Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014829.1 Kokia drynarioides strain JFW-HI SEQ_129871, 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: 469256
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 555 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:341167 original size:3 final size:3
Alignment explanation
Indices: 341161--341204 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
341151 TGGGTTGATG
341161 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
341205 GACGATAGAA
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:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:342301 original size:17 final size:18
Alignment explanation
Indices: 342264--342301 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
342254 CATTACCAAA
*
342264 AAATTCAAAATAATTTTT
1 AAATTCAAAATAATTTAT
342282 AAATTCAAAAT-ATTTAT
1 AAATTCAAAATAATTTAT
342299 AAA
1 AAA
342302 AAATTTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATTCAAAATAATTTAT
Found at i:342367 original size:17 final size:18
Alignment explanation
Indices: 342337--342379 Score: 63
Period size: 16 Copynumber: 2.5 Consensus size: 18
342327 GATTTTTTTA
342337 TTTAAAACTTTTAAATTT
1 TTTAAAACTTTTAAATTT
342355 TTTAAAA-TTTTAAA-TT
1 TTTAAAACTTTTAAATTT
*
342371 ATTAAAACT
1 TTTAAAACT
342380 AAAATTGCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAAAACTTTTAAATTT
Found at i:354771 original size:29 final size:28
Alignment explanation
Indices: 354725--354798 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
354715 ATTAGTAAGT
* *
354725 TATAATAATTAGATCAAATCAAAATTTCATA
1 TATAA-AATTACA-CAAATCAAAACTT-ATA
*
354756 TATAAAATTACACAAAATCAAAGCTTATA
1 TATAAAATTACAC-AAATCAAAACTTATA
*
354785 TATACAATTACACA
1 TATAAAATTACACA
354799 TTAAATTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
28 1 0.03
29 16 0.42
30 16 0.42
31 5 0.13
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.31
Consensus pattern (28 bp):
TATAAAATTACACAAATCAAAACTTATA
Found at i:354817 original size:31 final size:29
Alignment explanation
Indices: 354740--354820 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 29
354730 TAATTAGATC
*
354740 AAATCAAAATTTCATATATAAAATTACACA
1 AAATC-AAACTTCATATATAAAATTACACA
*
354770 AAATCAAAGCTT-ATATATACAATTACACA
1 AAATCAAA-CTTCATATATAAAATTACACA
*
354799 TTAAATTATAA-TTCATATATAA
1 --AAATCA-AACTTCATATATAA
354821 TTTTAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
29 19 0.45
30 9 0.21
31 12 0.29
32 2 0.05
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.33
Consensus pattern (29 bp):
AAATCAAACTTCATATATAAAATTACACA
Found at i:357371 original size:30 final size:30
Alignment explanation
Indices: 357331--357401 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
357321 TTAAATTAAT
*
357331 AATAAT-AAAATTATACTTTAAT-CTCTAAA
1 AATAATAAAAATT-TAATTTAATCCTCTAAA
*
357360 AATAATAAAAATTTAATTTAATCCTTTAAA
1 AATAATAAAAATTTAATTTAATCCTCTAAA
* *
357390 ATTTATAAAAAT
1 AATAATAAAAAT
357402 ATAAACTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 14 0.39
30 22 0.61
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (30 bp):
AATAATAAAAATTTAATTTAATCCTCTAAA
Found at i:357390 original size:29 final size:30
Alignment explanation
Indices: 357326--357405 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 30
357316 AAATTTTAAA
*
357326 TTAATAATAAT-AAAATTATACTTTAATCTC
1 TTAA-AATAATAAAAATTATAATTTAATCTC
*
357356 TAAAAATAATAAAAATT-TAATTTAATC-C
1 TTAAAATAATAAAAATTATAATTTAATCTC
*
357384 TTTAAAATTTATAAAAA-TATAA
1 -TTAAAA-TAATAAAAATTATAA
357406 ACTATTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
28 1 0.02
29 21 0.50
30 20 0.48
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (30 bp):
TTAAAATAATAAAAATTATAATTTAATCTC
Found at i:359086 original size:16 final size:16
Alignment explanation
Indices: 359062--359100 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
359052 TTTAAGTTTA
359062 TAATATTTTATATTATG
1 TAAT-TTTTATATTATG
*
359079 TTATTTTTATATTATG
1 TAATTTTTATATTATG
359095 TAATTT
1 TAATTT
359101 AGAACTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (16 bp):
TAATTTTTATATTATG
Found at i:364069 original size:18 final size:18
Alignment explanation
Indices: 364046--364080 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
364036 GAGTTAAACG
*
364046 AATTGAGTTTTTCGAGTT
1 AATTGAGTTATTCGAGTT
364064 AATTGAGTTATTCGAGT
1 AATTGAGTTATTCGAGT
364081 CAACTCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.46
Consensus pattern (18 bp):
AATTGAGTTATTCGAGTT
Found at i:364404 original size:19 final size:20
Alignment explanation
Indices: 364369--364406 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
364359 TCCCTAAAAA
*
364369 CCTTCAAAATTTTTTATTTT
1 CCTTCAAAATCTTTTATTTT
364389 CCTTCAAAA-CTTTTATTT
1 CCTTCAAAATCTTTTATTT
364407 CTCTCACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.55
Consensus pattern (20 bp):
CCTTCAAAATCTTTTATTTT
Found at i:365748 original size:20 final size:20
Alignment explanation
Indices: 365719--365758 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
365709 TTTTTTAGAA
*
365719 AGTTGGGTGATTGCTTTGAC
1 AGTTGAGTGATTGCTTTGAC
*
365739 AGTTGAGTGATTGTTTTGAC
1 AGTTGAGTGATTGCTTTGAC
365759 TCCAGATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.07, G:0.33, T:0.42
Consensus pattern (20 bp):
AGTTGAGTGATTGCTTTGAC
Found at i:366281 original size:68 final size:68
Alignment explanation
Indices: 366197--366330 Score: 241
Period size: 68 Copynumber: 2.0 Consensus size: 68
366187 TTAGAGAATC
*
366197 AAGTTTCAAATTAGGAGTGTTCAAACAGTTAATCGATCGGTTAATTGAACTGAACTAGCATTAAC
1 AAGTTTCAAATTAGGAGTATTCAAACAGTTAATCGATCGGTTAATTGAACTGAACTAGCATTAAC
366262 TGA
66 TGA
* *
366265 AAGTTTCAAATTAGGAGTATTCAAACAGTTAATCGATCGGTTAATTGAATTGAACTAGTATTAAC
1 AAGTTTCAAATTAGGAGTATTCAAACAGTTAATCGATCGGTTAATTGAACTGAACTAGCATTAAC
366330 T
66 T
366331 AAATTAACCT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (68 bp):
AAGTTTCAAATTAGGAGTATTCAAACAGTTAATCGATCGGTTAATTGAACTGAACTAGCATTAAC
TGA
Found at i:367781 original size:28 final size:27
Alignment explanation
Indices: 367728--367796 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
367718 TTGAGAGAAA
* * *
367728 GGTTCACTAATGTG-TTGGCGAGCTAGG
1 GGTTCACCAATCTGTTTGGCAAGCTA-G
*
367755 GGTTCACCAGTCTGTTTGGCAAGCTAG
1 GGTTCACCAATCTGTTTGGCAAGCTAG
*
367782 GGTTCGCCAATCTGT
1 GGTTCACCAATCTGT
367797 GTTGTGAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 25 0.71
28 10 0.29
ACGTcount: A:0.17, C:0.20, G:0.32, T:0.30
Consensus pattern (27 bp):
GGTTCACCAATCTGTTTGGCAAGCTAG
Found at i:376850 original size:9 final size:9
Alignment explanation
Indices: 376836--376860 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
376826 TAAAGTCAAG
376836 TTTATTTAA
1 TTTATTTAA
376845 TTTATTTAA
1 TTTATTTAA
376854 TTTATTT
1 TTTATTT
376861 TTGCAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTATTTAA
Found at i:377503 original size:8 final size:8
Alignment explanation
Indices: 377487--377538 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
377477 TTTTGTTAAG
*
377487 AAAACATA
1 AAAAAATA
377495 AAAAAATA
1 AAAAAATA
*
377503 AACAAATA
1 AAAAAATA
377511 AAAAAA-A
1 AAAAAATA
377518 GAGAAAAATA
1 -A-AAAAATA
*
377528 AATAAATA
1 AAAAAATA
377536 AAA
1 AAA
377539 GACATGAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
7 1 0.03
8 28 0.78
9 6 0.17
10 1 0.03
ACGTcount: A:0.81, C:0.04, G:0.04, T:0.12
Consensus pattern (8 bp):
AAAAAATA
Found at i:377515 original size:25 final size:25
Alignment explanation
Indices: 377487--377548 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
377477 TTTTGTTAAG
377487 AAAACATAAAAAAATAAACAAATAA
1 AAAACATAAAAAAATAAACAAATAA
* * * *
377512 AAAAAAGAGAAAAATAAATAAATAA
1 AAAACATAAAAAAATAAACAAATAA
* *
377537 AAGACATGAAAA
1 AAAACATAAAAA
377549 TCACATGACA
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.77, C:0.05, G:0.06, T:0.11
Consensus pattern (25 bp):
AAAACATAAAAAAATAAACAAATAA
Found at i:380603 original size:34 final size:34
Alignment explanation
Indices: 380559--380626 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
380549 TGAATTGAAG
*
380559 TTAATTTGACTGATCCCTATTCTCTAAAGTTACA
1 TTAATCTGACTGATCCCTATTCTCTAAAGTTACA
380593 TTAATCTGACTGATCCCTATTCTCTAAAGTTACA
1 TTAATCTGACTGATCCCTATTCTCTAAAGTTACA
380627 GGTTACGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (34 bp):
TTAATCTGACTGATCCCTATTCTCTAAAGTTACA
Found at i:395420 original size:13 final size:13
Alignment explanation
Indices: 395402--395435 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
395392 TGTTCATGGA
395402 GTTCATGGTTTCT
1 GTTCATGGTTTCT
*
395415 GTTCATGGTTTTT
1 GTTCATGGTTTCT
*
395428 GTGCATGG
1 GTTCATGG
395436 AGGACCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.12, G:0.29, T:0.50
Consensus pattern (13 bp):
GTTCATGGTTTCT
Found at i:400333 original size:66 final size:65
Alignment explanation
Indices: 400246--400406 Score: 214
Period size: 66 Copynumber: 2.5 Consensus size: 65
400236 ACCCTTATAT
* * *
400246 TGATACTTCCTTATCAAGGAATTACTCTGTAATACATTAACAGCGTTAAAAAAACCTTAATTTCT
1 TGATACTTCCTTATCAAGGAATTACTCTATAATACATTAACAGCATT-AAAAAACCTTAAGTTCT
400311 A
65 A
** * * *
400312 TGATACTTCCTTATTGAGGAATTACTCTATAATACATTACCAGCATTAAAAACCCTTACGTTCTA
1 TGATACTTCCTTATCAAGGAATTACTCTATAATACATTAACAGCATTAAAAAACCTTAAGTTCTA
* **
400377 TGAAACTTCCTCGTCAAGGAATTACTCTAT
1 TGATACTTCCTTATCAAGGAATTACTCTAT
400407 GCTCTTACCT
Statistics
Matches: 82, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
65 40 0.49
66 42 0.51
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (65 bp):
TGATACTTCCTTATCAAGGAATTACTCTATAATACATTAACAGCATTAAAAAACCTTAAGTTCTA
Found at i:400397 original size:65 final size:66
Alignment explanation
Indices: 400250--400406 Score: 208
Period size: 65 Copynumber: 2.4 Consensus size: 66
400240 TTATATTGAT
* * *
400250 ACTTCCTTATCAAGGAATTACTCTGTAATACATTAACAGCGTTAAAAAAACCTTAATTTCTATGA
1 ACTTCCTTATCAAGGAATTACTCTATAATACATTAACAGCATTAAAAAAACCTTAAGTTCTATGA
*
400315 T
66 A
** * * *
400316 ACTTCCTTATTGAGGAATTACTCTATAATACATTACCAGCATT-AAAAACCCTTACGTTCTATGA
1 ACTTCCTTATCAAGGAATTACTCTATAATACATTAACAGCATTAAAAAAACCTTAAGTTCTATGA
400380 A
66 A
**
400381 ACTTCCTCGTCAAGGAATTACTCTAT
1 ACTTCCTTATCAAGGAATTACTCTAT
400407 GCTCTTACCT
Statistics
Matches: 78, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
65 40 0.51
66 38 0.49
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (66 bp):
ACTTCCTTATCAAGGAATTACTCTATAATACATTAACAGCATTAAAAAAACCTTAAGTTCTATGA
A
Found at i:405641 original size:3 final size:3
Alignment explanation
Indices: 405633--405672 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
405623 TCAATTATCT
405633 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
405673 ATATGGTTTC
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:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:405810 original size:16 final size:15
Alignment explanation
Indices: 405769--405810 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
405759 AACTCGAACA
405769 ATTTCACTTG-ATTC
1 ATTTCACTTGAATTC
*
405783 GTTTCGACTTGAATTTC
1 ATTTC-ACTTGAA-TTC
405800 ATTTCACTTGA
1 ATTTCACTTGA
405811 CTCAAATCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 4 0.17
15 5 0.22
16 7 0.30
17 7 0.30
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (15 bp):
ATTTCACTTGAATTC
Found at i:406021 original size:22 final size:23
Alignment explanation
Indices: 405981--406024 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
405971 TTTCTATTTT
405981 TATTTTTAGAAATTCAATTATTC
1 TATTTTTAGAAATTCAATTATTC
* *
406004 TATTTTT-GAAGTTTAATTATT
1 TATTTTTAGAAATTCAATTATT
406025 AGTATCATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.57
Consensus pattern (23 bp):
TATTTTTAGAAATTCAATTATTC
Found at i:422693 original size:54 final size:55
Alignment explanation
Indices: 422634--422819 Score: 175
Period size: 54 Copynumber: 3.4 Consensus size: 55
422624 CTGTCATGCA
* * *
422634 CCTTCTCCCTTCTCCTTTCACCATCT-AGATCCCTGTCCCGGCTCTTCCCTCTCT
1 CCTTCTCCCTTCTCCTTTCACCATCTCAGATCCCTGTCCCGACTCCTCCCTCGCT
* * * * *
422688 CCTTCTCCCTTCTCCTTTC-CC-TCTCCAGTTCTCTTTCCCTACTCCTCTCTCGCT
1 CCTTCTCCCTTCTCCTTTCACCATCT-CAGATCCCTGTCCCGACTCCTCCCTCGCT
* * * * **
422742 CCTTCTCCCTTCTCCTTTCACCA-CTCATG-TCTCTATCTCTACTCCTTGCTCGCT
1 CCTTCTCCCTTCTCCTTTCACCATCTCA-GATCCCTGTCCCGACTCCTCCCTCGCT
* *
422796 CCCTCTCCCTTCTCCTCTCACCAT
1 CCTTCTCCCTTCTCCTTTCACCAT
422820 AAATCTCCCT
Statistics
Matches: 112, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
52 3 0.03
53 2 0.02
54 102 0.91
55 5 0.04
ACGTcount: A:0.07, C:0.49, G:0.05, T:0.39
Consensus pattern (55 bp):
CCTTCTCCCTTCTCCTTTCACCATCTCAGATCCCTGTCCCGACTCCTCCCTCGCT
Found at i:422711 original size:24 final size:24
Alignment explanation
Indices: 422684--422760 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 24
422674 GCTCTTCCCT
422684 CTCTCCTTCTCCCTTCTCCTTTCC
1 CTCTCCTTCTCCCTTCTCCTTTCC
* * *
422708 CTCTCCAGTTCTCTTTCCCTACTCCTCTCT
1 CTCTCC---T-TC--TCCCTTCTCCTTTCC
*
422738 CGCTCCTTCTCCCTTCTCCTTTC
1 CTCTCCTTCTCCCTTCTCCTTTC
422761 ACCACTCATG
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
24 18 0.44
26 2 0.05
27 2 0.05
28 2 0.05
30 17 0.41
ACGTcount: A:0.03, C:0.51, G:0.03, T:0.44
Consensus pattern (24 bp):
CTCTCCTTCTCCCTTCTCCTTTCC
Found at i:424314 original size:15 final size:15
Alignment explanation
Indices: 424294--424327 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
424284 TGCGGTGGCG
*
424294 GTGGTGACGATGTTT
1 GTGGTGACGATGCTT
*
424309 GTGGTGGCGATGCTT
1 GTGGTGACGATGCTT
424324 GTGG
1 GTGG
424328 CGTTTGGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.09, G:0.47, T:0.35
Consensus pattern (15 bp):
GTGGTGACGATGCTT
Found at i:424908 original size:16 final size:17
Alignment explanation
Indices: 424876--424917 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
424866 TTAAAAAATA
*
424876 TTAATA-TTATATTATT
1 TTAATATTTATATAATT
424892 TTAATATTTA-ATAATT
1 TTAATATTTATATAATT
424908 TTATATATTT
1 TTA-ATATTT
424918 TTTATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTAATATTTATATAATT
Found at i:424927 original size:28 final size:28
Alignment explanation
Indices: 424883--424953 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
424873 ATATTAATAT
*
424883 TATATTATTTTAATATTTAATAATTTTA
1 TATATTATTTTAATATTAAATAATTTTA
* **
424911 TATATT-TTTTATTTATTAAATTTTTTTA
1 TATATTATTTTA-ATATTAAATAATTTTA
424939 TATAGTTATTTTAAT
1 TATA-TTATTTTAAT
424954 GTTTACGTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 5 0.14
28 22 0.63
29 3 0.09
30 5 0.14
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (28 bp):
TATATTATTTTAATATTAAATAATTTTA
Found at i:428024 original size:14 final size:15
Alignment explanation
Indices: 428002--428035 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
427992 TATATGTTTT
*
428002 AAATTACATAATA-A
1 AAATAACATAATATA
428016 AAATAACATAATATA
1 AAATAACATAATATA
428031 AAATA
1 AAATA
428036 TTATAAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATAACATAATATA
Found at i:434878 original size:23 final size:22
Alignment explanation
Indices: 434848--434893 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
434838 ATAATGTTCT
434848 ATATAAATTT-TAAATATTATTTA
1 ATATAAATTTATAAA-ATT-TTTA
434871 ATATAAATTTATAAAATTTTTA
1 ATATAAATTTATAAAATTTTTA
434893 A
1 A
434894 CTAAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATAAATTTATAAAATTTTTA
Found at i:446179 original size:25 final size:25
Alignment explanation
Indices: 446151--446233 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
446141 TTTTATGTAG
446151 TTATACATTTTTGAATGTTTTTCTT
1 TTATACATTTTTGAATGTTTTTCTT
* ** * *
446176 TTATA-ATCTTTGGTTTTATTTTATGT
1 TTATACATTTTTGAATGT-TTTTCT-T
446202 AGTTATACATTTTTGAATGTTTTTCTT
1 --TTATACATTTTTGAATGTTTTTCTT
446229 TTATA
1 TTATA
446234 ATCTTTGGTG
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
24 8 0.19
25 15 0.35
26 1 0.02
27 1 0.02
28 10 0.23
29 8 0.19
ACGTcount: A:0.22, C:0.06, G:0.10, T:0.63
Consensus pattern (25 bp):
TTATACATTTTTGAATGTTTTTCTT
Found at i:446198 original size:53 final size:53
Alignment explanation
Indices: 446135--446242 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
446125 GATAGGTGAA
446135 GTTTTATTTTATGTAGTTATACATTTTTGAATGTTTTTCTTTTATAATCTTTG
1 GTTTTATTTTATGTAGTTATACATTTTTGAATGTTTTTCTTTTATAATCTTTG
446188 GTTTTATTTTATGTAGTTATACATTTTTGAATGTTTTTCTTTTATAATCTTTG
1 GTTTTATTTTATGTAGTTATACATTTTTGAATGTTTTTCTTTTATAATCTTTG
446241 GT
1 GT
446243 GAAGTTTTCT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.20, C:0.06, G:0.12, T:0.62
Consensus pattern (53 bp):
GTTTTATTTTATGTAGTTATACATTTTTGAATGTTTTTCTTTTATAATCTTTG
Found at i:449279 original size:16 final size:16
Alignment explanation
Indices: 449248--449284 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
449238 GTATGAACAA
449248 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
449264 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
449280 TATTA
1 TATTA
449285 AAATAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:450700 original size:26 final size:26
Alignment explanation
Indices: 450664--450729 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
450654 CCCGACCCAC
*
450664 AGCTCGTGTGAGCAGACGCATTTCAT
1 AGCTCGTGTGAGCAGACCCATTTCAT
450690 AGCTCGTGTGAGCAGACCCATTTCAT
1 AGCTCGTGTGAGCAGACCCATTTCAT
450716 AGCTCGTGTGAGCA
1 AGCTCGTGTGAGCA
450730 TATATGGTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (26 bp):
AGCTCGTGTGAGCAGACCCATTTCAT
Found at i:456138 original size:16 final size:16
Alignment explanation
Indices: 456093--456139 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
456083 AAGTTAAAAT
*
456093 TTTCTAAAATATTTTA
1 TTTCAAAAATATTTTA
**
456109 TTT-AGTAATAATTTTA
1 TTTCAAAAAT-ATTTTA
456125 TTTCAAAAATATTTT
1 TTTCAAAAATATTTT
456140 TTCCTTAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
15 3 0.12
16 17 0.71
17 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTCAAAAATATTTTA
Done.