Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000094.1 Hibiscus syriacus cultivar Beakdansim tig00000173_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: 111762
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3280 original size:805 final size:786
Alignment explanation
Indices: 1765--3361 Score: 2607
Period size: 804 Copynumber: 2.0 Consensus size: 786
1755 ATTGTACGCC
1765 CATTCATAGGTCATCTTTATGAATGATTCTTATCAAAAATCATTCCTTAAATATTCTGTTGATGA
1 CATTCATAGGTCATCTTTATGAATGATTCTTATCAAAAATCATTCCTTAAATATTCTGTTGATGA
1830 CCTAAAAAGAGAAGGAATCTCATAAGTAAAAGAATGATTAATGATAAATAAGTGAAAGAAGTACT
66 CCTAAAAAGAGAAGGAATCTCATAAGTAAAAGAATGATTAATGATAAATAAGTG-AAGAAGTACT
* *
1895 CCCTGTCTATATTTGCTGAATGGTCTAGAGTCATGTCTTTTGAAGACATATTATCTTTAATGATC
130 CACTGTCTATATTTGCTAAATGGTCTAGAGTCATGTCTTTTGAAGACATATTATCTTTAATGATC
1960 ATATCTCTTGGTACCCAAGGACATATGTTTGGTTCTTCAAAATCATGTCCATTGAATAAAAAGTT
195 ATATCTCTTGGTACCCAAGGACATATGTTTGGTTCTTCAAAATCATGTCCATTGAATAAAAAGTT
* *
2025 ATAGCTTTTGGTACTTTAAATGATAATTATCTTAATCTTCCTTGGATCATGCCTCTTGGTTCCTC
260 ATAGCTTTTGGTACTTTAAATGATAAATATCTTAAGCTTCCTTGGATCATGCCTCTTGGTTCCTC
* *
2090 TATTTGCAAGTTGTGTCCTTTGAATCATCCTTCATGCTTGATGCATCAATGTTAGGTAGGATAAT
325 TATTTGCAAGTTGTGTCCTTTGAATCATCCTTCATGCTTGATGCATCAACGTTAGGTAGGATAAA
2155 CCCATATATATGAATTGATTTCCTGCAAATTAAATCAAAGTTAGAATATGAAATAAACAAAATGA
390 CCCA-ATATATGAATTGATTTCCTGCAAATTAAATCAAAGTTAGAATATGAAATAAACAAAATGA
2220 ATAGAAATATCAAACCAAGGTGGATGTTTAATGGGAGTTGGTTGCTTAATGATGAGAACTCCATT
454 ATAGAAATATCAAACCAAGGTGGATGTTTAATGGGAGTTGGTTGCTTAATGATGAGAACTCCATT
* * *
2285 GGTTGTTGAATTCCCTTCAATATGTGCAGTGTATTTGGAATGTTAATGGTTGCTACTCATGGCCT
519 GGTTGTTAAATTCCCTTCAATATGTGCAGTGTATTTGGAATGTTAACGGTTGCTACTCATGGCAT
*
2350 TTCAATTGACACATCCTTTGAAATATCAAGAGACATGTTTTGTGGATCACCAAAAGTCACGTCTT
584 TTCAATTGACACATCCTTTGAAATATCAAGAGACATGTTTTGTGGATCACCAAAAGTCACATCTT
*
2415 TTGGTCCTTCAAAGCCATGATTCTTAATTCATCTCCTTGAAAAGATATGTCCCTTGAATGGTCCT
649 TTAGTCCTTCAAAGCCATGATTCTTAATTCATCTCCTTGAAAAGATATGTCCCTTGAATGGTCCT
* *
2480 CCAAAACAAAATGAAGGATATGGAGAAGAAAGGTTAGATAAAATTTGTTCTTCGCTCT-ATCTTT
714 CCAAAACAAAATGAAGGATA-GGAGAAGAAAGGTTAAAT-AAA-TTGTTCTCCGCTCTCATCTTT
2544 TTCTCCAAATT
776 TTCTCCAAATT
*
2555 CATTCATAGGTCATCTTTATGAAATGATTCTTATC-AAAATCACATTCCTTGAATAAGTTCCTTG
1 CATTCATAGGTCATCTTTATG-AATGATTCTTATCAAAAAT--CATTCCTTAAAT-A-TT-C-T-
* * *
2619 AGTGTCGATGACCT-TAAAGAGAAATGAATCTCATAAGTAAGAGAATGATTAATGATAAATAAGT
58 -GT-T-GATGACCTAAAAAGAG-AAGGAATCTCATAAGTAAAAGAATGATTAATGATAAATAAGT
*
2683 G-AGAAGTACTCACTGTCTATGTTTGCTAAATGGTCTAGAGTCATGTCTTTTGAAGACATATTAT
119 GAAGAAGTACTCACTGTCTATATTTGCTAAATGGTCTAGAGTCATGTCTTTTGAAGACATATTAT
2747 CTTTAATGATCATATCTCTTGGTACCCCAAAGGA-ATATTGTTTGGTTCTTCAAAAGTCATGTCC
184 CTTTAATGATCATATCTCTTGGTA-CCC-AAGGACATA-TGTTTGGTTCTTCAAAA-TCATGTCC
* *
2811 ATTGAATGAAAAGTTATAGCTTTTGGTACTTTAAATGATAAATCTCTTAAGCTTCCTTGGATCAT
245 ATTGAATAAAAAGTTATAGCTTTTGGTACTTTAAATGATAAATATCTTAAGCTTCCTTGGATCAT
2876 GCCTCTTGGTTCCTCTATTTGACAAGTTGTGTCCTTTGAATCATCCTTCATGCTTGATGCATCAA
310 GCCTCTTGGTTCCTCTATTTG-CAAGTTGTGTCCTTTGAATCATCCTTCATGCTTGATGCATCAA
*
2941 CGTTAGGTAGGATAAACCC-ATGTATGAATTGATTTCCTGCAAATTAAATCAAAGTTAGAATATG
374 CGTTAGGTAGGATAAACCCAATATATGAATTGATTTCCTGCAAATTAAATCAAAGTTAGAATAT-
*
3005 AGAAATTATAAACAAAATGAATGGAAATATCAAACCAAGGT-GATGTTTAATGGGAGTTGGTTGC
438 -G-AA--ATAAACAAAATGAATAGAAATATCAAACCAAGGTGGATGTTTAATGGGAGTTGGTTGC
3069 TTAATGATGGAGAACTCCATTGGTTGTTAAATTCCCTTCAATATGTGCAGTGT-TTTGGAATGTT
499 TTAATGAT-GAGAACTCCATTGGTTGTTAAATTCCCTTCAATATGTGCAGTGTATTTGGAATGTT
* * *
3133 AACGGTTGCTACTCTTGTCATTTCAATTGACACTTCCTTTGAAATATCAAGAGACATGTTTTGTG
563 AACGGTTGCTACTCATGGCATTTCAATTGACACATCCTTTGAAATATCAAGAGACATGTTTTGTG
*
3198 GATCACCAAAAGTCACATCTTTTAGTCCTTCAAAAGCCATGATTCTTGATTCATCTCCTTGAAAA
628 GATCACCAAAAGTCACATCTTTTAGTCCTTC-AAAGCCATGATTCTTAATTCATCTCCTTGAAAA
* **
3263 TATATGTCCCTTGAATGGTCCTGTAAAACAAAATGAAGGATAGGAGAAGAAAGGTTAAATAAATT
692 GATATGTCCCTTGAATGGTCCTCCAAAACAAAATGAAGGATAGGAGAAGAAAGGTTAAATAAATT
*
3328 GTTCTCCGCTCTCCTCTTTTTCTCCAAATT
757 GTTCTCCGCTCTCATCTTTTTCTCCAAATT
3358 CATT
1 CATT
3362 ATTCTCATTT
Statistics
Matches: 752, Mismatches: 30, Indels: 37
0.92 0.04 0.05
Matches are distributed among these distances:
790 26 0.03
791 13 0.02
792 11 0.01
793 1 0.00
794 2 0.00
795 1 0.00
796 1 0.00
798 86 0.11
799 13 0.02
800 114 0.15
801 90 0.12
802 74 0.10
803 25 0.03
804 148 0.20
805 147 0.20
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (786 bp):
CATTCATAGGTCATCTTTATGAATGATTCTTATCAAAAATCATTCCTTAAATATTCTGTTGATGA
CCTAAAAAGAGAAGGAATCTCATAAGTAAAAGAATGATTAATGATAAATAAGTGAAGAAGTACTC
ACTGTCTATATTTGCTAAATGGTCTAGAGTCATGTCTTTTGAAGACATATTATCTTTAATGATCA
TATCTCTTGGTACCCAAGGACATATGTTTGGTTCTTCAAAATCATGTCCATTGAATAAAAAGTTA
TAGCTTTTGGTACTTTAAATGATAAATATCTTAAGCTTCCTTGGATCATGCCTCTTGGTTCCTCT
ATTTGCAAGTTGTGTCCTTTGAATCATCCTTCATGCTTGATGCATCAACGTTAGGTAGGATAAAC
CCAATATATGAATTGATTTCCTGCAAATTAAATCAAAGTTAGAATATGAAATAAACAAAATGAAT
AGAAATATCAAACCAAGGTGGATGTTTAATGGGAGTTGGTTGCTTAATGATGAGAACTCCATTGG
TTGTTAAATTCCCTTCAATATGTGCAGTGTATTTGGAATGTTAACGGTTGCTACTCATGGCATTT
CAATTGACACATCCTTTGAAATATCAAGAGACATGTTTTGTGGATCACCAAAAGTCACATCTTTT
AGTCCTTCAAAGCCATGATTCTTAATTCATCTCCTTGAAAAGATATGTCCCTTGAATGGTCCTCC
AAAACAAAATGAAGGATAGGAGAAGAAAGGTTAAATAAATTGTTCTCCGCTCTCATCTTTTTCTC
CAAATT
Found at i:4264 original size:26 final size:26
Alignment explanation
Indices: 4235--4324 Score: 153
Period size: 26 Copynumber: 3.5 Consensus size: 26
4225 GGTTAGGGTC
4235 TAGAAATGGTTATGATAGGGGTAGGA
1 TAGAAATGGTTATGATAGGGGTAGGA
* *
4261 TAGAAATGTTTATGATAGGGATAGGA
1 TAGAAATGGTTATGATAGGGGTAGGA
4287 TAGAAATGGTTATGATAGGGGTAGGA
1 TAGAAATGGTTATGATAGGGGTAGGA
*
4313 TAGAAAAGGTTA
1 TAGAAATGGTTA
4325 AGAAATGGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 59 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (26 bp):
TAGAAATGGTTATGATAGGGGTAGGA
Found at i:4335 original size:52 final size:52
Alignment explanation
Indices: 4235--4335 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
4225 GGTTAGGGTC
* * * *
4235 TAGAAATGGTTATGATAGGGGTAGGATAGAAATGTTTATGATAGGGATAGGA
1 TAGAAATGGTTATGATAGGGGTAGGATAGAAAAGGTTAAGAAAGGGATAGGA
*
4287 TAGAAATGGTTATGATAGGGGTAGGATAGAAAAGGTTAAGAAATGGATA
1 TAGAAATGGTTATGATAGGGGTAGGATAGAAAAGGTTAAGAAAGGGATA
4336 AGGAAATGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.27
Consensus pattern (52 bp):
TAGAAATGGTTATGATAGGGGTAGGATAGAAAAGGTTAAGAAAGGGATAGGA
Found at i:5040 original size:35 final size:35
Alignment explanation
Indices: 5001--5102 Score: 105
Period size: 35 Copynumber: 2.9 Consensus size: 35
4991 ATTGGTGGTT
* *
5001 ATATAGGCATGAAATGGTGATAGAAGATGGTAATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTAATG
* * * * *
5036 ATATACGCGTGCAGTGGTAATGGAAGATGGTGATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTAATG
* * *
5071 TTATAGGCGTGAAAATAGTGATGGGAGATGGT
1 ATATAGGCGTG-AAATGGTGATGGAAGATGGT
5103 GATGTTTAGG
Statistics
Matches: 52, Mismatches: 14, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
35 37 0.71
36 15 0.29
ACGTcount: A:0.33, C:0.05, G:0.35, T:0.26
Consensus pattern (35 bp):
ATATAGGCGTGAAATGGTGATGGAAGATGGTAATG
Found at i:7038 original size:17 final size:17
Alignment explanation
Indices: 7016--7048 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
7006 GTCGGCTAAA
*
7016 AGAAATGGTTATGGTAT
1 AGAAATGGATATGGTAT
7033 AGAAATGGATATGGTA
1 AGAAATGGATATGGTA
7049 AAGGTAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.30
Consensus pattern (17 bp):
AGAAATGGATATGGTAT
Found at i:7317 original size:19 final size:20
Alignment explanation
Indices: 7289--7337 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
7279 GATGTAGGAG
*
7289 TTTTTTTTTTTTCTT-TTTC
1 TTTTTCTTTTTTCTTCTTTC
7308 TTTTTC-TTTTTCTTCTTTC
1 TTTTTCTTTTTTCTTCTTTC
*
7327 TTTTTGTTTTT
1 TTTTTCTTTTT
7338 GTTGCAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 8 0.31
19 14 0.54
20 4 0.15
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (20 bp):
TTTTTCTTTTTTCTTCTTTC
Found at i:7318 original size:25 final size:25
Alignment explanation
Indices: 7289--7337 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
7279 GATGTAGGAG
* *
7289 TTTTTTTTTTTTCTTTTTCTTTTTC
1 TTTTTCTTCTTTCTTTTTCTTTTTC
*
7314 TTTTTCTTCTTTCTTTTTGTTTTT
1 TTTTTCTTCTTTCTTTTTCTTTTT
7338 GTTGCAACAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (25 bp):
TTTTTCTTCTTTCTTTTTCTTTTTC
Found at i:7340 original size:6 final size:6
Alignment explanation
Indices: 7290--7337 Score: 69
Period size: 6 Copynumber: 7.8 Consensus size: 6
7280 ATGTAGGAGT
* *
7290 TTTTTT TTTTTC TTTTTC TTTTTC TTTTTC TTCTTTC TTTTTG TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC TTTTTC TTTTT
7338 GTTGCAACAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
6 33 0.85
7 6 0.15
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:10758 original size:19 final size:21
Alignment explanation
Indices: 10717--10766 Score: 77
Period size: 19 Copynumber: 2.5 Consensus size: 21
10707 AACCCCTTTA
10717 AAAATACATGATTTTTAAATG
1 AAAATACATGATTTTTAAATG
10738 AAAATACATGA-TTTT-AATG
1 AAAATACATGATTTTTAAATG
*
10757 AAGATACATG
1 AAAATACATG
10767 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 13 0.46
20 4 0.14
21 11 0.39
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (21 bp):
AAAATACATGATTTTTAAATG
Found at i:11694 original size:30 final size:31
Alignment explanation
Indices: 11653--11712 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
11643 ACATGTTGCC
**
11653 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
11684 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
11713 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:14200 original size:19 final size:21
Alignment explanation
Indices: 14171--14222 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 21
14161 CCTTGGCTTG
14171 TTTTC-TCTTTTTATTT-TC-
1 TTTTCTTCTTTTTATTTGTCT
14189 TTTTCTTC-TTTTATTTGTCT
1 TTTTCTTCTTTTTATTTGTCT
14209 TTTTCTTTCTTTTT
1 TTTTC-TTCTTTTT
14223 GCACTCCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 13 0.45
19 4 0.14
20 5 0.17
21 3 0.10
22 4 0.14
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTCTTCTTTTTATTTGTCT
Found at i:14956 original size:19 final size:21
Alignment explanation
Indices: 14913--14964 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
14903 GAAACCCCTT
*
14913 TGAAATTACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
14934 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
14953 TGAAGATACATG
1 TGAAAATACATG
14965 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:15084 original size:22 final size:22
Alignment explanation
Indices: 15042--15084 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
15032 GGTGCTAAAA
*
15042 TGAAGAGGAAGGAGTCTTTGGC
1 TGAAGAGGAAGGAATCTTTGGC
*
15064 TGAATAGGAA-GAATCTCTTGG
1 TGAAGAGGAAGGAATCT-TTGG
15085 TGTTTTGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.30, C:0.09, G:0.35, T:0.26
Consensus pattern (22 bp):
TGAAGAGGAAGGAATCTTTGGC
Found at i:21110 original size:26 final size:26
Alignment explanation
Indices: 21076--21134 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
21066 AAAGAAAGAA
21076 AAGACAAAAGAAGAAA-ATT-CATAAAAG
1 AAGA-AAAAGAA-AAAGATTCCA-AAAAG
21103 AAGAAAAAGAAAAAGATTCCAAAAAG
1 AAGAAAAAGAAAAAGATTCCAAAAAG
21129 -AGAAAA
1 AAGAAAA
21135 GCAAGCCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
25 9 0.30
26 15 0.50
27 6 0.20
ACGTcount: A:0.69, C:0.07, G:0.15, T:0.08
Consensus pattern (26 bp):
AAGAAAAAGAAAAAGATTCCAAAAAG
Found at i:33313 original size:91 final size:91
Alignment explanation
Indices: 33133--33306 Score: 267
Period size: 91 Copynumber: 1.9 Consensus size: 91
33123 GGTAGTTGAT
* *
33133 GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCATATGCAAGGTACATG
1 GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
33198 GGGACTGATCACATGCAAAACACATG
66 GGGACTGATCACATGCAAAACACATG
* ** *
33224 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGTGCCTAAATGATCCACATGCAAGGCACATG
1 GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
* * *
33289 GGGGCTGGTCATATGCAA
66 GGGACTGATCACATGCAA
33307 GGCACATCAG
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 74 1.00
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (91 bp):
GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
GGGACTGATCACATGCAAAACACATG
Found at i:36442 original size:27 final size:25
Alignment explanation
Indices: 36412--36471 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
36402 AAGAAAAGAC
*
36412 AAAAGAAGAGAAAAATCAGAAAATAAA
1 AAAAGAAAAGAAAAA-CA-AAAATAAA
* *
36439 AAAAGAAAAGAAAAAGAAAAATTAA
1 AAAAGAAAAGAAAAACAAAAATAAA
36464 AAAAGAAA
1 AAAAGAAA
36472 GCAAGCCAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 15 0.50
26 1 0.03
27 14 0.47
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (25 bp):
AAAAGAAAAGAAAAACAAAAATAAA
Found at i:36445 original size:13 final size:13
Alignment explanation
Indices: 36429--36471 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
36419 GAGAAAAATC
36429 AGAAAATAAAAAA
1 AGAAAATAAAAAA
* *
36442 AGAAAAGAAAAAG
1 AGAAAATAAAAAA
*
36455 A-AAAATTAAAAA
1 AGAAAATAAAAAA
36467 AGAAA
1 AGAAA
36472 GCAAGCCAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (13 bp):
AGAAAATAAAAAA
Found at i:39345 original size:23 final size:23
Alignment explanation
Indices: 39300--39345 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
39290 TTATACCTAT
*
39300 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
39323 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
39346 TATATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:40075 original size:39 final size:39
Alignment explanation
Indices: 40021--40103 Score: 159
Period size: 39 Copynumber: 2.2 Consensus size: 39
40011 GCCACATCAC
40021 ATGGCATGCACATGAGAGCCTTTGGCGCCAAACATGATA
1 ATGGCATGCACATGAGAGCCTTTGGCGCCAAACATGATA
40060 ATGGCATGCACATGAGAGCCTTTGGCGCCAAACATGATA
1 ATGGCATGCACATGAGAGCCTTTGGCGCCAAACATGATA
40099 A-GGCA
1 ATGGCA
40104 CATGACTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 4 0.09
39 40 0.91
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (39 bp):
ATGGCATGCACATGAGAGCCTTTGGCGCCAAACATGATA
Found at i:46958 original size:5 final size:6
Alignment explanation
Indices: 46941--46985 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
46931 GATGTATGAG
*
46941 TCTTTT TCTTTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
46986 TGTTGCTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
6 25 0.71
7 10 0.29
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:46973 original size:19 final size:18
Alignment explanation
Indices: 46943--46978 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
46933 TGTATGAGTC
46943 TTTTTCTTTTTCTTTTTG
1 TTTTTCTTTTTCTTTTTG
46961 TTTTTCTTCTTTCTTTTT
1 TTTTTCTT-TTTCTTTTT
46979 CTCTTTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (18 bp):
TTTTTCTTTTTCTTTTTG
Found at i:49632 original size:23 final size:23
Alignment explanation
Indices: 49606--49651 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
49596 TTATACCTAT
*
49606 AGATTCTTA-TTTCATATGTTATA
1 AGATACTTATTTTCATAT-TTATA
*
49629 AGATAGTTATTTTCATATTTATA
1 AGATACTTATTTTCATATTTATA
49652 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.52
Consensus pattern (23 bp):
AGATACTTATTTTCATATTTATA
Found at i:51522 original size:18 final size:19
Alignment explanation
Indices: 51479--51515 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
51469 TATTTTTTTT
51479 CAAAAAAAAAGCAAAAAAA
1 CAAAAAAAAAGCAAAAAAA
51498 CAAAAAAAAA-CAAAAAAA
1 CAAAAAAAAAGCAAAAAAA
51516 GCCAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (19 bp):
CAAAAAAAAAGCAAAAAAA
Found at i:56978 original size:10 final size:9
Alignment explanation
Indices: 56963--57023 Score: 50
Period size: 11 Copynumber: 6.0 Consensus size: 9
56953 ATTGGAGTGC
56963 AAAAAGAAA
1 AAAAAGAAA
56972 GAAAAAGAAA
1 -AAAAAGAAA
56982 AAAGAAGAGAA
1 AAA-AAGA-AA
*
56993 AAATCAGAAAA
1 AAA-AAG-AAA
57004 AAAAAGGAAAA
1 AAAAA-G-AAA
57015 AAAAAGAAA
1 AAAAAGAAA
57024 TTCAAAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
9 6 0.14
10 15 0.34
11 22 0.50
12 1 0.02
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:57016 original size:21 final size:21
Alignment explanation
Indices: 56977--57015 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
56967 AGAAAGAAAA
*
56977 AGAAAAAAGAAGAGAAAAATC
1 AGAAAAAAAAAGAGAAAAATC
56998 AGAAAAAAAAAG-GAAAAA
1 AGAAAAAAAAAGAGAAAAA
57016 AAAAGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (21 bp):
AGAAAAAAAAAGAGAAAAATC
Found at i:62221 original size:19 final size:19
Alignment explanation
Indices: 62194--62232 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
62184 ACATCGAATG
* *
62194 CATTTCATGCATCGATGCA
1 CATTCCATGCACCGATGCA
62213 CATTCCATGCACCGATGCA
1 CATTCCATGCACCGATGCA
62232 C
1 C
62233 TGAGTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (19 bp):
CATTCCATGCACCGATGCA
Found at i:62334 original size:17 final size:19
Alignment explanation
Indices: 62306--62354 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
62296 TATTTTGAAA
62306 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
62324 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
62343 CACCGATGCACT
1 CATCGATGCACT
62355 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:66756 original size:16 final size:15
Alignment explanation
Indices: 66692--66774 Score: 76
Period size: 16 Copynumber: 5.2 Consensus size: 15
66682 AAAGAAGAGA
*
66692 AAAAGAAGAAAAGAAG
1 AAAAGAA-AAAAAAAG
*
66708 AAAAGAAGAAAAGAAG
1 AAAAGAA-AAAAAAAG
*
66724 AAAAGAAGAAAAGAAG
1 AAAAGAA-AAAAAAAG
66740 AAAAGAAAAGAAAAAG
1 AAAAGAAAA-AAAAAG
* *
66756 AGAAGTTAAAAAAAAG
1 AAAAG-AAAAAAAAAG
66772 AAA
1 AAA
66775 GCAAGCCAAG
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
15 2 0.03
16 56 0.92
17 3 0.05
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AAAAGAAAAAAAAAG
Found at i:66756 original size:24 final size:23
Alignment explanation
Indices: 66680--66756 Score: 95
Period size: 24 Copynumber: 3.3 Consensus size: 23
66670 ATTGGAGTGC
*
66680 AAAAAGAAGAG-A-AAAAGAAGA
1 AAAAAGAAAAGAAGAAAAGAAGA
66701 AAAGAAGAAAAGAAGAAAAGAAGA
1 AAA-AAGAAAAGAAGAAAAGAAGA
*
66725 AAAGAAGAAAAGAAGAAAAGAAAA
1 AAA-AAGAAAAGAAGAAAAGAAGA
66749 GAAAAAGA
1 -AAAAAGA
66757 GAAGTTAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
21 3 0.06
22 7 0.14
23 1 0.02
24 36 0.72
25 3 0.06
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAGAAGAAAAGAAGA
Found at i:66759 original size:8 final size:8
Alignment explanation
Indices: 66692--66746 Score: 110
Period size: 8 Copynumber: 6.9 Consensus size: 8
66682 AAAGAAGAGA
66692 AAAAGAAG
1 AAAAGAAG
66700 AAAAGAAG
1 AAAAGAAG
66708 AAAAGAAG
1 AAAAGAAG
66716 AAAAGAAG
1 AAAAGAAG
66724 AAAAGAAG
1 AAAAGAAG
66732 AAAAGAAG
1 AAAAGAAG
66740 AAAAGAA
1 AAAAGAA
66747 AAGAAAAAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 47 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:76049 original size:19 final size:19
Alignment explanation
Indices: 76022--76060 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
76012 ACATCGAATG
* *
76022 CATTTCATGCATCGATGCA
1 CATTCCATGCACCGATGCA
76041 CATTCCATGCACCGATGCA
1 CATTCCATGCACCGATGCA
76060 C
1 C
76061 TGAGGATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (19 bp):
CATTCCATGCACCGATGCA
Found at i:76117 original size:19 final size:19
Alignment explanation
Indices: 76093--76144 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
76083 AATGCATTTG
76093 ATGCATCGATGCACCAACC
1 ATGCATCGATGCACCAACC
* *
76112 ATGCATCGATGCATCAGCC
1 ATGCATCGATGCACCAACC
76131 ATGCATCGATGCAC
1 ATGCATCGATGCAC
76145 TCTAGCTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.19
Consensus pattern (19 bp):
ATGCATCGATGCACCAACC
Found at i:77067 original size:15 final size:15
Alignment explanation
Indices: 77056--77084 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
77046 ACTCAAAAAT
77056 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
77071 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
77085 GTTGAAGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:81989 original size:24 final size:24
Alignment explanation
Indices: 81936--81990 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
81926 TCGTTGATCA
81936 CCAAAAGTAACAACTATTTGTTCT
1 CCAAAAGTAACAACTATTTGTTCT
** * *
81960 TTAAAAGTCACATCT-TTTAGTTCT
1 CCAAAAGTAACAACTATTT-GTTCT
81984 CCAAAAG
1 CCAAAAG
81991 CCATGATTCT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (24 bp):
CCAAAAGTAACAACTATTTGTTCT
Found at i:83204 original size:6 final size:6
Alignment explanation
Indices: 83193--83236 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
83183 GATGTAGGAG
*
83193 TCTTTT TC-TTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
83237 TGTTGCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:83216 original size:12 final size:12
Alignment explanation
Indices: 83193--83236 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
83183 GATGTAGGAG
83193 TCTTTTTC-TTT
1 TCTTTTTCTTTT
*
83204 TCTTTTTGTTTT
1 TCTTTTTCTTTT
83216 TCTTCTTTCTTTT
1 TCTT-TTTCTTTT
83229 TCTCTTTT
1 TCT-TTTT
83237 TGTTGCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.25
12 7 0.25
13 13 0.46
14 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:83660 original size:13 final size:13
Alignment explanation
Indices: 83642--83680 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
83632 ATATAGGCAT
83642 GAATGGTGATAGA
1 GAATGGTGATAGA
83655 GAATGGTGATAGA
1 GAATGGTGATAGA
**
83668 CTATGGTGATAGA
1 GAATGGTGATAGA
83681 AAGATAGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.03, G:0.36, T:0.26
Consensus pattern (13 bp):
GAATGGTGATAGA
Found at i:84140 original size:13 final size:12
Alignment explanation
Indices: 84121--84206 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
84111 ATATGGGCTT
84121 GATATGGTGATG
1 GATATGGTGATG
84133 GAATATGGTGAT-
1 G-ATATGGTGATG
*
84145 GATATAGGCG-T-
1 GATAT-GGTGATG
84156 GATAATGGTGATG
1 GAT-ATGGTGATG
84169 GACTATGGTGAT-
1 GA-TATGGTGATG
*
84181 GATATAGGCG-T-
1 GATAT-GGTGATG
84192 GATAATGGTGATG
1 GAT-ATGGTGATG
84205 GA
1 GA
84207 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:84176 original size:36 final size:36
Alignment explanation
Indices: 84103--84207 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
84093 ATTTATAAGT
* * * *
84103 TGGTGATAATATGGGCTTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
84138 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
84174 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
84208 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 18 0.28
36 47 0.72
ACGTcount: A:0.28, C:0.05, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:87613 original size:25 final size:24
Alignment explanation
Indices: 87584--87637 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
87574 ACTTGCTTCA
87584 CTTTTCTTTTGCTTTTGATTTTCTT
1 CTTTTCTTTT-CTTTTGATTTTCTT
**
87609 CTTTTTCTTTTCTTTTTTTTTTCTT
1 C-TTTTCTTTTCTTTTGATTTTCTT
87634 CTTT
1 CTTT
87638 CTTGTTGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 3 0.12
25 14 0.54
26 9 0.35
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.78
Consensus pattern (24 bp):
CTTTTCTTTTCTTTTGATTTTCTT
Found at i:87623 original size:11 final size:11
Alignment explanation
Indices: 87584--87640 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
87574 ACTTGCTTCA
*
87584 CTTTTCTTTTG
1 CTTTTCTTTTT
**
87595 CTTTTGATTTT
1 CTTTTCTTTTT
87606 C--TTCTTTTT
1 CTTTTCTTTTT
87615 CTTTTCTTTTT
1 CTTTTCTTTTT
*
87626 TTTTTCTTCTTT
1 CTTTTCTT-TTT
87638 CTT
1 CTT
87641 GTTGTTTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 7 0.19
11 24 0.67
12 5 0.14
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:87649 original size:25 final size:25
Alignment explanation
Indices: 87602--87652 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
87592 TTGCTTTTGA
*
87602 TTTTCTTCTTTTTCTTTTCTTTTTT
1 TTTTCTTCTTTTTCTTGTCTTTTTT
*
87627 TTTTCTTCTTTCTTGTTGT-TTTTTT
1 TTTTCTTCTTT-TTCTTGTCTTTTTT
87652 T
1 T
87653 GTTGTAGCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (25 bp):
TTTTCTTCTTTTTCTTGTCTTTTTT
Found at i:88070 original size:13 final size:12
Alignment explanation
Indices: 88051--88136 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
88041 ATATGGACGT
88051 GATATGGTGATG
1 GATATGGTGATG
88063 GAATATGGTGAT-
1 G-ATATGGTGATG
*
88075 GATATAGGCG-T-
1 GATAT-GGTGATG
88086 GATAATGGTGATG
1 GAT-ATGGTGATG
88099 GACTATGGTGAT-
1 GA-TATGGTGATG
*
88111 GATATAGGCG-T-
1 GATAT-GGTGATG
88122 GATAATGGTGATG
1 GAT-ATGGTGATG
88135 GA
1 GA
88137 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:88106 original size:36 final size:36
Alignment explanation
Indices: 88033--88137 Score: 169
Period size: 36 Copynumber: 2.9 Consensus size: 36
88023 ATTTATAAGT
* *
88033 TGGTGATAATAT-GGACGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGG-CGTGATAATGGTGATGGACTA
88068 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
88104 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
88138 AGATTGTATC
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
35 17 0.26
36 49 0.74
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:97903 original size:17 final size:18
Alignment explanation
Indices: 97881--97952 Score: 71
Period size: 17 Copynumber: 4.2 Consensus size: 18
97871 AATTAAGAGT
97881 TAGTTT-ATTAAATGAAC
1 TAGTTTAATTAAATGAAC
*
97898 TAGTTTGA-TAAATGAAC
1 TAGTTTAATTAAATGAAC
*
97915 TAGTTTAATT-AATCAAC
1 TAGTTTAATTAAATGAAC
* *
97932 TAACTTT-ATTCAATGAAC
1 T-AGTTTAATTAAATGAAC
97950 TAG
1 TAG
97953 ATGCATGAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
17 33 0.72
18 13 0.28
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (18 bp):
TAGTTTAATTAAATGAAC
Found at i:99156 original size:21 final size:21
Alignment explanation
Indices: 99132--99172 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
99122 GCTCATTTTC
99132 ACTCTCAAT-TCTCTTTTCAAT
1 ACTCTCAATGTCT-TTTTCAAT
99153 ACTCTCAATGTCTTTTTCAA
1 ACTCTCAATGTCTTTTTCAA
99173 CTCTCATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.24, C:0.27, G:0.02, T:0.46
Consensus pattern (21 bp):
ACTCTCAATGTCTTTTTCAAT
Found at i:99177 original size:19 final size:19
Alignment explanation
Indices: 99127--99183 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
99117 AATGTGCTCA
99127 TTTTC-ACTCTCAATTCTC
1 TTTTCAACTCTCAATTCTC
99145 TTTTCAATACTCTCAATGTCT-
1 TTTTC-A-ACTCTCAAT-TCTC
*
99166 TTTTCAACTCTCATTTCT
1 TTTTCAACTCTCAATTCT
99184 TCTTCATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 8 0.24
19 8 0.24
20 1 0.03
21 14 0.41
22 3 0.09
ACGTcount: A:0.19, C:0.28, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTTCAACTCTCAATTCTC
Found at i:102961 original size:17 final size:17
Alignment explanation
Indices: 102939--102991 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
102929 TATTAAGAGT
102939 TAGTTT-ATTAAATGAAC
1 TAGTTTAATT-AATGAAC
* *
102956 TAGTTTGATGAATGAAC
1 TAGTTTAATTAATGAAC
102973 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
102990 TA
1 TA
102992 ACTTTATTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 30 0.94
18 2 0.06
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:104234 original size:19 final size:19
Alignment explanation
Indices: 104178--104240 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 19
104168 TTTTTCAATG
104178 TTCTCATTTTC-ACTCTCAA
1 TTCTC-TTTTCAACTCTCAA
104197 TTCTCTTTTCAATACTCTCAA
1 TTCTCTTTTC-A-ACTCTCAA
*
104218 TGTCT-TTTTCAACTCTCAT
1 T-TCTCTTTTCAACTCTCAA
104237 TTCT
1 TTCT
104241 TCTTCTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 8 0.21
19 13 0.33
20 1 0.03
21 14 0.36
22 3 0.08
ACGTcount: A:0.19, C:0.29, G:0.02, T:0.51
Consensus pattern (19 bp):
TTCTCTTTTCAACTCTCAA
Found at i:109918 original size:9 final size:10
Alignment explanation
Indices: 109892--109917 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
109882 TTCCTTTGCC
109892 TTTTTTTGTT
1 TTTTTTTGTT
109902 TTTTTTTGTT
1 TTTTTTTGTT
109912 TTTTTT
1 TTTTTT
109918 GAAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTTTGTT
Done.