Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009038.1 Kokia drynarioides strain JFW-HI SEQ_123736, 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: 69074
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:1430 original size:20 final size:20
Alignment explanation
Indices: 1405--1449 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
1395 TAATAATATA
1405 AAAATATCATATTTTATGTG
1 AAAATATCATATTTTATGTG
1425 AAAATATCATATTTTATGTG
1 AAAATATCATATTTTATGTG
1445 AAAAT
1 AAAAT
1450 TAATAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.42
Consensus pattern (20 bp):
AAAATATCATATTTTATGTG
Found at i:2912 original size:18 final size:18
Alignment explanation
Indices: 2889--2924 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2879 GGGAACCAAG
*
2889 GTTCAGAATCAGTTCTTA
1 GTTCAGAAACAGTTCTTA
2907 GTTCAGAAACAGTTCTTA
1 GTTCAGAAACAGTTCTTA
2925 AGTGGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (18 bp):
GTTCAGAAACAGTTCTTA
Found at i:4241 original size:20 final size:20
Alignment explanation
Indices: 4216--4255 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
4206 TCAATTAATG
4216 ATGACATGGTATCTTGATCA
1 ATGACATGGTATCTTGATCA
*
4236 ATGACATGGTATGTTGATCA
1 ATGACATGGTATCTTGATCA
4256 TGCATAGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (20 bp):
ATGACATGGTATCTTGATCA
Found at i:4364 original size:21 final size:22
Alignment explanation
Indices: 4333--4374 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
4323 GATCAGTAAA
4333 AAAATATTTAAAATTTATTTAG
1 AAAATATTTAAAATTTATTTAG
*
4355 AAAAT-TTTAAATTTTATTTA
1 AAAATATTTAAAATTTATTTA
4375 AATGTGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
AAAATATTTAAAATTTATTTAG
Found at i:4438 original size:19 final size:18
Alignment explanation
Indices: 4414--4464 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
4404 AAAAGTTGTA
*
4414 AAAATTATAATAATTATTT
1 AAAATTATAATAAATA-TT
4433 AAAATTATAA-AAATATT
1 AAAATTATAATAAATATT
*
4450 AAATATTATTATAAA
1 AAA-ATTATAATAAA
4465 GAGCATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 5 0.18
18 10 0.36
19 13 0.46
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATTATAATAAATATT
Found at i:4458 original size:37 final size:37
Alignment explanation
Indices: 4370--4463 Score: 93
Period size: 37 Copynumber: 2.5 Consensus size: 37
4360 TTTAAATTTT
* *
4370 ATTTAAATGTGTATAAAAATTATTTTAAAATATTAAAA
1 ATTTAAATAT-TATAATAATTATTTTAAAATATTAAAA
* *
4408 GTTGTAAAAATTATAATAATTA-TTTAAAAT-TATAAAA
1 ATT-TAAATATTATAATAATTATTTTAAAATAT-TAAAA
*
4445 ATATTAAATATTATTATAA
1 AT-TTAAATATTATAATAA
4464 AGAGCATAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
36 1 0.02
37 27 0.59
38 13 0.28
39 5 0.11
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (37 bp):
ATTTAAATATTATAATAATTATTTTAAAATATTAAAA
Found at i:4459 original size:10 final size:9
Alignment explanation
Indices: 4394--4460 Score: 50
Period size: 10 Copynumber: 7.3 Consensus size: 9
4384 AAAAATTATT
4394 TTAAAA-TA
1 TTAAAATTA
*
4402 TTAAAAGTTG
1 TTAAAA-TTA
*
4412 TAAAAATTA
1 TTAAAATTA
4421 -TAATAATTA
1 TTAA-AATTA
4430 TTTAAAATTA
1 -TTAAAATTA
*
4440 -TAAAAATA
1 TTAAAATTA
4448 TTAAATATTA
1 TTAAA-ATTA
4458 TTA
1 TTA
4461 TAAAGAGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
8 15 0.33
9 11 0.24
10 17 0.37
11 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (9 bp):
TTAAAATTA
Found at i:4586 original size:20 final size:20
Alignment explanation
Indices: 4558--4611 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
4548 ATTACTATAA
4558 TTTTT-ACAATTTTAAATAT
1 TTTTTAACAATTTTAAATAT
**
4577 TTTTTAACAATTTTTTATAT
1 TTTTTAACAATTTTAAATAT
* *
4597 TTTTAAAAAATTTTA
1 TTTTTAACAATTTTA
4612 CAACTCTCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 5 0.17
20 24 0.83
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTAACAATTTTAAATAT
Found at i:5868 original size:28 final size:28
Alignment explanation
Indices: 5815--5868 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
5805 ACTTAACTAG
* **
5815 AAAAAAAACTCAAGTGTCAATTTGAAAA
1 AAAAAAAACTCAAGTATCAAAGTGAAAA
*
5843 AAAAAAAACTTAAGTATCAAAGTGAA
1 AAAAAAAACTCAAGTATCAAAGTGAA
5869 TATTAAAACC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.59, C:0.09, G:0.11, T:0.20
Consensus pattern (28 bp):
AAAAAAAACTCAAGTATCAAAGTGAAAA
Found at i:6279 original size:23 final size:23
Alignment explanation
Indices: 6249--6292 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
6239 TTATCATTCA
*
6249 TTTTTTTTTCGGTTTTACTTTCT
1 TTTTTTTTTAGGTTTTACTTTCT
*
6272 TTTTTTTTTAGTTTTTACTTT
1 TTTTTTTTTAGGTTTTACTTT
6293 TAAAAGTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.77
Consensus pattern (23 bp):
TTTTTTTTTAGGTTTTACTTTCT
Found at i:12744 original size:2 final size:2
Alignment explanation
Indices: 12737--12761 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12727 GCAAGTACTT
12737 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
12762 TTGTTTATTC
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:14302 original size:79 final size:77
Alignment explanation
Indices: 14067--14367 Score: 409
Period size: 75 Copynumber: 4.0 Consensus size: 77
14057 ATAAAAGGTG
* *
14067 AAGAGTTAAGGAAGATAAAAGGTGAAAAAGATTAATTATAATGA-A-CA-TCAACTTAATAATAT
1 AAGAGTTAAGGAAGATGAAAGGTGAAAAAGATTAATTATAATGACATCATTC-ACTTAATAGTAT
* *
14129 TCATAATACTGTG
65 TCATAACACTGTA
* * *
14142 AAGAGTTAAGAAAGATGAAAAGTGAAAAAGATTAATTATAAT-A-AGCATTCACTTAATAGTATT
1 AAGAGTTAAGGAAGATGAAAGGTGAAAAAGATTAATTATAATGACATCATTCACTTAATAGTATT
* *
14205 CGTAAAACTGTA
66 CATAACACTGTA
14217 AAGAGTTAAGGAAGATGAAAGGTGAAAAAGATTAATTATAATGAACATTCATTCACTTAATAGTA
1 AAGAGTTAAGGAAGATGAAAGGTGAAAAAGATTAATTATAATG-ACA-TCATTCACTTAATAGTA
*
14282 TTCGTAACACTGTA
64 TTCATAACACTGTA
* * *
14296 AAGAGTTAAGGAAGATGAAAGGTGAAAAAAATTAATTATAATG-CA-CATCCACTTATTAGTATT
1 AAGAGTTAAGGAAGATGAAAGGTGAAAAAGATTAATTATAATGACATCATTCACTTAATAGTATT
14359 CATAACACT
66 CATAACACT
14368 CCCCCTTGAA
Statistics
Matches: 205, Mismatches: 15, Indels: 12
0.88 0.06 0.05
Matches are distributed among these distances:
74 2 0.01
75 126 0.61
76 2 0.01
77 3 0.01
78 1 0.00
79 71 0.35
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.28
Consensus pattern (77 bp):
AAGAGTTAAGGAAGATGAAAGGTGAAAAAGATTAATTATAATGACATCATTCACTTAATAGTATT
CATAACACTGTA
Found at i:14349 original size:154 final size:150
Alignment explanation
Indices: 14067--14359 Score: 435
Period size: 154 Copynumber: 1.9 Consensus size: 150
14057 ATAAAAGGTG
14067 AAGAGTTAAGGAAGATAAAAGGTGAAAAAGATTAATTATAATGAACATCAACTTAATAATATTCA
1 AAGAGTTAAGGAAGATAAAAGGTGAAAAAGATTAATTATAATGAACATCAACTTAATAATATTCA
* * * *
14132 TAATACTGTGAAGAGTTAAGAAAGATGAAAAGTGAAAAAGATTAATTATAATAAGCATTCACTTA
66 TAACACTGTAAAGAGTTAAGAAAGATGAAAAGTGAAAAAAATTAATTATAATAAGCATCCACTTA
14197 ATAGTATTCGTAAAACTGTA
131 ATAGTATTCGTAAAACTGTA
* *
14217 AAGAGTTAAGGAAGATGAAAGGTGAAAAAGATTAATTATAATGAACATTCATTCACTTAATAGTA
1 AAGAGTTAAGGAAGATAAAAGGTGAAAAAGATTAATTATAATGAACA-TCA---ACTTAATAATA
* * * *
14282 TTCGTAACACTGTAAAGAGTTAAGGAAGATGAAAGGTGAAAAAAATTAATTATAATGCA-CATCC
62 TTCATAACACTGTAAAGAGTTAAGAAAGATGAAAAGTGAAAAAAATTAATTATAAT-AAGCATCC
*
14346 ACTTATTAGTATTC
126 ACTTAATAGTATTC
14360 ATAACACTCC
Statistics
Matches: 127, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
150 46 0.36
151 3 0.02
154 77 0.61
155 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.28
Consensus pattern (150 bp):
AAGAGTTAAGGAAGATAAAAGGTGAAAAAGATTAATTATAATGAACATCAACTTAATAATATTCA
TAACACTGTAAAGAGTTAAGAAAGATGAAAAGTGAAAAAAATTAATTATAATAAGCATCCACTTA
ATAGTATTCGTAAAACTGTA
Found at i:16302 original size:18 final size:18
Alignment explanation
Indices: 16275--16309 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16265 ATTTTCCAAC
* *
16275 AAAAAGTAAAAAGTTAAA
1 AAAAAATAAAAAATTAAA
16293 AAAAAATAAAAAATTAA
1 AAAAAATAAAAAATTAA
16310 TTATAATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (18 bp):
AAAAAATAAAAAATTAAA
Found at i:17314 original size:16 final size:16
Alignment explanation
Indices: 17293--17330 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
17283 TTTGGTTCGC
17293 TATAATAAAATAGAGT
1 TATAATAAAATAGAGT
* *
17309 TATAATATAATAGGGT
1 TATAATAAAATAGAGT
17325 TATAAT
1 TATAAT
17331 CAATATTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (16 bp):
TATAATAAAATAGAGT
Found at i:17564 original size:56 final size:57
Alignment explanation
Indices: 17497--17647 Score: 191
Period size: 56 Copynumber: 2.6 Consensus size: 57
17487 TTATTAAATT
* * * *
17497 TTAATAAAATTATTATTAAATATAATTTAATAAAAAATAAATATTTTAATCATATT-
1 TTAATATAATTATTATTAAATATAATTTAATAAAAAATAAATAATTTAATAACATTC
* *
17553 TTAACT-TAATTATTATTAAATATAATTTAATAAAATAGTATATAATTTAATAACATTC
1 TTAA-TATAATTATTATTAAATATAATTTAATAAAA-AATAAATAATTTAATAACATTC
17611 TTAATATAATTATTATTAAAATATGAA-TTAATAAAAA
1 TTAATATAATTATTATT-AAATAT-AATTTAATAAAAA
17648 TCATATTATA
Statistics
Matches: 83, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
56 32 0.39
57 18 0.22
58 16 0.19
59 15 0.18
60 2 0.02
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (57 bp):
TTAATATAATTATTATTAAATATAATTTAATAAAAAATAAATAATTTAATAACATTC
Found at i:20356 original size:11 final size:11
Alignment explanation
Indices: 20340--20372 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
20330 AGTATTGAGG
20340 GAAAAATAATT
1 GAAAAATAATT
*
20351 GAAAAATAATG
1 GAAAAATAATT
20362 GAAAAATAATT
1 GAAAAATAATT
20373 TTGTGAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (11 bp):
GAAAAATAATT
Found at i:31294 original size:24 final size:24
Alignment explanation
Indices: 31266--31313 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
31256 TTATTAAACC
*
31266 AATAATTAAAT-TAAAAATAATAAA
1 AATAACTAAATATAAAAAT-ATAAA
*
31290 AATAACTAAATATAATAATATAAA
1 AATAACTAAATATAAAAATATAAA
31314 TGAGCTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (24 bp):
AATAACTAAATATAAAAATATAAA
Found at i:32769 original size:2 final size:2
Alignment explanation
Indices: 32764--32788 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32754 GGTGATAATA
32764 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
32789 ATTAATCCAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33042 original size:11 final size:11
Alignment explanation
Indices: 33026--33050 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33016 AATATTTACC
33026 AAAAAGAAAAA
1 AAAAAGAAAAA
33037 AAAAAGAAAAA
1 AAAAAGAAAAA
33048 AAA
1 AAA
33051 GAAAAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:42281 original size:44 final size:44
Alignment explanation
Indices: 42233--42316 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
42223 TTGCTTGGTG
* *
42233 TATTGCTAGTTCCTGGTTTGGTCATTGTTGTTTAGTTGTGCAGC
1 TATTGCTAGTTCCTGGTTTGGTCATTGCTATTTAGTTGTGCAGC
* *
42277 TATTGCTGGTTTCTGGTTTGGTCATTGCTATTTAGTTGTG
1 TATTGCTAGTTCCTGGTTTGGTCATTGCTATTTAGTTGTG
42317 AAGCGAGGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.11, C:0.12, G:0.27, T:0.50
Consensus pattern (44 bp):
TATTGCTAGTTCCTGGTTTGGTCATTGCTATTTAGTTGTGCAGC
Found at i:42522 original size:94 final size:94
Alignment explanation
Indices: 42361--42547 Score: 374
Period size: 94 Copynumber: 2.0 Consensus size: 94
42351 ATTGAAGTCG
42361 CAATTCAGATGTCTTCTATTTTGATTTAAAAGGCGCGGTCTCCTTTGATTATTGAGTTTGATTTG
1 CAATTCAGATGTCTTCTATTTTGATTTAAAAGGCGCGGTCTCCTTTGATTATTGAGTTTGATTTG
42426 GTTACGGTATCGAATCGATTTAAGTATAA
66 GTTACGGTATCGAATCGATTTAAGTATAA
42455 CAATTCAGATGTCTTCTATTTTGATTTAAAAGGCGCGGTCTCCTTTGATTATTGAGTTTGATTTG
1 CAATTCAGATGTCTTCTATTTTGATTTAAAAGGCGCGGTCTCCTTTGATTATTGAGTTTGATTTG
42520 GTTACGGTATCGAATCGATTTAAGTATA
66 GTTACGGTATCGAATCGATTTAAGTATA
42548 GAAGTCTCGG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (94 bp):
CAATTCAGATGTCTTCTATTTTGATTTAAAAGGCGCGGTCTCCTTTGATTATTGAGTTTGATTTG
GTTACGGTATCGAATCGATTTAAGTATAA
Found at i:60351 original size:30 final size:32
Alignment explanation
Indices: 60309--60372 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 32
60299 AGTATTCAAT
*
60309 TTGACACTTTTTTTTAATTTGGTAC-TTAAAC
1 TTGACACTTTTTTTTAAGTTGGTACTTTAAAC
60340 TTGACA-TTTTTTTTAAGTTGGTACTTTAAAC
1 TTGACACTTTTTTTTAAGTTGGTACTTTAAAC
60371 TT
1 TT
60373 TTTTTTGATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.53
Consensus pattern (32 bp):
TTGACACTTTTTTTTAAGTTGGTACTTTAAAC
Found at i:60596 original size:28 final size:28
Alignment explanation
Indices: 60554--60607 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
60544 TTTTAATAAT
* *
60554 ATTTAATAAATTTAGGTACCAAATTAAA
1 ATTTAAAAAACTTAGGTACCAAATTAAA
*
60582 ATTTAAAAAACTTAGGTACTAAATTA
1 ATTTAAAAAACTTAGGTACCAAATTA
60608 GGAAAAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.35
Consensus pattern (28 bp):
ATTTAAAAAACTTAGGTACCAAATTAAA
Found at i:60692 original size:59 final size:60
Alignment explanation
Indices: 60561--60696 Score: 168
Period size: 61 Copynumber: 2.3 Consensus size: 60
60551 AATATTTAAT
* *
60561 AAATTTAGGTACCAAATTAAAATTTAAAAAACTTAGGTACTAAATTAGGAAAAAAAGTGCC
1 AAATTTAGGTACCAAATTAAAATTCAAAAAACTTAGGTACCAAATTAGG-AAAAAAGTGCC
* ** * *
60622 AAATTCAGGTACCAAATT-GGATTCAAAAAAGTTCAGGTACCAAATTAGG-AAAAAGTGTC
1 AAATTTAGGTACCAAATTAAAATTCAAAAAACTT-AGGTACCAAATTAGGAAAAAAGTGCC
*
60681 AAGTTTAGGTACCAAA
1 AAATTTAGGTACCAAA
60697 GTGGGTAAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 23 0.35
60 11 0.17
61 31 0.48
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (60 bp):
AAATTTAGGTACCAAATTAAAATTCAAAAAACTTAGGTACCAAATTAGGAAAAAAGTGCC
Found at i:60709 original size:59 final size:59
Alignment explanation
Indices: 60586--60726 Score: 158
Period size: 59 Copynumber: 2.4 Consensus size: 59
60576 ATTAAAATTT
* * * **
60586 AAAAAACTTAGGTACTAAATTAGGAAAAAAAGTGCCAAATTCAGGTACCAAATTGGATTC
1 AAAAAAATTAGGTACCAAATTAGG-AAAAAAGTGCCAAATTCAGGTACCAAAGTGGATAA
* * * * *
60646 AAAAAAGTTCAGGTACCAAATTAGG-AAAAAGTGTCAAGTTTAGGTACCAAAGTGGGTAA
1 AAAAAAATT-AGGTACCAAATTAGGAAAAAAGTGCCAAATTCAGGTACCAAAGTGGATAA
*
60705 AAAAAAAATAGGTACCAAATTA
1 AAAAAAATTAGGTACCAAATTA
60727 AAAAATATAT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
58 13 0.19
59 34 0.49
60 8 0.12
61 14 0.20
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.22
Consensus pattern (59 bp):
AAAAAAATTAGGTACCAAATTAGGAAAAAAGTGCCAAATTCAGGTACCAAAGTGGATAA
Found at i:64201 original size:39 final size:39
Alignment explanation
Indices: 64132--64209 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
64122 CAGTATTGTT
* *
64132 TTACGATATTTACAGTGTTACCGTCAATTCAATATTGCA
1 TTACGATATTTACAATGTTACCATCAATTCAATATTGCA
* * * *
64171 TTACGGTATTTACAATGTTACTATCGATTCAGTATTGCA
1 TTACGATATTTACAATGTTACCATCAATTCAATATTGCA
64210 GTGTTTACAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (39 bp):
TTACGATATTTACAATGTTACCATCAATTCAATATTGCA
Done.