Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010130.1 Kokia drynarioides strain JFW-HI SEQ_124925, 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: 132774
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Warning! 41 characters in sequence are not A, C, G, or T
Found at i:58 original size:3 final size:3
Alignment explanation
Indices: 1--40 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
41 AAACAGTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:486 original size:3 final size:3
Alignment explanation
Indices: 420--468 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
410 NNNNNNNNNN
420 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
468 A
1 A
469 AAACAGTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:798 original size:428 final size:418
Alignment explanation
Indices: 1--838 Score: 1586
Period size: 428 Copynumber: 2.0 Consensus size: 418
1 ATTATTATTATTATTATTATTATTATTATTATTATTATTAAAACAGTTATTATTATTAATACTTA
1 ATTATTATTATTATTATTATTATTATTATTATTATTATTAAAACAGTTATTATTATTAATACTTA
66 TTACAAACAATGTATTTAAAAAATGGAAATAAAGATGAAAAATAAAATGTAACTGATGAACGGTA
66 TTACAAACAATGTATTTAAAAAATGGAAATAAAGATGAAAAATAAAATGTAACTGATGAACGGTA
131 GGTATTCAATGCGTATATTAATGCATATTTGAAAATCCAAAGAGGTTAAATGTTGAGCTATCAAT
131 GGTATTCAATGCGTATATTAATGCATATTTGAAAATCCAAAGAGGTTAAATGTTGAGCTATCAAT
196 GGCAGTAATTATGCATTAAATGGTACCTGATCAGTTTCAATGCTTGAATGTTCTTGGTCGATTCG
196 GGCAGTAATTATGCATTAAATGGTACCTGATCAGTTTCAATGCTTGAATGTTCTTGGTCGATTCG
261 TGTATCTGATAGTCTGTTCGTGCTTAGACACTACCTCTTGGTTCTGCTTCTTTAGTAAACTCTAT
261 TGTATCTGATAGTCTGTTCGTGCTTAGACACTACCTCTTGGTTCTGCTTCTTTAGTAAACTCTAT
326 GATATTATTAAAGAGGCTATTTCTTGTATTGATCTTTTAGGTTTCAAAAGTACAAAGAAAAGAAC
326 GATATTATTAAAGAGGCTATTTCTTGTATTGATCTTTTAGGTTTCAAAAGTACAAAGAAAAGAAC
391 CCTTCTCCAAAAAAAAAAANNNNNNNNNNATTATTATT
391 CCTTCTCCAAAAAAAAAAA----------ATTATTATT
429 ATTATTATTATTATTATTATTATTATTATTATTATTATTAAAACAGTTATTATTATTAATACTTA
1 ATTATTATTATTATTATTATTATTATTATTATTATTATTAAAACAGTTATTATTATTAATACTTA
494 TTACAAACAATGTATTTAAAAAATGGAAATAAAGATGAAAAATAAAATGTAACTGATGAACGGTA
66 TTACAAACAATGTATTTAAAAAATGGAAATAAAGATGAAAAATAAAATGTAACTGATGAACGGTA
559 GGTATTCAATGCGTATATTAATGCATATTTGAAAATCCAAAGAGGTTAAATGTTGAGCTATCAAT
131 GGTATTCAATGCGTATATTAATGCATATTTGAAAATCCAAAGAGGTTAAATGTTGAGCTATCAAT
624 GGCAGTAATTATGCATTAAATGGTACCTGATCAGTTTCAATGCTTGAATGTTCTTGGTCGATTCG
196 GGCAGTAATTATGCATTAAATGGTACCTGATCAGTTTCAATGCTTGAATGTTCTTGGTCGATTCG
689 TGTATCTGATAGTCTGTTCGTGCTTAGACACTACCTCTTGGTTCTGCTTCTTTAGTAAACTCTAT
261 TGTATCTGATAGTCTGTTCGTGCTTAGACACTACCTCTTGGTTCTGCTTCTTTAGTAAACTCTAT
754 GATATTATTAAAGAGGCTATTTCTTGTATTGATCTTTTAGGTTTCAAAAGTACAAAGAAAAGAAC
326 GATATTATTAAAGAGGCTATTTCTTGTATTGATCTTTTAGGTTTCAAAAGTACAAAGAAAAGAAC
819 CCTTCTCCAAAAAAAAAAAA
391 CCTTCTCCAAAAAAAAAAAA
839 GTCTCTTTCC
Statistics
Matches: 410, Mismatches: 0, Indels: 10
0.98 0.00 0.02
Matches are distributed among these distances:
418 1 0.00
428 409 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.37
Consensus pattern (418 bp):
ATTATTATTATTATTATTATTATTATTATTATTATTATTAAAACAGTTATTATTATTAATACTTA
TTACAAACAATGTATTTAAAAAATGGAAATAAAGATGAAAAATAAAATGTAACTGATGAACGGTA
GGTATTCAATGCGTATATTAATGCATATTTGAAAATCCAAAGAGGTTAAATGTTGAGCTATCAAT
GGCAGTAATTATGCATTAAATGGTACCTGATCAGTTTCAATGCTTGAATGTTCTTGGTCGATTCG
TGTATCTGATAGTCTGTTCGTGCTTAGACACTACCTCTTGGTTCTGCTTCTTTAGTAAACTCTAT
GATATTATTAAAGAGGCTATTTCTTGTATTGATCTTTTAGGTTTCAAAAGTACAAAGAAAAGAAC
CCTTCTCCAAAAAAAAAAAATTATTATT
Found at i:1169 original size:6 final size:6
Alignment explanation
Indices: 1158--1252 Score: 67
Period size: 6 Copynumber: 16.7 Consensus size: 6
1148 TTTGGACGTT
* * *
1158 AATTTA AATTTA AATTT- AACTCA AATTTA TAA--TA AATTTA AATTTT
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA
* * * * *
1204 AA-GTA AATTTA AACTTA AA-ATA AATTTA ATTTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
1249 AATT
1 AATT
1253 CTGTTGAGCC
Statistics
Matches: 67, Mismatches: 15, Indels: 14
0.70 0.16 0.15
Matches are distributed among these distances:
4 2 0.03
5 16 0.24
6 47 0.70
7 2 0.03
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:1200 original size:17 final size:17
Alignment explanation
Indices: 1158--1252 Score: 109
Period size: 17 Copynumber: 5.6 Consensus size: 17
1148 TTTGGACGTT
* *
1158 AATTTAAATTTAAATTT
1 AATTTAAATTTAAAATA
* * *
1175 AACTCAAATTTATAATA
1 AATTTAAATTTAAAATA
* *
1192 AATTTAAATTTTAAGTA
1 AATTTAAATTTAAAATA
*
1209 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
*
1226 AATTTAATTTTAAAATA
1 AATTTAAATTTAAAATA
1243 AATTTAAATT
1 AATTTAAATT
1253 CTGTTGAGCC
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 62 1.00
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:5346 original size:26 final size:25
Alignment explanation
Indices: 5316--5377 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 25
5306 TTTAAAAAAA
*
5316 AATATTTATTTATTTTATTTTATTTT
1 AATATTTATTTATTTTA-TATATTTT
* *
5342 AATATTTAATAATTTTATATATTTT
1 AATATTTATTTATTTTATATATTTT
*
5367 -TTATTTATTTA
1 AATATTTATTTA
5378 AATTTTTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
24 8 0.27
25 7 0.23
26 15 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
AATATTTATTTATTTTATATATTTT
Found at i:8044 original size:15 final size:15
Alignment explanation
Indices: 8009--8042 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 15
7999 AGAGAGGACT
8009 AAATTGTAAAAGTGTA
1 AAATTGTAAAAGTG-A
8025 AAATTGTAAAGAGTGA
1 AAATTGTAAA-AGTGA
8041 AA
1 AA
8043 TTACTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (15 bp):
AAATTGTAAAAGTGA
Found at i:26554 original size:32 final size:33
Alignment explanation
Indices: 26518--26592 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
26508 GCTCTCACGA
* *
26518 GTCCACAGCTCGCCAT-CCCCTGTCCGCCTGAT
1 GTCCACAGCTCGCCATCCCCCCGTCCACCTGAT
*
26550 GTCCACAGCTCGTCATCCCCCCGTCCACCTGAT
1 GTCCACAGCTCGCCATCCCCCCGTCCACCTGAT
26583 GTCCACAGCT
1 GTCCACAGCT
26593 TATCCGCGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 15 0.38
33 24 0.62
ACGTcount: A:0.15, C:0.47, G:0.17, T:0.21
Consensus pattern (33 bp):
GTCCACAGCTCGCCATCCCCCCGTCCACCTGAT
Found at i:26604 original size:82 final size:81
Alignment explanation
Indices: 26467--26644 Score: 252
Period size: 82 Copynumber: 2.2 Consensus size: 81
26457 CGCCTGTCCA
* * * * *
26467 ATGTCCACAGCTCGCATCCTCCTGTCCAGCTGATGTCAGCAGCTCTCACGAGTCCACAGCTCGCC
1 ATGTCCACAGCTCGCATCCCCCCGTCCACCTGATGTCAGCAGCTATCACGAGTCCACAACTCGCC
26532 ATCCCCTGTCCGCCTG
66 ATCCCCTGTCCGCCTG
*
26548 ATGTCCACAGCTCGTCATCCCCCCGTCCACCTGATGTCCA-CAGCTTATC-CGCGTCCACAACTC
1 ATGTCCACAGCTCG-CATCCCCCCGTCCACCTGATGT-CAGCAGC-TATCACGAGTCCACAACTC
*
26611 GTCATCCCCTGTCCGCCTG
63 GCCATCCCCTGTCCGCCTG
26630 ATGTCCACAGCTCGC
1 ATGTCCACAGCTCGC
26645 CATCTCCTTA
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
81 15 0.17
82 67 0.77
83 5 0.06
ACGTcount: A:0.16, C:0.43, G:0.18, T:0.22
Consensus pattern (81 bp):
ATGTCCACAGCTCGCATCCCCCCGTCCACCTGATGTCAGCAGCTATCACGAGTCCACAACTCGCC
ATCCCCTGTCCGCCTG
Found at i:36748 original size:23 final size:22
Alignment explanation
Indices: 36722--36769 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
36712 TTGTAGGTTC
*
36722 AAATTTCATTATGTTTATGATAA
1 AAATTTCATTA-ATTTATGATAA
* *
36745 AAATTTTATTAATTTATTATAA
1 AAATTTCATTAATTTATGATAA
36767 AAA
1 AAA
36770 ATAAAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (22 bp):
AAATTTCATTAATTTATGATAA
Found at i:37951 original size:96 final size:93
Alignment explanation
Indices: 37717--37990 Score: 338
Period size: 96 Copynumber: 2.9 Consensus size: 93
37707 CACGAGTTCA
* * *
37717 TTTTTTCATTTCAATGACAATGGTAAAATTTCAGTTTTTGT--TTCTCTAATAAACTTAAATTTA
1 TTTTTTCATTTCAATGATAATGGTAAAATTTCAGTTTTGGTCCTT-T-TGATAAACTTAAATTTA
* * * **
37780 ATATTTAATTTTTATATTTTTACGTTCATT
64 AGATTTAATCTTTATATTTTTATGCCCATT
* * * * *
37810 TTTTTT-ATTTCAATTATAATGGTAAAATTTTATTTTTGATCCTTTTGTTAAACTTAAATTTAAG
1 TTTTTTCATTTCAATGATAATGGTAAAATTTCAGTTTTGGTCCTTTTGATAAACTTAAATTTAAG
37874 ATTTAATCTTTATATTTTTATGCCCACTT
66 ATTTAATCTTTATATTTTTATGCCCA-TT
* * *
37903 TTGTTTTCCATTTCAATGATAATGATAAAATTTCAGTTTTGGTCCTTTTGCTAAACTAAAATTTA
1 TT-TTTT-CATTTCAATGATAATGGTAAAATTTCAGTTTTGGTCCTTTTGATAAACTTAAATTTA
37968 AGATTTAATCTTTATATTTTTAT
64 AGATTTAATCTTTATATTTTTAT
37991 TTGACATAAT
Statistics
Matches: 155, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
92 66 0.43
93 11 0.07
94 6 0.04
96 72 0.46
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (93 bp):
TTTTTTCATTTCAATGATAATGGTAAAATTTCAGTTTTGGTCCTTTTGATAAACTTAAATTTAAG
ATTTAATCTTTATATTTTTATGCCCATT
Found at i:38805 original size:25 final size:23
Alignment explanation
Indices: 38752--38807 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
38742 ACTTATTTAA
*
38752 AAATAAATATTTTAATTTAATTG
1 AAATAAATATTATAATTTAATTG
** *
38775 GTATAAATAATTATATATTTATTTG
1 AAATAAAT-ATTATA-ATTTAATTG
38800 AAATAAAT
1 AAATAAAT
38808 GGGGGATAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 6 0.24
24 5 0.20
25 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.46
Consensus pattern (23 bp):
AAATAAATATTATAATTTAATTG
Found at i:39629 original size:24 final size:25
Alignment explanation
Indices: 39596--39643 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
39586 CTCAAGATTA
*
39596 TTTCAATTAAATTC-TGTTTATTTG
1 TTTCAATTAAATTCTTGTTAATTTG
* *
39620 TTTCAGTTAAGTTCTTGTTAATTT
1 TTTCAATTAAATTCTTGTTAATTT
39644 AGGTTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.23, C:0.08, G:0.10, T:0.58
Consensus pattern (25 bp):
TTTCAATTAAATTCTTGTTAATTTG
Found at i:50690 original size:22 final size:22
Alignment explanation
Indices: 50665--50710 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
50655 TGATGTTTGG
50665 AACTATATTGATCTCGAGTTCA
1 AACTATATTGATCTCGAGTTCA
50687 AACTATATTGATCTCGAGTTCA
1 AACTATATTGATCTCGAGTTCA
50709 AA
1 AA
50711 AATAATGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (22 bp):
AACTATATTGATCTCGAGTTCA
Found at i:52235 original size:9 final size:9
Alignment explanation
Indices: 52221--52250 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
52211 GTCTTGCATT
52221 TTTTTTTTG
1 TTTTTTTTG
52230 TTTTTTTTG
1 TTTTTTTTG
52239 TTTTTTTT-
1 TTTTTTTTG
52247 TTTT
1 TTTT
52251 GTGTTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:52237 original size:13 final size:13
Alignment explanation
Indices: 52219--52252 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
52209 AAGTCTTGCA
52219 TTTTTTT-TTTGT
1 TTTTTTTGTTTGT
*
52231 TTTTTTTGTTTTT
1 TTTTTTTGTTTGT
52244 TTTTTTTGT
1 TTTTTTTGT
52253 GTTATTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (13 bp):
TTTTTTTGTTTGT
Found at i:56589 original size:19 final size:18
Alignment explanation
Indices: 56565--56607 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
56555 TATTTTTTTA
56565 TATAATACTTAAAATCATT
1 TATAATACTTAAAA-CATT
**
56584 TATAATTTTTAAAACATT
1 TATAATACTTAAAACATT
56602 TA-AATA
1 TATAATA
56608 GGAGATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 3 0.14
18 6 0.29
19 12 0.57
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAATACTTAAAACATT
Found at i:56998 original size:76 final size:76
Alignment explanation
Indices: 56872--57026 Score: 310
Period size: 76 Copynumber: 2.0 Consensus size: 76
56862 CAAACAAGTA
56872 TCACGATAGTGGATGAGAAAAAAGTCTTGAGTATGAAATTGGAAAAAAACTAAACGTACTAAGTT
1 TCACGATAGTGGATGAGAAAAAAGTCTTGAGTATGAAATTGGAAAAAAACTAAACGTACTAAGTT
56937 GAAAAGAGGAG
66 GAAAAGAGGAG
56948 TCACGATAGTGGATGAGAAAAAAGTCTTGAGTATGAAATTGGAAAAAAACTAAACGTACTAAGTT
1 TCACGATAGTGGATGAGAAAAAAGTCTTGAGTATGAAATTGGAAAAAAACTAAACGTACTAAGTT
57013 GAAAAGAGGAG
66 GAAAAGAGGAG
57024 TCA
1 TCA
57027 AATTCAGGAC
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 79 1.00
ACGTcount: A:0.46, C:0.08, G:0.25, T:0.21
Consensus pattern (76 bp):
TCACGATAGTGGATGAGAAAAAAGTCTTGAGTATGAAATTGGAAAAAAACTAAACGTACTAAGTT
GAAAAGAGGAG
Found at i:62479 original size:19 final size:19
Alignment explanation
Indices: 62455--62492 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
62445 ATTAGTTTTT
*
62455 GTTAATTAAGTATAATTAA
1 GTTAATTAAATATAATTAA
*
62474 GTTAATTAAATCTAATTAA
1 GTTAATTAAATATAATTAA
62493 CTAATCCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (19 bp):
GTTAATTAAATATAATTAA
Found at i:69813 original size:29 final size:29
Alignment explanation
Indices: 69780--69839 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
69770 TCATGTGATG
69780 TTATAACACTAAATTTAATAGATCTAAAC
1 TTATAACACTAAATTTAATAGATCTAAAC
69809 TTATAACACTAAATTTAATAGATCTAAAC
1 TTATAACACTAAATTTAATAGATCTAAAC
69838 TT
1 TT
69840 TCTCCATCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (29 bp):
TTATAACACTAAATTTAATAGATCTAAAC
Found at i:73494 original size:5 final size:5
Alignment explanation
Indices: 73480--73512 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
73470 TGTTGTAAGC
73480 AAAA- AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
73513 AGAGATCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:83381 original size:20 final size:20
Alignment explanation
Indices: 83332--83383 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
83322 ATAACATATC
83332 TAATATTATT-AAATAATGT
1 TAATATTATTAAAATAATGT
83351 TAAT-TGATATTAAAATTAAT-T
1 TAATAT--TATTAAAA-TAATGT
83372 TAATATTATTAA
1 TAATATTATTAA
83384 TATTTAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
18 1 0.04
19 4 0.14
20 10 0.36
21 8 0.29
22 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (20 bp):
TAATATTATTAAAATAATGT
Found at i:83454 original size:18 final size:18
Alignment explanation
Indices: 83427--83469 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
83417 ATAATGTTAT
*
83427 ATAATATTAATTTAATTA
1 ATAATATTAAGTTAATTA
* *
83445 ATAATGTTAAGTTATTTA
1 ATAATATTAAGTTAATTA
*
83463 ATTATAT
1 ATAATAT
83470 CTGATGATTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
ATAATATTAAGTTAATTA
Found at i:85515 original size:13 final size:14
Alignment explanation
Indices: 85492--85531 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
85482 CAACAGCAGC
85492 CGTTT-TCTTTCTT
1 CGTTTCTCTTTCTT
85505 -GTTTCTCTTTCTT
1 CGTTTCTCTTTCTT
*
85518 CCTTTCTC-TTCTT
1 CGTTTCTCTTTCTT
85531 C
1 C
85532 ACGCAATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 4 0.17
13 14 0.58
14 6 0.25
ACGTcount: A:0.00, C:0.30, G:0.05, T:0.65
Consensus pattern (14 bp):
CGTTTCTCTTTCTT
Found at i:91137 original size:17 final size:19
Alignment explanation
Indices: 91108--91142 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
91098 TCCTTTCGAA
91108 CAGTAGTCTT-CCCTTGAG
1 CAGTAGTCTTCCCCTTGAG
91126 CAGTAG-CTTCCCCTTGA
1 CAGTAGTCTTCCCCTTGA
91143 ACAATGGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.17, C:0.31, G:0.20, T:0.31
Consensus pattern (19 bp):
CAGTAGTCTTCCCCTTGAG
Found at i:92805 original size:19 final size:19
Alignment explanation
Indices: 92781--92821 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
92771 CAACTAAGGA
*
92781 AATAATATCTCTTAATTAG
1 AATAATATATCTTAATTAG
92800 AATAATATATCTTAATTAG
1 AATAATATATCTTAATTAG
92819 AAT
1 AAT
92822 GTCTTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (19 bp):
AATAATATATCTTAATTAG
Found at i:94181 original size:15 final size:16
Alignment explanation
Indices: 94163--94193 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
94153 CTGTTTCATT
94163 TGATT-TTGTTTTCTA
1 TGATTCTTGTTTTCTA
94178 TGATTCTTGTTTTCTA
1 TGATTCTTGTTTTCTA
94194 CAGTTAGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.13, C:0.10, G:0.13, T:0.65
Consensus pattern (16 bp):
TGATTCTTGTTTTCTA
Found at i:97586 original size:3 final size:3
Alignment explanation
Indices: 97578--97632 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
97568 TATGCCCTTG
97578 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
97626 AAT AAT A
1 AAT AAT A
97633 TTATTATTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:97975 original size:32 final size:32
Alignment explanation
Indices: 97938--98006 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
97928 TATCTGCAGC
97938 AAAGAAGAGCATAAAAGTCATTATATCACTTG
1 AAAGAAGAGCATAAAAGTCATTATATCACTTG
97970 AAAGAAGAGCATAAAAGTCATTATATCACTTG
1 AAAGAAGAGCATAAAAGTCATTATATCACTTG
98002 AAAGA
1 AAAGA
98007 CTTCCCAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.23
Consensus pattern (32 bp):
AAAGAAGAGCATAAAAGTCATTATATCACTTG
Found at i:98926 original size:36 final size:36
Alignment explanation
Indices: 98879--98954 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
98869 AACTTCATAG
* *
98879 ACTTAGCTAACTTTAACGTAAAAATGTGACTGAATA
1 ACTTAGCTAACTTGAACGTAAAAATGAGACTGAATA
* *
98915 ACTTAGCTAACTTGAATGTAAAAATGAGGCTGAATA
1 ACTTAGCTAACTTGAACGTAAAAATGAGACTGAATA
98951 ACTT
1 ACTT
98955 TAATGTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (36 bp):
ACTTAGCTAACTTGAACGTAAAAATGAGACTGAATA
Found at i:108057 original size:28 final size:28
Alignment explanation
Indices: 108012--108065 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
108002 AAACCTAAAC
* *
108012 CTCCTAAGATTTAGTC-AACTATCTTGCA
1 CTCCTAAGATCTACTCAAACTA-CTTGCA
108040 CTCCTAAGATCTACTCAAACTACTTG
1 CTCCTAAGATCTACTCAAACTACTTG
108066 ACATGCAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (28 bp):
CTCCTAAGATCTACTCAAACTACTTGCA
Found at i:110701 original size:121 final size:120
Alignment explanation
Indices: 110547--110842 Score: 423
Period size: 121 Copynumber: 2.5 Consensus size: 120
110537 TAGAAAAGTT
*
110547 AACATTATATTTTTGTTTGAATGATTTGATTTGTGTTAAAAGTAATATTAAGATTGGTCCGGTAG
1 AACATTATATTTTTGTTTGAATGATTAGATTTGTGTTAAAAGTAATATTAAGATTGGTCCGGTAG
* * * * * * * *
110612 TGTATGTTTTTTTTTATATTGTAATAATAATTTGTATGTTTTTAGATGTAA-ATTG
66 TATATG-TTTTTTTTACATTGTAATAATAAATTATATATTTTAAGATATAACATTA
* **
110667 AACATTATATTTTTAGTTTGAATGATTAGATTTGTGTTGAAAGTAATATTAAGATTGGTTTGGTA
1 AACATTATATTTTT-GTTTGAATGATTAGATTTGTGTTAAAAGTAATATTAAGATTGGTCCGGTA
110732 GTATATGTTTTTTTTACATTGTAATAATAAATTATATATTTTAAGATATAACATTA
65 GTATATGTTTTTTTTACATTGTAATAATAAATTATATATTTTAAGATATAACATTA
* * *
110788 AACATTAGATTTTTGTTTGGATTATTAGATTTGTGTTAAAAAGTAATATTAAGAT
1 AACATTATATTTTTGTTTGAATGATTAGATTTGTGTT-AAAAGTAATATTAAGAT
110843 ATAATTTAAA
Statistics
Matches: 157, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
120 73 0.46
121 84 0.54
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (120 bp):
AACATTATATTTTTGTTTGAATGATTAGATTTGTGTTAAAAGTAATATTAAGATTGGTCCGGTAG
TATATGTTTTTTTTACATTGTAATAATAAATTATATATTTTAAGATATAACATTA
Found at i:124052 original size:39 final size:39
Alignment explanation
Indices: 124003--124092 Score: 162
Period size: 39 Copynumber: 2.3 Consensus size: 39
123993 ATGATCCGTA
*
124003 CCTTATTTTGCCCCCACAAACCTTCGCCCCCATAGATCC
1 CCTTATTTTGCCCCCACAAACCTTCACCCCCATAGATCC
*
124042 CCTTATTTTGCCCCCACAAACCTTCACCCCCATAGGTCC
1 CCTTATTTTGCCCCCACAAACCTTCACCCCCATAGATCC
124081 CCTTATTTTGCC
1 CCTTATTTTGCC
124093 ATGGTATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.19, C:0.44, G:0.08, T:0.29
Consensus pattern (39 bp):
CCTTATTTTGCCCCCACAAACCTTCACCCCCATAGATCC
Found at i:131054 original size:24 final size:24
Alignment explanation
Indices: 131019--131067 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
131009 AGATAAAACT
131019 AAACCTCGAAAATC-TAAAAACAAA
1 AAACCTCGAAAA-CGTAAAAACAAA
*
131043 AAACTCTC-AAAACGTAAACACAAA
1 AAAC-CTCGAAAACGTAAAAACAAA
131067 A
1 A
131068 TTCTCCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 1 0.05
24 18 0.82
25 3 0.14
ACGTcount: A:0.61, C:0.22, G:0.04, T:0.12
Consensus pattern (24 bp):
AAACCTCGAAAACGTAAAAACAAA
Found at i:131223 original size:24 final size:24
Alignment explanation
Indices: 131186--131245 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
131176 TAAACTAATA
*
131186 AGAGTTTGACTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
131210 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
131234 AAAATTTAACTG
1 AGAGTTTAACTG
131246 GAAGATTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:132446 original size:22 final size:22
Alignment explanation
Indices: 132392--132490 Score: 128
Period size: 23 Copynumber: 4.4 Consensus size: 22
132382 GCTGGGGAAA
132392 CAGTAAGCACACACAGTGCAAT
1 CAGTAAGCACACACAGTGCAAT
132414 CCAGTAAGCACACACAGTGCAAT
1 -CAGTAAGCACACACAGTGCAAT
* *
132437 CAGTAGGCACACACAGCGCAAAT
1 CAGTAAGCACACACAGTGC-AAT
*
132460 CAGTAAGCACACGA-AGTGCGAAA
1 CAGTAAGCACAC-ACAGTGC-AAT
132483 CAGTAAGC
1 CAGTAAGC
132491 GTGCTAGCGT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
22 17 0.25
23 50 0.74
24 1 0.01
ACGTcount: A:0.40, C:0.27, G:0.21, T:0.11
Consensus pattern (22 bp):
CAGTAAGCACACACAGTGCAAT
Found at i:132478 original size:45 final size:46
Alignment explanation
Indices: 132366--132490 Score: 141
Period size: 45 Copynumber: 2.7 Consensus size: 46
132356 AAGTACTTGA
*
132366 CAGTAAGCACACA-AGTGCTGGGGAAACAGTAAGCACACACAGTGCAATC
1 CAGTAAGCACACACAGTGC----GAAACAGTAAGCACACACAGCGCAATC
* *
132415 CAGTAAGCACACACAGTGC-AATCAGTAGGCACACACAGCGCAAAT-
1 CAGTAAGCACACACAGTGCGAAACAGTAAGCACACACAGCGC-AATC
132460 CAGTAAGCACACGA-AGTGCGAAACAGTAAGC
1 CAGTAAGCACAC-ACAGTGCGAAACAGTAAGC
132491 GTGCTAGCGT
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
45 36 0.54
46 13 0.19
49 13 0.19
50 5 0.07
ACGTcount: A:0.40, C:0.26, G:0.23, T:0.11
Consensus pattern (46 bp):
CAGTAAGCACACACAGTGCGAAACAGTAAGCACACACAGCGCAATC
Done.