Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016495.1 Corchorus capsularis cultivar CVL-1 contig16516, 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: 112321
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3090 original size:13 final size:13
Alignment explanation
Indices: 3072--3113 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
3062 TTTATTACTA
*
3072 TTTTATTAATATG
1 TTTTATTAAAATG
*
3085 TTTTA-TAAAAGG
1 TTTTATTAAAATG
*
3097 TTTTAATAAAATG
1 TTTTATTAAAATG
3110 TTTT
1 TTTT
3114 GGGTGCATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.55
Consensus pattern (13 bp):
TTTTATTAAAATG
Found at i:11448 original size:31 final size:31
Alignment explanation
Indices: 11409--11517 Score: 182
Period size: 31 Copynumber: 3.5 Consensus size: 31
11399 AAGCTTAATC
*
11409 ATTGGTCCTGATATACCGTCATGACCCAACA
1 ATTGGTCCTGATATACCGTCAGGACCCAACA
* *
11440 GTTGGTCCTGATATACCGTCAGGACCTAACA
1 ATTGGTCCTGATATACCGTCAGGACCCAACA
*
11471 ATTTGTCCTGATATACCGTCAGGACCCAACA
1 ATTGGTCCTGATATACCGTCAGGACCCAACA
11502 ATTGGTCCTGATATAC
1 ATTGGTCCTGATATAC
11518 TCTGAGTTCT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.28
Consensus pattern (31 bp):
ATTGGTCCTGATATACCGTCAGGACCCAACA
Found at i:16041 original size:27 final size:27
Alignment explanation
Indices: 15991--16042 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
15981 ATGATTTAGG
* *
15991 GGTTACTAACTCTCTTTTTCTTTTTGA
1 GGTTACTAACACTCTTATTCTTTTTGA
16018 GGTTACTAACACTCATTATT-TTTTT
1 GGTTACTAACACTC-TTATTCTTTTT
16043 CAGAGGGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54
Consensus pattern (27 bp):
GGTTACTAACACTCTTATTCTTTTTGA
Found at i:16614 original size:9 final size:9
Alignment explanation
Indices: 16600--16638 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
16590 TTAATTTCTT
*
16600 TTAATTTAA
1 TTAATTAAA
16609 TTAATTAAA
1 TTAATTAAA
**
16618 TTAAAGAAA
1 TTAATTAAA
16627 TTAATTAAA
1 TTAATTAAA
16636 TTA
1 TTA
16639 TGATGAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (9 bp):
TTAATTAAA
Found at i:19788 original size:12 final size:12
Alignment explanation
Indices: 19771--19795 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19761 GCCGGTTGCT
19771 CCATGCGATGGC
1 CCATGCGATGGC
19783 CCATGCGATGGC
1 CCATGCGATGGC
19795 C
1 C
19796 GGTCATGTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.32, T:0.16
Consensus pattern (12 bp):
CCATGCGATGGC
Found at i:35636 original size:13 final size:13
Alignment explanation
Indices: 35618--35642 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35608 ATCTCCCTAA
35618 TCTCTTAAACAAC
1 TCTCTTAAACAAC
35631 TCTCTTAAACAA
1 TCTCTTAAACAA
35643 ATTAAGTTCC
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:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (13 bp):
TCTCTTAAACAAC
Found at i:39468 original size:26 final size:26
Alignment explanation
Indices: 39439--39506 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
39429 AGACTGATTT
39439 CAGTTTCTGAAATCAGAATCTGAAAG
1 CAGTTTCTGAAATCAGAATCTGAAAG
*
39465 CAGTTTCTGAAATCAGAATCTGAAAT
1 CAGTTTCTGAAATCAGAATCTGAAAG
*
39491 CAGATTCTGAAATCAG
1 CAGTTTCTGAAATCAG
39507 TCTGATTTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (26 bp):
CAGTTTCTGAAATCAGAATCTGAAAG
Found at i:39487 original size:39 final size:37
Alignment explanation
Indices: 39444--39530 Score: 111
Period size: 39 Copynumber: 2.3 Consensus size: 37
39434 GATTTCAGTT
39444 TCTGAAATCAGAATCTGAAAGCAGTTTCTGAAATCAGAA
1 TCTGAAATCAGAATCTGAAAGCAG--TCTGAAATCAGAA
* * **
39483 TCTGAAATCAGATTCTGAAATCAGTCTGATTTCAGAA
1 TCTGAAATCAGAATCTGAAAGCAGTCTGAAATCAGAA
*
39520 ACTGAAATCAG
1 TCTGAAATCAG
39531 TTTTTTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
37 21 0.49
39 22 0.51
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (37 bp):
TCTGAAATCAGAATCTGAAAGCAGTCTGAAATCAGAA
Found at i:39530 original size:13 final size:13
Alignment explanation
Indices: 39444--39530 Score: 97
Period size: 13 Copynumber: 6.8 Consensus size: 13
39434 GATTTCAGTT
39444 TCTGAAATCAGAA
1 TCTGAAATCAGAA
* **
39457 TCTGAAAGCAGTT
1 TCTGAAATCAGAA
39470 TCTGAAATCAGAA
1 TCTGAAATCAGAA
*
39483 TCTGAAATCAGAT
1 TCTGAAATCAGAA
39496 TCTGAAATCAG--
1 TCTGAAATCAGAA
**
39507 TCTGATTTCAGAA
1 TCTGAAATCAGAA
*
39520 ACTGAAATCAG
1 TCTGAAATCAG
39531 TTTTTTTTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
11 9 0.15
13 51 0.85
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (13 bp):
TCTGAAATCAGAA
Found at i:42262 original size:21 final size:21
Alignment explanation
Indices: 42238--42286 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
42228 TTTTCCTATA
*
42238 TGCTACGAGCTTATTTGCATT
1 TGCTACGAGCTTATTTACATT
*
42259 TGCTACGAGTTTATTTACATT
1 TGCTACGAGCTTATTTACATT
42280 TGCTACG
1 TGCTACG
42287 GACATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.43
Consensus pattern (21 bp):
TGCTACGAGCTTATTTACATT
Found at i:60573 original size:16 final size:16
Alignment explanation
Indices: 60548--60578 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60538 GGTTATAGCA
*
60548 AACAATTAATCTTTTG
1 AACAACTAATCTTTTG
60564 AACAACTAATCTTTT
1 AACAACTAATCTTTT
60579 AAGGATATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (16 bp):
AACAACTAATCTTTTG
Found at i:61086 original size:22 final size:22
Alignment explanation
Indices: 60929--61141 Score: 84
Period size: 22 Copynumber: 9.8 Consensus size: 22
60919 GTGTGGAGTA
* * * *
60929 ATCAAGATTTTATAGGGAGGTT
1 ATCAAAATTTCATAAGGAAGTT
*
60951 ATCAAAATTTCATAA-GAAGGCT
1 ATCAAAATTTCATAAGGAA-GTT
** ***
60973 ATTGAAATTTCATAATTTAGTT
1 ATCAAAATTTCATAAGGAAGTT
* * **
60995 TTCAAAATTTTAT-AGGGGGATT
1 ATCAAAATTTCATAAGGAAG-TT
* **
61017 ATCAAAACTTCAT-AGTGTGGTT
1 ATCAAAATTTCATAAG-GAAGTT
* * *
61039 A--AAATTTTCAT-AGTATGTAT
1 ATCAAAATTTCATAAGGAAGT-T
61059 ATCAAAATTTCATAAGGAAGTT
1 ATCAAAATTTCATAAGGAAGTT
* *
61081 AACAAAATTT-ATTAATGAAGTT
1 ATCAAAATTTCA-TAAGGAAGTT
* *
61103 ATCAAGAA--TCATATGGAGGTT
1 ATCAA-AATTTCATAAGGAAGTT
*
61124 ATCAAAATTTAATAAGGA
1 ATCAAAATTTCATAAGGA
61142 GCTTTAAAAA
Statistics
Matches: 140, Mismatches: 38, Indels: 26
0.69 0.19 0.13
Matches are distributed among these distances:
19 2 0.01
20 14 0.10
21 18 0.13
22 95 0.68
23 11 0.08
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAAGGAAGTT
Found at i:61276 original size:44 final size:44
Alignment explanation
Indices: 61218--61309 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 44
61208 ATTTTTACAA
* * * *
61218 TGTGATTACTAACATTTCATAACGATGTTCCCAAAATTTCATAG
1 TGTGATTACCAACATTTCACAACGAGGTTACCAAAATTTCATAG
* * * *
61262 TGTGTTTACCAACATTTCACAAGGAGGTTATCAAAATTTCATTG
1 TGTGATTACCAACATTTCACAACGAGGTTACCAAAATTTCATAG
61306 TGTG
1 TGTG
61310 GTTATCAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (44 bp):
TGTGATTACCAACATTTCACAACGAGGTTACCAAAATTTCATAG
Found at i:61300 original size:22 final size:22
Alignment explanation
Indices: 61231--61394 Score: 100
Period size: 22 Copynumber: 7.4 Consensus size: 22
61221 GATTACTAAC
* * **
61231 ATTTCATAACGATGTTCCCAAA
1 ATTTCATAAGGAGGTTATCAAA
* * * *
61253 ATTTCAT-AGTGTGTTTACCAAC
1 ATTTCATAAG-GAGGTTATCAAA
*
61275 ATTTCACAAGGAGGTTATCAAA
1 ATTTCATAAGGAGGTTATCAAA
* *
61297 ATTTCAT-TGTGTGGTTATCAAAAA
1 ATTTCATAAG-GAGGTTATC--AAA
* **
61321 AATTCATTGGGAGGTTATCAAA
1 ATTTCATAAGGAGGTTATCAAA
*
61343 ATTTCATAATGAGGGTT-TCAAA
1 ATTTCATAAGGA-GGTTATCAAA
* * *
61365 ATTGCATAAAGAGGTTAACAAA
1 ATTTCATAAGGAGGTTATCAAA
61387 ATTTCATA
1 ATTTCATA
61395 GAAAGCTCCT
Statistics
Matches: 109, Mismatches: 25, Indels: 16
0.73 0.17 0.11
Matches are distributed among these distances:
21 6 0.06
22 79 0.72
23 6 0.06
24 17 0.16
25 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (22 bp):
ATTTCATAAGGAGGTTATCAAA
Found at i:61326 original size:24 final size:24
Alignment explanation
Indices: 61284--61343 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
61274 CATTTCACAA
*
61284 GGAGGTTATC--AAAATTTCATTG
1 GGAGGTTATCAAAAAAATTCATTG
* *
61306 TGTGGTTATCAAAAAAATTCATTG
1 GGAGGTTATCAAAAAAATTCATTG
61330 GGAGGTTATCAAAA
1 GGAGGTTATCAAAA
61344 TTTCATAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 8 0.26
24 23 0.74
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (24 bp):
GGAGGTTATCAAAAAAATTCATTG
Found at i:61810 original size:76 final size:74
Alignment explanation
Indices: 61723--61872 Score: 248
Period size: 77 Copynumber: 2.0 Consensus size: 74
61713 TAAAATTGGC
61723 AATTGCAAGCCT-GAATTTTTTTAAGGACAAATTATCCATTTTTGATTGATATTAGTAGTTTAGG
1 AATTGCAAGCCTGGAATTTTTTTAAGGACAAATTATCCATTTTTGATTGATA-T--TAGTTTAGG
61787 AAATGAAAAGAT
63 AAATGAAAAGAT
*
61799 AATTGCAAGCCTGGATTTTTTTTAAGGACAAATTATCCATTTTTGATTGATATTAGTTTAGGAAA
1 AATTGCAAGCCTGGAATTTTTTTAAGGACAAATTATCCATTTTTGATTGATATTAGTTTAGGAAA
*
61864 TGGAAAGAT
66 TGAAAAGAT
61873 TAACGGTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
74 20 0.28
76 13 0.18
77 38 0.54
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (74 bp):
AATTGCAAGCCTGGAATTTTTTTAAGGACAAATTATCCATTTTTGATTGATATTAGTTTAGGAAA
TGAAAAGAT
Found at i:62205 original size:20 final size:21
Alignment explanation
Indices: 62180--62219 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
62170 TAGTATATAA
*
62180 TTTCTTTTTT-TTTTTTTTGC
1 TTTCTTTTTTCTTGTTTTTGC
62200 TTTCTTTTTTCTTGTTTTTG
1 TTTCTTTTTTCTTGTTTTTG
62220 GGTAAGGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.82
Consensus pattern (21 bp):
TTTCTTTTTTCTTGTTTTTGC
Found at i:63152 original size:19 final size:19
Alignment explanation
Indices: 63128--63179 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
63118 AAAAAGAACG
63128 TTAGATTTTACATTTAATA
1 TTAGATTTTACATTTAATA
63147 TTAGATTTTACATTTAATA
1 TTAGATTTTACATTTAATA
63166 TATAG-TTTT-CATTT
1 T-TAGATTTTACATTT
63180 TTTAAATGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.16
19 24 0.75
20 3 0.09
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (19 bp):
TTAGATTTTACATTTAATA
Found at i:63217 original size:20 final size:20
Alignment explanation
Indices: 63192--63239 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
63182 TAAATGGGTA
* *
63192 TTTTTTTAATTGAGTGGTTT
1 TTTTTTTAAATGAGTAGTTT
*
63212 TTTTTTCAAATGAGTAGTTT
1 TTTTTTTAAATGAGTAGTTT
63232 TTATTTTT
1 TT-TTTTT
63240 GGTTTTTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.19, C:0.02, G:0.15, T:0.65
Consensus pattern (20 bp):
TTTTTTTAAATGAGTAGTTT
Found at i:63352 original size:1 final size:1
Alignment explanation
Indices: 63346--63370 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
63336 TTCCTTCACG
63346 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
63371 CCCGGATGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:63698 original size:42 final size:43
Alignment explanation
Indices: 63618--63705 Score: 160
Period size: 43 Copynumber: 2.1 Consensus size: 43
63608 AATCCCAATT
63618 ATCTCATCTTTTTCTTCTTCTTTTTTTGTACCGCTTCTTCTTC
1 ATCTCATCTTTTTCTTCTTCTTTTTTTGTACCGCTTCTTCTTC
*
63661 ATCTCATCTTTTTCTTCTTCTTTTTTT-TTCCGCTTCTTCTTC
1 ATCTCATCTTTTTCTTCTTCTTTTTTTGTACCGCTTCTTCTTC
63703 ATC
1 ATC
63706 ATAATAATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 17 0.39
43 27 0.61
ACGTcount: A:0.07, C:0.28, G:0.03, T:0.61
Consensus pattern (43 bp):
ATCTCATCTTTTTCTTCTTCTTTTTTTGTACCGCTTCTTCTTC
Found at i:68656 original size:21 final size:21
Alignment explanation
Indices: 68632--68696 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
68622 GTAAAGGAAA
*
68632 TCTAAATATATGA-AAGAAACC
1 TCTAAATATA-AATAAGAAACC
*
68653 TCTAATTATAAATAAGAAACC
1 TCTAAATATAAATAAGAAACC
*
68674 TCCAAATATAAATAAGAAACC
1 TCTAAATATAAATAAGAAACC
68695 TC
1 TC
68697 CAACATAGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 1 0.03
21 38 0.97
ACGTcount: A:0.52, C:0.17, G:0.06, T:0.25
Consensus pattern (21 bp):
TCTAAATATAAATAAGAAACC
Found at i:68697 original size:21 final size:21
Alignment explanation
Indices: 68645--68699 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
68635 AAATATATGA
* *
68645 AAGAAACCTCTAATTATAAAT
1 AAGAAACCTCCAAATATAAAT
68666 AAGAAACCTCCAAATATAAAT
1 AAGAAACCTCCAAATATAAAT
68687 AAGAAACCTCCAA
1 AAGAAACCTCCAA
68700 CATAGGATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (21 bp):
AAGAAACCTCCAAATATAAAT
Found at i:72697 original size:30 final size:30
Alignment explanation
Indices: 72661--72720 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
72651 CAAAGGATCA
72661 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGGCATCTTTGGTGCGATTCCTCCATCC
*
72691 AATGGCATCTTTGGTGTGATTCCTCCATCC
1 AATGGCATCTTTGGTGCGATTCCTCCATCC
72721 TTTGATGTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.35
Consensus pattern (30 bp):
AATGGCATCTTTGGTGCGATTCCTCCATCC
Found at i:80318 original size:17 final size:17
Alignment explanation
Indices: 80296--80343 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
80286 TGAAAAAGAC
80296 GAGAAT-TGAGAGAACAA
1 GAGAATATG-GAGAACAA
*
80313 GAGAATATGGAGAAGAA
1 GAGAATATGGAGAACAA
80330 GAGAATATGGAGAA
1 GAGAATATGGAGAA
80344 TGAGAAAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 27 0.93
18 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.33, T:0.12
Consensus pattern (17 bp):
GAGAATATGGAGAACAA
Found at i:81950 original size:19 final size:19
Alignment explanation
Indices: 81926--81966 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
81916 TATTCACTAT
*
81926 GAGGGAGTAAGTGGGAGGA
1 GAGGGACTAAGTGGGAGGA
* *
81945 GAGGGACTTAGTGGGGGGA
1 GAGGGACTAAGTGGGAGGA
81964 GAG
1 GAG
81967 AGAAGAGGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.59, T:0.12
Consensus pattern (19 bp):
GAGGGACTAAGTGGGAGGA
Found at i:84473 original size:35 final size:35
Alignment explanation
Indices: 84426--84523 Score: 151
Period size: 35 Copynumber: 2.8 Consensus size: 35
84416 AACAATAGTA
* *
84426 GCTCTTCCGGAGCCTTCAATTAAATTTGAATACTG
1 GCTCTTCTGGAGCCTTCAATCAAATTTGAATACTG
* * *
84461 GCTCTTCTGGAGCCTTCAATCAATTTTAAATATTG
1 GCTCTTCTGGAGCCTTCAATCAAATTTGAATACTG
84496 GCTCTTCTGGAGCCTTCAATCAAATTTG
1 GCTCTTCTGGAGCCTTCAATCAAATTTG
84524 CACAATCTGA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (35 bp):
GCTCTTCTGGAGCCTTCAATCAAATTTGAATACTG
Found at i:85274 original size:54 final size:54
Alignment explanation
Indices: 85213--85379 Score: 253
Period size: 54 Copynumber: 3.0 Consensus size: 54
85203 CGCTTTTCCT
*
85213 TTCCTATTTTCTTTTTTCCTTCAAAACTCTTCAGATGGTATAAATTTTATTTAA
1 TTCCTATTTTCTTTTTTCCTTCAAATCTCTTCAGATGGTATAAATTTTATTTAA
* *
85267 TTTCTATTTTCTTTTTTCCTTCAAATCTCTTTAGATGGTATAAATTTTATTTAA
1 TTCCTATTTTCTTTTTTCCTTCAAATCTCTTCAGATGGTATAAATTTTATTTAA
*
85321 TTCCTATTTTCTTTTTTCCTTCAAATCTCTTCTCTTTATATGGTATAAATTTTATTTAA
1 TTCCTATTTTCTTTTTTCCTTCAAATCTC-T-TC---AGATGGTATAAATTTTATTTAA
85380 GGAAAAATGA
Statistics
Matches: 102, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
54 79 0.77
55 1 0.01
56 1 0.01
59 21 0.21
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.56
Consensus pattern (54 bp):
TTCCTATTTTCTTTTTTCCTTCAAATCTCTTCAGATGGTATAAATTTTATTTAA
Found at i:85770 original size:85 final size:85
Alignment explanation
Indices: 85627--85783 Score: 296
Period size: 85 Copynumber: 1.8 Consensus size: 85
85617 TCTACTCAGC
* *
85627 TAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTATTTTACCATTTTAC
1 TAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAATTTACCATTTTAC
85692 TATTTTACTCAACTAAAAAG
66 TATTTTACTCAACTAAAAAG
85712 TAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAATTTACCATTTTAC
1 TAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAATTTACCATTTTAC
85777 TATTTTA
66 TATTTTA
85784 ACTAAAAAAC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.50
Consensus pattern (85 bp):
TAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAATTTACCATTTTAC
TATTTTACTCAACTAAAAAG
Found at i:88168 original size:48 final size:47
Alignment explanation
Indices: 88087--88178 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 47
88077 TGAAGACTAG
**
88087 TTGGTATAAAAAGGGATAGATTTGATTTAAATAATCAAAACAAAAAT
1 TTGGTATAAAAAGGGATAGATTTGATTTAAATAAAAAAAACAAAAAT
* *
88134 TTGGTGTAAAAAGGGGTAGAGTTTGATTTAAATAAAAAAAACAAA
1 TTGGTATAAAAAGGGATAGA-TTTGATTTAAATAAAAAAAACAAA
88179 TCATAACAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 18 0.45
48 22 0.55
ACGTcount: A:0.50, C:0.03, G:0.18, T:0.28
Consensus pattern (47 bp):
TTGGTATAAAAAGGGATAGATTTGATTTAAATAAAAAAAACAAAAAT
Found at i:89230 original size:20 final size:20
Alignment explanation
Indices: 89163--89216 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
89153 TTATTTCCCA
89163 CAATTTCAAGAGTCACAAAT
1 CAATTTCAAGAGTCACAAAT
89183 CAATTTCAAGAGTCACAAAT
1 CAATTTCAAGAGTCACAAAT
89203 CAATTTCAAGAGTC
1 CAATTTCAAGAGTC
89217 CAAGATAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (20 bp):
CAATTTCAAGAGTCACAAAT
Found at i:89435 original size:54 final size:54
Alignment explanation
Indices: 89356--89458 Score: 197
Period size: 54 Copynumber: 1.9 Consensus size: 54
89346 ATATAATTTA
89356 AAGTGGATAGTATGACAACTTCAGGTGTCAAACTTTAGCAACAATTAAAGTTTT
1 AAGTGGATAGTATGACAACTTCAGGTGTCAAACTTTAGCAACAATTAAAGTTTT
*
89410 AAGTGGATAGTATGACAACTTCAGGTGTCAAACTTTGGCAACAATTAAA
1 AAGTGGATAGTATGACAACTTCAGGTGTCAAACTTTAGCAACAATTAAA
89459 CAAATATTTC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (54 bp):
AAGTGGATAGTATGACAACTTCAGGTGTCAAACTTTAGCAACAATTAAAGTTTT
Found at i:89580 original size:33 final size:33
Alignment explanation
Indices: 89543--89606 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
89533 CACTATATTT
* *
89543 TTGATGTGACAACTTCGGGTGCCACTAATATGC
1 TTGATGTAACAACTTCAGGTGCCACTAATATGC
89576 TTGATGTAACAACTTCAGGTGCCACTAATAT
1 TTGATGTAACAACTTCAGGTGCCACTAATAT
89607 TCAAGATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (33 bp):
TTGATGTAACAACTTCAGGTGCCACTAATATGC
Found at i:89707 original size:32 final size:33
Alignment explanation
Indices: 89641--89714 Score: 105
Period size: 32 Copynumber: 2.2 Consensus size: 33
89631 TAATTTTTTA
* *
89641 ATGATAAAAGAAAGGTAGAAGGAGGAGATTATGC
1 ATGAT-AAAGAAAGGTAGAAGGAAGAGATCATGC
89675 ATGATAAAGAAAGGTAGAA-GAAGAGATCATGC
1 ATGATAAAGAAAGGTAGAAGGAAGAGATCATGC
*
89707 ATGTTAAA
1 ATGATAAA
89715 TAAACTTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 18 0.49
33 14 0.38
34 5 0.14
ACGTcount: A:0.49, C:0.04, G:0.28, T:0.19
Consensus pattern (33 bp):
ATGATAAAGAAAGGTAGAAGGAAGAGATCATGC
Found at i:89906 original size:17 final size:17
Alignment explanation
Indices: 89881--89932 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
89871 TATGGAAAAG
*
89881 ACAATAGAAT-TGAGAGA
1 ACAAGAGAATATG-GAGA
89898 ACAAGAGAATATGGAGA
1 ACAAGAGAATATGGAGA
*
89915 AGAAGAGAATATGGAGA
1 ACAAGAGAATATGGAGA
89932 A
1 A
89933 TGAGAAAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 30 0.94
18 2 0.06
ACGTcount: A:0.54, C:0.04, G:0.29, T:0.13
Consensus pattern (17 bp):
ACAAGAGAATATGGAGA
Found at i:91102 original size:31 final size:31
Alignment explanation
Indices: 91064--91123 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
91054 CCCTTCTCTG
91064 TTCTTCATCTTCTTCCTCCCTTCTCCTTTAT
1 TTCTTCATCTTCTTCCTCCCTTCTCCTTTAT
91095 TTCTTCATCTTCTTCCTCCCTTCTCCTTT
1 TTCTTCATCTTCTTCCTCCCTTCTCCTTT
91124 CTTTGATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.05, C:0.40, G:0.00, T:0.55
Consensus pattern (31 bp):
TTCTTCATCTTCTTCCTCCCTTCTCCTTTAT
Found at i:91125 original size:27 final size:27
Alignment explanation
Indices: 91052--91126 Score: 98
Period size: 31 Copynumber: 2.6 Consensus size: 27
91042 TCCCCGACCT
91052 CTCCCTTCT-CTGTTCTTCATCTTCTTC
1 CTCCCTTCTCCT-TTCTTCATCTTCTTC
91079 CTCCCTTCTCCTTTATTTCTTCATCTTCTTC
1 CTCCCTTCTCC----TTTCTTCATCTTCTTC
91110 CTCCCTTCTCCTTTCTT
1 CTCCCTTCTCCTTTCTT
91127 TGATTCAACA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
27 15 0.35
28 1 0.02
31 26 0.60
32 1 0.02
ACGTcount: A:0.04, C:0.41, G:0.01, T:0.53
Consensus pattern (27 bp):
CTCCCTTCTCCTTTCTTCATCTTCTTC
Found at i:94061 original size:14 final size:14
Alignment explanation
Indices: 94042--94085 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
94032 TTTATGAATG
*
94042 TTTTATTAAATTGT
1 TTTTATTAAATTAT
94056 TTTTA-TAAATTAT
1 TTTTATTAAATTAT
*
94069 TTTTATTAAATGAT
1 TTTTATTAAATTAT
94083 TTT
1 TTT
94086 GGGTGCATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 12 0.44
14 15 0.56
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (14 bp):
TTTTATTAAATTAT
Found at i:96344 original size:2 final size:2
Alignment explanation
Indices: 96337--96366 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
96327 AAATCTATGC
96337 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
96367 AAATAAGGAA
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):
TA
Found at i:96941 original size:21 final size:21
Alignment explanation
Indices: 96896--96951 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
96886 GTCTCTGTGT
*
96896 GGTTATCAAAATTGAATAAGAA
1 GGTTATCAAAATT-CATAAGAA
* * *
96918 GGTTGTCACAATTCATAAGGA
1 GGTTATCAAAATTCATAAGAA
96939 GGTTATCAAAATT
1 GGTTATCAAAATT
96952 TTACAGTGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (21 bp):
GGTTATCAAAATTCATAAGAA
Found at i:97081 original size:22 final size:22
Alignment explanation
Indices: 97053--97288 Score: 201
Period size: 22 Copynumber: 10.8 Consensus size: 22
97043 GTTATAAGGA
97053 GGTTATCAAAATTTCATATTGT
1 GGTTATCAAAATTTCATATTGT
** *
97075 GGTTATCAAAATTTCATAAAGG
1 GGTTATCAAAATTTCATATTGT
* *
97097 GGTTATCAAAATCTCATATAGT
1 GGTTATCAAAATTTCATATTGT
*
97119 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATATTGT
* * * * *
97141 AGTTTTCAAATTTTCAT-TGGGA
1 GGTTATCAAAATTTCATAT-TGT
* *
97163 GGTTATCAAAATTTCATAATGA
1 GGTTATCAAAATTTCATATTGT
* * *
97185 GGTTATC-AATTTTCACAGTGT
1 GGTTATCAAAATTTCATATTGT
* * *
97206 GATTATCAAAATTTCATGTGGAT
1 GGTTATCAAAATTTCATATTG-T
* *
97229 -GTTA-CAAAATTACATAATGT
1 GGTTATCAAAATTTCATATTGT
* * *
97249 GGTTATCAAAATTTTATACTGA
1 GGTTATCAAAATTTCATATTGT
*
97271 GGTTAACAAAATTTCATA
1 GGTTATCAAAATTTCATA
97289 AAGAAGTTAT
Statistics
Matches: 167, Mismatches: 41, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
20 1 0.01
21 31 0.19
22 134 0.80
23 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (22 bp):
GGTTATCAAAATTTCATATTGT
Found at i:97167 original size:66 final size:64
Alignment explanation
Indices: 97053--97287 Score: 228
Period size: 66 Copynumber: 3.6 Consensus size: 64
97043 GTTATAAGGA
* **
97053 GGTTATCAAAATTTCATATTGTGGTTATCAAAATTTCATAAAGG-GGTTATCAAAATCTCAT-AT
1 GGTTATCAAAATTTCATAGTGT-GTTATCAAAATTTCAT-TGGGAGGTTATCAAAAT-TCATAAT
97116 AGT
63 -GT
* *
97119 GGTTATCAAAATTTCATAGTGTAGTTTTCAAATTTTCATTGGGAGGTTATCAAAATTTCATAATG
1 GGTTATCAAAATTTCATAGTGT-GTTATCAAAATTTCATTGGGAGGTTATCAAAA-TTCATAATG
*
97184 A
64 T
* * *
97185 GGTTATC-AATTTTCACAGTGTGATTATCAAAATTTCA-TGTGGATGTTA-CAAAATTACATAAT
1 GGTTATCAAAATTTCATAGTGTG-TTATCAAAATTTCATTG-GGAGGTTATCAAAATT-CATAAT
97247 GT
63 GT
* * * *
97249 GGTTATCAAAATTTTATACTGAGGTTAACAAAATTTCAT
1 GGTTATCAAAATTTCATAGTG-TGTTATCAAAATTTCAT
97288 AAAGAAGTTA
Statistics
Matches: 141, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
63 2 0.01
64 22 0.16
65 55 0.39
66 59 0.42
67 3 0.02
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.39
Consensus pattern (64 bp):
GGTTATCAAAATTTCATAGTGTGTTATCAAAATTTCATTGGGAGGTTATCAAAATTCATAATGT
Found at i:97253 original size:21 final size:21
Alignment explanation
Indices: 97046--97309 Score: 138
Period size: 22 Copynumber: 12.1 Consensus size: 21
97036 TAAGAAGGTT
*
97046 ATAAGGAGGTTATCAAAATTTC
1 ATAATGAGGTTA-CAAAATTTC
* *
97068 ATATTGTGGTTATCAAAATTTC
1 ATAATGAGGTTA-CAAAATTTC
* * *
97090 ATAAAGGGGTTATCAAAATCTC
1 ATAATGAGGTTA-CAAAATTTC
*
97112 AT-ATAGTGGTTATCAAAATTTC
1 ATAAT-GAGGTTA-CAAAATTTC
* * * *
97134 ATAGTGTAGTTTTCAAATTTTC
1 ATAATG-AGGTTACAAAATTTC
***
97156 ATTGGGAGGTTATCAAAATTTC
1 ATAATGAGGTTA-CAAAATTTC
*
97178 ATAATGAGGTTATC-AATTTTC
1 ATAATGAGGTTA-CAAAATTTC
* * * *
97199 ACAGTGTGATTATCAAAATTTC
1 ATAATGAGGTTA-CAAAATTTC
* * *
97221 AT-GTGGATGTTACAAAATTAC
1 ATAAT-GAGGTTACAAAATTTC
* *
97242 ATAATGTGGTTATCAAAATTTT
1 ATAATGAGGTTA-CAAAATTTC
*
97264 ATACTGAGGTTAACAAAATTTC
1 ATAATGAGGTT-ACAAAATTTC
* * *
97286 ATAAAGAAGTTATCGAAATTTC
1 ATAATGAGGTTA-CAAAATTTC
97308 AT
1 AT
97310 GAGGTTATCA
Statistics
Matches: 186, Mismatches: 46, Indels: 20
0.74 0.18 0.08
Matches are distributed among these distances:
21 39 0.21
22 142 0.76
23 5 0.03
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (21 bp):
ATAATGAGGTTACAAAATTTC
Found at i:100404 original size:22 final size:23
Alignment explanation
Indices: 100344--100431 Score: 65
Period size: 22 Copynumber: 3.9 Consensus size: 23
100334 GTATTTTAGA
*
100344 GAATGTTATCAAAATTTCATAGTT
1 GAATGTTATTAAAATTTCATAG-T
** *
100368 TTAT-TTACTAAAATTTCATA-T
1 GAATGTTATTAAAATTTCATAGT
* *
100389 GAATGTTATTAAAATTTTATTGT
1 GAATGTTATTAAAATTTCATAGT
* **
100412 GAA-GTAATCGAAATTTCATA
1 GAATGTTATTAAAATTTCATA
100432 AGGAGGTTAT
Statistics
Matches: 48, Mismatches: 14, Indels: 6
0.71 0.21 0.09
Matches are distributed among these distances:
21 3 0.06
22 25 0.52
23 18 0.38
24 2 0.04
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (23 bp):
GAATGTTATTAAAATTTCATAGT
Found at i:100834 original size:15 final size:15
Alignment explanation
Indices: 100814--100843 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
100804 TGAAAACAAT
*
100814 GAACTGATGATTGTA
1 GAACTGAAGATTGTA
100829 GAACTGAAGATTGTA
1 GAACTGAAGATTGTA
100844 TTGAATAATG
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:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (15 bp):
GAACTGAAGATTGTA
Found at i:102446 original size:16 final size:15
Alignment explanation
Indices: 102427--102490 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 15
102417 TCCAATTCGA
102427 AACCCGAATGACCCG
1 AACCCGAATGACCCG
*
102442 TAACCCGAGTGACCCG
1 -AACCCGAATGACCCG
* *
102458 AGACCCGTATGACCGG
1 A-ACCCGAATGACCCG
* *
102474 AAATCCGAATAACCCG
1 -AACCCGAATGACCCG
102490 A
1 A
102491 GAAGTTAACC
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
15 2 0.05
16 35 0.92
17 1 0.03
ACGTcount: A:0.33, C:0.34, G:0.22, T:0.11
Consensus pattern (15 bp):
AACCCGAATGACCCG
Found at i:103355 original size:9 final size:8
Alignment explanation
Indices: 103336--103452 Score: 88
Period size: 7 Copynumber: 14.9 Consensus size: 8
103326 AATCCGTCCA
103336 ACCCG-AG
1 ACCCGAAG
103343 ACCCGATAG
1 ACCCGA-AG
103352 ACCCGAA-
1 ACCCGAAG
103359 ACCCGAATG
1 ACCCGAA-G
103368 ACCCGAA-
1 ACCCGAAG
103375 ACCCGAATG
1 ACCCGAA-G
103384 ACCCG-AG
1 ACCCGAAG
*
103391 ACCCAAATG
1 ACCCGAA-G
103400 ACCCG-AG
1 ACCCGAAG
*
103407 ACCCAAATG
1 ACCCGAA-G
103416 ACCCG-AG
1 ACCCGAAG
*
103423 ACCCGTATG
1 ACCCG-AAG
*
103432 ACCCG-GG
1 ACCCGAAG
103439 ACCCGAA-
1 ACCCGAAG
103446 ACCCGAA
1 ACCCGAA
103453 TAACACGAAT
Statistics
Matches: 90, Mismatches: 7, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
7 48 0.53
8 6 0.07
9 36 0.40
ACGTcount: A:0.34, C:0.38, G:0.21, T:0.06
Consensus pattern (8 bp):
ACCCGAAG
Found at i:103357 original size:16 final size:16
Alignment explanation
Indices: 103336--103445 Score: 150
Period size: 16 Copynumber: 6.9 Consensus size: 16
103326 AATCCGTCCA
103336 ACCCGAGACCCG-ATAG
1 ACCCGAGACCCGAAT-G
*
103352 ACCCGAAACCCGAATG
1 ACCCGAGACCCGAATG
*
103368 ACCCGAAACCCGAATG
1 ACCCGAGACCCGAATG
*
103384 ACCCGAGACCCAAATG
1 ACCCGAGACCCGAATG
*
103400 ACCCGAGACCCAAATG
1 ACCCGAGACCCGAATG
*
103416 ACCCGAGACCCGTATG
1 ACCCGAGACCCGAATG
*
103432 ACCCGGGACCCGAA
1 ACCCGAGACCCGAA
103446 ACCCGAATAA
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
16 84 0.98
17 2 0.02
ACGTcount: A:0.34, C:0.38, G:0.22, T:0.06
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:103491 original size:16 final size:16
Alignment explanation
Indices: 103438--103493 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
103428 TATGACCCGG
*
103438 GACCCGAAACCCGAAT
1 GACCCGAAACCAGAAT
* * *
103454 AACACGAATCCAG-AT
1 GACCCGAAACCAGAAT
* *
103469 GAACCGAAACCTGAAT
1 GACCCGAAACCAGAAT
103485 GACCCGAAA
1 GACCCGAAA
103494 AAGCTACCTG
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.43, C:0.30, G:0.18, T:0.09
Consensus pattern (16 bp):
GACCCGAAACCAGAAT
Found at i:111838 original size:55 final size:55
Alignment explanation
Indices: 111748--111853 Score: 167
Period size: 55 Copynumber: 1.9 Consensus size: 55
111738 AACGAGAGAT
* * * *
111748 AACAATGCAAACTAACACATGATAAGGAACTCTGCAATTATAAGTTTCATGTGGA
1 AACAATGCAAACTAACACATGATAAGGAACACTGCAAATACAACTTTCATGTGGA
*
111803 AACAGTGCAAACTAACACATGATAAGGAACACTGCAAATACAACTTTCATG
1 AACAATGCAAACTAACACATGATAAGGAACACTGCAAATACAACTTTCATG
111854 GCAACTTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (55 bp):
AACAATGCAAACTAACACATGATAAGGAACACTGCAAATACAACTTTCATGTGGA
Found at i:111839 original size:27 final size:27
Alignment explanation
Indices: 111748--111840 Score: 68
Period size: 27 Copynumber: 3.4 Consensus size: 27
111738 AACGAGAGAT
*
111748 AACAATGCAAACTAACACATGATAAGG
1 AACACTGCAAACTAACACATGATAAGG
* **
111775 AACTCTGCAATTA-TAAGTTTCATG-T--GG
1 AACACTGCAA--ACTAA--CACATGATAAGG
*
111802 AAACAGTGCAAACTAACACATGATAAGG
1 -AACACTGCAAACTAACACATGATAAGG
111830 AACACTGCAAA
1 AACACTGCAAA
111841 TACAACTTTC
Statistics
Matches: 48, Mismatches: 9, Indels: 18
0.64 0.12 0.24
Matches are distributed among these distances:
25 4 0.08
26 2 0.04
27 23 0.48
28 13 0.27
29 2 0.04
30 4 0.08
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.20
Consensus pattern (27 bp):
AACACTGCAAACTAACACATGATAAGG
Done.