Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003028.1 Hibiscus syriacus cultivar Beakdansim tig00006301_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: 48724
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:427 original size:9 final size:9
Alignment explanation
Indices: 389--420 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
379 ATATATTGTT
389 TATAT-ATA
1 TATATAATA
397 -ATATAATA
1 TATATAATA
405 TATATAATA
1 TATATAATA
414 TATATAA
1 TATATAA
421 AGTATATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 4 0.18
8 3 0.14
9 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TATATAATA
Found at i:507 original size:2 final size:2
Alignment explanation
Indices: 389--491 Score: 68
Period size: 2 Copynumber: 51.5 Consensus size: 2
379 ATATATTGTT
* *
389 TA TA TA TA -A TA TA -A TA TA TA TA -A TA TA TA TA AA GTA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * ** * * *
429 TA TG TA TA TA TA AA CTA CC TA TA TGG TT TA TA TA TA TC TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
*
473 TA TA TA TA TC TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
492 GTATGTAAAC
Statistics
Matches: 76, Mismatches: 19, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
1 3 0.04
2 70 0.92
3 3 0.04
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:945 original size:58 final size:57
Alignment explanation
Indices: 866--988 Score: 144
Period size: 58 Copynumber: 2.1 Consensus size: 57
856 TATAAAGATC
* * * *
866 AAATTGAACAAATTTTAAATATGAAG-TTTAATTAATAACTGTAA-TATTAAATTTGGACT
1 AAATTGAAAAAAGTTGAAATAT-AAGCTTAAATTAAT-ACTG-AATTATT-AATTTGGACT
*
925 -AATTGAAAAAAGTTGAAATATAAGCTTAAATTAATATTGAATTATTAATTTGGACT
1 AAATTGAAAAAAGTTGAAATATAAGCTTAAATTAATACTGAATTATTAATTTGGACT
981 AAATTGAA
1 AAATTGAA
989 CAAATTTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
56 12 0.21
57 17 0.30
58 27 0.48
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.37
Consensus pattern (57 bp):
AAATTGAAAAAAGTTGAAATATAAGCTTAAATTAATACTGAATTATTAATTTGGACT
Found at i:1014 original size:57 final size:57
Alignment explanation
Indices: 866--1015 Score: 148
Period size: 57 Copynumber: 2.6 Consensus size: 57
856 TATAAAGATC
*
866 AAATTGAACAAATTTTAAATATGAAGTTTAATTAATAACTGTAATATTAAATTTGGACT
1 AAATTGAACAAAGTTTAAATA-GAAG-TTAATTAATAACTGTAATATTAAATTTGGACT
* * * *
925 -AATTGAAAAAAGTTGAAATATAAGCTTAAATTAAT-ATTG-AATTATT-AATTTGGACT
1 AAATTGAACAAAGTTTAAATAGAAG-TT-AATTAATAACTGTAA-TATTAAATTTGGACT
981 AAATTGAACAAA-TTTAAACTAGAAGATGTAATTAA
1 AAATTGAACAAAGTTTAAA-TAGAAG-T-TAATTAA
1016 ATCAGCCCCA
Statistics
Matches: 76, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
56 17 0.22
57 34 0.45
58 25 0.33
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (57 bp):
AAATTGAACAAAGTTTAAATAGAAGTTAATTAATAACTGTAATATTAAATTTGGACT
Found at i:1362 original size:20 final size:20
Alignment explanation
Indices: 1334--1381 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1324 CATCGCCCTG
*
1334 CTCGTGCACGCCCGACATCA
1 CTCGAGCACGCCCGACATCA
1354 CTCGAGCACGCCCGACATCA
1 CTCGAGCACGCCCGACATCA
1374 CTCGAGCA
1 CTCGAGCA
1382 ACCCAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.44, G:0.21, T:0.12
Consensus pattern (20 bp):
CTCGAGCACGCCCGACATCA
Found at i:4987 original size:16 final size:16
Alignment explanation
Indices: 4968--5006 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
4958 TGAGTCAATT
*
4968 ACAGGTCAGGTTCATA
1 ACAGGTCAGGTTCAAA
*
4984 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTCAAA
5000 ACAGGTC
1 ACAGGTC
5007 GGTATACCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTCAAA
Found at i:9927 original size:23 final size:23
Alignment explanation
Indices: 9880--9929 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
9870 AATAACATAT
* **
9880 TAGGTAGCGCTTAGATAATGTAA
1 TAGGAAGCGCTTAGATAATAAAA
*
9903 TAGGAAGCGCTTATATAATAAAA
1 TAGGAAGCGCTTAGATAATAAAA
9926 TAGG
1 TAGG
9930 CATTTAACCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (23 bp):
TAGGAAGCGCTTAGATAATAAAA
Found at i:9984 original size:23 final size:23
Alignment explanation
Indices: 9958--10005 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
9948 ATTAAGTACA
9958 ATAA-CAAATTAGGTAGCGCTTAT
1 ATAATCAAA-TAGGTAGCGCTTAT
**
9981 ATAATGTAATAGGTAGCGCTTAT
1 ATAATCAAATAGGTAGCGCTTAT
10004 AT
1 AT
10006 TGACCTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAATCAAATAGGTAGCGCTTAT
Found at i:9991 original size:87 final size:87
Alignment explanation
Indices: 9845--10005 Score: 277
Period size: 87 Copynumber: 1.9 Consensus size: 87
9835 ATGTTATATC
*
9845 TTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTAGATAATGTAATAGGAAG
1 TTTAACCGGAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTAGATAATGTAATAGGAAG
9910 CGCTTATATAATAAAATAGGCA
66 CGCTTATATAATAAAATAGGCA
* * * *
9932 TTTAACCGGAAATATTATTAAGTACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGGTAG
1 TTTAACCGGAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTAGATAATGTAATAGGAAG
9997 CGCTTATAT
66 CGCTTATAT
10006 TGACCTATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (87 bp):
TTTAACCGGAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTAGATAATGTAATAGGAAG
CGCTTATATAATAAAATAGGCA
Found at i:10371 original size:198 final size:200
Alignment explanation
Indices: 10027--10479 Score: 542
Period size: 198 Copynumber: 2.3 Consensus size: 200
10017 CTCATAAAAA
* * * * * * * *
10027 CGGTAAATTTAAATCGGTTACATTATAAATTGACCTATTAGATTATAAATATCGGTTTCGATATT
1 CGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATATT
* *** *
10092 TTCAGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCAACTCGTTTGTGTTTTATTT
66 TTCAGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTACAACTCGTTTGCCATTCATTT
* * * *
10157 TAGAAAAAAAGTATCGACACATATTTAA-AGAGTGTCGATACATAATGTAT-ACCTATT-TGCTA
131 TAGAAAAAAAGTATCGACACAAATTAAACAAAGTATCGATACATAATGT-TGACCTATTCT-CTA
*
10219 ATTAA-C
194 ATGAACC
* * *
10225 CGGTATATTTTAACCGGTTACATTGTAAATTTACCTGTTACATAATAATTATCGATTTCGATGTT
1 CGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATATT
* * *
10290 TTGAGGATCGATAC-TTTTTAAAAATGTATCGACACTTTATGCGTACACCTCGTTTGCCATTCAT
66 TTCAGGATCGATACAATTTT--AAATGTATCGACACTTTATGCGTACAACTCGTTTGCCATTCAT
* * * *
10354 TTT-GAAAAAATGTATCGACACAAATTAAACAAAGTATCGATACTTTATGTTGACCTATTCTCTC
129 TTTAGAAAAAAAGTATCGACACAAATTAAACAAAGTATCGATACATAATGTTGACCTATTCTCTA
10418 ATGAACC
194 ATGAACC
* *
10425 CGGTATATTTCT-ACCGGTTACATTGAAAATTTACCTATTACATTATATTTATCGA
1 CGGTATATTT-TAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGA
10480 CACAAAATCT
Statistics
Matches: 216, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
197 4 0.02
198 91 0.42
199 69 0.32
200 51 0.24
201 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (200 bp):
CGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATATT
TTCAGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTACAACTCGTTTGCCATTCATTT
TAGAAAAAAAGTATCGACACAAATTAAACAAAGTATCGATACATAATGTTGACCTATTCTCTAAT
GAACC
Found at i:10503 original size:200 final size:199
Alignment explanation
Indices: 10095--10506 Score: 446
Period size: 199 Copynumber: 2.1 Consensus size: 199
10085 CGATATTTTC
* * *** *
10095 AGGATCGATACAATTTT--AAATGTATCGACACTTTATGCGTGCAACTCGTTTGTGTTTTATTTT
1 AGGATCGATAC-TTTTTAAAAATGTATCGACACTTTATGCGTACAACTCGTTTGCCATTCATTTT
* * * * *
10158 AGAAAAAAAGTATCGACACATATTTAAAGAGTGTCGATACATAATGTATACCTATTTGCTAATTA
65 AGAAAAAAAGTATCGACACAAATTAAAAAAGTATCGATACATAATGTATACCTATTTGCTAATGA
* * ** * *
10223 ACCGGTATATTTTAACCGGTTACATTGTAAATTTACCTGTTACATAATAATTATCGATTTCGATG
130 ACCGGTATATTTTAACCGGTTACATTGAAAATTTACCTATTACATAATAATTATCGATCACAATC
**
10288 TTTTG
195 TAATG
*
10293 AGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTACACCTCGTTTGCCATTCATTTT-
1 AGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTACAACTCGTTTGCCATTCATTTTA
* * * *
10357 GAAAAAATGTATCGACACAAATTAAACAAAGTATCGATACTTTATGT-TGACCTATTCT-CTCAT
66 GAAAAAAAGTATCGACACAAATTAAA-AAAGTATCGATACATAATGTAT-ACCTATT-TGCTAAT
* *
10420 GAACCCGGTATATTTCT-ACCGGTTACATTGAAAATTTACCTATTACATTATATTTATCGA-CAC
128 GAA-CCGGTATATTT-TAACCGGTTACATTGAAAATTTACCTATTACATAATAATTATCGATCAC
10483 AAAATCTAAT-
191 --AATCTAATG
10493 AGTG-TCGATACTTT
1 AG-GATCGATACTTT
10507 ATGTTAACCT
Statistics
Matches: 178, Mismatches: 26, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
197 4 0.02
198 35 0.20
199 70 0.39
200 63 0.35
201 6 0.03
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (199 bp):
AGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTACAACTCGTTTGCCATTCATTTTA
GAAAAAAAGTATCGACACAAATTAAAAAAGTATCGATACATAATGTATACCTATTTGCTAATGAA
CCGGTATATTTTAACCGGTTACATTGAAAATTTACCTATTACATAATAATTATCGATCACAATCT
AATG
Found at i:12170 original size:182 final size:182
Alignment explanation
Indices: 11634--12172 Score: 830
Period size: 182 Copynumber: 3.0 Consensus size: 182
11624 ATTTGTATGG
* * *
11634 TCGACACTTTTTAGGCGCTATAATTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTA
1 TCGACACCTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTA
* * *
11699 ATTTATCGACACTTTCAATATATCCGGTATCTTTTTACCGGTTTTATCATTTCGATACCTCTTTT
66 ATTTATCGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGACACCTGTTTT
* * * *
11764 GTCATATTATTACCGGATATATTACTATGGATCGATACATTTGTATAAAGTA
131 GTCATATTATTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTA
**
11816 TCGACA-CTTTTCAACCGCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATT
1 TCGACACCTTTT-AGGCGCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATT
*
11880 AATTTATCGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTT
65 AATTTATCGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGACACCTGTTT
*
11945 TGTCATATTATTACCTGTTATATTGCTATGGATCGACACATTTTTATAAAGTA
130 TGTCATATTATTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTA
* *
11998 TTGACACCTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGACACTTATATTA
1 TCGACACCTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTA
* ** * *
12063 ATTTATCGACACTTTCAATATATCTGGTAGCGCTTTACCGGTTTTATCATAAT-GACACCGGTTT
66 ATTTATCGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCAT-TTCGACACCTGTTT
* * *
12127 TATCATATTTTTACATGTTATATTGCTATGGATCGATACATTTTTA
130 TGTCATATTATTACCTGTTATATTGCTATGGATCGATACATTTTTA
12173 ATTTGTATCA
Statistics
Matches: 327, Mismatches: 27, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
181 4 0.01
182 317 0.97
183 6 0.02
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (182 bp):
TCGACACCTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTA
ATTTATCGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGACACCTGTTTT
GTCATATTATTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTA
Found at i:15119 original size:16 final size:16
Alignment explanation
Indices: 15047--15129 Score: 62
Period size: 16 Copynumber: 5.0 Consensus size: 16
15037 AATGATTATT
*
15047 TTATAACTTTTAATAA
1 TTATAAATTTTAATAA
15063 TTA-AAATTTTTAATAA
1 TTATAAA-TTTTAATAA
** *
15079 TT-TATAATTAAAAATTATC
1 TTATA-AATT-TTAA-TA-A
15098 TTATAAATTTTAATAA
1 TTATAAATTTTAATAA
*
15114 TTATAAAATTTAATAA
1 TTATAAATTTTAATAA
15130 AATAATATCT
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
15 2 0.04
16 32 0.62
17 6 0.12
18 4 0.08
19 6 0.12
20 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATAAATTTTAATAA
Found at i:15606 original size:23 final size:23
Alignment explanation
Indices: 15580--15627 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
15570 ATAAAGTACA
*
15580 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
15603 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
15626 AT
1 AT
15628 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:16029 original size:21 final size:22
Alignment explanation
Indices: 16004--16055 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
15994 ACACTTTACA
*
16004 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
16027 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
16050 ATATAA
1 ATATAA
16056 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:16040 original size:23 final size:23
Alignment explanation
Indices: 16014--16076 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
16004 ATATAACCAC
16014 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
16037 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
16060 TACCTATTACATCATAT
1 TACCTATTACATTATAT
16077 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:16530 original size:39 final size:39
Alignment explanation
Indices: 16476--16601 Score: 234
Period size: 39 Copynumber: 3.2 Consensus size: 39
16466 TCAAGTTGTA
16476 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
16515 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
* *
16554 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
16593 GATTTTGAT
1 GATTTTGAT
16602 GAGCATCGGA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 85 1.00
ACGTcount: A:0.17, C:0.13, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
Found at i:17147 original size:25 final size:25
Alignment explanation
Indices: 17119--17169 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
17109 TTAATCCAAA
*
17119 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
17144 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
17169 T
1 T
17170 GATTGTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:17459 original size:21 final size:22
Alignment explanation
Indices: 17434--17485 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
17424 ACACTTTACA
*
17434 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
17457 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
17480 ATATAA
1 ATATAA
17486 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:17470 original size:23 final size:23
Alignment explanation
Indices: 17444--17506 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
17434 ATATAACCAC
17444 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
17467 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
17490 TACCTATTACATCATAT
1 TACCTATTACATTATAT
17507 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:17904 original size:23 final size:23
Alignment explanation
Indices: 17874--17936 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
17864 AATATACCAC
17874 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
17897 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
17920 TACCTATTACATCATAT
1 TACCTATTACATTATAT
17937 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:18067 original size:430 final size:431
Alignment explanation
Indices: 17203--18462 Score: 2374
Period size: 430 Copynumber: 2.9 Consensus size: 431
17193 GAATTATTTG
*
17203 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATA-TTTATAAAATAAT-ATTA
1 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATAATAATTA
17266 GAATTTTTAATTTAATAATAATATATACCGTAACGT-AAAAATAAATCATTAGACGCCTATAATT
66 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
17330 ACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAA
131 ACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAA
*
17395 AAGTATGGACACTTTTATAAAAAGGATATACACTTTACAATATAACCACTACCTATTACATTATA
196 AAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATA
17460 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
261 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
17525 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
326 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
*
17590 ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTG
391 ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTA
*
17631 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTAATTA
1 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATAATAATTA
17696 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
66 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
17761 ACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAA
131 ACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAA
17826 AAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATAT-ACCACTACCTATTACATTATA
196 AAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATA
17890 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
261 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
17955 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
326 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
18020 ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTA
391 ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTA
* *
18061 ATTTAATAATTTAATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATAATATTTA
1 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATAATAATTA
* *
18126 GAATTTTTAATTTAATAATAATATATATCGTAACGTAAGAAATAAATCATTAGACGCCTATAATT
66 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
*
18191 ACTAAATTAATATCTTAAAACTCACTCAAAGGATAACCTTAAATTAATGTTTTCCACAGTG-AAA
131 ACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAA
18255 AAGTATGGACACTTTTAT-AAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATA
196 AAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATA
*
18319 TAAACGATACCTATTACATTATATAAGGGGTACCTATTACATCATATGTTTACCTATTATATTGA
261 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
18384 AAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAACTTATGTAATTTATGTTTCA
326 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
18448 A-TTTTTTAACAGTGT
391 ATTTTTTTAACAGTGT
18463 ACTGCGAATT
Statistics
Matches: 817, Mismatches: 11, Indels: 9
0.98 0.01 0.01
Matches are distributed among these distances:
427 14 0.02
428 100 0.12
429 152 0.19
430 416 0.51
431 135 0.17
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (431 bp):
ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATAATAATTA
GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
ACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAA
AAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATA
TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTA
Found at i:18313 original size:21 final size:20
Alignment explanation
Indices: 18288--18341 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
18278 GATAGACACT
18288 TTACAATATAACCACTACCTA
1 TTACAATATAACCA-TACCTA
*
18309 TTACATTATATAAACGATACCTA
1 TTACA--ATAT-AACCATACCTA
*
18332 TTACATTATA
1 TTACAATATA
18342 TAAGGGGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
23 15 0.54
24 4 0.14
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (20 bp):
TTACAATATAACCATACCTA
Found at i:18329 original size:23 final size:23
Alignment explanation
Indices: 18303--18365 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
18293 ATATAACCAC
18303 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
18326 TACCTATTACATTATATAAGGGG
1 TACCTATTACATTATATAAACGA
*
18349 TACCTATTACATCATAT
1 TACCTATTACATTATAT
18366 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:21521 original size:22 final size:23
Alignment explanation
Indices: 21490--21532 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
21480 TTCCACAGTG
21490 AAAAAAGTATCGACAC-TTTTAT
1 AAAAAAGTATCGACACATTTTAT
*
21512 AAAAAGGTATCGACACATTTT
1 AAAAAAGTATCGACACATTTT
21533 TATACCGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (23 bp):
AAAAAAGTATCGACACATTTTAT
Found at i:21836 original size:183 final size:183
Alignment explanation
Indices: 21528--22222 Score: 1241
Period size: 183 Copynumber: 3.8 Consensus size: 183
21518 GTATCGACAC
21528 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
21593 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
21658 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
21711 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
21776 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
21841 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
*
21894 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
* *
21959 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCTAATCTGGACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
*
22024 AATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
* *
22077 ATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTTTTTT
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATG---TGT
* * * * *
22142 CAA--TCGACACTTTTTTAAATGGTATCGACACATTTTTCTTTCATTCTGGACATAAAGTACAGA
63 AAATGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGA
*
22205 CACAATATTAAAAAGTGT
128 CACAATATTAGAAAGTGT
22223 GAAAACTTTG
Statistics
Matches: 496, Mismatches: 13, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
183 419 0.84
184 73 0.15
186 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (183 bp):
ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
Found at i:23430 original size:3 final size:3
Alignment explanation
Indices: 23422--23493 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
23412 ACTTGTTTGG
* * * **
23422 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
23470 AGC TTC ATC GTC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC
23494 TGTTAAAAGA
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.25, C:0.35, G:0.06, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:25605 original size:198 final size:198
Alignment explanation
Indices: 24926--26094 Score: 2234
Period size: 198 Copynumber: 5.9 Consensus size: 198
24916 TATTTAAATT
24926 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
*
24991 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTGGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
25056 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTCCATTCATTCTGGGA
25121 AAAA
195 AAAA
25125 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
25190 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
*
25255 ATCGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTTATTCTGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
25318 AAA
196 AAA
25321 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
25386 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
*
25451 ATCGACTCTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
25516 AAA
196 AAA
*
25519 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTG
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
25584 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
25649 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
25714 AAA
196 AAA
25717 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
25782 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
25847 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTCCATTCATTCTGGGA
25912 AAAA
195 AAAA
*
25916 AGTATCGACACAAACTATATTAGTGTCAACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
25981 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
* *
26046 ATTGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
131 ATCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
26095 GGCCATATTG
Statistics
Matches: 956, Mismatches: 10, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
196 158 0.17
197 36 0.04
198 428 0.45
199 297 0.31
200 37 0.04
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (198 bp):
AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
AAA
Found at i:26259 original size:19 final size:19
Alignment explanation
Indices: 26213--26261 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
26203 TTATATTCAC
*
26213 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
26232 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
26251 ATACAAAATTA
1 ATACAAAATTA
26262 ACTCGACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:28089 original size:33 final size:33
Alignment explanation
Indices: 28052--28117 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
28042 CATCTTAATA
*
28052 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
28085 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
28118 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:28191 original size:21 final size:21
Alignment explanation
Indices: 28151--28215 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
28141 CCCCTTATTC
* *
28151 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
28172 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
28193 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
28214 CT
1 CT
28216 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:30503 original size:20 final size:19
Alignment explanation
Indices: 30447--30494 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 19
30437 ATCCGGTATC
30447 ATTTTACCGGTTTTATCAT
1 ATTTTACCGGTTTTATCAT
30466 ATTGTTACCGGTTTTATCAT
1 ATT-TTACCGGTTTTATCAT
30486 AATTTTACC
1 -ATTTTACC
30495 TGTTATATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.11
20 21 0.78
21 3 0.11
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (19 bp):
ATTTTACCGGTTTTATCAT
Found at i:30641 original size:20 final size:20
Alignment explanation
Indices: 30615--30660 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
30605 CACTTTTAAA
30615 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
30634 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
30655 TTTACC
1 TTTACC
30661 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:31547 original size:28 final size:25
Alignment explanation
Indices: 31491--31552 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
31481 ATGAAATAAA
31491 AAAAATAAATATTAGATGTAATTTT
1 AAAAATAAATATTAGATGTAATTTT
*
31516 -AAAATAAATAATTATATGTATGATTTT
1 AAAAATAAAT-ATTAGATGTA--ATTTT
31543 GAAAAATAAA
1 -AAAAATAAA
31553 ACACGGATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 9 0.29
25 9 0.29
27 5 0.16
29 8 0.26
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (25 bp):
AAAAATAAATATTAGATGTAATTTT
Found at i:33327 original size:31 final size:31
Alignment explanation
Indices: 33257--33327 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
33247 TATGTGAATG
*
33257 AAAATTTTATTAATTTGATTATTAAAATTAA
1 AAAATTTTATTAATTTAATTATTAAAATTAA
*
33288 AAATATTTT-TTAATTTTAATTATTTAAA-TAA
1 AAA-ATTTTATTAA-TTTAATTATTAAAATTAA
33319 TAAAATTTT
1 -AAAATTTT
33328 CAAATAGGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 15 0.43
32 20 0.57
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (31 bp):
AAAATTTTATTAATTTAATTATTAAAATTAA
Found at i:40758 original size:16 final size:16
Alignment explanation
Indices: 40737--40779 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
40727 CGTTTAGTTC
*
40737 TTATTAATGTAATATA
1 TTATTAATATAATATA
40753 TTATTAATATAATATA
1 TTATTAATATAATATA
40769 TTATTAA-ATAA
1 TTATTAATATAA
40780 AATAAATATG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TTATTAATATAATATA
Found at i:48132 original size:140 final size:144
Alignment explanation
Indices: 47957--48240 Score: 483
Period size: 144 Copynumber: 2.0 Consensus size: 144
47947 AATAAATACT
47957 TTGTCGTAGGAAAATAAATTCATTTGTTAATCAGTGATTTTACG-AATAATGTC-TTTTCGTGAA
1 TTGTCGTAGGAAAATAAATTCATTTGTTAATCAGTGATTTTACGAAATAATGTCTTTTTCGTGAA
48020 ATCTTTTCATAAC-AT-ATA-ATATATGTTATTTTCATGCATAAATACTGAT-AAAACTAAAACT
66 ATCTTTTCATAACTATAATATA-ATATGTTATTTTCATGCATAAATACTGATAAAAACT-AAACT
48081 AAGTAAAATAAACTAAA
129 AAGTAAAAT-AACTAAA
*
48098 TTGTTGTAGGAAAATAAATTCA-TTGTTAATCAGTGATTTTACGAAATAATGTCTTTTTCGTGAA
1 TTGTCGTAGGAAAATAAATTCATTTGTTAATCAGTGATTTTACGAAATAATGTCTTTTTCGTGAA
48162 ATCTTTTCATAACTATAATATAATATGTTATTTTCATGCATAAATACTGATAAAAACTAAACTAA
66 ATCTTTTCATAACTATAATATAATATGTTATTTTCATGCATAAATACTGATAAAAACTAAACTAA
48227 GTAAAATAACTAAA
131 GTAAAATAACTAAA
48241 ATAGTTATAG
Statistics
Matches: 136, Mismatches: 1, Indels: 10
0.93 0.01 0.07
Matches are distributed among these distances:
140 21 0.15
141 30 0.22
142 23 0.17
143 9 0.07
144 46 0.34
145 7 0.05
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (144 bp):
TTGTCGTAGGAAAATAAATTCATTTGTTAATCAGTGATTTTACGAAATAATGTCTTTTTCGTGAA
ATCTTTTCATAACTATAATATAATATGTTATTTTCATGCATAAATACTGATAAAAACTAAACTAA
GTAAAATAACTAAA
Done.