Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002962.1 Hibiscus syriacus cultivar Beakdansim tig00006130_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: 206078
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:9403 original size:65 final size:66
Alignment explanation
Indices: 9298--9431 Score: 252
Period size: 65 Copynumber: 2.0 Consensus size: 66
9288 GTCTTGTAAA
9298 TTAACATCTTTAAAAATTATACTTCTTAATATTAATATTAAAAATAAAAAATAATTTAATACCGA
1 TTAACATCTTTAAAAATTATACTTCTTAATATTAATATTAAAAATAAAAAATAATTTAATACCGA
9363 T
66 T
*
9364 TTAACATCTTT-AAAATTCTACTTCTTAATATTAATATTAAAAATAAAAAATAATTTAATACCGA
1 TTAACATCTTTAAAAATTATACTTCTTAATATTAATATTAAAAATAAAAAATAATTTAATACCGA
9428 T
66 T
9429 TTA
1 TTA
9432 TTCTTAAAAT
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
65 56 0.84
66 11 0.16
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.40
Consensus pattern (66 bp):
TTAACATCTTTAAAAATTATACTTCTTAATATTAATATTAAAAATAAAAAATAATTTAATACCGA
T
Found at i:15593 original size:19 final size:19
Alignment explanation
Indices: 15569--15610 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
15559 TATTAGTTTG
15569 ATGCATGGTCGTGAATATA
1 ATGCATGGTCGTGAATATA
15588 ATGCATGGTCGTGAATATA
1 ATGCATGGTCGTGAATATA
15607 ATGC
1 ATGC
15611 CTGGAGACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (19 bp):
ATGCATGGTCGTGAATATA
Found at i:17421 original size:27 final size:27
Alignment explanation
Indices: 17390--17444 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
17380 CACTAGACTA
17390 TATTTAAACGATTAATGCCATATGTGT
1 TATTTAAACGATTAATGCCATATGTGT
* * * * *
17417 TATTTTAAGGTTTAATGTCATTTGTGT
1 TATTTAAACGATTAATGCCATATGTGT
17444 T
1 T
17445 TTGATTCATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.49
Consensus pattern (27 bp):
TATTTAAACGATTAATGCCATATGTGT
Found at i:17734 original size:32 final size:33
Alignment explanation
Indices: 17677--17744 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 33
17667 TTTATAATCT
*
17677 TTAGATAAAATTTAATAATTATTTTGTAACA-A
1 TTAGATAAAATTTAATAATCATTTTGTAACATA
* *
17709 TTAGATAAAATTTAATGATCGTTTTGTAACATA
1 TTAGATAAAATTTAATAATCATTTTGTAACATA
17742 TTA
1 TTA
17745 TAAGTTTAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 28 0.88
33 4 0.12
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (33 bp):
TTAGATAAAATTTAATAATCATTTTGTAACATA
Found at i:18680 original size:2 final size:2
Alignment explanation
Indices: 18673--18748 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
18663 ATACAACTAA
18673 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
18715 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
18749 TTTAAATCGA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20125 original size:23 final size:23
Alignment explanation
Indices: 20088--20145 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
20078 AGAACGTTAA
* * *
20088 ATAAATTTTAAACGAATATGTTT
1 ATAAATATTAAACGAACATATTT
* *
20111 GTAAATATTATACGAACATATTT
1 ATAAATATTAAACGAACATATTT
20134 ATAAATATTAAA
1 ATAAATATTAAA
20146 TAAATATATT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (23 bp):
ATAAATATTAAACGAACATATTT
Found at i:23229 original size:21 final size:21
Alignment explanation
Indices: 23182--23223 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
23172 TATTAAATTA
23182 TAAAA-TAGATAAAAATACAT
1 TAAAATTAGATAAAAATACAT
23202 TAAAATTAGATAAATAAT-CAT
1 TAAAATTAGATAAA-AATACAT
23223 T
1 T
23224 CTAATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 12 0.60
22 3 0.15
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (21 bp):
TAAAATTAGATAAAAATACAT
Found at i:44924 original size:3 final size:3
Alignment explanation
Indices: 44916--44945 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
44906 GATGTGGCAT
44916 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44946 GAGAAAATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:45131 original size:20 final size:21
Alignment explanation
Indices: 45087--45161 Score: 84
Period size: 20 Copynumber: 3.7 Consensus size: 21
45077 ATCAGTTTCC
* *
45087 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGAATCATG
*
45108 AAAATCGCAATGCGAAT-ATG
1 AAAATCGCAACGCGAATCATG
*
45128 AAAATCGCAACGCGAA-CA-C
1 AAAATCGCAACGCGAATCATG
45147 ATAAATCGCAACGCG
1 A-AAATCGCAACGCG
45162 TATCCGTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.02
20 31 0.66
21 15 0.32
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (21 bp):
AAAATCGCAACGCGAATCATG
Found at i:45171 original size:20 final size:20
Alignment explanation
Indices: 45129--45338 Score: 228
Period size: 20 Copynumber: 10.5 Consensus size: 20
45119 GCGAATATGA
* *
45129 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
45149 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
45169 AAACCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
45189 AAATAGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
45209 AAATCGCAATGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
45229 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
45249 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
45269 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
45289 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
45309 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
45329 AAATCACAAC
1 AAATCGCAAC
45339 ACTGAAATTT
Statistics
Matches: 162, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
19 1 0.01
20 159 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:45912 original size:19 final size:19
Alignment explanation
Indices: 45843--45980 Score: 152
Period size: 19 Copynumber: 7.7 Consensus size: 19
45833 GCAACGAGAG
*
45843 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
45862 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
45876 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
45896 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
45915 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
45929 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
45949 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
45968 AATCGCATTGCGA
1 AATCGCAATGCGA
45981 TTCTCTCGTT
Statistics
Matches: 102, Mismatches: 5, Indels: 24
0.78 0.04 0.18
Matches are distributed among these distances:
14 22 0.22
15 1 0.01
16 2 0.02
17 4 0.04
19 44 0.43
20 29 0.28
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:45972 original size:53 final size:53
Alignment explanation
Indices: 45843--45974 Score: 221
Period size: 53 Copynumber: 2.5 Consensus size: 53
45833 GCAACGAGAG
* *
45843 AATCACAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGCGGAAATGAA
*
45896 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAAC-ATGAAAATCGCAATGCGGAAATGAA
45949 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
45975 TTGCGATTCT
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
53 74 0.99
54 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGCGGAAATGAA
Found at i:46014 original size:53 final size:52
Alignment explanation
Indices: 45951--46066 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
45941 GAAATGAAAA
*
45951 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
46003 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
46056 TCGCATTGCGA
1 TCGCATTGCGA
46067 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:46081 original size:53 final size:53
Alignment explanation
Indices: 45970--46087 Score: 220
Period size: 53 Copynumber: 2.2 Consensus size: 53
45960 GAAATGAAAA
45970 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
46023 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
46075 TCCGCATTGCGAT
1 T-CGCATTGCGAT
46088 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 19 0.30
53 45 0.70
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:46095 original size:20 final size:19
Alignment explanation
Indices: 45989--46087 Score: 136
Period size: 20 Copynumber: 5.4 Consensus size: 19
45979 GATTCTCTCG
45989 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
46009 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
46028 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
46042 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
46061 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
46081 TTGCGAT
1 TTGCGAT
46088 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 25 0.35
20 26 0.37
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:46213 original size:14 final size:14
Alignment explanation
Indices: 46194--46230 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
46184 CATCAATTAA
46194 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
46208 ACAAATCATCTTTT
1 ACAAATCAACTTTT
46222 ACAAATCAA
1 ACAAATCAA
46231 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:47664 original size:21 final size:21
Alignment explanation
Indices: 47634--47694 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
47624 GTGAATCGGG
47634 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGGAC
* * ** *
47655 CTCTTCAATGATGACAGTGAC
1 CTCTTGAATGGTGGGAGGGAC
*
47676 CTCTTGAACGGTGGGAGGG
1 CTCTTGAATGGTGGGAGGG
47695 GACTCTCGAG
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGAC
Found at i:48266 original size:14 final size:14
Alignment explanation
Indices: 48247--48303 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
48237 GCGAAATGAA
*
48247 AATCGCAACGACAG
1 AATCGCAACGAAAG
48261 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
48278 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
48294 AATCGCAACG
1 AATCGCAACG
48304 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:48274 original size:33 final size:33
Alignment explanation
Indices: 48228--48317 Score: 162
Period size: 33 Copynumber: 2.7 Consensus size: 33
48218 GCGAAACCAA
48228 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
48261 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
48294 AATCGCAACGCGAAATGAAAATCG
1 AATCGCAACGCGAAATGAAAATCG
48318 TAATGCGATT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:48317 original size:52 final size:52
Alignment explanation
Indices: 48187--48325 Score: 138
Period size: 52 Copynumber: 2.7 Consensus size: 52
48177 AACGCGAAAT
* * * *
48187 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
* ** * **
48239 GA-AAT-GAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAACGA-A-AATCGCAATGCGAAACCAAAATCGCAACGA
* *
48291 GAGAATCGCAACGCGAAATGAAAATCGTAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
48326 TTTTGGTTTC
Statistics
Matches: 67, Mismatches: 16, Indels: 8
0.74 0.18 0.09
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 42 0.63
53 4 0.06
54 9 0.13
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
Found at i:48325 original size:19 final size:19
Alignment explanation
Indices: 48153--48317 Score: 152
Period size: 19 Copynumber: 9.2 Consensus size: 19
48143 TAGTTTACTT
* *
48153 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
48173 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
48192 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
48211 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
48230 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
48249 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
48263 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
48282 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
48296 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
48315 TCG
1 TCG
48318 TAATGCGATT
Statistics
Matches: 121, Mismatches: 14, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
14 18 0.15
15 1 0.01
16 7 0.06
17 7 0.06
18 1 0.01
19 75 0.62
20 12 0.10
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:48343 original size:19 final size:18
Alignment explanation
Indices: 48321--48412 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
48311 AAAATCGTAA
48321 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
48340 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
48354 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
48373 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
48387 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
48406 TGCGATT
1 TGCGATT
48413 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:48356 original size:14 final size:14
Alignment explanation
Indices: 48337--48395 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
48327 TTTGGTTTCG
48337 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
48351 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
48368 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
48384 CGTTGCGATTTT
1 CGTTGCGATTTT
48396 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:48363 original size:33 final size:33
Alignment explanation
Indices: 48321--48444 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
48311 AAAATCGTAA
*
48321 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
48354 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
48387 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
48420 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
48445 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:48422 original size:14 final size:14
Alignment explanation
Indices: 48370--48426 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
48360 TTTGGTTTCG
*
48370 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
48384 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
48403 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
48417 CGTTGCGATT
1 CGTTGCGATT
48427 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:50395 original size:20 final size:20
Alignment explanation
Indices: 50365--50471 Score: 113
Period size: 19 Copynumber: 5.7 Consensus size: 20
50355 TTTTGGTTGA
50365 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
**
50385 AATGACTATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
50405 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
50424 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
50439 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
50458 AATGAAAATCGCAA
1 AATGAAAATCGCAA
50472 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 30 0.39
20 18 0.24
21 13 0.17
ACGTcount: A:0.48, C:0.19, G:0.22, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:50416 original size:21 final size:21
Alignment explanation
Indices: 50363--50427 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
50353 TCTTTTGGTT
50363 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
**
50384 G-AATGACTATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
50404 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
50425 GAA
1 GAA
50428 TCGCAACGCG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 18 0.46
21 21 0.54
ACGTcount: A:0.49, C:0.15, G:0.25, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:50507 original size:14 final size:14
Alignment explanation
Indices: 50488--50544 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
50478 TTTGGTTTCG
50488 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
50502 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
50521 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
50535 CGTTGCGATT
1 CGTTGCGATT
50545 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:50520 original size:33 final size:33
Alignment explanation
Indices: 50472--50551 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
50462 AAAATCGCAA
**
50472 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
50505 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
50538 TGCGATTTTCATTT
1 TGCGATTTTCATTT
50552 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:50557 original size:21 final size:21
Alignment explanation
Indices: 50532--50605 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
50522 GTTGCGATTC
50532 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
50553 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
50574 TCGCGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTT
50595 TCTCGTTGCGA
1 TCTCGTTGCGA
50606 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:50727 original size:33 final size:33
Alignment explanation
Indices: 50685--50755 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
50675 CATACTAACT
50685 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
*
50718 TGAAAATCGCAACGAGAGAATCGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
50751 TGAAA
1 TGAAA
50756 TTTAAGTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.48, C:0.18, G:0.24, T:0.10
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:50731 original size:19 final size:19
Alignment explanation
Indices: 50707--50755 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 19
50697 CGAGAGAATA
50707 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
50726 GCAA--CG--A-GAGAATC
1 GCAACGCGAAATGAAAATC
50740 GCAACGCGAAATGAAA
1 GCAACGCGAAATGAAA
50756 TTTAAGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 10
0.66 0.06 0.29
Matches are distributed among these distances:
14 10 0.43
15 1 0.04
16 2 0.09
17 2 0.09
18 1 0.04
19 7 0.30
ACGTcount: A:0.47, C:0.20, G:0.24, T:0.08
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:50741 original size:14 final size:14
Alignment explanation
Indices: 50689--50745 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
50679 CTAACTTGAA
50689 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
50703 AATAGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
50722 AATCGCAACGAGAG
1 AATCGCAACGAGAG
50736 AATCGCAACG
1 AATCGCAACG
50746 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.46, C:0.21, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:51162 original size:20 final size:20
Alignment explanation
Indices: 51137--51347 Score: 264
Period size: 20 Copynumber: 10.5 Consensus size: 20
51127 TTAAAAATCA
*
51137 CGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGGATACG
* *
51157 CGTTGCGATTTTACGTAT-TG
1 CGTTGCGA-TTTACGGATACG
51177 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTACGGATACG
51198 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
51218 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
51238 CATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
51258 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
* *
51278 TGTTGCGGTTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
51298 CGTTGCGATTTATGTG-TTCG
1 CGTTGCGATTTACG-GATACG
* ** *
51318 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGGATACG
51338 CGTTGCGATT
1 CGTTGCGATT
51348 CTGGAAAATC
Statistics
Matches: 167, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
20 150 0.90
21 17 0.10
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:52343 original size:3 final size:3
Alignment explanation
Indices: 52335--52360 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52325 ATCAAAAGTA
52335 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
52361 ACATATAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:59958 original size:2 final size:2
Alignment explanation
Indices: 59914--59942 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59904 ATACACACAC
59914 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
59943 AACAAATATT
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:61408 original size:65 final size:65
Alignment explanation
Indices: 61304--61433 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
61294 GGTACGATCG
61304 AATACTTTCTACTACAATATTTATCGTTAATCAAGATCAAAAGTGAACTCAAGAGTCGATTACAC
1 AATACTTTCTACTACAATATTTATCGTTAATCAAGATCAAAAGTGAACTCAAGAGTCGATTACAC
61369 AATACTTTCTACTACAATATTTATCGTTAATCAAGATCAAAAGTGAACTCAAGAGTCGATTACAC
1 AATACTTTCTACTACAATATTTATCGTTAATCAAGATCAAAAGTGAACTCAAGAGTCGATTACAC
61434 GTGAAAAAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (65 bp):
AATACTTTCTACTACAATATTTATCGTTAATCAAGATCAAAAGTGAACTCAAGAGTCGATTACAC
Found at i:61767 original size:3 final size:3
Alignment explanation
Indices: 61761--61798 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
61751 AATTCTAACA
61761 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
61799 CGACAAGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:62234 original size:2 final size:2
Alignment explanation
Indices: 62227--62260 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
62217 AATAACTTTG
62227 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
62261 TAAGCACATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65252 original size:254 final size:255
Alignment explanation
Indices: 64775--65265 Score: 846
Period size: 254 Copynumber: 1.9 Consensus size: 255
64765 TTCATTTTGG
64775 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAATATATAATTTTACCT
1 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAATATATAATTTTACCT
*
64840 TATATATTTAGGAATAATTACAATAATACATCTCTATATATAATTTTTTCCAATTAAGTCACTGT
66 TATATATTTAGGAATAATTACAATAATACACCTCTATATATAATTTTTTCCAATTAAGT-ACTGT
*
64905 TTTTATTGAATAAAAATAAATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATT
130 TTTTATTGAATAAAAAT-AATTTTTGTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATT
*
64970 CGGGTCGGATCGGGTGAAACTTTATTTTGGTC-GAGTCGGGTCGGTTTTTTTAAGTGTGATAT
194 CGGGTCGGATCGGGTGAAACATTATTTTGGTCAG-GTCGGGTCGGTTTTTTTAAGTGTGATAT
*
65032 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAAATATATAATTTTACG
1 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCC-AAAAATATATAATTTTACC
* *
65097 TTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCAATTAAGT-C-G
65 TTATATATTTAGGAATAATTACAATAATACACCTCTATATATAA-TTTTTTCCAATTAAGTACTG
65160 TTTTTATTGAATAAAAAT-ATTTTTGTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATT
129 TTTTTATTGAATAAAAATAATTTTTGTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATT
*
65224 CGGGTCGGGTCGGGTGAAACATTATTTTGGTCAGGTCGGGTC
194 CGGGTCGGATCGGGTGAAACATTATTTTGGTCAGGTCGGGTC
65266 TCGGATGGAG
Statistics
Matches: 224, Mismatches: 7, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
254 83 0.37
255 1 0.00
256 19 0.08
257 46 0.21
258 60 0.27
259 15 0.07
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (255 bp):
TCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAATATATAATTTTACCT
TATATATTTAGGAATAATTACAATAATACACCTCTATATATAATTTTTTCCAATTAAGTACTGTT
TTTATTGAATAAAAATAATTTTTGTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCG
GGTCGGATCGGGTGAAACATTATTTTGGTCAGGTCGGGTCGGTTTTTTTAAGTGTGATAT
Found at i:65624 original size:44 final size:44
Alignment explanation
Indices: 65561--65681 Score: 215
Period size: 44 Copynumber: 2.8 Consensus size: 44
65551 TATGTCTGCG
65561 AACCAAACAGAATATGGAATTGGATTCCAATTCAATTTCATGCC
1 AACCAAACAGAATATGGAATTGGATTCCAATTCAATTTCATGCC
*
65605 AACCAAACAGAATATGGAATTGGATTCCAATTCAATTTCCTGCC
1 AACCAAACAGAATATGGAATTGGATTCCAATTCAATTTCATGCC
* *
65649 AACCAAACAGAATATGAAATTGGATTCAAATTC
1 AACCAAACAGAATATGGAATTGGATTCCAATTC
65682 CTGACAGATT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 74 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (44 bp):
AACCAAACAGAATATGGAATTGGATTCCAATTCAATTTCATGCC
Found at i:76559 original size:22 final size:20
Alignment explanation
Indices: 76530--76583 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
76520 AAAAAATTTA
*
76530 ATTTAAAAAACTTAAAACTAT
1 ATTTAAAAAA-ATAAAACTAT
76551 ATTTAAAAACAATAAAACTAT
1 ATTTAAAAA-AATAAAACTAT
*
76572 AATTAAAAAAAT
1 ATTTAAAAAAAT
76584 TCGAATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 3 0.10
21 26 0.87
22 1 0.03
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (20 bp):
ATTTAAAAAAATAAAACTAT
Found at i:76772 original size:29 final size:29
Alignment explanation
Indices: 76730--76799 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
76720 GTTTAGGATC
76730 TAAGGAAGAAAACCATCGCTTGTCACCCT
1 TAAGGAAGAAAACCATCGCTTGTCACCCT
*
76759 TAAGGAAGAAAACCATCGTTTGTCACCCT
1 TAAGGAAGAAAACCATCGCTTGTCACCCT
*
76788 TGAGGAAGAAAA
1 TAAGGAAGAAAA
76800 ACATTCAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (29 bp):
TAAGGAAGAAAACCATCGCTTGTCACCCT
Found at i:77121 original size:2 final size:2
Alignment explanation
Indices: 77114--77153 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
77104 TAAAAATTTA
77114 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
77154 GTGTGTGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77963 original size:124 final size:122
Alignment explanation
Indices: 77722--77973 Score: 434
Period size: 124 Copynumber: 2.0 Consensus size: 122
77712 TCATCTCTGC
77722 ATATTTTTATGAGCCTTTGTCTCTTGAGATATGATGATGTTAGGTTTTGTTTAAATTATATAGTA
1 ATATTTTTATGAGCCTTTGTCTCTTGAGATATGATGATGTTAGGTTTTGTTTAAATTATATAGTA
* * * *
77787 TATTTTTAAAATAAATATTTAAAATATATTATAGATATTTATTTTTTTTAAAAAGTAA
66 TATTTTTAAAATAAATATTTAAAATATATTATAAATATATATATTTTCT-AAAAGTAA
77845 ATATTATTTATGAGCCTTTGTCTCTTGAGATATGATGATGTTAGGTTTTGTTTAAATTATATAGT
1 ATATT-TTTATGAGCCTTTGTCTCTTGAGATATGATGATGTTAGGTTTTGTTTAAATTATATAGT
77910 ATATTTTTAAAAGTAAATATTTAAAATATATTATAAATATATA-ATTTTCTAAAAGTAA
65 ATATTTTTAAAA-TAAATATTTAAAATATATTATAAATATATATATTTTCTAAAAGTAA
77968 ATATTT
1 ATATTT
77974 AGAATTATCA
Statistics
Matches: 123, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
122 1 0.01
123 18 0.15
124 76 0.62
125 28 0.23
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (122 bp):
ATATTTTTATGAGCCTTTGTCTCTTGAGATATGATGATGTTAGGTTTTGTTTAAATTATATAGTA
TATTTTTAAAATAAATATTTAAAATATATTATAAATATATATATTTTCTAAAAGTAA
Found at i:83677 original size:23 final size:22
Alignment explanation
Indices: 83628--83674 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
83618 TTCCAATTAC
83628 ATTATTAAAAACAATATTTCAA
1 ATTATTAAAAACAATATTTCAA
83650 ATTATTAAACTAACAA-ATTT-AA
1 ATTATTAAA--AACAATATTTCAA
83672 ATT
1 ATT
83675 TATGTTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 14 0.61
23 4 0.17
24 5 0.22
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTATTAAAAACAATATTTCAA
Found at i:94269 original size:2 final size:2
Alignment explanation
Indices: 94262--94291 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
94252 TAAACATTTA
94262 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
94292 TGAAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:95318 original size:21 final size:21
Alignment explanation
Indices: 95294--95335 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
95284 AAAAGTTTCG
95294 GACCGTGAACC-GACCTAATTC
1 GACCGTG-ACCGGACCTAATTC
*
95315 GACCGTGACCGGCCCTAATTC
1 GACCGTGACCGGACCTAATTC
95336 CCAGTGCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
GACCGTGACCGGACCTAATTC
Found at i:95465 original size:14 final size:14
Alignment explanation
Indices: 95446--95509 Score: 60
Period size: 14 Copynumber: 4.4 Consensus size: 14
95436 TTTAGAAATA
95446 TACATTTGAGTATT
1 TACATTTGAGTATT
*
95460 TACATTTGATTTTAAATT
1 TACATTTGA--GT--ATT
*
95478 TA-ATTT-ATTATT
1 TACATTTGAGTATT
95490 TACATTTGAGTATT
1 TACATTTGAGTATT
95504 TACATT
1 TACATT
95510 CGATTTAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
12 5 0.12
13 4 0.10
14 22 0.52
16 2 0.05
17 4 0.10
18 5 0.12
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (14 bp):
TACATTTGAGTATT
Found at i:96060 original size:33 final size:33
Alignment explanation
Indices: 96023--96099 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 33
96013 TGTTTTGTGT
*
96023 TTTTGATA-TTGTTTGTTCACTGTAAAT-ATTCCA
1 TTTTGATAGTTG-TAGTTCACTGTAAATGATT-CA
* *
96056 TTTTGACAGTTGTAGTTCACTGTAATTGATTCA
1 TTTTGATAGTTGTAGTTCACTGTAAATGATTCA
96089 TTTTGATAGTT
1 TTTTGATAGTT
96100 TTTCTAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 32 0.84
34 6 0.16
ACGTcount: A:0.23, C:0.10, G:0.16, T:0.51
Consensus pattern (33 bp):
TTTTGATAGTTGTAGTTCACTGTAAATGATTCA
Found at i:99548 original size:17 final size:16
Alignment explanation
Indices: 99506--99548 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
99496 AGCTAGTCTA
99506 TTAATATTT-TTATTT
1 TTAATATTTATTATTT
*
99521 TTAATACTTTATTGTTT
1 TTAATA-TTTATTATTT
99538 TTAAGTATTTA
1 TTAA-TATTTA
99549 ATAATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 6 0.25
16 3 0.12
17 13 0.54
18 2 0.08
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (16 bp):
TTAATATTTATTATTT
Found at i:100604 original size:29 final size:29
Alignment explanation
Indices: 100562--100650 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 29
100552 TACCGGGGGT
*
100562 AGGTCGCCATGCACGCCCGGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
***
100591 AGGTCGCCATGCACGCCCAGCGACCTGGT
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* *
100620 AGGTCGCCATGCATGCCCTGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
100649 AG
1 AG
100651 CCAACGACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.18, C:0.40, G:0.28, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:100680 original size:10 final size:10
Alignment explanation
Indices: 100665--100690 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
100655 CGACCTCCAT
100665 GCCCATGCAC
1 GCCCATGCAC
100675 GCCCATGCAC
1 GCCCATGCAC
100685 GCCCAT
1 GCCCAT
100691 CTCGCCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.50, G:0.19, T:0.12
Consensus pattern (10 bp):
GCCCATGCAC
Found at i:100726 original size:41 final size:41
Alignment explanation
Indices: 100675--100752 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
100665 GCCCATGCAC
100675 GCCCATGCACGCCCATCTCGCCAAAGGTCACCATGCACCAT
1 GCCCATGCACGCCCATCTCGCCAAAGGTCACCATGCACCAT
100716 GCCCATGCACGCCCATCTCGCCAAAGGTCACCATGCA
1 GCCCATGCACGCCCATCTCGCCAAAGGTCACCATGCA
100753 ATGCACGTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.24, C:0.44, G:0.18, T:0.14
Consensus pattern (41 bp):
GCCCATGCACGCCCATCTCGCCAAAGGTCACCATGCACCAT
Found at i:100769 original size:33 final size:33
Alignment explanation
Indices: 100710--100785 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
100700 GGTCACCATG
* *
100710 CACCATGCCCATGCACGCCCATCTCGCCAAAGGT
1 CACCATG-CAATGCACGCCCAGCTCGCCAAAGGT
*
100744 CACCATGCAATGCACGTCCAGCTCGCCAAAGGT
1 CACCATGCAATGCACGCCCAGCTCGCCAAAGGT
100777 CACCATGCA
1 CACCATGCA
100786 GTCCATGCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 32 0.82
34 7 0.18
ACGTcount: A:0.26, C:0.41, G:0.18, T:0.14
Consensus pattern (33 bp):
CACCATGCAATGCACGCCCAGCTCGCCAAAGGT
Found at i:100996 original size:12 final size:11
Alignment explanation
Indices: 100976--101011 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
100966 GAAATCAACT
100976 GCATTATTGCA
1 GCATTATTGCA
*
100987 GCACTTATTGCT
1 GCA-TTATTGCA
100999 GCATTATTGCA
1 GCATTATTGCA
101010 GC
1 GC
101012 CCGTGAACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (11 bp):
GCATTATTGCA
Found at i:101340 original size:28 final size:27
Alignment explanation
Indices: 101301--101353 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
101291 ATATTAAAAA
101301 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
101329 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
101354 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:101359 original size:27 final size:29
Alignment explanation
Indices: 101300--101364 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
101290 TATATTAAAA
101300 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
101329 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
101355 AAATAGTTAA
1 AAATAATTAA
101365 GTTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:101503 original size:18 final size:18
Alignment explanation
Indices: 101480--101534 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
101470 AATAATTATT
101480 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
101498 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
101510 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
101527 TAAATTAG
1 TAAATTAG
101535 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:101587 original size:21 final size:21
Alignment explanation
Indices: 101562--101601 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
101552 GTTAATTAGT
101562 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
101583 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
101602 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:101843 original size:30 final size:30
Alignment explanation
Indices: 101775--101848 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 30
101765 ATGAGTTAAT
* *
101775 TAGTTTTTTAGTAGTAAATTATAATTAAAAA
1 TAGTTTATTAGT-TTAAATTATAATTAAAAA
*
101806 TCA-TTTATTAGTTTAATTTAT-ATTAAAGAA
1 T-AGTTTATTAGTTTAAATTATAATTAAA-AA
101836 TAGTTTATTAGTT
1 TAGTTTATTAGTT
101849 GTTTAAGGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
29 7 0.19
30 20 0.54
31 9 0.24
32 1 0.03
ACGTcount: A:0.39, C:0.01, G:0.09, T:0.50
Consensus pattern (30 bp):
TAGTTTATTAGTTTAAATTATAATTAAAAA
Found at i:102268 original size:49 final size:49
Alignment explanation
Indices: 102215--102610 Score: 378
Period size: 49 Copynumber: 7.2 Consensus size: 49
102205 GAGCAACGAG
102215 TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAA
1 TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAA
102264 TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAA
1 TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAA
102313 TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAA
1 TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAA
*
102362 TCATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATCATT
1 TCATTACT--ATCA--A--ATC--AT--TA-AAAATTAATAATAATTTC------A-T--T-ATT
102427 ACTAAA
45 ACT-AA
102433 TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAA
1 TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAA
*
102482 TCATTACTAAGTCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATCATT
1 TCATTACT-A-TCA--A--ATC--AT--TA-AAAATTAATAATAATTTC------A-T--T-ATT
102547 ACTAAA
45 ACT-AA
102553 TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAA
1 TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAA
102602 TCATTACTA
1 TCATTACTA
102611 AATCATTACT
Statistics
Matches: 299, Mismatches: 4, Indels: 88
0.76 0.01 0.23
Matches are distributed among these distances:
49 127 0.42
50 13 0.04
51 9 0.03
53 4 0.01
54 2 0.01
55 6 0.02
57 4 0.01
59 4 0.01
60 68 0.23
61 4 0.01
63 4 0.01
65 6 0.02
66 2 0.01
67 4 0.01
69 9 0.03
70 13 0.04
71 20 0.07
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (49 bp):
TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAA
Found at i:102380 original size:60 final size:60
Alignment explanation
Indices: 102305--102630 Score: 586
Period size: 60 Copynumber: 5.5 Consensus size: 60
102295 TAATTTCATT
102305 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
102364 ATTACTAAATCATTACTATCAAATCA-TACATAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTA-AAAATTAATAATAATTTCATTATTACTAATC
102424 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* *
102484 ATTACTAAGTCATTACTATCAAATCA-TACATAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTA-AAAATTAATAATAATTTCATTATTACTAATC
102544 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
102604 ATTACTAAATCATTACTATCAAATCAT
1 ATTACTAAATCATTACTATCAAATCAT
102631 CAAATTACTA
Statistics
Matches: 256, Mismatches: 6, Indels: 9
0.94 0.02 0.03
Matches are distributed among these distances:
59 10 0.04
60 242 0.95
61 4 0.02
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:102639 original size:19 final size:19
Alignment explanation
Indices: 102615--102654 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
102605 TTACTAAATC
102615 ATTACTATCAAATCATCAA
1 ATTACTATCAAATCATCAA
* *
102634 ATTACTATTAAATCATTAA
1 ATTACTATCAAATCATCAA
102653 AT
1 AT
102655 ATTAATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTACTATCAAATCATCAA
Found at i:105559 original size:28 final size:28
Alignment explanation
Indices: 105528--105581 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
105518 ATAATCTAAT
*
105528 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
105556 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
105582 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:105588 original size:28 final size:28
Alignment explanation
Indices: 105524--105588 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
105514 TTATATAATC
*
105524 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
105552 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
105580 TAATTTATA
1 TAATATATA
105589 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:105591 original size:21 final size:21
Alignment explanation
Indices: 105558--105606 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
105548 TTAATATAAT
105558 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
105579 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
105600 ATTAACT
1 A-TAACT
105607 AAATTTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:106283 original size:30 final size:30
Alignment explanation
Indices: 106247--106404 Score: 181
Period size: 30 Copynumber: 5.0 Consensus size: 30
106237 GCGAGCTGGG
106247 CGTGCATGGAGGTCGTTGGGCGTGCATGGC
1 CGTGCATGGAGGTCGTTGGGCGTGCATGGC
* * *
106277 CGTGCATGGAGGTCGTTGGACGTGCCTGGG
1 CGTGCATGGAGGTCGTTGGGCGTGCATGGC
*
106307 CATGCATGGAGGTCGTTGGGCGTGCATGGGC
1 CGTGCATGGAGGTCGTTGGGCGTGCAT-GGC
* *
106338 GTGCATGGAGGTCATGGAGGTCGTTGGGCGTGCATGGG
1 ---C---G-TG-CATGGAGGTCGTTGGGCGTGCATGGC
106376 CGTGCATGGAGGTCGTTGGGCGTGCATGG
1 CGTGCATGGAGGTCGTTGGGCGTGCATGG
106405 GCGTTGGCTG
Statistics
Matches: 108, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
30 76 0.70
31 3 0.03
32 1 0.01
34 1 0.01
35 1 0.01
38 3 0.03
39 23 0.21
ACGTcount: A:0.11, C:0.18, G:0.47, T:0.23
Consensus pattern (30 bp):
CGTGCATGGAGGTCGTTGGGCGTGCATGGC
Found at i:106338 original size:10 final size:10
Alignment explanation
Indices: 106323--106408 Score: 67
Period size: 10 Copynumber: 8.7 Consensus size: 10
106313 TGGAGGTCGT
106323 TGGGCGTGCA
1 TGGGCGTGCA
106333 TGGGCGTGCA
1 TGGGCGTGCA
106343 TGGAG-GT-CA
1 TGG-GCGTGCA
*
106352 TGGAG-GT-CGT
1 TGG-GCGTGC-A
106362 TGGGCGTGCA
1 TGGGCGTGCA
106372 TGGGCGTGCA
1 TGGGCGTGCA
*
106382 TGGAG-GT-CGT
1 TGG-GCGTGC-A
106392 TGGGCGTGCA
1 TGGGCGTGCA
106402 TGGGCGT
1 TGGGCGT
106409 TGGCTGGTAG
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
9 13 0.20
10 47 0.73
11 4 0.06
ACGTcount: A:0.10, C:0.16, G:0.50, T:0.23
Consensus pattern (10 bp):
TGGGCGTGCA
Found at i:106355 original size:39 final size:39
Alignment explanation
Indices: 106311--106389 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
106301 CCTGGGCATG
106311 CATGGAGGTCGTTGGGCGTGCATGGGCGTGCATGGAGGT
1 CATGGAGGTCGTTGGGCGTGCATGGGCGTGCATGGAGGT
106350 CATGGAGGTCGTTGGGCGTGCATGGGCGTGCATGGAGGT
1 CATGGAGGTCGTTGGGCGTGCATGGGCGTGCATGGAGGT
106389 C
1 C
106390 GTTGGGCGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.13, C:0.16, G:0.48, T:0.23
Consensus pattern (39 bp):
CATGGAGGTCGTTGGGCGTGCATGGGCGTGCATGGAGGT
Found at i:106376 original size:69 final size:70
Alignment explanation
Indices: 106263--106408 Score: 240
Period size: 69 Copynumber: 2.1 Consensus size: 70
106253 TGGAGGTCGT
* *
106263 TGGGCGTGCATGGCCGTGCATGGAGGTCGTTGGACGTGCCTGGGCATGCATGGAGGTCGTTGGGC
1 TGGGCGTGCATGGACGTGCATGGAGGTCGTTGGACGTGCATGGGCATGCATGGAGGTCGTTGGGC
106328 GTGCA
66 GTGCA
* * *
106333 TGGGCGTGCATGGAGGT-CATGGAGGTCGTTGGGCGTGCATGGGCGTGCATGGAGGTCGTTGGGC
1 TGGGCGTGCATGGACGTGCATGGAGGTCGTTGGACGTGCATGGGCATGCATGGAGGTCGTTGGGC
106397 GTGCA
66 GTGCA
106402 TGGGCGT
1 TGGGCGT
106409 TGGCTGGTAG
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
69 56 0.79
70 15 0.21
ACGTcount: A:0.11, C:0.18, G:0.48, T:0.23
Consensus pattern (70 bp):
TGGGCGTGCATGGACGTGCATGGAGGTCGTTGGACGTGCATGGGCATGCATGGAGGTCGTTGGGC
GTGCA
Found at i:107312 original size:22 final size:20
Alignment explanation
Indices: 107287--107343 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
107277 TTTATATTTT
107287 TTAAAAATTTAATTTAAAAAA
1 TTAAAAATTTAATTT-AAAAA
* *
107308 CTTAAAACTAT-ATTTAAAAA
1 -TTAAAAATTTAATTTAAAAA
*
107328 TAAAAAATTCTAATTT
1 TTAAAAATT-TAATTT
107344 CTCTAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 6 0.21
20 6 0.21
21 8 0.29
22 8 0.29
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
TTAAAAATTTAATTTAAAAA
Found at i:107822 original size:2 final size:2
Alignment explanation
Indices: 107815--107856 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
107805 TAAAAATTTA
107815 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
107857 GTGTGTGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:109002 original size:15 final size:16
Alignment explanation
Indices: 108965--109014 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
108955 AACAAAAATA
108965 TTAAAA-AATATAATAT
1 TTAAAATAATAT-ATAT
*
108981 TTTAAATAATATA-AT
1 TTAAAATAATATATAT
* *
108996 TTAAAATATTATATTT
1 TTAAAATAATATATAT
109012 TTA
1 TTA
109015 TCATATTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 13 0.46
16 10 0.36
17 5 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAAATAATATATAT
Found at i:113319 original size:63 final size:63
Alignment explanation
Indices: 113234--113484 Score: 466
Period size: 63 Copynumber: 4.0 Consensus size: 63
113224 TCAAATTACC
* * *
113234 TTGTAGAGTGAAGTTTTGGCTGATCTCACACGAGGACAACTCCAAATACTTTAAAGAAGAAAG
1 TTGTAGAGTGAAGTTTTGGCTGATCTCACATGAGGACAACTCCAAATGCTTCAAAGAAGAAAG
113297 TTGTAGAGTGAAGTTTTGGCTGATCTCACATGAGGACAACTCCAAATGCTTCAAAGAAGAAAG
1 TTGTAGAGTGAAGTTTTGGCTGATCTCACATGAGGACAACTCCAAATGCTTCAAAGAAGAAAG
113360 TTGTAGAGTGAAGTTTTGGCTGATCTCACATGAGGACAACTCCAAATGCTTCAAAGAAGAAAG
1 TTGTAGAGTGAAGTTTTGGCTGATCTCACATGAGGACAACTCCAAATGCTTCAAAGAAGAAAG
*
113423 TTGTAGAGTGAAGTTTTGGCTGATCTCACATGAGGACAACCCCAAATGCTTCAAAGAAGAAA
1 TTGTAGAGTGAAGTTTTGGCTGATCTCACATGAGGACAACTCCAAATGCTTCAAAGAAGAAA
113485 ATTCTCTTGG
Statistics
Matches: 184, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 184 1.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.25
Consensus pattern (63 bp):
TTGTAGAGTGAAGTTTTGGCTGATCTCACATGAGGACAACTCCAAATGCTTCAAAGAAGAAAG
Found at i:113780 original size:22 final size:21
Alignment explanation
Indices: 113755--113797 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
113745 ATTACATTTT
113755 TTAAA-AACAACATTTCAAATTA
1 TTAAACAACAA-ATTT-AAATTA
113777 TTAAACTAACAAATTTAAATT
1 TTAAAC-AACAAATTTAAATT
113798 TATGTTGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.53
23 4 0.21
24 5 0.26
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (21 bp):
TTAAACAACAAATTTAAATTA
Found at i:116570 original size:2 final size:2
Alignment explanation
Indices: 116563--116601 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
116553 AGTAATTTTA
116563 AT AT 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 AT AT A
116602 GTTTAAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:117915 original size:65 final size:69
Alignment explanation
Indices: 117774--117915 Score: 152
Period size: 72 Copynumber: 2.1 Consensus size: 69
117764 AATAATTTAC
* *
117774 TAATATTTTAAAAATAAAACTTAATTATATAAAATATATATATTTGGGTCAGTATATCAAAAAAT
1 TAATATTTTAAAAATAAAACTTAATTATAT--AATATATATATTTGGAT-AGTATATCAAAAAAA
** *
117839 AATTTAC
63 AATAGAA
117846 TAATATTTTAAAAATAAAACTTAATTATAT-ATATATAT-TTCAT-GAT-GTA-A-CAAAAAAAA
1 TAATATTTTAAAAATAAAACTTAATTATATAATATATATATT--TGGATAGTATATCAAAAAAAA
117905 ATAGAA
64 ATAGAA
117911 TAATA
1 TAATA
117916 ATATTATTCT
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
65 16 0.25
66 1 0.02
67 3 0.05
68 2 0.03
69 10 0.16
70 1 0.02
72 30 0.48
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (69 bp):
TAATATTTTAAAAATAAAACTTAATTATATAATATATATATTTGGATAGTATATCAAAAAAAAAT
AGAA
Found at i:118277 original size:470 final size:470
Alignment explanation
Indices: 117397--118288 Score: 1628
Period size: 470 Copynumber: 1.9 Consensus size: 470
117387 ATATATTTTA
117397 TAATTATATATATATATTTCATGATGTAACAAAAAATAGAATAATAATATTATTCTATAATATTT
1 TAATTATATATATATATTTCATGATGTAACAAAAAATAGAATAATAATATTATTCTATAATATTT
*
117462 GGGTCAGTATATCAAAAAATAATAATGTTATTCACCGCTACACACGTTAATGTATATATGATTTT
66 GGGTCAGTATATCAAAAAATAATAATGTTATTCACCGCTACACACATTAATGTATATATGATTTT
* *
117527 TTTAAAATAAATTTAGAGGGAATATAAGATAATATATATTGAAAGACTCCTAGTTATTTGATAAT
131 TTTAAAATAAATTTAGAGGGAATATAAGATAATATATATTGAAAGACTCCTAATTATTTAATAAT
* * *
117592 AAATATTTATATCTTTTTTATATGTGATGTTGAAACTTAAAAACCTCAAGGAATAATAACAAATC
196 AAATATTTATATCTTTTTTATATGTCATGCTGAAACTTAAAAACCTCAAGAAATAATAACAAATC
117657 TCTTAATCACTAAGATTGCTTAATTTATGTATATACGAATCATCAGTATTAAGGTTTTGGATAAA
261 TCTTAATCACTAAGATTGCTTAATTTATGTATATACGAATCATCAGTATTAAGGTTTTGGATAAA
117722 ATATTTATAATGTATACATGCTTATCTGAATTATAAAATTTAAATAATTTACTAATATTTTAAAA
326 ATATTTATAATGTATACATGCTTATCTGAATTATAAAATTTAAATAATTTACTAATATTTTAAAA
117787 ATAAAACTTAATTATATAAAATATATATATTTGGGTCAGTATATCAAAAAATAATTTACTAATAT
391 ATAAAACTTAATTATATAAAATATATATATTTGGGTCAGTATATCAAAAAATAATTTACTAATAT
117852 TTTAAAAATAAAACT
456 TTTAAAAATAAAACT
117867 TAATTATATATATATATTTCATGATGTAACAAAAAAAAATAGAATAATAATATTATTCTATAATA
1 TAATTATATATATATATTTCATGATGTAAC---AAAAAATAGAATAATAATATTATTCTATAATA
117932 TTTGGGTCAGTATATCAAAAAATAATAATGTTATTCACCGCTACACACATTAATGTATATATGA-
63 TTTGGGTCAGTATATCAAAAAATAATAATGTTATTCACCGCTACACACATTAATGTATATATGAT
*
117996 TTTTTT-AAATAAATTTAGAGTGAATATAAGATAATATATATTGAAAGACTCCTAATTATTTAAT
128 TTTTTTAAAATAAATTTAGAGGGAATATAAGATAATATATATTGAAAGACTCCTAATTATTTAAT
*
118060 AATAAATATTTATATTTTTTTTATATGTCATGCTGAAACTT-AAAACCTCAAGAAATAATAACAA
193 AATAAATATTTATATCTTTTTTATATGTCATGCTGAAACTTAAAAACCTCAAGAAATAATAACAA
* * *
118124 ATCTCTTAATTATTAAGATTGCTTAATTTATGTATATATGAATCATCAGTATTAAGGTTTTGGAT
258 ATCTCTTAATCACTAAGATTGCTTAATTTATGTATATACGAATCATCAGTATTAAGGTTTTGGAT
*
118189 AAAATATTTATAATTTATACATGCTTATCTGAATTATAAAATTTAAATAATTTACTAATATTTTA
323 AAAATATTTATAATGTATACATGCTTATCTGAATTATAAAATTTAAATAATTTACTAATATTTTA
118254 AAAATAAAACTTAATTATATAAAATATATATATTT
388 AAAATAAAACTTAATTATATAAAATATATATATTT
118289 TTTAAAAGAA
Statistics
Matches: 407, Mismatches: 12, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
470 213 0.52
471 93 0.23
472 6 0.01
473 95 0.23
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (470 bp):
TAATTATATATATATATTTCATGATGTAACAAAAAATAGAATAATAATATTATTCTATAATATTT
GGGTCAGTATATCAAAAAATAATAATGTTATTCACCGCTACACACATTAATGTATATATGATTTT
TTTAAAATAAATTTAGAGGGAATATAAGATAATATATATTGAAAGACTCCTAATTATTTAATAAT
AAATATTTATATCTTTTTTATATGTCATGCTGAAACTTAAAAACCTCAAGAAATAATAACAAATC
TCTTAATCACTAAGATTGCTTAATTTATGTATATACGAATCATCAGTATTAAGGTTTTGGATAAA
ATATTTATAATGTATACATGCTTATCTGAATTATAAAATTTAAATAATTTACTAATATTTTAAAA
ATAAAACTTAATTATATAAAATATATATATTTGGGTCAGTATATCAAAAAATAATTTACTAATAT
TTTAAAAATAAAACT
Found at i:119132 original size:14 final size:14
Alignment explanation
Indices: 119113--119146 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
119103 TACTTTAAAA
119113 CTAAATTTAAATCT
1 CTAAATTTAAATCT
119127 CTAAATTTAAATCT
1 CTAAATTTAAATCT
119141 CTAAAT
1 CTAAAT
119147 AACCCAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (14 bp):
CTAAATTTAAATCT
Found at i:120629 original size:29 final size:28
Alignment explanation
Indices: 120596--120660 Score: 71
Period size: 31 Copynumber: 2.3 Consensus size: 28
120586 AAAATTTACA
120596 TAATTTAAAA-ATCTTTTAAAAATAAAACT
1 TAATTTAAAATATCTTTTAAAAA-AAAA-T
* *
120625 TAATTATAAAATATTTTTTTAAAAAAAAT
1 TAATT-TAAAATATCTTTTAAAAAAAAAT
120654 T-ATTTAA
1 TAATTTAA
120661 TTAACAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 3 0.09
28 3 0.09
29 7 0.22
30 9 0.28
31 10 0.31
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (28 bp):
TAATTTAAAATATCTTTTAAAAAAAAAT
Found at i:120743 original size:21 final size:21
Alignment explanation
Indices: 120719--120760 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
120709 AAAAGTTTCG
120719 GACCGTGAACC-GACCTAATTC
1 GACCGTG-ACCGGACCTAATTC
*
120740 GACCGTGACCGGCCCTAATTC
1 GACCGTGACCGGACCTAATTC
120761 CCAGTGCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
GACCGTGACCGGACCTAATTC
Found at i:120890 original size:14 final size:14
Alignment explanation
Indices: 120871--120939 Score: 61
Period size: 14 Copynumber: 4.8 Consensus size: 14
120861 TTTAGAAATA
*
120871 TACATTTGACTATT
1 TACATTTGATTATT
120885 TACATTTGATTTTAAATT
1 TACATTTGA--TT--ATT
120903 TA-ATTT-ATTATT
1 TACATTTGATTATT
*
120915 TACATTTGAGTATT
1 TACATTTGATTATT
*
120929 TACATTCGATT
1 TACATTTGATT
120940 TAAATCAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
12 5 0.11
13 4 0.09
14 25 0.56
16 2 0.04
17 4 0.09
18 5 0.11
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (14 bp):
TACATTTGATTATT
Found at i:121504 original size:33 final size:33
Alignment explanation
Indices: 121462--121524 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
121452 TATATTGTTT
121462 GTTCACTGTAAAT-ATTCCATTTTGACAGTTGTA
1 GTTCACTGTAAATGATT-CATTTTGACAGTTGTA
*
121495 GTTCACTGTAAATGATTCATTTTGATAGTT
1 GTTCACTGTAAATGATTCATTTTGACAGTT
121525 CTTCTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 25 0.89
34 3 0.11
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (33 bp):
GTTCACTGTAAATGATTCATTTTGACAGTTGTA
Found at i:124979 original size:17 final size:16
Alignment explanation
Indices: 124937--124979 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
124927 AGCTAGTCTA
124937 TTAATATTT-TTATTT
1 TTAATATTTATTATTT
*
124952 TTAATACTTTATTGTTT
1 TTAATA-TTTATTATTT
124969 TTAAGTATTTA
1 TTAA-TATTTA
124980 ATAATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 6 0.25
16 3 0.12
17 13 0.54
18 2 0.08
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (16 bp):
TTAATATTTATTATTT
Found at i:126692 original size:22 final size:20
Alignment explanation
Indices: 126667--126723 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
126657 TTTATATTTT
126667 TTAAAAATTTAATTTAAAAAA
1 TTAAAAATTTAATTT-AAAAA
* *
126688 CTTAAAACTAT-ATTTAAAAA
1 -TTAAAAATTTAATTTAAAAA
*
126708 TAAAAAATTCTAATTT
1 TTAAAAATT-TAATTT
126724 CTCTAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 6 0.21
20 6 0.21
21 8 0.29
22 8 0.29
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
TTAAAAATTTAATTTAAAAA
Found at i:127202 original size:2 final size:2
Alignment explanation
Indices: 127195--127252 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
127185 TAAAAATTTA
127195 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
127237 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
127253 GTCACGTATC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128064 original size:125 final size:124
Alignment explanation
Indices: 127831--128069 Score: 426
Period size: 125 Copynumber: 1.9 Consensus size: 124
127821 TCTCTGCATA
127831 TATTTATGAGCTTTGTCTCTTGAGATATGATGATGTTAGGTTTTGTTTAAATTATATAGTATATT
1 TATTTATGAGCTTTGTCTCTTGAGATATGATGATGTTAGGTTTTGTTTAAATTATATAGTATATT
* *
127896 TTTAAAATAAATATTTAAAATATATTATAAATATTTATTTTTTTAAAAAAAGTAAATAT
66 TTTAAAATAAATATTTAAAATATATTATAAATATATATATTTTTAAAAAAAGTAAATAT
127955 TATTTATGAGCCTTTGTCTCTTGAGATATGATGATGTTAGGTTTTGTTTAAATTATATAGTATAT
1 TATTTATGAG-CTTTGTCTCTTGAGATATGATGATGTTAGGTTTTGTTTAAATTATATAGTATAT
*
128020 TTTTAAAAATAAATATTTAAAATATATTATAAATATATA-ATTTTTTAAAA
65 TTTT-AAAATAAATATTTAAAATATATTATAAATATATATATTTTTAAAAA
128070 GTAATATTTA
Statistics
Matches: 110, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
124 10 0.09
125 67 0.61
126 33 0.30
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.48
Consensus pattern (124 bp):
TATTTATGAGCTTTGTCTCTTGAGATATGATGATGTTAGGTTTTGTTTAAATTATATAGTATATT
TTTAAAATAAATATTTAAAATATATTATAAATATATATATTTTTAAAAAAAGTAAATAT
Found at i:128066 original size:28 final size:29
Alignment explanation
Indices: 128035--128105 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
128025 AAAATAAATA
128035 TTTAAAA-T-ATATTATA-AATATATAATTT
1 TTTAAAAGTAATATT-TAGAAT-TATAATTT
*
128063 TTTAAAAGTAATATTTAGAATTATCATTT
1 TTTAAAAGTAATATTTAGAATTATAATTT
128092 TTTAAGAAG-AATAT
1 TTTAA-AAGTAATAT
128106 AGATGGTGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 7 0.18
29 20 0.53
30 11 0.29
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.46
Consensus pattern (29 bp):
TTTAAAAGTAATATTTAGAATTATAATTT
Found at i:135678 original size:29 final size:28
Alignment explanation
Indices: 135640--135721 Score: 67
Period size: 32 Copynumber: 2.7 Consensus size: 28
135630 AATAATTCTG
*
135640 TCATACTCAATATAATCATAAAATTGAT-A
1 TCATCCTCAATATAAT-ATAAAATT-ATAA
*
135669 TCATCCTCAAAATTAATATTATAAAATTATAA
1 TCATCCTC--AA-T-ATAATATAAAATTATAA
*
135701 TCATCCTAAAATATAATATAA
1 TCATCCT-CAATATAATATAA
135722 TATTTTTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
29 15 0.35
30 1 0.02
31 6 0.14
32 17 0.40
33 4 0.09
ACGTcount: A:0.50, C:0.13, G:0.01, T:0.35
Consensus pattern (28 bp):
TCATCCTCAATATAATATAAAATTATAA
Found at i:135693 original size:32 final size:32
Alignment explanation
Indices: 135657--135719 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
135647 CAATATAATC
135657 ATAAAATTGAT-ATCATCCTCAAAAT-TAATATT
1 ATAAAATT-ATAATCATCCT-AAAATATAATATT
135689 ATAAAATTATAATCATCCTAAAATATAATAT
1 ATAAAATTATAATCATCCTAAAATATAATAT
135720 AATATTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.37
Consensus pattern (32 bp):
ATAAAATTATAATCATCCTAAAATATAATATT
Found at i:135715 original size:16 final size:16
Alignment explanation
Indices: 135668--135717 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
135658 TAAAATTGAT
135668 ATCATCCTCAAAAT-TA
1 ATCATCCT-AAAATATA
**
135684 AT-ATTATAAAATTATA
1 ATCATCCTAAAA-TATA
135700 ATCATCCTAAAATATA
1 ATCATCCTAAAATATA
135716 AT
1 AT
135718 ATAATATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 4 0.15
15 4 0.15
16 12 0.44
17 7 0.26
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (16 bp):
ATCATCCTAAAATATA
Found at i:139868 original size:22 final size:21
Alignment explanation
Indices: 139843--139885 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
139833 ATTACATTTT
139843 TTAAA-AACAATATTTCAAATTA
1 TTAAACAACAA-ATTT-AAATTA
139865 TTAAACTAACAAATTTAAATT
1 TTAAAC-AACAAATTTAAATT
139886 TATGTTGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.53
23 4 0.21
24 5 0.26
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (21 bp):
TTAAACAACAAATTTAAATTA
Found at i:140386 original size:11 final size:11
Alignment explanation
Indices: 140365--140398 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
140355 GCGTATTACA
140365 TTATA-TATAT
1 TTATATTATAT
140375 TTATATTATAT
1 TTATATTATAT
140386 TTATATTATAT
1 TTATATTATAT
140397 TT
1 TT
140399 TTGGTACCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATATTATAT
Found at i:147820 original size:63 final size:63
Alignment explanation
Indices: 147712--147839 Score: 186
Period size: 63 Copynumber: 2.0 Consensus size: 63
147702 TCAAATTACC
*
147712 TTGTAGAGTGAAGTCTTGGCTGATCTCACACCCATACAAGATCAAATGCTTCAAAGAAGAAAA
1 TTGTAGAGTGAAGTCTTGGCTGATCTCACACCCATACAACATCAAATGCTTCAAAGAAGAAAA
* * * * *
147775 TTGTATAGTGAAGTTTTGGCTGATCTCACACTCGA-ACAACCTCAAATGCTTCAAAGAGGAAAA
1 TTGTAGAGTGAAGTCTTGGCTGATCTCACAC-CCATACAACATCAAATGCTTCAAAGAAGAAAA
147838 TT
1 TT
147840 CTCTTGGACT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 56 0.97
64 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (63 bp):
TTGTAGAGTGAAGTCTTGGCTGATCTCACACCCATACAACATCAAATGCTTCAAAGAAGAAAA
Found at i:148113 original size:27 final size:27
Alignment explanation
Indices: 148069--148127 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
148059 TATATTTTTT
* *
148069 AATTACTTTATTTCTTTAGAAAATTCC
1 AATTACTTTATTTCTTTAAAAAATTCA
*
148096 AATTACATTT-TTTTTTTAAAAAATTCA
1 AATTAC-TTTATTTCTTTAAAAAATTCA
148123 AATTA
1 AATTA
148128 TTAAACTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (27 bp):
AATTACTTTATTTCTTTAAAAAATTCA
Found at i:150717 original size:12 final size:12
Alignment explanation
Indices: 150700--150725 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
150690 ACAATATGCT
150700 ATTGTTGAAGGG
1 ATTGTTGAAGGG
150712 ATTGTTGAAGGG
1 ATTGTTGAAGGG
150724 AT
1 AT
150726 CCACCCCCAA
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:0.27, C:0.00, G:0.38, T:0.35
Consensus pattern (12 bp):
ATTGTTGAAGGG
Found at i:153316 original size:22 final size:23
Alignment explanation
Indices: 153274--153319 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
153264 TATTTTTACC
*
153274 TTAAAACTAAATTTTTAATATTT
1 TTAAAACTAAATTATTAATATTT
153297 TTAAAACTAAA-TATTAATATTT
1 TTAAAACTAAATTATTAATATTT
153319 T
1 T
153320 AATATTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAAAACTAAATTATTAATATTT
Found at i:158175 original size:21 final size:21
Alignment explanation
Indices: 158125--158167 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
158115 TTTATTTAAA
158125 TAAAATTTTAAAATATATATT
1 TAAAATTTTAAAATATATATT
*
158146 TGAAATTTTAAAATA-AT-TT
1 TAAAATTTTAAAATATATATT
158165 TAA
1 TAA
158168 TAAGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 2 0.10
21 14 0.70
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TAAAATTTTAAAATATATATT
Found at i:159977 original size:7 final size:7
Alignment explanation
Indices: 159965--159994 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
159955 GAGTGGCCTT
159965 TTATTTA
1 TTATTTA
159972 TTATTTA
1 TTATTTA
159979 TTATTTA
1 TTATTTA
*
159986 TTATATA
1 TTATTTA
159993 TT
1 TT
159995 TACTTTCCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTATTTA
Found at i:160664 original size:33 final size:33
Alignment explanation
Indices: 160627--160703 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 33
160617 TGTTTTATGT
*
160627 TTTTGATA-TTGTTTGTTCACTGTAAAT-ATTCCA
1 TTTTGATAGTTG-TAGTTCACTGTAAATGATT-CA
*
160660 TTTTGACAGTTGTAGTTCACTGTAAATGATTCA
1 TTTTGATAGTTGTAGTTCACTGTAAATGATTCA
160693 TTTTGATAGTT
1 TTTTGATAGTT
160704 CTTCTGATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
33 33 0.85
34 6 0.15
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (33 bp):
TTTTGATAGTTGTAGTTCACTGTAAATGATTCA
Found at i:173127 original size:180 final size:185
Alignment explanation
Indices: 172912--173279 Score: 674
Period size: 186 Copynumber: 2.0 Consensus size: 185
172902 CACCGCCGAT
172912 GATTGTTTCTTCACCACGTCCATTTCTGG-AAAAAAAATCAAAACAGAAAAG-AAAAGATTGAAA
1 GATTGTTTCTTCACCACGTCCATTTCTGGAAAAAAAAATCAAAACAGAAAAGAAAAAGATTGAAA
172975 CTTC-TTTTTGGCGCTCGGTTGGATTCCAAGACAGACAGATATCTCAAAGCTCCACCGAG-CACA
66 CTTCTTTTTTGGCGCTCGGTTGGATTCCAAGACAGACAGATATCTCAAAGCTCCACCGAGACACA
*
173038 CACTCTGTGTCTCCCACCTCCCCCACAACAGCGATTCTTGCAGGCAAATTCTTTA
131 CACTCTGTCTCTCCCACCTCCCCCACAACAGCGATTCTTGCAGGCAAATTCTTTA
173093 GATTGTTTCTTCA-CACGTCCATTTCTGGAAAAAAAAATCAAAACAGAAAAGAAAAAAGATTGAA
1 GATTGTTTCTTCACCACGTCCATTTCTGGAAAAAAAAATCAAAACAGAAAAG-AAAAAGATTGAA
173157 ACTTCTTTTTTGGCGCTCGGTTGGATTCCAAGACAGACAGATATCTCAAAGCTCCACCGAGCACA
65 ACTTCTTTTTTGGCGCTCGGTTGGATTCCAAGACAGACAGATATCTCAAAGCTCCACCGAG-ACA
173222 CACACTCTGTCTCTCCCACCTCCCCCACAACAGCGATTCTTGCAGGCAAATTCTTTA
129 CACACTCTGTCTCTCCCACCTCCCCCACAACAGCGATTCTTGCAGGCAAATTCTTTA
173279 G
1 G
173280 GAACCAAACT
Statistics
Matches: 180, Mismatches: 1, Indels: 7
0.96 0.01 0.04
Matches are distributed among these distances:
180 15 0.08
181 35 0.19
183 16 0.09
184 55 0.31
186 59 0.33
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (185 bp):
GATTGTTTCTTCACCACGTCCATTTCTGGAAAAAAAAATCAAAACAGAAAAGAAAAAGATTGAAA
CTTCTTTTTTGGCGCTCGGTTGGATTCCAAGACAGACAGATATCTCAAAGCTCCACCGAGACACA
CACTCTGTCTCTCCCACCTCCCCCACAACAGCGATTCTTGCAGGCAAATTCTTTA
Found at i:174963 original size:163 final size:162
Alignment explanation
Indices: 174677--175003 Score: 618
Period size: 163 Copynumber: 2.0 Consensus size: 162
174667 CCCACCGTTA
*
174677 AAAAATTAATGATTATATTGATATGTCGTCATAAGGTAATGTCATCTCATCATTGAATTTTAAAA
1 AAAAATTAATGATTATATTAATATGTCGTCATAAGGTAATGTCATCTCATCATTGAATTTTAAAA
174742 AAAAATACTACGTCAACATTTTGTTAATTTTTTAACATGAGTGACTAAAACAAAATTAAAATATA
66 AAAAATACTACGTCAACATTTTGTTAATTTTTTAACATGAGTGACTAAAACAAAATTAAAATATA
174807 ATATTAGATATGATTTTAAAAAATAATAATTC
131 ATATTAGATATGATTTTAAAAAATAATAATTC
* *
174839 AAAAATTAATGATTATATTAATATGTCGTCATAAGGTAATGTCATCTCATCATTGATTTTTTTAA
1 AAAAATTAATGATTATATTAATATGTCGTCATAAGGTAATGTCATCTCATCATTGA-ATTTTAAA
174904 AAAAAATACTACGTCAACATTTTGTTAATTTTTTAACATGAGTGACTAAAACAAAATTAAAATAT
65 AAAAAATACTACGTCAACATTTTGTTAATTTTTTAACATGAGTGACTAAAACAAAATTAAAATAT
174969 AATATTAGATATGATTTTAAAAAATAATAATTC
130 AATATTAGATATGATTTTAAAAAATAATAATTC
175002 AA
1 AA
175004 TAATAAAAAC
Statistics
Matches: 161, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
162 55 0.34
163 106 0.66
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (162 bp):
AAAAATTAATGATTATATTAATATGTCGTCATAAGGTAATGTCATCTCATCATTGAATTTTAAAA
AAAAATACTACGTCAACATTTTGTTAATTTTTTAACATGAGTGACTAAAACAAAATTAAAATATA
ATATTAGATATGATTTTAAAAAATAATAATTC
Found at i:180378 original size:15 final size:15
Alignment explanation
Indices: 180340--180378 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
180330 TCTTCCGAAT
180340 ATTTGAATATAATTA
1 ATTTGAATATAATTA
*
180355 TTTTGAATATACATTA
1 ATTTGAATATA-ATTA
180371 ATTT-AATA
1 ATTTGAATA
180379 ATTGAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (15 bp):
ATTTGAATATAATTA
Found at i:194302 original size:2 final size:2
Alignment explanation
Indices: 194295--194323 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
194285 TCATTTTGGA
194295 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
194324 ATGATGAACA
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
Done.