Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008512.1 Hibiscus syriacus cultivar Beakdansim tig00111372_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: 1759229
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 9
Found at i:3597 original size:15 final size:15
Alignment explanation
Indices: 3577--3609 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3567 ATTAAAAATA
3577 TAACATTTTCAGTTG
1 TAACATTTTCAGTTG
3592 TAACATTTTCAGTTG
1 TAACATTTTCAGTTG
3607 TAA
1 TAA
3610 TCGAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (15 bp):
TAACATTTTCAGTTG
Found at i:6402 original size:2 final size:2
Alignment explanation
Indices: 6395--6422 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6385 TTGTTCGTGC
6395 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
6423 TCCGATATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6907 original size:21 final size:21
Alignment explanation
Indices: 6883--6925 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6873 ATTGTCATAG
**
6883 GGGAACCGATTTCCTGCTACA
1 GGGAACCGATACCCTGCTACA
*
6904 GGGAACTGATACCCTGCTACA
1 GGGAACCGATACCCTGCTACA
6925 G
1 G
6926 TACTGCTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.21
Consensus pattern (21 bp):
GGGAACCGATACCCTGCTACA
Found at i:9927 original size:18 final size:18
Alignment explanation
Indices: 9894--9962 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
9884 CGGGACAAAC
* *
9894 AGTGGTCATTCAGAACAT
1 AGTGGTCCTTCGGAACAT
*
9912 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGAAC-AT
* * *
9931 CAATGGTCCTTCGGGATAT
1 -AGTGGTCCTTCGGAACAT
9950 AGTGGTCCTTCGG
1 AGTGGTCCTTCGG
9963 GACAAATATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 25 0.61
19 4 0.10
20 12 0.29
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGAACAT
Found at i:9938 original size:38 final size:38
Alignment explanation
Indices: 9874--9968 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 38
9864 AGGGATTATC
*
9874 AGTGG-TCATTCGGGACAAACAGTGGTCATTCAGAACAT
1 AGTGGTTC-TTCGGGACAAACAATGGTCATTCAGAACAT
* * * * * *
9912 AGTGGTTCTTCGGAACAATCAATGGTCCTTCGGGATAT
1 AGTGGTTCTTCGGGACAAACAATGGTCATTCAGAACAT
*
9950 AGTGGTCCTTCGGGACAAA
1 AGTGGTTCTTCGGGACAAA
9969 TATTCAGTGC
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
38 44 0.96
39 2 0.04
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (38 bp):
AGTGGTTCTTCGGGACAAACAATGGTCATTCAGAACAT
Found at i:11801 original size:18 final size:19
Alignment explanation
Indices: 11755--11801 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
11745 GGACTCTCAG
*
11755 TGCATCGATGCACTAAGAG
1 TGCATCGATGCACTAAGAA
11774 TGCATCGATGCA-TAA-AA
1 TGCATCGATGCACTAAGAA
11791 TGCATTCGATG
1 TGCA-TCGATG
11802 TTTTGAAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 9 0.35
19 12 0.46
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCACTAAGAA
Found at i:20582 original size:19 final size:20
Alignment explanation
Indices: 20539--20591 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
20529 AATAGCCTGA
*
20539 GTGCATCGATGCATGGTCTT
1 GTGCATCGATGCATGGTCAT
20559 GTGCATCGATGCATGGT-AT
1 GTGCATCGATGCATGGTCAT
20578 GTGCATCGATGCAT
1 GTGCATCGATGCAT
20592 AAAATGCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATGGTCAT
Found at i:23656 original size:63 final size:63
Alignment explanation
Indices: 23555--23684 Score: 206
Period size: 63 Copynumber: 2.1 Consensus size: 63
23545 TTATTGGCTG
* * * *
23555 TTTGATCTTTGGGGTTTCCTTTTTTTAGTTTCTTGGTATTATTTGTTATTAAAGTTTGAAGAT
1 TTTGATCTTTGGGGTTTCCCTCTTTTAGTTTCTGGGTATTAATTGTTATTAAAGTTTGAAGAT
* *
23618 TTTGATCTTTGGGTTTTCCCTCTTTTAGTTTCTGGGTATTAATTGTTATTAAGGTTTGAAGAT
1 TTTGATCTTTGGGGTTTCCCTCTTTTAGTTTCTGGGTATTAATTGTTATTAAAGTTTGAAGAT
23681 TTTG
1 TTTG
23685 GTCTATGGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.17, C:0.08, G:0.20, T:0.55
Consensus pattern (63 bp):
TTTGATCTTTGGGGTTTCCCTCTTTTAGTTTCTGGGTATTAATTGTTATTAAAGTTTGAAGAT
Found at i:27647 original size:30 final size:27
Alignment explanation
Indices: 27574--27653 Score: 70
Period size: 30 Copynumber: 2.8 Consensus size: 27
27564 TATTTCATAC
*
27574 TCAGAAATCAGATACAGAAATATAGTAA
1 TCAGAAATCAGATA-AAAAATATAGTAA
* * *
27602 TCATAGATCATATAAAAAATATACAGTAAA
1 TCAGAAATCAGATAAAAAATAT--AGT-AA
* *
27632 TCAGATATCAGATAAATAATAT
1 TCAGAAATCAGATAAAAAATAT
27654 TAAGAAAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
27 7 0.17
28 11 0.27
29 3 0.07
30 20 0.49
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (27 bp):
TCAGAAATCAGATAAAAAATATAGTAA
Found at i:28833 original size:30 final size:30
Alignment explanation
Indices: 28790--28846 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
28780 TTTGGATTCA
* *
28790 AATTTAATCAAAATTTTATTTTGGTCCCCT
1 AATTTAATCAAAATTTTAATTTAGTCCCCT
* *
28820 AATTTAGTTAAAATTTTAATTTAGTCC
1 AATTTAATCAAAATTTTAATTTAGTCC
28847 TCAAAATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47
Consensus pattern (30 bp):
AATTTAATCAAAATTTTAATTTAGTCCCCT
Found at i:38713 original size:210 final size:207
Alignment explanation
Indices: 38289--38741 Score: 677
Period size: 210 Copynumber: 2.2 Consensus size: 207
38279 CTTATTCATA
*
38289 TATTGAATAAAAATATTTTTTTATTATTTCGGGTC--G-GGTTTCTAATTCATATATTCGGGTCG
1 TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTGGTTTCTAATTCATATATTCGGGTCG
* *
38351 GGTGAAACTTTATTTTGGTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCG
66 GATGAAACTTTATTTTAGTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCG
* * *
38416 GGTTTAGGGTGAAAAAAACCGGTCTGATCCGAAAATATATATATAATTCAGGTCGGGTCGGATTA
131 GGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATATAATTCAGGTCGGGTCGGATTA
38481 AGTCACTGTTTT
196 AGTCACTGTTTT
*
38493 TATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTTGGATTTCTAATTCATATATTAGAGT
1 TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGG-TGG-TTTCTAATTCATATA-T----T
* *
38558 CGGGTCGGATGAAACTTTATTTTATTCGGGTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTC
59 CGGGTCGGATGAAACTTTATTTTAGTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTC
* * **
38622 -GGTTCGGGTTTAGGGTGAAGAAAATCGGACCGACCCG-AAA-ATATATATAATTTGGGTCGGGT
124 GGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATATAATTCAGGTCGGGT
38684 CGGATTAAGTCACTGTTTT
189 CGGATTAAGTCACTGTTTT
38703 TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGT
1 TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGT
38742 CGGGTTTTTT
Statistics
Matches: 225, Mismatches: 14, Indels: 15
0.89 0.06 0.06
Matches are distributed among these distances:
204 33 0.15
206 1 0.00
208 2 0.01
209 16 0.07
210 77 0.34
211 3 0.01
212 32 0.14
213 24 0.11
214 37 0.16
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (207 bp):
TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTGGTTTCTAATTCATATATTCGGGTCG
GATGAAACTTTATTTTAGTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCG
GGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATATAATTCAGGTCGGGTCGGATTA
AGTCACTGTTTT
Found at i:40318 original size:75 final size:75
Alignment explanation
Indices: 40168--40353 Score: 255
Period size: 75 Copynumber: 2.5 Consensus size: 75
40158 CAAAGCCAAA
* * * * **
40168 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
40233 TTTGGCTCCGAG
64 TTTGGCTCCGAG
* *
40245 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACATTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
40310 TTGTTCCGAG
66 TGGCTCCGAG
*
40320 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCC
40354 TGTTCAACGG
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
75 72 0.74
77 25 0.26
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:41745 original size:37 final size:37
Alignment explanation
Indices: 41703--41776 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
41693 ATATTTCAAC
*
41703 AAACATCTACCAAATTTTGAAAA-AATCTTTTTCAAAG
1 AAACATCTACCAAACTTTGAAAACAAT-TTTTTCAAAG
* *
41740 AAACATTTACCAAACTTTGAAAACCATTTTTTCAAAG
1 AAACATCTACCAAACTTTGAAAACAATTTTTTCAAAG
41777 TTGGTTGCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 31 0.94
38 2 0.06
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (37 bp):
AAACATCTACCAAACTTTGAAAACAATTTTTTCAAAG
Found at i:44823 original size:19 final size:19
Alignment explanation
Indices: 44799--44836 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
44789 TTTTGGTGCA
*
44799 GAGGGAATCGATCCCCCCT
1 GAGGGAACCGATCCCCCCT
*
44818 GAGGGAACCGATTCCCCCT
1 GAGGGAACCGATCCCCCCT
44837 TTGAAGGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.37, G:0.26, T:0.16
Consensus pattern (19 bp):
GAGGGAACCGATCCCCCCT
Found at i:47630 original size:75 final size:75
Alignment explanation
Indices: 47480--47665 Score: 255
Period size: 75 Copynumber: 2.5 Consensus size: 75
47470 CAAAGCCAAA
* * * * **
47480 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
47545 TTTGGCTCCGAG
64 TTTGGCTCCGAG
* *
47557 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACATTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
47622 TTGTTCCGAG
66 TGGCTCCGAG
*
47632 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCC
47666 CCCAGAGGGT
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
75 72 0.74
77 25 0.26
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:47687 original size:75 final size:76
Alignment explanation
Indices: 47480--47689 Score: 253
Period size: 75 Copynumber: 2.8 Consensus size: 76
47470 CAAAGCCAAA
* * * * * **
47480 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCCAGA-GAGGAACCGATTCCCCCCTAAACAG
47545 TTTGGCTCCGAG
65 TTTGGCTCCGAG
* ** *
47557 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAG-GAGGAACCGATTCCCCCCTAAACATT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCCAGAGAGGAACCGATTCCCCCCTAAACAGT
* *
47621 TTTGTTCCGAG
66 TTGGCTCCGAG
* *
47632 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCCCCCAGAG-GGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCCAGAGAGGAACCGATTCCCCCCT
47690 GTTCAACGGT
Statistics
Matches: 113, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
75 58 0.51
76 23 0.20
77 32 0.28
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.21
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCCAGAGAGGAACCGATTCCCCCCTAAACAGT
TTGGCTCCGAG
Found at i:49627 original size:21 final size:21
Alignment explanation
Indices: 49603--49644 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
49593 TATGAGAAAT
*
49603 TGTTTTAAAATAT-AAAAATGA
1 TGTTTCAAAAT-TGAAAAATGA
49624 TGTTTCAAAATTGAAAAATGA
1 TGTTTCAAAATTGAAAAATGA
49645 AAACAAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (21 bp):
TGTTTCAAAATTGAAAAATGA
Found at i:53517 original size:21 final size:21
Alignment explanation
Indices: 53491--53530 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53481 CCCCCTTTGA
*
53491 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
53512 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
53531 TGGGATTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:56279 original size:75 final size:74
Alignment explanation
Indices: 56115--56299 Score: 244
Period size: 75 Copynumber: 2.5 Consensus size: 74
56105 CAAAGCCAAA
* * * * **
56115 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCTAAACAGT
56180 TTGGCTCCGAG
64 TTGGCTCCGAG
* *
56191 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACATTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATT-CCCCCTAAACAGTT
* *
56256 TTGTTCCGAG
65 TGGCTCCGAG
*
56266 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCC
56300 CCAGAGGGTA
Statistics
Matches: 96, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
74 21 0.22
75 50 0.52
76 25 0.26
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (74 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
GGCTCCGAG
Found at i:56315 original size:75 final size:76
Alignment explanation
Indices: 56115--56322 Score: 242
Period size: 75 Copynumber: 2.8 Consensus size: 76
56105 CAAAGCCAAA
* * * * * **
56115 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCCAGA-GAGGAACCGATTCCCCCCTAAACAG
56179 TTTGGCTCCGAG
65 TTTGGCTCCGAG
* ** *
56191 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAG-GAGGAACCGATTCCCCCCTAAACATT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCCAGAGAGGAACCGATTCCCCCCTAAACAGT
* *
56255 TTTGTTCCGAG
66 TTGGCTCCGAG
* * *
56266 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCCCCAGAG-GGTATCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCCAGAGAGGAACCGATTCCCCCCT
56323 GTTCAACGGT
Statistics
Matches: 111, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
74 12 0.11
75 67 0.60
76 32 0.29
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.22
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCCAGAGAGGAACCGATTCCCCCCTAAACAGT
TTGGCTCCGAG
Found at i:57740 original size:37 final size:37
Alignment explanation
Indices: 57671--57745 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
57661 ATATTTCAAC
*
57671 AAACATCTACCAAATTTTGAAAAAATCATTTTTCAAAG
1 AAACATCTACCAAACTTTGAAAAAAT-ATTTTTCAAAG
* *
57709 AAACATTTACCAAACTTTGAAAACCAT-TTTTTCAAAG
1 AAACATCTACCAAACTTTGAAAA-AATATTTTTCAAAG
57746 TTGGTTGCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 10 0.30
38 21 0.64
39 2 0.06
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.32
Consensus pattern (37 bp):
AAACATCTACCAAACTTTGAAAAAATATTTTTCAAAG
Found at i:62331 original size:35 final size:35
Alignment explanation
Indices: 62256--62358 Score: 152
Period size: 35 Copynumber: 2.9 Consensus size: 35
62246 ATATTTCAAC
*
62256 AAACATCTACCAAACTTTGAAAAAACCATTTTTCAAAG
1 AAACATTTACCAAACTTT--AAAAACCA-TTTTCAAAG
*
62294 AAACATTTACTAAACTTTAAAAACCATTTTCAAAG
1 AAACATTTACCAAACTTTAAAAACCATTTTCAAAG
*
62329 AAACATTTACCAAACTTTGAAAACCATTTT
1 AAACATTTACCAAACTTTAAAAACCATTTT
62359 TTCAAAGTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 37 0.61
36 8 0.13
38 16 0.26
ACGTcount: A:0.47, C:0.19, G:0.04, T:0.30
Consensus pattern (35 bp):
AAACATTTACCAAACTTTAAAAACCATTTTCAAAG
Found at i:68047 original size:21 final size:21
Alignment explanation
Indices: 68033--68072 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
68023 AATAGGTTAA
*
68033 TAAAATGTCTGAATAGATAAT
1 TAAAATATCTGAATAGATAAT
*
68054 TAAAATATCTGATTAGATA
1 TAAAATATCTGAATAGATA
68073 TTATCTTGTA
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:0.47, C:0.05, G:0.12, T:0.35
Consensus pattern (21 bp):
TAAAATATCTGAATAGATAAT
Found at i:70279 original size:15 final size:15
Alignment explanation
Indices: 70261--70309 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
70251 GTGAAATTCT
*
70261 AATTATTTAAATAAA
1 AATTATTTATATAAA
*
70276 AATTATTTATACAAA
1 AATTATTTATATAAA
70291 AATTATTTATATAAA
1 AATTATTTATATAAA
70306 AATT
1 AATT
70310 CATCGATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTATTTATATAAA
Found at i:71414 original size:23 final size:21
Alignment explanation
Indices: 71388--71429 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
71378 ATATAAAAAT
71388 TATTTCTTATTAAATATTTTTGG
1 TATTT-TTATTAAAT-TTTTTGG
*
71411 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
71430 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 8 0.44
23 5 0.28
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:71816 original size:15 final size:15
Alignment explanation
Indices: 71796--71851 Score: 103
Period size: 15 Copynumber: 3.7 Consensus size: 15
71786 CTCCTACTTG
71796 AAGAAAGCATCAGAC
1 AAGAAAGCATCAGAC
71811 AAGAAAGCATCAGAC
1 AAGAAAGCATCAGAC
71826 AAGAAAGCATCAGAC
1 AAGAAAGCATCAGAC
*
71841 AAGGAAGCATC
1 AAGAAAGCATC
71852 TTTAAGTTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.52, C:0.20, G:0.21, T:0.07
Consensus pattern (15 bp):
AAGAAAGCATCAGAC
Found at i:74948 original size:17 final size:18
Alignment explanation
Indices: 74911--74951 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
74901 ATATTATGTA
*
74911 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
74929 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
74946 TTTACT
1 TTTACT
74952 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:76657 original size:18 final size:18
Alignment explanation
Indices: 76630--76683 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
76620 ACAGCAGCCA
76630 CCGCAGCCATTTATGATG
1 CCGCAGCCATTTATGATG
* *
76648 CCGCAACCATTTATAATG
1 CCGCAGCCATTTATGATG
*
76666 CCGCAGCCATATATGATG
1 CCGCAGCCATTTATGATG
76684 TCGCCATCGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (18 bp):
CCGCAGCCATTTATGATG
Found at i:77044 original size:15 final size:15
Alignment explanation
Indices: 77020--77049 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
77010 ACCTGCTCAG
*
77020 GACGATGACGATGAC
1 GACGACGACGATGAC
77035 GACGACGACGATGAC
1 GACGACGACGATGAC
77050 AGCGAGGAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.23, G:0.33, T:0.10
Consensus pattern (15 bp):
GACGACGACGATGAC
Found at i:77304 original size:35 final size:33
Alignment explanation
Indices: 77265--77349 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
77255 ATATTTCAGT
77265 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
77300 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
77335 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
77350 TAAATACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:85466 original size:24 final size:25
Alignment explanation
Indices: 85433--85485 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
85423 AATTTGAAAA
* *
85433 ATTAATTTTTAAATTAATAT-TTTT
1 ATTAAATTTTAAAATAATATCTTTT
85457 ATTAAATTTTAAAATAATATCCTTTT
1 ATTAAATTTTAAAATAATAT-CTTTT
85483 ATT
1 ATT
85486 TTATGTAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 18 0.72
26 7 0.28
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTAAATTTTAAAATAATATCTTTT
Found at i:89409 original size:78 final size:78
Alignment explanation
Indices: 89291--89438 Score: 199
Period size: 78 Copynumber: 1.9 Consensus size: 78
89281 ATGCAGTTAA
*
89291 TATAATATTAATATTCTTTGAATGTATCAATTCTCCTATGATGTTCAATATTATAAAATTTTATG
1 TATAATATTAATATTCTTTGAATGTATCAATTCTACTATGATGTTCAATATTATAAAATTTTATG
89356 AAAAAACTGTATG
66 AAAAAACTGTATG
*** * * * * *
89369 TATAATATTAATATTCTTTGAA-GTTATTTGTTTTATTATGATGTTCAGTATTTTGAAATTTTAT
1 TATAATATTAATATTCTTTGAATG-TATCAATTCTACTATGATGTTCAATATTATAAAATTTTAT
89433 GAAAAA
65 GAAAAA
89439 TTCGATACAT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
77 1 0.02
78 59 0.98
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.47
Consensus pattern (78 bp):
TATAATATTAATATTCTTTGAATGTATCAATTCTACTATGATGTTCAATATTATAAAATTTTATG
AAAAAACTGTATG
Found at i:93373 original size:15 final size:15
Alignment explanation
Indices: 93353--93391 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
93343 TTTCAAAGGC
93353 TTTGGGTTTTCAGAG
1 TTTGGGTTTTCAGAG
93368 TTTGGGTTTTCAGAG
1 TTTGGGTTTTCAGAG
93383 TTTGGGTTT
1 TTTGGGTTT
93392 AATCATTAAG
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:0.10, C:0.05, G:0.33, T:0.51
Consensus pattern (15 bp):
TTTGGGTTTTCAGAG
Found at i:99200 original size:31 final size:31
Alignment explanation
Indices: 99165--99228 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
99155 GTCATAACCC
*
99165 GACCCGACCCGA-CTCGTTTACCCGACCCATT
1 GACCCGACCCGACCT-GTTGACCCGACCCATT
*
99196 GACCCGACCCGACCTGTTGACCCGACCCGTT
1 GACCCGACCCGACCTGTTGACCCGACCCATT
99227 GA
1 GA
99229 TCGTTGACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.19, C:0.44, G:0.20, T:0.17
Consensus pattern (31 bp):
GACCCGACCCGACCTGTTGACCCGACCCATT
Found at i:99205 original size:18 final size:18
Alignment explanation
Indices: 99184--99224 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
99174 CGACTCGTTT
99184 ACCCGACCCATTGACCCG
1 ACCCGACCCATTGACCCG
**
99202 ACCCGACCTGTTGACCCG
1 ACCCGACCCATTGACCCG
99220 ACCCG
1 ACCCG
99225 TTGATCGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.49, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCCATTGACCCG
Found at i:101806 original size:24 final size:24
Alignment explanation
Indices: 101733--101806 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
101723 TCGATTTGAA
* *
101733 TTCTGATCTGATACTTGACATGGA-
1 TTCTGATATGATACTTGACCT-GAT
101757 TTCTGATAT-ATTACTTGACCTGAT
1 TTCTGATATGA-TACTTGACCTGAT
101781 TTCTGATATGATACTTGACCTGAT
1 TTCTGATATGATACTTGACCTGAT
101805 TT
1 TT
101807 ATGTTTTGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
23 3 0.07
24 41 0.91
25 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (24 bp):
TTCTGATATGATACTTGACCTGAT
Found at i:103916 original size:13 final size:13
Alignment explanation
Indices: 103898--103933 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
103888 TTATAACCCG
103898 ACCCGACCCGTTT
1 ACCCGACCCGTTT
*
103911 ACCCGACCCATTT
1 ACCCGACCCGTTT
*
103924 ACCCAACCCG
1 ACCCGACCCG
103934 ACCTGTTGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.22, C:0.50, G:0.11, T:0.17
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:103916 original size:18 final size:17
Alignment explanation
Indices: 103893--103951 Score: 54
Period size: 18 Copynumber: 3.6 Consensus size: 17
103883 ACCGGTTATA
103893 ACCCGACCCGACCCGTTT
1 ACCCGACCCGA-CCGTTT
103911 ACCCGACCC-A---TTT
1 ACCCGACCCGACCGTTT
* *
103924 ACCCAACCCGACCTGTTG
1 ACCCGACCCGACC-GTTT
103942 ACCCGACCCG
1 ACCCGACCCG
103952 TTGATCGGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
13 11 0.33
14 1 0.03
17 1 0.03
18 20 0.61
ACGTcount: A:0.20, C:0.49, G:0.15, T:0.15
Consensus pattern (17 bp):
ACCCGACCCGACCGTTT
Found at i:106506 original size:48 final size:48
Alignment explanation
Indices: 106442--106533 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
106432 TTCGATTTGA
106442 ATTCTGATCTGATACTTGACATGGA-TTCTGATATGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACAT-GATTTCTGATATGATACTTGACTTGG
* *
106490 ATTCTGATCTGTTACTTGACCTGATTTCTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGACATGATTTCTGATATGATACTTGAC
106534 CTGATTTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
47 2 0.05
48 39 0.95
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.41
Consensus pattern (48 bp):
ATTCTGATCTGATACTTGACATGATTTCTGATATGATACTTGACTTGG
Found at i:106540 original size:24 final size:24
Alignment explanation
Indices: 106442--106536 Score: 129
Period size: 24 Copynumber: 4.0 Consensus size: 24
106432 TTCGATTTGA
* *
106442 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATATGATACTTGACCTGG
*
106466 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACCTGG
* *
106490 ATTCTGATCTGTTACTTGACCT-G
1 ATTCTGATATGATACTTGACCTGG
106513 ATTTCTGATATGATACTTGACCTG
1 A-TTCTGATATGATACTTGACCTG
106537 ATTTATATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.03
24 60 0.97
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:111488 original size:20 final size:21
Alignment explanation
Indices: 111450--111488 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
111440 TAACTTTTTC
*
111450 TTTTCTCTTTCTTTATTAATT
1 TTTTCTCTTTCATTATTAATT
111471 TTTTCTCTTTCATT-TTAA
1 TTTTCTCTTTCATTATTAA
111489 CTTGTACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAATT
Found at i:114819 original size:24 final size:24
Alignment explanation
Indices: 114792--114841 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
114782 TGGTGGTTGA
*
114792 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
114816 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
114840 TT
1 TT
114842 GGTTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:115944 original size:17 final size:15
Alignment explanation
Indices: 115908--115946 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
115898 GGTGTGCAAA
*
115908 TCCGGGTACCCAATT
1 TCCGGGTACCCAACT
115923 TCCGGGTACCCAGAACT
1 TCCGGGTACCC--AACT
115940 TCCGGGT
1 TCCGGGT
115947 CGATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.52
17 10 0.48
ACGTcount: A:0.18, C:0.33, G:0.26, T:0.23
Consensus pattern (15 bp):
TCCGGGTACCCAACT
Found at i:115994 original size:17 final size:16
Alignment explanation
Indices: 115972--116040 Score: 70
Period size: 15 Copynumber: 4.3 Consensus size: 16
115962 CCGTGTCCCG
*
115972 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
*
115989 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
*
116004 ACCCGGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
*
116021 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
116036 ACCCG
1 ACCCG
116041 ATACCCGGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
15 21 0.48
16 6 0.14
17 17 0.39
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.22
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:116004 original size:15 final size:15
Alignment explanation
Indices: 115984--116040 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
115974 CCGGATGTTA
115984 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
**
115999 CGGGTACCCGGATTTT
1 CGGGTACCCGG-TAAT
116015 GCGGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
116031 CGGGTACCCG
1 CGGGTACCCG
116041 ATACCCGGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 21 0.58
16 4 0.11
17 11 0.31
ACGTcount: A:0.16, C:0.28, G:0.35, T:0.21
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:116009 original size:32 final size:32
Alignment explanation
Indices: 115972--116040 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
115962 CCGTGTCCCG
115972 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
* *
116004 ACCCGGATTTTGCGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
116036 ACCCG
1 ACCCG
116041 ATACCCGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.22
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACCCGGTAATCGGGT
Found at i:116412 original size:8 final size:8
Alignment explanation
Indices: 116381--116411 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
116371 TTTTTAGATC
116381 CGGGTCGA
1 CGGGTCGA
116389 CGGGTCGA
1 CGGGTCGA
*
116397 CGGGTCGG
1 CGGGTCGA
116405 CGGGTCG
1 CGGGTCG
116412 GGTCAACCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.06, C:0.26, G:0.55, T:0.13
Consensus pattern (8 bp):
CGGGTCGA
Found at i:116580 original size:3 final size:3
Alignment explanation
Indices: 116572--116617 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
116562 TAAAACAAAA
*
116572 AAT AAT AAT ATT AAT AAT -AT AAT ATAT AAAT AAT AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AAT AAT AAT
116617 A
1 A
116618 CTTTATTTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 4 0.11
3 28 0.76
4 4 0.11
5 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:116600 original size:7 final size:7
Alignment explanation
Indices: 116572--116785 Score: 72
Period size: 7 Copynumber: 29.0 Consensus size: 7
116562 TAAAACAAAA
116572 AATA-AT
1 AATATAT
116578 AATAT-T
1 AATATAT
116584 AATAATAT
1 AAT-ATAT
116592 AATATAT
1 AATATAT
116599 AA-ATAAT
1 AATAT-AT
116606 AATATAAT
1 AATAT-AT
116614 AATACT-T
1 AATA-TAT
* *
116621 TATTTACT
1 AATATA-T
116629 ACATATA-
1 A-ATATAT
116636 AACTATA-
1 AA-TATAT
116643 AATACTAT
1 AATA-TAT
116651 ACACTATATAT
1 A-A---TATAT
116662 AATATATT
1 AATATA-T
116670 AATAT-T
1 AATATAT
*
116676 -ATATAA
1 AATATAT
*
116682 AGATATAA
1 A-ATATAT
116690 AATACTAT
1 AATA-TAT
116698 AA-ATAT
1 AATATAT
* *
116704 ATTATAC
1 AATATAT
116711 AA-ATACT
1 AATATA-T
116718 ATATATAT
1 A-ATATAT
*
116726 ACTATAT
1 AATATAT
116733 AATATATTGT
1 AATATA---T
116743 AATATAT
1 AATATAT
*
116750 AATGTAAAT
1 AA--TATAT
*
116759 ACTATAT
1 AATATAT
116766 AATATAT
1 AATATAT
116773 AATATA-
1 AATATAT
116779 AATATAT
1 AATATAT
116786 GTTATATAAC
Statistics
Matches: 161, Mismatches: 16, Indels: 61
0.68 0.07 0.26
Matches are distributed among these distances:
5 4 0.02
6 28 0.17
7 66 0.41
8 35 0.22
9 14 0.09
10 8 0.05
11 4 0.02
12 2 0.01
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (7 bp):
AATATAT
Found at i:116603 original size:16 final size:17
Alignment explanation
Indices: 116573--116617 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
116563 AAAACAAAAA
*
116573 ATAATAATATTAATAAT
1 ATAATAATATAAATAAT
*
116590 ATAATATATAAATAATAAT
1 ATAATA-ATATA-AATAAT
116609 ATAATAATA
1 ATAATAATA
116618 CTTTATTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.25
18 6 0.25
19 12 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATAATATAAATAAT
Found at i:116674 original size:8 final size:9
Alignment explanation
Indices: 116573--116773 Score: 68
Period size: 9 Copynumber: 22.1 Consensus size: 9
116563 AAAACAAAAA
116573 ATAATA-AT
1 ATAATATAT
116581 ATTAATA-AT
1 A-TAATATAT
116590 AT-A-ATAT
1 ATAATATAT
116597 ATAA-ATA-
1 ATAATATAT
116604 ATAATATA-
1 ATAATATAT
116612 ATAATACTTTAT
1 ATAATA---TAT
* * *
116624 TTACTACAT
1 ATAATATAT
116633 ATAA-ACTAT
1 ATAATA-TAT
116642 A-AATACTAT
1 ATAATA-TAT
* *
116651 ACACTATAT
1 ATAATATAT
116660 ATAATATAT
1 ATAATATAT
116669 -TAATATTAT
1 ATAATA-TAT
*
116678 ATAA-AGAT
1 ATAATATAT
*
116686 ATAAAATACT
1 ATAATATA-T
116696 ATAA-ATAT
1 ATAATATAT
* * *
116704 ATTATACAA
1 ATAATATAT
*
116713 ATACTATAT
1 ATAATATAT
116722 AT-ATACTAT
1 ATAATA-TAT
116731 ATAATATATT
1 ATAATATA-T
*
116741 GTAATATAT
1 ATAATATAT
116750 AATGTAAATACTAT
1 -A--T-AATA-TAT
116764 ATAATATAT
1 ATAATATAT
116773 A
1 A
116774 ATATAAATAT
Statistics
Matches: 148, Mismatches: 21, Indels: 47
0.69 0.10 0.22
Matches are distributed among these distances:
6 1 0.01
7 9 0.06
8 35 0.24
9 61 0.41
10 26 0.18
11 3 0.02
12 5 0.03
13 5 0.03
14 3 0.02
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (9 bp):
ATAATATAT
Found at i:116720 original size:11 final size:10
Alignment explanation
Indices: 116685--116736 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 10
116675 TATATAAAGA
116685 TATAAAATAC
1 TATAAAATAC
*
116695 TATAAATATAT
1 TATAAA-ATAC
116706 TATACAAATAC
1 TATA-AAATAC
*
116717 TATATATATAC
1 TATA-AAATAC
*
116728 TATATAATA
1 TATAAAATA
116737 TATTGTAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 9 0.26
11 23 0.68
12 2 0.06
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (10 bp):
TATAAAATAC
Found at i:116791 original size:13 final size:14
Alignment explanation
Indices: 116656--116785 Score: 72
Period size: 13 Copynumber: 8.9 Consensus size: 14
116646 ACTATACACT
116656 ATATATAATATATTA
1 ATATATAATATA-TA
*
116671 ATAT-T-ATATAAA
1 ATATATAATATATA
*
116683 GATATAAAATACTATA
1 -ATATATAATA-TATA
* *
116699 A-ATATATTATACA
1 ATATATAATATATA
116712 A-ATACTATATATATA
1 ATATA-TA-ATATATA
*
116727 CTATATAATATATTGTA
1 ATATATAATATA---TA
*
116744 ATATATAATGTAAATA
1 ATATATAA--TATATA
*
116760 CTATATAATATATA
1 ATATATAATATATA
116774 ATATA-AATATAT
1 ATATATAATATAT
116786 GTTATATAAC
Statistics
Matches: 89, Mismatches: 14, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
12 1 0.01
13 23 0.26
14 23 0.26
15 15 0.17
16 15 0.17
17 9 0.10
19 3 0.03
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (14 bp):
ATATATAATATATA
Found at i:116793 original size:2 final size:2
Alignment explanation
Indices: 116655--116785 Score: 52
Period size: 2 Copynumber: 69.5 Consensus size: 2
116645 TACTATACAC
* * *
116655 TA TA TA TA -A TA TA T- TA -A TA T- TA TA TA AA GA TA TA -A AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
116692 TA CTA TA AA TA TA T- TA TA CA AA TA CTA TA TA TA TA CTA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA
* * *
116734 -A TA TA T- TG TA -A TA TA TA -A TG TA AA TA CTA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
*
116772 TA -A TA TA AA TA TA T
1 TA TA TA TA TA TA TA T
116786 GTTATATAAC
Statistics
Matches: 97, Mismatches: 16, Indels: 32
0.67 0.11 0.22
Matches are distributed among these distances:
1 12 0.12
2 77 0.79
3 8 0.08
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (2 bp):
TA
Found at i:118187 original size:11 final size:11
Alignment explanation
Indices: 118164--118192 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
118154 GGATCTAATG
118164 GACTCGA-CTC
1 GACTCGAGCTC
118174 GACTCGAGCTC
1 GACTCGAGCTC
118185 GACTCGAG
1 GACTCGAG
118193 TTCTTAACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.21, C:0.34, G:0.28, T:0.17
Consensus pattern (11 bp):
GACTCGAGCTC
Found at i:119255 original size:20 final size:20
Alignment explanation
Indices: 119230--119273 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
119220 GGAATGTAAA
119230 ATTATCAGT-AGAAATAAAAG
1 ATTATCAGTGAG-AATAAAAG
119250 ATTATCAGTGAGAATAAAAG
1 ATTATCAGTGAGAATAAAAG
119270 ATTA
1 ATTA
119274 CCAGAGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.52, C:0.05, G:0.16, T:0.27
Consensus pattern (20 bp):
ATTATCAGTGAGAATAAAAG
Found at i:119282 original size:18 final size:19
Alignment explanation
Indices: 119242--119284 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
119232 TATCAGTAGA
*
119242 AATAAAAGATTATCAGTGAG
1 AATAAAAGATTACCAG-GAG
119262 AATAAAAGATTACCA-GAG
1 AATAAAAGATTACCAGGAG
119280 AATAA
1 AATAA
119285 GATTACCGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
20 14 0.64
ACGTcount: A:0.56, C:0.07, G:0.16, T:0.21
Consensus pattern (19 bp):
AATAAAAGATTACCAGGAG
Found at i:119509 original size:37 final size:38
Alignment explanation
Indices: 119429--119509 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 38
119419 AACAAGTTGA
* *
119429 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAAATTGAAAATCAT
*
119468 -AAAATTTATATAATTTT-TTTACAAAATTGAAAAT-AT
1 AAAAATTTATAT-ATTTTCTTTAAAAAATTGAAAATCAT
119504 AAAAAT
1 AAAAAT
119510 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 2 0.05
37 27 0.73
38 8 0.22
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (38 bp):
AAAAATTTATATATTTTCTTTAAAAAATTGAAAATCAT
Found at i:140422 original size:42 final size:42
Alignment explanation
Indices: 140375--140462 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
140365 CATGGCGGGG
*
140375 TGGCAACGTGGCATGGGTCTGGGCGAGGTTGGAGTCTCTGCA
1 TGGCAACGTGGCATGGGTCTGGGCGAGATTGGAGTCTCTGCA
140417 TGGCAACGTGGCATGGGTCTGGGCGAGATTGGAGTCTCTGCA
1 TGGCAACGTGGCATGGGTCTGGGCGAGATTGGAGTCTCTGCA
140459 TGGC
1 TGGC
140463 TGTGCATGGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.15, C:0.19, G:0.42, T:0.24
Consensus pattern (42 bp):
TGGCAACGTGGCATGGGTCTGGGCGAGATTGGAGTCTCTGCA
Found at i:140570 original size:29 final size:30
Alignment explanation
Indices: 140487--140570 Score: 120
Period size: 29 Copynumber: 2.9 Consensus size: 30
140477 TGCAACGTGG
*
140487 GTAGGTCG-CAAGGGAATCCCAACAACATT
1 GTAGGTCGCCAAGGGAATCCCAACGACATT
* *
140516 GTAGGTCGCC-AGGGCATCCCAGCGACATT
1 GTAGGTCGCCAAGGGAATCCCAACGACATT
140545 GTAGGTCGCCAAGGG-ATCCCAACGAC
1 GTAGGTCGCCAAGGGAATCCCAACGAC
140571 CTATGCCTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.15
Consensus pattern (30 bp):
GTAGGTCGCCAAGGGAATCCCAACGACATT
Found at i:140645 original size:12 final size:11
Alignment explanation
Indices: 140625--140660 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
140615 TAAATCAGCT
140625 GCATTATTGCA
1 GCATTATTGCA
*
140636 GCACTTATTGCT
1 GCA-TTATTGCA
140648 GCATTATTGCA
1 GCATTATTGCA
140659 GC
1 GC
140661 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:140876 original size:8 final size:9
Alignment explanation
Indices: 140846--140883 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
140836 GGTAAGTTTT
140846 TTTTAATTA
1 TTTTAATTA
140855 TTTTAATTA
1 TTTTAATTA
*
140864 GTTT-ATTA
1 TTTTAATTA
140872 TTTTAAATTA
1 TTTT-AATTA
140882 TT
1 TT
140884 AGTTTGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTAATTA
Found at i:141005 original size:28 final size:27
Alignment explanation
Indices: 140966--141018 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
140956 ATATTAAAAA
140966 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
140994 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
141019 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:141024 original size:27 final size:29
Alignment explanation
Indices: 140965--141029 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
140955 TATATTAAAA
140965 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
140994 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
141020 AAATAGTTAA
1 AAATAATTAA
141030 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:141252 original size:21 final size:21
Alignment explanation
Indices: 141227--141266 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
141217 GTTAATTAGT
141227 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
141248 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
141267 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:141512 original size:30 final size:30
Alignment explanation
Indices: 141444--141547 Score: 115
Period size: 30 Copynumber: 3.4 Consensus size: 30
141434 ATTAGTTAAT
* *
141444 TAGTTTTTTAGTAGTAAATTATAATTAAA-AA
1 TAGTTTATTAGT-TTAAATTAT-ATTAAAGAA
*
141475 TCA-TTTATTAGTTTAATTTATATTAAAGAA
1 T-AGTTTATTAGTTTAAATTATATTAAAGAA
*
141505 TAGTTTATTAG-TTAACGTTATATTAAAGAA
1 TAGTTTATTAGTTTAA-ATTATATTAAAGAA
141535 TAGTTTATTAGTT
1 TAGTTTATTAGTT
141548 GTTTAAGGGA
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
29 11 0.17
30 42 0.66
31 10 0.16
32 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (30 bp):
TAGTTTATTAGTTTAAATTATATTAAAGAA
Found at i:143889 original size:11 final size:14
Alignment explanation
Indices: 143859--143906 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
143849 TTCAAGTCGT
143859 AAATCATTACTATC
1 AAATCATTACTATC
143873 AAATCATTA-T-T-
1 AAATCATTACTATC
143884 AAATCATTACTATC
1 AAATCATTACTATC
143898 AAATCATTA
1 AAATCATTA
143907 AATATTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.29
12 2 0.06
13 2 0.06
14 18 0.58
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:143922 original size:21 final size:22
Alignment explanation
Indices: 143858--143964 Score: 74
Period size: 25 Copynumber: 4.6 Consensus size: 22
143848 GTTCAAGTCG
*
143858 TAAATCATTACTATCAAATCATTAT
1 TAAATCATTAATATCAAATC---AT
*
143883 TAAATCATTACTATCAAATCAT
1 TAAATCATTAATATCAAATCAT
* *
143905 TAAAT-ATTAATAATAAATTATTAT
1 TAAATCATTAAT-ATCAA--ATCAT
*
143929 TACTAATCATTACTATCAAATCAT
1 TA--AATCATTAATATCAAATCAT
*
143953 TAAA-AATTAATA
1 TAAATCATTAATA
143965 ATAATTTTAT
Statistics
Matches: 68, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
21 11 0.16
22 13 0.19
24 12 0.18
25 20 0.29
26 7 0.10
27 5 0.07
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATCATTAATATCAAATCAT
Found at i:143939 original size:48 final size:48
Alignment explanation
Indices: 143873--143992 Score: 190
Period size: 48 Copynumber: 2.5 Consensus size: 48
143863 CATTACTATC
* *
143873 AAATCATTATTA--AATCATTACTATCAAATCATTAAATATTAATAAT
1 AAATTATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAAT
143919 AAATTATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAAT
1 AAATTATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAAT
*
143967 AATTTTATTATTACTAATCATTACTA
1 AA-ATTATTATTACTAATCATTACTA
143993 ATCATTACTA
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
46 11 0.16
48 35 0.51
49 22 0.32
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (48 bp):
AAATTATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAAT
Found at i:143989 original size:10 final size:10
Alignment explanation
Indices: 143976--144012 Score: 74
Period size: 10 Copynumber: 3.7 Consensus size: 10
143966 TAATTTTATT
143976 ATTACTAATC
1 ATTACTAATC
143986 ATTACTAATC
1 ATTACTAATC
143996 ATTACTAATC
1 ATTACTAATC
144006 ATTACTA
1 ATTACTA
144013 TCAAATCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:144063 original size:49 final size:49
Alignment explanation
Indices: 143996--144110 Score: 221
Period size: 49 Copynumber: 2.3 Consensus size: 49
143986 ATTACTAATC
143996 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
144045 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
144094 AATACTAATCATTACTA
1 ATTACTAATCATTACTA
144111 AATCATTAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:144124 original size:60 final size:60
Alignment explanation
Indices: 143927--144483 Score: 570
Period size: 60 Copynumber: 9.2 Consensus size: 60
143917 ATAAATTATT
*
143927 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
143986 ATTACTAATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 A-T--T-A-C--TA--AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
144051 AATC
57 AATC
* * * * * * *
144055 ATTACTATCAAATCATTA--A--AAATTAATAATAATT--TCATTAATACTAATCATTACTAAAT
1 ATTAC--T-AAATCATTACTATCAAATCATTAAAAATTAAT-AATAAT-TTCATTATTACT-AAT
144114 C
60 C
* * * * * * * *
144115 ATTA--ATATCA--AATCATTAAAT-ATTAATAA-TAATTTCATTATTACTAATCATTACTAATC
1 ATTACTAAATCATTACT-ATCAAATCATTAAAAATTAA--TAATAATT--TCATTATTACTAATC
*
144174 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * * * *
144233 ATTACTAAATTATTATTATCAAATCATTAAAAATTATTAATGATTTCATTATTACTATTC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
144293 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
144353 ATTACTGAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * *
144413 ATTACT--ATCAAATTACAATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATC
1 ATTACTAAATC--ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
144473 ATTACTAAATC
1 ATTACTAAATC
144484 TTATAAATAC
Statistics
Matches: 423, Mismatches: 39, Indels: 69
0.80 0.07 0.13
Matches are distributed among these distances:
53 1 0.00
55 5 0.01
56 2 0.00
57 8 0.02
58 12 0.03
59 52 0.12
60 244 0.58
61 13 0.03
62 13 0.03
63 12 0.03
64 3 0.01
65 2 0.00
66 2 0.00
68 1 0.00
69 53 0.13
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:144134 original size:178 final size:178
Alignment explanation
Indices: 143927--144425 Score: 748
Period size: 178 Copynumber: 2.8 Consensus size: 178
143917 ATAAATTATT
*
143927 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
143991 TAATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
66 TAATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
144056 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTAATACTAATC
131 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTAATACTAATC
* *
144104 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
*
144169 TAATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACTAATCA
66 TAATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
* * * *
144234 TTACTAAATTATTATTATCAAATCATTAAAAATTATTAATGATTTCATTATTACTATTC
131 TTAC-----------TATCAAATCATTAAAAATTAATAATAATTTCATTAATACTAATC
144293 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA-T--
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
*
144355 T-A-C--T--GAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
66 TAATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
144414 TTACTATCAAAT
131 TTACTATCAAAT
144426 TACAATCAAA
Statistics
Matches: 298, Mismatches: 12, Indels: 32
0.87 0.04 0.09
Matches are distributed among these distances:
169 8 0.03
177 6 0.02
178 123 0.41
180 57 0.19
182 1 0.00
184 1 0.00
185 1 0.00
186 1 0.00
188 1 0.00
189 99 0.33
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.41
Consensus pattern (178 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
TAATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
TTACTATCAAATCATTAAAAATTAATAATAATTTCATTAATACTAATC
Found at i:144169 original size:10 final size:10
Alignment explanation
Indices: 144154--144190 Score: 74
Period size: 10 Copynumber: 3.7 Consensus size: 10
144144 TAATTTCATT
144154 ATTACTAATC
1 ATTACTAATC
144164 ATTACTAATC
1 ATTACTAATC
144174 ATTACTAATC
1 ATTACTAATC
144184 ATTACTA
1 ATTACTA
144191 TCAAATCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:144250 original size:24 final size:24
Alignment explanation
Indices: 144218--144271 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
144208 AATAATAATT
* *
144218 TTATTATTA-CTAATCATTACTAAA
1 TTATTATTATCAAATCATTA-AAAA
144242 TTATTATTATCAAATCATTAAAAA
1 TTATTATTATCAAATCATTAAAAA
144266 TTATTA
1 TTATTA
144272 ATGATTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 18 0.67
25 9 0.33
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.46
Consensus pattern (24 bp):
TTATTATTATCAAATCATTAAAAA
Found at i:144324 original size:120 final size:119
Alignment explanation
Indices: 143874--144483 Score: 724
Period size: 120 Copynumber: 5.1 Consensus size: 119
143864 ATTACTATCA
* *
143874 AATCATTATTAAATCATTACTATCAAATCATTAAATATTAATAAT-A----A--ATTA-T--T-A
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
*
143928 TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACT
66 TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
143982 AATCATTACTAATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC-----
1 AATCA-T--T-A-C--TA--AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTAT
*
144042 -A-T--T-ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTAATACT
57 TACTAATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
* *
144100 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC------A-T--T-A
*
144165 TTACTAATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACT
56 TTACTAATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
* * * * *
144229 AATCATTACTAAATTATTATTATCAAATCATTAAAAATTATTAATGATTTCATTATTACTATTCA
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
144294 TTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
66 TTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
*
144349 AATCATTACTGAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
* * *
144414 TTACT-ATCAAATTACAATCAAATCATTAAATATTAATAATAATTTCATCATTACT
66 TTACTAATC--ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
144469 AATCATTACTAAATC
1 AATCATTACTAAATC
144484 TTATAAATAC
Statistics
Matches: 440, Mismatches: 25, Indels: 62
0.83 0.05 0.12
Matches are distributed among these distances:
108 5 0.01
109 39 0.09
111 3 0.01
112 1 0.00
113 1 0.00
114 1 0.00
115 3 0.01
117 34 0.08
118 65 0.15
119 15 0.03
120 169 0.38
122 1 0.00
123 1 0.00
125 1 0.00
126 1 0.00
128 1 0.00
129 99 0.22
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (119 bp):
AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
Found at i:147589 original size:28 final size:28
Alignment explanation
Indices: 147558--147611 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
147548 ATAATCTAAT
*
147558 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
147586 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
147612 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:147618 original size:28 final size:28
Alignment explanation
Indices: 147554--147618 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
147544 TTATATAATC
*
147554 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
147582 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
147610 TAATTTATA
1 TAATATATA
147619 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:147621 original size:21 final size:21
Alignment explanation
Indices: 147588--147636 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
147578 TTAATATAAT
147588 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
147609 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
147630 ATTAACT
1 A-TAACT
147637 AAATTTCTAT
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:148301 original size:29 final size:29
Alignment explanation
Indices: 148262--148333 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
148252 GGACGTCGGC
*
148262 GTGCATGGCGACCTATAAGGTCG-TCGGGA
1 GTGCATGGCGACCTACAAGGTCGCT-GGGA
* *
148291 TTGCTTGGCGACCTACAAGGTCGCTGGGA
1 GTGCATGGCGACCTACAAGGTCGCTGGGA
148320 GTGCATGGCGACCT
1 GTGCATGGCGACCT
148334 TGTAGATTGC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 36 0.97
30 1 0.03
ACGTcount: A:0.18, C:0.24, G:0.36, T:0.22
Consensus pattern (29 bp):
GTGCATGGCGACCTACAAGGTCGCTGGGA
Found at i:148412 original size:13 final size:13
Alignment explanation
Indices: 148394--148418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
148384 CATGCACGAC
148394 ACGATCCTCGTCA
1 ACGATCCTCGTCA
148407 ACGATCCTCGTC
1 ACGATCCTCGTC
148419 GGAGCCACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.40, G:0.16, T:0.24
Consensus pattern (13 bp):
ACGATCCTCGTCA
Found at i:148432 original size:17 final size:18
Alignment explanation
Indices: 148410--148444 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
148400 CTCGTCAACG
148410 ATCCTCGTC-GGAGCCAC
1 ATCCTCGTCGGGAGCCAC
148427 ATCCTCGTCGGGAGCCAC
1 ATCCTCGTCGGGAGCCAC
148445 GTCGTAGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.17, C:0.40, G:0.26, T:0.17
Consensus pattern (18 bp):
ATCCTCGTCGGGAGCCAC
Found at i:149230 original size:27 final size:26
Alignment explanation
Indices: 149200--149250 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
149190 CGTAAAACGC
*
149200 GAGATCATAATTGTTTTTTTAAAAAGG
1 GAGATCATAA-GGTTTTTTTAAAAAGG
**
149227 GAGATTTTAAGGTTTTTTTAAAAA
1 GAGATCATAAGGTTTTTTTAAAAA
149251 AAATTGATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (26 bp):
GAGATCATAAGGTTTTTTTAAAAAGG
Found at i:160285 original size:61 final size:61
Alignment explanation
Indices: 160211--160332 Score: 201
Period size: 61 Copynumber: 2.0 Consensus size: 61
160201 GACGCCATCC
* * *
160211 ATCGATTCGAGTCTTAAGATTCGGATTACA-ACATCTGCAATCCTTTCCCTGTAATTAGCAG
1 ATCGATTCAAGTCTTAAGACTCGGATTA-AGACATCTGCAATCCTTTACCTGTAATTAGCAG
160272 ATCGATTCAAGTCTTAAGACTCGGATTAAGACATCTGCAATCCTTTACCTGTAATTAGCAG
1 ATCGATTCAAGTCTTAAGACTCGGATTAAGACATCTGCAATCCTTTACCTGTAATTAGCAG
160333 CACGAAAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
60 1 0.02
61 56 0.98
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (61 bp):
ATCGATTCAAGTCTTAAGACTCGGATTAAGACATCTGCAATCCTTTACCTGTAATTAGCAG
Found at i:164980 original size:23 final size:22
Alignment explanation
Indices: 164945--164995 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
164935 AATTAGTATA
* *
164945 TTATTT-ACATAAAAGATTTTTT
1 TTATTTAACATAAAA-AATATTT
164967 TTATTTAACATAAAAAATATTT
1 TTATTTAACATAAAAAATATTT
164989 TTATTTA
1 TTATTTA
164996 GTTTTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
TTATTTAACATAAAAAATATTT
Found at i:165731 original size:58 final size:57
Alignment explanation
Indices: 165621--165732 Score: 131
Period size: 58 Copynumber: 1.9 Consensus size: 57
165611 ATTGGTGGCC
*
165621 ATTTTATAACTTTAATAGTTAATGGAATTAACAAAACACATCCTATAATCGATGTACT
1 ATTTTATAACTTTAATAGTTAATGGAATTAACAAAAAACA-CCTATAATCGATGTACT
* *
165679 ATTTTATAATTTTTAATAGTTGAA-GG-ATTCAACAAAATAACA-CTATAGTCGATG
1 ATTTTATAA-CTTTAATAGTT-AATGGAATT-AACAAAA-AACACCTATAATCGATG
165733 GGTCATTTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
58 23 0.49
59 19 0.40
60 5 0.11
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.37
Consensus pattern (57 bp):
ATTTTATAACTTTAATAGTTAATGGAATTAACAAAAAACACCTATAATCGATGTACT
Found at i:180684 original size:29 final size:29
Alignment explanation
Indices: 180641--180723 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
180631 CTCACCTAAC
*
180641 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
180671 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
180700 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
180724 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:185437 original size:29 final size:29
Alignment explanation
Indices: 185394--185476 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
185384 CTCACCTAAC
*
185394 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
185424 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
* *
185453 TAAATGATGTAAGTAATGATATCA
1 TAAATGATGTAAGCAATGACATCA
185477 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:189102 original size:15 final size:15
Alignment explanation
Indices: 189082--189124 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
189072 CTCCGGAGTA
*
189082 TTTCTTTTTCTTCCT
1 TTTCTTCTTCTTCCT
189097 TTTCTTCTTCTTCCT
1 TTTCTTCTTCTTCCT
**
189112 CGTCTTCTTCTTC
1 TTTCTTCTTCTTC
189125 AGCCACCTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTCTTCTTCTTCCT
Found at i:194297 original size:86 final size:85
Alignment explanation
Indices: 194135--194301 Score: 210
Period size: 86 Copynumber: 2.0 Consensus size: 85
194125 CACGGTTGAG
* * * *
194135 AAATAGTATAAACATTTCATGAAAGTTAATTACAGACCGTACTGTACGGTTTGTGACAAGATCTT
1 AAATACTATAAACATTTCATGAAAGTTAATCACAGACCGTACCGTACGGTTTGTGACAAGATCCT
*
194200 CATAATGCAAAACCATCAAA
66 CATAATACAAAACCATCAAA
* * * *
194220 AAATACTATTAAACATTTCGTGAAAGTTAGTCACCAG-CCTTACCGTATGGTTTGTGACAAGATC
1 AAATACTA-TAAACATTTCATGAAAGTTAATCA-CAGACCGTACCGTACGGTTTGTGACAAGATC
* *
194284 CTCGTAGTACAAAACCAT
64 CTCATAATACAAAACCAT
194302 GTGACGGGTG
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
85 7 0.10
86 59 0.86
87 3 0.04
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (85 bp):
AAATACTATAAACATTTCATGAAAGTTAATCACAGACCGTACCGTACGGTTTGTGACAAGATCCT
CATAATACAAAACCATCAAA
Found at i:195713 original size:10 final size:10
Alignment explanation
Indices: 195698--195727 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
195688 TACTCAATTA
195698 AATATTTAAT
1 AATATTTAAT
195708 AATATTTAAT
1 AATATTTAAT
*
195718 AATTTTTAAT
1 AATATTTAAT
195728 TTAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
AATATTTAAT
Found at i:196561 original size:15 final size:15
Alignment explanation
Indices: 196538--196577 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
196528 AAATGCCCCC
196538 AACTATTAATATATT
1 AACTATTAATATATT
* *
196553 AACTCTTAATATATG
1 AACTATTAATATATT
*
196568 AAGTATTAAT
1 AACTATTAAT
196578 CTATCTATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (15 bp):
AACTATTAATATATT
Found at i:197375 original size:2 final size:2
Alignment explanation
Indices: 197368--197418 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
197358 TATCCACCTC
197368 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
197410 TA TA TA TA T
1 TA TA TA TA T
197419 GTAACAACCC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:198204 original size:13 final size:13
Alignment explanation
Indices: 198183--198212 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
198173 GACCGGTCAC
*
198183 GACCTGACCCGTT
1 GACCCGACCCGTT
198196 GACCCGACCCGTT
1 GACCCGACCCGTT
198209 GACC
1 GACC
198213 AATGCTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:198257 original size:29 final size:29
Alignment explanation
Indices: 198215--198315 Score: 148
Period size: 29 Copynumber: 3.5 Consensus size: 29
198205 CGTTGACCAA
* *** *
198215 TGCTATTCTAGTAAATAATTCTAATTTAG
1 TGCTATTCTGGTAAATAATTCGGTTTTGG
198244 TGCTATTCTGGTAAATAATTCGGTTTTGG
1 TGCTATTCTGGTAAATAATTCGGTTTTGG
*
198273 TGCTATTATGGTAAATAATTCGGTTTTGG
1 TGCTATTCTGGTAAATAATTCGGTTTTGG
198302 TGCTATTCTGGTAA
1 TGCTATTCTGGTAA
198316 TTATTTTAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.45
Consensus pattern (29 bp):
TGCTATTCTGGTAAATAATTCGGTTTTGG
Found at i:205542 original size:29 final size:29
Alignment explanation
Indices: 205495--205597 Score: 161
Period size: 29 Copynumber: 3.6 Consensus size: 29
205485 CCCGTTGACC
* *
205495 GGTGCTATTCTAGTAAATAATTCGATTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
* *
205524 AGTGATATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
205553 GGTGCTATTATGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
205582 GGTGCTATTCTGGTAA
1 GGTGCTATTCTGGTAA
205598 TTATTTTAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.44
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:207396 original size:110 final size:110
Alignment explanation
Indices: 207203--207419 Score: 380
Period size: 110 Copynumber: 2.0 Consensus size: 110
207193 TATAAGATAA
* *
207203 TATATGTTAAAAAAATTCTTGATTATTTAACAATGAACATTCATACATAACATATACGGTGCTCG
1 TATATGTTAAAAAAACTCTTGATTATTTAACAATGAACATTCATACATAACATACACGGTGCTCG
207268 AACCTTTCCATCTCACTTCACAAAACGAGACAGCATTCACTTCTT
66 AACCTTTCCATCTCACTTCACAAAACGAGACAGCATTCACTTCTT
* *
207313 TATATGTTAAAAAAACTCTTGATTATTTAATAATGAACATTCATACTTAACATACACGGTGCTCG
1 TATATGTTAAAAAAACTCTTGATTATTTAACAATGAACATTCATACATAACATACACGGTGCTCG
* *
207378 AACCTTTTCATCTCACTTCACAAAACGAGACATCATTCACTT
66 AACCTTTCCATCTCACTTCACAAAACGAGACAGCATTCACTT
207420 TTTTCTATAG
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
110 101 1.00
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (110 bp):
TATATGTTAAAAAAACTCTTGATTATTTAACAATGAACATTCATACATAACATACACGGTGCTCG
AACCTTTCCATCTCACTTCACAAAACGAGACAGCATTCACTTCTT
Found at i:212055 original size:11 final size:11
Alignment explanation
Indices: 211967--212048 Score: 51
Period size: 12 Copynumber: 7.1 Consensus size: 11
211957 CATAAGAATG
211967 AAAATAAAAAT
1 AAAATAAAAAT
*
211978 AATAATAATAAT
1 AA-AATAAAAAT
* *
211990 -AAATCAAAAG
1 AAAATAAAAAT
212000 AAAA-AGAAAAT
1 AAAATA-AAAAT
*
212011 CAAAATCAAAAT
1 -AAAATAAAAAT
*
212023 CAAAAAGGAAAAAT
1 --AAAA-TAAAAAT
212037 AAAATAAAAAT
1 AAAATAAAAAT
212048 A
1 A
212049 CATTAAATAA
Statistics
Matches: 53, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
10 6 0.11
11 17 0.32
12 21 0.40
13 4 0.08
14 5 0.09
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:212090 original size:10 final size:10
Alignment explanation
Indices: 212077--212156 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
212067 AAAAAATACG
*
212077 ATAAAAAAGA
1 ATAAAAAAAA
212087 ATAAATAAAAA
1 ATAAA-AAAAA
*
212098 ATAAGAAAAA
1 ATAAAAAAAA
** *
212108 AGGAAAATAA
1 ATAAAAAAAA
212118 ATCAAAGAAAAA
1 AT-AAA-AAAAA
* *
212130 ATGAAATAAA
1 ATAAAAAAAA
*
212140 ACAAAAAAAA
1 ATAAAAAAAA
*
212150 TTAAAAA
1 ATAAAAA
212157 TTAAAAAATA
Statistics
Matches: 51, Mismatches: 16, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
10 33 0.65
11 12 0.24
12 6 0.12
ACGTcount: A:0.78, C:0.03, G:0.07, T:0.12
Consensus pattern (10 bp):
ATAAAAAAAA
Found at i:212092 original size:36 final size:37
Alignment explanation
Indices: 212019--212118 Score: 96
Period size: 37 Copynumber: 2.7 Consensus size: 37
212009 ATCAAAATCA
* *
212019 AAATCAAAAAGGAAAAATAAAATAAAAATACATTAAAT
1 AAATC-AAAAGAAAAAATAAAATAAAAATACAATAAAT
** *
212057 AAATCAAAAGAAAAAATACGATAAAAA-AGAATAAAT
1 AAATCAAAAGAAAAAATAAAATAAAAATACAATAAAT
* *
212093 AAA-AAATAAGAAAAAAGGAAAATAAA
1 AAATCAA-AAGAAAAAA-TAAAATAAA
212119 TCAAAGAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
35 2 0.04
36 19 0.37
37 25 0.49
38 5 0.10
ACGTcount: A:0.74, C:0.04, G:0.08, T:0.14
Consensus pattern (37 bp):
AAATCAAAAGAAAAAATAAAATAAAAATACAATAAAT
Found at i:212125 original size:22 final size:21
Alignment explanation
Indices: 212089--212149 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
212079 AAAAAAGAAT
*
212089 AAATAAAAAATAAGAAAAAAGG
1 AAATAAAACA-AAGAAAAAAGG
* *
212111 AAAATAAATCAAAGAAAAAATG
1 -AAATAAAACAAAGAAAAAAGG
212133 AAATAAAACAAA-AAAAA
1 AAATAAAACAAAGAAAAA
212150 TTAAAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.15
21 11 0.32
22 10 0.29
23 8 0.24
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.10
Consensus pattern (21 bp):
AAATAAAACAAAGAAAAAAGG
Found at i:212155 original size:59 final size:58
Alignment explanation
Indices: 212053--212164 Score: 140
Period size: 58 Copynumber: 1.9 Consensus size: 58
212043 AAAATACATT
* *
212053 AAATAAATCAAAAGAAAAAATACGATAAAAAAGAATAAATAAAAAATAAGAAAAAAGGA
1 AAATAAATCAAAAGAAAAAATACAATAAAAAAGAAAAAATAAAAAATAA-AAAAAAGGA
* *
212112 AAATAAATC-AAAGAAAAAATGA-AATAAAACAA-AAAAAATTAAAAATTAAAAAA
1 AAATAAATCAAAAGAAAAAAT-ACAATAAAA-AAGAAAAAATAAAAAATAAAAAAA
212165 TATTTTAAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
57 5 0.11
58 30 0.64
59 12 0.26
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.13
Consensus pattern (58 bp):
AAATAAATCAAAAGAAAAAATACAATAAAAAAGAAAAAATAAAAAATAAAAAAAAGGA
Found at i:212157 original size:21 final size:21
Alignment explanation
Indices: 212081--212155 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
212071 AATACGATAA
*
212081 AAAAGAAT-AAATAAAAAATAAG
1 AAAA-AATAAAATAAAACA-AAG
* *
212103 AAAAAAGGAAAATAAATCAAAG
1 AAAAAA-TAAAATAAAACAAAG
*
212125 AAAAAATGAAATAAAACAAA-
1 AAAAAATAAAATAAAACAAAG
*
212145 AAAAATTAAAA
1 AAAAAATAAAA
212156 ATTAAAAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
20 9 0.21
21 13 0.30
22 13 0.30
23 8 0.19
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.12
Consensus pattern (21 bp):
AAAAAATAAAATAAAACAAAG
Found at i:213192 original size:13 final size:15
Alignment explanation
Indices: 213156--213192 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
213146 AAATTCAATG
213156 TAAATATACATATTA
1 TAAATATACATATTA
213171 TATAATATA-AT-TTA
1 TA-AATATACATATTA
213185 TAAATATA
1 TAAATATA
213193 TTATATAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.29
14 5 0.24
15 4 0.19
16 6 0.29
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAATATACATATTA
Found at i:213997 original size:84 final size:84
Alignment explanation
Indices: 213824--214567 Score: 938
Period size: 84 Copynumber: 8.9 Consensus size: 84
213814 GTAAAATGGC
* * * * * * * * * * *
213824 GTGCCTTTGAGCTGAGTGAAATTGAACTCGAAGGTC-TTTGTTGACAAATAGCCATTTTTGCCTT
1 GTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTT
* *
213888 GAGCTATGTTGCAAATGAT
66 GAGTTATGCTGCAAATGAT
* * *
213907 GTGCCTTAGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTAGTTGGCAGATAACCCTTCTAGCCTT
1 GTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTT
*
213972 GAGTTATGCTGCAAATAAT
66 GAGTTATGCTGCAAATGAT
* * * * *
213991 ATGCCTTGGAGCTGAGCGTTGTCGAACTTGAAGGTCTTTTGGTGGCAGATAGCCCTTCTAGCCTT
1 GTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTT
*
214056 GA-TCTATGCTGAAAATGAT
66 GAGT-TATGCTGCAAATGAT
** * *
214075 GTAACTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAACCTT
1 GTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTT
214140 GAGTTATGCTGCAAATGAT
66 GAGTTATGCTGCAAATGAT
* *
214159 GTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTAGCCTT
1 GTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTT
* *
214224 GAGCTATGCTGTAAATGAT
66 GAGTTATGCTGCAAATGAT
* * ** *
214243 ATGCCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTAACAGATAACCTTTCTAGCCTT
1 GTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTT
214308 GAGTTATGCTGCAAATGAT
66 GAGTTATGCTGCAAATGAT
* * * * * * *
214327 GTGCCTTGGAG-TAGAGCGTAGTCAAACTTGAAGGTC-TGTGTTTGGAAAATAGCCCTTCTTGCC
1 GTGCCTTGGAGCT-GAGCGTAGTCGAACTCGAAGGTCTTTTG-TTGGCAGATAACCCTTCTAGCC
*
214390 TTGAGTTATGTTGCAAATGAT
64 TTGAGTTATGCTGCAAATGAT
* * * **
214411 GTGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGATCTTTGGTTGAAAGATAACCCTTCTAGCCTT
1 GTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTT
214476 GAGTTATGCTGCAAATGAT
66 GAGTTATGCTGCAAATGAT
* * * * * *
214495 ATGCCTTGTAGCTGAGCGTAATCGAACTCAAAGGTTTTTTGTTGGCAAATAACCCTTCTAGCCTT
1 GTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTT
214560 GAGTTATG
66 GAGTTATG
214568 TTGCCGATAG
Statistics
Matches: 568, Mismatches: 86, Indels: 13
0.85 0.13 0.02
Matches are distributed among these distances:
83 35 0.06
84 529 0.93
85 4 0.01
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (84 bp):
GTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTT
GAGTTATGCTGCAAATGAT
Found at i:215897 original size:95 final size:95
Alignment explanation
Indices: 215700--215960 Score: 348
Period size: 95 Copynumber: 2.7 Consensus size: 95
215690 AGCTAGCTGA
* * ** **
215700 ATCCATTAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGTTCAA--TATCGTTGTAGATA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCT-TTATTGT--ATA
*
215763 TTATAATCACCATTATCAGGCTAGCTGAATATT
63 TTATAATCACCATTATCAGGCTAGCTGAACATT
215796 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
* * *
215861 TAATCACCTTTATTAGGCTAGCTGAACCTT
66 TAATCACCATTATCAGGCTAGCTGAACATT
* *
215891 ATCCATAAA-TCTGGGGCGTTTAACCAATTGCTTTAGAGGGACATCTCAAGCTTTATTGTATATA
1 ATCCATAAAGTC-GGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-
215955 TATAAT
64 TATAAT
215961 ATTATAATCT
Statistics
Matches: 149, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
94 2 0.01
95 90 0.60
96 51 0.34
97 5 0.03
98 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (95 bp):
ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACCATTATCAGGCTAGCTGAACATT
Found at i:230394 original size:38 final size:38
Alignment explanation
Indices: 230303--230395 Score: 159
Period size: 38 Copynumber: 2.4 Consensus size: 38
230293 GTAAACATGT
*
230303 AATTAATTTGTAAGCATGACTAAGCATATTAATATTTA
1 AATTAATTTGTAAGTATGACTAAGCATATTAATATTTA
*
230341 AATTAATTTGTAAGTATGACTGAGCATATTAATATTTA
1 AATTAATTTGTAAGTATGACTAAGCATATTAATATTTA
*
230379 AATTAATTTGCAAGTAT
1 AATTAATTTGTAAGTAT
230396 ATTTTGCATG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (38 bp):
AATTAATTTGTAAGTATGACTAAGCATATTAATATTTA
Found at i:235134 original size:22 final size:22
Alignment explanation
Indices: 235104--235158 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
235094 ATTCAGCTGT
*
235104 TATAACTCCTGAAATTATATCA
1 TATAACTCCTGAAATTAAATCA
*
235126 TGTAACTCCTGAAATTAAATCA
1 TATAACTCCTGAAATTAAATCA
*
235148 TATATCTCCTG
1 TATAACTCCTG
235159 TAACTCCTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.36
Consensus pattern (22 bp):
TATAACTCCTGAAATTAAATCA
Found at i:241258 original size:35 final size:36
Alignment explanation
Indices: 241212--241281 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 36
241202 GTTTCAACAA
* *
241212 TGGTACCGATACTATCCTTAT-GGTATCGGTACCCT
1 TGGTACCGATACTACCCTTATGGGTATCGATACCCT
* *
241247 TGGTATCGATACTACCCTTCTGGGTATCGATACCC
1 TGGTACCGATACTACCCTTATGGGTATCGATACCC
241282 CTTGAATATC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 18 0.60
36 12 0.40
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (36 bp):
TGGTACCGATACTACCCTTATGGGTATCGATACCCT
Found at i:241465 original size:35 final size:36
Alignment explanation
Indices: 241419--241488 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 36
241409 GTTTCAACAA
* *
241419 TGGTACCGATACTATCCTTAT-GGTATCGGTACCCT
1 TGGTACCGATACTACCCTTATGGGTATCGATACCCT
* *
241454 TGGTATCGATACTACCCTTCTGGGTATCGATACCC
1 TGGTACCGATACTACCCTTATGGGTATCGATACCC
241489 CTTGAATATC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 18 0.60
36 12 0.40
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (36 bp):
TGGTACCGATACTACCCTTATGGGTATCGATACCCT
Found at i:241537 original size:207 final size:209
Alignment explanation
Indices: 241182--241599 Score: 822
Period size: 207 Copynumber: 2.0 Consensus size: 209
241172 ATTGATACCT
241182 TTTTTGCATTCGAAATCCTTGTTTCAACAATGGTACCGATACTATCCTTATGGTATCGGTACCCT
1 TTTTTGCATTCGAAATCCTTGTTTCAACAATGGTACCGATACTATCCTTATGGTATCGGTACCCT
241247 TGGTATCGATACTACCCTTCTGGGTATCGATACCCCTTGAATATCTTATCAAGTTTTTTGCTTAG
66 TGGTATCGATACTACCCTTCTGGGTATCGATACCCCTTGAATATCTTATCAAGTTTTTTGCTTAG
241312 GGTATCGATACTGATTCACAAAGTACCAATACCCTCCCTCAAATA-TGACCATTTTCTTCTT-AA
131 GGTATCGATACTGATTCACAAAGTACCAATACCCTCCCTCAAATATTGACCATTTTCTTCTTAAA
241375 GTATTGGTACTAGA
196 GTATTGGTACTAGA
241389 TTTTTGCATTCGAAATCCTTGTTTCAACAATGGTACCGATACTATCCTTATGGTATCGGTACCCT
1 TTTTTGCATTCGAAATCCTTGTTTCAACAATGGTACCGATACTATCCTTATGGTATCGGTACCCT
241454 TGGTATCGATACTACCCTTCTGGGTATCGATACCCCTTGAATATCTTATCAAGTTTTTTGCTTAG
66 TGGTATCGATACTACCCTTCTGGGTATCGATACCCCTTGAATATCTTATCAAGTTTTTTGCTTAG
241519 GGTATCGATACTGATTCACAAAGTACCAATACCCTCCCTCAAATATTGACCATTTTCTTCTTAAA
131 GGTATCGATACTGATTCACAAAGTACCAATACCCTCCCTCAAATATTGACCATTTTCTTCTTAAA
241584 GTATTGGTACTAGA
196 GTATTGGTACTAGA
241598 TT
1 TT
241600 AACAGTACTG
Statistics
Matches: 209, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
207 175 0.84
208 16 0.08
209 18 0.09
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (209 bp):
TTTTTGCATTCGAAATCCTTGTTTCAACAATGGTACCGATACTATCCTTATGGTATCGGTACCCT
TGGTATCGATACTACCCTTCTGGGTATCGATACCCCTTGAATATCTTATCAAGTTTTTTGCTTAG
GGTATCGATACTGATTCACAAAGTACCAATACCCTCCCTCAAATATTGACCATTTTCTTCTTAAA
GTATTGGTACTAGA
Found at i:243015 original size:23 final size:23
Alignment explanation
Indices: 242989--243048 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
242979 ACTTAGACTT
242989 TGTCCCGAAGGACCGTGTAGAAA
1 TGTCCCGAAGGACCGTGTAGAAA
243012 TGTCCCGAAGGACCGTGTAGAAA
1 TGTCCCGAAGGACCGTGTAGAAA
243035 TGTCCCGAAGGACC
1 TGTCCCGAAGGACC
243049 ACATATCACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.28, C:0.25, G:0.30, T:0.17
Consensus pattern (23 bp):
TGTCCCGAAGGACCGTGTAGAAA
Found at i:246815 original size:23 final size:23
Alignment explanation
Indices: 246789--246833 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
246779 CACCACAGCT
*
246789 CGTATAAATGCACC-TAAGTGCCG
1 CGTAGAAATGCACCGT-AGTGCCG
*
246812 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGTAGTGCC
246834 ATATAAGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGTAGTGCCG
Found at i:247103 original size:31 final size:30
Alignment explanation
Indices: 247059--247118 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
247049 TATTGTATAG
*
247059 ACATATAATTTCCATACCTT-TATCACATAA
1 ACATATAATTTCCAT-CATTGTATCACATAA
*
247089 ACATATCATGTTCCATCATTGTATCACATA
1 ACATATAAT-TTCCATCATTGTATCACATA
247119 GATTATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCATTGTATCACATAA
Found at i:257164 original size:2 final size:2
Alignment explanation
Indices: 257159--257184 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
257149 TTGGTGTGTG
257159 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
257185 CACTTGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:260262 original size:15 final size:15
Alignment explanation
Indices: 260238--260272 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
260228 GCACTATTAA
*
260238 ATTAATTTATAAAAT
1 ATTAAGTTATAAAAT
*
260253 GTTAAGTTATAAAAT
1 ATTAAGTTATAAAAT
260268 ATTAA
1 ATTAA
260273 ACGTATAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (15 bp):
ATTAAGTTATAAAAT
Found at i:260717 original size:22 final size:23
Alignment explanation
Indices: 260673--260729 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
260663 ATTAAATTAC
*
260673 ATTTAGATTTTTAGCTAATTTATA
1 ATTTA-ATGTTTAGCTAATTTATA
*
260697 A-TTATATGTTTAG-TACTTTATA
1 ATTTA-ATGTTTAGCTAATTTATA
260719 ATTTAATGTTT
1 ATTTAATGTTT
260730 TATAAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 15 0.52
23 13 0.45
24 1 0.03
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.56
Consensus pattern (23 bp):
ATTTAATGTTTAGCTAATTTATA
Found at i:260731 original size:23 final size:25
Alignment explanation
Indices: 260673--260731 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 25
260663 ATTAAATTAC
260673 ATTTAGAT-TTTTAGCTAATTTATA
1 ATTTAGATGTTTTAGCTAATTTATA
* *
260697 A-TTATATG-TTTAG-TACTTTATA
1 ATTTAGATGTTTTAGCTAATTTATA
260719 ATTTA-ATGTTTTA
1 ATTTAGATGTTTTA
260732 TAAATTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
22 12 0.40
23 17 0.57
24 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.56
Consensus pattern (25 bp):
ATTTAGATGTTTTAGCTAATTTATA
Found at i:264220 original size:25 final size:25
Alignment explanation
Indices: 264189--264241 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
264179 GGTGAAGCTC
*
264189 GAGGGAGTGACGTAGCATCTAGGAG
1 GAGGGAGTGACGTAACATCTAGGAG
*
264214 GAGGGAGTGGCGTAACATCTAGGAG
1 GAGGGAGTGACGTAACATCTAGGAG
264239 GAG
1 GAG
264242 CTCGTGCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.28, C:0.11, G:0.45, T:0.15
Consensus pattern (25 bp):
GAGGGAGTGACGTAACATCTAGGAG
Found at i:270953 original size:15 final size:15
Alignment explanation
Indices: 270933--270970 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
270923 CTCCAACAAT
270933 CCTTCTTTAAGTGAC
1 CCTTCTTTAAGTGAC
270948 CCTTCTTTAAGTGAC
1 CCTTCTTTAAGTGAC
270963 CCTTCTTT
1 CCTTCTTT
270971 CCACAATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.16, C:0.29, G:0.11, T:0.45
Consensus pattern (15 bp):
CCTTCTTTAAGTGAC
Done.