Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007494.1 Kokia drynarioides strain JFW-HI SEQ_122118, 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: 68515
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 207 characters in sequence are not A, C, G, or T
Found at i:4526 original size:77 final size:77
Alignment explanation
Indices: 4438--4588 Score: 257
Period size: 77 Copynumber: 2.0 Consensus size: 77
4428 GTTGAATCAG
*
4438 ATATTGCTTGAAAAGAAAAGAAAGTAATAAAAACATAATTTGAAACTTGATATACAACATTTAAG
1 ATATTGCTTGAAAAGAAAAGAAAGTAATAAAAACATAATTTGAAACCTGATATACAACATTTAAG
4503 AAGCCCTTACAT
66 AAGCCCTTACAT
* * * *
4515 ATATTGCTTGAAAAGAAAAGAAAGTAATAAAAATATAATTTGAAACCTGATATACGATATTTGAG
1 ATATTGCTTGAAAAGAAAAGAAAGTAATAAAAACATAATTTGAAACCTGATATACAACATTTAAG
4580 AAGCCCTTA
66 AAGCCCTTA
4589 TATGAGCACT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 69 1.00
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (77 bp):
ATATTGCTTGAAAAGAAAAGAAAGTAATAAAAACATAATTTGAAACCTGATATACAACATTTAAG
AAGCCCTTACAT
Found at i:4626 original size:31 final size:30
Alignment explanation
Indices: 4583--4671 Score: 97
Period size: 31 Copynumber: 2.9 Consensus size: 30
4573 ATTTGAGAAG
* *
4583 CCCTTATATGAGCACTTTTGAAAAGTTTTGG
1 CCCTTATTTGAGCA-TTTTGAAAAGTTTTGA
* * *
4614 CTCTTATTTGAGCATGTTCGAAAAGGTTTGA
1 CCCTTATTTGAGCAT-TTTGAAAAGTTTTGA
* *
4645 CCCTTATTTGACCATTTTGAAAGGTTT
1 CCCTTATTTGAGCATTTTGAAAAGTTT
4672 GGCCTTCTTT
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
30 10 0.21
31 37 0.79
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTGAAAAGTTTTGA
Found at i:6580 original size:12 final size:13
Alignment explanation
Indices: 6563--6591 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6553 CTGCTGATTC
6563 TTTTCTTTTTC-T
1 TTTTCTTTTTCAT
6575 TTTTCTTTTTCAT
1 TTTTCTTTTTCAT
6588 TTTT
1 TTTT
6592 GCAGGAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTTTTTCAT
Found at i:9536 original size:69 final size:66
Alignment explanation
Indices: 9387--9579 Score: 181
Period size: 66 Copynumber: 2.9 Consensus size: 66
9377 CCGTACTATC
* * * *
9387 CTCAATATTCCGTTAGCCACCGTAACGACCACTCAGCTCCGTCTTTTGCACCAGCGGCTGAGTCT
1 CTCAATATTCCGTTAGCCACCGTAACGACCACTCAGCTCCGTCTTTCGCACCAACGGCTCACTCT
9452 T
66 T
* * * * * *
9453 TTCAATATTCCGTTAGCCGCCGTAACGACCATTTAGATCCTCC-TCCTTTCGCGCCAATGGCTCA
1 CTCAATATTCCGTTAGCCACCGTAACGACCACTCAG---CTCCGT-CTTTCGCACCAACGGCTCA
9517 CTCTT
62 CTCTT
* * *** * * *
9522 CTCAATATTCCGTTAGTCACCATAACGGTTACTCAGATCCGTCTTTTGCGCCAACGGC
1 CTCAATATTCCGTTAGCCACCGTAACGACCACTCAGCTCCGTCTTTCGCACCAACGGC
9580 ACCGTCTTTT
Statistics
Matches: 100, Mismatches: 22, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
66 49 0.49
67 1 0.01
68 1 0.01
69 49 0.49
ACGTcount: A:0.20, C:0.34, G:0.17, T:0.30
Consensus pattern (66 bp):
CTCAATATTCCGTTAGCCACCGTAACGACCACTCAGCTCCGTCTTTCGCACCAACGGCTCACTCT
T
Found at i:9634 original size:135 final size:135
Alignment explanation
Indices: 9387--9653 Score: 309
Period size: 135 Copynumber: 2.0 Consensus size: 135
9377 CCGTACTATC
* * * **
9387 CTCAATATTCCGTTAGCCACCGTAACGACCACTCAGCTCCGTCTTTTGCACCAGCGGCTGAGTCT
1 CTCAATATTCCGTTAGCCACCATAACGACCACTCAGATCCGTCTTTTGCACCAACGGCACAGTCT
* * * *
9452 TTTCAATATTCCGTTAGCCGCCGTAACGACCATTTAGATCCTCCTCCTTTCGCGCCAATGGCTCA
66 TTTCAATATTACGTTAGCCGCCATAACGACCACTCAGATCCTCCTCCTTTCGCGCCAATGGCTCA
9517 CTCTT
131 CTCTT
* *** * *
9522 CTCAATATTCCGTTAGTCACCATAACGGTTACTCAGATCCGTCTTTTGCGCCAACGGCACCGTCT
1 CTCAATATTCCGTTAGCCACCATAACGACCACTCAGATCCGTCTTTTGCACCAACGGCACAGTCT
* * *** * *
9587 TTTGAATATTACGTTAGCGGCCATAACGGTTACTCAGATCCTTCTCCTCCTTTAGCGCCAACGGC
66 TTTCAATATTACGTTAGCCGCCATAACGACCACTCAGAT-C--CTCCTCCTTTCGCGCCAATGGC
9652 TC
128 TC
9654 CACCTGAAGC
Statistics
Matches: 107, Mismatches: 22, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
135 84 0.79
136 1 0.01
138 22 0.21
ACGTcount: A:0.20, C:0.33, G:0.17, T:0.30
Consensus pattern (135 bp):
CTCAATATTCCGTTAGCCACCATAACGACCACTCAGATCCGTCTTTTGCACCAACGGCACAGTCT
TTTCAATATTACGTTAGCCGCCATAACGACCACTCAGATCCTCCTCCTTTCGCGCCAATGGCTCA
CTCTT
Found at i:30403 original size:17 final size:16
Alignment explanation
Indices: 30350--30403 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
30340 TATCATTGAA
*
30350 AAAAATAAAAATAACAT
1 AAAAATAAAAATAA-TT
*
30367 AAAAATAGAAGAATACTT
1 AAAAATA-AA-AATAATT
30385 AAAAATAAAAATTAATT
1 AAAAATAAAAA-TAATT
30402 AA
1 AA
30404 TCTATTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 2 0.06
17 15 0.48
18 10 0.32
19 4 0.13
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (16 bp):
AAAAATAAAAATAATT
Found at i:32782 original size:4 final size:4
Alignment explanation
Indices: 32773--32816 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
32763 AGCCATGAAC
* * *
32773 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ATAT AAAT ATAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
32817 GCGTACCTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (4 bp):
ACAT
Found at i:38495 original size:3 final size:3
Alignment explanation
Indices: 38487--38530 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
38477 TTATATCATC
38487 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
38531 TAAAACATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:42402 original size:22 final size:22
Alignment explanation
Indices: 42377--42450 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
42367 AATATATTGT
42377 TGTTTTGGTGTTATTTTTTTAC
1 TGTTTTGGTGTTATTTTTTTAC
* *
42399 TGTTTTGATTGCTATTTTTTT-C
1 TGTTTTG-GTGTTATTTTTTTAC
**
42421 TGTTTTGGTGTT-GCTTTTTAC
1 TGTTTTGGTGTTATTTTTTTAC
42442 TGTTTTGGT
1 TGTTTTGGT
42451 TTTTTATTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 5 0.11
21 13 0.30
22 15 0.34
23 11 0.25
ACGTcount: A:0.07, C:0.07, G:0.20, T:0.66
Consensus pattern (22 bp):
TGTTTTGGTGTTATTTTTTTAC
Found at i:42456 original size:16 final size:16
Alignment explanation
Indices: 42435--42467 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42425 TTGGTGTTGC
42435 TTTTTACTGTTTTGGT
1 TTTTTACTGTTTTGGT
*
42451 TTTTTATTGTTTTGGT
1 TTTTTACTGTTTTGGT
42467 T
1 T
42468 GCTGTTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.03, G:0.18, T:0.73
Consensus pattern (16 bp):
TTTTTACTGTTTTGGT
Found at i:42475 original size:21 final size:20
Alignment explanation
Indices: 42392--42475 Score: 59
Period size: 21 Copynumber: 4.2 Consensus size: 20
42382 TGGTGTTATT
* *
42392 TTTTTACTGTTTTGATTGCTAT
1 TTTTTACTGTTTTG-GTGCT-G
* *
42414 TTTTTTCTGTTTTGGTGTTG
1 TTTTTACTGTTTTGGTGCTG
42434 CTTTTTACTGTTTT-G-G-T-
1 -TTTTTACTGTTTTGGTGCTG
*
42451 TTTTTATTGTTTTGGTTGCTG
1 TTTTTACTGTTTTGG-TGCTG
42472 TTTT
1 TTTT
42476 GGTACTTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
16 12 0.24
17 1 0.02
18 1 0.02
19 2 0.04
20 2 0.04
21 19 0.38
22 13 0.26
ACGTcount: A:0.06, C:0.07, G:0.19, T:0.68
Consensus pattern (20 bp):
TTTTTACTGTTTTGGTGCTG
Found at i:42515 original size:24 final size:22
Alignment explanation
Indices: 42482--42573 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 22
42472 TTTTGGTACT
*
42482 TTTTTATTGTTTTTGAGGCTGTTA
1 TTTTTGTTGTTTTT--GGCTGTTA
42506 TTTTTGTTG-TTTT-GCTGTTA
1 TTTTTGTTGTTTTTGGCTGTTA
*
42526 TTTTTGTTGTTGTTTTGGTTGTTA
1 TTTTTGTTG-T-TTTTGGCTGTTA
*
42550 -TTTTGATTG--TTTGGATGTTA
1 TTTTTG-TTGTTTTTGGCTGTTA
42570 TTTT
1 TTTT
42574 ATGCGTTTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
20 26 0.44
21 3 0.05
23 13 0.22
24 17 0.29
ACGTcount: A:0.09, C:0.02, G:0.22, T:0.67
Consensus pattern (22 bp):
TTTTTGTTGTTTTTGGCTGTTA
Found at i:42516 original size:12 final size:12
Alignment explanation
Indices: 42515--42553 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
42505 ATTTTTGTTG
*
42515 TTTTGCTGTTAT
1 TTTTGTTGTTAT
*
42527 TTTTGTTGTTGT
1 TTTTGTTGTTAT
*
42539 TTTGGTTGTTAT
1 TTTTGTTGTTAT
42551 TTT
1 TTT
42554 GATTGTTTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.05, C:0.03, G:0.21, T:0.72
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:42537 original size:23 final size:24
Alignment explanation
Indices: 42498--42553 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
42488 TTGTTTTTGA
42498 GGCTGTTA--TTT-TTGTTGTTTT
1 GGCTGTTATTTTTGTTGTTGTTTT
42519 -GCTGTTATTTTTGTTGTTGTTTT
1 GGCTGTTATTTTTGTTGTTGTTTT
*
42542 GGTTGTTATTTT
1 GGCTGTTATTTT
42554 GATTGTTTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.23
22 3 0.10
23 10 0.33
24 10 0.33
ACGTcount: A:0.05, C:0.04, G:0.23, T:0.68
Consensus pattern (24 bp):
GGCTGTTATTTTTGTTGTTGTTTT
Found at i:42554 original size:12 final size:12
Alignment explanation
Indices: 42521--42560 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
42511 GTTGTTTTGC
*
42521 TGTTATTTTTGT
1 TGTTATTTTGGT
*
42533 TGTTGTTTTGGT
1 TGTTATTTTGGT
*
42545 TGTTATTTTGAT
1 TGTTATTTTGGT
42557 TGTT
1 TGTT
42561 TGGATGTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.07, C:0.00, G:0.23, T:0.70
Consensus pattern (12 bp):
TGTTATTTTGGT
Found at i:42725 original size:27 final size:27
Alignment explanation
Indices: 42689--42767 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
42679 ATATAAAGAA
42689 TTTTTAATGTATTTTAAATTTGTTT-AT
1 TTTTTAATGT-TTTTAAATTTGTTTGAT
* *
42716 TTTTTAATGTTTTTAAGTTTATTTGAT
1 TTTTTAATGTTTTTAAATTTGTTTGAT
* * *
42743 ATATTATATGTTTTTTCAATTTGTT
1 TTTTTA-ATG-TTTTTAAATTTGTT
42768 GTATATAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
26 12 0.29
27 16 0.38
28 3 0.07
29 11 0.26
ACGTcount: A:0.24, C:0.01, G:0.09, T:0.66
Consensus pattern (27 bp):
TTTTTAATGTTTTTAAATTTGTTTGAT
Found at i:60052 original size:20 final size:20
Alignment explanation
Indices: 60029--60067 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
60019 GAATTTAACT
*
60029 ATACATATTTAAAAAAATAA
1 ATACATATATAAAAAAATAA
*
60049 ATACATATATAAAATAATA
1 ATACATATATAAAAAAATA
60068 CTAATTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
ATACATATATAAAAAAATAA
Found at i:61521 original size:18 final size:20
Alignment explanation
Indices: 61477--61526 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
61467 GACTTATCTC
*
61477 TTTCTTTCTTCTCCCGTTTT
1 TTTCTTTCTTCTCCCGTTCT
61497 TTCTCTTTCTTCT-CC-TTCT
1 TT-TCTTTCTTCTCCCGTTCT
61516 TTTCTTTCTTC
1 TTTCTTTCTTC
61527 CTTTCCTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 9 0.32
19 5 0.18
20 4 0.14
21 10 0.36
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTCTTTCTTCTCCCGTTCT
Found at i:62396 original size:279 final size:283
Alignment explanation
Indices: 61898--62459 Score: 690
Period size: 279 Copynumber: 2.0 Consensus size: 283
61888 AAGCCAATAC
61898 AAAGAAGCTAAACACTAGTGAAAGAACACAAGCACGCCTAGAACCAATGTGCAGCAAGAACAAAT
1 AAAGAAGCTAAACACTAGTGAAAGAACACAAGCACGCCTAGAACCAATGTGCAGCAAGAACAAAT
* * *
61963 TGAAGTTAAAGTGTCCCTCTTTCAATGTTACTAATTAAAAAGAAAGTCTGAAGATGTAAGCTTCA
66 T-AAG-T-AA-----CCTCTTTCAATGTTACTAATGAAAAAGAAACTCTGAAGATATAAGCTTCA
* * *
62028 CTATCCATTAAATGATATTTCCCATTATATAACTTGCATGATTCTTTGTTCCATTCTCCAAAGCA
123 CAATCCATTAAATGA-ATTTCCCATTATATAACTTGCATGATTCTTTGTTCAACTCTCCAAAGCA
* * * * * *
62093 AATTTAGATGTAGCTTTGGTACAAGTTAGGTTTCATGCTCAAGCAACATTTCACCATGAGCAAAA
187 AAATTACATGCAGCTTTAGTACAAGCTAGGTTTCATGCTCAAGCAACATTCCACCATGAGCAAAA
* *
62158 TGCAATTAT-ACTAGATTCTAGCTAATACAAAG
252 CGCAATT-TCACTAAATTCTAGCTAATACAAAG
** *
62190 AAAGAAGCTAAACTGTAGTGAAAGAACACAAGCAGGCCTAGAACCAATGTGCAGCAAGAACAAA-
1 AAAGAAGCTAAACACTAGTGAAAGAACACAAGCACGCCTAGAACCAATGTGCAGCAAGAACAAAT
* * *
62254 T-CG-AA-CTCTTTCACTGTTACTAATGAATAAA-AAACTCATTGGAGATATAAGCTTCACAATC
66 TAAGTAACCTCTTTCAATGTTACTAATGAA-AAAGAAACTC--TGAAGATATAAGCTTCACAATC
* * ****
62315 TATTAAATG-A-TTCCCATTATATAACTTGCATGATTTTTTGTTCAACTCTCCTGTTCAAAATTA
128 CATTAAATGAATTTCCCATTATATAACTTGCATGATTCTTTGTTCAACTCTCCAAAGCAAAATTA
** *
62378 CATGCAGCTTTAGTACAAGCTAGGTTTCATTTTCAAGCAACATTCCACCATGGGCAAAACGCAAT
193 CATGCAGCTTTAGTACAAGCTAGGTTTCATGCTCAAGCAACATTCCACCATGAGCAAAACGCAAT
62443 TTCACTAAATTCTAGCT
258 TTCACTAAATTCTAGCT
62460 TATATCTTCA
Statistics
Matches: 237, Mismatches: 29, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
278 1 0.00
279 115 0.49
280 26 0.11
281 3 0.01
282 27 0.11
286 2 0.01
289 1 0.00
291 1 0.00
292 61 0.26
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (283 bp):
AAAGAAGCTAAACACTAGTGAAAGAACACAAGCACGCCTAGAACCAATGTGCAGCAAGAACAAAT
TAAGTAACCTCTTTCAATGTTACTAATGAAAAAGAAACTCTGAAGATATAAGCTTCACAATCCAT
TAAATGAATTTCCCATTATATAACTTGCATGATTCTTTGTTCAACTCTCCAAAGCAAAATTACAT
GCAGCTTTAGTACAAGCTAGGTTTCATGCTCAAGCAACATTCCACCATGAGCAAAACGCAATTTC
ACTAAATTCTAGCTAATACAAAG
Found at i:64341 original size:19 final size:19
Alignment explanation
Indices: 64314--64352 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
64304 ATGACTTTAA
* *
64314 TTTGGCATAGGTTAATTCC
1 TTTGACATAGCTTAATTCC
64333 TTTGACATAGCTTAATTCC
1 TTTGACATAGCTTAATTCC
64352 T
1 T
64353 CTATCTTTAG
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:0.23, C:0.18, G:0.15, T:0.44
Consensus pattern (19 bp):
TTTGACATAGCTTAATTCC
Found at i:66603 original size:18 final size:18
Alignment explanation
Indices: 66563--66605 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
66553 GTTCAAGATG
66563 TAATTAATTCAAAATTTT
1 TAATTAATTCAAAATTTT
* *
66581 CAATTAATT-AAATTTATT
1 TAATTAATTCAAAATT-TT
66599 TAATTAA
1 TAATTAA
66606 AAATCTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTAATTCAAAATTTT
Found at i:68363 original size:11 final size:11
Alignment explanation
Indices: 68347--68403 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
68337 GGGGACCAAC
* *
68347 GAAAAATGAAG
1 GAAAAAAGAAA
68358 GAAAAAAGAAA
1 GAAAAAAGAAA
68369 GAAAAAAGAGAGA
1 GAAAAAAGA-A-A
68382 GAAAGAAAGAAA
1 GAAA-AAAGAAA
*
68394 GAAAGAAGAA
1 GAAAAAAGAA
68404 GGAAGAAGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 23 0.57
12 6 0.15
13 6 0.15
14 5 0.12
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:68371 original size:4 final size:4
Alignment explanation
Indices: 68358--68400 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
68348 AAAAATGAAG
68358 GAAA -AAA GAAA GAAA -AAA GAGAGA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GA-A-A GAAA GAAA GAAA GAAA GAA
68401 GAAGGAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 6 0.17
4 24 0.69
5 2 0.06
6 3 0.09
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:68419 original size:9 final size:9
Alignment explanation
Indices: 68397--68442 Score: 69
Period size: 9 Copynumber: 5.3 Consensus size: 9
68387 AAAGAAAGAA
68397 AGAAGAA-G
1 AGAAGAAGG
68405 -GAAGAAGG
1 AGAAGAAGG
68413 AGAAGAAGG
1 AGAAGAAGG
*
68422 ATAAGAAGG
1 AGAAGAAGG
68431 AGAAGAAGG
1 AGAAGAAGG
68440 AGA
1 AGA
68443 GGAAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
7 6 0.18
8 1 0.03
9 27 0.79
ACGTcount: A:0.57, C:0.00, G:0.41, T:0.02
Consensus pattern (9 bp):
AGAAGAAGG
Found at i:68427 original size:18 final size:17
Alignment explanation
Indices: 68384--68440 Score: 75
Period size: 18 Copynumber: 3.5 Consensus size: 17
68374 AAGAGAGAGA
*
68384 AAGAAAGAAAGAA--AG
1 AAGAAGGAAAGAAGGAG
68399 AAGAAGG-AAGAAGGAG
1 AAGAAGGAAAGAAGGAG
68415 AAGAAGGATAAGAAGGAG
1 AAGAAGGA-AAGAAGGAG
68433 AAGAAGGA
1 AAGAAGGA
68441 GAGGAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
14 5 0.14
15 6 0.16
16 9 0.24
18 17 0.46
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (17 bp):
AAGAAGGAAAGAAGGAG
Done.