Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009895.1 Kokia drynarioides strain JFW-HI SEQ_124631, 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: 69357
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:286 original size:7 final size:7
Alignment explanation
Indices: 249--302 Score: 62
Period size: 7 Copynumber: 8.3 Consensus size: 7
239 ACTCTTTTTT
249 TTCCTTC
1 TTCCTTC
256 -TCCTTC
1 TTCCTTC
*
262 TTCC-CC
1 TTCCTTC
268 TT-CTTC
1 TTCCTTC
274 -TCCTTC
1 TTCCTTC
280 TTCCTTC
1 TTCCTTC
287 TTCCTTC
1 TTCCTTC
*
294 TTCTTTC
1 TTCCTTC
301 TT
1 TT
303 TCTTTCTTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 2 0.05
6 14 0.35
7 24 0.60
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (7 bp):
TTCCTTC
Found at i:301 original size:4 final size:4
Alignment explanation
Indices: 294--332 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
284 TTCTTCCTTC
*
294 TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
333 CTTCATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:305 original size:25 final size:25
Alignment explanation
Indices: 248--306 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
238 TACTCTTTTT
*
248 TTTCCTTC-TCCTTCTTCC-CCTTC
1 TTTCCTTCTTCCTTCTTCCTTCTTC
271 TTCTCCTTCTTCCTTCTTCCTTCTTC
1 TT-TCCTTCTTCCTTCTTCCTTCTTC
*
297 TTTCTTTCTT
1 TTTCCTTCTT
307 TCTTTCTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 2 0.06
24 6 0.19
25 17 0.55
26 6 0.19
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTCCTTCTTCCTTCTTCCTTCTTC
Found at i:316 original size:21 final size:20
Alignment explanation
Indices: 292--336 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
282 CCTTCTTCCT
292 TCTTCTTTCTTTCTTTCTTTC
1 TCTTCTTTCTTTCTTT-TTTC
*
313 TCTTTTTTCTTTCTTTTTTC
1 TCTTCTTTCTTTCTTTTTTC
333 -CTTC
1 TCTTC
337 ATTTTTCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 4 0.18
21 15 0.68
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (20 bp):
TCTTCTTTCTTTCTTTTTTC
Found at i:341 original size:12 final size:11
Alignment explanation
Indices: 287--343 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
277 TTCTTCCTTC
*
287 TTCCTTCTTCT
1 TTCCTTCTTTT
*
298 TTCTTTCTTTCT
1 TTCCTTCTTT-T
310 TT-C-TCTTTT
1 TTCCTTCTTTT
*
319 TTCTTTCTTTT
1 TTCCTTCTTTT
*
330 TTCCTTCATTT
1 TTCCTTCTTTT
341 TTC
1 TTC
344 GTTGGTTCCC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 3 0.08
10 5 0.14
11 26 0.70
12 3 0.08
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (11 bp):
TTCCTTCTTTT
Found at i:341 original size:21 final size:21
Alignment explanation
Indices: 287--341 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 21
277 TTCTTCCTTC
287 TTCCTTCTTCTTTCTTTCTTTCT
1 TTCCTTC-T-TTTCTTTCTTTCT
310 TTCTCTT-TTTTCTTTCTTT-T
1 TTC-CTTCTTTTCTTTCTTTCT
330 TTCCTTCATTTT
1 TTCCTTC-TTTT
342 TCGTTGGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 3 0.10
20 4 0.14
21 15 0.52
22 1 0.03
23 3 0.10
24 3 0.10
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (21 bp):
TTCCTTCTTTTCTTTCTTTCT
Found at i:2475 original size:40 final size:40
Alignment explanation
Indices: 2420--2496 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
2410 GATGCCAAAT
2420 TGCCACCTCTAGGTTGAATACTAAGTAGTTTTTAAGTAAC
1 TGCCACCTCTAGGTTGAATACTAAGTAGTTTTTAAGTAAC
*
2460 TGCCACCTCTAGGTTGAATGCTAAGTAGTTTTTAAGT
1 TGCCACCTCTAGGTTGAATACTAAGTAGTTTTTAAGT
2497 TTCCTATTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (40 bp):
TGCCACCTCTAGGTTGAATACTAAGTAGTTTTTAAGTAAC
Found at i:10860 original size:18 final size:17
Alignment explanation
Indices: 10839--10876 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
10829 CACGTCAGCA
10839 AAAAAT-TAATTATTTTT
1 AAAAATATAATT-TTTTT
*
10856 TAAAATATAATTTTTTT
1 AAAAATATAATTTTTTT
10873 AAAA
1 AAAA
10877 TATTTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAAAATATAATTTTTTT
Found at i:10884 original size:10 final size:11
Alignment explanation
Indices: 10864--10904 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
10854 TTTAAAATAT
*
10864 AATTTTTTTAA
1 AATTATTTTAA
10875 AA-TATTTTAA
1 AATTATTTTAA
*
10885 AATTAATTTAA
1 AATTATTTTAA
10896 AATTATTTT
1 AATTATTTT
10905 TTAAATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTATTTTAA
Found at i:15192 original size:2 final size:2
Alignment explanation
Indices: 15185--15210 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15175 CATGGATTTG
15185 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
15211 GGATTGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17941 original size:29 final size:31
Alignment explanation
Indices: 17885--17943 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
17875 ATATATTTGA
* *
17885 ATCACAATTAGAATTTTGTGTGTACAATTGT
1 ATCACAATTAGAAATTTATGTGTACAATTGT
17916 ATCA-AATTA-AAATTTATGTGTACAATTG
1 ATCACAATTAGAAATTTATGTGTACAATTG
17944 CACATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 17 0.65
30 5 0.19
31 4 0.15
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (31 bp):
ATCACAATTAGAAATTTATGTGTACAATTGT
Found at i:17954 original size:31 final size:29
Alignment explanation
Indices: 17903--17965 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
17893 TAGAATTTTG
* *
17903 TGTGTACAATTGTATCAAATTAAAATTTA
1 TGTGTACAATTGCATCAAATTAAAATTAA
*
17932 TGTGTACAATTGCACATTAAATTAAAATTAA
1 TGTGTACAATTG--CATCAAATTAAAATTAA
17963 TGT
1 TGT
17966 ATAATTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 12 0.41
31 17 0.59
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (29 bp):
TGTGTACAATTGCATCAAATTAAAATTAA
Found at i:18075 original size:16 final size:16
Alignment explanation
Indices: 18056--18099 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
18046 TAAATAAAAC
* *
18056 TGTAATGAAATAGGGT
1 TGTAATGAAATAGAGA
18072 TGTAATGAAATAGAGA
1 TGTAATGAAATAGAGA
*
18088 TGTAATGTAATA
1 TGTAATGAAATA
18100 AAATTGTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.25, T:0.32
Consensus pattern (16 bp):
TGTAATGAAATAGAGA
Found at i:18107 original size:16 final size:16
Alignment explanation
Indices: 18047--18109 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
18037 CATTGGAATT
*
18047 AAATAAAACTGTAATG
1 AAATAAAATTGTAATG
***
18063 AAATAGGGTTGTAATG
1 AAATAAAATTGTAATG
*
18079 AAATAGAGA-TGTAATG
1 AAATA-AAATTGTAATG
*
18095 TAATAAAATTGTAAT
1 AAATAAAATTGTAAT
18110 TAATAATTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
15 2 0.05
16 34 0.92
17 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.19, T:0.30
Consensus pattern (16 bp):
AAATAAAATTGTAATG
Found at i:18741 original size:15 final size:15
Alignment explanation
Indices: 18721--18751 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18711 TATTAAAAAG
*
18721 AATTAAATAAATTTA
1 AATTAAATAAAATTA
18736 AATTAAATAAAATTA
1 AATTAAATAAAATTA
18751 A
1 A
18752 CATGTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATTAAATAAAATTA
Found at i:19576 original size:19 final size:18
Alignment explanation
Indices: 19552--19624 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 18
19542 TTTAACTAAC
*
19552 TTATATATTGTTTTAATTT
1 TTATAAATT-TTTTAATTT
* *
19571 TTATATA-TTTTTAA--A
1 TTATAAATTTTTTAATTT
* *
19586 ATATAAATTTTTGAATTT
1 TTATAAATTTTTTAATTT
19604 TTATAAATTATTTTAATTT
1 TTATAAATT-TTTTAATTT
19623 TT
1 TT
19625 GTTGTATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
15 5 0.12
16 6 0.14
17 6 0.14
18 9 0.21
19 17 0.40
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TTATAAATTTTTTAATTT
Found at i:23605 original size:18 final size:18
Alignment explanation
Indices: 23582--23650 Score: 61
Period size: 18 Copynumber: 3.7 Consensus size: 18
23572 AGGTCTTCGC
23582 CAATCAATTATTTAATTA
1 CAATCAATTATTTAATTA
*
23600 CAATCAATTAAATAATAATT-
1 CAATCAATT--AT-TTAATTA
*
23620 CAAAACAA-TATTTAATTA
1 C-AATCAATTATTTAATTA
*
23638 CAATCAAATATTT
1 CAATCAATTATTT
23651 TAAAGGTCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
17 10 0.24
18 17 0.41
20 4 0.10
21 10 0.24
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.38
Consensus pattern (18 bp):
CAATCAATTATTTAATTA
Found at i:25092 original size:28 final size:28
Alignment explanation
Indices: 25052--25106 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
25042 ATATGCTATC
25052 ATTTTGAATTTTTTATATTTT-TAATTTG
1 ATTTTGAATTTTTT-TATTTTATAATTTG
* *
25080 ATTTTGATTTTTTTTTTTTTATAATTT
1 ATTTTGAATTTTTTTATTTTATAATTT
25107 TTATATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (28 bp):
ATTTTGAATTTTTTTATTTTATAATTTG
Found at i:29578 original size:29 final size:29
Alignment explanation
Indices: 29483--29791 Score: 191
Period size: 29 Copynumber: 10.8 Consensus size: 29
29473 AGACGGATTC
* * * *
29483 AAAAT-GTGATTTTTGGATGCTCGGGGGT
1 AAAATGGTAATTTTTGGAAGTTCGGGGTT
* *
29511 AAAATGGTAA--TCTGGACA-TTCGGGGGT
1 AAAATGGTAATTTTTGGA-AGTTCGGGGTT
29538 AAAATGGTAA-TTTTGGAATGTTCGGGGTTT
1 AAAATGGTAATTTTTGGAA-GTTCGGGG-TT
* *
29568 AAAATGG-AATTTTTAGACA-TCCGAGGGTT
1 AAAATGGTAATTTTTGGA-AGTTCG-GGGTT
*
29597 -AAATGGTAATCTTTGGAAGGTTCGGGGTT
1 AAAATGGTAATTTTTGGAA-GTTCGGGGTT
* * ** *
29626 AAAAGTAG-AATTTTTAGATA-TTTAGGGTCA
1 AAAA-TGGTAATTTTTGGA-AGTTCGGGGT-T
*
29656 AAAATGG-AATTTTTGAAAGTTC-GGGTGT
1 AAAATGGTAATTTTTGGAAGTTCGGGGT-T
**
29684 AAAATGGTAATTTTTGGAAAATCGGGGTT
1 AAAATGGTAATTTTTGGAAGTTCGGGGTT
*
29713 AAAATGG-AATTTTTGGAAGCTCAGGGG-T
1 AAAATGGTAATTTTTGGAAGTTC-GGGGTT
** *
29741 AAAATGGTAA-TTTTGGAAAGTTTAGGGTC
1 AAAATGGTAATTTTTGG-AAGTTCGGGGTT
*
29770 AAAAT-GTGATTTTTGGATAGTT
1 AAAATGGTAATTTTTGGA-AGTT
29792 TAAAGACCTC
Statistics
Matches: 223, Mismatches: 33, Indels: 49
0.73 0.11 0.16
Matches are distributed among these distances:
27 24 0.11
28 63 0.28
29 93 0.42
30 39 0.17
31 4 0.02
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.35
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGAAGTTCGGGGTT
Found at i:29768 original size:28 final size:28
Alignment explanation
Indices: 29507--29775 Score: 126
Period size: 28 Copynumber: 9.4 Consensus size: 28
29497 GGATGCTCGG
* * *
29507 GGGTAAAATGGTAA-TCTGGACA-TTCGG
1 GGGTAAAATGGTAATTTTGGAAAGTTC-A
* *
29534 GGGTAAAATGGTAATTTTGGAATGTTCG
1 GGGTAAAATGGTAATTTTGGAAAGTTCA
* * *
29562 GGGTTTAAAATGG-AATTTTTAGACA-TCCGA
1 GGG--TAAAATGGTAA-TTTTGGAAAGTTC-A
* * *
29592 GGGTTAAATGGTAATCTTTGGAAGGTTCG
1 GGGTAAAATGGTAAT-TTTGGAAAGTTCA
* * * *
29621 GGGTTAAAAGTAG-AATTTTTAGATA-TTTA
1 GGG-TAAAA-TGGTAA-TTTTGGAAAGTTCA
* *
29650 GGGTCAAAAATGG-AATTTTTGAAAGTTCG
1 GGGT--AAAATGGTAATTTTGGAAAGTTCA
* *
29679 GGTGTAAAATGGTAATTTTTGGAAA-ATCG
1 GG-GTAAAATGGTAA-TTTTGGAAAGTTCA
*
29708 GGGTTAAAATGG-AATTTTTGG-AAGCTCA
1 GGG-TAAAATGGTAA-TTTTGGAAAGTTCA
*
29736 GGGGTAAAATGGTAATTTTGGAAAGTTTA
1 -GGGTAAAATGGTAATTTTGGAAAGTTCA
29765 GGGTCAAAATG
1 GGGT-AAAATG
29776 TGATTTTTGG
Statistics
Matches: 186, Mismatches: 32, Indels: 46
0.70 0.12 0.17
Matches are distributed among these distances:
27 16 0.09
28 62 0.33
29 61 0.33
30 44 0.24
31 3 0.02
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTGGAAAGTTCA
Found at i:29774 original size:57 final size:57
Alignment explanation
Indices: 29481--29786 Score: 186
Period size: 57 Copynumber: 5.3 Consensus size: 57
29471 ATAGACGGAT
* * * * **
29481 TCAAAATGTG-ATTTTTGGATGCTCGGGGGTAAAATGGTAA--TCTGGACATTCGGGGG
1 TCAAAATG-GAATTTTTGGAAGCTCGGGTGTAAAATGGTAATTTTTGGAAATT-TAGGG
* * * * **
29537 T-AAAATGGTAA-TTTTGGAATGTTCGGGGTTTAAAATGG-AATTTTTAGACATCCGAGGG
1 TCAAAATGG-AATTTTTGGAA-GCTC-GGGTGTAAAATGGTAATTTTTGGAAAT-TTAGGG
* * * * * *
29595 T-TAAATGGTAATCTTTGGAAGGTTCGGG-GTTAAAAGTAG-AATTTTTAGATATTTAGGG
1 TCAAAATGG-AATTTTTGGAA-GCTCGGGTG-TAAAA-TGGTAATTTTTGGAAATTTAGGG
* * * **
29653 TCAAAAATGGAATTTTTGAAAGTTCGGGTGTAAAATGGTAATTTTTGGAAAATCGGGG
1 TC-AAAATGGAATTTTTGGAAGCTCGGGTGTAAAATGGTAATTTTTGGAAATTTAGGG
*
29711 TTAAAATGGAATTTTTGGAAGCTCAGGG-GTAAAATGGTAA-TTTTGGAAAGTTTAGGG
1 TCAAAATGGAATTTTTGGAAGCTC-GGGTGTAAAATGGTAATTTTTGGAAA-TTTAGGG
29768 TCAAAATGTG-ATTTTTGGA
1 TCAAAATG-GAATTTTTGGA
29787 TAGTTTAAAG
Statistics
Matches: 201, Mismatches: 32, Indels: 33
0.76 0.12 0.12
Matches are distributed among these distances:
54 1 0.00
55 13 0.06
56 16 0.08
57 65 0.32
58 65 0.32
59 35 0.17
60 6 0.03
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.34
Consensus pattern (57 bp):
TCAAAATGGAATTTTTGGAAGCTCGGGTGTAAAATGGTAATTTTTGGAAATTTAGGG
Found at i:31725 original size:24 final size:23
Alignment explanation
Indices: 31697--31744 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
31687 AAATTGTTTC
*
31697 AAATATAA-TTAAATTCAAATTTAA
1 AAATA-AATTTAAAATC-AATTTAA
31721 AAATAAATTTAAAATCAATTTAA
1 AAATAAATTTAAAATCAATTTAA
31744 A
1 A
31745 CCTAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (23 bp):
AAATAAATTTAAAATCAATTTAA
Found at i:33510 original size:27 final size:27
Alignment explanation
Indices: 33480--33533 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
33470 TTTACTATGT
33480 TTTTCATATACCACAACTTTAAATTTA
1 TTTTCATATACCACAACTTTAAATTTA
33507 TTTTCATATACCACAACTTTAAATTTA
1 TTTTCATATACCACAACTTTAAATTTA
33534 AATATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (27 bp):
TTTTCATATACCACAACTTTAAATTTA
Found at i:37684 original size:18 final size:18
Alignment explanation
Indices: 37661--37697 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
37651 TAGTACGCTT
37661 TTTAATTTTGCTTATGCA
1 TTTAATTTTGCTTATGCA
*
37679 TTTAATTTTGCTTTTGCA
1 TTTAATTTTGCTTATGCA
37697 T
1 T
37698 GTGATTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.59
Consensus pattern (18 bp):
TTTAATTTTGCTTATGCA
Found at i:37704 original size:18 final size:18
Alignment explanation
Indices: 37663--37705 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
37653 GTACGCTTTT
*
37663 TAATTTTGCTTATGCATT
1 TAATTTTGCTTATGCATG
*
37681 TAATTTTGCTTTTGCATG
1 TAATTTTGCTTATGCATG
*
37699 TGATTTT
1 TAATTTT
37706 AGGGTTGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.09, G:0.14, T:0.58
Consensus pattern (18 bp):
TAATTTTGCTTATGCATG
Found at i:39631 original size:48 final size:48
Alignment explanation
Indices: 39560--39839 Score: 398
Period size: 48 Copynumber: 5.8 Consensus size: 48
39550 TGGAGGTGGT
*
39560 TTCACAACGGGAGGACTTGGGTATACAGGAGGCGTTGGTGTTGGCGGC
1 TTCACAATGGGAGGACTTGGGTATACAGGAGGCGTTGGTGTTGGCGGC
39608 TTCACAATGGGAGGACTTGGGTATACAGGAGGCGTTGGTGTTGGCGGC
1 TTCACAATGGGAGGACTTGGGTATACAGGAGGCGTTGGTGTTGGCGGC
* *
39656 TTCACAATGGGAGGACTAGGGTATACAGGAGGTGTTGGTGTTGGCGGC
1 TTCACAATGGGAGGACTTGGGTATACAGGAGGCGTTGGTGTTGGCGGC
* * *
39704 TTCACAATGGGAGGACTTGGGTATACAGGAGGCTTTGGAGCTGGCGGC
1 TTCACAATGGGAGGACTTGGGTATACAGGAGGCGTTGGTGTTGGCGGC
* * * * * *
39752 TTCACAATGGGAGGACTGGGGTAGACGGGAGTCTTTGGTGATGGCGGC
1 TTCACAATGGGAGGACTTGGGTATACAGGAGGCGTTGGTGTTGGCGGC
* * * * * *
39800 TTTACAATAGGAGGACTGGGGTAGACGGGAGGCTTTGGTG
1 TTCACAATGGGAGGACTTGGGTATACAGGAGGCGTTGGTG
39840 GTGGTGAAGT
Statistics
Matches: 215, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 215 1.00
ACGTcount: A:0.20, C:0.14, G:0.42, T:0.24
Consensus pattern (48 bp):
TTCACAATGGGAGGACTTGGGTATACAGGAGGCGTTGGTGTTGGCGGC
Found at i:40817 original size:4 final size:4
Alignment explanation
Indices: 40808--40856 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
40798 TTAAATCCAA
40808 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
40856 C
1 C
40857 CGTAAACCAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.24, C:0.51, G:0.00, T:0.24
Consensus pattern (4 bp):
CATC
Found at i:41388 original size:6 final size:6
Alignment explanation
Indices: 41379--41419 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
41369 AAATTAAAAT
41379 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTT
41420 GAATTCTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:51309 original size:3 final size:3
Alignment explanation
Indices: 51301--51328 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
51291 GAGTTCATTA
51301 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
51329 TGTCGCTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:55372 original size:29 final size:29
Alignment explanation
Indices: 55329--55624 Score: 209
Period size: 29 Copynumber: 10.2 Consensus size: 29
55319 ACTCGAGGGC
* *
55329 AAAATGGTAATTTTTGCAAGTTTCGGGATCA
1 AAAATGG-AATTTTTGAAAGTTTCGGGGT-A
*
55360 AAAATGGAATTTTT-AGAAGTTTGGGGGT-
1 AAAATGGAATTTTTGA-AAGTTTCGGGGTA
* **
55388 AAAATGTAATTTTTGGAAA-TTTTAGGGTCA
1 AAAATGGAATTTTT-GAAAGTTTCGGGGT-A
55418 AAAATGGAATTTTTGAAAGTTT-GAGGGTA
1 AAAATGGAATTTTTGAAAGTTTCG-GGGTA
* * *
55447 AAAATGTATTTTTTGGAAG-TTCGGGGTA
1 AAAATGGAATTTTTGAAAGTTTCGGGGTA
* *
55475 AAAATGTG-ATTTTTGGAAGTTTCGAGGTTA
1 AAAATG-GAATTTTTGAAAGTTTCG-GGGTA
**
55505 AAAATGGAATTTTCAAAAGTTT-GAGGGTA
1 AAAATGGAATTTTTGAAAGTTTCG-GGGTA
* *
55534 AAAATGTAATTTTTAGAAA-TTTGGGGGT-
1 AAAATGGAATTTTT-GAAAGTTTCGGGGTA
* ** *
55562 AAAATGTAATTTTT-AGAAGTTTTAGGGTC
1 AAAATGGAATTTTTGA-AAGTTTCGGGGTA
* * *
55591 AAAATGGAACTTTAGAGAAGTTT-GGGGTC
1 AAAATGGAATTTTTGA-AAGTTTCGGGGTA
55620 AAAAT
1 AAAAT
55625 ATAATTACTA
Statistics
Matches: 220, Mismatches: 27, Indels: 38
0.77 0.09 0.13
Matches are distributed among these distances:
26 1 0.00
27 2 0.01
28 64 0.29
29 75 0.34
30 71 0.32
31 7 0.03
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGAAAGTTTCGGGGTA
Found at i:55419 original size:58 final size:59
Alignment explanation
Indices: 55329--55630 Score: 257
Period size: 58 Copynumber: 5.2 Consensus size: 59
55319 ACTCGAGGGC
* * *
55329 AAAATGGTAATTTTT-GCAAGTTTCGGGATCAAAAATGGAATTTTTAGAAGTTTGGGGGT-
1 AAAAT-GTAATTTTTGGAAATTTTAGGG-TCAAAAATGGAATTTTTAGAAGTTTGGGGGTA
*
55388 AAAATGTAATTTTTGGAAATTTTAGGGTCAAAAATGGAATTTTT-GAAAGTTTGAGGGTA
1 AAAATGTAATTTTTGGAAATTTTAGGGTCAAAAATGGAATTTTTAG-AAGTTTGGGGGTA
* * ** * * *
55447 AAAATGTATTTTTTGG-AAGTTCGGGGT-AAAAATGTG-ATTTTTGGAAGTTTCGAGGTTA
1 AAAATGTAATTTTTGGAAATTTTAGGGTCAAAAATG-GAATTTTTAGAAGTTT-GGGGGTA
* ** * * *
55505 AAAATGGAA-TTTTCAAAAGTTTGAGGGT-AAAAATGTAATTTTTAGAAATTTGGGGGT-
1 AAAATGTAATTTTTGGAAA-TTTTAGGGTCAAAAATGGAATTTTTAGAAGTTTGGGGGTA
* * ** *
55562 AAAATGTAATTTTTAGAAGTTTTAGGGTC-AAAATGGAACTTTAGAGAAGTTT-GGGGTC
1 AAAATGTAATTTTTGGAAATTTTAGGGTCAAAAATGGAA-TTTTTAGAAGTTTGGGGGTA
*
55620 AAAATATAATT
1 AAAATGTAATT
55631 ACTAGATAGT
Statistics
Matches: 199, Mismatches: 31, Indels: 27
0.77 0.12 0.11
Matches are distributed among these distances:
57 53 0.27
58 92 0.46
59 54 0.27
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.36
Consensus pattern (59 bp):
AAAATGTAATTTTTGGAAATTTTAGGGTCAAAAATGGAATTTTTAGAAGTTTGGGGGTA
Found at i:55466 original size:87 final size:86
Alignment explanation
Indices: 55329--55630 Score: 340
Period size: 87 Copynumber: 3.5 Consensus size: 86
55319 ACTCGAGGGC
* * *
55329 AAAATGGTAATTTTTGCAAGTTTCGGGATCAAAAATGGAATTTTTAGAAGTTTGGGGGTAAAATG
1 AAAATGG-AATTTTTGAAAGTTT-GGGGT-AAAAATGTAATTTTTAGAAGTTTGGGGGTAAAATG
55394 TAATTTTTGGAAATTTTAGGGTCA
63 TAATTTTTGGAAATTTTAGGGTCA
* * *
55418 AAAATGGAATTTTTGAAAGTTTGAGGGTAAAAATGTATTTTTTGGAAG-TTCGGGGTAAAAATGT
1 AAAATGGAATTTTTGAAAGTTTG-GGGTAAAAATGTAATTTTTAGAAGTTTGGGGGT-AAAATGT
* * * *
55482 GATTTTTGG-AAGTTTCGAGGTTA
64 AATTTTTGGAAATTTTAG-GGTCA
** *
55505 AAAATGGAATTTTCAAAAGTTTGAGGGTAAAAATGTAATTTTTAGAAATTTGGGGGTAAAATGTA
1 AAAATGGAATTTTTGAAAGTTTG-GGGTAAAAATGTAATTTTTAGAAGTTTGGGGGTAAAATGTA
* *
55570 ATTTTTAGAAGTTTTAGGGTC-
65 ATTTTTGGAAATTTTAGGGTCA
* * * *
55591 AAAATGGAACTTTAGAGAAGTTTGGGGTCAAAATATAATT
1 AAAATGGAATTTTTGA-AAGTTTGGGGTAAAAATGTAATT
55631 ACTAGATAGT
Statistics
Matches: 180, Mismatches: 27, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
86 40 0.22
87 104 0.58
88 29 0.16
89 7 0.04
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.36
Consensus pattern (86 bp):
AAAATGGAATTTTTGAAAGTTTGGGGTAAAAATGTAATTTTTAGAAGTTTGGGGGTAAAATGTAA
TTTTTGGAAATTTTAGGGTCA
Found at i:57449 original size:17 final size:17
Alignment explanation
Indices: 57424--57457 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
57414 TTTTTAATTC
57424 AATTCAAATTCAAACTT
1 AATTCAAATTCAAACTT
* *
57441 AATTTAAATTTAAACTT
1 AATTCAAATTCAAACTT
57458 TTCTTTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTCAAATTCAAACTT
Found at i:57450 original size:6 final size:6
Alignment explanation
Indices: 57441--57491 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
57431 ATTCAAACTT
* **
57441 AATTTA AATTTA AACTTTT CTTTTA AAGTTTA AATTTA AA-TTA AATTTA
1 AATTTA AATTTA AA-TTTA AATTTA AA-TTTA AATTTA AATTTA AATTTA
57490 AA
1 AA
57492 CCCAAAATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
5 5 0.14
6 22 0.61
7 9 0.25
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (6 bp):
AATTTA
Found at i:60115 original size:15 final size:16
Alignment explanation
Indices: 60083--60116 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
60073 AATATTTTTA
*
60083 TAAAATAATATAATAT
1 TAAAATAATATAAAAT
60099 TAAAATAA-ATAAAAT
1 TAAAATAATATAAAAT
60114 TAA
1 TAA
60117 TTAATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAAATAATATAAAAT
Done.