Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015282.1 Kokia drynarioides strain JFW-HI SEQ_130327, 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: 423680
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 323 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:349131 original size:29 final size:29
Alignment explanation
Indices: 349095--349164 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
349085 AACCCAAATC
* *
349095 TAAACCTTAAATCATAAACCCCTAATCCT
1 TAAACCTTAAACCATAAACCCATAATCCT
* *
349124 TAAACCTTAAACCATAAACTCATAGTCCT
1 TAAACCTTAAACCATAAACCCATAATCCT
*
349153 TAAACTTTAAAC
1 TAAACCTTAAAC
349165 ATTTAGTCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.43, C:0.27, G:0.01, T:0.29
Consensus pattern (29 bp):
TAAACCTTAAACCATAAACCCATAATCCT
Found at i:351401 original size:18 final size:17
Alignment explanation
Indices: 351378--351411 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
351368 AATAAATTTG
351378 TAATTAAATAAATTTAAT
1 TAATTAAA-AAATTTAAT
351396 TAATTAAAAAATTTAA
1 TAATTAAAAAATTTAA
351412 ACTCTAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATTAAAAAATTTAAT
Found at i:353021 original size:31 final size:31
Alignment explanation
Indices: 352986--353094 Score: 78
Period size: 31 Copynumber: 3.2 Consensus size: 31
352976 ATTCATTCTT
352986 TTTATTAGATACAAATAATTTATAAATCTAG
1 TTTATTAGATACAAATAATTTATAAATCTAG
** *
353017 TTTATTATTTTGATTTAAATTTAAATATTA-AATGATTCT-T
1 TTTATTA----GATACAAA--T-AAT-TTATAA--A-TCTAG
353057 TTTATTAGATACAAATAATTTATAAATCTAG
1 TTTATTAGATACAAATAATTTATAAATCTAG
353088 TTTATTA
1 TTTATTA
353095 TTTTGATTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 26
0.65 0.07 0.29
Matches are distributed among these distances:
30 3 0.05
31 15 0.25
32 3 0.05
33 5 0.08
34 1 0.02
35 6 0.10
36 6 0.10
37 1 0.02
38 5 0.08
39 3 0.05
40 8 0.14
41 3 0.05
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.50
Consensus pattern (31 bp):
TTTATTAGATACAAATAATTTATAAATCTAG
Found at i:353096 original size:71 final size:71
Alignment explanation
Indices: 352980--353124 Score: 290
Period size: 71 Copynumber: 2.0 Consensus size: 71
352970 TCGACAATTC
352980 ATTCTTTTTATTAGATACAAATAATTTATAAATCTAGTTTATTATTTTGATTTAAATTTAAATAT
1 ATTCTTTTTATTAGATACAAATAATTTATAAATCTAGTTTATTATTTTGATTTAAATTTAAATAT
353045 TAAATG
66 TAAATG
353051 ATTCTTTTTATTAGATACAAATAATTTATAAATCTAGTTTATTATTTTGATTTAAATTTAAATAT
1 ATTCTTTTTATTAGATACAAATAATTTATAAATCTAGTTTATTATTTTGATTTAAATTTAAATAT
353116 TAAATG
66 TAAATG
353122 ATT
1 ATT
353125 AAGTATTAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (71 bp):
ATTCTTTTTATTAGATACAAATAATTTATAAATCTAGTTTATTATTTTGATTTAAATTTAAATAT
TAAATG
Found at i:356568 original size:28 final size:28
Alignment explanation
Indices: 356536--356608 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
356526 ATGCTTTAAT
356536 ATATTATTGAAAAGGTATATCCGAAAGG
1 ATATTATTGAAAAGGTATATCCGAAAGG
*
356564 ATATTATTAAAAAGGTATATCCGAAAGG
1 ATATTATTGAAAAGGTATATCCGAAAGG
* *
356592 ATAATAAATGAAAAGGT
1 AT-ATTATTGAAAAGGT
356609 TAAAAAGGAC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 29 0.73
29 11 0.28
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.27
Consensus pattern (28 bp):
ATATTATTGAAAAGGTATATCCGAAAGG
Found at i:360636 original size:14 final size:14
Alignment explanation
Indices: 360619--360648 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
360609 GTGTGTTTGT
360619 GAGAGAGAGGGAGC
1 GAGAGAGAGGGAGC
*
360633 GAGAGGGAGGGAGC
1 GAGAGAGAGGGAGC
360647 GA
1 GA
360649 ACCTGCTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.60, T:0.00
Consensus pattern (14 bp):
GAGAGAGAGGGAGC
Found at i:366803 original size:11 final size:11
Alignment explanation
Indices: 366787--366825 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
366777 AAGAGGAGGA
366787 TTTTTTTTTTC
1 TTTTTTTTTTC
*
366798 TTTTTTTTTAC
1 TTTTTTTTTTC
*
366809 TTTTTTATTTTA
1 TTTTTT-TTTTC
366821 TTTTT
1 TTTTT
366826 CCGCATAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.08, C:0.05, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:372946 original size:18 final size:18
Alignment explanation
Indices: 372925--372959 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
372915 ACTTTACTAA
* *
372925 TCAAGTGATGCCTTCAAC
1 TCAAATGATGCCCTCAAC
372943 TCAAATGATGCCCTCAA
1 TCAAATGATGCCCTCAA
372960 ATTCTGTGAG
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:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (18 bp):
TCAAATGATGCCCTCAAC
Found at i:378421 original size:22 final size:22
Alignment explanation
Indices: 378353--378411 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
378343 ATGCTAGCGA
*
378353 GCTTACTGATCAGCACTGTGTGT
1 GCTT-CTGTTCAGCACTGTGTGT
378376 GCTTCTGTTCAGCACTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
* *
378398 GCTTTTGTTTAGCA
1 GCTTCTGTTCAGCA
378412 TGTTTTGTGC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.41
Consensus pattern (22 bp):
GCTTCTGTTCAGCACTGTGTGT
Found at i:378476 original size:41 final size:41
Alignment explanation
Indices: 378417--378494 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
378407 TAGCATGTTT
*
378417 TGTGCCCTTTGATCAGCACTTCGTGTGCCCTCTGTTATTTG
1 TGTGCCCTCTGATCAGCACTTCGTGTGCCCTCTGTTATTTG
* *
378458 TGTGCCCTCTGATTAGCACTTTGTGTGCCCTCTGTTA
1 TGTGCCCTCTGATCAGCACTTCGTGTGCCCTCTGTTA
378495 CCCAGCACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.10, C:0.27, G:0.22, T:0.41
Consensus pattern (41 bp):
TGTGCCCTCTGATCAGCACTTCGTGTGCCCTCTGTTATTTG
Found at i:378484 original size:23 final size:23
Alignment explanation
Indices: 378358--378491 Score: 88
Period size: 23 Copynumber: 6.1 Consensus size: 23
378348 AGCGAGCTTA
* * *
378358 CTGATCAGCACTGTGTGTG-CTT
1 CTGATTAGCACTTTGTGTGCCCT
* *
378380 CTG-TTCAGCACTGTGTGTG-CTT
1 CTGATT-AGCACTTTGTGTGCCCT
* * *
378402 TTGTTTAGCA-TGTTTTGTGCCCT
1 CTGATTAGCACT-TTGTGTGCCCT
* * *
378425 TTGATCAGCACTTCGTGTGCCCT
1 CTGATTAGCACTTTGTGTGCCCT
378448 CTG-TT---A-TTTGTGTGCCCT
1 CTGATTAGCACTTTGTGTGCCCT
378466 CTGATTAGCACTTTGTGTGCCCT
1 CTGATTAGCACTTTGTGTGCCCT
378489 CTG
1 CTG
378492 TTACCCAGCA
Statistics
Matches: 90, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
18 14 0.16
19 3 0.03
21 2 0.02
22 32 0.36
23 38 0.42
24 1 0.01
ACGTcount: A:0.10, C:0.24, G:0.24, T:0.42
Consensus pattern (23 bp):
CTGATTAGCACTTTGTGTGCCCT
Found at i:382293 original size:41 final size:41
Alignment explanation
Indices: 382247--382326 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
382237 ATTAGAGATA
382247 ACAGTCATTAACAGAAATACAAAATGATAATTAATTCTTAC
1 ACAGTCATTAACAGAAATACAAAATGATAATTAATTCTTAC
*
382288 ACAGTCATTAACAGAAATACAAATTGATAATTAATTCTT
1 ACAGTCATTAACAGAAATACAAAATGATAATTAATTCTT
382327 TCTTCCATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.31
Consensus pattern (41 bp):
ACAGTCATTAACAGAAATACAAAATGATAATTAATTCTTAC
Found at i:384020 original size:48 final size:48
Alignment explanation
Indices: 383949--384047 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
383939 CATTGTTGCA
383949 GGTAGGGAGTAATGGCTTGTTGCTCAGAGATGAATCTCAGACTTTGGT
1 GGTAGGGAGTAATGGCTTGTTGCTCAGAGATGAATCTCAGACTTTGGT
383997 GGTAGGGAGTAATGGCTTGTTGCTCAGAGATGAATCTCAGACTTTGGT
1 GGTAGGGAGTAATGGCTTGTTGCTCAGAGATGAATCTCAGACTTTGGT
384045 GGT
1 GGT
384048 CTGTTTTAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.22, C:0.12, G:0.34, T:0.31
Consensus pattern (48 bp):
GGTAGGGAGTAATGGCTTGTTGCTCAGAGATGAATCTCAGACTTTGGT
Found at i:387103 original size:17 final size:18
Alignment explanation
Indices: 387081--387118 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
387071 GAAACAGAAG
387081 AAGGAGAAG-AAGAAAGA
1 AAGGAGAAGAAAGAAAGA
*
387098 AAGGAGAAGAAAGAGAGA
1 AAGGAGAAGAAAGAAAGA
387116 AAG
1 AAG
387119 ATTAGAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (18 bp):
AAGGAGAAGAAAGAAAGA
Found at i:393641 original size:16 final size:16
Alignment explanation
Indices: 393615--393647 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
393605 ATGGCTTTGG
393615 AAAGAAAGGT-ATAAT
1 AAAGAAAGGTAATAAT
393630 AAAGAGAAGGTAATAAT
1 AAAGA-AAGGTAATAAT
393647 A
1 A
393648 GAAACACCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 5 0.31
17 6 0.38
ACGTcount: A:0.61, C:0.00, G:0.21, T:0.18
Consensus pattern (16 bp):
AAAGAAAGGTAATAAT
Found at i:397799 original size:57 final size:57
Alignment explanation
Indices: 397732--397845 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
397722 TTTCTGCATA
397732 GTAAAACGGATAAATTAGATAGCTAAACACAGATATTGGTAAGGGACAAGGTCCTGG
1 GTAAAACGGATAAATTAGATAGCTAAACACAGATATTGGTAAGGGACAAGGTCCTGG
397789 GTAAAACGGATAAATTAGATAGCTAAACACAGATATTGGTAAGGGACAAGGTCCTGG
1 GTAAAACGGATAAATTAGATAGCTAAACACAGATATTGGTAAGGGACAAGGTCCTGG
397846 CACAACAGCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.21
Consensus pattern (57 bp):
GTAAAACGGATAAATTAGATAGCTAAACACAGATATTGGTAAGGGACAAGGTCCTGG
Found at i:398328 original size:27 final size:27
Alignment explanation
Indices: 398298--398350 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
398288 CCCCTCCCAT
398298 TCCTCCACCTTCACCCCCACCACCACC
1 TCCTCCACCTTCACCCCCACCACCACC
* *
398325 TCCTCCAGCTTCACCCCCACCTCCAC
1 TCCTCCACCTTCACCCCCACCACCAC
398351 TCGGCATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.64, G:0.02, T:0.17
Consensus pattern (27 bp):
TCCTCCACCTTCACCCCCACCACCACC
Found at i:401313 original size:23 final size:23
Alignment explanation
Indices: 401280--401323 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
401270 ATATTTGCAT
*
401280 AAAAATGAAATTAAT-TAAAATAG
1 AAAAATAAAATT-ATCTAAAATAG
401303 AAAAATAAAATTATCTAAAAT
1 AAAAATAAAATTATCTAAAAT
401324 TTCAAGTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (23 bp):
AAAAATAAAATTATCTAAAATAG
Found at i:404607 original size:16 final size:15
Alignment explanation
Indices: 404582--404614 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
404572 ATAACAATTA
404582 AATTATTAAAATATT
1 AATTATTAAAATATT
404597 AATTATATAAAATATT
1 AATTAT-TAAAATATT
404613 AA
1 AA
404615 AAAAATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTATTAAAATATT
Found at i:405358 original size:22 final size:22
Alignment explanation
Indices: 405314--405358 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
405304 AAAATACTTT
*
405314 TAAAATAATATAATTTATTTTA
1 TAAAATAATATAATTTATATTA
*
405336 TAAAATAATAGTATTTTA-ATTA
1 TAAAATAATA-TAATTTATATTA
405358 T
1 T
405359 TATTTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TAAAATAATATAATTTATATTA
Found at i:406158 original size:17 final size:18
Alignment explanation
Indices: 406133--406167 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
406123 TAATTCTAGG
406133 AAATGAAAAAG-TAAAAT
1 AAATGAAAAAGATAAAAT
*
406150 AAATTAAAAAGATAAAAT
1 AAATGAAAAAGATAAAAT
406168 TATTTTCCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (18 bp):
AAATGAAAAAGATAAAAT
Found at i:406522 original size:31 final size:31
Alignment explanation
Indices: 406484--406570 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 31
406474 TTAATGACGG
***
406484 GTGTCTAAAATAAAAATAATTTTTAATGGTA
1 GTGTCTAAAATAAAAATAATTTTTAATAACA
* * *
406515 GTGTCTAAAGTGAAAATGATTTTTAATAACA
1 GTGTCTAAAATAAAAATAATTTTTAATAACA
* *
406546 GTGCCTAAAATAAAAAAAATATTTT
1 GTGTCTAAAATAAAAATAAT-TTTT
406571 TAGACACCTA
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
31 40 0.91
32 4 0.09
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.36
Consensus pattern (31 bp):
GTGTCTAAAATAAAAATAATTTTTAATAACA
Found at i:406630 original size:5 final size:5
Alignment explanation
Indices: 406624--406655 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
406614 ATATAATTAA
*
406624 AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
406656 GAGCAATACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:419813 original size:4 final size:4
Alignment explanation
Indices: 419804--419888 Score: 75
Period size: 4 Copynumber: 21.2 Consensus size: 4
419794 AAATAAACGG
* * *
419804 GAAA GAAA GAAA -AAA AAAA GAAA GAAA GGAA GAAA GAGAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* * * *
419852 GGAA GAAG GAGAG GAAA GAAA G-AA GAAG GAAA GAAA G
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G
419889 GAAATGTGTT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
3 6 0.09
4 53 0.80
5 7 0.11
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:419849 original size:9 final size:8
Alignment explanation
Indices: 419820--419892 Score: 50
Period size: 9 Copynumber: 9.4 Consensus size: 8
419810 AAGAAAAAAA
*
419820 AAAGAAAG
1 AAAGAAGG
419828 AAAGGAA-G
1 AAA-GAAGG
419836 AAAGAGAGG
1 AAAGA-AGG
419845 AAAGAAAGG
1 AAAG-AAGG
419854 -AAGAAGG
1 AAAGAAGG
419861 --AG-AGG
1 AAAGAAGG
*
419866 AAAGAAAG
1 AAAGAAGG
419874 -AAGAAGG
1 AAAGAAGG
419881 AAAGAAAGG
1 AAAG-AAGG
419890 AAA
1 AAA
419893 TGTGTTTATT
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
5 3 0.06
6 2 0.04
7 14 0.26
8 16 0.30
9 18 0.33
10 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (8 bp):
AAAGAAGG
Found at i:419849 original size:21 final size:21
Alignment explanation
Indices: 419823--419878 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
419813 AAAAAAAAAA
419823 GAAAGAAAGGAAGAAAGAGAG
1 GAAAGAAAGGAAGAAAGAGAG
*
419844 GAAAGAAAGGAAGAAGGAGAG
1 GAAAGAAAGGAAGAAAGAGAG
419865 GAAAGAAA-GAAGAA
1 GAAAGAAAGGAAGAA
419879 GGAAAGAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 6 0.18
21 28 0.82
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGGAAGAAAGAGAG
Found at i:419872 original size:25 final size:22
Alignment explanation
Indices: 419804--419888 Score: 78
Period size: 21 Copynumber: 4.2 Consensus size: 22
419794 AAATAAACGG
*
419804 GAAAGAAA-GAA-AAA-AAAAA
1 GAAAGAAAGGAAGAAAGAGAAA
*
419823 GAAAGAAAGGAAGAAAGAG-AG
1 GAAAGAAAGGAAGAAAGAGAAA
* *
419844 GAAAGAAAGGAAGAAGGAG-AG
1 GAAAGAAAGGAAGAAAGAGAAA
419865 GAAAGAAA-GAAG-AAG-GAAA
1 GAAAGAAAGGAAGAAAGAGAAA
419884 GAAAG
1 GAAAG
419889 GAAATGTGTT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.02
19 16 0.28
20 7 0.12
21 32 0.56
22 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (22 bp):
GAAAGAAAGGAAGAAAGAGAAA
Found at i:419973 original size:19 final size:19
Alignment explanation
Indices: 419928--419973 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
419918 GTATGATATC
*
419928 TTTTTAAAATCGTATTTTA
1 TTTTTAAAATCGTATTTAA
**
419947 TTTATTAAAATTTTATTTAA
1 TTT-TTAAAATCGTATTTAA
419967 TTTTTAA
1 TTTTTAA
419974 CAGATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTTAAAATCGTATTTAA
Found at i:422996 original size:28 final size:28
Alignment explanation
Indices: 422964--423044 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
422954 CCTTAATCAA
*
422964 TCTAGTGTTTACGGTTT-AGAGTTTTAAG
1 TCTAGTGTTTACGATTTAAG-GTTTTAAG
* *
422992 TCTAGTGGTTATGATTTAAGGTTTTAAG
1 TCTAGTGTTTACGATTTAAGGTTTTAAG
* * **
423020 TTTAGGGTTTATAATTT-AGGTTTTA
1 TCTAGTGTTTACGATTTAAGGTTTTA
423045 GGGTTTAATG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
27 8 0.18
28 35 0.78
29 2 0.04
ACGTcount: A:0.23, C:0.04, G:0.23, T:0.49
Consensus pattern (28 bp):
TCTAGTGTTTACGATTTAAGGTTTTAAG
Found at i:423028 original size:14 final size:14
Alignment explanation
Indices: 422977--423044 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
422967 AGTGTTTACG
*
422977 GTTTAGAGTTTTAA
1 GTTTAGGGTTTTAA
* * *
422991 GTCTAGTGGTTATGA
1 GTTTAG-GGTTTTAA
*
423006 -TTTAAGGTTTTAA
1 GTTTAGGGTTTTAA
423019 GTTTAGGGTTTATAA
1 GTTTAGGGTTT-TAA
423034 -TTTA-GGTTTTA
1 GTTTAGGGTTTTA
423045 GGGTTTAATG
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
12 2 0.05
13 11 0.26
14 21 0.50
15 8 0.19
ACGTcount: A:0.25, C:0.01, G:0.24, T:0.50
Consensus pattern (14 bp):
GTTTAGGGTTTTAA
Found at i:423389 original size:45 final size:45
Alignment explanation
Indices: 423309--423438 Score: 152
Period size: 45 Copynumber: 2.9 Consensus size: 45
423299 GGGAGGAATA
* * ****
423309 GAGTATCGCGGTGGCTCGTCAAATTCATCCCGATATCCTTCCCTT
1 GAGTATTGCGGTGGCTCGTCAAATTGAGGTTGATATCCTTCCCTT
**
423354 GAGTATTGCGGTGGCTCGTCAAATTGAGGTTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAATTGAGGTTGATATCCTTCCCTT
* * * *
423399 GAATATTACGGTGGCTCTTCAAACTGAGGTTGATATCCTT
1 GAGTATTGCGGTGGCTCGTCAAATTGAGGTTGATATCCTT
423439 GGCTTGATGA
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 73 1.00
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.34
Consensus pattern (45 bp):
GAGTATTGCGGTGGCTCGTCAAATTGAGGTTGATATCCTTCCCTT
Found at i:423439 original size:45 final size:45
Alignment explanation
Indices: 423340--423445 Score: 158
Period size: 45 Copynumber: 2.4 Consensus size: 45
423330 AATTCATCCC
** * * *
423340 GATATCCTTCCCTTGAGTATTGCGGTGGCTCGTCAAATTGAGGTT
1 GATATCCTTGGCTTGAATATTACGGTGGCTCGTCAAACTGAGGTT
*
423385 GATATCCTTGGCTTGAATATTACGGTGGCTCTTCAAACTGAGGTT
1 GATATCCTTGGCTTGAATATTACGGTGGCTCGTCAAACTGAGGTT
423430 GATATCCTTGGCTTGA
1 GATATCCTTGGCTTGA
423446 TGAGCTATGC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (45 bp):
GATATCCTTGGCTTGAATATTACGGTGGCTCGTCAAACTGAGGTT
Done.