Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001627.1 Kokia drynarioides strain JFW-HI SEQ_113264, 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: 288041
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 7 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:273640 original size:16 final size:17
Alignment explanation
Indices: 273615--273670 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
273605 TTTTTATAGT
*
273615 TTTAAAATTTAT-TTAA
1 TTTAATATTTATATTAA
*
273631 TTTAATATTTATCTTAA
1 TTTAATATTTATATTAA
*
273648 --TAGTATTT-TATTAA
1 TTTAATATTTATATTAA
273662 TTTAATATT
1 TTTAATATT
273671 AAAGCGATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 17 0.52
17 4 0.12
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTAATATTTATATTAA
Found at i:275374 original size:22 final size:22
Alignment explanation
Indices: 275297--275380 Score: 80
Period size: 22 Copynumber: 3.7 Consensus size: 22
275287 TAAAAGAAAT
275297 AAAAATAAAAGGATTAAATTTTA
1 AAAAATAAAAGGATT-AATTTTA
* * * **
275320 AAACA-AAAGGGTTTAATTAAAAA
1 AAAAATAAAAGGATTAATT--TTA
275343 AACAAATAAAAGGATTAATTTTA
1 AA-AAATAAAAGGATTAATTTTA
275366 AAAAATAAAAGGATT
1 AAAAATAAAAGGATT
275381 TAGTTTTTCA
Statistics
Matches: 47, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
21 4 0.09
22 20 0.43
23 10 0.21
24 2 0.04
25 11 0.23
ACGTcount: A:0.61, C:0.02, G:0.11, T:0.26
Consensus pattern (22 bp):
AAAAATAAAAGGATTAATTTTA
Found at i:275398 original size:23 final size:23
Alignment explanation
Indices: 275297--275387 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 23
275287 TAAAAGAAAT
*
275297 AAAAATAAAAGGATTAAATTTT-
1 AAAAATAAAAGGATTTAATTTTA
* * **
275319 -AAAACAAAAGGGTTTAATTAAAAA
1 AAAAATAAAAGGATTTAATT--TTA
275343 AACAAATAAAAGGA-TTAATTTTA
1 AA-AAATAAAAGGATTTAATTTTA
*
275366 AAAAATAAAAGGATTTAGTTTT
1 AAAAATAAAAGGATTTAATTTT
275388 TCAGAATAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 11
0.72 0.14 0.15
Matches are distributed among these distances:
21 16 0.30
22 11 0.21
23 10 0.19
25 7 0.13
26 9 0.17
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (23 bp):
AAAAATAAAAGGATTTAATTTTA
Found at i:275426 original size:21 final size:21
Alignment explanation
Indices: 275402--275442 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
275392 AATAAAATGA
*
275402 TTAATAAAAAATAAAAAAAAT
1 TTAATAAAAAACAAAAAAAAT
**
275423 TTAATTTAAAACAAAAAAAA
1 TTAATAAAAAACAAAAAAAA
275443 AAGTTAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
TTAATAAAAAACAAAAAAAAT
Found at i:275432 original size:23 final size:23
Alignment explanation
Indices: 275406--275449 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
275396 AAATGATTAA
*
275406 TAAAA-AATAAAAAAAATTTAATT
1 TAAAACAA-AAAAAAAAGTTAATT
275429 TAAAACAAAAAAAAAAGTTAA
1 TAAAACAAAAAAAAAAGTTAA
275450 AATGGGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (23 bp):
TAAAACAAAAAAAAAAGTTAATT
Found at i:275498 original size:5 final size:5
Alignment explanation
Indices: 275490--275514 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
275480 CAGTGGAGAT
275490 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
275515 AGGGCATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:277323 original size:42 final size:42
Alignment explanation
Indices: 277276--277576 Score: 324
Period size: 42 Copynumber: 7.2 Consensus size: 42
277266 TGTGTGGCTG
*
277276 CAATCTGACCCTCTAGATTAGGGGTAAAAGATTGGATGAATT
1 CAATCTGACCCTCTAGATTAGGGGTAAAAGATTGGATGACTT
*
277318 CAATCT-ACCCCTCTAGATTAGGGGTAAAAGATTGGATGGCTT
1 CAATCTGA-CCCTCTAGATTAGGGGTAAAAGATTGGATGACTT
* * *
277360 CAATCTG-CTCCTCTGGATTAGGAGTAAAAGATTGGATGGCTT
1 CAATCTGAC-CCTCTAGATTAGGGGTAAAAGATTGGATGACTT
* * *
277402 CAATCTG-CTCTTCTAGATTAGGGGTAAAAGACTAGATGACTT
1 CAATCTGAC-CCTCTAGATTAGGGGTAAAAGATTGGATGACTT
* *
277444 CAAT-TTACCCCTCTAGATTAGGGGTAAATGATTGGATGACTT
1 CAATCTGA-CCCTCTAGATTAGGGGTAAAAGATTGGATGACTT
* *
277486 CAATCTGCCCCTCTAGATTAGGGGTAAAAGACTGGAT-ACCTT
1 CAATCTGACCCTCTAGATTAGGGGTAAAAGATTGGATGA-CTT
* * * * * ** **
277528 TAATTTGCCCCTTTGGATTAAAGGTAAAAGATCAGATGACTT
1 CAATCTGACCCTCTAGATTAGGGGTAAAAGATTGGATGACTT
*
277570 TAATCTG
1 CAATCTG
277577 CCGCTTTGGA
Statistics
Matches: 222, Mismatches: 29, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
41 4 0.02
42 215 0.97
43 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (42 bp):
CAATCTGACCCTCTAGATTAGGGGTAAAAGATTGGATGACTT
Found at i:277417 original size:84 final size:83
Alignment explanation
Indices: 277270--277578 Score: 357
Period size: 84 Copynumber: 3.7 Consensus size: 83
277260 GAGTTGTGTG
* * *
277270 TGGCTGCAATCTGACCCTCTAGATTAGGGGTAAAAGATTGGATGAATTCAATCTACCCCTCTAGA
1 TGGCTTCAATCTG-CCCTCTAGATTAGGGGTAAAAGATTGGATGACTTCAATCTGCCCCTCTAGA
*
277335 TTAGGGGTAAAAGATTGGA
65 TTAGGGGTAAAAGACTGGA
* * * * *
277354 TGGCTTCAATCTGCTCCTCTGGATTAGGAGTAAAAGATTGGATGGCTTCAATCTGCTCTTCTAGA
1 TGGCTTCAATCTGC-CCTCTAGATTAGGGGTAAAAGATTGGATGACTTCAATCTGCCCCTCTAGA
*
277419 TTAGGGGTAAAAGACTAGA
65 TTAGGGGTAAAAGACTGGA
* * * *
277438 TGACTTCAATTTACCCCTCTAGATTAGGGGTAAATGATTGGATGACTTCAATCTGCCCCTCTAGA
1 TGGCTTCAATCT-GCCCTCTAGATTAGGGGTAAAAGATTGGATGACTTCAATCTGCCCCTCTAGA
277503 TTAGGGGTAAAAGACTGGA
65 TTAGGGGTAAAAGACTGGA
** * * * * ** ** *
277522 TACCTTTAATTTGCCCCTTTGGATTAAAGGTAAAAGATCAGATGACTTTAATCTGCC
1 TGGCTTCAATCTG-CCCTCTAGATTAGGGGTAAAAGATTGGATGACTTCAATCTGCC
277579 GCTTTGGATT
Statistics
Matches: 190, Mismatches: 32, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
83 1 0.01
84 188 0.99
85 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (83 bp):
TGGCTTCAATCTGCCCTCTAGATTAGGGGTAAAAGATTGGATGACTTCAATCTGCCCCTCTAGAT
TAGGGGTAAAAGACTGGA
Found at i:277440 original size:126 final size:126
Alignment explanation
Indices: 277270--277522 Score: 382
Period size: 126 Copynumber: 2.0 Consensus size: 126
277260 GAGTTGTGTG
* *
277270 TGGCTGCAATCTGACCCTCTAGATTAGGGGTAAAAGATTGGATGAATTCAATCTACCCCTCTAGA
1 TGGCTGCAATCTGACCCTCTAGATTAGGGGTAAAAGACTAGATGAATTCAATCTACCCCTCTAGA
* * * *
277335 TTAGGGGTAAAAGATTGGATGGCTTCAATCTGCTCCTCTGGATTAGGAGTAAAAGATTGGA
66 TTAGGGGTAAAAGATTGGATGACTTCAATCTGCCCCTCTAGATTAGGAGTAAAAGACTGGA
* * * *
277396 TGGCTTCAATCTG-CTCTTCTAGATTAGGGGTAAAAGACTAGATGACTTCAATTTACCCCTCTAG
1 TGGCTGCAATCTGAC-CCTCTAGATTAGGGGTAAAAGACTAGATGAATTCAATCTACCCCTCTAG
* *
277460 ATTAGGGGTAAATGATTGGATGACTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGACTGGA
65 ATTAGGGGTAAAAGATTGGATGACTTCAATCTGCCCCTCTAGATTAGGAGTAAAAGACTGGA
277522 T
1 T
277523 ACCTTTAATT
Statistics
Matches: 114, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
125 1 0.01
126 113 0.99
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (126 bp):
TGGCTGCAATCTGACCCTCTAGATTAGGGGTAAAAGACTAGATGAATTCAATCTACCCCTCTAGA
TTAGGGGTAAAAGATTGGATGACTTCAATCTGCCCCTCTAGATTAGGAGTAAAAGACTGGA
Found at i:277547 original size:126 final size:125
Alignment explanation
Indices: 277276--277575 Score: 379
Period size: 126 Copynumber: 2.4 Consensus size: 125
277266 TGTGTGGCTG
* *
277276 CAATCTGACCC-TCTAGATTAGGGGTAAAAGATTGGATGAATTCAATCTACCCCTCTAGATTAGG
1 CAATCTG-CCCTTCTAGATTAGGGGTAAAAGA-TAGATGACTTCAATCTACCCCTCTAGATTAGG
* * * * **
277340 GGTAAAAGATTGGATGGCTTCAATCTGCTCCTCTGGATTAGGAGTAAAAGATTGGATGGCTT
64 GGTAAAAGATTGGATGACTTCAATCTGCCCCTCTAGATTAGGAGTAAAAGACTGGATACCTT
* *
277402 CAATCTGCTCTTCTAGATTAGGGGTAAAAGACTAGATGACTTCAATTTACCCCTCTAGATTAGGG
1 CAATCTGCCCTTCTAGATTAGGGGTAAAAGA-TAGATGACTTCAATCTACCCCTCTAGATTAGGG
* *
277467 GTAAATGATTGGATGACTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGACTGGATACCTT
65 GTAAAAGATTGGATGACTTCAATCTGCCCCTCTAGATTAGGAGTAAAAGACTGGATACCTT
* * * ** *
277528 TAATTTGCCCCTT-TGGATTAAAGGTAAAAGATCAGATGACTTTAATCT
1 CAATCTG-CCCTTCTAGATTAGGGGTAAAAGAT-AGATGACTTCAATCT
277576 GCCGCTTTGG
Statistics
Matches: 150, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
125 3 0.02
126 143 0.95
127 4 0.03
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (125 bp):
CAATCTGCCCTTCTAGATTAGGGGTAAAAGATAGATGACTTCAATCTACCCCTCTAGATTAGGGG
TAAAAGATTGGATGACTTCAATCTGCCCCTCTAGATTAGGAGTAAAAGACTGGATACCTT
Found at i:280341 original size:16 final size:15
Alignment explanation
Indices: 280315--280344 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
280305 GTAATTAACT
280315 TTTAACCTTTTTCAA
1 TTTAACCTTTTTCAA
280330 TTTAATCCTTTTTCA
1 TTTAA-CCTTTTTCA
280345 TTAATTAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAACCTTTTTCAA
Found at i:280725 original size:42 final size:42
Alignment explanation
Indices: 280655--280850 Score: 187
Period size: 42 Copynumber: 4.5 Consensus size: 42
280645 GTTGTTACAG
* * * * * * * *
280655 GATTAAGGATAAAAGACTGGATGACTTCAATCAGCCCTTTTA
1 GATTAGGGGTAAAAGATTTGATGGCTTCAATCTGCCCCTCTA
280697 GATTAGGGGTAAAAGATTTGATGGCTTCAATCTGCCCCTCTA
1 GATTAGGGGTAAAAGATTTGATGGCTTCAATCTGCCCCTCTA
* * *
280739 GATTAGGGGTAAAAGATTGGTGGTGGTTTCAATCTGTCCCTCTTA
1 GATTAGGGGTAAAAGATT--TGATGGCTTCAATCTGCCCCTC-TA
* * * *
280784 -ATTAAGGGTAAAAGATTGGGTGGTGGTTTCAATCTGCCCCTCTG
1 GATTAGGGGTAAAAGATT---TGATGGCTTCAATCTGCCCCTCTA
*
280828 GATTAGGGGTAAAAGATTGGATG
1 GATTAGGGGTAAAAGATTTGATG
280851 TGGTGATGTA
Statistics
Matches: 132, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
42 55 0.42
44 36 0.27
45 41 0.31
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (42 bp):
GATTAGGGGTAAAAGATTTGATGGCTTCAATCTGCCCCTCTA
Found at i:280825 original size:45 final size:45
Alignment explanation
Indices: 280680--280847 Score: 222
Period size: 45 Copynumber: 3.8 Consensus size: 45
280670 ACTGGATGAC
* * * *
280680 TTCAATCAG-CCCTTTTAGATTAGGGGTAAAAGATT--TGATGGC
1 TTCAATCTGCCCCTCTTAGATTAGGGGTAAAAGATTGGTGGTGGT
280722 TTCAATCTGCCCCTC-TAGATTAGGGGTAAAAGATTGGTGGTGGT
1 TTCAATCTGCCCCTCTTAGATTAGGGGTAAAAGATTGGTGGTGGT
* *
280766 TTCAATCTGTCCCTCTTA-ATTAAGGGTAAAAGATTGGGTGGTGGT
1 TTCAATCTGCCCCTCTTAGATTAGGGGTAAAAGATT-GGTGGTGGT
*
280811 TTCAATCTGCCCCTC-TGGATTAGGGGTAAAAGATTGG
1 TTCAATCTGCCCCTCTTAGATTAGGGGTAAAAGATTGG
280848 ATGTGGTGAT
Statistics
Matches: 111, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
42 28 0.25
43 4 0.04
44 38 0.34
45 41 0.37
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (45 bp):
TTCAATCTGCCCCTCTTAGATTAGGGGTAAAAGATTGGTGGTGGT
Found at i:280854 original size:89 final size:86
Alignment explanation
Indices: 280680--280847 Score: 239
Period size: 89 Copynumber: 1.9 Consensus size: 86
280670 ACTGGATGAC
* *
280680 TTCAATCAGCCCTTTTAGATTAGGGGTAAAAGATTTGATGGCTTCAATCTGCCCCTCTAGATTAG
1 TTCAATCAGCCCTCTTAGATTAAGGGTAAAAGATTTGATGGCTTCAATCTGCCCCTCTAGATTAG
280745 GGGTAAAAGATTGGTGGTGGT
66 GGGTAAAAGATTGGTGGTGGT
* * * *
280766 TTCAATCTGTCCCTCTTA-ATTAAGGGTAAAAGATTGGGTGGTGGTTTCAATCTGCCCCTCTGGA
1 TTCAATCAG-CCCTCTTAGATTAAGGGTAAAAGATT---TGATGGCTTCAATCTGCCCCTCTAGA
280830 TTAGGGGTAAAAGATTGG
62 TTAGGGGTAAAAGATTGG
280848 ATGTGGTGAT
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
86 24 0.33
87 7 0.10
89 41 0.57
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (86 bp):
TTCAATCAGCCCTCTTAGATTAAGGGTAAAAGATTTGATGGCTTCAATCTGCCCCTCTAGATTAG
GGGTAAAAGATTGGTGGTGGT
Found at i:282146 original size:53 final size:53
Alignment explanation
Indices: 282064--282470 Score: 519
Period size: 53 Copynumber: 7.6 Consensus size: 53
282054 GTAAATGCAA
* * * * **
282064 AAAGGTCCGATGACTCTGTGCCATTGTGAGTTATATGGATCCTATTATGGATT
1 AAAGGTCTGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACAGATT
* * * *
282117 AAAGGTTTGATGACTCTGTTTCATGGTGAGTTATATGAACCCTATTACAGATT
1 AAAGGTCTGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACAGATT
* * * *
282170 AAAGGTCTGATGACTTTGTGTCATCATAAGTTATATGAATCCTATTACAAATT
1 AAAGGTCTGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACAGATT
* * * *
282223 AAAGGTCTGATGACTCTGTGTCATCGTGACTTATAAGAATCCTATTACTGACT
1 AAAGGTCTGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACAGATT
* * * *
282276 AAAGGTCTGATGACTTTGTGTCATCGTGAGTTAGATGAGTCCTATTACGGATT
1 AAAGGTCTGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACAGATT
* * * *
282329 AAAGATCCGATGACTCTGTGTCATCGTGAGTTATATGAATCTTATTATAGATT
1 AAAGGTCTGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACAGATT
*
282382 AAAGGTCTGATGACTCTTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
1 AAAGGTCTGATGACTC-TGTGTCATCGTGAGTTATATGAATCCTATTACAGATT
* *
282436 AAAAAGT-TCGATGACTCAGTGTCATCGTGAGTTAT
1 -AAAGGTCT-GATGACTCTGTGTCATCGTGAGTTAT
282471 CAAATGTGAA
Statistics
Matches: 304, Mismatches: 47, Indels: 5
0.85 0.13 0.01
Matches are distributed among these distances:
53 239 0.79
54 52 0.17
55 13 0.04
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.36
Consensus pattern (53 bp):
AAAGGTCTGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACAGATT
Found at i:283636 original size:49 final size:49
Alignment explanation
Indices: 283551--284287 Score: 643
Period size: 49 Copynumber: 15.1 Consensus size: 49
283541 CAGTCTTTAA
* * * * * *
283551 ATTCGCCTTTGTGGCTTCAAT-TTTCTTCTCCTCATCTTTAGGGTATAAG
1 ATTCGCCATTGCGGCTTCAATCTTTC-CCTTCACATCTCTAGGGTATAAG
*** * * *
283600 ATTTATCGTTACGGCTTCAATCTTTCCCTTCACATCTCTATGGTATAAG
1 ATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAG
* * * * *
283649 GTTCGCCATTGCGACTTCAACCTTTCCCTCCACATCTCTAAGGTATAAG
1 ATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAG
* **** * * * *
283698 TTTCATTGTTGCGACTTCAATCTTTCCCATGACATCTCTAAGGTATAAG
1 ATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAG
* * * * * *
283747 GTTCGTCATTGCAGCTTTAACCTTTCCCTCCACATCTCTAGGGTATAAG
1 ATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAG
** * * * * * *
283796 ATTCATCGTTGCAGCTTTAATCTTTCCCATCACATTTCTAAGGTATAAG
1 ATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAG
* * * * * *
283845 GTTAGCCGTTGCGGCTTCAACCTTTCCCTCCACATGTCTAGGGTATAAG
1 ATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAG
* * * * * * * * *
283894 GTTCGTCGTTGCGGCTTCAACCTTTTCGTTCATATCTCCAAGGTATAAG
1 ATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAG
* * * * *
283943 ATTCGCCGTTGCGACTTCAATCTTTCCCTTCACATCTTTAGGGCATGAG
1 ATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAG
* * * * **
283992 ATTCACCATTGCGGCTTCAATCCTTCCCTTTACATCTCTAGGGCACGAG
1 ATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAG
* * * * * *
284041 ATTCACCATTGCGGCTTCAATCTTTCCCATCATATTTGTAGGGTACAAG
1 ATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAG
* * *
284090 ATTTGCCATTGTGGTTTCAATCTTTCCCTTCACATCTCTAGGGTATAAG
1 ATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAG
* *
284139 ATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGCATGAG
1 ATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAG
* * * *
284188 ATTTGTCATT-CGGCTTCAATCTTTCCCTTCACATCTCTAGGGCATGAG
1 ATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAG
** ** * * * *
284236 ATTCATCATTGCAACTTCAGTCTCTCCCTTCATATCTCTAAGGTAT-AG
1 ATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAG
284284 ATTC
1 ATTC
284288 AATGTTTCTT
Statistics
Matches: 564, Mismatches: 122, Indels: 5
0.82 0.18 0.01
Matches are distributed among these distances:
48 52 0.09
49 508 0.90
50 4 0.01
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (49 bp):
ATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAG
Found at i:285336 original size:21 final size:21
Alignment explanation
Indices: 285304--285360 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 21
285294 CATCTTAATC
*
285304 TCTCCTTT-T-TTTTTTTCCT
1 TCTCCTTTCTATTTTTTTTCT
285323 TCT-CTTTCTA-TTTTTTTCT
1 TCTCCTTTCTATTTTTTTTCT
*
285342 TTTCCTTTCTATTTTTTTT
1 TCTCCTTTCTATTTTTTTT
285361 ATTTTTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 4 0.12
19 14 0.44
20 7 0.22
21 7 0.22
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (21 bp):
TCTCCTTTCTATTTTTTTTCT
Found at i:285337 original size:25 final size:23
Alignment explanation
Indices: 285309--285368 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 23
285299 TAATCTCTCC
285309 TTTTTTTTTTTCCTTCTCT-TTCTAT
1 TTTTTTTTTTTCCTT-TCTATT-T-T
*
285334 TTTTTTCTTTTCCTTTCTATTTT
1 TTTTTTTTTTTCCTTTCTATTTT
285357 TTTTATTTTTTT
1 TTTT-TTTTTTT
285369 GAAGATAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 5 0.16
24 10 0.32
25 16 0.52
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTTTTTTTCCTTTCTATTTT
Found at i:285338 original size:20 final size:20
Alignment explanation
Indices: 285304--285359 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
285294 CATCTTAATC
285304 TCTCCTTT-T-TTTTTTTCCT
1 TCTCCTTTCTATTTTTTT-CT
285323 TCT-CTTTCTATTTTTTTCT
1 TCTCCTTTCTATTTTTTTCT
*
285342 TTTCCTTTCTATTTTTTT
1 TCTCCTTTCTATTTTTTT
285360 TATTTTTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 4 0.12
19 8 0.24
20 21 0.64
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (20 bp):
TCTCCTTTCTATTTTTTTCT
Found at i:285340 original size:10 final size:10
Alignment explanation
Indices: 285327--285368 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
285317 TTTCCTTCTC
285327 TTTCTATTTT
1 TTTCTATTTT
*
285337 TTTCT-TTTCC
1 TTTCTATTT-T
285347 TTTCTATTTT
1 TTTCTATTTT
285357 TTT-TATTTT
1 TTTCTATTTT
285366 TTT
1 TTT
285369 GAAGATAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 12 0.43
10 13 0.46
11 3 0.11
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTCTATTTT
Found at i:286225 original size:48 final size:48
Alignment explanation
Indices: 286115--286214 Score: 200
Period size: 48 Copynumber: 2.1 Consensus size: 48
286105 TCCGTATGAC
286115 TTTTGCTCAAATTTTTTCAACATTCCCACATTATCTTGATTTGTCATG
1 TTTTGCTCAAATTTTTTCAACATTCCCACATTATCTTGATTTGTCATG
286163 TTTTGCTCAAATTTTTTCAACATTCCCACATTATCTTGATTTGTCATG
1 TTTTGCTCAAATTTTTTCAACATTCCCACATTATCTTGATTTGTCATG
286211 TTTT
1 TTTT
286215 CTCTCAATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.22, C:0.20, G:0.08, T:0.50
Consensus pattern (48 bp):
TTTTGCTCAAATTTTTTCAACATTCCCACATTATCTTGATTTGTCATG
Found at i:287062 original size:22 final size:21
Alignment explanation
Indices: 287015--287131 Score: 58
Period size: 21 Copynumber: 5.2 Consensus size: 21
287005 TAAAAGAAAT
*
287015 AAAAATAAAAGGATTAAATTT
1 AAAAATAAAAGGATTAAATTA
* * *
287036 TAAAATAAAAGGGTTTAATTAAAA
1 AAAAATAAAAGGATTAAATT---A
* *
287060 AAACGAATAAAAGGATTTAATTTTT
1 AAA--AATAAAAGGA-TTAA-ATTA
*
287085 CAAAATAAAAGGATT-AA-TA
1 AAAAATAAAAGGATTAAATTA
* *
287104 AAAAATAAAAAAGATATAATTTA
1 AAAAAT-AAAAGGAT-TAAATTA
287127 AAAAA
1 AAAAA
287132 AAAGATACAA
Statistics
Matches: 70, Mismatches: 15, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
19 6 0.09
20 7 0.10
21 19 0.27
22 3 0.04
23 17 0.24
24 2 0.03
25 2 0.03
26 9 0.13
27 3 0.04
28 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAAATAAAAGGATTAAATTA
Found at i:287072 original size:47 final size:47
Alignment explanation
Indices: 287018--287108 Score: 132
Period size: 47 Copynumber: 1.9 Consensus size: 47
287008 AAGAAATAAA
*
287018 AATAAAAGGA-TTAAATTTT-AAAATAAAAGGGTTTAATTAAAAAAACG
1 AATAAAAGGATTTAAATTTTCAAAATAAAA-GGATTAA-TAAAAAAACG
*
287065 AATAAAAGGATTTAATTTTTCAAAATAAAAGGATTAATAAAAAA
1 AATAAAAGGATTTAAATTTTCAAAATAAAAGGATTAATAAAAAA
287109 TAAAAAAGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
47 17 0.43
48 14 0.35
49 9 0.22
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.29
Consensus pattern (47 bp):
AATAAAAGGATTTAAATTTTCAAAATAAAAGGATTAATAAAAAAACG
Found at i:287123 original size:21 final size:19
Alignment explanation
Indices: 287086--287137 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
287076 TTAATTTTTC
*
287086 AAAATAAAAGGATTAATAA
1 AAAATAAAAAGATTAATAA
**
287105 AAAATAAAAAAGATATAATTT
1 AAAAT-AAAAAGAT-TAATAA
287126 AAAA-AAAAAGAT
1 AAAATAAAAAGAT
287138 ACAAGGGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 13 0.46
20 7 0.25
21 8 0.29
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (19 bp):
AAAATAAAAAGATTAATAA
Done.