Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001888.1 Hibiscus syriacus cultivar Beakdansim tig00003831_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: 86993
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2897 original size:22 final size:22
Alignment explanation
Indices: 2869--3203 Score: 397
Period size: 22 Copynumber: 15.3 Consensus size: 22
2859 TATTTTAAAT
*
2869 TTTTAAAATATAGATTGATTTA
1 TTTTAAAATATGGATTGATTTA
*
2891 TTTTAAAATATGAATTGATTTA
1 TTTTAAAATATGGATTGATTTA
* *
2913 TTTTAAAATATTGATTTATTTA
1 TTTTAAAATATGGATTGATTTA
* ***
2935 TTTTAAATTATGGAAAAATTTA
1 TTTTAAAATATGGATTGATTTA
* *
2957 TTTTAAAATATGAATTAATTTA
1 TTTTAAAATATGGATTGATTTA
2979 TTTTAAAATATGGATTGATTTA
1 TTTTAAAATATGGATTGATTTA
***
3001 TTTTAAAATAT-GAAAAATTTTA
1 TTTTAAAATATGGATTGA-TTTA
*
3023 TTTTAAAATATGGATTGGTTTA
1 TTTTAAAATATGGATTGATTTA
3045 TTTTAAAATATGGATTGATTTA
1 TTTTAAAATATGGATTGATTTA
** **
3067 TTTTAAAATAT-GA-AAAAATA
1 TTTTAAAATATGGATTGATTTA
*
3087 TTTTAAAATATGAATTGATTTA
1 TTTTAAAATATGGATTGATTTA
***
3109 TTTTAAAATATGGAAAAATTTA
1 TTTTAAAATATGGATTGATTTA
3131 TTTTAAAATATGGATTGATTTA
1 TTTTAAAATATGGATTGATTTA
*** *
3153 TTTTAAAATATGGAAAAAGTTA
1 TTTTAAAATATGGATTGATTTA
*
3175 TTTTAAAATATAGATTGATTTA
1 TTTTAAAATATGGATTGATTTA
3197 TTTTAAA
1 TTTTAAA
3204 GAGAAAATAA
Statistics
Matches: 260, Mismatches: 49, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.05
21 6 0.02
22 238 0.92
23 2 0.01
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (22 bp):
TTTTAAAATATGGATTGATTTA
Found at i:3365 original size:21 final size:21
Alignment explanation
Indices: 3349--3425 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
3339 GCGTTGCATT
3349 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
3370 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
* *
3390 TCGCGTTGCTATAGTTAAAAA
1 TCGCGTTGCGATAGTTGAAAA
3411 TCGCGTTGCGATAGT
1 TCGCGTTGCGATAGT
3426 CTACAATGTC
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:3390 original size:41 final size:41
Alignment explanation
Indices: 3345--3422 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
3335 ATTCGCGTTG
*
3345 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTAAAAATCGCGTTGCGATTTTC
*
3386 CATTTCGCGTTGCTATAGTTAAAAATCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTAAAAATCGCGTTGCGAT
3423 AGTCTACAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTAAAAATCGCGTTGCGATTTTC
Found at i:3480 original size:22 final size:22
Alignment explanation
Indices: 3453--3505 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
3443 TTTTCCAAAT
**
3453 TCGTTGCGGTAGTCTACAGTTG
1 TCGTTGCGAAAGTCTACAGTTG
* *
3475 TTGTTGCGAAAGTTTACAGTTG
1 TCGTTGCGAAAGTCTACAGTTG
3497 TCGTTGCGA
1 TCGTTGCGA
3506 TTTTCCAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.38
Consensus pattern (22 bp):
TCGTTGCGAAAGTCTACAGTTG
Found at i:4277 original size:41 final size:41
Alignment explanation
Indices: 4230--4325 Score: 131
Period size: 41 Copynumber: 2.3 Consensus size: 41
4220 GCAACGAATT
4230 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CAACTGTCA-ACTATCGCAACGCGAAA
* * * *
4272 TGAAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
4313 TGGAAAATCGCAA
1 TGGAAAATCGCAA
4326 TGCGATTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
41 33 0.69
42 15 0.31
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.17
Consensus pattern (41 bp):
TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
Found at i:4283 original size:20 final size:20
Alignment explanation
Indices: 4258--4330 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
4248 ACTGTAGACT
4258 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
** * **
4278 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
*
4299 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
*
4319 ATCGCAATGCGA
1 ATCGCAACGCGA
4331 TTTTTGGTCA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:4331 original size:41 final size:41
Alignment explanation
Indices: 4255--4334 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
4245 ACAACTGTAG
4255 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
* *
4296 ACTATCGCAACGCGAAATGGAAAATCGCAATGCGATTTT
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTT
4335 TGGTCACTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
Found at i:4467 original size:22 final size:22
Alignment explanation
Indices: 4460--4536 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
4450 ATGGAAAAAG
4460 TTATTTTAAAATATAGATTGAT
1 TTATTTTAAAATATAGATTGAT
4482 TTATTTTAAAATATAGATTGAT
1 TTATTTTAAAATATAGATTGAT
* *
4504 TTATTTTAAAATATGGTTTGAT
1 TTATTTTAAAATATAGATTGAT
4526 TTATTTTAAAA
1 TTATTTTAAAA
4537 AAAATTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
TTATTTTAAAATATAGATTGAT
Found at i:4619 original size:31 final size:31
Alignment explanation
Indices: 4562--4620 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
4552 AGTTGTATGG
*
4562 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
*
4593 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
4621 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:16060 original size:20 final size:20
Alignment explanation
Indices: 16035--16083 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
16025 GGAAGTTATT
*
16035 ATTTTTTGGCACAATTTGGA
1 ATTTTTGGGCACAATTTGGA
16055 ATTTTTGGGCACAATTTGGA
1 ATTTTTGGGCACAATTTGGA
*
16075 CTTTTTGGG
1 ATTTTTGGG
16084 TGAGTAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.10, G:0.24, T:0.45
Consensus pattern (20 bp):
ATTTTTGGGCACAATTTGGA
Found at i:16237 original size:12 final size:12
Alignment explanation
Indices: 16220--16244 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16210 GTCAAATAAT
16220 TTAGGCACCAAA
1 TTAGGCACCAAA
16232 TTAGGCACCAAA
1 TTAGGCACCAAA
16244 T
1 T
16245 GGTGCTTTGT
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:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:22053 original size:32 final size:33
Alignment explanation
Indices: 22017--22082 Score: 125
Period size: 32 Copynumber: 2.0 Consensus size: 33
22007 TATTTTCCCT
22017 CTATTTAAGTTTATAAATG-TTTTTTAATGAGG
1 CTATTTAAGTTTATAAATGTTTTTTTAATGAGG
22049 CTATTTAAGTTTATAAATGTTTTTTTAATGAGG
1 CTATTTAAGTTTATAAATGTTTTTTTAATGAGG
22082 C
1 C
22083 GCATGTCTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 19 0.58
33 14 0.42
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (33 bp):
CTATTTAAGTTTATAAATGTTTTTTTAATGAGG
Found at i:29346 original size:20 final size:20
Alignment explanation
Indices: 29321--29363 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
29311 TCTACCTTTC
29321 TAGGTATTTGTTTGATTCTG
1 TAGGTATTTGTTTGATTCTG
29341 TAGGTATTTGTTTGATTCTG
1 TAGGTATTTGTTTGATTCTG
29361 TAG
1 TAG
29364 TGTCACATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.05, G:0.26, T:0.53
Consensus pattern (20 bp):
TAGGTATTTGTTTGATTCTG
Found at i:29530 original size:21 final size:20
Alignment explanation
Indices: 29506--29547 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
29496 GTCATGCAAT
*
29506 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
29527 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
29547 T
1 T
29548 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:35091 original size:20 final size:20
Alignment explanation
Indices: 35066--35104 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
35056 CAAGTGGGAG
35066 ATTATTAGTTGTCATGCAAA
1 ATTATTAGTTGTCATGCAAA
35086 ATTATTAGTTGTCATGCAA
1 ATTATTAGTTGTCATGCAA
35105 CTAATAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (20 bp):
ATTATTAGTTGTCATGCAAA
Found at i:35130 original size:21 final size:20
Alignment explanation
Indices: 35106--35147 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
35096 GTCATGCAAC
*
35106 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
35127 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
35147 T
1 T
35148 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:38006 original size:13 final size:13
Alignment explanation
Indices: 37988--38014 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
37978 CTATAAATAG
37988 CCATTGTAACTCA
1 CCATTGTAACTCA
38001 CCATTGTAACTCA
1 CCATTGTAACTCA
38014 C
1 C
38015 GATTTACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.30
Consensus pattern (13 bp):
CCATTGTAACTCA
Found at i:38365 original size:18 final size:17
Alignment explanation
Indices: 38326--38368 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
38316 ATTATATGGA
38326 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
38342 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
38360 TATTATTAT
1 TATTATTAT
38369 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:38851 original size:38 final size:40
Alignment explanation
Indices: 38800--38879 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
38790 CGTGAGAGGG
* *
38800 TAGCTTTTCTATTTT-TAAATA-TTTGGTGTGTATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
38838 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
38878 TA
1 TA
38880 TATATATTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 12 0.33
39 7 0.19
40 17 0.47
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:38950 original size:31 final size:30
Alignment explanation
Indices: 38915--38981 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
38905 CTATATATAA
38915 TTATTACTTTACTATTT-TTTTTTCC-TTTATC
1 TTATTA-TTTA-T-TTTATTTTTTCCTTTTATC
38946 TTATTTATTTATTTTATTTTTTCCTTTTATC
1 TTA-TTATTTATTTTATTTTTTCCTTTTATC
38977 TTATT
1 TTATT
38982 TGTTTTCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
29 3 0.09
30 11 0.33
31 16 0.48
32 3 0.09
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (30 bp):
TTATTATTTATTTTATTTTTTCCTTTTATC
Found at i:42025 original size:22 final size:22
Alignment explanation
Indices: 42002--42063 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
41992 CAAAAAGGGC
42002 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAA-AAAAGAAGCA
* *
42025 AAAAAGGAAAAAACAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
42046 AAAAAGAAAGAACAAAAA
1 AAAAAGAAA-AA-AAAAA
42064 TAAAAAAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 8 0.24
23 15 0.45
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:42054 original size:20 final size:20
Alignment explanation
Indices: 42002--42071 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
41992 CAAAAAGGGC
*
42002 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAG-AAAAA-ACAAGAA-CA
42025 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAGAACA
* * *
42046 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
42066 AAAAAG
1 AAAAAG
42072 GGAACAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 18 0.43
21 7 0.17
22 6 0.14
23 10 0.24
24 1 0.02
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:43579 original size:36 final size:36
Alignment explanation
Indices: 43539--43660 Score: 106
Period size: 36 Copynumber: 3.4 Consensus size: 36
43529 ACTCATGATT
* * *
43539 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
1 GTTTCTCTTAAAACAAGATTTGTCTCCCTTGAGACA
* * * * *
43575 GTTT-TCACTAGAA-GAGTTTTGTCTCTCTTGAGACA
1 GTTTCTC-TTAAAACAAGATTTGTCTCCCTTGAGACA
* *
43610 GTTTCCCTTGAAACAA-ATTTTGTCTCCCTTGAGACA
1 GTTTCTCTTAAAACAAGA-TTTGTCTCCCTTGAGACA
*
43646 GTTTCTCTTGAAACA
1 GTTTCTCTTAAAACA
43661 TAAACATTGA
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
35 27 0.40
36 41 0.60
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (36 bp):
GTTTCTCTTAAAACAAGATTTGTCTCCCTTGAGACA
Found at i:43739 original size:37 final size:36
Alignment explanation
Indices: 43676--43800 Score: 171
Period size: 36 Copynumber: 3.4 Consensus size: 36
43666 ATTGAAAACA
* * *
43676 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
43712 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
* *
43749 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAG
43785 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
43801 ATCTTTGAAT
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
35 4 0.05
36 43 0.54
37 33 0.41
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:43743 original size:138 final size:138
Alignment explanation
Indices: 43589--43863 Score: 374
Period size: 138 Copynumber: 2.0 Consensus size: 138
43579 TCACTAGAAG
* *
43589 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTT-GTCTCCCTTGAGACAGTTTCTC
1 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AATTTTCGTCTACCTTGAGACAGTTTCCC
* * * * * * *
43653 TTGAAACATAAA-CATTGAAAACATTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAGTTTCT
65 TTGAAACA-AAATCATTGAAAACATTTCCCCTAAAACAAATTTCGTCTCCCTTGAGACAATTACT
43717 CTTGAAACAA
129 CTTGAAACAA
* *
43727 AGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATTTTCGTCTATCTTGAGACAGTTTCCCT
1 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAATTTTCGTCTACCTTGAGACAGTTTCCCT
* *** *
43792 TGAAACAAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAATTACTCT
66 TGAAACAAAATCATTGAAAACATTTCCCCTAAAACAAATTTCGTCTCCCTTGAGACAATTACTCT
43857 TGAAACA
131 TGAAACA
43864 CAAAATCTTC
Statistics
Matches: 119, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
137 9 0.08
138 110 0.92
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (138 bp):
AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAATTTTCGTCTACCTTGAGACAGTTTCCCT
TGAAACAAAATCATTGAAAACATTTCCCCTAAAACAAATTTCGTCTCCCTTGAGACAATTACTCT
TGAAACAA
Found at i:43862 original size:65 final size:67
Alignment explanation
Indices: 43758--43915 Score: 196
Period size: 67 Copynumber: 2.4 Consensus size: 67
43748 GTTTCTCTTG
** * * **
43758 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCC
1 AAACAAATTTT-GTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCC
43820 CTA
65 CTA
* *
43823 AAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
43888 TA
66 TA
*
43890 AAACATAATTTTGTTTCCCTTGAGAC
1 AAACA-AATTTTGTCTCCCTTGAGAC
43916 CGTTTCTCAT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 24 0.30
66 8 0.10
67 29 0.36
68 19 0.24
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:43892 original size:67 final size:65
Alignment explanation
Indices: 43749--43915 Score: 192
Period size: 65 Copynumber: 2.5 Consensus size: 65
43739 CTTGAGACAG
* * ** * * **
43749 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTT
1 TTTCCCTTAAAACAAATTTT-GTCTCCCTTGAGACAATTACCCTTGAAACAAAATCTTCAAATTT
43813 A
65 A
* *
43814 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTG-AA-ACAAAATCTTCAAATT
43879 TA
64 TA
*
43881 TTTCCCTTAAAACATAATTTTGTTTCCCTTGAGAC
1 TTTCCCTTAAAACA-AATTTTGTCTCCCTTGAGAC
43916 CGTTTCTCAT
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
65 30 0.35
66 8 0.09
67 29 0.34
68 19 0.22
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (65 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACAAAATCTTCAAATTTA
Found at i:44707 original size:105 final size:103
Alignment explanation
Indices: 44536--45381 Score: 1099
Period size: 105 Copynumber: 8.3 Consensus size: 103
44526 GCCATCCGCG
* * * *
44536 ATTTCAACTCCACAACGGAGGATATCGTGGCACTCGAGACAACGCAAGTTCAACTTCACGAGGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
44601 GGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
63 GGGACCGCTGCTTGTCAACAACAACTT-CCAAT-TCAGAGCCA
* *
44644 ATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
44709 ACCGCTGCTTATCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAAC-TTCCAAT-TCAGAGCCA
44749 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
44814 ACCGCTGCTTGTCAACAA-AA-TTTC-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCAATTCAGAGCCA
* *
44849 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
44914 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAAAGCCA
66 ACCGCTGCTTGTCAACAACAAC-TTCCAAT-TCAGAGCCA
*
44954 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
45019 GCCGCTGCTTGTCAACAA-AA-TTTC-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCAATTCAGAGCCA
* *
45054 ATTTCAACTTCACAGCGAAGGATATTGGACT-C---C-A-G--A---CAA--T-GCGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
45105 ACCGTTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTT-CCAAT-TCAGAGCCA
*
45145 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
45210 ACCGCTGCTTGTCAACAA-AA-TTTC-ATTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCAATTCAGAGCCA
* * *
45245 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * **
45310 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTT-CCAATT-CAGAGCCA
* *
45351 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
45382 TGGAACAATG
Statistics
Matches: 657, Mismatches: 50, Indels: 64
0.85 0.06 0.08
Matches are distributed among these distances:
86 25 0.04
87 3 0.00
88 2 0.00
89 4 0.01
90 2 0.00
91 37 0.06
92 2 0.00
94 1 0.00
95 2 0.00
96 2 0.00
97 1 0.00
99 2 0.00
100 208 0.32
101 10 0.02
102 12 0.02
103 7 0.01
104 10 0.02
105 264 0.40
106 40 0.06
108 23 0.04
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (103 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCAATTCAGAGCCA
Found at i:44896 original size:205 final size:205
Alignment explanation
Indices: 44536--45381 Score: 1211
Period size: 205 Copynumber: 4.2 Consensus size: 205
44526 GCCATCCGCG
* * * *
44536 ATTTCAACTCCACAACGGAGGATATCGTGGCACTCGAGACAACGCAAGTTCAACTTCACGAGGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
44601 GGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGA
63 GGGACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGAGCCAATTTCAACTTCACAACGAAGGA
* *
44666 TATTGGACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTATCAACAACAAC
123 TATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAAC
44731 TTTCCAATCTCAGAGCCA
188 TTTCCAATCTCAGAGCCA
44749 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
44814 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
44879 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
*
44944 CTCAAAGCCA
196 CTCAGAGCCA
*
44954 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
45019 GCCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* * *
45084 TCCAGACAAT----G----------CGACGAAGGGACCGTTGTTTGTCAACAACAACTTCCCAAT
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
*
45135 CCCAGAGCCA
196 CTCAGAGCCA
*
45145 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
45210 ACCGCTGCTTGTCAACAAAATTTCATTCAGATTCAATTTCAACTTCACAACGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* ** * * * *
45275 TCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCCCG
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTT-CCA
*
45339 GT-TCCAGAGCCA
194 ATCT-CAGAGCCA
* *
45351 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
45382 TGGAACAATG
Statistics
Matches: 582, Mismatches: 34, Indels: 41
0.89 0.05 0.06
Matches are distributed among these distances:
191 179 0.31
195 1 0.00
201 1 0.00
205 272 0.47
206 46 0.08
207 1 0.00
208 2 0.00
209 2 0.00
210 52 0.09
211 3 0.01
213 23 0.04
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (205 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
CTCAGAGCCA
Found at i:45228 original size:191 final size:191
Alignment explanation
Indices: 44904--45283 Score: 670
Period size: 191 Copynumber: 2.0 Consensus size: 191
44894 TTCAACTTCA
* *
44904 CGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTCAAAGCCAATTTCAACTTCACAA
1 CGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCCCAAAGCCAATTTCAACTTCACAA
*
44969 CGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGGCCGCTGCTTGTCAA
66 CGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA
*
45034 CAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATG
131 CAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATG
* * *
45095 CGACGAAGGGACCGTTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCAATTTCAACTTCACAA
1 CGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCCCAAAGCCAATTTCAACTTCACAA
45160 CGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA
66 CGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA
** *
45225 CAAAATTTCATTCAGATTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAA
131 CAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA
45284 CACAAGTTCA
Statistics
Matches: 179, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
191 179 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (191 bp):
CGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCCCAAAGCCAATTTCAACTTCACAA
CGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA
CAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATG
Found at i:46420 original size:18 final size:17
Alignment explanation
Indices: 46381--46423 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
46371 ATTATATGGA
46381 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
46397 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
46415 TATTATTAT
1 TATTATTAT
46424 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:46899 original size:38 final size:40
Alignment explanation
Indices: 46847--46927 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
46837 AAGTGAGAGG
* *
46847 ATAGCTTTTCTATTTT-TAAATA-TTTGGTGTGTATATAT
1 ATAGCTTTTCTATTTTATAAATACTTTGATGTATATATAT
*
46885 ATAGCTTATT-TATTTTATTAATACTTTGATGTATATATAT
1 ATAGCTT-TTCTATTTTATAAATACTTTGATGTATATATAT
46925 ATA
1 ATA
46928 TATATATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 13 0.35
39 7 0.19
40 17 0.46
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (40 bp):
ATAGCTTTTCTATTTTATAAATACTTTGATGTATATATAT
Found at i:46923 original size:2 final size:2
Alignment explanation
Indices: 46916--46940 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46906 TACTTTGATG
46916 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
46941 CCTTTTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47010 original size:27 final size:27
Alignment explanation
Indices: 46982--47033 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
46972 ACTTTACTAT
*
46982 TTTTTTCC-TTTATCTTATTTATTTTA
1 TTTTTCCCTTTTATCTTATTTATTTTA
*
47008 TTTTTCCCTTTTATCTTATTTGTTTT
1 TTTTTCCCTTTTATCTTATTTATTTT
47034 CTTTACCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.12, C:0.13, G:0.02, T:0.73
Consensus pattern (27 bp):
TTTTTCCCTTTTATCTTATTTATTTTA
Found at i:47047 original size:27 final size:27
Alignment explanation
Indices: 46990--47050 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
46980 ATTTTTTTCC
* *
46990 TTTATCTTATTTATTTTATTTTTCCCT
1 TTTATCTTATTTATTTTACTTTACCCT
* *
47017 TTTATCTTATTTGTTTT-CTTTACCTT
1 TTTATCTTATTTATTTTACTTTACCCT
47043 GTTTATCT
1 -TTTATCT
47051 AACACATTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 6 0.21
27 23 0.79
ACGTcount: A:0.13, C:0.15, G:0.03, T:0.69
Consensus pattern (27 bp):
TTTATCTTATTTATTTTACTTTACCCT
Found at i:48784 original size:18 final size:18
Alignment explanation
Indices: 48761--48802 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
48751 AAGCAAAAGC
48761 ATATAAGAT-AAACCCATA
1 ATATAAGATCAAA-CCATA
*
48779 ATATAAGATCAAACCATT
1 ATATAAGATCAAACCATA
48797 ATATAA
1 ATATAA
48803 TATATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.55, C:0.14, G:0.05, T:0.26
Consensus pattern (18 bp):
ATATAAGATCAAACCATA
Found at i:53328 original size:2 final size:2
Alignment explanation
Indices: 53323--53365 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
53313 AACTATTTAT
53323 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
53365 T
1 T
53366 GTGTGTGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:62829 original size:25 final size:26
Alignment explanation
Indices: 62789--62838 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
62779 AATTGTATCA
*
62789 AATTTTATATTTTA-TTATTGAAATAG
1 AATTTTATATTATATTTATT-AAATAG
62815 AATTTTAT-TTATATTTATTAAATA
1 AATTTTATATTATATTTATTAAATA
62839 TATTTTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (26 bp):
AATTTTATATTATATTTATTAAATAG
Found at i:62845 original size:25 final size:24
Alignment explanation
Indices: 62790--62845 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
62780 ATTGTATCAA
62790 ATTTTATATTTTATTATTGAAATAG
1 ATTTT-TATTTTATTATTGAAATAG
* *
62815 AATTTTATTTATATTTATT-AAATAT
1 ATTTTTATTT-TA-TTATTGAAATAG
62840 ATTTTT
1 ATTTTT
62846 CAATCTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 5 0.19
25 16 0.62
26 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
ATTTTTATTTTATTATTGAAATAG
Found at i:65148 original size:67 final size:67
Alignment explanation
Indices: 65040--65174 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 67
65030 AGCTAATCCT
* *
65040 GTGTTTCGTGACCTTGACAATTAAGAGAGTGGTTGAACTATGGTCCTGTCTATGGACCCGGTTCT
1 GTGTTTCGTGACCTTGACAATTAAGAGAGTGGTTAAACTATGATCCTGTCTATGGACCCGGTTCT
65105 TC
66 TC
*
65107 GTGTTTCGTGACCTTGACAATTAAGAGAGTGGTTAAACTATGATTCTGTCTATGGACCCGGTTCT
1 GTGTTTCGTGACCTTGACAATTAAGAGAGTGGTTAAACTATGATCCTGTCTATGGACCCGGTTCT
65172 TC
66 TC
65174 G
1 G
65175 GGTCACGGAG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (67 bp):
GTGTTTCGTGACCTTGACAATTAAGAGAGTGGTTAAACTATGATCCTGTCTATGGACCCGGTTCT
TC
Found at i:71171 original size:13 final size:13
Alignment explanation
Indices: 71155--71180 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
71145 TCTTTTATTT
71155 TTTATTTTTTTCA
1 TTTATTTTTTTCA
71168 TTTATTTTTTTCA
1 TTTATTTTTTTCA
71181 ATACTTAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTTTTTCA
Found at i:71287 original size:30 final size:30
Alignment explanation
Indices: 71253--71314 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
71243 TTGTGATTAT
* *
71253 TTTAGATACTGACGAATTTTTTTCATCGTC
1 TTTAGATACTGACGAACTCTTTTCATCGTC
*
71283 TTTAGATACTGATGAACTCTTTTCATCGTC
1 TTTAGATACTGACGAACTCTTTTCATCGTC
71313 TT
1 TT
71315 CTACTACTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.47
Consensus pattern (30 bp):
TTTAGATACTGACGAACTCTTTTCATCGTC
Found at i:83674 original size:43 final size:43
Alignment explanation
Indices: 83626--83708 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
83616 GACCCGAACC
*
83626 GAAAATTTTATATCATTCACCCGATCCGACCTGAAAAGTACCT
1 GAAAATTTTATATCATTCACCCGATCCGACCGGAAAAGTACCT
* *
83669 GAAAATTTTATATCATTCACTCGATCTGACCGGAAAAGTA
1 GAAAATTTTATATCATTCACCCGATCCGACCGGAAAAGTA
83709 TATTTCCACC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (43 bp):
GAAAATTTTATATCATTCACCCGATCCGACCGGAAAAGTACCT
Found at i:85074 original size:46 final size:46
Alignment explanation
Indices: 84997--85089 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 46
84987 GTGAAATGGG
*
84997 TAGTCGATATGTTTAACGGTGAAGCGAATGAGGAACATCTCGAGAA
1 TAGTCGATATGTTTAACGGTGAAGCGAATGAGGAACACCTCGAGAA
* * *
85043 TAGTCGATATGTTTAACGGTGAA-CTGGATGAGGGACACCTCGGGAA
1 TAGTCGATATGTTTAACGGTGAAGC-GAATGAGGAACACCTCGAGAA
85089 T
1 T
85090 GTACTACTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 1 0.02
46 41 0.98
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (46 bp):
TAGTCGATATGTTTAACGGTGAAGCGAATGAGGAACACCTCGAGAA
Found at i:86387 original size:15 final size:15
Alignment explanation
Indices: 86367--86398 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
86357 TGGGGGGTTC
86367 CTCTTAAATTTTAGT
1 CTCTTAAATTTTAGT
86382 CTCTTAAATTTTAGT
1 CTCTTAAATTTTAGT
86397 CT
1 CT
86399 GGATGAAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (15 bp):
CTCTTAAATTTTAGT
Done.