Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000737.1 Hibiscus syriacus cultivar Beakdansim tig00001427_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: 278038
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:164656 original size:19 final size:19
Alignment explanation
Indices: 164634--164708 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
164624 TCGGGTCGGG
164634 TCAGACCGGTCAAACCGGC
1 TCAGACCGGTCAAACCGGC
164653 TCAGACCGGTCAAACCGGC
1 TCAGACCGGTCAAACCGGC
*
164672 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGC
* *
164691 TGAAACCGGTCAAACCGG
1 TCAGACCGGTCAAACCGG
164709 TTAAACCGGT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.28, C:0.33, G:0.27, T:0.12
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGC
Found at i:164709 original size:19 final size:19
Alignment explanation
Indices: 164638--164718 Score: 110
Period size: 19 Copynumber: 4.3 Consensus size: 19
164628 GTCGGGTCAG
*
164638 ACCGGTCAAACCGGCTCAG
1 ACCGGTCAAACCGGCTCAA
*
164657 ACCGGTCAAACCGGCTCAG
1 ACCGGTCAAACCGGCTCAA
* *
164676 ACCGGTCAAACCGGTTGAA
1 ACCGGTCAAACCGGCTCAA
*
164695 ACCGGTCAAACCGG-TTAA
1 ACCGGTCAAACCGGCTCAA
164713 ACCGGT
1 ACCGGT
164719 TTCCAGCAGC
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
18 9 0.16
19 49 0.84
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (19 bp):
ACCGGTCAAACCGGCTCAA
Found at i:164709 original size:28 final size:28
Alignment explanation
Indices: 164638--164719 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 28
164628 GTCGGGTCAG
*
164638 ACCGGTCAAACCGGCTCAGACCGG-TCAA
1 ACCGGTCAAACCGG-TCAAACCGGTTCAA
* *
164666 ACCGGCTCAGACCGGTCAAACCGGTTGAA
1 ACCGG-TCAAACCGGTCAAACCGGTTCAA
*
164695 ACCGGTCAAACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTCAAACCGGTT
164720 TCCAGCAGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
28 31 0.66
29 16 0.34
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.15
Consensus pattern (28 bp):
ACCGGTCAAACCGGTCAAACCGGTTCAA
Found at i:164719 original size:9 final size:9
Alignment explanation
Indices: 164632--164718 Score: 102
Period size: 9 Copynumber: 9.3 Consensus size: 9
164622 GGTCGGGTCG
*
164632 GGTCAGACC
1 GGTCAAACC
164641 GGTCAAACC
1 GGTCAAACC
*
164650 GGCTCAGACC
1 GG-TCAAACC
164660 GGTCAAACC
1 GGTCAAACC
*
164669 GGCTCAGACC
1 GG-TCAAACC
164679 GGTCAAACC
1 GGTCAAACC
*
164688 GGTTGAAACC
1 GG-TCAAACC
164698 GGTCAAACC
1 GGTCAAACC
*
164707 GGTTAAACC
1 GGTCAAACC
164716 GGT
1 GGT
164719 TTCCAGCAGC
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
9 43 0.64
10 24 0.36
ACGTcount: A:0.28, C:0.31, G:0.28, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:166502 original size:18 final size:18
Alignment explanation
Indices: 166436--166494 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
166426 TTCATTTAGG
166436 GGGGAATCGATACCCCCA
1 GGGGAATCGATACCCCCA
*
166454 GGGGAATCTG-T--TCCC-
1 GGGGAATC-GATACCCCCA
166469 GGGGAATCGATACCCCCA
1 GGGGAATCGATACCCCCA
166487 GGGGAATC
1 GGGGAATC
166495 TGTACCCCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 1 0.03
15 9 0.26
16 3 0.09
17 3 0.09
18 17 0.50
19 1 0.03
ACGTcount: A:0.24, C:0.29, G:0.32, T:0.15
Consensus pattern (18 bp):
GGGGAATCGATACCCCCA
Found at i:169569 original size:31 final size:31
Alignment explanation
Indices: 169543--169747 Score: 356
Period size: 31 Copynumber: 6.6 Consensus size: 31
169533 TCCATAGATT
* *
169543 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
169574 CCGAAGAACATAGGTAAACAGTCTATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
169605 CCGAAGAATATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
169636 CCGAAGAACATAGGTAAACAGCCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
169667 CCGAATAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
169698 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
169729 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
169748 CCTCGACCCT
Statistics
Matches: 164, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 164 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:170723 original size:19 final size:19
Alignment explanation
Indices: 170699--170768 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 19
170689 TTCATTTAAG
170699 GGGGAATC-GATACCCCCCA
1 GGGGAATCTG-TACCCCCCA
* *
170718 GGGGAATCTGT---TCTC-
1 GGGGAATCTGTACCCCCCA
170733 GGGGAATC-GATACCCCCCA
1 GGGGAATCTG-TACCCCCCA
170752 GGGGAATCTGTACCCCC
1 GGGGAATCTGTACCCCC
170769 TGGACATTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
14 1 0.03
15 9 0.22
16 2 0.05
18 2 0.05
19 24 0.60
20 2 0.05
ACGTcount: A:0.21, C:0.33, G:0.29, T:0.17
Consensus pattern (19 bp):
GGGGAATCTGTACCCCCCA
Found at i:172981 original size:2 final size:2
Alignment explanation
Indices: 172974--173019 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
172964 AATTAATGTA
172974 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
173016 AT AT
1 AT AT
173020 CATTTCTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:181469 original size:23 final size:21
Alignment explanation
Indices: 181382--181491 Score: 91
Period size: 23 Copynumber: 5.0 Consensus size: 21
181372 ACAGCTTGTA
*
181382 ATTTGCACCGAAGTGCCACAT
1 ATTTGCACCGAAGTACCACAT
* *
181403 AATTGTC-CCGAA-TGACCACAAA
1 ATTTG-CACCGAAGT-ACCAC-AT
*
181425 AGTTTGCACCGAAGTGCCACAT
1 A-TTTGCACCGAAGTACCACAT
181447 AGGTTTGCACCGAAGTACCACAT
1 A--TTTGCACCGAAGTACCACAT
*
181470 ATTTGTC-CCGAAGGACCACAT
1 ATTTG-CACCGAAGTACCACAT
181491 A
1 A
181492 AAACCCTCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 16
0.75 0.08 0.16
Matches are distributed among these distances:
20 1 0.01
21 31 0.42
22 7 0.10
23 33 0.45
24 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (21 bp):
ATTTGCACCGAAGTACCACAT
Found at i:182077 original size:19 final size:20
Alignment explanation
Indices: 182034--182085 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
182024 TACCTTTACA
*
182034 GTATCGATACTTCTCTTCAAGG
1 GTATCGATAC--CTCCTCAAGG
182056 GTATCGATACCTCCTC-AGG
1 GTATCGATACCTCCTCAAGG
*
182075 GTACCGATACC
1 GTATCGATACC
182086 GAATTGGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 13 0.46
20 5 0.18
22 10 0.36
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (20 bp):
GTATCGATACCTCCTCAAGG
Found at i:182143 original size:20 final size:21
Alignment explanation
Indices: 182118--182210 Score: 88
Period size: 20 Copynumber: 4.5 Consensus size: 21
182108 TCTTAAAAAT
182118 GTATCGATACCATCCTC-CTA
1 GTATCGATACCATCCTCACTA
* *
182138 GTATCGATACTACCCT-A-TCA
1 GTATCGATACCATCCTCACT-A
*
182158 GTATCGATACCCTCCTCTACTA
1 GTATCGATACCATCCTC-ACTA
*
182180 GTATCGATA-CTTCCCTCAC-A
1 GTATCGATACCAT-CCTCACTA
182200 GTATCGATACC
1 GTATCGATACC
182211 CACTTCAACT
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
19 1 0.02
20 38 0.63
21 5 0.08
22 15 0.25
23 1 0.02
ACGTcount: A:0.26, C:0.33, G:0.11, T:0.30
Consensus pattern (21 bp):
GTATCGATACCATCCTCACTA
Found at i:182185 original size:22 final size:22
Alignment explanation
Indices: 182118--182231 Score: 84
Period size: 20 Copynumber: 5.5 Consensus size: 22
182108 TCTTAAAAAT
*
182118 GTATCGATACCATCCTC--CTA
1 GTATCGATACCCTCCTCTACTA
182138 GTATCGATA--CTACC-CTA-TCA
1 GTATCGATACCCT-CCTCTACT-A
182158 GTATCGATACCCTCCTCTACTA
1 GTATCGATACCCTCCTCTACTA
*
182180 GTATCGATA-CTTCC-CTCAC-A
1 GTATCGATACCCTCCTCT-ACTA
* * * *
182200 GTATCGATACCCACTTCAACTG
1 GTATCGATACCCTCCTCTACTA
182222 GTATCGATAC
1 GTATCGATAC
182232 TTCCCTTAAG
Statistics
Matches: 75, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
18 2 0.03
19 3 0.04
20 31 0.41
21 12 0.16
22 26 0.35
23 1 0.01
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.30
Consensus pattern (22 bp):
GTATCGATACCCTCCTCTACTA
Found at i:182202 original size:42 final size:41
Alignment explanation
Indices: 182118--182237 Score: 154
Period size: 42 Copynumber: 2.9 Consensus size: 41
182108 TCTTAAAAAT
* *
182118 GTATCGATACCATCCTC-CTAGTATCGATACTACCCTATCA
1 GTATCGATACCCTCCTCACTAGTATCGATACTTCCCTATCA
182158 GTATCGATACCCTCCTCTACTAGTATCGATACTTCCCTCA-CA
1 GTATCGATACCCTCCTC-ACTAGTATCGATACTTCCCT-ATCA
* * *
182200 GTATCGATACCCACTTCAACTGGTATCGATACTTCCCT
1 GTATCGATACCCTCCTC-ACTAGTATCGATACTTCCCT
182238 TAAGAATTAC
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
40 16 0.23
42 54 0.76
43 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.11, T:0.31
Consensus pattern (41 bp):
GTATCGATACCCTCCTCACTAGTATCGATACTTCCCTATCA
Found at i:185056 original size:2 final size:2
Alignment explanation
Indices: 185049--185083 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
185039 ATTATGCCTC
185049 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
185084 AAAAGTACCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:191808 original size:25 final size:24
Alignment explanation
Indices: 191780--191830 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
191770 TAATAATGTG
*
191780 AAATATTGGATATATAAAAAATTAT
1 AAATATTGGATAT-TAAAAAAATAT
* *
191805 AAATATTTGTTATTAAAAAAATAT
1 AAATATTGGATATTAAAAAAATAT
191829 AA
1 AA
191831 CAAATTTCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
AAATATTGGATATTAAAAAAATAT
Found at i:192686 original size:29 final size:29
Alignment explanation
Indices: 192652--192710 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
192642 CCTAAATTAA
192652 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
192681 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
192710 T
1 T
192711 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:197361 original size:29 final size:29
Alignment explanation
Indices: 197327--197385 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
197317 CCTAAATTAA
197327 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
197356 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
197385 T
1 T
197386 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:198731 original size:28 final size:28
Alignment explanation
Indices: 198699--198755 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
198689 GATAGTATTG
198699 TCATATATAGTTATAGATCTAGAAATAT
1 TCATATATAGTTATAGATCTAGAAATAT
198727 TCATATATAGTTATAGATCTAGAAATAT
1 TCATATATAGTTATAGATCTAGAAATAT
198755 T
1 T
198756 TTTAATAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (28 bp):
TCATATATAGTTATAGATCTAGAAATAT
Found at i:200463 original size:2 final size:2
Alignment explanation
Indices: 200456--200488 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
200446 GAATTTTCTA
200456 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
200489 AATCTACGCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:206729 original size:23 final size:23
Alignment explanation
Indices: 206686--206729 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
206676 CCAATTATTA
* *
206686 TTTAAAAGAAAATCTTGTTATAT
1 TTTAAAAAAAAATATTGTTATAT
206709 TTTAAAAAAATAATATT-TTAT
1 TTTAAAAAAA-AATATTGTTAT
206730 CATTAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (23 bp):
TTTAAAAAAAAATATTGTTATAT
Found at i:209331 original size:2 final size:2
Alignment explanation
Indices: 209324--209382 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
209314 AATAATGATA
209324 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
209366 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
209383 AACGGGACAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:213948 original size:2 final size:2
Alignment explanation
Indices: 213941--213980 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
213931 ACTAATAATA
213941 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
213981 ATCGTAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:229322 original size:26 final size:26
Alignment explanation
Indices: 229266--229323 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
229256 CATGTAACTC
*
229266 ATAAAATGATTTATCAATATACATAT
1 ATAAAATGATTTATCAATATAAATAT
*
229292 ATAAAATAGATTT-TCATATTTAAATAT
1 ATAAAAT-GATTTATCA-ATATAAATAT
229319 -TAAAA
1 ATAAAA
229324 CAAAATACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 15 0.54
27 13 0.46
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (26 bp):
ATAAAATGATTTATCAATATAAATAT
Found at i:229912 original size:24 final size:24
Alignment explanation
Indices: 229885--229996 Score: 59
Period size: 24 Copynumber: 4.7 Consensus size: 24
229875 TATATCAAAA
*
229885 ATCAAAACATAATTCAAGTCAAGT
1 ATCAAAACAAAATTCAAGTCAAGT
* * * *
229909 ATCATATCAAAATTCAGGTCATGT
1 ATCAAAACAAAATTCAAGTCAAGT
* * *
229933 ATCAGATCAGAA-TCAATGTCAA-T
1 ATCAAAACAAAATTCAA-GTCAAGT
* * * * *
229956 ATCATATCAGAATCCATGTC-AGAT
1 ATCAAAACAAAATTCAAGTCAAG-T
*
229980 ATCATAACAAAATTCAA
1 ATCAAAACAAAATTCAA
229997 ATCAGAAATC
Statistics
Matches: 68, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
22 1 0.01
23 18 0.26
24 49 0.72
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.28
Consensus pattern (24 bp):
ATCAAAACAAAATTCAAGTCAAGT
Found at i:233176 original size:18 final size:18
Alignment explanation
Indices: 233153--233204 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
233143 TTACCCGTTT
233153 ACCTGACCCGTTGACCCG
1 ACCTGACCCGTTGACCCG
233171 ACCTGACCCGTTGACCCG
1 ACCTGACCCGTTGACCCG
*
233189 ACCCGACCCGTTGACC
1 ACCTGACCCGTTGACC
233205 GTTGACCGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.17, C:0.46, G:0.21, T:0.15
Consensus pattern (18 bp):
ACCTGACCCGTTGACCCG
Found at i:233275 original size:29 final size:29
Alignment explanation
Indices: 233217--233287 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
233207 TGACCGGTGT
*** *
233217 TATTCTGGGAATTAATTCGGTTTTTATGC
1 TATTCTGGGAATTAATTCGAAATGTATGC
*
233246 TATTCTGGGAATTAATTCGAAATGTGTGC
1 TATTCTGGGAATTAATTCGAAATGTATGC
* *
233275 TATTTTGGTAATT
1 TATTCTGGGAATT
233288 TTTTTAAAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.24, C:0.08, G:0.21, T:0.46
Consensus pattern (29 bp):
TATTCTGGGAATTAATTCGAAATGTATGC
Found at i:236292 original size:18 final size:17
Alignment explanation
Indices: 236269--236305 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
236259 TCAAGTGGCA
*
236269 AAAAAAAATTTGATATTT
1 AAAAAAAA-TTAATATTT
236287 AAAAAAAATTAATATTT
1 AAAAAAAATTAATATTT
236304 AA
1 AA
236306 TTAATATGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
AAAAAAAATTAATATTT
Found at i:241111 original size:19 final size:19
Alignment explanation
Indices: 241087--241130 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
241077 TCGATTATGG
241087 AGAGAAGAGAAACCAAAAA
1 AGAGAAGAGAAACCAAAAA
*
241106 AGAGAAGAGAAACCAGAAA
1 AGAGAAGAGAAACCAAAAA
*
241125 GGAGAA
1 AGAGAA
241131 ATGAAGGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.64, C:0.09, G:0.27, T:0.00
Consensus pattern (19 bp):
AGAGAAGAGAAACCAAAAA
Found at i:241554 original size:28 final size:28
Alignment explanation
Indices: 241485--241565 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
241475 AAATTTGTTT
*
241485 TGAACTTTGAAGTATTGAAGTTACTAAA
1 TGAAATTTGAAGTATTGAAGTTACTAAA
* *
241513 TGAAATCT-ATAGTATTGAAGTTACTCTAA
1 TGAAATTTGA-AGTATTGAAGTTACT-AAA
* *
241542 -GATATTTGAAGTATTAAAGTTACT
1 TGAAATTTGAAGTATTGAAGTTACT
241566 TATAAAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
27 1 0.02
28 40 0.91
29 3 0.07
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.38
Consensus pattern (28 bp):
TGAAATTTGAAGTATTGAAGTTACTAAA
Found at i:246771 original size:60 final size:59
Alignment explanation
Indices: 246606--246771 Score: 158
Period size: 60 Copynumber: 2.8 Consensus size: 59
246596 GAAATGGTCA
* * * * *
246606 AAAAGTTTGAGGACTAATTTTAAATTAAGGTCATAGTTTGAGTATGAAAATGAACTATTC
1 AAAAGTTTGAGGACTAA-TTTAAAATAATGTCATAATTTAAGGATGAAAATGAACTATTC
* * * * *
246666 AAAA-TCTTGAGGACTAATTTAGAATATATGTTATAATTTAGGGATGAAATTGGAA-TATTT
1 AAAAGT-TTGAGGACTAATTTAAAATA-ATGTCATAATTTAAGGATGAAAAT-GAACTATTC
*
246726 AAAAGTTT-AGGAACTAATTTAAAATAACTGTCATACTTTAAGGATG
1 AAAAGTTTGAGG-ACTAATTTAAAATAA-TGTCATAATTTAAGGATG
246772 TATGATGCAA
Statistics
Matches: 86, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
59 12 0.14
60 70 0.81
61 4 0.05
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36
Consensus pattern (59 bp):
AAAAGTTTGAGGACTAATTTAAAATAATGTCATAATTTAAGGATGAAAATGAACTATTC
Found at i:247190 original size:14 final size:14
Alignment explanation
Indices: 247136--247202 Score: 64
Period size: 14 Copynumber: 4.8 Consensus size: 14
247126 AAGGTTTAGG
247136 GTTTAGGGTTTAT-
1 GTTTAGGGTTTATA
* * *
247149 GATTTATGATTTAGA
1 G-TTTAGGGTTTATA
* *
247164 GGTTATGGTTTATA
1 GTTTAGGGTTTATA
247178 GTTTAGGGTTTATA
1 GTTTAGGGTTTATA
*
247192 ATTTAGGGTTT
1 GTTTAGGGTTT
247203 TAAGTTAGGG
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
13 1 0.02
14 41 0.95
15 1 0.02
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (14 bp):
GTTTAGGGTTTATA
Found at i:247202 original size:21 final size:21
Alignment explanation
Indices: 247130--247202 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
247120 TGAGTTAAGG
247130 TTTAGGGTTTAGGGTTTATGA
1 TTTAGGGTTTAGGGTTTATGA
* * *
247151 TTTATGATTTAGAGG-TTATGG
1 TTTAGGGTTTAG-GGTTTATGA
** *
247172 TTTATAGTTTAGGGTTTATAA
1 TTTAGGGTTTAGGGTTTATGA
247193 TTTAGGGTTT
1 TTTAGGGTTT
247203 TAAGTTAGGG
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 2 0.05
21 37 0.90
22 2 0.05
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (21 bp):
TTTAGGGTTTAGGGTTTATGA
Found at i:247214 original size:14 final size:14
Alignment explanation
Indices: 247165--247212 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
247155 TGATTTAGAG
*
247165 GTTATGGTTTAT-A
1 GTTAGGGTTTATAA
247178 GTTTAGGGTTTATAA
1 G-TTAGGGTTTATAA
*
247193 TTTAGGGTTT-TAA
1 GTTAGGGTTTATAA
247206 GTTAGGG
1 GTTAGGG
247213 GTATGATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 10 0.33
14 19 0.63
15 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (14 bp):
GTTAGGGTTTATAA
Found at i:249138 original size:25 final size:24
Alignment explanation
Indices: 249079--249148 Score: 97
Period size: 25 Copynumber: 2.9 Consensus size: 24
249069 GAGTCGAGGG
*
249079 TTCTACGCGGTGCTTCGGGAC-AA
1 TTCTACGCGGTCCTTCGGGACAAA
* *
249102 TTCTATGTGGTCCTTCGGGACAAA
1 TTCTACGCGGTCCTTCGGGACAAA
249126 TTTCTACGCGGTCCTTCGGGACA
1 -TTCTACGCGGTCCTTCGGGACA
249149 TTTTCTATGT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 18 0.45
24 2 0.05
25 20 0.50
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.30
Consensus pattern (24 bp):
TTCTACGCGGTCCTTCGGGACAAA
Found at i:249162 original size:24 final size:23
Alignment explanation
Indices: 249091--249167 Score: 91
Period size: 25 Copynumber: 3.2 Consensus size: 23
249081 CTACGCGGTG
*
249091 CTTCGGGACAATTCTATGTGGTC
1 CTTCGGGACATTTCTATGTGGTC
* *
249114 CTTCGGGACAAATTTCTACGCGGTC
1 CTTCGGGAC--ATTTCTATGTGGTC
249139 CTTCGGGACATTTTCTATGTGGTC
1 CTTCGGGACA-TTTCTATGTGGTC
*
249163 TTTCG
1 CTTCG
249168 AGATATTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
23 10 0.22
24 15 0.33
25 20 0.44
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (23 bp):
CTTCGGGACATTTCTATGTGGTC
Found at i:249191 original size:47 final size:47
Alignment explanation
Indices: 249082--249191 Score: 107
Period size: 47 Copynumber: 2.3 Consensus size: 47
249072 TCGAGGGTTC
** *
249082 TACGCGGTGCTTCGGGACAATTCTATGTGGTCCTTCGGGACAAATTTC
1 TACGCGGACCTTCGGGACAATTCTATGTGGTCCTTC-GGACAAATTTA
* * * * *
249130 TACGCGGTCCTTCGGGACATTTTCTATGTGGTCTTTC-GAGATATTTA
1 TACGCGGACCTTCGGGACA-ATTCTATGTGGTCCTTCGGACAAATTTA
249177 TACGC-GACACTTCGG
1 TACGCGGAC-CTTCGG
249192 TGCATATTCT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
46 2 0.04
47 18 0.34
48 18 0.34
49 15 0.28
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (47 bp):
TACGCGGACCTTCGGGACAATTCTATGTGGTCCTTCGGACAAATTTA
Found at i:252889 original size:28 final size:28
Alignment explanation
Indices: 252857--252923 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
252847 ACATGTTTTT
*
252857 AATAAATTCATCAATGGTTAGTTGATTG
1 AATAAATTCATCAATGGTTAGTTAATTG
*
252885 AATAAATTCATTAATGGTTAGTTAATTG
1 AATAAATTCATCAATGGTTAGTTAATTG
252913 AATAAATTCAT
1 AATAAATTCAT
252924 ATACCTTTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.40
Consensus pattern (28 bp):
AATAAATTCATCAATGGTTAGTTAATTG
Found at i:253831 original size:21 final size:21
Alignment explanation
Indices: 253807--253846 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
253797 TAAAAATAAA
253807 TTAAAACATTATTATTTTTAC
1 TTAAAACATTATTATTTTTAC
*
253828 TTAAAACATTATTGTTTTT
1 TTAAAACATTATTATTTTT
253847 TAATATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TTAAAACATTATTATTTTTAC
Found at i:258150 original size:2 final size:2
Alignment explanation
Indices: 258143--258170 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
258133 TCTGTGCTCG
258143 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
258171 GTATTCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:264887 original size:165 final size:165
Alignment explanation
Indices: 264550--265228 Score: 934
Period size: 165 Copynumber: 4.1 Consensus size: 165
264540 CAAACTCGTC
* * * * *
264550 AGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTCGGAG
1 AGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTCCAAATGATGTGCCCTCGAAG
* * * * * * * * * **
264614 CTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGTTG
66 CTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTG
*
264679 CAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTCAA
127 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
*
264718 AGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTCCAAATGATGTGCCCTCGAAG
1 AGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTCCAAATGATGTGCCCTCGAAG
*
264783 CTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATACTGCAAA
66 CTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAA
* *
264848 TGATATGCCTTAGAGCTGAGCGTAGTCGAACTCAA
131 TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
* * * *
264883 AGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATG-TCGTAAATGATGTGCCCTCGA
1 AGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTC-CAAATGATGTGCCCTCGA
* *
264946 AGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
64 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCA
*
265011 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGA
129 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
* * * **
265048 AGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAA
1 AGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTCCAAATGATGTGCCCTCGAA
*
265112 GCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATATCCCTTCTCGACTTAAGCTATACTGCAA
65 GCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAA
* * *
265177 ATGATGTGCCTTGGAGTTGAGCATAGTCGAACTCGA
130 ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
265213 AGGTCTTTGGTTGGCA
1 AGGTCTTTGGTTGGCA
265229 AATAGTCCTT
Statistics
Matches: 471, Mismatches: 35, Indels: 13
0.91 0.07 0.03
Matches are distributed among these distances:
164 7 0.01
165 376 0.80
166 6 0.01
167 1 0.00
168 53 0.11
169 28 0.06
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (165 bp):
AGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTCCAAATGATGTGCCCTCGAAG
CTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAA
TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
Found at i:265263 original size:84 final size:84
Alignment explanation
Indices: 264550--265240 Score: 746
Period size: 84 Copynumber: 8.3 Consensus size: 84
264540 CAAACTCGTC
*
264550 AGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCGGAGC
1 AGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTCGGAGC
*
264615 TGAGCGTAGTCAAACTCGA
66 TGAGCGTAGTCGAACTCGA
* * * * * * *
264634 AGGTCTTTGGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGTTGCAAATGATGTACCTTGGAGC
1 AGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTCGGAGC
*
264699 TGAGCGTAGTCGAACTCAA
66 TGAGCGTAGTCGAACTCGA
* * *
264718 AGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTCCAAATGATGTGCCCTCGAAG
1 AGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTCGGAG
* *
264783 CTGAGTGTAATCGAACTCGA
65 CTGAGCGTAGTCGAACTCGA
* * * **
264803 GGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGTTATACTGCAAATGATATGCCTTAGAGC
1 AGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTCGGAGC
*
264864 TGAGCGTAGTCGAACTCAA
66 TGAGCGTAGTCGAACTCGA
* * * * * * *
264883 AGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATG-TCGTAAATGATGTGCCCTCGA
1 AGGTC-TTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCT-GCAAATGATGTG-CCTCGG
* * *
264946 AGCTGAGTGTAATCGAACTCGG
63 AGCTGAGCGTAGTCGAACTCGA
* * *
264968 GGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
1 AGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTCGGAGC
265029 TGAGCGTAGTCGAACTCGA
66 TGAGCGTAGTCGAACTCGA
* * * * * ** *
265048 AGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAA
1 AGGTC-TTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTCGGA
* *
265112 GCTGAGTGTAATCGAACTCGA
64 GCTGAGCGTAGTCGAACTCGA
* * * * * *
265133 GGGTC--T--TTGGCAGATATCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGT
1 AGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTCGGAGC
*
265194 TGAGCATAGTCGAACTCGA
66 TGAGCGTAGTCGAACTCGA
* *
265213 AGGTCTTTGGTTGGCAAATAGTCCTTCT
1 AGGTCTTTGGTTGGCAGATAGCCCTTCT
265241 TGTCTTGAGC
Statistics
Matches: 490, Mismatches: 96, Indels: 42
0.78 0.15 0.07
Matches are distributed among these distances:
80 79 0.16
81 114 0.23
82 4 0.01
83 4 0.01
84 209 0.43
85 80 0.16
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (84 bp):
AGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTCGGAGC
TGAGCGTAGTCGAACTCGA
Found at i:269149 original size:20 final size:21
Alignment explanation
Indices: 269108--269149 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
269098 AAATTACCCC
*
269108 TAAAAAGATAAAAATATTATA
1 TAAAAAGATAAAAATATAATA
269129 TAAAAA-ATAAGAAATA-AATA
1 TAAAAAGATAA-AAATATAATA
269149 T
1 T
269150 TAAATAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (21 bp):
TAAAAAGATAAAAATATAATA
Found at i:270797 original size:81 final size:82
Alignment explanation
Indices: 270525--271184 Score: 688
Period size: 81 Copynumber: 8.0 Consensus size: 82
270515 AGGTCTTTGG
270525 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTCGGAGCTGAGCGTAG
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGGAGCTGAGCGTAG
*
270589 TCAAACTCGAAGGTCTTT
66 TCGAACTCGAAGGTC-TT
* *** * * * *
270607 GTTGGCAAATAGCCCTTCTTTCCTTGAGCTATGTTGCAAATGATGT-ACCTTGGAGCTGAGCGTA
1 -TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGGAGCTGAGCGTA
*
270671 GTCGAACTCAAAGGTCTTT
65 GTCGAACTCGAAGGTC-TT
* * * *
270690 GGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGT
1 --TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGGAGCTGAGCGT
* *
270755 AATCGAACTCGAGGGTC-T
64 AGTCGAACTCGAAGGTCTT
* * **
270773 TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATG-CCTTAGAGCTGAGCGTAG
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGGAGCTGAGCGTAG
*
270837 TCGAACTCAAAGGTCTT
66 TCGAACTCGAAGGTCTT
* * * * * * * * ** *
270854 TTGGTGACATATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCAAAGCTGAGTG
1 TT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGGAGCTGAGCG
* **
270919 TAATCGAACTCGGGGGTC-T
63 TAGTCGAACTCGAAGGTCTT
* *
270938 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGCAG
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGGAGCTGAGCGTAG
271002 TCGAACTCGAAGGTCTT
66 TCGAACTCGAAGGTCTT
* * * * * ** * *
271019 TTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTG
1 TT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGGAGCTGAGCG
* *
271084 TAATCGAACTCGAGGGTC-T
63 TAGTCGAACTCGAAGGTCTT
* * * * *
271103 TTGGCAGATATCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTGGAGTTGAGCATAG
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGGAGCTGAGCGTAG
271167 TCGAACTCGAAGGTCTT
66 TCGAACTCGAAGGTCTT
271184 T
1 T
271185 GGTTGGCAAA
Statistics
Matches: 467, Mismatches: 96, Indels: 30
0.79 0.16 0.05
Matches are distributed among these distances:
80 77 0.16
81 118 0.25
82 4 0.01
83 77 0.16
84 111 0.24
85 80 0.17
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (82 bp):
TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGGAGCTGAGCGTAG
TCGAACTCGAAGGTCTT
Found at i:270870 original size:165 final size:165
Alignment explanation
Indices: 270515--271184 Score: 923
Period size: 165 Copynumber: 4.0 Consensus size: 165
270505 CGAACTCGTC
* * * * *
270515 AGGTC-TTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTCGGA
1 AGGTCTTTTGG-TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAA
* * * * * *** * **
270578 GCTGAGCGTAGTCAAACTCGAAGGTCTTTGTTGGCAAATAGCCCTTCTTTCCTTGAGCTATGTTG
65 GCTGAGTGTAATCGAACTCGAGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTG
*
270643 CAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTCAA
127 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
* *
270682 AGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAA
1 AGGTCTTTTGG-TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAA
270746 GCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAA
65 GCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAA
* *
270811 ATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCAA
130 ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
* * * * * *
270847 AGGTCTTTTGGTGACATATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCAAAG
1 AGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAG
* *
270912 CTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAA
66 CTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAA
* *
270977 TGATGTGCCTTGGAGCTGAGCGCAGTCGAACTCGA
131 TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
* * **
271012 AGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAG
1 AGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAG
*
271077 CTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATATCCCTTCTCGACTTAAGCTATACTGCAAA
66 CTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAA
* * *
271142 TGATGTGCCTTGGAGTTGAGCATAGTCGAACTCGA
131 TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
271177 AGGTCTTT
1 AGGTCTTT
271185 GGTTGGCAAA
Statistics
Matches: 460, Mismatches: 41, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
165 372 0.81
166 6 0.01
167 54 0.12
168 28 0.06
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
AGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAG
CTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAA
TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
Found at i:271062 original size:84 final size:82
Alignment explanation
Indices: 270504--271187 Score: 714
Period size: 84 Copynumber: 8.3 Consensus size: 82
270494 CTGAATGAAA
*
270504 TCGAACTCGTCAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
1 TCGAACTCG-AAGGTCTTTGG-T-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
270569 TGCCTCGGAGCTGAGCGTAG
63 TGCCTCGGAGCTGAGCGTAG
* * * *** * * *
270589 TCAAACTCGAAGGTCTTTGTTGGCAAATAGCCCTTCTTTCCTTGAGCTATGTTGCAAATGATGTA
1 TCGAACTCGAAGGTCTTTGGT-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
270654 CCTTGGAGCTGAGCGTAG
65 CCTCGGAGCTGAGCGTAG
* * *
270672 TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGG-T-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * *
270737 GCCCTCGAAGCTGAGTGTAA
64 G-CCTCGGAGCTGAGCGTAG
* * *
270757 TCGAACTCGAGGGTCTTT-G-GCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATGC
1 TCGAACTCGAAGGTCTTTGGTGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
**
270820 CTTAGAGCTGAGCGTAG
66 CTCGGAGCTGAGCGTAG
* * * * * * * * *
270837 TCGAACTCAAAGGTCTTTTGGTGACATATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGGTG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
** * *
270902 GCCCTCAAAGCTGAGTGTAA
64 G-CCTCGGAGCTGAGCGTAG
**
270922 TCGAACTCGGGGGTCTTT-G-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
1 TCGAACTCGAAGGTCTTTGGTGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
* *
270985 CTTGGAGCTGAGCGCAG
66 CTCGGAGCTGAGCGTAG
* * * * * **
271002 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGT
1 TCGAACTCGAAGGTC-TTTGGTG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * *
271067 GCCCTCGAAGCTGAGTGTAA
64 G-CCTCGGAGCTGAGCGTAG
* * *
271087 TCGAACTCGAGGGTCTTT-G-GCAGATATCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGC
1 TCGAACTCGAAGGTCTTTGGTGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
* * *
271150 CTTGGAGTTGAGCATAG
66 CTCGGAGCTGAGCGTAG
271167 TCGAACTCGAAGGTCTTTGGT
1 TCGAACTCGAAGGTCTTTGGT
271188 TGGCAAATAG
Statistics
Matches: 484, Mismatches: 101, Indels: 31
0.79 0.16 0.05
Matches are distributed among these distances:
80 80 0.17
81 114 0.24
82 4 0.01
83 76 0.16
84 119 0.25
85 91 0.19
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (82 bp):
TCGAACTCGAAGGTCTTTGGTGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
CTCGGAGCTGAGCGTAG
Found at i:274968 original size:6 final size:6
Alignment explanation
Indices: 274957--274995 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
274947 TTAATTGCGA
274957 AAATTT AAATTT --ATTT AAATTT AAATTT AAATTT AAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATT
274996 ATTCGATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.13
6 27 0.87
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:276201 original size:23 final size:22
Alignment explanation
Indices: 276161--276215 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
276151 TGGACCTGCA
276161 AAAATAAAAAATATTAATAAT-
1 AAAATAAAAAATATTAATAATG
276182 AATAATAAATAAAT-TATAATAATG
1 AA-AATAAA-AAATAT-TAATAATG
276206 AAAATAAAAA
1 AAAATAAAAA
276216 TATAAAACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 2 0.07
22 9 0.30
23 17 0.57
24 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAATAAAAAATATTAATAATG
Found at i:277030 original size:76 final size:75
Alignment explanation
Indices: 276889--277081 Score: 300
Period size: 76 Copynumber: 2.6 Consensus size: 75
276879 AAACTTAAAG
* * * *
276889 CTAAATTTTGAA-AGGGGTACTAAAATGAAACAAAAGCTAAAGTTTTAACGGTGGGCACTAAAAT
1 CTAAATTTTTAACATGGGTACTAAAATGAAACAAAAACTAAAGTTTTAACGATGGGCACTAAAAT
276953 GAAACAAAAA
66 GAAACAAAAA
*
276963 CTAAAATTTTTAAC-TGCGGTACTAAAATGAAACAAAAACTAAAGTTTTAACGATGGGTACTAAA
1 CT-AAATTTTTAACATG-GGTACTAAAATGAAACAAAAACTAAAGTTTTAACGATGGGCACTAAA
277027 ATGAAACAAAAA
64 ATGAAACAAAAA
277039 CTAAATTTTTAACATTGGGTACTAAAATGAAACAAAAACTAAA
1 CTAAATTTTTAACA-TGGGTACTAAAATGAAACAAAAACTAAA
277082 TTGTAGGTAT
Statistics
Matches: 109, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
74 2 0.02
75 21 0.19
76 84 0.77
77 2 0.02
ACGTcount: A:0.50, C:0.11, G:0.15, T:0.24
Consensus pattern (75 bp):
CTAAATTTTTAACATGGGTACTAAAATGAAACAAAAACTAAAGTTTTAACGATGGGCACTAAAAT
GAAACAAAAA
Found at i:277082 original size:38 final size:37
Alignment explanation
Indices: 276889--277083 Score: 268
Period size: 38 Copynumber: 5.2 Consensus size: 37
276879 AAACTTAAAG
* * *
276889 CTAAATTTTGAA-AGGGGTACTAAAATGAAACAAAAG
1 CTAAATTTTTAACATGGGTACTAAAATGAAACAAAAA
* * *
276925 CTAAAGTTTTAACGGTGGGCACTAAAATGAAACAAAAA
1 CTAAATTTTTAAC-ATGGGTACTAAAATGAAACAAAAA
276963 CTAAAATTTTTAAC-TGCGGTACTAAAATGAAACAAAAA
1 CT-AAATTTTTAACATG-GGTACTAAAATGAAACAAAAA
*
277001 CTAAAGTTTTAACGATGGGTACTAAAATGAAACAAAAA
1 CTAAATTTTTAAC-ATGGGTACTAAAATGAAACAAAAA
277039 CTAAATTTTTAACATTGGGTACTAAAATGAAACAAAAA
1 CTAAATTTTTAACA-TGGGTACTAAAATGAAACAAAAA
277077 CTAAATT
1 CTAAATT
277084 GTAGGTATTG
Statistics
Matches: 142, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
36 10 0.07
37 13 0.09
38 107 0.75
39 12 0.08
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.25
Consensus pattern (37 bp):
CTAAATTTTTAACATGGGTACTAAAATGAAACAAAAA
Done.