Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014625.1 Kokia drynarioides strain JFW-HI SEQ_129664, 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: 378628
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 251 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:296282 original size:15 final size:17
Alignment explanation
Indices: 296249--296283 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
296239 TTTTTTTAAT
296249 TATTAGTTATTATAAAA
1 TATTAGTTATTATAAAA
296266 TATTAGTTA-TA-AAAA
1 TATTAGTTATTATAAAA
296281 TAT
1 TAT
296284 AAAAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 2 0.11
17 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
TATTAGTTATTATAAAA
Found at i:296757 original size:14 final size:14
Alignment explanation
Indices: 296738--296769 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
296728 AGAGTTACAA
296738 GGGAATGAATTTGG
1 GGGAATGAATTTGG
296752 GGGAATGAATTTGG
1 GGGAATGAATTTGG
296766 GGGA
1 GGGA
296770 TTTGAGAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.47, T:0.25
Consensus pattern (14 bp):
GGGAATGAATTTGG
Found at i:299350 original size:13 final size:13
Alignment explanation
Indices: 299327--299351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
299317 CATTATTTAA
299327 TTTTATTATTATG
1 TTTTATTATTATG
299340 TTTTATTATTAT
1 TTTTATTATTAT
299352 TTATTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTTATTATTATG
Found at i:300277 original size:16 final size:18
Alignment explanation
Indices: 300256--300290 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
300246 TTGTTTTCAA
*
300256 ATTTTTTTAT-TTTTTAT
1 ATTTTTTAATATTTTTAT
300273 ATTTTTTAATATTTTTAT
1 ATTTTTTAATATTTTTAT
300291 GATATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
ATTTTTTAATATTTTTAT
Found at i:300284 original size:10 final size:9
Alignment explanation
Indices: 300256--300288 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
300246 TTGTTTTCAA
300256 ATTTTTT-T
1 ATTTTTTAT
300264 ATTTTTTAT
1 ATTTTTTAT
300273 ATTTTTTAAT
1 ATTTTTT-AT
300283 ATTTTT
1 ATTTTT
300289 ATGATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 7 0.30
9 8 0.35
10 8 0.35
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:301009 original size:14 final size:14
Alignment explanation
Indices: 300985--301027 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
300975 AATTTATATT
300985 ATTAAATAAATTAAA
1 ATTAAA-AAATTAAA
*
301000 ATTAAAAAATTTAA
1 ATTAAAAAATTAAA
*
301014 ATT-ATAAATTAAA
1 ATTAAAAAATTAAA
301027 A
1 A
301028 GGGTCAGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 9 0.36
14 10 0.40
15 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATTAAAAAATTAAA
Found at i:301069 original size:23 final size:22
Alignment explanation
Indices: 301037--301083 Score: 85
Period size: 23 Copynumber: 2.1 Consensus size: 22
301027 AGGGTCAGTC
301037 AAAAAAGTATGTTAATTAATCA
1 AAAAAAGTATGTTAATTAATCA
301059 AAAAAAGGTATGTTAATTAATCA
1 AAAAAA-GTATGTTAATTAATCA
301082 AA
1 AA
301084 GGCATACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.55, C:0.04, G:0.11, T:0.30
Consensus pattern (22 bp):
AAAAAAGTATGTTAATTAATCA
Found at i:313856 original size:23 final size:23
Alignment explanation
Indices: 313826--313961 Score: 195
Period size: 23 Copynumber: 6.0 Consensus size: 23
313816 GCTCTTTATT
*
313826 ATTAGCACTGTGTGTACTCTCTG
1 ATTAGCACTTTGTGTACTCTCTG
*
313849 ATTAGCACTTTGTGTGCTCTCTG
1 ATTAGCACTTTGTGTACTCTCTG
*
313872 ATTAGCACTTTGTGTGCTCTCTG
1 ATTAGCACTTTGTGTACTCTCTG
313895 ATTAGCACTTTGTGTACTCTCTG
1 ATTAGCACTTTGTGTACTCTCTG
* * *
313918 TTTAGCACTGTGTGTGCTCTCTG
1 ATTAGCACTTTGTGTACTCTCTG
*
313941 -TTAGTACTTTG-GTACTCTCTG
1 ATTAGCACTTTGTGTACTCTCTG
313962 TTTGTTCCGT
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
21 9 0.09
22 9 0.09
23 86 0.83
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (23 bp):
ATTAGCACTTTGTGTACTCTCTG
Found at i:316578 original size:2 final size:2
Alignment explanation
Indices: 316573--316614 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
316563 CATTTTTTTC
316573 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
316615 TCAAATGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:320018 original size:22 final size:21
Alignment explanation
Indices: 319976--320027 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
319966 AAGTCCATCC
319976 ATATTATTTTTTTAAATATTT
1 ATATTATTTTTTTAAATATTT
* *
319997 ATATTGTTTTATTTTAATATTT
1 ATATTATTTT-TTTAAATATTT
*
320019 A-ATAATTTT
1 ATATTATTTT
320028 ATATATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
ATATTATTTTTTTAAATATTT
Found at i:320042 original size:16 final size:16
Alignment explanation
Indices: 319996--320042 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
319986 TTTAAATATT
319996 TATATTGTTTTATTTTA
1 TATATT-TTTTATTTTA
* *
320013 -ATATTTAATAATTTTA
1 TATATTT-TTTATTTTA
320029 TATATTTTTTATTT
1 TATATTTTTTATTT
320043 ATTAAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATATTTTTTATTTTA
Found at i:322510 original size:23 final size:21
Alignment explanation
Indices: 322484--322528 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
322474 TTGTAAATAA
*
322484 TTATTTATTTGATTTACTTTTTT
1 TTATTTATTT-ATATA-TTTTTT
322507 TTATTTATTTATATATTTTTT
1 TTATTTATTTATATATTTTTT
322528 T
1 T
322529 AAAAATCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 4 0.19
23 10 0.48
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (21 bp):
TTATTTATTTATATATTTTTT
Found at i:334770 original size:17 final size:17
Alignment explanation
Indices: 334739--334802 Score: 92
Period size: 17 Copynumber: 3.8 Consensus size: 17
334729 GGGCCCAATG
*
334739 AAATTTGAATTTATTTT
1 AAATTTAAATTTATTTT
* *
334756 AAAATTAAGTTTATTTT
1 AAATTTAAATTTATTTT
*
334773 AAATTTAAATTTATTAT
1 AAATTTAAATTTATTTT
334790 AAATTTAAATTTA
1 AAATTTAAATTTA
334803 AATGTCCAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:334779 original size:6 final size:6
Alignment explanation
Indices: 334739--334805 Score: 52
Period size: 6 Copynumber: 11.7 Consensus size: 6
334729 GGGCCCAATG
* * * * *
334739 AAATTT GAATTT -ATTTT AAAATT AAGTTT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
334785 --ATTAT AAATTT AAATTT AAAT
1 AAATT-T AAATTT AAATTT AAAT
334806 GTCCAATTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
4 3 0.06
5 9 0.19
6 33 0.69
7 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:335397 original size:3 final size:3
Alignment explanation
Indices: 335389--335470 Score: 62
Period size: 3 Copynumber: 27.3 Consensus size: 3
335379 AAAACGATTC
* * *
335389 ATA ATA ATA ATA ATA ATA ATGA AT- ATG ATA ATA TTA ATA ATA AGA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
* * *
335434 GTA ATGA AT- TTA TTA ATA ATA ATAA ATA AT- ATA ATA A
1 ATA AT-A ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA A
335471 ATAAAAAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
2 5 0.08
3 50 0.78
4 9 0.14
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:335426 original size:24 final size:25
Alignment explanation
Indices: 335392--335469 Score: 83
Period size: 24 Copynumber: 3.2 Consensus size: 25
335382 ACGATTCATA
*
335392 ATAATAATAATAATAATGAAT-ATG
1 ATAATATTAATAATAATGAATAATG
*
335416 ATAATATTAATAATAA-GAGTAATG
1 ATAATATTAATAATAATGAATAATG
* *
335440 A-ATTTATTAATAATAATAAATAAT-
1 ATA-ATATTAATAATAATGAATAATG
335464 ATAATA
1 ATAATA
335470 AATAAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
23 4 0.09
24 34 0.77
25 6 0.14
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (25 bp):
ATAATATTAATAATAATGAATAATG
Found at i:335429 original size:30 final size:31
Alignment explanation
Indices: 335384--335473 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 31
335374 TTCAAAAAAC
*
335384 GATTCATAATAATAATAATAATAATGAATAT
1 GATTAATAATAATAATAATAATAATGAATAT
* * *
335415 GA-TAATATTAATAATAAGAGTAATGAAT-T
1 GATTAATAATAATAATAATAATAATGAATAT
* *
335444 TATTAATAATAATAAATAAT-ATAATAAATA
1 GATTAATAATAAT-AATAATAATAATGAATA
335474 AAAAAAATGG
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
29 2 0.04
30 38 0.81
31 7 0.15
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.36
Consensus pattern (31 bp):
GATTAATAATAATAATAATAATAATGAATAT
Found at i:336528 original size:30 final size:29
Alignment explanation
Indices: 336461--336747 Score: 282
Period size: 29 Copynumber: 9.8 Consensus size: 29
336451 GGAGGTCCCT
*
336461 AAACTGTCCGAAAATTCCATTTTT-ACACCC-
1 AAACT-TCCAAAAATT-CATTTTTGAC-CCCA
*
336491 GAACTTCCAAAAATCTCATTTTTGACCCCA
1 AAACTTCCAAAAAT-TCATTTTTGACCCCA
*
336521 AAACTTCCAAAAATTCCATTTTTGACCTCA
1 AAACTTCCAAAAATT-CATTTTTGACCCCA
** *
336551 AAACTTCCAAAAATTCAAAATTTAACCCCA
1 AAACTTCCAAAAATTC-ATTTTTGACCCCA
*
336581 AAACTTCCAAAAATTCCATTTTT-ACCCCC
1 AAACTTCCAAAAATT-CATTTTTGACCCCA
* * *
336610 AAACTTCAAAAAATCCA-TTTTGACCTCA
1 AAACTTCCAAAAATTCATTTTTGACCCCA
* * *
336638 AAACTTCTAAAATTTCCATTTTT-ACCCCT
1 AAACTTCCAAAAATT-CATTTTTGACCCCA
*
336667 AAACTTCCAAAAATCTTATTTTTGACCCCA
1 AAACTTCCAAAAAT-TCATTTTTGACCCCA
* *
336697 AAAC-TCCAAAAATTTCATTTTTGACCTCG
1 AAACTTCCAAAAA-TTCATTTTTGACCCCA
336726 AAAC-TCCAAAAATTCCATTTTT
1 AAACTTCCAAAAATT-CATTTTT
336748 ACCTCGAATG
Statistics
Matches: 217, Mismatches: 27, Indels: 27
0.80 0.10 0.10
Matches are distributed among these distances:
27 4 0.02
28 20 0.09
29 101 0.47
30 91 0.42
31 1 0.00
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCATTTTTGACCCCA
Found at i:336765 original size:29 final size:28
Alignment explanation
Indices: 336471--336785 Score: 133
Period size: 30 Copynumber: 10.8 Consensus size: 28
336461 AAACTGTCCG
*
336471 AAAATTCCATTTTTACACC-CG-AACTTCCA
1 AAAATTTCATTTTTA-ACCTCGAAAC-T-CA
* * * *
336500 AAAATCTCATTTTTGACCCCAAAACTTCCA
1 AAAATTTCATTTTTAACCTCGAAAC-T-CA
* * *
336530 AAAATTCCATTTTTGACCTCAAAACTTCCA
1 AAAATTTCATTTTTAACCTCGAAAC-T-CA
** * *
336560 AAAA-TTCAAAATTTAACCCCAAAACTTCCA
1 AAAATTTC-ATTTTTAACCTCGAAAC-T-CA
* * *
336590 AAAATTCCATTTTT-ACCCCCAAACTTCA
1 AAAATTTCATTTTTAACCTCGAAAC-TCA
* * * * *
336618 AAAAATCCA-TTTTGACCTCAAAACTTCT
1 AAAATTTCATTTTTAACCTCGAAAC-TCA
* *
336646 AAAATTTCCATTTTT-ACCCCTAAACTTCCA
1 AAAATTT-CATTTTTAACCTCGAAAC-T-CA
* * *
336676 AAAATCTT-ATTTTTGACCCCAAAACTCCA
1 AAAAT-TTCATTTTTAACCTCGAAACT-CA
*
336705 AAAATTTCATTTTTGACCTCGAAACTCCA
1 AAAATTTCATTTTTAACCTCGAAACT-CA
* **
336734 AAAATTCCATTTTT-ACCTCGAATGTCTA
1 AAAATTTCATTTTTAACCTCGAAACTC-A
336762 AAAATTTCATCTTTTAACCTCGAA
1 AAAATTTCAT-TTTTAACCTCGAA
336786 CTTCCCTAAA
Statistics
Matches: 240, Mismatches: 32, Indels: 27
0.80 0.11 0.09
Matches are distributed among these distances:
27 5 0.02
28 50 0.21
29 89 0.37
30 92 0.38
31 4 0.02
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (28 bp):
AAAATTTCATTTTTAACCTCGAAACTCA
Found at i:336766 original size:116 final size:117
Alignment explanation
Indices: 336461--336777 Score: 335
Period size: 116 Copynumber: 2.7 Consensus size: 117
336451 GGAGGTCCCT
* * * *
336461 AAACTGTCCGAAAATTCCATTTTTACACCCGAACTTCC-AAAAATCTCATTTTTGACCCCAAAAC
1 AAACT-TCCAAAAATTCCATTTTTACCCCCAAAC-TCCAAAAAATC-CA-TTTTGACCTCAAAAC
* *
336525 TTCCAAAAA-TTCCATTTTTGACCTCAAAACTTCCAAAAATTCAAAATTTAACCCCA
62 TTCTAAAAATTTCCATTTTT-ACCCCAAAACTTCCAAAAATTCAAAATTTAACCCCA
*
336581 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCAAAAAATCCATTTTGACCTCAAAACTTCT
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTCCAAAAAATCCATTTTGACCTCAAAACTTCT
* * ** *
336646 -AAAATTTCCATTTTTACCCCTAAACTTCCAAAAA-TCTTATTTTTGACCCCA
66 AAAAATTTCCATTTTTACCCCAAAACTTCCAAAAATTC-AAAATTTAACCCCA
* * * * * *
336697 AAAC-TCCAAAAATTTCATTTTTGACCTCGAAACTCCAAAAATTCCATTTTTACCTC-GAA-TGT
1 AAACTTCCAAAAATTCCATTTTT-ACCCCCAAACTCCAAAAAATCCATTTTGACCTCAAAACT-T
336759 CTAAAAATTT-CATCTTTTA
64 CTAAAAATTTCCAT-TTTTA
336778 ACCTCGAACT
Statistics
Matches: 171, Mismatches: 19, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
114 1 0.01
115 27 0.16
116 75 0.44
117 27 0.16
118 4 0.02
119 32 0.19
120 5 0.03
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (117 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCAAACTCCAAAAAATCCATTTTGACCTCAAAACTTCT
AAAAATTTCCATTTTTACCCCAAAACTTCCAAAAATTCAAAATTTAACCCCA
Found at i:336784 original size:30 final size:28
Alignment explanation
Indices: 336471--336785 Score: 204
Period size: 29 Copynumber: 10.8 Consensus size: 28
336461 AAACTGTCCG
* *
336471 AAAATTCCATTTTTACACCCG-AACTTCCA
1 AAAATTTCATTTTTAC-CTCGAAAC-TCCA
* * *
336500 AAAATCTCATTTTTGACCCCAAAACTTCCA
1 AAAATTTCATTTTT-ACCTCGAAAC-TCCA
* *
336530 AAAATTCCATTTTTGACCTCAAAACTTCCA
1 AAAATTTCATTTTT-ACCTCGAAAC-TCCA
* * * *
336560 AAAA-TTCAAAATTTAACCCCAAAACTTCCA
1 AAAATTTC--ATTTTTACCTCGAAAC-TCCA
* * * *
336590 AAAATTCCATTTTTACCCCCAAACTTCA
1 AAAATTTCATTTTTACCTCGAAACTCCA
* * * * * *
336618 AAAAATCCATTTTGACCTCAAAACTTCT
1 AAAATTTCATTTTTACCTCGAAACTCCA
* *
336646 AAAATTTCCATTTTTACCCCTAAACTTCCA
1 AAAATTT-CATTTTTACCTCGAAAC-TCCA
* *
336676 AAAATCTT-ATTTTTGACCCCAAAACTCCA
1 AAAAT-TTCATTTTT-ACCTCGAAACTCCA
336705 AAAATTTCATTTTTGACCTCGAAACTCCA
1 AAAATTTCATTTTT-ACCTCGAAACTCCA
* ** *
336734 AAAATTCCATTTTTACCTCGAATGTCTA
1 AAAATTTCATTTTTACCTCGAAACTCCA
336762 AAAATTTCATCTTTTAACCTCGAA
1 AAAATTTCAT-TTTT-ACCTCGAA
336786 CTTCCCTAAA
Statistics
Matches: 239, Mismatches: 35, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
28 53 0.22
29 95 0.40
30 83 0.35
31 8 0.03
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (28 bp):
AAAATTTCATTTTTACCTCGAAACTCCA
Found at i:337933 original size:23 final size:23
Alignment explanation
Indices: 337883--337935 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
337873 AAATTAGGTC
* **
337883 AAATT-AAATTATAATTTTTACG
1 AAATTAAAAATATAATTTTTAAA
*
337905 ATATTAAAAATATAATTTTTAAA
1 AAATTAAAAATATAATTTTTAAA
337928 AAATTAAA
1 AAATTAAA
337936 TCAAAATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
AAATTAAAAATATAATTTTTAAA
Found at i:338651 original size:17 final size:17
Alignment explanation
Indices: 338612--338654 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
338602 GATCGAATCG
*
338612 AATTTATTTATTTTTAA
1 AATTTATTTAGTTTTAA
338629 ATATTT-TTTAGTTTTAA
1 A-ATTTATTTAGTTTTAA
338646 TAATTTATT
1 -AATTTATT
338655 CAATTGAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
AATTTATTTAGTTTTAA
Found at i:340628 original size:17 final size:18
Alignment explanation
Indices: 340605--340658 Score: 76
Period size: 17 Copynumber: 3.1 Consensus size: 18
340595 TCAAACTCAT
*
340605 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAAA
*
340623 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAAA
340640 TTTAAATTTA-TTTAAAA
1 TTTAAATTTATTTTAAAA
340657 TT
1 TT
340659 ATTTTCAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 24 0.75
18 8 0.25
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:340654 original size:28 final size:28
Alignment explanation
Indices: 340623--340688 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
340613 TATTTTAAGA
* *
340623 TTAAATTTGTTTTAAAATTTAAATTTAT
1 TTAAATTTATTTTAAAATTTAAAATTAT
* *
340651 TTAAAATTATTTTCAAATTTAAAATTAT
1 TTAAATTTATTTTAAAATTTAAAATTAT
340679 TATAAATTTA
1 T-TAAATTTA
340689 AAATAAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 25 0.78
29 7 0.22
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (28 bp):
TTAAATTTATTTTAAAATTTAAAATTAT
Found at i:340687 original size:17 final size:18
Alignment explanation
Indices: 340649--340692 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
340639 ATTTAAATTT
*
340649 ATTTAAAATTATTTTCAA
1 ATTTAAAATTATTATCAA
340667 ATTTAAAATTATTAT-AA
1 ATTTAAAATTATTATCAA
340684 ATTTAAAAT
1 ATTTAAAAT
340693 AAATAAAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTTAAAATTATTATCAA
Found at i:341472 original size:30 final size:30
Alignment explanation
Indices: 341437--341524 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
341427 TAATTATTTT
* * *
341437 AATAATAATAATATTATTATTATTAAT-ATT
1 AATAATAATAATAATATT-TAATAAATAATT
* *
341467 GATAATAATTATAATATTTAATAAATAATT
1 AATAATAATAATAATATTTAATAAATAATT
* *
341497 AATAATAATAATAATAATAAATAAATAA
1 AATAATAATAATAATATTTAATAAATAA
341525 AAAGGAAGAC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
29 6 0.12
30 42 0.88
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (30 bp):
AATAATAATAATAATATTTAATAAATAATT
Found at i:341525 original size:4 final size:3
Alignment explanation
Indices: 341422--341516 Score: 64
Period size: 3 Copynumber: 30.7 Consensus size: 3
341412 TATTAATAGC
* ** * * * * * *
341422 AAT AAT AAT TAT TTT AAT AAT AAT AAT ATT ATT ATT ATT AAT ATT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
341470 AAT AAT TAT AAT ATTT AAT AAAT AATT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT A-AT AAT -AAT AA-T AAT AAT AAT AAT AAT AAT AA
341517 ATAAATAAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
3 67 0.89
4 8 0.11
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (3 bp):
AAT
Found at i:342564 original size:30 final size:29
Alignment explanation
Indices: 342516--342699 Score: 192
Period size: 30 Copynumber: 6.2 Consensus size: 29
342506 CTGAAAACTA
**
342516 CATTTTTACCCATGAACTTCCAAAAATCC
1 CATTTTTACCCAAAAACTTCCAAAAATCC
342545 CATTTTTGACCCAAAAACTTCCAAAAATCC
1 CATTTTT-ACCCAAAAACTTCCAAAAATCC
342575 CATTTTTGACCTC-AAAACTTCCAAAAATCC
1 CATTTTT-ACC-CAAAAACTTCCAAAAATCC
*** *
342605 CATTTTTACCCCCGAACTTCTAAAAATCC
1 CATTTTTACCCAAAAACTTCCAAAAATCC
* *
342634 CAATTTTACCCTCAAAACTTCCAAAAAATCC
1 CATTTTTACCC-AAAAACTTCC-AAAAATCC
** **
342665 CAAATTTACCCCTAAACTTCCAAAAA-CTC
1 CATTTTTACCCAAAAACTTCCAAAAATC-C
342694 CATTTT
1 CATTTT
342700 CGACCTCAAA
Statistics
Matches: 136, Mismatches: 13, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
28 2 0.01
29 44 0.32
30 71 0.52
31 19 0.14
ACGTcount: A:0.37, C:0.32, G:0.02, T:0.29
Consensus pattern (29 bp):
CATTTTTACCCAAAAACTTCCAAAAATCC
Found at i:342631 original size:59 final size:59
Alignment explanation
Indices: 342530--342712 Score: 235
Period size: 60 Copynumber: 3.1 Consensus size: 59
342520 TTTACCCATG
**
342530 AACTTCCAAAAATCCCATTTTTGACCCAAAAACTTCCAAAAATCCCATTTTTGACCTCAA
1 AACTTCCAAAAATCCCATTTTT-ACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCAA
* * *
342590 AACTTCCAAAAATCCCATTTTTACCCCCGAACTTCTAAAAATCCCAATTTT-ACCCTCAA
1 AACTTCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA-CCTCAA
** * *
342649 AACTTCCAAAAAATCCCAAATTTACCCCTAAACTTCCAAAAA-CTCCATTTTCGACCTCAA
1 AACTTCC-AAAAATCCCATTTTTACCCCCAAACTTCCAAAAATC-CCATTTTTGACCTCAA
342709 AACT
1 AACT
342713 CTCAAAATTA
Statistics
Matches: 107, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
58 1 0.01
59 38 0.36
60 67 0.63
61 1 0.01
ACGTcount: A:0.38, C:0.32, G:0.02, T:0.27
Consensus pattern (59 bp):
AACTTCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCAA
Found at i:342651 original size:89 final size:89
Alignment explanation
Indices: 342509--342699 Score: 244
Period size: 89 Copynumber: 2.1 Consensus size: 89
342499 AAACTATCTG
* * *
342509 AAAACTACATTTTTACCCATGAACTTCCAAAAATCCCATTTTTGACCCAAAAACTTCC-AAAAAT
1 AAAACTCCATTTTTACCCACGAACTTCCAAAAATCCCAATTTTGACCCAAAAACTTCCAAAAAAT
** *
342573 CCCATTTTTGACCTCAAAACTTCCA
66 CCCAAATTT-ACCCCAAAACTTCCA
* * *
342598 AAAA-TCCCATTTTTACCCCCGAACTTCTAAAAATCCCAATTTT-ACCCTCAAAACTTCCAAAAA
1 AAAACT-CCATTTTTACCCACGAACTTCCAAAAATCCCAATTTTGACCC-AAAAACTTCCAAAAA
*
342661 ATCCCAAATTTACCCCTAAACTTCCA
64 ATCCCAAATTTACCCCAAAACTTCCA
342687 AAAACTCCATTTT
1 AAAACTCCATTTT
342700 CGACCTCAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
88 5 0.06
89 69 0.78
90 14 0.16
ACGTcount: A:0.38, C:0.31, G:0.02, T:0.29
Consensus pattern (89 bp):
AAAACTCCATTTTTACCCACGAACTTCCAAAAATCCCAATTTTGACCCAAAAACTTCCAAAAAAT
CCCAAATTTACCCCAAAACTTCCA
Found at i:343195 original size:96 final size:97
Alignment explanation
Indices: 343055--343240 Score: 263
Period size: 96 Copynumber: 1.9 Consensus size: 97
343045 AAAACTTTAA
* * * *
343055 AATCGAGGCAATGTTCTGTTACTTCGAGTTTCGAAAATTTGCGCCTTAACTTCCTAGGTGCAA-T
1 AATCGAGGCAATGTTCTCTTACTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTACAACC
*
343119 TTTTCTTCAAATTGAAATAATCGAATACCCTT
66 TTTTCTTCAAATCGAAATAATCGAATACCCTT
343151 AATCGAGGCAATGTT-TCCTTATCTTCGA--TTCTGAAAATTTGCGCCTTAACTTACTAGGTACA
1 AATCGAGGCAATGTTCT-CTTA-CTTCGAGTTTC-GAAAATTTGCGCCTTAACTTACTAGGTACA
*
343213 ACCTTTTCTTCAAATCGAGATAATCGAA
63 ACCTTTTCTTCAAATCGAAATAATCGAA
343241 CATCCTTTCC
Statistics
Matches: 80, Mismatches: 6, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
95 4 0.05
96 47 0.59
97 29 0.36
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (97 bp):
AATCGAGGCAATGTTCTCTTACTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTACAACC
TTTTCTTCAAATCGAAATAATCGAATACCCTT
Found at i:344713 original size:52 final size:52
Alignment explanation
Indices: 344625--344916 Score: 458
Period size: 52 Copynumber: 5.6 Consensus size: 52
344615 TTCTCATTTA
* * * * *
344625 ATACTCATGATGACACATTGTCATCGGACCTCATAATCCGAAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATACGTAAAGGATTCAT
* * * *
344677 ATGCTCACGATGATACATAGTCGTCGGACCTTATAATTCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATACGTAAAGGATTCAT
* *
344729 ATACTCACGATAACACATATTCATCGGACCTTATAATACGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATACGTAAAGGATTCAT
*
344781 ATACTCACGATGACACATATTCATCGGACCTTATAATACGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATACGTAAAGGATTCAT
* *
344833 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATACGTAAAGGATTCAT
344885 ATACTCACGATGACACATAGTCATCGGACCTT
1 ATACTCACGATGACACATAGTCATCGGACCTT
344917 TTGCATTTAC
Statistics
Matches: 222, Mismatches: 18, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
52 222 1.00
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTTATAATACGTAAAGGATTCAT
Found at i:348292 original size:32 final size:32
Alignment explanation
Indices: 348212--348272 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
348202 ATAATCACAT
*
348212 CTCTTAAATAGATATAACCATTCAAGTAAGAC
1 CTCTTAAATAGATATAACAATTCAAGTAAGAC
* *
348244 CTCATAAATAAATATAACAATTCAAGTAA
1 CTCTTAAATAGATATAACAATTCAAGTAA
348273 TATTACTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (32 bp):
CTCTTAAATAGATATAACAATTCAAGTAAGAC
Found at i:352608 original size:17 final size:18
Alignment explanation
Indices: 352572--352610 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
352562 ATTGCTTCTC
* *
352572 AAAAGTATTTTTGGGCAA
1 AAAAGTACTTTTGAGCAA
352590 AAAAGTACTTTTGAG-AA
1 AAAAGTACTTTTGAGCAA
352607 AAAA
1 AAAA
352611 CTAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.28
Consensus pattern (18 bp):
AAAAGTACTTTTGAGCAA
Found at i:360272 original size:9 final size:9
Alignment explanation
Indices: 360258--360285 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
360248 GTAGATTGCT
360258 TGAAGAGTA
1 TGAAGAGTA
360267 TGAAGAGTA
1 TGAAGAGTA
360276 TGAAGAGTA
1 TGAAGAGTA
360285 T
1 T
360286 TGGTTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (9 bp):
TGAAGAGTA
Found at i:360854 original size:262 final size:262
Alignment explanation
Indices: 360389--360916 Score: 1056
Period size: 262 Copynumber: 2.0 Consensus size: 262
360379 TCAAATTTTC
360389 ATGTGAGGAGATGACTGTAACGCTTGAAGATTTTACTTTAATAATTGACCTTCCAAACAATGTGC
1 ATGTGAGGAGATGACTGTAACGCTTGAAGATTTTACTTTAATAATTGACCTTCCAAACAATGTGC
360454 AAGCAATAATTGGAGTTAGCAACATTGACATGGGGTACGAATGTGATCGACTATTTGACGTTGTC
66 AAGCAATAATTGGAGTTAGCAACATTGACATGGGGTACGAATGTGATCGACTATTTGACGTTGTC
360519 TTATCTAAGGATAAAGACAATAATAAATTAGATGAAAATTGGGTGAAATATATACGATTGAAGAG
131 TTATCTAAGGATAAAGACAATAATAAATTAGATGAAAATTGGGTGAAATATATACGATTGAAGAG
360584 GCTTGTCAAACCAATCTCTCTAACGCATACAATTGTGTAGGAGATGGATCGATATACTAGAACAT
196 GCTTGTCAAACCAATCTCTCTAACGCATACAATTGTGTAGGAGATGGATCGATATACTAGAACAT
360649 AA
261 AA
360651 ATGTGAGGAGATGACTGTAACGCTTGAAGATTTTACTTTAATAATTGACCTTCCAAACAATGTGC
1 ATGTGAGGAGATGACTGTAACGCTTGAAGATTTTACTTTAATAATTGACCTTCCAAACAATGTGC
360716 AAGCAATAATTGGAGTTAGCAACATTGACATGGGGTACGAATGTGATCGACTATTTGACGTTGTC
66 AAGCAATAATTGGAGTTAGCAACATTGACATGGGGTACGAATGTGATCGACTATTTGACGTTGTC
360781 TTATCTAAGGATAAAGACAATAATAAATTAGATGAAAATTGGGTGAAATATATACGATTGAAGAG
131 TTATCTAAGGATAAAGACAATAATAAATTAGATGAAAATTGGGTGAAATATATACGATTGAAGAG
360846 GCTTGTCAAACCAATCTCTCTAACGCATACAATTGTGTAGGAGATGGATCGATATACTAGAACAT
196 GCTTGTCAAACCAATCTCTCTAACGCATACAATTGTGTAGGAGATGGATCGATATACTAGAACAT
360911 AA
261 AA
360913 ATGT
1 ATGT
360917 TTTAGATAGT
Statistics
Matches: 266, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
262 266 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (262 bp):
ATGTGAGGAGATGACTGTAACGCTTGAAGATTTTACTTTAATAATTGACCTTCCAAACAATGTGC
AAGCAATAATTGGAGTTAGCAACATTGACATGGGGTACGAATGTGATCGACTATTTGACGTTGTC
TTATCTAAGGATAAAGACAATAATAAATTAGATGAAAATTGGGTGAAATATATACGATTGAAGAG
GCTTGTCAAACCAATCTCTCTAACGCATACAATTGTGTAGGAGATGGATCGATATACTAGAACAT
AA
Found at i:361369 original size:20 final size:22
Alignment explanation
Indices: 361344--361385 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
361334 TTTTTACTTT
*
361344 TTCAAATTTTAA-AAT-TTAAA
1 TTCAAATGTTAACAATATTAAA
361364 TTCAAATGTTAACAATATTAAA
1 TTCAAATGTTAACAATATTAAA
361386 ATTATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 3 0.16
22 5 0.26
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.40
Consensus pattern (22 bp):
TTCAAATGTTAACAATATTAAA
Found at i:374854 original size:59 final size:59
Alignment explanation
Indices: 374762--374881 Score: 195
Period size: 59 Copynumber: 2.0 Consensus size: 59
374752 TTTCGAGGCC
* * * *
374762 ATAGTCAATCTGCATTGCATATTGTAATTGAAGTGGATTGTCACTTTGTTCGGGATGCA
1 ATAGTCAATCTACATTGCATATTGCAATCGAAGTGGATTGTCACTTTGTTAGGGATGCA
*
374821 ATAGTCAATCTACGTTGCATATTGCAATCGAAGTGGATTGTCACTTTGTTAGGGATGCA
1 ATAGTCAATCTACATTGCATATTGCAATCGAAGTGGATTGTCACTTTGTTAGGGATGCA
374880 AT
1 AT
374882 CTTGTAATGA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (59 bp):
ATAGTCAATCTACATTGCATATTGCAATCGAAGTGGATTGTCACTTTGTTAGGGATGCA
Found at i:375340 original size:23 final size:23
Alignment explanation
Indices: 375296--375341 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
375286 GGTAATAAAA
*
375296 TATACATGTGTAAAAATTATATT
1 TATACATGTGTAAAAATAATATT
*
375319 TATACATTTGT-AAAATAAATATT
1 TATACATGTGTAAAAAT-AATATT
375342 AATTTACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (23 bp):
TATACATGTGTAAAAATAATATT
Found at i:375445 original size:12 final size:12
Alignment explanation
Indices: 375428--375461 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
375418 ATAAAAGAAT
375428 AAAGAAAGAAAA
1 AAAGAAAGAAAA
*
375440 AAAGAAACAAAA
1 AAAGAAAGAAAA
*
375452 GAAGAAAGAA
1 AAAGAAAGAA
375462 CAGAGGCTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAAA
Found at i:375979 original size:3 final size:3
Alignment explanation
Indices: 375971--375997 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
375961 AATAGTGTAA
375971 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
375998 TTAGCTAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:377668 original size:3 final size:3
Alignment explanation
Indices: 377660--377731 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
377650 AATAGTGTAA
*
377660 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
377708 ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT
377732 GTAACTAGTA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
ATT
Done.