Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008166.1 Hibiscus syriacus cultivar Beakdansim tig00110747_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: 2544747
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 10
Found at i:1975 original size:20 final size:21
Alignment explanation
Indices: 1931--1976 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
1921 AATAGAGTCA
* *
1931 ATACCATGGTATGGTAGTATTG
1 ATACCATGGTAAGG-AGTATCG
1953 ATACCATGGTAAGG-GTATCG
1 ATACCATGGTAAGGAGTATCG
1973 ATAC
1 ATAC
1977 TATTGAGCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
22 13 0.59
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.30
Consensus pattern (21 bp):
ATACCATGGTAAGGAGTATCG
Found at i:2957 original size:81 final size:81
Alignment explanation
Indices: 2461--2940 Score: 768
Period size: 81 Copynumber: 6.0 Consensus size: 81
2451 TTTGAATAAT
* * *
2461 TTTGAGTAAAAGATTAATGGCCTAGCTGTGTATTTGACAGAAATGTGTCAATTATGGCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
2526 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
*
2542 TTTGAGT-AAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
*
2606 TG-AAGGTTAAATACT
66 TGAAAGGTTAAATACC
* * * *
2621 TTTTAGTAAAATATTAATGGCCTAGCTGTGCATTTGACAGAAAGATGTCAATTATGCCAATTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
*
2686 TGAAAGGTTAAATACA
66 TGAAAGGTTAAATACC
*
2702 TTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
2767 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* *
2783 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTATCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
*
2848 TGAAATGTTAAATACC
66 TGAAAGGTTAAATACC
* * *
2864 TTTGAGTAAAAGATTAATGGCCTAGATGTGCATTTGACAAAAAGGTGTCAATTATGTCAG-TAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
* *
2928 TGAATGATTAAAT
66 TGAAAGGTTAAAT
2941 GCTTGTGGGG
Statistics
Matches: 368, Mismatches: 29, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
79 18 0.05
80 124 0.34
81 226 0.61
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (81 bp):
TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
TGAAAGGTTAAATACC
Found at i:5403 original size:2 final size:2
Alignment explanation
Indices: 5398--5432 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5388 AATGTCAGAA
5398 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
5433 ACTTTTCTGG
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:7898 original size:81 final size:81
Alignment explanation
Indices: 7763--8729 Score: 1405
Period size: 81 Copynumber: 12.0 Consensus size: 81
7753 GAATAATTAA
* * * *
7763 TTGAGTAAAATATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGGCAGTTAGAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
7828 GAAAGGTTAAATACCT
66 GAAAGGTTAAATACCT
*
7844 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
*
7909 GAAAGGTTAAATACTT
66 GAAAGGTTAAATACCT
* * * * * *
7925 TTTAGTAAAATATTAATGGCCTAGCTATGCATTTGACAGAAAGATGTCAATTATGTCAATTAGAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
* *
7990 AAAAGGTTAAATACAT
66 GAAAGGTTAAATACCT
* * *
8006 TTGAGTAAAATATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAG
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
* *
8071 GAAATGTTAAATATCT
66 GAAAGGTTAAATACCT
* * * * ** *
8087 TTGAGTAAAAGATTAATGTCCTAGTTGTGCATTTGACAGAAAGGTGTCGATTATTCCTTTTAAAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
*
8152 GAAAAGTTAAATACCT
66 GAAAGGTTAAATACCT
* * * * * *
8168 TAGAGT-AAAGATTAATGGCCTAGTTGTGAATTTGACATAAAGGTTTCAATTATGCCAATTAGAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
8232 GAAAGGTTAAATACCT
66 GAAAGGTTAAATACCT
* * * *
8248 TTGAGTAAAAGATTAATGGCCTAACTGTGCATTTGACAGAAAGATGTCAATTATGCCAATTATAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
8313 GAAAGGTTAAATACCT
66 GAAAGGTTAAATACCT
*
8329 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
*
8394 GAAACGTTAAATACCT
66 GAAAGGTTAAATACCT
* * *
8410 ATGAGTAAAATATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
8475 GAAAGGTTAAATACCT
66 GAAAGGTTAAATACCT
* * *
8491 TTGAGTAAAAGATTAATGGCCTAGCAGTGCATTTGACAGAAATGTGTCAATTATGTCAGTTAGAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
*
8556 GAAAGGTTAAATACTT
66 GAAAGGTTAAATACCT
* * * * * *
8572 TTTAGTAAAATATTAATGGCCTAGCTATGCATTTGACAGAAAGATGTCAATTATGTCAATTAGAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
* *
8637 AAAAGGTTAAATACAT
66 GAAAGGTTAAATACCT
* * *
8653 TTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTAACAGAAAGGTGTCAATTATGCCAGTTAGAG
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
*
8718 GAAAGATTAAAT
66 GAAAGGTTAAAT
8730 GTTTGTGGGG
Statistics
Matches: 795, Mismatches: 90, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
80 69 0.09
81 726 0.91
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (81 bp):
TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
GAAAGGTTAAATACCT
Found at i:9537 original size:19 final size:20
Alignment explanation
Indices: 9494--9539 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
9484 TACTATGCTG
*
9494 GAAATTAATGTTAGAATGTT
1 GAAATTGATGTTAGAATGTT
*
9514 GAAATTGATGTTATAATG-T
1 GAAATTGATGTTAGAATGTT
9533 GAAATTG
1 GAAATTG
9540 GGTCATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.39, C:0.00, G:0.22, T:0.39
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Found at i:19139 original size:18 final size:18
Alignment explanation
Indices: 19116--19150 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
19106 GATGTTACGT
19116 TAACCATTTCAAAATTTG
1 TAACCATTTCAAAATTTG
19134 TAACCATTTCAAAATTT
1 TAACCATTTCAAAATTT
19151 TCTTGTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (18 bp):
TAACCATTTCAAAATTTG
Found at i:21210 original size:18 final size:18
Alignment explanation
Indices: 21176--21265 Score: 84
Period size: 18 Copynumber: 5.2 Consensus size: 18
21166 ACCGGTCACA
*
21176 ACCCGACCCGA-CCGTTT
1 ACCCGACCCGACCCGTTG
21193 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
* *
21210 ----TACCCGACCTGTTG
1 ACCCGACCCGACCCGTTG
21224 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
21242 ACCCGACCCGTTGACCCGTTG
1 ACCCGACCC---GACCCGTTG
21263 ACC
1 ACC
21266 GTTGACCCGT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
13 11 0.18
17 11 0.18
18 26 0.43
21 12 0.20
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.17
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:21216 original size:13 final size:13
Alignment explanation
Indices: 21197--21259 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 13
21187 CCGTTTACCC
21197 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
21210 TACCCGACCTGTT
1 GACCCGACCCGTT
21223 GACCCGACCCGACCCGTT
1 G-----ACCCGACCCGTT
21241 GACCCGACCCGTT
1 GACCCGACCCGTT
21254 GACCCG
1 GACCCG
21260 TTGACCGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 29 0.71
18 12 0.29
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:21231 original size:31 final size:30
Alignment explanation
Indices: 21180--21259 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 30
21170 GTCACAACCC
*
21180 GACCCGACCGTTTACCCGACCCGACCCGTT
1 GACCCGACCGTTGACCCGACCCGACCCGTT
*
21210 TACCCGACCTGTTGACCCGACCCGACCCGTT
1 GACCCGACC-GTTGACCCGACCCGACCCGTT
21241 GACCCGACCCGTTGACCCG
1 GACCCGA-CCGTTGACCCG
21260 TTGACCGTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 8 0.18
31 35 0.78
32 2 0.04
ACGTcount: A:0.16, C:0.46, G:0.21, T:0.16
Consensus pattern (30 bp):
GACCCGACCGTTGACCCGACCCGACCCGTT
Found at i:21244 original size:8 final size:8
Alignment explanation
Indices: 21233--21287 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
21223 GACCCGACCC
21233 GACCCGTT
1 GACCCGTT
21241 GACCC---
1 GACCCGTT
21246 GACCCGTT
1 GACCCGTT
21254 GACCCGTT
1 GACCCGTT
21262 GA-CCGTT
1 GACCCGTT
21269 GACCCGTT
1 GACCCGTT
21277 GA-CCGTT
1 GACCCGTT
21284 GACC
1 GACC
21288 GGAGTTGACC
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
5 5 0.12
7 14 0.33
8 23 0.55
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:21269 original size:7 final size:7
Alignment explanation
Indices: 21249--21288 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
21239 TTGACCCGAC
21249 CCGTTGA
1 CCGTTGA
21256 CCCGTTGA
1 -CCGTTGA
21264 CCGTTGA
1 CCGTTGA
21271 CCCGTTGA
1 -CCGTTGA
21279 CCGTTGA
1 CCGTTGA
21286 CCG
1 CCG
21289 GAGTTGACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 17 0.55
8 14 0.45
ACGTcount: A:0.12, C:0.35, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:21269 original size:15 final size:15
Alignment explanation
Indices: 21249--21287 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
21239 TTGACCCGAC
21249 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
21264 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
21279 CCGTTGACC
1 CCGTTGACC
21288 GGAGTTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.13, C:0.36, G:0.26, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:23867 original size:24 final size:24
Alignment explanation
Indices: 23773--23872 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
23763 ATATTTTATC
* *
23773 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
* * * *
23797 TAACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTCTGTTT
* * * *
23821 TGAT-TCCTAAACTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTCTGTTT
*
23845 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTT
23869 TGAT
1 TGAT
23873 TTTTGATATC
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 54 0.96
25 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:26049 original size:13 final size:13
Alignment explanation
Indices: 26048--26110 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 13
26038 CCGTTTACCC
26048 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
26061 TACCCGACCTGTT
1 GACCCGACCCGTT
26074 GACCCGACCCGACCCGTT
1 G-----ACCCGACCCGTT
26092 GACCCGACCCGTT
1 GACCCGACCCGTT
26105 GACCCG
1 GACCCG
26111 TTGACCGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 29 0.71
18 12 0.29
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:26049 original size:18 final size:18
Alignment explanation
Indices: 26026--26116 Score: 93
Period size: 18 Copynumber: 5.2 Consensus size: 18
26016 ACCGGTCACA
*
26026 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
26044 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
* *
26061 ----TACCCGACCTGTTG
1 ACCCGACCCGACCCGTTG
26075 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
26093 ACCCGACCCGTTGACCCGTTG
1 ACCCGACCC---GACCCGTTG
26114 ACC
1 ACC
26117 GTTGACCCGT
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
13 11 0.18
18 38 0.62
21 12 0.20
ACGTcount: A:0.16, C:0.47, G:0.20, T:0.16
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:26067 original size:31 final size:31
Alignment explanation
Indices: 26030--26110 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
26020 GTCACAACCC
*
26030 GACCCGACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* *
26061 TACCCGACCTGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
26092 GACCCGACCCGTTGACCCG
1 GACCCGACCCGTTGACCCG
26111 TTGACCGTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.16, C:0.47, G:0.21, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:26095 original size:8 final size:8
Alignment explanation
Indices: 26084--26138 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
26074 GACCCGACCC
26084 GACCCGTT
1 GACCCGTT
26092 GACCC---
1 GACCCGTT
26097 GACCCGTT
1 GACCCGTT
26105 GACCCGTT
1 GACCCGTT
26113 GA-CCGTT
1 GACCCGTT
26120 GACCCGTT
1 GACCCGTT
26128 GA-CCGTT
1 GACCCGTT
26135 GACC
1 GACC
26139 GGAGTTGACC
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
5 5 0.12
7 14 0.33
8 23 0.55
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:26120 original size:7 final size:7
Alignment explanation
Indices: 26100--26139 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
26090 TTGACCCGAC
26100 CCGTTGA
1 CCGTTGA
26107 CCCGTTGA
1 -CCGTTGA
26115 CCGTTGA
1 CCGTTGA
26122 CCCGTTGA
1 -CCGTTGA
26130 CCGTTGA
1 CCGTTGA
26137 CCG
1 CCG
26140 GAGTTGACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 17 0.55
8 14 0.45
ACGTcount: A:0.12, C:0.35, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:26120 original size:15 final size:15
Alignment explanation
Indices: 26100--26138 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
26090 TTGACCCGAC
26100 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
26115 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
26130 CCGTTGACC
1 CCGTTGACC
26139 GGAGTTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.13, C:0.36, G:0.26, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:28721 original size:24 final size:24
Alignment explanation
Indices: 28627--28726 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
28617 ATATTTTATC
* *
28627 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
* * * *
28651 TAACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTCTGTTT
* * * *
28675 TGAT-TCCTAAACTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTCTGTTT
*
28699 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTT
28723 TGAT
1 TGAT
28727 TTTTGATATC
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 54 0.96
25 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:34955 original size:25 final size:25
Alignment explanation
Indices: 34921--34978 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
34911 TTGTCTGTAC
34921 TAATCTCTCTCCCGAAGCCATCGAA
1 TAATCTCTCTCCCGAAGCCATCGAA
*
34946 TAATCTCTCTCCGGAAGCCATCGAA
1 TAATCTCTCTCCCGAAGCCATCGAA
34971 TAATCTCT
1 TAATCTCT
34979 AATAAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.28, C:0.33, G:0.12, T:0.28
Consensus pattern (25 bp):
TAATCTCTCTCCCGAAGCCATCGAA
Found at i:41047 original size:12 final size:12
Alignment explanation
Indices: 41026--41051 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41016 TTGAGGAATA
41026 GGAGGAGGATTT
1 GGAGGAGGATTT
41038 GGAGGAGGATTT
1 GGAGGAGGATTT
41050 GG
1 GG
41052 TTGACGACTA
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:0.23, C:0.00, G:0.54, T:0.23
Consensus pattern (12 bp):
GGAGGAGGATTT
Found at i:41800 original size:21 final size:21
Alignment explanation
Indices: 41747--41808 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
41737 ATTTCCCTGT
41747 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
**
41770 GGGGGAATCGGTTCCCTCATG
1 GGGGGAATCGGTTCCCTCAAA
* *
41791 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
41809 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 19 0.54
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:52589 original size:13 final size:13
Alignment explanation
Indices: 52533--52581 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
52523 TCTATGACGT
52533 GCATTTATGACAC
1 GCATTTATGACAC
52546 GCATTTATGACAC
1 GCATTTATGACAC
*
52559 ACATTTATGACAC
1 GCATTTATGACAC
*
52572 TCATTTATGA
1 GCATTTATGA
52582 TGCGCATTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (13 bp):
GCATTTATGACAC
Found at i:61193 original size:29 final size:28
Alignment explanation
Indices: 61103--61193 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 28
61093 CAAAATATAT
* *
61103 AACTTTTAAAAATTATACTTTGGTCCCTA
1 AACTTTTAAAATTTATACTTT-GTCACTA
* * * * *
61132 AACATCTACAATTTTATACTTTGATTACCA
1 AACTTTTA-AAATTTATACTTTG-TCACTA
*
61162 AACTTTTAAAATTTATATTTTAGTCACTA
1 AACTTTTAAAATTTATACTTT-GTCACTA
61191 AAC
1 AAC
61194 AAAATTTGAG
Statistics
Matches: 46, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 25 0.54
30 21 0.46
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.42
Consensus pattern (28 bp):
AACTTTTAAAATTTATACTTTGTCACTA
Found at i:61980 original size:13 final size:13
Alignment explanation
Indices: 61962--61990 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
61952 CTGATCACAC
61962 TAATTGTTGATGG
1 TAATTGTTGATGG
61975 TAATTGTTGATGG
1 TAATTGTTGATGG
61988 TAA
1 TAA
61991 AAAGTCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (13 bp):
TAATTGTTGATGG
Found at i:63083 original size:23 final size:22
Alignment explanation
Indices: 63057--63109 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 22
63047 ACTGCAAGTT
63057 TATAATAACATATTA-TTATTAAA
1 TATAATAA-AT-TTATTTATTAAA
*
63080 TAT-ATAAATTTATTTTTTAAA
1 TATAATAAATTTATTTATTAAA
63101 TATATATAA
1 TATA-ATAA
63110 TACTATCGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.12
21 12 0.46
22 4 0.15
23 7 0.27
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TATAATAAATTTATTTATTAAA
Found at i:63846 original size:46 final size:44
Alignment explanation
Indices: 63796--63888 Score: 114
Period size: 46 Copynumber: 2.1 Consensus size: 44
63786 AAGTTGTAAT
*
63796 TTTTTATTACCTTACATAAATATATTTATTTCATTTATGTATCATA
1 TTTTTATTACCTTACATAAATATATCTATTTCATTTATG--TCATA
** ** *
63842 TTTTTATTATTTTACATTGATATATCTATTTTATTTATGTCATA
1 TTTTTATTACCTTACATAAATATATCTATTTCATTTATGTCATA
63886 TTT
1 TTT
63889 AAATTATTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 8 0.20
46 33 0.80
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (44 bp):
TTTTTATTACCTTACATAAATATATCTATTTCATTTATGTCATA
Found at i:63849 original size:28 final size:26
Alignment explanation
Indices: 63818--63884 Score: 64
Period size: 28 Copynumber: 2.5 Consensus size: 26
63808 TACATAAATA
* *
63818 TATTTATTTCATTTATGTATCATATTT
1 TATTTATTTCATTGATATATC-TATTT
63845 T-TATTATTTTACATTGATATATCTATTT
1 TAT-TTA-TTT-CATTGATATATCTATTT
*
63873 TATTTATGTCAT
1 TATTTATTTCAT
63885 ATTTAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
26 4 0.12
27 6 0.18
28 12 0.36
29 11 0.33
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.61
Consensus pattern (26 bp):
TATTTATTTCATTGATATATCTATTT
Found at i:64694 original size:6 final size:6
Alignment explanation
Indices: 64683--64801 Score: 195
Period size: 6 Copynumber: 19.7 Consensus size: 6
64673 CCACTAAAAA
64683 CTCTTC CTCTTC C-CTTC AACTCTTC CTCTTC CTCTTC CTCTTC CTCTTC
1 CTCTTC CTCTTC CTCTTC --CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC
64732 CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC
1 CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC
* *
64780 CTCTTC TTATTC CTCTTC CTCT
1 CTCTTC CTCTTC CTCTTC CTCT
64802 CCAAAGTGAA
Statistics
Matches: 106, Mismatches: 4, Indels: 6
0.91 0.03 0.05
Matches are distributed among these distances:
5 4 0.04
6 97 0.92
7 1 0.01
8 4 0.04
ACGTcount: A:0.03, C:0.48, G:0.00, T:0.50
Consensus pattern (6 bp):
CTCTTC
Found at i:65605 original size:20 final size:20
Alignment explanation
Indices: 65555--65605 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
65545 CATAGTCGTG
* *
65555 AGTATCGATATTGTACCAAC
1 AGTATCGATACTGGACCAAC
* * *
65575 AGTTTCTATACTGGACCAGC
1 AGTATCGATACTGGACCAAC
65595 AGTATCGATAC
1 AGTATCGATAC
65606 CAATCACCTA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTGGACCAAC
Found at i:71683 original size:19 final size:20
Alignment explanation
Indices: 71659--71696 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
71649 CCCACCAGAC
*
71659 ACTTTTCCTCTTCC-CTTTA
1 ACTTTTCATCTTCCTCTTTA
71678 ACTTTTCATCTTCCTCTTT
1 ACTTTTCATCTTCCTCTTT
71697 CTTTCCAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.11, C:0.34, G:0.00, T:0.55
Consensus pattern (20 bp):
ACTTTTCATCTTCCTCTTTA
Found at i:77448 original size:58 final size:61
Alignment explanation
Indices: 77386--77520 Score: 188
Period size: 60 Copynumber: 2.3 Consensus size: 61
77376 TAAACTTTAA
* * *
77386 AACATTTTAATTTCATCCTTAA-TTATGA-GTATC-TTTTAAATTAGTCCTCAAAATTTTT-
1 AACATTTCAATTTCATCCTTAAGTTATGACAT-TCATTTTAAATTAGTCCCCAAAATTTTTG
*
77444 AACATTTCAATTTCATCCTTAAGTTATGACATTCATTTTAAATTAGTCCCCAAACTTTTTG
1 AACATTTCAATTTCATCCTTAAGTTATGACATTCATTTTAAATTAGTCCCCAAAATTTTTG
*
77505 AACATTCCAATTTCAT
1 AACATTTCAATTTCAT
77521 TCCAAAATAT
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
58 21 0.31
59 8 0.12
60 24 0.35
61 15 0.22
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.44
Consensus pattern (61 bp):
AACATTTCAATTTCATCCTTAAGTTATGACATTCATTTTAAATTAGTCCCCAAAATTTTTG
Found at i:77743 original size:60 final size:60
Alignment explanation
Indices: 77675--77837 Score: 161
Period size: 60 Copynumber: 2.7 Consensus size: 60
77665 AAATAGGAAT
** *
77675 ATTTAAAAGTTTTGGGACCAATTCAATAAAAAG-GTTATAGTTTAGGGATGAAATTAAAAC
1 ATTTAAAAGTTTAAGGACCAATTCAA-AAAAAGAGTTATAATTTAGGGATGAAATTAAAAC
* * * * * *
77735 ATTTAAAAGTTTAAGGACTAATTTAAAATAAGAGTTATAATTTATGGATGAAATTAGAAT
1 ATTTAAAAGTTTAAGGACCAATTCAAAAAAAGAGTTATAATTTAGGGATGAAATTAAAAC
* * * *
77795 ATTCAAAA-TTTAAGGATCAACTTAAAAATAAATA-TTATAATTT
1 ATTTAAAAGTTTAAGGACCAA-TTCAAAA-AAAGAGTTATAATTT
77838 GAGGACATGT
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
59 15 0.18
60 67 0.79
61 3 0.04
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.35
Consensus pattern (60 bp):
ATTTAAAAGTTTAAGGACCAATTCAAAAAAAGAGTTATAATTTAGGGATGAAATTAAAAC
Found at i:83282 original size:233 final size:235
Alignment explanation
Indices: 82816--83287 Score: 695
Period size: 233 Copynumber: 2.0 Consensus size: 235
82806 TGATTTCATT
* * * *
82816 ATTGAATCAAGTGAAAATCCACAAACCCTAACCCATATACTATTCAGCCGTGGGAAATAAATTAA
1 ATTGAATCAACTGAAAATCCACAAAACCTAACCCA-ATACTATTCAGCCATGGGAAATAAACTAA
** *
82881 GGGAAAATATGGAACCTCTAATCTTATAAATGATAAAAGATTCTACAAGCTTTAGAATGTTATTT
65 GGGAAAATATAAAACCCCTAATCTTATAAATGATAAAAGA-TCTACAAGCTTTAGAATGTTATTT
* *
82946 GGACCTATTTATAATTTTGTTAAAGTTGGGGACCTATTTAGTAATTATAGAAAATTATGAGATCA
129 GGACCTATTTATAATTTTGTTAAAGTTGGGGACCTATTCAATAATTATAGAAAATTATGAGATCA
* * *
83011 ATGTATAATTGATCAATAGTTTATGGACTATACTGAAAATTA
194 ATGTATAATTGATCAATAATTGATAGACTATACTGAAAATTA
*
83053 ATTGAATCAACTGAAAATCCGCAAAACCTAACCC-ATACTA-TCAGCCATGGGAAA-AAACTAAG
1 ATTGAATCAACTGAAAATCCACAAAACCTAACCCAATACTATTCAGCCATGGGAAATAAACTAAG
*
83115 GGAAAATATAAAACCCCTAATCTTATAAATGATATTTGAAAG-T-TAGAAGCTTTAGAATGTTAT
66 GGAAAATATAAAACCCCTAATCTTATAAATGATA----AAAGATCTACAAGCTTTAGAATGTTAT
* *
83178 TTGGACCTATTTGTAATTTTGTTAAAGTTGGGGACCTATTCAATAATTAT-GTAAATTATGAGAT
127 TTGGACCTATTTATAATTTTGTTAAAGTTGGGGACCTATTCAATAATTATAGAAAATTATGAGAT
*
83242 CAATGTATAATTGTTCAATAATTGATAGACTATACTGAAAATTA
192 CAATGTATAATTGATCAATAATTGATAGACTATACTGAAAATTA
83286 AT
1 AT
83288 GTTAGAGTGT
Statistics
Matches: 214, Mismatches: 17, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
233 93 0.43
234 79 0.37
235 7 0.03
237 35 0.16
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (235 bp):
ATTGAATCAACTGAAAATCCACAAAACCTAACCCAATACTATTCAGCCATGGGAAATAAACTAAG
GGAAAATATAAAACCCCTAATCTTATAAATGATAAAAGATCTACAAGCTTTAGAATGTTATTTGG
ACCTATTTATAATTTTGTTAAAGTTGGGGACCTATTCAATAATTATAGAAAATTATGAGATCAAT
GTATAATTGATCAATAATTGATAGACTATACTGAAAATTA
Found at i:84856 original size:70 final size:69
Alignment explanation
Indices: 84741--84936 Score: 257
Period size: 70 Copynumber: 2.8 Consensus size: 69
84731 CTTAATGCAA
* * * * *
84741 CACTAGAGTTTAAACCCAATACACTTAGTGCAGATGGTGGACACGAGCTTATGTGTCATATTCGG
1 CACTAGAGTGTATA-CCAACACACTTAGTGCATATGGTGGGCACGAGCTTATGTGTCATATTCGG
84806 TTTAG
65 TTTAG
84811 CACTAGAGTGTATATCCAACACACTTAGTGCATATGGTGGGCACGAGCTTATGTGTCATATTCGG
1 CACTAGAGTGTATA-CCAACACACTTAGTGCATATGGTGGGCACGAGCTTATGTGTCATATTCGG
84876 TTTAG
65 TTTAG
* * ** * * *
84881 CACTAGAGTGCATACCGAAGACACTTAGTGTGTATGGTAGGCACAACCTTATGTGT
1 CACTAGAGTGTATACC-AACACACTTAGTGCATATGGTGGGCACGAGCTTATGTGT
84937 ATTAGCACTT
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
69 2 0.02
70 110 0.98
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (69 bp):
CACTAGAGTGTATACCAACACACTTAGTGCATATGGTGGGCACGAGCTTATGTGTCATATTCGGT
TTAG
Found at i:86162 original size:35 final size:35
Alignment explanation
Indices: 86114--86193 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
86104 AACATATTCA
86114 TCAATTACATTCTAAACCCCAAAATAC-AAAATACT
1 TCAATTACATTCTAAACCCC-AAATACTAAAATACT
* * *
86149 TTAATTACATTCTAAACCTCAAATTCTAAAATACT
1 TCAATTACATTCTAAACCCCAAATACTAAAATACT
86184 TCAATTACAT
1 TCAATTACAT
86194 GCCCAACCCG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 5 0.12
35 35 0.88
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.33
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATACTAAAATACT
Found at i:86208 original size:35 final size:35
Alignment explanation
Indices: 86114--86209 Score: 88
Period size: 35 Copynumber: 2.7 Consensus size: 35
86104 AACATATTCA
* * * *
86114 TCAATTACATTCTAAACCCCAAAATAC-AAAATACT
1 TCAATTACATGCCAAACCTC-AAATTCTAAAATACT
* * *
86149 TTAATTACATTCTAAACCTCAAATTCTAAAATACT
1 TCAATTACATGCCAAACCTCAAATTCTAAAATACT
*
86184 TCAATTACATGCCCAACC-CGAAATTC
1 TCAATTACATGCCAAACCTC-AAATTC
86210 ATAATTCATT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
34 6 0.12
35 46 0.88
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.29
Consensus pattern (35 bp):
TCAATTACATGCCAAACCTCAAATTCTAAAATACT
Found at i:86553 original size:148 final size:147
Alignment explanation
Indices: 86377--86780 Score: 684
Period size: 148 Copynumber: 2.7 Consensus size: 147
86367 CAATTCAGTG
*
86377 TATAAAATAGTTGACTCGAAATTTTTTCGAATTGAGTTTATAAAATTTAAATCAAGTCGAATTGG
1 TATAAAATAGTTGACTC-AAATTTTTTCGAATTGAGTTTATAAAATTTAAATCAAGTCGAATTGA
86442 ATTAAATTTTTGAGTTTCTTTTTAAATTTAATTATAAATATTTACCACATTACAATATTATTTGA
65 ATTAAATTTTTGAGTTTCTTTTTAAATTTAATTATAAATATTTACCACATTACAATATTATTTGA
86507 TTCTAATTCAGTTCAATT
130 TTCTAATTCAGTTCAATT
86525 TATAAAATAGTTGACTCAAATTTTTTTCGAATTGAGTTTATAAAATTTAAATCAAGTCGAATTGA
1 TATAAAATAGTTGACTCAAA-TTTTTTCGAATTGAGTTTATAAAATTTAAATCAAGTCGAATTGA
*
86590 ATTAAATTTTTGAGTTTCTTTTTAAATTTAATTATAAATATTTATCACATTACAATATTATTTGA
65 ATTAAATTTTTGAGTTTCTTTTTAAATTTAATTATAAATATTTACCACATTACAATATTATTTGA
86655 TTCTAATTCAGTTCAATT
130 TTCTAATTCAGTTCAATT
** *
86673 TATAAAATAGTTGACTCAAAAAATTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAATTGA
1 TATAAAATAGTTGACTC-AAATTTTTTCGAATTGAGTTTATAAAATTTAAATCAAGTCGAATTGA
* * * * *
86738 AATGAATTTTCGAGTTTCTGTTTAAACTTAATTAT-AATATTTA
65 ATTAAATTTTTGAGTTTCTTTTTAAATTTAATTATAAATATTTA
86781 TAATACTATA
Statistics
Matches: 244, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
147 11 0.05
148 230 0.94
149 3 0.01
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (147 bp):
TATAAAATAGTTGACTCAAATTTTTTCGAATTGAGTTTATAAAATTTAAATCAAGTCGAATTGAA
TTAAATTTTTGAGTTTCTTTTTAAATTTAATTATAAATATTTACCACATTACAATATTATTTGAT
TCTAATTCAGTTCAATT
Found at i:88574 original size:26 final size:27
Alignment explanation
Indices: 88508--88575 Score: 95
Period size: 25 Copynumber: 2.6 Consensus size: 27
88498 AGTCGAGGGT
*
88508 TCTACGTGGTCCTTCGAACATATGTGT
1 TCTACGTGGTCCTTCGAACATATGTGC
88535 TCTACGT-GTCCTTCG-ACATATGTGC
1 TCTACGTGGTCCTTCGAACATATGTGC
* *
88560 TCTATGTGGTACTTCG
1 TCTACGTGGTCCTTCG
88576 GGACATAGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 15 0.41
26 15 0.41
27 7 0.19
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (27 bp):
TCTACGTGGTCCTTCGAACATATGTGC
Found at i:89870 original size:35 final size:35
Alignment explanation
Indices: 89831--89910 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
89821 GGGGTTGGGC
* *
89831 ATGTAATTGAAGTATTTTGGAATTTGAGGTTTAGA
1 ATGTAATTGAAGTATTTTAGAATTTGAGGTGTAGA
* *
89866 ATGTAATTAAAGTATTTTAGAATTTGGGGTGTAGA
1 ATGTAATTGAAGTATTTTAGAATTTGAGGTGTAGA
89901 ATGTAATTGA
1 ATGTAATTGA
89911 TGGTTGTGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTAGAATTTGAGGTGTAGA
Found at i:91398 original size:2 final size:2
Alignment explanation
Indices: 91391--91419 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
91381 ATACTAAATA
91391 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
91420 ACGTATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:92234 original size:21 final size:19
Alignment explanation
Indices: 92209--92260 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
92199 ATTAAGTTAC
92209 TAATAAAATATATTTAATAGT
1 TAATAAAATATATTT-A-AGT
*
92230 TAATATAA-ATATTTAAGT
1 TAATAAAATATATTTAAGT
*
92248 TAATAATATATAT
1 TAATAAAATATAT
92261 ATATATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 9 0.33
19 5 0.19
20 6 0.22
21 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (19 bp):
TAATAAAATATATTTAAGT
Found at i:92255 original size:42 final size:44
Alignment explanation
Indices: 92200--92281 Score: 107
Period size: 42 Copynumber: 1.9 Consensus size: 44
92190 ATTTTTTTAA
* *
92200 TTAAGTTACTAATA-AAATATATTTA-ATAGT-TAATATAAATAT
1 TTAAGTTAATAATATAAATATATATATATA-TATAATATAAATAT
*
92242 TTAAGTTAATAATATATATATATATATATATATAATATAA
1 TTAAGTTAATAATATAAATATATATATATATATAATATAA
92282 TATGAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 13 0.38
43 10 0.29
44 11 0.32
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (44 bp):
TTAAGTTAATAATATAAATATATATATATATATAATATAAATAT
Found at i:92260 original size:2 final size:2
Alignment explanation
Indices: 92253--92284 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
92243 TAAGTTAATA
92253 AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
92285 GAATTTAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:92262 original size:21 final size:20
Alignment explanation
Indices: 92209--92262 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
92199 ATTAAGTTAC
92209 TAATAA-AATATATTTAATAGT
1 TAATAATAATATATTT-A-AGT
92230 TAAT-ATAA-ATATTTAAGT
1 TAATAATAATATATTTAAGT
92248 TAATAATATATATAT
1 TAATAATA-ATATAT
92263 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 7 0.24
19 4 0.14
20 8 0.28
21 10 0.34
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (20 bp):
TAATAATAATATATTTAAGT
Found at i:99450 original size:39 final size:39
Alignment explanation
Indices: 99393--99484 Score: 130
Period size: 39 Copynumber: 2.4 Consensus size: 39
99383 CTACAAGTTC
* *
99393 TTCTCATTATGAATTTATTCTCCTTTTTTGAATGAGCTA
1 TTCTCATTATGAACTTATTCTCCTTATTTGAATGAGCTA
* * * *
99432 TTCTCATTTTGAACTTATTCTCCTTATTTGGATGAGTTT
1 TTCTCATTATGAACTTATTCTCCTTATTTGAATGAGCTA
99471 TTCTCATTATGAAC
1 TTCTCATTATGAAC
99485 CCTTCCATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.22, C:0.16, G:0.11, T:0.51
Consensus pattern (39 bp):
TTCTCATTATGAACTTATTCTCCTTATTTGAATGAGCTA
Found at i:99739 original size:121 final size:122
Alignment explanation
Indices: 99518--99756 Score: 280
Period size: 121 Copynumber: 2.0 Consensus size: 122
99508 CTCCTAGTGT
* * *
99518 GATTTGAGTAAAAGGTCGAACAAGTTCTTCTCTTTCTGAACTTATATTCCTTTGATTATACTGGT
1 GATTTGAGTAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTATATTCCTTTGATTATACTGAT
* *
99583 CCCCTCTTCTATGAACTCTACAAGAATGACAATATTGA-CCACCTTCTTCTGTGATG
66 CCCCTCTTCTATGAAATCTACAAGAATGACAATATTGATCCACCTCCTTCTGTGATG
*
99639 GATTTGAGTAAAAGGTCG-A-AAGTTC-T-TCATTATG-ACTCT-TCTTCCTTTGATTATGA-TG
1 GATTTGAGTAAAAGGTCGAACAAGTTCTTCTCATTATGAACT-TATATTCCTTTGATTAT-ACTG
*
99697 ATCCACCTCTTTCTGTGATGAAATCTAACAAGGATGAC-ATATTGATCCACCTCCTTCTGT
64 ATCC-CCTC-TTC--T-ATGAAATCT-ACAAGAATGACAATATTGATCCACCTCCTTCTGT
99757 TATTGATCAA
Statistics
Matches: 102, Mismatches: 7, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
116 22 0.22
117 12 0.12
118 4 0.04
119 6 0.06
120 2 0.02
121 33 0.32
122 23 0.23
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.37
Consensus pattern (122 bp):
GATTTGAGTAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTATATTCCTTTGATTATACTGAT
CCCCTCTTCTATGAAATCTACAAGAATGACAATATTGATCCACCTCCTTCTGTGATG
Found at i:100001 original size:157 final size:156
Alignment explanation
Indices: 99775--100171 Score: 459
Period size: 157 Copynumber: 2.5 Consensus size: 156
99765 AAACAAAAGT
* *
99775 TGAACAAGCTCTTCT-TTATGAACTCATTCTCACTCTTCAGACGAGTTCTTCTCATTAT-AACCA
1 TGAACAAGTTCTTCTCTTATGAAC-C-TTCTCACTCTTCAGACGAGTTCTTCTCATTATGAACCC
* * *
99838 TCCATTGGAAATGATGATCCACCTCAT-TCTGTGATGGATTCAATCAAAATGATGATGCTGATCT
64 TACATTGGAAATGATGATCCACCTC-TGTCTATGATGGATTCAATCAAAATGATGATGCTGATAT
* *
99902 ATCTCCTTATGTGATAG-AGTCGAGAAATGGG
128 ATCTCC-T-TCTGATAGAAGTC-AGAAAAGGG
99933 TGAACAAGTTCTTCTCATTAT-AA-CTTCTCACTCTTCAGACGAGTTCTTCTCATTATGAACCCT
1 TGAACAAGTTCTTCTC-TTATGAACCTTCTCACTCTTCAGACGAGTTCTTCTCATTATGAACCCT
* * * * *
99996 TCATTGGAAATGACGATCCACCTCTGTCTATGATGGATTCGATCAAAATGCTGATGTTGATATAT
65 ACATTGGAAATGATGATCCACCTCTGTCTATGATGGATTCAATCAAAATGATGATGCTGATATAT
* * *
100061 CTTCTTCTGATAGAATTCATAAAAGGG
130 CTCCTTCTGATAGAAGTCAGAAAAGGG
* ** * * *
100088 TGAACAAGTTCTTCTCTTATGAACCTCTTCTCCCTCTT-AGTTGAGTTATTCTTATTATGAACTC
1 TGAACAAGTTCTTCTCTTATGAA-C-CTTCTCACTCTTCAGACGAGTTCTTCTCATTATGAACCC
*
100152 TAC-TTGGAAATGCTGATCCA
64 TACATTGGAAATGATGATCCA
100172 TTTCCTTCTA
Statistics
Matches: 207, Mismatches: 23, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
154 4 0.02
155 32 0.15
156 52 0.25
157 88 0.43
158 25 0.12
159 2 0.01
160 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (156 bp):
TGAACAAGTTCTTCTCTTATGAACCTTCTCACTCTTCAGACGAGTTCTTCTCATTATGAACCCTA
CATTGGAAATGATGATCCACCTCTGTCTATGATGGATTCAATCAAAATGATGATGCTGATATATC
TCCTTCTGATAGAAGTCAGAAAAGGG
Found at i:102647 original size:14 final size:14
Alignment explanation
Indices: 102617--102678 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
102607 TTTTTCTTTT
*
102617 TTTTTATTTTTCTTC
1 TTTTTATTTCTC-TC
102632 TTTTTATTTCTCTC
1 TTTTTATTTCTCTC
*
102646 TTTTTATTTTTCT-
1 TTTTTATTTCTCTC
* *
102659 TTTTTCTTTTCTTTC
1 TTTTT-ATTTCTCTC
102674 TTTTT
1 TTTTT
102679 TTTTTATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 5 0.12
14 19 0.47
15 16 0.40
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTATTTCTCTC
Found at i:102674 original size:32 final size:33
Alignment explanation
Indices: 102597--102713 Score: 104
Period size: 33 Copynumber: 3.7 Consensus size: 33
102587 TGAACCCTCC
*
102597 TTTCATTTCTTT-TTTCTTTTT-TTTTAT-TTT
1 TTTCTTTTCTTTCTTTCTTTTTATTTTATCTTT
* *
102627 TCTTCTTTTTATTTCTCTCTTTTTATTTT-TCTTT
1 T-TTC-TTTTCTTTCTTTCTTTTTATTTTATCTTT
* *
102661 TTTCTTTTCTTTCTTTTTTTTTTATTTTCTCTTT
1 TTTCTTTTCTTTC-TTTCTTTTTATTTTATCTTT
*
102695 TAT-TTTTC-TTC-TTCTTTTT
1 TTTCTTTTCTTTCTTTCTTTTT
102714 TCTCTTTTCT
Statistics
Matches: 72, Mismatches: 8, Indels: 14
0.77 0.09 0.15
Matches are distributed among these distances:
30 8 0.11
31 3 0.04
32 17 0.24
33 29 0.40
34 15 0.21
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (33 bp):
TTTCTTTTCTTTCTTTCTTTTTATTTTATCTTT
Found at i:102674 original size:45 final size:44
Alignment explanation
Indices: 102607--102720 Score: 128
Period size: 45 Copynumber: 2.6 Consensus size: 44
102597 TTTCATTTCT
*
102607 TTTTTCTTTTTT-TTTATTTTTC-TTCTTTTTATTTCTCTCTTTTTA
1 TTTTTCTTTTTTCTTT-TCTTTCTTTCTTTTTATTT-TCTC-TTTTA
*
102652 TTTTTCTTTTTTCTTTTCTTTCTTTTTTTTTTATTTTCTCTTTTA
1 TTTTTCTTTTTTCTTTTCTTTC-TTTCTTTTTATTTTCTCTTTTA
*
102697 TTTTTC-TTCTTCTTTT-TTCTCTTT
1 TTTTTCTTTTTTCTTTTCTT-TCTTT
102721 TCTTCAGGTG
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
43 5 0.08
44 11 0.18
45 28 0.45
46 7 0.11
47 11 0.18
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (44 bp):
TTTTTCTTTTTTCTTTTCTTTCTTTCTTTTTATTTTCTCTTTTA
Found at i:102702 original size:33 final size:31
Alignment explanation
Indices: 102609--102724 Score: 112
Period size: 29 Copynumber: 3.7 Consensus size: 31
102599 TCATTTCTTT
* *
102609 TTTCTTTTTTTTTATTTTTC--TTCTTTTTA
1 TTTCTTTTTTTTTATTTTTCTTTTATTTTTC
* * *
102638 TTTCTCTCTTTTTATTTTTCTTTTTTCTTTTC
1 TTTCTTTTTTTTTATTTTTCTTTTAT-TTTTC
102670 TTTCTTTTTTTTTTATTTTCTCTTTTATTTTTC
1 TTTC-TTTTTTTTTATTTT-TCTTTTATTTTTC
* *
102703 -TTCTTCTTTTTTCTCTTTTCTT
1 TTTCTTTTTTTTTAT-TTTTCTT
102725 CAGGTGTAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
29 18 0.25
31 16 0.22
32 14 0.19
33 17 0.24
34 7 0.10
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (31 bp):
TTTCTTTTTTTTTATTTTTCTTTTATTTTTC
Found at i:110467 original size:162 final size:162
Alignment explanation
Indices: 110061--110442 Score: 449
Period size: 157 Copynumber: 2.4 Consensus size: 162
110051 AAGCTCTTCT
* * * * * *
110061 TTAT-AAACTCCTTATCACTCTTCATACGAGTTCTTCTCATTATGAACCATTCCATTAGAAATGA
1 TTATGAAACT-CTTCTCACTCTTCAGATGAGTTCCTCTCATTATGAACCCTTCCATTGGAAATGA
* ** * * *
110125 CGATCCACCTTATTCTATGATGG-----ATCAAAATGTTGATGCTGATCTATATTCTTCTGCAAT
65 CAATCCACCTCCTTATATGATGGATCCAATCAAAATGTTGATGCTCATCTATATCCTTCTGCAAT
*
110185 AGATCGAGAAAAAGGGTGAACAAGTTCTTCTCA
130 AGATCGAGAAAAAGGGTGAACAAGTTATTCTCA
* * *
110218 TTATGAAATTCTTCTCACTCTTCAGATGAGTTCTTCTCATTTTGAACCCTTCCATTGGAAATGAC
1 TTATGAAACTCTTCTCACTCTTCAGATGAGTTCCTCTCATTATGAACCCTTCCATTGGAAATGAC
* *
110283 AATCCACCTCCTTATATGATGGATCCAATCAAAATGTTGATGCTCATCTATCTCCTTCTGCGATA
66 AATCCACCTCCTTATATGATGGATCCAATCAAAATGTTGATGCTCATCTATATCCTTCTGCAATA
* *
110348 GAATCTAG-CAAAGGGTTGAACAAGTTATTCTCA
131 G-ATCGAGAAAAAGGG-TGAACAAGTTATTCTCA
* * * *
110381 TTATGAACCTCTTCTCCCTC-TCAGGATGAGTTCCTCTCATTATGAACTC-TCTATTGGAAATG
1 TTATGAAACTCTTCTCACTCTTCA-GATGAGTTCCTCTCATTATGAACCCTTCCATTGGAAATG
110443 TTGATCCATT
Statistics
Matches: 191, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
157 71 0.37
158 4 0.02
162 56 0.29
163 60 0.31
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (162 bp):
TTATGAAACTCTTCTCACTCTTCAGATGAGTTCCTCTCATTATGAACCCTTCCATTGGAAATGAC
AATCCACCTCCTTATATGATGGATCCAATCAAAATGTTGATGCTCATCTATATCCTTCTGCAATA
GATCGAGAAAAAGGGTGAACAAGTTATTCTCA
Found at i:112697 original size:83 final size:82
Alignment explanation
Indices: 112558--112719 Score: 256
Period size: 83 Copynumber: 2.0 Consensus size: 82
112548 GGAATTTTGA
*
112558 GAGAGTTTTACTCACTCTAAAACTCCTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAA
1 GAGAGTTTTACTCACACTAAAACTCCTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAA
112623 ATTTAAAATATTAAACCT
66 ATTT-AAATATTAAACCT
* *
112641 GAGAGTTTTACTC-CAACT-AAACATCTTTTAATATCTAAATTTAAACAACTAATAATATCTTTT
1 GAGAGTTTTACTCAC-ACTAAAAC-TCCTTTAATATCTAAATTTAAACAAATAATAATATCTTTT
112704 AAATTTAAATATTAAA
64 AAATTTAAATATTAAA
112720 TAGATATACA
Statistics
Matches: 74, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
82 15 0.20
83 59 0.80
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.39
Consensus pattern (82 bp):
GAGAGTTTTACTCACACTAAAACTCCTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAA
ATTTAAATATTAAACCT
Found at i:115987 original size:13 final size:13
Alignment explanation
Indices: 115954--116041 Score: 97
Period size: 13 Copynumber: 6.5 Consensus size: 13
115944 AACCCGACCC
115954 GACCCGACCCGTT
1 GACCCGACCCGTT
*
115967 TA-CCGACCCGTT
1 GACCCGACCCGTT
* *
115979 TACCCGACCAGTT
1 GACCCGACCCGTT
115992 GACCCGACCCAACCCGTT
1 GACCCG-----ACCCGTT
116010 GACCCGACCCGTT
1 GACCCGACCCGTT
116023 GACCCGACCCGTT
1 GACCCGACCCGTT
116036 GACCCG
1 GACCCG
116042 TTGACCGTTG
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
12 12 0.18
13 41 0.63
18 12 0.18
ACGTcount: A:0.18, C:0.45, G:0.20, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:116014 original size:8 final size:8
Alignment explanation
Indices: 116003--116055 Score: 57
Period size: 8 Copynumber: 7.5 Consensus size: 8
115993 ACCCGACCCA
116003 ACCCGTTG
1 ACCCGTTG
116011 ACCC---G
1 ACCCGTTG
116016 ACCCGTTG
1 ACCCGTTG
116024 ACCC---G
1 ACCCGTTG
116029 ACCCGTTG
1 ACCCGTTG
116037 ACCCGTTG
1 ACCCGTTG
116045 A-CCGTTG
1 ACCCGTTG
116052 ACCC
1 ACCC
116056 ACGTTGACCA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
5 10 0.26
7 7 0.18
8 21 0.55
ACGTcount: A:0.15, C:0.43, G:0.23, T:0.19
Consensus pattern (8 bp):
ACCCGTTG
Found at i:116015 original size:31 final size:31
Alignment explanation
Indices: 115972--116032 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
115962 CCGTTTACCG
*
115972 ACCCGTTTACCCGACCAGTTGACCCGACCCA
1 ACCCGTTGACCCGACCAGTTGACCCGACCCA
*
116003 ACCCGTTGACCCGACCCGTTGACCCGACCC
1 ACCCGTTGACCCGACCAGTTGACCCGACCC
116033 GTTGACCCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.20, C:0.48, G:0.18, T:0.15
Consensus pattern (31 bp):
ACCCGTTGACCCGACCAGTTGACCCGACCCA
Found at i:116030 original size:44 final size:43
Alignment explanation
Indices: 115949--116041 Score: 141
Period size: 44 Copynumber: 2.1 Consensus size: 43
115939 GTCATAACCC
* * *
115949 GACCCGACCCGACCCGTTTACCGACCCGTTTACCCGACCAGTT
1 GACCCGACCCAACCCGTTGACCGACCCGTTGACCCGACCAGTT
*
115992 GACCCGACCCAACCCGTTGACCCGACCCGTTGACCCGACCCGTT
1 GACCCGACCCAACCCGTTGA-CCGACCCGTTGACCCGACCAGTT
116036 GACCCG
1 GACCCG
116042 TTGACCGTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
43 18 0.40
44 27 0.60
ACGTcount: A:0.18, C:0.46, G:0.20, T:0.15
Consensus pattern (43 bp):
GACCCGACCCAACCCGTTGACCGACCCGTTGACCCGACCAGTT
Found at i:116033 original size:18 final size:18
Alignment explanation
Indices: 115980--116020 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
115970 CGACCCGTTT
115980 ACCCGACCAGTTGACCCG
1 ACCCGACCAGTTGACCCG
* *
115998 ACCCAACCCGTTGACCCG
1 ACCCGACCAGTTGACCCG
116016 ACCCG
1 ACCCG
116021 TTGACCCGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.22, C:0.49, G:0.20, T:0.10
Consensus pattern (18 bp):
ACCCGACCAGTTGACCCG
Found at i:117359 original size:18 final size:18
Alignment explanation
Indices: 117333--117368 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
117323 TCGAAAGGAC
*
117333 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
117351 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
117369 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:118535 original size:23 final size:23
Alignment explanation
Indices: 118509--118582 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
118499 AATTCTATTA
*
118509 TGATCCTGACCTGGATTCTGATC
1 TGATCATGACCTGGATTCTGATC
*
118532 TGAT-ATTGACATGGATTCTGATC
1 TGATCA-TGACCTGGATTCTGATC
*
118555 TGATACATGACCTGGATTCTGATA
1 TGAT-CATGACCTGGATTCTGATC
118579 TGAT
1 TGAT
118583 ACTTGACTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
23 24 0.55
24 19 0.43
25 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (23 bp):
TGATCATGACCTGGATTCTGATC
Found at i:118570 original size:24 final size:24
Alignment explanation
Indices: 118515--118589 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
118505 ATTATGATCC
118515 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* *
118538 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
*
118562 TGACCTGGATTCTGATATGATACT
1 TGACCTGGATTCTGATCTGATACT
118586 TGAC
1 TGAC
118590 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:120799 original size:13 final size:13
Alignment explanation
Indices: 120780--120868 Score: 106
Period size: 13 Copynumber: 6.5 Consensus size: 13
120770 AACCCGACCC
120780 GACCCGACCCGTT
1 GACCCGACCCGTT
*
120793 TACCCGACCCGTT
1 GACCCGACCCGTT
* *
120806 TACCCGACCAGTT
1 GACCCGACCCGTT
120819 GACCCGACCCAACCCGTT
1 GACCCG-----ACCCGTT
120837 GACCCGACCCGTT
1 GACCCGACCCGTT
120850 GACCCGACCCGTT
1 GACCCGACCCGTT
120863 GACCCG
1 GACCCG
120869 TTGACCGTTG
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
13 55 0.82
18 12 0.18
ACGTcount: A:0.18, C:0.46, G:0.20, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:120834 original size:31 final size:31
Alignment explanation
Indices: 120794--120859 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
120784 CGACCCGTTT
* *
120794 ACCCGACCCGTTTACCCGACCAGTTGACCCG
1 ACCCAACCCGTTGACCCGACCAGTTGACCCG
*
120825 ACCCAACCCGTTGACCCGACCCGTTGACCCG
1 ACCCAACCCGTTGACCCGACCAGTTGACCCG
120856 ACCC
1 ACCC
120860 GTTGACCCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.20, C:0.48, G:0.18, T:0.14
Consensus pattern (31 bp):
ACCCAACCCGTTGACCCGACCAGTTGACCCG
Found at i:120841 original size:8 final size:8
Alignment explanation
Indices: 120830--120882 Score: 57
Period size: 8 Copynumber: 7.5 Consensus size: 8
120820 ACCCGACCCA
120830 ACCCGTTG
1 ACCCGTTG
120838 ACCC---G
1 ACCCGTTG
120843 ACCCGTTG
1 ACCCGTTG
120851 ACCC---G
1 ACCCGTTG
120856 ACCCGTTG
1 ACCCGTTG
120864 ACCCGTTG
1 ACCCGTTG
120872 A-CCGTTG
1 ACCCGTTG
120879 ACCC
1 ACCC
120883 ACGTTGACCA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
5 10 0.26
7 7 0.18
8 21 0.55
ACGTcount: A:0.15, C:0.43, G:0.23, T:0.19
Consensus pattern (8 bp):
ACCCGTTG
Found at i:120842 original size:44 final size:44
Alignment explanation
Indices: 120775--120868 Score: 152
Period size: 44 Copynumber: 2.1 Consensus size: 44
120765 GTCATAACCC
* * *
120775 GACCCGACCCGACCCGTTTACCCGACCCGTTTACCCGACCAGTT
1 GACCCGACCCAACCCGTTGACCCGACCCGTTGACCCGACCAGTT
*
120819 GACCCGACCCAACCCGTTGACCCGACCCGTTGACCCGACCCGTT
1 GACCCGACCCAACCCGTTGACCCGACCCGTTGACCCGACCAGTT
120863 GACCCG
1 GACCCG
120869 TTGACCGTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.15
Consensus pattern (44 bp):
GACCCGACCCAACCCGTTGACCCGACCCGTTGACCCGACCAGTT
Found at i:120860 original size:18 final size:18
Alignment explanation
Indices: 120807--120847 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
120797 CGACCCGTTT
120807 ACCCGACCAGTTGACCCG
1 ACCCGACCAGTTGACCCG
* *
120825 ACCCAACCCGTTGACCCG
1 ACCCGACCAGTTGACCCG
120843 ACCCG
1 ACCCG
120848 TTGACCCGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.22, C:0.49, G:0.20, T:0.10
Consensus pattern (18 bp):
ACCCGACCAGTTGACCCG
Found at i:122199 original size:18 final size:18
Alignment explanation
Indices: 122173--122208 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
122163 TCGAAAGGAC
*
122173 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
122191 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
122209 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:123398 original size:22 final size:22
Alignment explanation
Indices: 123368--123435 Score: 100
Period size: 22 Copynumber: 3.0 Consensus size: 22
123358 ATTATGATCC
123368 TGACCTGGATTCTGATCTGATA
1 TGACCTGGATTCTGATCTGATA
*
123390 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGAT--A
*
123414 TGACCTGGATTCTGATATGATA
1 TGACCTGGATTCTGATCTGATA
123436 CTTGACTTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
22 21 0.51
24 20 0.49
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35
Consensus pattern (22 bp):
TGACCTGGATTCTGATCTGATA
Found at i:123422 original size:24 final size:24
Alignment explanation
Indices: 123368--123441 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
123358 ATTATGATCC
123368 TGACCTGGATTCTGATCTGAT--A
1 TGACCTGGATTCTGATCTGATACA
*
123390 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACA
* *
123414 TGACCTGGATTCTGATATGATACT
1 TGACCTGGATTCTGATCTGATACA
123438 TGAC
1 TGAC
123442 TTGAATTATG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 20 0.43
24 26 0.57
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACA
Found at i:147120 original size:23 final size:21
Alignment explanation
Indices: 147090--147171 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 21
147080 AAAAAAGAAA
147090 AAAAAAGAAAAAAATGAATAATG
1 AAAAAAGAAAAAAAT-AA-AATG
*
147113 AAAAAAGAGAAAAATAAAGA-G
1 AAAAAAGAAAAAAATAAA-ATG
*
147134 AAAGAAA-AGAAAAAAGAAAAT-
1 AAA-AAAGA-AAAAAATAAAATG
*
147155 TAAAAAGAAAAAAATAA
1 AAAAAAGAAAAAAATAA
147172 TAAAAGGGGG
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
20 11 0.22
21 10 0.20
22 14 0.29
23 14 0.29
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (21 bp):
AAAAAAGAAAAAAATAAAATG
Found at i:147153 original size:28 final size:27
Alignment explanation
Indices: 147080--147177 Score: 76
Period size: 28 Copynumber: 3.5 Consensus size: 27
147070 AAGAAGAGAT
147080 AAAAAAGAAAAAA-AAAGAA-AAAAATG-
1 AAAAAAGAAAAAAGAAA-AATAAAAA-GA
* * *
147106 AATAATGAAAAAAGAGAAAAATAAAGAGA
1 AAAAAAG-AAAAA-AGAAAAATAAAAAGA
*
147135 AAGAAAAGAAAAAAGAAAATTAAAAAGA
1 AA-AAAAGAAAAAAGAAAAATAAAAAGA
*
147163 AAAAAATAATAAAAG
1 AAAAAAGAA-AAAAG
147178 GGGGCTAAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
26 5 0.09
27 11 0.19
28 24 0.42
29 14 0.25
30 3 0.05
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (27 bp):
AAAAAAGAAAAAAGAAAAATAAAAAGA
Found at i:148436 original size:37 final size:37
Alignment explanation
Indices: 148381--148496 Score: 175
Period size: 37 Copynumber: 3.2 Consensus size: 37
148371 AGGTTCCTTC
*
148381 GAAGTAAGTCAATCTTAAGCCTTCAC-GAAGGAGTAGT
1 GAAGCAAGTCAATCTTAAGCCTTCACGGAA-GAGTAGT
148418 GAAGCAAGTCAATCTTAAGCCTTCACGGAAGAGTAGT
1 GAAGCAAGTCAATCTTAAGCCTTCACGGAAGAGTAGT
* *
148455 AAAGCAAATC-ATCTT-AGCCTTCACGGAAGAGTAGT
1 GAAGCAAGTCAATCTTAAGCCTTCACGGAAGAGTAGT
148490 GAAGCAA
1 GAAGCAA
148497 ATCAGTCTCG
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
35 26 0.35
36 5 0.07
37 40 0.54
38 3 0.04
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (37 bp):
GAAGCAAGTCAATCTTAAGCCTTCACGGAAGAGTAGT
Found at i:148481 original size:35 final size:36
Alignment explanation
Indices: 148392--148500 Score: 168
Period size: 35 Copynumber: 3.0 Consensus size: 36
148382 AAGTAAGTCA
*
148392 ATCTTAAGCCTTCAC-GAAGGAGTAGTGAAGCAAGTC
1 ATCTTAAGCCTTCACGGAA-GAGTAGTGAAGCAAATC
*
148428 AATCTTAAGCCTTCACGGAAGAGTAGTAAAGCAAATC
1 -ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
148465 ATCTT-AGCCTTCACGGAAGAGTAGTGAAGCAAATC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
148500 A
1 A
148501 GTCTCGAGTC
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 30 0.44
36 5 0.07
37 30 0.44
38 3 0.04
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (36 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
Found at i:148662 original size:55 final size:54
Alignment explanation
Indices: 148504--148692 Score: 161
Period size: 55 Copynumber: 3.5 Consensus size: 54
148494 CAAATCAGTC
* * * *
148504 TCGAGTCTGAT-CTCCCTGAAAGAAGAGGAAGCATACCCA-TTTTCAGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGA-CCATTTTTC-GAAGATTGT
* * * * * **
148558 TAGAGTTTTGTACTCCCTGAAATAATAGGGAG-TGAACC-TGGTTACCGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAG-ACCAT--TTTTCGAAGATTGT
148613 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACTCATTTTTCGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGAC-CATTTTTCGAAGATTGT
* ** *
148668 TTGAGTCCAATACTCCTTGAAAGAA
1 TCGAGTCTTATACTCCCTGAAAGAA
148693 AAAGGAGTGG
Statistics
Matches: 105, Mismatches: 22, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
54 9 0.09
55 90 0.86
56 5 0.05
57 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (54 bp):
TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACCATTTTTCGAAGATTGT
Found at i:149126 original size:11 final size:11
Alignment explanation
Indices: 149110--149134 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
149100 TTGGCAGAAG
149110 TAAATGAGGAA
1 TAAATGAGGAA
149121 TAAATGAGGAA
1 TAAATGAGGAA
149132 TAA
1 TAA
149135 TATATCAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.20
Consensus pattern (11 bp):
TAAATGAGGAA
Found at i:151286 original size:30 final size:30
Alignment explanation
Indices: 151250--151316 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
151240 TAAAGTTTAA
* *
151250 AAAAGTTTAGTGACTAAAAGGGTAATTTTT
1 AAAAGTTTAGGGACTAAAAGGGTAATTTTC
* **
151280 AAAAGTTTAGGGACTATAAGTTTAATTTTC
1 AAAAGTTTAGGGACTAAAAGGGTAATTTTC
151310 AAAAGTT
1 AAAAGTT
151317 ATGTATTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.37
Consensus pattern (30 bp):
AAAAGTTTAGGGACTAAAAGGGTAATTTTC
Found at i:152306 original size:20 final size:21
Alignment explanation
Indices: 152278--152316 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
152268 TGATGTACTA
152278 TGCTGGAAATTAATGTTAGAG
1 TGCTGGAAATTAATGTTAGAG
*
152299 TGCT-GAAATTGATGTTAG
1 TGCTGGAAATTAATGTTAG
152317 GATGTGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.36
Consensus pattern (21 bp):
TGCTGGAAATTAATGTTAGAG
Found at i:152326 original size:19 final size:20
Alignment explanation
Indices: 152278--152328 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
152268 TGATGTACTA
*
152278 TGCTGGAAATTAATGTTAGAG
1 TGCT-GAAATTGATGTTAGAG
152299 TGCTGAAATTGATGTTAG-G
1 TGCTGAAATTGATGTTAGAG
152318 ATG-TGAAATTG
1 -TGCTGAAATTG
152329 GGTCATTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 9 0.32
20 15 0.54
21 4 0.14
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.35
Consensus pattern (20 bp):
TGCTGAAATTGATGTTAGAG
Found at i:153590 original size:22 final size:22
Alignment explanation
Indices: 153563--153607 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
153553 CACTAGTTAT
153563 TATATATGATGTTTATCATGAA
1 TATATATGATGTTTATCATGAA
*
153585 TATATATGATGTTTATTATGAA
1 TATATATGATGTTTATCATGAA
153607 T
1 T
153608 GTTATTTCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (22 bp):
TATATATGATGTTTATCATGAA
Found at i:157401 original size:21 final size:21
Alignment explanation
Indices: 157376--157415 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
157366 AAGACTTTAT
157376 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
157397 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
157416 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:161208 original size:23 final size:21
Alignment explanation
Indices: 161182--161260 Score: 70
Period size: 23 Copynumber: 3.6 Consensus size: 21
161172 TAGTGCATAA
161182 TGCATCGATGCATCCCTTGAATG
1 TGCATCGATGCAT-CCTT-AATG
* * *
161205 TGCATCGATACA-CCATATAGG
1 TGCATCGATGCATCCTTA-ATG
*
161226 TGCACCGATGCATTCCTTAAATG
1 TGCATCGATGCA-TCCTT-AATG
161249 TGCATCGATGCA
1 TGCATCGATGCA
161261 CCCATCGGGT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
20 1 0.02
21 15 0.34
23 27 0.61
24 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (21 bp):
TGCATCGATGCATCCTTAATG
Found at i:164044 original size:64 final size:64
Alignment explanation
Indices: 163923--164055 Score: 155
Period size: 63 Copynumber: 2.1 Consensus size: 64
163913 CACCCATTTT
* ** *
163923 GAATGCATTTTCTGTATCGATGCACAAGCATGCATCGATGCACTCTTGAATATTTTG-AACGTC
1 GAATGCATTTTCTGTATCGATGCACAACCATGCATCGATGCACTCCAGAATATTTTGAAACATC
* **
163986 GAATGCATTTTTTGTA-CTGATGCACAGACCATGCATCGATGCACTCCAGGCT-TGTTTGAAACA
1 GAATGCATTTTCTGTATC-GATGCACA-ACCATGCATCGATGCACTCCAGAATAT-TTTGAAACA
164049 TC
63 TC
164051 GAATG
1 GAATG
164056 TAATTAGTGC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
62 1 0.02
63 24 0.41
64 24 0.41
65 10 0.17
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (64 bp):
GAATGCATTTTCTGTATCGATGCACAACCATGCATCGATGCACTCCAGAATATTTTGAAACATC
Found at i:167080 original size:44 final size:45
Alignment explanation
Indices: 166960--167085 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
166950 TATAAAATCC
*
166960 CTTACCATTTATTTCATAAGCTCGTAAGCTTATTTTAACAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
* * *
167005 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
* * *
167052 CTTGCCA-TTATTCCAAAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
167086 ATATGCTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 37 0.51
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
Found at i:171160 original size:17 final size:17
Alignment explanation
Indices: 171138--171197 Score: 102
Period size: 17 Copynumber: 3.5 Consensus size: 17
171128 TAATTTAATA
171138 AATGAACTAGTTTGATG
1 AATGAACTAGTTTGATG
171155 AATGAACTAGTTTGATG
1 AATGAACTAGTTTGATG
* *
171172 AATGAACTAGTTTAATT
1 AATGAACTAGTTTGATG
171189 AATGAACTA
1 AATGAACTA
171198 CTTCCCTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (17 bp):
AATGAACTAGTTTGATG
Found at i:171210 original size:34 final size:34
Alignment explanation
Indices: 171135--171215 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
171125 AGTTAATTTA
* * **
171135 ATAAATGAACTAGTTTGATGAATGAACTAGTTTG
1 ATAAATGAACTAGTTTAATGAATGAACTACTTCC
* *
171169 ATGAATGAACTAGTTTAATTAATGAACTACTTCC
1 ATAAATGAACTAGTTTAATGAATGAACTACTTCC
*
171203 CTAAATGAACTAG
1 ATAAATGAACTAG
171216 ATGATTTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (34 bp):
ATAAATGAACTAGTTTAATGAATGAACTACTTCC
Found at i:185969 original size:77 final size:78
Alignment explanation
Indices: 185868--186014 Score: 185
Period size: 77 Copynumber: 1.9 Consensus size: 78
185858 ATAAAAAAAT
* *
185868 CTTATTTAATTAATTCATATTAAATATTC-ATT-AAAGACTTATAATATGAATTACAATC-TTTA
1 CTTATTTAATTAATTCAAATTAAATA-TCGATTAAAAGACTTATAAT-CGAATTACAATCTTTTA
185930 ACGTTTATTTAAACA
64 ACGTTTATTTAAACA
* * *
185945 CTTATTTAATT-ATTCCAAATTAAATATCGATTAAAAGAGTTGTAATCGAATTACATTCTTTTAA
1 CTTATTTAATTAATT-CAAATTAAATATCGATTAAAAGACTTATAATCGAATTACAATCTTTTAA
*
186009 TGTTTA
65 CGTTTA
186015 CTTATTATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
76 5 0.08
77 34 0.57
78 21 0.35
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.44
Consensus pattern (78 bp):
CTTATTTAATTAATTCAAATTAAATATCGATTAAAAGACTTATAATCGAATTACAATCTTTTAAC
GTTTATTTAAACA
Found at i:198420 original size:21 final size:20
Alignment explanation
Indices: 198396--198434 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
198386 TTTAATACAC
198396 AAGGGATCGATCCGTTTATGA
1 AAGGGATCGATCC-TTTATGA
198417 AAGGGATCGATCCTTTAT
1 AAGGGATCGATCCTTTAT
198435 CAAATAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (20 bp):
AAGGGATCGATCCTTTATGA
Found at i:198502 original size:21 final size:22
Alignment explanation
Indices: 198478--198536 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 22
198468 TCTATTAGAG
198478 GAAGGGATCAATCCTTTTGCT-
1 GAAGGGATCAATCCTTTTGCTC
* *
198499 GAAGGGATCAATCATTTTTCTC
1 GAAGGGATCAATCCTTTTGCTC
198521 G-AGGGATCAATCCTTT
1 GAAGGGATCAATCCTTT
198537 GGTGAGGGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (22 bp):
GAAGGGATCAATCCTTTTGCTC
Found at i:205198 original size:41 final size:41
Alignment explanation
Indices: 205153--205332 Score: 166
Period size: 41 Copynumber: 4.4 Consensus size: 41
205143 GCTGCATCAC
* *
205153 TTCACAATCCGATTCAGTTCAATCATAACAACATGCAATAA
1 TTCACAATCCGATTCAATTCAATCATGACAACATGCAATAA
* * * * *
205194 TTCACCATTCGACTCAATTCGATCATGGCAACATGCAATAA
1 TTCACAATCCGATTCAATTCAATCATGACAACATGCAATAA
* * *
205235 TTCACAATTCGATTCAATTCAATCATTGA-AACATGCATTTA
1 TTCACAATCCGATTCAATTCAATCA-TGACAACATGCAATAA
* * ** ***
205276 TTCACAAACCAATTCAATT-AGATCATGGTAACATGTGTTAA
1 TTCACAATCCGATTCAATTCA-ATCATGACAACATGCAATAA
*
205317 TTCACAATCCAATTCA
1 TTCACAATCCGATTCA
205333 GTTTAAATCA
Statistics
Matches: 115, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.03
41 110 0.96
42 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.31
Consensus pattern (41 bp):
TTCACAATCCGATTCAATTCAATCATGACAACATGCAATAA
Found at i:205293 original size:82 final size:82
Alignment explanation
Indices: 205153--205332 Score: 200
Period size: 82 Copynumber: 2.2 Consensus size: 82
205143 GCTGCATCAC
* * ** * *
205153 TTCACAATCCGATTCAGTTCAATCATAACAACATGCAATAATTCACCATTCGACTCAATTCGATC
1 TTCACAATCCGATTCAATTCAATCATAACAACATGCAATAATTCACAAACCAACTCAATTAGATC
205218 ATGGCAACATGCAATAA
66 ATGGCAACATGCAATAA
* * * * *
205235 TTCACAATTCGATTCAATTCAATCATTGA-AACATGCATTTATTCACAAACCAATTCAATTAGAT
1 TTCACAATCCGATTCAATTCAATCA-TAACAACATGCAATAATTCACAAACCAACTCAATTAGAT
* ***
205299 CATGGTAACATGTGTTAA
65 CATGGCAACATGCAATAA
*
205317 TTCACAATCCAATTCA
1 TTCACAATCCGATTCA
205333 GTTTAAATCA
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
82 78 0.98
83 2 0.03
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.31
Consensus pattern (82 bp):
TTCACAATCCGATTCAATTCAATCATAACAACATGCAATAATTCACAAACCAACTCAATTAGATC
ATGGCAACATGCAATAA
Found at i:208674 original size:20 final size:20
Alignment explanation
Indices: 208649--208686 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
208639 AATGAGTAAA
208649 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
208669 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
208687 TAATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:208761 original size:2 final size:2
Alignment explanation
Indices: 208748--208782 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
208738 AAAATAGGAA
*
208748 AT AT AT AA 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
208783 ATAACACTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:209273 original size:37 final size:36
Alignment explanation
Indices: 209230--209331 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
209220 ATAGTATAAC
209230 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
209267 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
209301 TCTATCATATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
209332 TATGACGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 32 0.53
37 28 0.47
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:210178 original size:105 final size:105
Alignment explanation
Indices: 209879--210815 Score: 1382
Period size: 105 Copynumber: 9.0 Consensus size: 105
209869 CATTGTTCCA
* * * ** * * * *
209879 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTTTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTGTTGACAAG
* * * *
209944 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * **
209985 AGTCCAATATCCTTTGTTATGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
210045 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
210085 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTATTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
210150 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
210190 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAGATT-AGGAAGTTGTTATTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAGTTGTTGTTGACAAG
* *
210254 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGA
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
210295 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGAAAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
210360 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
210400 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
210465 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
210505 AGTCCAATATCCTTCATTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGATAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
210570 AGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
210610 AGTCCATTATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGATAGGT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
210675 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
210715 AGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * *
210780 CAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
210816 CCTCGAGTGC
Statistics
Matches: 766, Mismatches: 57, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
100 82 0.11
101 3 0.00
102 4 0.01
103 2 0.00
104 3 0.00
105 599 0.78
106 73 0.10
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:211593 original size:67 final size:66
Alignment explanation
Indices: 211458--211615 Score: 201
Period size: 68 Copynumber: 2.4 Consensus size: 66
211448 AAGATATCTG
* * **
211458 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA-
211523 TT
65 TT
* * * * *
211525 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGATAAAATT-TGTTTTAGGGGAAATAAATTCAAAGG
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
211589 TT
65 TT
*
211591 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
211616 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 23 0.29
68 31 0.39
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:211631 original size:65 final size:67
Alignment explanation
Indices: 211459--211851 Score: 189
Period size: 65 Copynumber: 5.7 Consensus size: 67
211449 AGATATCTGT
* * * * * ** *
211459 TGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATT-TGTTTTAAGGGAAATAAATTCAAAGAGT
211524 TTG
65 TTG
* * * *
211527 TGTTTCAAGAGTAACTGTCTCAAGGGAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAG-GTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
211591 T-
66 TG
* * * * *
211592 TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACT--GTCTCAAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-GAAAATTTGTTTTAAGGGAAA-TAAAT-TCAA-AG
*
211654 AGACAAAACTT-
62 AG------TTTG
* * * * * * * * * * *
211665 AGTTCCAAAAGAAACTGTCTCAAGGGAGACG-GAATTTGTTTCAAAGAAAACATATTCAAATA-T
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-GAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGT
211728 TT-
65 TTG
* * * * *
211730 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACT--GTCTCAAGATA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAA-TAAAT-TC-A-A-A
*
211793 GACGAAATT-
61 GA-G--TTTG
* *
211802 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAA
211852 CTGTCTCAAG
Statistics
Matches: 252, Mismatches: 49, Indels: 44
0.73 0.14 0.13
Matches are distributed among these distances:
64 2 0.01
65 84 0.33
66 11 0.04
67 24 0.10
68 33 0.13
72 54 0.21
73 43 0.17
74 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
TG
Found at i:211642 original size:36 final size:35
Alignment explanation
Indices: 211591--211871 Score: 272
Period size: 36 Copynumber: 8.0 Consensus size: 35
211581 TTCAAAGGTT
* *
211591 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
211627 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
211662 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
211700 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
211729 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
211764 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
211801 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
211836 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
211872 CTCTTCTAGT
Statistics
Matches: 204, Mismatches: 25, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 10 0.05
36 134 0.66
37 33 0.16
38 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:211701 original size:138 final size:137
Alignment explanation
Indices: 211539--211852 Score: 423
Period size: 138 Copynumber: 2.3 Consensus size: 137
211529 TTTCAAGAGT
* * * * *
211539 AACTGTCTCAAGGGAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* *
211604 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
211668 TCCAAAAGA
129 TCCAAAAGA
** * * * *
211677 AACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * * * *
211742 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
211807 CAAGAGA
131 CAAAAGA
*
211814 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
211853 TGTCTCAAGA
Statistics
Matches: 151, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
137 49 0.32
138 102 0.68
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:211815 original size:102 final size:102
Alignment explanation
Indices: 211627--211815 Score: 290
Period size: 102 Copynumber: 1.9 Consensus size: 102
211617 TAGACGAAAA
*
211627 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
*
211692 GACGGAATTTGTTTCAAAGAAAACATATTCAAATATT
66 GACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
* * * ** *
211729 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGGGAAACTGTCTCAAGATA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
211793 GACGAAATTTGTTTCAAGAGAAA
66 GACGAAATTTGTTTCAA-AGAAA
211816 CTGTCTCAAG
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 36 0.46
102 42 0.54
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (102 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
GACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
Found at i:211893 original size:35 final size:36
Alignment explanation
Indices: 211733--211905 Score: 172
Period size: 36 Copynumber: 4.8 Consensus size: 36
211723 AATATTTTGT
* * **
211733 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * * * *
211769 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* *
211805 TTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGGA-AAACTGTCTCAAGAGAGACAAAATCTGC
*
211841 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CT-C
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * *
211875 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAG-GAAAACTGTCTCAAGAGAGACAAA
211906 TCTTGTTTTA
Statistics
Matches: 121, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
34 5 0.04
35 23 0.19
36 92 0.76
37 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (36 bp):
TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
Found at i:212827 original size:22 final size:22
Alignment explanation
Indices: 212801--212849 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
212791 TTGTGTTTGG
* *
212801 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
212823 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
212845 TCAAA
1 TCAAA
212850 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:212856 original size:22 final size:22
Alignment explanation
Indices: 212813--212856 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
212803 AAAGGTTTGG
* * *
212813 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
212835 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
212857 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:213516 original size:23 final size:22
Alignment explanation
Indices: 213489--213569 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 22
213479 TTTTTGTCCC
213489 TTTTTCTTTTTGATTTTTGCTCT
1 TTTTTCTTTTTG-TTTTTGCTCT
* * *
213512 TTTTTCCTTTTGTTCTTGTTTCT
1 TTTTTCTTTTTGTTTTTG-CTCT
*
213535 CTTTTTCTTTGTTTTTTTTTGCT-T
1 -TTTTTC-TT-TTTGTTTTTGCTCT
*
213559 TTTTGCTTTTT
1 TTTTTCTTTTT
213570 TGCTTCTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
21 3 0.07
22 7 0.15
23 19 0.41
24 7 0.15
25 2 0.04
26 8 0.17
ACGTcount: A:0.01, C:0.14, G:0.09, T:0.77
Consensus pattern (22 bp):
TTTTTCTTTTTGTTTTTGCTCT
Found at i:213521 original size:8 final size:7
Alignment explanation
Indices: 213509--213586 Score: 68
Period size: 8 Copynumber: 10.1 Consensus size: 7
213499 TGATTTTTGC
213509 TCTTTTT
1 TCTTTTT
213516 TCCTTTTGT
1 T-CTTTT-T
*
213525 TCTTGTT
1 TCTTTTT
213532 TCTCTTTT
1 TCT-TTTT
213540 TCTTTGTT
1 TCTTT-TT
213548 T-TTTTT
1 TCTTTTT
213554 TGCTTTTT
1 T-CTTTTT
213562 TGCTTTTT
1 T-CTTTTT
213570 TGCTTCTTT
1 T-CTT-TTT
213579 TCTTTTT
1 TCTTTTT
213586 T
1 T
213587 GTTCTTGATT
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
6 3 0.05
7 14 0.23
8 39 0.63
9 6 0.10
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (7 bp):
TCTTTTT
Found at i:213522 original size:16 final size:17
Alignment explanation
Indices: 213503--213557 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
213493 TCTTTTTGAT
*
213503 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
213519 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
* *
213536 TTTTTCT-TTGTTT-TT
1 TTTTGCTCTTGTTTCTC
213551 TTTTGCT
1 TTTTGCT
213558 TTTTTGCTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
15 7 0.22
16 19 0.59
17 6 0.19
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.75
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:213570 original size:16 final size:16
Alignment explanation
Indices: 213549--213592 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
213539 TTCTTTGTTT
213549 TTTTTTGCTT-TTTTGC
1 TTTTTTGCTTCTTTT-C
213565 TTTTTTGCTTCTTTTC
1 TTTTTTGCTTCTTTTC
213581 TTTTTTG-TTCTT
1 TTTTTTGCTTCTT
213593 GATTGGGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.19
16 18 0.67
17 4 0.15
ACGTcount: A:0.00, C:0.14, G:0.09, T:0.77
Consensus pattern (16 bp):
TTTTTTGCTTCTTTTC
Found at i:213581 original size:47 final size:46
Alignment explanation
Indices: 213488--213585 Score: 112
Period size: 46 Copynumber: 2.1 Consensus size: 46
213478 TTTTTTGTCC
213488 CTTTTTCTTTTTGATTTTTGCTCTTTTTTCCTTTTGTTCTTGTTTCT
1 CTTTTTCTTTTTGATTTTTGC-CTTTTTTCCTTTTGTTCTTGTTTCT
** * *
213535 CTTTTTCTTTGTTTTTTTTTG-CTTTTTTGCTTTT-TTGCTTCTTT-T
1 CTTTTTCTTT-TTGATTTTTGCCTTTTTTCCTTTTGTT-CTTGTTTCT
213580 CTTTTT
1 CTTTTT
213586 TGTTCTTGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
45 9 0.20
46 18 0.40
47 10 0.22
48 8 0.18
ACGTcount: A:0.01, C:0.15, G:0.08, T:0.76
Consensus pattern (46 bp):
CTTTTTCTTTTTGATTTTTGCCTTTTTTCCTTTTGTTCTTGTTTCT
Found at i:216804 original size:16 final size:18
Alignment explanation
Indices: 216772--216806 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
216762 ATATAAAAAC
216772 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
216790 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
216806 A
1 A
216807 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:216842 original size:20 final size:20
Alignment explanation
Indices: 216817--216854 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
216807 AATGAGTAAA
216817 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
216837 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
216855 TAATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:216961 original size:2 final size:2
Alignment explanation
Indices: 216917--216941 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
216907 AAAATAGGAA
216917 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 A
216942 ACAATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:217398 original size:37 final size:37
Alignment explanation
Indices: 217348--217486 Score: 167
Period size: 37 Copynumber: 3.8 Consensus size: 37
217338 GTGCTTGTGG
* * * * *
217348 ATCCTATCTTTAGGAATTTAAATACTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAATTCT
** * *
217385 ATCCTATTTTTAGGAGTTTGAATCCTAACAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAATTCT
217422 ATCCTATTTTTAGGAGTTTGAATCCTA--A-AATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAATTCT
*
217456 ATCATATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
217487 GACGAAAAAT
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
34 31 0.35
35 1 0.01
36 1 0.01
37 55 0.62
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAATTCT
Found at i:217464 original size:34 final size:34
Alignment explanation
Indices: 217382--217482 Score: 157
Period size: 34 Copynumber: 2.9 Consensus size: 34
217372 CTAGTAGAAC
217382 TCTATCCTATTTTTAGGAGTTTGAATCCTAACAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAAT
*
217419 TTTATCCTATTTTTAGGAGTTTGAATCCTAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAT
*
217453 TCTATCATATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
217483 GTAGGACGAA
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.45
Consensus pattern (34 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAT
Found at i:218882 original size:21 final size:21
Alignment explanation
Indices: 218853--218911 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
218843 ATTCTGACTA
*
218853 TCGCATTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
218874 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
218895 TCGCGTTGCGATTTTCC
1 TCGCGTTGCGATTTTCC
218912 GACTATCGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCAAAT
Found at i:219028 original size:20 final size:20
Alignment explanation
Indices: 218912--219045 Score: 146
Period size: 20 Copynumber: 6.7 Consensus size: 20
218902 GCGATTTTCC
*
218912 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
218932 GTA-AATCGCAATGCGAGTAT
1 G-ACTATCGCAATGCGATTAT
*
218952 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
*
218972 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
*
218992 GACTATCGCAATGCGATTCT
1 GACTATCGCAATGCGATTAT
* *
219012 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTAT
* *
219032 AACTGTCGCAATGC
1 GACTATCGCAATGC
219046 TGAATTTCAA
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.96
21 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:219029 original size:40 final size:40
Alignment explanation
Indices: 218912--219007 Score: 183
Period size: 40 Copynumber: 2.4 Consensus size: 40
218902 GCGATTTTCC
*
218912 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
218952 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
218992 GACTATCGCAATGCGA
1 GACTATCGCAATGCGA
219008 TTCTGACTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (40 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
Found at i:219897 original size:24 final size:24
Alignment explanation
Indices: 219865--219918 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
219855 GTATTCGAAA
219865 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
219889 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
219913 TTTGAT
1 TTTGAT
219919 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:220137 original size:14 final size:14
Alignment explanation
Indices: 220108--220144 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
220098 AGAAAAAGAA
220108 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
220123 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
220137 GAAGAAAA
1 GAAGAAAA
220145 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:222196 original size:18 final size:18
Alignment explanation
Indices: 222173--222207 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
222163 AGGAAAAGAC
*
222173 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
222191 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
222208 CAACCGGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Done.