842877 GATAATTACG
1842887 AAAATTAAATTATATCAAAATTTAATATAT
1 AAAATTAAATTATATCAAAATTTAATATAT
* * * *
1842917 AAAATTACATAATATTAAAATTT-ATTTAT
1 AAAATTAAATTATATCAAAATTTAATATAT
* * *
1842946 AATATTACACATTAAAACAAAATTTATATCATGTAT
1 AAAATTA-A-ATTATATCAAAATTTA-AT-A--TAT
1842982 AAAATTAAA
1 AAAATTAAA
1842991 AATCTAACAA
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
29 11 0.20
30 20 0.36
31 11 0.20
33 2 0.04
34 1 0.02
35 1 0.02
36 9 0.16
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (30 bp):
AAAATTAAATTATATCAAAATTTAATATAT
Found at i:1848569 original size:31 final size:31
Alignment explanation
Indices: 1848532--1848602 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
1848522 TTTATACAAT
*
1848532 TATACACATGAAACTTTGATCATGGTTCAAG
1 TATACACATGAAACTTTGATCATGATTCAAG
* * * *
1848563 TGTACACATGAAATTTTGATTATGATTCAAT
1 TATACACATGAAACTTTGATCATGATTCAAG
1848594 TATACACAT
1 TATACACAT
1848603 TTAAATAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (31 bp):
TATACACATGAAACTTTGATCATGATTCAAG
Found at i:1851998 original size:20 final size:20
Alignment explanation
Indices: 1851961--1851997 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
1851951 ATGCATTTTT
1851961 TATAGATTTAATCCTTTTAC
1 TATAGATTTAATCCTTTTAC
*
1851981 TATA-ATTTAATCATTTT
1 TATAGATTTAATCCTTTT
1851998 TTGTTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.54
Consensus pattern (20 bp):
TATAGATTTAATCCTTTTAC
Found at i:1853589 original size:22 final size:24
Alignment explanation
Indices: 1853561--1853604 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1853551 TATGGCAAGA
1853561 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGTTAGAAAAGTAAGTATG
1853583 AATTAAGTTAGAAAAGTAAGTA
1 AATTAAGTTAGAAAAGTAAGTA
1853605 AACCTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (24 bp):
AATTAAGTTAGAAAAGTAAGTATG
Found at i:1853999 original size:36 final size:37
Alignment explanation
Indices: 1853915--1854010 Score: 124
Period size: 37 Copynumber: 2.6 Consensus size: 37
1853905 GAATATACGT
* *
1853915 GTGAAATTGAAATGAATAT-TGACTTGAAAATGGAAAA
1 GTGAAATTGAATTGAAT-TGTGACTTGAAAATGAAAAA
*
1853952 GTGAATTTTGAATTGAATTGTGA-TTGAAAATGAAAAA
1 GTGAA-ATTGAATTGAATTGTGACTTGAAAATGAAAAA
*
1853989 GTGAAATTGAATTGAAATGTGA
1 GTGAAATTGAATTGAATTGTGA
1854011 ATTTGGAGAC
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
36 15 0.29
37 24 0.46
38 13 0.25
ACGTcount: A:0.45, C:0.01, G:0.23, T:0.31
Consensus pattern (37 bp):
GTGAAATTGAATTGAATTGTGACTTGAAAATGAAAAA
Found at i:1860248 original size:59 final size:58
Alignment explanation
Indices: 1860178--1860292 Score: 178
Period size: 59 Copynumber: 2.0 Consensus size: 58
1860168 CATATTTTAG
* * *
1860178 TTTCCATATCATATCTAAAATGGATATTTA-ACTTTTTTAATTTTTAATATCATATCAA
1 TTTCCATATCATATCTAAAATAGATATTTAGA-TCTTTTAATTTTCAATATCATATCAA
1860236 TTTCCGATATCATATCTAAAATAGATATTTAGATCTTTTAATTTTCAATATCATATC
1 TTTCC-ATATCATATCTAAAATAGATATTTAGATCTTTTAATTTTCAATATCATATC
1860293 TAAAATGAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
58 5 0.10
59 46 0.88
60 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (58 bp):
TTTCCATATCATATCTAAAATAGATATTTAGATCTTTTAATTTTCAATATCATATCAA
Found at i:1886046 original size:16 final size:17
Alignment explanation
Indices: 1886025--1886056 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1886015 TATCTGAAGA
1886025 AATGAAAAAG-AAATAT
1 AATGAAAAAGTAAATAT
1886041 AATGAAAAAGTAAATA
1 AATGAAAAAGTAAATA
1886057 GATGAAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (17 bp):
AATGAAAAAGTAAATAT
Found at i:1895094 original size:20 final size:20
Alignment explanation
Indices: 1895071--1895114 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1895061 TGTTGCTATT
* *
1895071 TTTTTTTAATTTTAT-AACTA
1 TTTTTATAATGTTATGAAC-A
1895091 TTTTTATAATGTTATGAACA
1 TTTTTATAATGTTATGAACA
1895111 TTTT
1 TTTT
1895115 ATTATTAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTTATAATGTTATGAACA
Found at i:1896690 original size:27 final size:29
Alignment explanation
Indices: 1896629--1896691 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
1896619 AAGAAAATTA
* * *
1896629 AAATATTGAATAAATTTGTCAAGAAATAT
1 AAATATGGAATAAATTGGTCAAGAAATAG
*
1896658 ATATATGGAATAAATTGGTC-A-AAATAG
1 AAATATGGAATAAATTGGTCAAGAAATAG
1896685 AAATATG
1 AAATATG
1896692 TAATTCAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 11 0.38
28 1 0.03
29 17 0.59
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (29 bp):
AAATATGGAATAAATTGGTCAAGAAATAG
Found at i:1898979 original size:110 final size:110
Alignment explanation
Indices: 1898812--1899122 Score: 334
Period size: 110 Copynumber: 2.9 Consensus size: 110
1898802 AAAAAAAAAA
* *
1898812 TTGGGTGCTGGCCTGTTAATGGCCGGCACCCAGTAAACAGTAATTTTTTTTTCTTTTTTTTCGTG
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTAAACAGTAATTTTTTCTTCTTTTTTTTCGTG
*
1898877 TCAGAGTCAGATATAAAAATACGAAAAAAAATTTAAAATTTTTTT
66 TCAGAATCAGATATAAAAATACGAAAAAAAATTTAAAATTTTTTT
* * *
1898922 TTGGGTGCTGGCCTGTCAGTGGTCGGCACCCAGTGAACAGTAAATTTTTTCTT-TTTTTTTTCGT
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTAAACAGT-AATTTTTTCTTCTTTTTTTTCGT
* ** ****
1898986 GTCAGAATCAGATATAAAAATAGGAAAAAAATAAAATAAAATAAAAAAATT
65 GTCAGAATCAGATATAAAAATACG-AAAAAA-AATTTAAAAT---TTTTTT
* * * * *
1899037 TTGGGTGCTGGCCTATCAATGGCCGGCACCAAATGAACAGTAA-------AT-TTTTTTTTCGTG
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTAAACAGTAATTTTTTCTTCTTTTTTTTCGTG
*
1899094 TCAGAATTAGATATAAAAATACGAAAAAA
66 TCAGAATCAGATATAAAAATACGAAAAAA
1899123 TAAAAAAAAA
Statistics
Matches: 174, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
106 6 0.03
107 34 0.20
110 70 0.40
111 16 0.09
112 8 0.05
114 2 0.01
115 38 0.22
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (110 bp):
TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTAAACAGTAATTTTTTCTTCTTTTTTTTCGTG
TCAGAATCAGATATAAAAATACGAAAAAAAATTTAAAATTTTTTT
Found at i:1899492 original size:104 final size:105
Alignment explanation
Indices: 1899241--1899682 Score: 523
Period size: 111 Copynumber: 4.2 Consensus size: 105
1899231 AAGTCTTATA
* ******
1899241 AAATTTTTTTA--TTTTTTCGTATTTTTATATTTGATTCTGACACGAAAAAAAAGAATTTTTTTT
1 AAATTTTTTTATTTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAATT
* * *
1899304 TACTGTGT-ATTGGGTGCCGACCATTGACAGGCCAGCACCT
66 TACTGT-TCACTGGGTGCCGGCCATTGACAGGCCAGCACCC
* *
1899344 AAA----TTT-TTTTTTTTCGTATTTTTATATCTGATTCTTACACGAAAAAAAAAGAAAAAAATT
1 AAATTTTTTTATTTTTTTTCGTATTTTTATATCTGATTCTGACACG-AAAAAAAAGAAAAAAAAT
1899404 TTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCA-CC
65 TTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCC
* *
1899444 -AATTTTTTTATTTTTTTTCGTATTTTTATATCTGATTTTGACACGAAAAAAAAAAAGAAAAAAT
1 AAATTTTTTTATTTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAA-AAAAAAT
* *
1899508 TCACTGTTCACTGGGTGCCGGCTATTGACAGGCCAGCACCC
65 TTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCC
* *
1899549 AAAAAATTTTTTTTAAAATTTTTTT-GTATTTTTATATCTGACTCTGACACGAAAAAAAAGAAAA
1 ---AAA-TTTTTTT--ATTTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAG-AAA
*
1899613 AAAAATTTACTGTTTACTGGGTGCCGGCCATTGACAGGCCAGCACCC
59 AAAAATTTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCC
1899660 AAATTTTTTT-TTCTTTTTT-GTAT
1 AAATTTTTTTATT-TTTTTTCGTAT
1899683 ATCAGTATTA
Statistics
Matches: 295, Mismatches: 24, Indels: 38
0.83 0.07 0.11
Matches are distributed among these distances:
99 5 0.02
100 33 0.11
101 47 0.16
103 16 0.05
104 76 0.26
105 12 0.04
107 7 0.02
108 3 0.01
109 2 0.01
110 7 0.02
111 77 0.26
112 10 0.03
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (105 bp):
AAATTTTTTTATTTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAATT
TACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCC
Found at i:1899616 original size:111 final size:107
Alignment explanation
Indices: 1899240--1899671 Score: 498
Period size: 104 Copynumber: 4.1 Consensus size: 107
1899230 CAAGTCTTAT
* * ******
1899240 AAAATTTTTTT-A-TTTTTTCGTATTTTTATATTTGATTCTGACACGAAAAAAAAGAATTTTTTT
1 AAAATTTTTTTAATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAAAAAAAAAAT
* *
1899303 TTACTGTGT-ATTGGGTGCCGACCATTGACAGGCCAGCA-CC-
66 TTACTGT-TCACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
* * *
1899343 TAAA---TTTT--TTTTTTTCGTATTTTTATATCTGATTCTTACACGAAAAAAAAAGAAAAAAAT
1 AAAATTTTTTTAATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAA-AAAAAAAA
1899403 TTTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCA-CC-
65 TTTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
* *
1899444 --AATTTTTTTATTTTTTTTCGTATTTTTATATCTGATTTTGACACGAAAAAAAAAAAGAAAAAA
1 AAAATTTTTTTAATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAAAA-AAAAAA
* *
1899507 TTCACTGTTCACTGGGTGCCGGCTATTGACAGGCCAGCACCCAA
65 TTTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCC-A
*
1899551 AAAATTTTTTTTAAAATTTTTTT-GTATTTTTATATCTGACTCTGACACGAAAAAAAAGAAAAAA
1 AAAA-TTTTTTT--AATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAA-AAAAAA
*
1899615 AAATTTACTGTTTACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
62 AAATTTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
**
1899661 AATTTTTTTTT
1 AAAATTTTTTT
1899672 CTTTTTTGTA
Statistics
Matches: 287, Mismatches: 24, Indels: 30
0.84 0.07 0.09
Matches are distributed among these distances:
99 2 0.01
100 44 0.15
101 40 0.14
102 4 0.01
103 5 0.02
104 83 0.29
105 2 0.01
109 9 0.03
110 10 0.03
111 77 0.27
112 11 0.04
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (107 bp):
AAAATTTTTTTAATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAAAAAAAAAAT
TTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
Found at i:1904711 original size:34 final size:35
Alignment explanation
Indices: 1904673--1904739 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
1904663 CAGTAAAATA
*
1904673 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
1904707 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
1904740 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:1905655 original size:18 final size:18
Alignment explanation
Indices: 1905632--1905689 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
1905622 AAAATATTTT
1905632 TAATTTTATGTTTTTTAA
1 TAATTTTATGTTTTTTAA
**
1905650 TAATTTTAATGATTTTAAAAA
1 TAATTTT-ATG-TTTT-TTAA
* *
1905671 TATTTTTATTTTTTTTAA
1 TAATTTTATGTTTTTTAA
1905689 T
1 T
1905690 TTTAAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
18 10 0.32
19 7 0.23
20 6 0.19
21 8 0.26
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TAATTTTATGTTTTTTAA
Found at i:1908386 original size:13 final size:14
Alignment explanation
Indices: 1908368--1908396 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1908358 TAAAAATTCA
1908368 AAATATAA-TTCTT
1 AAATATAACTTCTT
1908381 AAATATAACTTCTT
1 AAATATAACTTCTT
1908395 AA
1 AA
1908397 GAGTTTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATAACTTCTT
Found at i:1910472 original size:31 final size:29
Alignment explanation
Indices: 1910402--1910475 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
1910392 GGCTCAGGTT
* *
1910402 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
1910431 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
1910462 ACATTTTAGTCACT
1 ACATTTTAGTCACT
1910476 GAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:1911037 original size:31 final size:29
Alignment explanation
Indices: 1911001--1911099 Score: 90
Period size: 31 Copynumber: 3.3 Consensus size: 29
1910991 TTAACGACTC
* *
1911001 AGTGACTAAAATGTTACAATACGATAACGTA
1 AGTGACTAAAATGTAACAATAC-A-AACATA
* * *
1911032 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAATACAAACATA
* * *
1911061 AGTGACTAAAATATAACCTAAGACAAACAAA
1 AGTGACTAAAATGTAA-C-AATACAAACATA
1911092 AGTGACTA
1 AGTGACTA
1911100 TTTTGATAGT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
29 19 0.35
30 2 0.04
31 34 0.62
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.22
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAATACAAACATA
Found at i:1914338 original size:24 final size:24
Alignment explanation
Indices: 1914310--1914360 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1914300 TCTTTCTAGA
**
1914310 ATATTTAGTATTTATGAGAATAAT
1 ATATTTAACATTTATGAGAATAAT
* *
1914334 ATATTTAACATTTATTAGCATAAT
1 ATATTTAACATTTATGAGAATAAT
1914358 ATA
1 ATA
1914361 CTTGACTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (24 bp):
ATATTTAACATTTATGAGAATAAT
Found at i:1922951 original size:20 final size:20
Alignment explanation
Indices: 1922928--1922969 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1922918 TCGATCATAG
1922928 ATGATAGATTTTGAGGACCC
1 ATGATAGATTTTGAGGACCC
1922948 ATGATAGATTTTGAGGACCC
1 ATGATAGATTTTGAGGACCC
1922968 AT
1 AT
1922970 TGGTTCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (20 bp):
ATGATAGATTTTGAGGACCC
Found at i:1927717 original size:19 final size:17
Alignment explanation
Indices: 1927685--1927719 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
1927675 TTATTTATTG
1927685 TATATTATTTTTAAATA
1 TATATTATTTTTAAATA
1927702 TATATCTATATTTTAAAT
1 TATAT-TAT-TTTTAAAT
1927720 TATCACAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATTATTTTTAAATA
Found at i:1932127 original size:26 final size:27
Alignment explanation
Indices: 1932086--1932147 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 27
1932076 TTTAAAATAC
* *
1932086 TTTTAAAATAATTTTTTTATTTTTTAT
1 TTTTAAAATAATTTTTTTAATGTTTAT
1932113 TTTTAAAATAA-TTTTTTAATGTTTAT
1 TTTTAAAATAATTTTTTTAATGTTTAT
*
1932139 TTTAAAAAT
1 TTTTAAAAT
1932148 GGGTCGGGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 21 0.66
27 11 0.34
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTTAAAATAATTTTTTTAATGTTTAT
Found at i:1947631 original size:23 final size:25
Alignment explanation
Indices: 1947587--1947634 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1947577 AACGTACGTT
* *
1947587 TATATTTTTGTTAATTTGAAATTTA
1 TATATATTTGTTAAGTTGAAATTTA
1947612 TATATATTT-TTAAGTT-AAATTTA
1 TATATATTTGTTAAGTTGAAATTTA
1947635 GTCATTAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (25 bp):
TATATATTTGTTAAGTTGAAATTTA
Found at i:1947985 original size:17 final size:19
Alignment explanation
Indices: 1947956--1947996 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
1947946 TTATTTTTAG
1947956 TATTTAGTATTATA-TAAT
1 TATTTAGTATTATATTAAT
1947974 TATTTA-TATTATATTAAT
1 TATTTAGTATTATATTAAT
1947992 T-TTTA
1 TATTTA
1947997 CAAGATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TATTTAGTATTATATTAAT
Found at i:1950244 original size:31 final size:32
Alignment explanation
Indices: 1950192--1950283 Score: 84
Period size: 31 Copynumber: 2.9 Consensus size: 32
1950182 ACAAAAGAAA
* ** *
1950192 ATTAGATACCAAATTGTGAAAATAA-GTCAAG
1 ATTACATACCAAATTAAGAAAAAAATGTCAAG
1950223 ATTACATACCAAATTAAGAAAAAAATGTCAAG
1 ATTACATACCAAATTAAGAAAAAAATGTCAAG
* *
1950255 -TT-CAAGTACCAAATT-AGATAAAAGTGTCA
1 ATTAC-A-TACCAAATTAAGAAAAAAATGTCA
1950284 TATTCAAGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
30 1 0.02
31 36 0.69
32 15 0.29
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (32 bp):
ATTACATACCAAATTAAGAAAAAAATGTCAAG
Found at i:1950290 original size:31 final size:32
Alignment explanation
Indices: 1950229--1950299 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
1950219 CAAGATTACA
1950229 TACCAAATTAAGAAAAAAATGTCAAGTTCAAG
1 TACCAAATTAAGAAAAAAATGTCAAGTTCAAG
* *
1950261 TACCAAATT-AGATAAAAGTGTCATA-TTCAAG
1 TACCAAATTAAGAAAAAAATGTCA-AGTTCAAG
*
1950292 TATCAAAT
1 TACCAAAT
1950300 GTTATATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 25 0.71
32 10 0.29
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27
Consensus pattern (32 bp):
TACCAAATTAAGAAAAAAATGTCAAGTTCAAG
Found at i:1958939 original size:19 final size:18
Alignment explanation
Indices: 1958896--1958943 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
1958886 GTTTTGGATT
1958896 TTAAA-TTTTAAATTTTA
1 TTAAATTTTTAAATTTTA
*
1958913 -TATGATTTTTAGAATTTTA
1 TTA-AATTTTTA-AATTTTA
1958932 TTAAATTTTTAA
1 TTAAATTTTTAA
1958944 TATATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
16 2 0.08
17 1 0.04
18 6 0.24
19 14 0.56
20 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (18 bp):
TTAAATTTTTAAATTTTA
Found at i:1967263 original size:3 final size:3
Alignment explanation
Indices: 1967255--1967298 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1967245 TTGTATTTGA
1967255 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1967299 ACGAAAAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1976101 original size:194 final size:193
Alignment explanation
Indices: 1975767--1976154 Score: 740
Period size: 194 Copynumber: 2.0 Consensus size: 193
1975757 AACTCACAAG
*
1975767 TTGGTAAGACTAATACAGTTGGTTAGTGACATCAAATCTCCGGATAAATTATTGTTTTCTATTCT
1 TTGGTAAGACTAATACAGTTGATTAGTGACATCAAATCTCCGGATAAATTATTGTTTTCTATTCT
1975832 CCTGCATTATATAGAACCAGCAGCTTATAAACAAGAGCAAATATTCTATTCTAAGTCAAGACCAT
66 CCTGCATTATATAGAACCAGCAGCTTATAAACAAGAGCAAATATTCTATTCTAAGTCAAGACCAT
1975897 ATAAGATATTTAGGCACATGAGGTGTTTTGCTAGAGCGTTAAGGTTTTGCGAAGGCCATAAAA
131 ATAAGATATTTAGGCACATGAGGTGTTTTGCTAGAGCGTTAAGGTTTTGCGAAGGCCATAAAA
*
1975960 TTGGTAAAGACTAATACAGTTGATTAGTGACATCAAATCTCCGGATGAATTATTGTTTTCTATTC
1 TTGGT-AAGACTAATACAGTTGATTAGTGACATCAAATCTCCGGATAAATTATTGTTTTCTATTC
1976025 TCCTGCATTATATAGAACCAGCAGCTTATAAACAAGAGCAAATATTCTATTCTAAGTCAAGACCA
65 TCCTGCATTATATAGAACCAGCAGCTTATAAACAAGAGCAAATATTCTATTCTAAGTCAAGACCA
*
1976090 TATAAGATATTTAGGCATATGAGGTGTTTTGCTAGAGCGTTAAGGTTTTGCGAAGGCCATAAAA
130 TATAAGATATTTAGGCACATGAGGTGTTTTGCTAGAGCGTTAAGGTTTTGCGAAGGCCATAAAA
1976154 T
1 T
1976155 GCCACCATTT
Statistics
Matches: 191, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
193 5 0.03
194 186 0.97
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (193 bp):
TTGGTAAGACTAATACAGTTGATTAGTGACATCAAATCTCCGGATAAATTATTGTTTTCTATTCT
CCTGCATTATATAGAACCAGCAGCTTATAAACAAGAGCAAATATTCTATTCTAAGTCAAGACCAT
ATAAGATATTTAGGCACATGAGGTGTTTTGCTAGAGCGTTAAGGTTTTGCGAAGGCCATAAAA
Found at i:1998626 original size:11 final size:9
Alignment explanation
Indices: 1998580--1998621 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
1998570 TTGAATCAAG
*
1998580 ATTTTTAAA
1 ATTTTTAAT
1998589 ATTTTTGAA-
1 ATTTTT-AAT
1998598 ATTTTTAAT
1 ATTTTTAAT
1998607 ATTTTTAAT
1 ATTTTTAAT
1998616 ATTTTT
1 ATTTTT
1998622 TTAATTAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 2 0.06
9 27 0.87
10 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:2006721 original size:15 final size:15
Alignment explanation
Indices: 2006701--2006731 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2006691 GCACCAACTA
*
2006701 ATAACATAGTGACAC
1 ATAACATAATGACAC
2006716 ATAACATAATGACAC
1 ATAACATAATGACAC
2006731 A
1 A
2006732 ACCTCATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (15 bp):
ATAACATAATGACAC
Found at i:2008881 original size:16 final size:18
Alignment explanation
Indices: 2008862--2008899 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2008852 TATATTATAC
2008862 AAAAACTAT-AA-AAAAT
1 AAAAACTATAAATAAAAT
*
2008878 AAAAATTATAAATAAAAT
1 AAAAACTATAAATAAAAT
2008896 AAAA
1 AAAA
2008900 TAAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 2 0.11
18 9 0.47
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAAACTATAAATAAAAT
Found at i:2008980 original size:68 final size:66
Alignment explanation
Indices: 2008840--2008998 Score: 250
Period size: 66 Copynumber: 2.4 Consensus size: 66
2008830 TTATGTATAA
* *
2008840 AATATTTATTTTTATATTATACAAAAACTATAAAAAATAAAAATTATAAATAAAATAAAATAAAA
1 AATATTTATTTTTATATTATACAAAAACCATAAAAAATAAAAATTAAAAATAAAATAAAATAAAA
2008905 T
66 T
2008906 AATATTTATTTTTATATTATACAAAAACCATAAAAAAATAAAAA-TAAAAATTATAAATAAAATA
1 AATATTTATTTTTATATTATACAAAAACCAT-AAAAAATAAAAATTAAAAA-TA-AAATAAAATA
2008970 AAAT
63 AAAT
*
2008974 AATATTTATTTTTATACTATA-AAAA
1 AATATTTATTTTTATATTATACAAAA
2008999 TCAAATTTAA
Statistics
Matches: 87, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
66 35 0.40
67 18 0.21
68 34 0.39
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (66 bp):
AATATTTATTTTTATATTATACAAAAACCATAAAAAATAAAAATTAAAAATAAAATAAAATAAAA
T
Found at i:2009013 original size:73 final size:67
Alignment explanation
Indices: 2008840--2008998 Score: 223
Period size: 68 Copynumber: 2.4 Consensus size: 67
2008830 TTATGTATAA
* * * *
2008840 AATATTTATTTTTATATTATACAAAAACTAT-AAAAAATAAAAATTATAAATAAAATAAAATAAA
1 AATATTTATTTTTATACTATAAAAAAACAATAAAAAAATAAAAATTAAAAATAAAATAAAATAAA
2008904 AT
66 AT
* * *
2008906 AATATTTATTTTTATATTATACAAAAACCATAAAAAAATAAAAA-TAAAAATTATAAATAAAATA
1 AATATTTATTTTTATACTATAAAAAAACAATAAAAAAATAAAAATTAAAAA-TA-AAATAAAATA
2008970 AAAT
64 AAAT
2008974 AATATTTATTTTTATACTATAAAAA
1 AATATTTATTTTTATACTATAAAAA
2008999 TCAAATTTAA
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
66 35 0.41
67 14 0.16
68 37 0.43
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (67 bp):
AATATTTATTTTTATACTATAAAAAAACAATAAAAAAATAAAAATTAAAAATAAAATAAAATAAA
AT
Found at i:2013484 original size:5 final size:6
Alignment explanation
Indices: 2013469--2013493 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2013459 CGAAGCTTGA
2013469 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
2013494 GACCGGCGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:2015268 original size:16 final size:16
Alignment explanation
Indices: 2015235--2015268 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2015225 AGTAAATGTT
* *
2015235 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
2015251 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
2015267 AA
1 AA
2015269 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:2018094 original size:21 final size:21
Alignment explanation
Indices: 2018068--2018108 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2018058 AGACGAGCAA
* *
2018068 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2018089 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2018109 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:2028266 original size:21 final size:21
Alignment explanation
Indices: 2028240--2028299 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
2028230 ATATTTGATG
2028240 ATAGAACTTTGGAAGATACAA
1 ATAGAACTTTGGAAGATACAA
2028261 ATAGAA-----GAAGATACAA
1 ATAGAACTTTGGAAGATACAA
2028277 ATAGAACTTTGGAAGATACAA
1 ATAGAACTTTGGAAGATACAA
2028298 AT
1 AT
2028300 GGAAGTATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 16 0.47
21 18 0.53
ACGTcount: A:0.52, C:0.08, G:0.18, T:0.22
Consensus pattern (21 bp):
ATAGAACTTTGGAAGATACAA
Found at i:2028272 original size:16 final size:16
Alignment explanation
Indices: 2028251--2028282 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2028241 TAGAACTTTG
2028251 GAAGATACAAATAGAA
1 GAAGATACAAATAGAA
2028267 GAAGATACAAATAGAA
1 GAAGATACAAATAGAA
2028283 CTTTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.19, T:0.12
Consensus pattern (16 bp):
GAAGATACAAATAGAA
Found at i:2031815 original size:91 final size:91
Alignment explanation
Indices: 2031677--2031884 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
2031667 TTGATTTTAG
* *
2031677 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
2031742 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
2031769 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
2031834 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
2031860 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
2031885 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:2031853 original size:26 final size:28
Alignment explanation
Indices: 2031799--2031859 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
2031789 TATTATCAAG
* *
2031799 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
2031827 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
2031853 AATTATA
1 AATTATA
2031860 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:2031859 original size:44 final size:43
Alignment explanation
Indices: 2031717--2031859 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
2031707 GAATTTTATG
* *
2031717 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
2031761 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
2031808 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
2031852 AAATTATA
1 AAATTATA
2031860 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:2031977 original size:59 final size:57
Alignment explanation
Indices: 2031911--2032099 Score: 152
Period size: 59 Copynumber: 3.2 Consensus size: 57
2031901 ATTTTATTAA
2031911 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGT
* * ** * *
2031970 ATCATATATTATGATTTTAGTAAATTCATATAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTA-ATTA--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATTTTTATAGT
* * * *
2032031 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
2032090 ATCATATATT
1 ATCATATATT
2032100 ATGATTTGAG
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
59 22 0.22
60 4 0.04
61 12 0.12
63 4 0.04
64 5 0.05
65 6 0.06
66 17 0.17
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGT
Found at i:2032008 original size:66 final size:64
Alignment explanation
Indices: 2031938--2032136 Score: 177
Period size: 66 Copynumber: 3.2 Consensus size: 64
2031928 AAATATATTT
2031938 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAA
2032003 G
64 G
* * * * * **
2032004 AATATTAATTATTAAGAATT-TTATTA-A--ATTATATATT-TTA-ATTA-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTATTTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAAG
* * *
2032058 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAA
2032123 G
64 G
*
2032124 AATATTGATTATT
1 AATATTAATTATT
2032137 AAGAATTTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 29
0.68 0.13 0.20
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 12 0.12
60 4 0.04
61 11 0.11
62 1 0.01
63 3 0.03
64 5 0.05
65 7 0.07
66 27 0.27
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (64 bp):
AATATTAATTATTTAAATTATTTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAAG
Found at i:2032024 original size:120 final size:120
Alignment explanation
Indices: 2031900--2032197 Score: 508
Period size: 120 Copynumber: 2.5 Consensus size: 120
2031890 AATTATTTTA
* * *
2031900 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
*
2031964 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
2032020 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
*
2032085 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
2032140 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
2032198 ATGATTAAAT
Statistics
Matches: 167, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
120 160 0.96
121 7 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:2032040 original size:61 final size:61
Alignment explanation
Indices: 2031973--2032160 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
2031963 TTATAGTATC
2031973 ATATATTATGATTTTAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTTAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * * * *
2032034 ATATATTTTAATTATAATATATTTA-ATAATAATTATGTTAA-T-TT-A-TATTTTA-TAGTATC
1 ATATATTATGATTTTAGTAAATTCATATAAGAA-TA--TTAATTATTAAGAATTTTATTA-AATT
* *
2032093 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTTAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
2032154 ATATATT
1 ATATATT
2032161 TTAATTAAAA
Statistics
Matches: 95, Mismatches: 22, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
57 3 0.03
58 3 0.03
59 30 0.32
60 14 0.15
61 38 0.40
62 3 0.03
63 4 0.04
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTTAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:2032060 original size:15 final size:15
Alignment explanation
Indices: 2032025--2032076 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
2032015 TTAAGAATTT
*
2032025 TATTAAATTAT-ATA
1 TATTTAATTATAATA
2032039 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
2032053 TATTTAATAATAAT-
1 TATTTAATTATAATA
2032067 TATGTTAATT
1 TAT-TTAATT
2032077 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:2032157 original size:59 final size:58
Alignment explanation
Indices: 2031974--2032157 Score: 155
Period size: 59 Copynumber: 3.1 Consensus size: 58
2031964 TATAGTATCA
*
2031974 TATATTATGATTTTAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TATATTATGATTTAAGTAAATTCATATAAGAATATT-ATTATTAAGAATTTTATTAAAT
* * * * * *
2032033 TATA-TAT--TTTAATTATAATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 TATATTATGATTTAAGTA-AAT-TCATATAAGAAT-ATTA--TT-ATTAAGAATTTTATTA-AAT
*
2032092 CATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTAAGTAAATTCATATAAGAATATT-ATTATTAAGAATTTTATTAAAT
2032153 TATAT
1 TATAT
2032158 ATTTTAATTA
Statistics
Matches: 95, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
56 6 0.06
57 12 0.13
58 9 0.09
59 19 0.20
60 8 0.08
61 14 0.15
62 9 0.09
63 12 0.13
64 6 0.06
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (58 bp):
TATATTATGATTTAAGTAAATTCATATAAGAATATTATTATTAAGAATTTTATTAAAT
Found at i:2032169 original size:18 final size:17
Alignment explanation
Indices: 2032141--2032175 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2032131 ATTATTAAGA
*
2032141 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
2032158 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
2032176 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:2032423 original size:45 final size:44
Alignment explanation
Indices: 2032340--2032430 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
2032330 ACCTCTATTC
* *
2032340 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACATCTATTCCATTA
*** *
2032384 CATTCAACCAAACAGTTGATTTGCTATTACACATCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACATCTATTCCATTA
2032429 CA
1 CA
2032431 CCTCTATTCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACATCTATTCCATTA
Found at i:2032430 original size:16 final size:16
Alignment explanation
Indices: 2032409--2032468 Score: 93
Period size: 16 Copynumber: 3.8 Consensus size: 16
2032399 TTGATTTGCT
*
2032409 ATTACACATCTATTCC
1 ATTACACCTCTATTCC
2032425 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
2032441 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
*
2032457 AATACACCTCTA
1 ATTACACCTCTA
2032469 ATTCAATACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:2032469 original size:16 final size:16
Alignment explanation
Indices: 2032411--2032478 Score: 82
Period size: 16 Copynumber: 4.2 Consensus size: 16
2032401 GATTTGCTAT
* * *
2032411 TACACATCTATTCCAT
1 TACACCTCTAATCCAA
* *
2032427 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
2032443 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
2032459 TACACCTCTAATTCAA
1 TACACCTCTAATCCAA
2032475 TACA
1 TACA
2032479 GTGAACCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:2045105 original size:24 final size:23
Alignment explanation
Indices: 2045078--2045130 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 23
2045068 ATTTTTAGAA
2045078 TTTAAAAAATTCAAAAAATTATTT
1 TTTAAAAAATT-AAAAAATTATTT
*
2045102 TTTAAAAAAATTATAAAATTATTT
1 TTT-AAAAAATTAAAAAATTATTT
2045126 TTTAA
1 TTTAA
2045131 TTTAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 2 0.07
24 17 0.63
25 8 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAAAAATTAAAAAATTATTT
Found at i:2046060 original size:24 final size:24
Alignment explanation
Indices: 2045995--2046048 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2045985 TCTTTCTAGA
* * *
2045995 ATATTTAGTATTTATGAGTATAAT
1 ATATTTAGCATTTATTAGCATAAT
2046019 ATATTTAGCATTTATTAGCATAAT
1 ATATTTAGCATTTATTAGCATAAT
2046043 ATATTT
1 ATATTT
2046049 GACTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (24 bp):
ATATTTAGCATTTATTAGCATAAT
Found at i:2048930 original size:35 final size:35
Alignment explanation
Indices: 2048890--2048963 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
2048880 TTTAATAAAA
2048890 TAAACCATATAAAATAAAAATTTTAAAGTCCAAAC
1 TAAACCATATAAAATAAAAATTTTAAAGTCCAAAC
*
2048925 TAAACCATATAAAATAAAAATTTTAAAGTCCAAAT
1 TAAACCATATAAAATAAAAATTTTAAAGTCCAAAC
2048960 TAAA
1 TAAA
2048964 AGCAGTCCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.27
Consensus pattern (35 bp):
TAAACCATATAAAATAAAAATTTTAAAGTCCAAAC
Found at i:2050659 original size:19 final size:19
Alignment explanation
Indices: 2050607--2050662 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
2050597 TTAATTTTTT
*
2050607 AAAATT-TTAAAAATGTCAA
1 AAAATTATTAAAAATAT-AA
*
2050626 AAAA-TA--AAAATTATAA
1 AAAATTATTAAAAATATAA
2050642 AAAATTATTAAAAATATAA
1 AAAATTATTAAAAATATAA
2050661 AA
1 AA
2050663 TAATATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
16 6 0.20
17 8 0.27
18 1 0.03
19 15 0.50
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATTATTAAAAATATAA
Found at i:2051119 original size:16 final size:18
Alignment explanation
Indices: 2051098--2051137 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2051088 TTTTTTAATT
2051098 TAAAAA-TATCAAAAA-A
1 TAAAAATTATCAAAAATA
*
2051114 TAAAAATTATTAAAAATA
1 TAAAAATTATCAAAAATA
2051132 TAAAAA
1 TAAAAA
2051138 ATATTATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 8 0.38
18 7 0.33
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAAAATTATCAAAAATA
Found at i:2051128 original size:9 final size:9
Alignment explanation
Indices: 2051097--2051143 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
2051087 ATTTTTTAAT
2051097 TTAAAAATA
1 TTAAAAATA
*
2051106 TCAAAAA-A
1 TTAAAAATA
2051114 -TAAAAATTA
1 TTAAAAA-TA
2051123 TTAAAAATA
1 TTAAAAATA
*
2051132 TAAAAAATA
1 TTAAAAATA
2051141 TTA
1 TTA
2051144 TTTGCTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
7 5 0.16
8 1 0.03
9 19 0.61
10 6 0.19
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (9 bp):
TTAAAAATA
Found at i:2051134 original size:18 final size:16
Alignment explanation
Indices: 2051098--2051143 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
2051088 TTTTTTAATT
*
2051098 TAAAAATATCAAAAAA
1 TAAAAATATTAAAAAA
2051114 TAAAAATTATTAAAAATA
1 TAAAAA-TATTAAAAA-A
2051132 TAAAAAATATTA
1 T-AAAAATATTA
2051144 TTTGCTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 6 0.23
17 8 0.31
18 7 0.27
19 5 0.19
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAAAATATTAAAAAA
Found at i:2053089 original size:17 final size:17
Alignment explanation
Indices: 2053069--2053107 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2053059 TTTAAAACAC
*
2053069 TAAAAATTGT-AAATTTT
1 TAAAAATT-TAAAATTAT
2053086 TAAAAATTTAAAATTAT
1 TAAAAATTTAAAATTAT
2053103 TAAAA
1 TAAAA
2053108 TAAAAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TAAAAATTTAAAATTAT
Found at i:2053108 original size:16 final size:16
Alignment explanation
Indices: 2053069--2053131 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
2053059 TTTAAAACAC
* *
2053069 TAAAAATTGTAAATTTT
1 TAAAAATT-TAAAATTA
2053086 TAAAAATTTAAAATTA
1 TAAAAATTTAAAATTA
* ** *
2053102 TTAAAATAAAAAATTG
1 TAAAAATTTAAAATTA
2053118 TAAAAATATTAAAA
1 TAAAAAT-TTAAAA
2053132 AAGTGTTCTC
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
16 24 0.67
17 12 0.33
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
TAAAAATTTAAAATTA
Found at i:2053383 original size:39 final size:40
Alignment explanation
Indices: 2053340--2053416 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 40
2053330 AAAGTTGTTG
* *
2053340 AAAAATTATAAAAATGTAAAAAG-TATTAAAAATATATTT
1 AAAAATTATAAAAATATAAAAAGTTATAAAAAATATATTT
* * *
2053379 AAAAATTGTAAAATTATTAAAAGTTATAAAAAATATAT
1 AAAAATTATAAAAATATAAAAAGTTATAAAAAATATAT
2053417 AATTTTTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
39 19 0.59
40 13 0.41
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (40 bp):
AAAAATTATAAAAATATAAAAAGTTATAAAAAATATATTT
Found at i:2053577 original size:11 final size:10
Alignment explanation
Indices: 2053561--2053616 Score: 53
Period size: 11 Copynumber: 5.5 Consensus size: 10
2053551 AAAAAAAATC
2053561 ATTTTTAGTAA
1 ATTTTTA-TAA
*
2053572 ATTTTTACAA
1 ATTTTTATAA
2053582 ATTTTTAATAA
1 ATTTTT-ATAA
*
2053593 A-TTTTA-CA
1 ATTTTTATAA
2053601 ATTTTCTATAA
1 ATTTT-TATAA
2053612 ATTTT
1 ATTTT
2053617 AATATATGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 2 0.05
9 4 0.11
10 14 0.38
11 17 0.46
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (10 bp):
ATTTTTATAA
Found at i:2053605 original size:19 final size:20
Alignment explanation
Indices: 2053561--2053617 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
2053551 AAAAAAAATC
*
2053561 ATTTTTAGTAAATTTTTACAA
1 ATTTTTAATAAA-TTTTACAA
2053582 ATTTTTAATAAATTTTAC-A
1 ATTTTTAATAAATTTTACAA
2053601 ATTTTCT-ATAAATTTTA
1 ATTTT-TAATAAATTTTA
2053618 ATATATGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 16 0.47
20 7 0.21
21 11 0.32
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTTTTAATAAATTTTACAA
Found at i:2053811 original size:20 final size:17
Alignment explanation
Indices: 2053784--2053841 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 17
2053774 TTGGTATTAC
2053784 TTAGAAATTTGGATATCA
1 TTAGAAATTT-GATATCA
2053802 TGTGAGAAATATTGATATTCA
1 T-T-AGAAAT-TTGATA-TCA
*
2053823 TTATAAATTTTGATATCA
1 TTAGAAA-TTTGATATCA
2053841 T
1 T
2053842 ATTAGAAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
18 5 0.15
19 11 0.32
20 12 0.35
21 6 0.18
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (17 bp):
TTAGAAATTTGATATCA
Found at i:2053835 original size:19 final size:19
Alignment explanation
Indices: 2053764--2053838 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
2053754 TTTTGTATGT
* *
2053764 ATTAAAAATTTTGGTATT-
1 ATTAGAAATTTTGATATTC
*
2053782 ACTTAGAAATTTGGATA-TC
1 A-TTAGAAATTTTGATATTC
*
2053801 ATGTGAGAAATATTGATATTC
1 AT-T-AGAAATTTTGATATTC
*
2053822 ATTATAAATTTTGATAT
1 ATTAGAAATTTTGATAT
2053839 CATATTAGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.07
19 26 0.58
20 12 0.27
21 4 0.09
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.44
Consensus pattern (19 bp):
ATTAGAAATTTTGATATTC
Found at i:2055084 original size:5 final size:5
Alignment explanation
Indices: 2055074--2055098 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2055064 GTATATCCAT
2055074 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
2055099 TATTGGTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:2055214 original size:6 final size:6
Alignment explanation
Indices: 2055203--2055229 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2055193 TTTAGTAAAT
2055203 TATTTA TATTTA TATTTA TATTTA TAT
1 TATTTA TATTTA TATTTA TATTTA TAT
2055230 AAAGTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:2058850 original size:23 final size:23
Alignment explanation
Indices: 2058784--2058869 Score: 67
Period size: 23 Copynumber: 4.0 Consensus size: 23
2058774 CCTGATCAGT
*
2058784 ATACAACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
* *
2058805 A-ACGACATA-AGAAGTG-CT-TG
1 ATACGACACATA-AAGTGCCTGAG
* *
2058825 ATATGACCCATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
*
2058848 ATACGGCACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
2058870 TAGGCAAAGC
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
20 9 0.19
21 16 0.33
22 3 0.06
23 20 0.42
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:2059985 original size:22 final size:21
Alignment explanation
Indices: 2059960--2060009 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
2059950 CTTCCCCTGT
2059960 TTTCGTCTCTT-TCTCTGTTTC
1 TTTCGTCTCTTCTCT-TGTTTC
2059981 GTTTCTGT-TCTTCTCTTGTTTC
1 -TTTC-GTCTCTTCTCTTGTTTC
2060003 TTT-GTCT
1 TTTCGTCT
2060010 TTTTATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
19 2 0.08
20 1 0.04
21 3 0.12
22 14 0.56
23 5 0.20
ACGTcount: A:0.00, C:0.24, G:0.12, T:0.64
Consensus pattern (21 bp):
TTTCGTCTCTTCTCTTGTTTC
Found at i:2060197 original size:5 final size:5
Alignment explanation
Indices: 2060189--2060247 Score: 64
Period size: 5 Copynumber: 11.6 Consensus size: 5
2060179 TTATTTTATT
* * * * *
2060189 TAATA TAATA TAATA TATTA TATTA TATTA TATTA TAAAA TAATA TATATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA-ATA
2060240 TAATA TAA
1 TAATA TAA
2060248 AAATCTAAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
5 44 0.90
6 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (5 bp):
TAATA
Found at i:2060215 original size:15 final size:15
Alignment explanation
Indices: 2060192--2060247 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
2060182 TTTTATTTAA
2060192 TATAATATAATATAT
1 TATAATATAATATAT
* *
2060207 TATATTATATTATAT
1 TATAATATAATATAT
*
2060222 TATAAAATAATATAT
1 TATAATATAATATAT
2060237 ATATAATATAA
1 -TATAATATAA
2060248 AAATCTAAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
15 25 0.74
16 9 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TATAATATAATATAT
Found at i:2066743 original size:25 final size:26
Alignment explanation
Indices: 2066694--2066753 Score: 95
Period size: 25 Copynumber: 2.3 Consensus size: 26
2066684 AAAAAATAAC
2066694 CAAAATATTATAACTTTTTTTATTTAT
1 CAAAATATTATAAC-TTTTTTATTTAT
2066721 CAAAATATTATAA-TTTTTTATTTAT
1 CAAAATATTATAACTTTTTTATTTAT
*
2066746 TAAAATAT
1 CAAAATAT
2066754 ACCAAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 19 0.59
27 13 0.41
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (26 bp):
CAAAATATTATAACTTTTTTATTTAT
Found at i:2067395 original size:23 final size:23
Alignment explanation
Indices: 2067369--2067440 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
2067359 ACTCTATTTT
2067369 AATTTAATAAACTATTCTCATCA
1 AATTTAATAAACTATTCTCATCA
* * * **
2067392 AA-TTACTTAAA-AACTCT-ATTTT
1 AATTTA-ATAAACTATTCTCA-TCA
2067414 AATTTAATAAACTATTCTCATCA
1 AATTTAATAAACTATTCTCATCA
2067437 AATT
1 AATT
2067441 ACCAAAATAG
Statistics
Matches: 34, Mismatches: 10, Indels: 10
0.63 0.19 0.19
Matches are distributed among these distances:
21 1 0.03
22 14 0.41
23 18 0.53
24 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.42
Consensus pattern (23 bp):
AATTTAATAAACTATTCTCATCA
Found at i:2067468 original size:15 final size:15
Alignment explanation
Indices: 2067448--2067497 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
2067438 ATTACCAAAA
2067448 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
2067463 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
*
2067478 GAGAATAGTTTATTAAAT
1 TAG---AGTTTATTAAAT
2067496 TA
1 TA
2067498 AAATAGAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 17 0.57
18 13 0.43
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (15 bp):
TAGAGTTTATTAAAT
Found at i:2067502 original size:18 final size:18
Alignment explanation
Indices: 2067466--2067503 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2067456 ATTAAATTAG
*
2067466 AGTTTATTAAATGAGAAT
1 AGTTTATTAAATGAAAAT
*
2067484 AGTTTATTAAATTAAAAT
1 AGTTTATTAAATGAAAAT
2067502 AG
1 AG
2067504 AGTTATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (18 bp):
AGTTTATTAAATGAAAAT
Found at i:2072046 original size:42 final size:42
Alignment explanation
Indices: 2071980--2072060 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
2071970 TATTTATCCA
* *
2071980 ATGATGCACTTACATATCAGTATATTTTCTTCAGTATATCGT
1 ATGATGCACTTACATACCAGTATATTTGCTTCAGTATATCGT
* * *
2072022 ATGATGCACTTACATGCCATTATATTTGCTTCGGTATAT
1 ATGATGCACTTACATACCAGTATATTTGCTTCAGTATAT
2072061 ACTGGCATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (42 bp):
ATGATGCACTTACATACCAGTATATTTGCTTCAGTATATCGT
Found at i:2072978 original size:21 final size:21
Alignment explanation
Indices: 2072954--2072999 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2072944 GTTTTAATAT
*
2072954 TAAAATCT-AATTTTGAAAAAA
1 TAAAATCTCAAATTTG-AAAAA
2072975 TAAAATCTCAAATTTGAAAAA
1 TAAAATCTCAAATTTGAAAAA
2072996 TAAA
1 TAAA
2073000 TTTGGGTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (21 bp):
TAAAATCTCAAATTTGAAAAA
Found at i:2077327 original size:20 final size:20
Alignment explanation
Indices: 2077302--2077349 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2077292 ATTTTCTCTT
2077302 TTCATCAAGAATATCAATAA
1 TTCATCAAGAATATCAATAA
* *
2077322 TTCATCATGAATATCAATAC
1 TTCATCAAGAATATCAATAA
2077342 TTCATCAA
1 TTCATCAA
2077350 TTATCATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (20 bp):
TTCATCAAGAATATCAATAA
Found at i:2080412 original size:24 final size:24
Alignment explanation
Indices: 2080351--2080429 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
2080341 CTGATTTTAT
*
2080351 TTTTTTG-ATTGCTTCTTTCTTTTATC
1 TTTTTTGTATTGC--CTTT-TTTTTTC
*
2080377 TGTTTTTCTATTGCCTTTTTTTTTC
1 T-TTTTTGTATTGCCTTTTTTTTTC
**
2080402 TTTTTTGTATT-ATTTTTTTCTTTC
1 TTTTTTGTATTGCCTTTTTT-TTTC
2080426 TTTT
1 TTTT
2080430 CGAAAAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
23 6 0.13
24 17 0.38
25 7 0.16
26 5 0.11
27 5 0.11
28 5 0.11
ACGTcount: A:0.06, C:0.13, G:0.06, T:0.75
Consensus pattern (24 bp):
TTTTTTGTATTGCCTTTTTTTTTC
Found at i:2080779 original size:31 final size:32
Alignment explanation
Indices: 2080743--2080803 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
2080733 TGGACGGTTG
*
2080743 TTTATTATTTATTATTTT-TATTTTGGTTTTA
1 TTTATTATTTATTATTTTGTATTTGGGTTTTA
*
2080774 TTTATTATTTATTTTTTTGTATTTGGGTTT
1 TTTATTATTTATTATTTTGTATTTGGGTTT
2080804 CTGTTTGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.74
Consensus pattern (32 bp):
TTTATTATTTATTATTTTGTATTTGGGTTTTA
Found at i:2081132 original size:88 final size:89
Alignment explanation
Indices: 2081011--2081182 Score: 251
Period size: 88 Copynumber: 1.9 Consensus size: 89
2081001 CTGTGTTTTG
* * *
2081011 TTTTTTTGTACTCATATGGGTACTTGAACTTTCAAAATGCAT-AAAAAAGCCTTCAAACTTTTTC
1 TTTTTTTGCACTCATATGGGTACTTGAACTTTCAAAATGCATCAAAAAAACCCTCAAACTTTTTC
2081075 -AAAAAAGCAATTAAGCCCTACTT
66 AAAAAAAGCAATTAAGCCCTACTT
* *
2081098 TTTTTTCTGCACTCA-ATTGGGTACTTGAATTTTCAAAATGCATCAAAAAAACCCTCAAATTTTT
1 TTTTTT-TGCACTCATA-TGGGTACTTGAACTTTCAAAATGCATCAAAAAAACCCTCAAACTTTT
*
2081162 TCAAAAAAAGTAATTAAGCCC
64 TCAAAAAAAGCAATTAAGCCC
2081183 CTGCTTTTAT
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
87 7 0.09
88 32 0.43
89 19 0.25
90 17 0.23
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (89 bp):
TTTTTTTGCACTCATATGGGTACTTGAACTTTCAAAATGCATCAAAAAAACCCTCAAACTTTTTC
AAAAAAAGCAATTAAGCCCTACTT
Found at i:2081217 original size:11 final size:10
Alignment explanation
Indices: 2081189--2081355 Score: 73
Period size: 10 Copynumber: 16.8 Consensus size: 10
2081179 GCCCCTGCTT
*
2081189 TTATTAAAAA
1 TTATAAAAAA
2081199 TTATAAAAAA
1 TTATAAAAAA
2081209 TTATAAAAAA
1 TTATAAAAAA
2081219 TT-TAAAATAA
1 TTATAAAA-AA
*
2081229 --AT-AAAAT
1 TTATAAAAAA
* *
2081236 TTAT-ATATA
1 TTATAAAAAA
* **
2081245 TTATTAAATT
1 TTATAAAAAA
2081255 TTAATAAAAAA
1 TT-ATAAAAAA
*
2081266 TTCAAATATTAAAATT
1 TT---ATA--AAAA-A
*
2081282 TTATTAAAAA
1 TTATAAAAAA
2081292 TTA-AAAAAA
1 TTATAAAAAA
*
2081301 TTGTAAAAAA
1 TTATAAAAAA
2081311 -TAT-AAAAA
1 TTATAAAAAA
* **
2081319 TTGTAAAATT
1 TTATAAAAAA
2081329 TTAT-AAAAA
1 TTATAAAAAA
*
2081338 TTGTAAAAAA
1 TTATAAAAAA
2081348 TTATAAAA
1 TTATAAAA
2081356 TATATAGAAA
Statistics
Matches: 118, Mismatches: 24, Indels: 30
0.69 0.14 0.17
Matches are distributed among these distances:
7 1 0.01
8 8 0.07
9 31 0.26
10 55 0.47
11 11 0.09
13 6 0.05
15 4 0.03
16 2 0.02
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:2081217 original size:19 final size:19
Alignment explanation
Indices: 2081189--2081355 Score: 87
Period size: 19 Copynumber: 8.9 Consensus size: 19
2081179 GCCCCTGCTT
*
2081189 TTATTAAAAATTATAAAAAA
1 TTATAAAAAATTAT-AAAAA
2081209 TTATAAAAAATT-T-AAAA
1 TTATAAAAAATTATAAAAA
* *
2081226 -TA-AATAAAATTTATATATA
1 TTATAA-AAAA-TTATAAAAA
* **
2081245 TTATTAAATTTTAATAAAAA
1 TTATAAAAAATT-ATAAAAA
* * * **
2081265 AT-TCAAATATTA-AAATT
1 TTATAAAAAATTATAAAAA
* *
2081282 TTATTAAAAATTAAAAAAA
1 TTATAAAAAATTATAAAAA
*
2081301 TTGTAAAAAA-TATAAAAA
1 TTATAAAAAATTATAAAAA
* **
2081319 TTGTAAAATTTTATAAAAA
1 TTATAAAAAATTATAAAAA
*
2081338 TTGTAAAAAATTATAAAA
1 TTATAAAAAATTATAAAA
2081356 TATATAGAAA
Statistics
Matches: 112, Mismatches: 25, Indels: 21
0.71 0.16 0.13
Matches are distributed among these distances:
15 2 0.02
16 6 0.05
17 10 0.09
18 25 0.22
19 47 0.42
20 21 0.19
21 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (19 bp):
TTATAAAAAATTATAAAAA
Found at i:2081239 original size:47 final size:47
Alignment explanation
Indices: 2081188--2081355 Score: 150
Period size: 46 Copynumber: 3.6 Consensus size: 47
2081178 AGCCCCTGCT
2081188 TTTATTAAAAATTATAAAAAATTATAAAAAATTTAAAATAAATAAAA
1 TTTATTAAAAATTATAAAAAATTATAAAAAATTTAAAATAAATAAAA
* * * ** * *
2081235 TTTA-TATATATTATTAAATTTTAATAAAAAA-TTCAAAT-ATTAAAA
1 TTTATTAAAAATTATAAAAAATT-ATAAAAAATTTAAAATAAATAAAA
* * **
2081280 TTTTATTAAAAATTA-AAAAAATTGTAAAAAATATAAAA-ATTGTAAAA
1 -TTTATTAAAAATTATAAAAAATTATAAAAAATTTAAAATA-AATAAAA
*
2081327 TTT-TATAAAAATTGTAAAAAATTATAAAA
1 TTTAT-TAAAAATTATAAAAAATTATAAAA
2081356 TATATAGAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
45 14 0.15
46 43 0.46
47 37 0.39
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.38
Consensus pattern (47 bp):
TTTATTAAAAATTATAAAAAATTATAAAAAATTTAAAATAAATAAAA
Done.