Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015241.1 Kokia drynarioides strain JFW-HI SEQ_130286, 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: 171737
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 392 characters in sequence are not A, C, G, or T
Found at i:4396 original size:3 final size:3
Alignment explanation
Indices: 4390--4415 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4380 TAATAATAAT
4390 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
4416 CTAAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5918 original size:16 final size:17
Alignment explanation
Indices: 5892--5924 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5882 GAACCGTTCG
*
5892 TATTGATTTTTGTATAA
1 TATTGATTTTTATATAA
5909 TATT-ATTTTTATATAA
1 TATTGATTTTTATATAA
5925 AAACAGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
TATTGATTTTTATATAA
Found at i:10443 original size:12 final size:12
Alignment explanation
Indices: 10426--10452 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
10416 ACTGAAATTA
10426 AAAAAAAAAAAG
1 AAAAAAAAAAAG
10438 AAAAAAAAAAAG
1 AAAAAAAAAAAG
10450 AAA
1 AAA
10453 GGGAAAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:19392 original size:18 final size:19
Alignment explanation
Indices: 19356--19394 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
19346 TAAAATATTT
*
19356 AAAATGTTACTTAAAAATA
1 AAAATATTACTTAAAAATA
*
19375 AAAATATTAC-TAATAATA
1 AAAATATTACTTAAAAATA
19393 AA
1 AA
19395 TTTTATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAATATTACTTAAAAATA
Found at i:19425 original size:18 final size:18
Alignment explanation
Indices: 19379--19425 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
19369 AAAATAAAAA
19379 TATTACTAATAATAAATTT
1 TATTA-TAATAATAAATTT
*
19398 TATTAAAATAATAAATTAT
1 TATTATAATAATAAATT-T
19417 TA-TATAATA
1 TATTATAATA
19426 TATTATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TATTATAATAATAAATTT
Found at i:39203 original size:29 final size:29
Alignment explanation
Indices: 39170--39226 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
39160 AAAAAATACC
*
39170 AAGTTCATGTACCAAATTAGGTCCAAAAA
1 AAGTTCAGGTACCAAATTAGGTCCAAAAA
* *
39199 AAGTTTAGGTACCAAATTGGGTCCAAAA
1 AAGTTCAGGTACCAAATTAGGTCCAAAA
39227 TATATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.25
Consensus pattern (29 bp):
AAGTTCAGGTACCAAATTAGGTCCAAAAA
Found at i:39281 original size:31 final size:32
Alignment explanation
Indices: 39240--39340 Score: 106
Period size: 31 Copynumber: 3.3 Consensus size: 32
39230 ATATATATAT
39240 AGGTACCAAATTAAG-AAAAAATGTCAAGTTC
1 AGGTACCAAATTAAGTAAAAAATGTCAAGTTC
* ** *
39271 AGGTATCAAATTGGGTAAAAAA----AAGTTT
1 AGGTACCAAATTAAGTAAAAAATGTCAAGTTC
*
39299 AGATACCAAA-TAAGTAAAAAATGTCAAGTTC
1 AGGTACCAAATTAAGTAAAAAATGTCAAGTTC
*
39330 AAGTACCAAAT
1 AGGTACCAAAT
39341 GTTATATTAA
Statistics
Matches: 53, Mismatches: 11, Indels: 11
0.71 0.15 0.15
Matches are distributed among these distances:
27 9 0.17
28 13 0.25
31 25 0.47
32 6 0.11
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.24
Consensus pattern (32 bp):
AGGTACCAAATTAAGTAAAAAATGTCAAGTTC
Found at i:42459 original size:24 final size:25
Alignment explanation
Indices: 42409--42462 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
42399 AATAATCTTT
*
42409 AAAATGTCATAAAATAGATAAAAAA
1 AAAATGTCATAAAATAGACAAAAAA
* *
42434 AAAATTTCATAAGA-AGACAAAGAAA
1 AAAATGTCATAAAATAGACAAA-AAA
42459 AAAA
1 AAAA
42463 ATTTAATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.17
Consensus pattern (25 bp):
AAAATGTCATAAAATAGACAAAAAA
Found at i:50915 original size:34 final size:34
Alignment explanation
Indices: 50876--50940 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
50866 TTTACATAAA
*
50876 TTTTGATATATAAATA-ATTTTGTATCATATTAAT
1 TTTTGAAATATAAATACA-TTTGTATCATATTAAT
**
50910 TTTTGAAATATCTATACATTTGTATCATATT
1 TTTTGAAATATAAATACATTTGTATCATATT
50941 CATATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 26 0.96
35 1 0.04
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (34 bp):
TTTTGAAATATAAATACATTTGTATCATATTAAT
Found at i:69102 original size:10 final size:11
Alignment explanation
Indices: 69084--69117 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
69074 GGTGACGAAG
69084 AAATAAAAGGA
1 AAATAAAAGGA
69095 AAAT-AAAGG-
1 AAATAAAAGGA
69104 AAATAAAAGGA
1 AAATAAAAGGA
69115 AAA
1 AAA
69118 GAATTGTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 4 0.19
10 10 0.48
11 7 0.33
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.09
Consensus pattern (11 bp):
AAATAAAAGGA
Found at i:71845 original size:117 final size:117
Alignment explanation
Indices: 71211--71817 Score: 872
Period size: 117 Copynumber: 5.2 Consensus size: 117
71201 GTTTCCTTCG
* * * * ** *
71211 TCGTCACTAGGTGGTTTCTTGCCGGCGACTGGACTTTCTTTCTCAACGTCTTCTAGTAATCGTTC
1 TCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCTTCCTCAACGTCTTCTAGTTTTCGTTT
* * *
71276 CTCACGGATGAACTCAATGTCTTTTAGTAATCTTTTTGGGGGATTATCTCCT
66 CTTACCGATGACCTCAATGTCTTTTAGTAATCTTTTTGGGGGATTATCTCCT
* * * * **
71328 TCATCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCTTCCTCGACGTCTGCTTGTAATAACCG
1 TCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCTTCCTCAACGTCTTCTAGT--T-TTCG
* * * * *
71393 TTTTTTACCGATGACCTCAATGTCTTTTAGTAATCTTTTAGGAGGATTGTCTCCC
63 TTTCTTACCGATGACCTCAATGTCTTTTAGTAATCTTTTTGGGGGATTATCTCCT
* *
71448 TCGTCACTAGGTGGTTTCTCACCGGCGAATGGACTCTCTTCCTCAACGTCTTCTAGTTTTCGTAT
1 TCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCTTCCTCAACGTCTTCTAGTTTTCGTTT
* *
71513 CTTACCGATGACCTCAATGTCTTTTAGTAATCTTTTAGGAGGATTATCTCCT
66 CTTACCGATGACCTCAATGTCTTTTAGTAATCTTTTTGGGGGATTATCTCCT
** *
71565 TCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCTTCCTCAACGTCTTCTAACTTTCGTAT
1 TCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCTTCCTCAACGTCTTCTAGTTTTCGTTT
* *
71630 CTTACCGATGACCTCAATGTCTTTTAGTAATCTTTTTGGGGGATTGTCACCT
66 CTTACCGATGACCTCAATGTCTTTTAGTAATCTTTTTGGGGGATTATCTCCT
* * * *
71682 TCGTCACTTGGTGGTTTCTCGCCGGCGAATGGACTCTCTTTCTCAACATCTTGTAGTTTTCGTTT
1 TCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCTTCCTCAACGTCTTCTAGTTTTCGTTT
*
71747 CTTACCGATGACCTCAATGTCTTTTAGTAATCTTTTTGGGGGCTTATCTCCT
66 CTTACCGATGACCTCAATGTCTTTTAGTAATCTTTTTGGGGGATTATCTCCT
71799 TCGTCACTAGGTGGTTTCT
1 TCGTCACTAGGTGGTTTCT
71818 TACCAGCAAA
Statistics
Matches: 439, Mismatches: 48, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
117 337 0.77
118 1 0.00
120 101 0.23
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (117 bp):
TCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCTTCCTCAACGTCTTCTAGTTTTCGTTT
CTTACCGATGACCTCAATGTCTTTTAGTAATCTTTTTGGGGGATTATCTCCT
Found at i:81445 original size:51 final size:51
Alignment explanation
Indices: 81368--81667 Score: 420
Period size: 51 Copynumber: 5.9 Consensus size: 51
81358 ACTCCCTTAC
* *
81368 TTCCCTTGCTGCTGATGATGGCTCCCCTGTTTCAGCCATTGAAGATGGTTCT
1 TTCCCTT-TTGCTGATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCT
** * *
81420 TTCCCTTTTATTGATGATGACTCCCCTGTTTCGGCCATTGAAGATGGTTGT
1 TTCCCTTTTGCTGATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCT
* * * * *
81471 TTCCCTTTTGCTGCTGGTGACTCCCCTGTTTCGGCCATCGAAGACGGTTCT
1 TTCCCTTTTGCTGATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCT
* *
81522 TTCCCTTTTGCTGCTGGTGACTCCCCTGTTTCAGCCATTGAAGATGGTTCT
1 TTCCCTTTTGCTGATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCT
* * * *
81573 TTCCCTTTGGCTGCTGGTGACTCCCCTGTTTCAGCCATTGAAGATAGTTCT
1 TTCCCTTTTGCTGATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCT
* *
81624 TTCCCTTTTGCTGAAGATGACTCCCCTTTTTCAGCCATTGAAGA
1 TTCCCTTTTGCTGATGATGACTCCCCTGTTTCAGCCATTGAAGA
81668 CAGAAAAAGA
Statistics
Matches: 225, Mismatches: 23, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
51 218 0.97
52 7 0.03
ACGTcount: A:0.14, C:0.27, G:0.21, T:0.38
Consensus pattern (51 bp):
TTCCCTTTTGCTGATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCT
Found at i:82164 original size:48 final size:48
Alignment explanation
Indices: 82069--82164 Score: 111
Period size: 48 Copynumber: 2.0 Consensus size: 48
82059 TGTATTTGAG
* * * **
82069 AAAATTTTCGAACTTTGGTGAAAGACTTGTTCACAAGTCAGGTTATCC
1 AAAATTTCCGAACTTTGGTGAAAGACCTATTCACAAGTCAGACTATCC
* * * *
82117 AAAATTTCCGAACTTTGGTGATAGGCCTATTCATAAGTTAGACTATCC
1 AAAATTTCCGAACTTTGGTGAAAGACCTATTCACAAGTCAGACTATCC
82165 GTCTATATTC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (48 bp):
AAAATTTCCGAACTTTGGTGAAAGACCTATTCACAAGTCAGACTATCC
Found at i:84692 original size:30 final size:31
Alignment explanation
Indices: 84653--84719 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
84643 TGATGATGAA
*
84653 TCCCCTGTTTCAGCCATTGAAGATGGTTC-T
1 TCCCTTGTTTCAGCCATTGAAGATGGTTCTT
* *
84683 TCCCTTGTTTCATCCATTGAAGATTGTTCTT
1 TCCCTTGTTTCAGCCATTGAAGATGGTTCTT
84714 TCCCTT
1 TCCCTT
84720 TTGCTAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 26 0.79
31 7 0.21
ACGTcount: A:0.15, C:0.27, G:0.15, T:0.43
Consensus pattern (31 bp):
TCCCTTGTTTCAGCCATTGAAGATGGTTCTT
Found at i:84764 original size:51 final size:51
Alignment explanation
Indices: 84683--85164 Score: 624
Period size: 51 Copynumber: 9.5 Consensus size: 51
84673 AGATGGTTCT
* * *
84683 TCCCTTGTTTCATCCATTGAAGATTGTTCTTTCCCTTTTGCTAATGATGAC
1 TCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTAATGATGAC
* * *** *
84734 TCCCCTGTTTCAGTCATTGAATATGGTTCTTTCCCTGCCGCTAATGGTGAC
1 TCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTAATGATGAC
* *
84785 TCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTAATAATGAC
1 TCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTAATGATGAC
* *
84836 TCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTAATAATGAC
1 TCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTAATGATGAC
* * *** ** * *
84887 TCCCCTGTTTCAGTCATTGAAGATGGTTCTTCCCCTGCCGCTGCTGGTAAC
1 TCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTAATGATGAC
* *
84938 TCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTTCTGATGATGAC
1 TCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTAATGATGAC
* * *** ** *
84989 TCCTCTGTTTCAGTCATTGAAGATGGTTCTTTCCCTGCCGCTGCTGGTGAC
1 TCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTAATGATGAC
*
85040 TCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTAAT-ACTGAC
1 TCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTAATGA-TGAC
* *
85091 TCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCGCTTTTGCTGATGATGAC
1 TCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTAATGATGAC
*
85142 TCCCCTGTTTCGGCCATTGAAGA
1 TCCCCTGTTTCAGCCATTGAAGA
85165 AAGAAAAATA
Statistics
Matches: 372, Mismatches: 57, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
51 371 1.00
52 1 0.00
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.39
Consensus pattern (51 bp):
TCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTAATGATGAC
Found at i:87342 original size:73 final size:73
Alignment explanation
Indices: 87223--87370 Score: 296
Period size: 73 Copynumber: 2.0 Consensus size: 73
87213 TATATGGAAA
87223 AGCATGACAAAACAGTGGGCGTGCCGGAGTGGTTATCGGGCATGACTAGAAATCATGTGGGCTCT
1 AGCATGACAAAACAGTGGGCGTGCCGGAGTGGTTATCGGGCATGACTAGAAATCATGTGGGCTCT
87288 GCCCGCGC
66 GCCCGCGC
87296 AGCATGACAAAACAGTGGGCGTGCCGGAGTGGTTATCGGGCATGACTAGAAATCATGTGGGCTCT
1 AGCATGACAAAACAGTGGGCGTGCCGGAGTGGTTATCGGGCATGACTAGAAATCATGTGGGCTCT
87361 GCCCGCGC
66 GCCCGCGC
87369 AG
1 AG
87371 GTTCGAATCC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.24, C:0.23, G:0.34, T:0.19
Consensus pattern (73 bp):
AGCATGACAAAACAGTGGGCGTGCCGGAGTGGTTATCGGGCATGACTAGAAATCATGTGGGCTCT
GCCCGCGC
Found at i:95309 original size:12 final size:12
Alignment explanation
Indices: 95287--95319 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
95277 AAGAGCTGAA
95287 TCTTATGGCGTCT
1 TCTT-TGGCGTCT
95300 TCTTTGGCGTCT
1 TCTTTGGCGTCT
95312 TCTTTGGC
1 TCTTTGGC
95320 TTCTCCGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.03, C:0.24, G:0.24, T:0.48
Consensus pattern (12 bp):
TCTTTGGCGTCT
Found at i:100578 original size:2 final size:2
Alignment explanation
Indices: 100523--100570 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
100513 CACCATCTAC
100523 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
100565 AT AT AT
1 AT AT AT
100571 GAATATATGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:103681 original size:16 final size:17
Alignment explanation
Indices: 103662--103696 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
103652 AAATTTTTGT
103662 AAATGAAAAA-AATATA
1 AAATGAAAAATAATATA
*
103678 AAATTAAAAATAATATA
1 AAATGAAAAATAATATA
103695 AA
1 AA
103697 TATTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (17 bp):
AAATGAAAAATAATATA
Found at i:103942 original size:3 final size:3
Alignment explanation
Indices: 103934--103959 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
103924 TATTGCTTTA
103934 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
103960 ATTAATCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:106507 original size:31 final size:30
Alignment explanation
Indices: 106467--106539 Score: 76
Period size: 32 Copynumber: 2.4 Consensus size: 30
106457 GATTTTACTA
106467 TTTAAATT-AATACAATATTAAAAATATATT
1 TTTAAATTAAATACAATATTAAAAA-ATATT
** *
106497 TTTATAATTAAATTTAATTTTAAAAAATATT
1 TTTA-AATTAAATACAATATTAAAAAATATT
* *
106528 TTTTATTTAAAT
1 TTTAAATTAAAT
106540 TGAATTTGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 11 0.31
31 12 0.33
32 13 0.36
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (30 bp):
TTTAAATTAAATACAATATTAAAAAATATT
Found at i:106540 original size:30 final size:32
Alignment explanation
Indices: 106484--106546 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
106474 TAATACAATA
*
106484 TTAAAAATATATTTTTATAATTAAATTTAATT
1 TTAAAAATATATTTTTATAATTAAATTGAATT
*
106516 TTAAAAA-ATATTTTT-TATTTAAATTGAATT
1 TTAAAAATATATTTTTATAATTAAATTGAATT
106546 T
1 T
106547 GGGTCAACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 14 0.48
31 8 0.28
32 7 0.24
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (32 bp):
TTAAAAATATATTTTTATAATTAAATTGAATT
Found at i:106986 original size:17 final size:18
Alignment explanation
Indices: 106952--106987 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
106942 TTTGGTATTG
106952 TTTTTATCAAGATTGTTTT
1 TTTTTATCAAGA-TGTTTT
106971 TTTTTATCAAGA-GTTTT
1 TTTTTATCAAGATGTTTT
106988 AGTGGGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
19 12 0.71
ACGTcount: A:0.22, C:0.06, G:0.11, T:0.61
Consensus pattern (18 bp):
TTTTTATCAAGATGTTTT
Found at i:109875 original size:57 final size:54
Alignment explanation
Indices: 109773--109938 Score: 176
Period size: 57 Copynumber: 3.0 Consensus size: 54
109763 TGACCATTGA
* *
109773 TGCCATTTTTTCCGGTATCCTCAAATCC--AACAATCGAACTTGATTTTCCCTTTCT
1 TGCCA-TTTTCCCGG-ATCCTCAAATCCTTAACAACCGAACTTGATTTTCCCTTT-T
* *
109828 TGCCATTTTCCCCGGATCCTCAAATCCATTAACAACCGAGCTTGATTTCCCCTTTT
1 TGCCATTTT-CCCGGATCCTCAAATCC-TTAACAACCGAACTTGATTTTCCCTTTT
* * *
109884 TGACCCATTTTCCTGGATCCTCCAACCCGTTAACAACCGAACTTGA-TTTCCCTTT
1 TG--CCATTTTCCCGGATCCTCAAATCC-TTAACAACCGAACTTGATTTTCCCTTT
109939 GTTAGTACTC
Statistics
Matches: 95, Mismatches: 10, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
54 16 0.17
55 9 0.09
56 11 0.12
57 52 0.55
58 7 0.07
ACGTcount: A:0.22, C:0.33, G:0.10, T:0.36
Consensus pattern (54 bp):
TGCCATTTTCCCGGATCCTCAAATCCTTAACAACCGAACTTGATTTTCCCTTTT
Found at i:111581 original size:17 final size:16
Alignment explanation
Indices: 111550--111584 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
111540 AATTGGCCGA
111550 TTAAAAATATAAAAAT
1 TTAAAAATATAAAAAT
*
111566 TTAAAATATCTAAAAAT
1 TTAAAA-ATATAAAAAT
111583 TT
1 TT
111585 GGAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAAAATATAAAAAT
Found at i:115730 original size:19 final size:20
Alignment explanation
Indices: 115686--115729 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
115676 TAATTTTTAA
*
115686 TTTTTTAACAACTTTTATAC
1 TTTTTTAACAACTTTTAGAC
*
115706 TTTTTTAAC-TCTTTTAGA-
1 TTTTTTAACAACTTTTAGAC
115724 TTTTTT
1 TTTTTT
115730 TTTGAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 7 0.32
20 9 0.41
ACGTcount: A:0.23, C:0.11, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTTTAACAACTTTTAGAC
Found at i:123902 original size:79 final size:79
Alignment explanation
Indices: 123771--123931 Score: 277
Period size: 79 Copynumber: 2.0 Consensus size: 79
123761 AGAAGCAACT
* **
123771 AATGGCTCACATATTGCCTATCGCTATGACTGTGGAACACAATCAGATCACAGATTAACTTTTGA
1 AATGGCTCACATATCGCCTATCGCTATGACTGAAGAACACAATCAGATCACAGATTAACTTTTGA
123836 GCACTTCATGAATC
66 GCACTTCATGAATC
* *
123850 AATGGTTCACATATCGCCTATTGCTATGACTGAAGAACACAATCAGATCACAGATTAACTTTTGA
1 AATGGCTCACATATCGCCTATCGCTATGACTGAAGAACACAATCAGATCACAGATTAACTTTTGA
123915 GCACTTCATGAATC
66 GCACTTCATGAATC
123929 AAT
1 AAT
123932 TAAATACTCG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.29
Consensus pattern (79 bp):
AATGGCTCACATATCGCCTATCGCTATGACTGAAGAACACAATCAGATCACAGATTAACTTTTGA
GCACTTCATGAATC
Found at i:127805 original size:19 final size:20
Alignment explanation
Indices: 127758--127808 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
127748 TTAAACCCAC
*
127758 ATATATATTATTTAGTTTAA
1 ATATATATTTTTTAGTTTAA
127778 ATATA-ATTTTTTA-TTTAA
1 ATATATATTTTTTAGTTTAA
*
127796 ATTTATATTTTTT
1 ATATATATTTTTT
127809 CAATATCCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 9 0.32
19 14 0.50
20 5 0.18
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
ATATATATTTTTTAGTTTAA
Found at i:131121 original size:7 final size:7
Alignment explanation
Indices: 131109--131135 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
131099 AAATCCAATC
131109 TCATGTT
1 TCATGTT
131116 TCATGTT
1 TCATGTT
131123 TCATGTT
1 TCATGTT
131130 TCATGT
1 TCATGT
131136 ATTTCAAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (7 bp):
TCATGTT
Found at i:140399 original size:14 final size:15
Alignment explanation
Indices: 140371--140409 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
140361 AATTTTAAGT
140371 TTAAATATTAATTTG
1 TTAAATATTAATTTG
*
140386 TTAAA-ATTATTTTG
1 TTAAATATTAATTTG
140400 TTAAAT-TTAA
1 TTAAATATTAA
140410 GTTTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (15 bp):
TTAAATATTAATTTG
Found at i:140801 original size:30 final size:30
Alignment explanation
Indices: 140765--140826 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
140755 GGATTTGAAA
*
140765 TTTAAAATCTAAAAA-ATAAAAAATTAAAAT
1 TTTAAAATATAAAAATA-AAAAAATTAAAAT
* *
140795 TTTAAAATATAAATATAAAAAAATTCAAAT
1 TTTAAAATATAAAAATAAAAAAATTAAAAT
140825 TT
1 TT
140827 ATGAGAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (30 bp):
TTTAAAATATAAAAATAAAAAAATTAAAAT
Found at i:141229 original size:31 final size:31
Alignment explanation
Indices: 141191--141249 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
141181 TTTATTTGTG
*
141191 TTAAATTTAA-CTTTTAATCTTTTAAAAAAAT
1 TTAAATTTAATC-ATTAATCTTTTAAAAAAAT
*
141222 TTAAATTTAATCATTAATTTTTTAAAAA
1 TTAAATTTAATCATTAATCTTTTAAAAA
141250 GAGTCGAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (31 bp):
TTAAATTTAATCATTAATCTTTTAAAAAAAT
Found at i:143386 original size:4 final size:4
Alignment explanation
Indices: 143377--143408 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
143367 CCCAACTTAC
143377 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
143409 GCTAAATGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:146189 original size:4 final size:4
Alignment explanation
Indices: 146180--146209 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
146170 TACAAATGAA
146180 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
146210 GTATGTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:146558 original size:191 final size:191
Alignment explanation
Indices: 146234--146593 Score: 549
Period size: 191 Copynumber: 1.9 Consensus size: 191
146224 GTGATAAGCA
* * *
146234 CTGAAATTTCAAGGAATGTATTACTATTGCAGTGAATAGATAGCAATGTTTAGCTCTTATATGCC
1 CTGAAATTTCAAGGAAAGTATTACTATTGCAGTGAATAGATAGCAATGTTTAGCTATTACATGCC
* * * *
146299 TTCAATTGAATACATTCCAGCAAAGACTTGTTAAATGGTCTAATTCCACTTTTAGCAACTCCTAA
66 TTCAATTCAATACATTCAAGCAAAGACTAGTTAAATGGTCCAATTCCACTTTTAGCAACTCCTAA
* * *
146364 ACCTTAATAATTCATTTTAATCCCTTTTATCTCCTTTATATATATATAGTTATAATAACCC
131 ACCTTAATAATTCAATTTAATCCCCTTTAGCTCCTTTATATATATATAGTTATAATAACCC
** * * * *
146425 CTGAAATTTCTTGGAAAGTATTGCTGTTGCAGTGAATGGATAGCCATGTTTAGCTATTACATGCC
1 CTGAAATTTCAAGGAAAGTATTACTATTGCAGTGAATAGATAGCAATGTTTAGCTATTACATGCC
* * *
146490 TTCAATTCAATACATTCAAGCAAAGACTAGTTAGATGGTCCAATTTCACTTTTAGCCACTCCTAA
66 TTCAATTCAATACATTCAAGCAAAGACTAGTTAAATGGTCCAATTCCACTTTTAGCAACTCCTAA
146555 ACCTTAATAATTCAATTTAATCCCCTTTAGCTCCTTTAT
131 ACCTTAATAATTCAATTTAATCCCCTTTAGCTCCTTTAT
146594 TAAATGGAAA
Statistics
Matches: 150, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
191 150 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (191 bp):
CTGAAATTTCAAGGAAAGTATTACTATTGCAGTGAATAGATAGCAATGTTTAGCTATTACATGCC
TTCAATTCAATACATTCAAGCAAAGACTAGTTAAATGGTCCAATTCCACTTTTAGCAACTCCTAA
ACCTTAATAATTCAATTTAATCCCCTTTAGCTCCTTTATATATATATAGTTATAATAACCC
Found at i:148720 original size:22 final size:22
Alignment explanation
Indices: 148683--148725 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
148673 ATGCTAAATT
*
148683 ATTTATAAATAATTAT-TTTAA
1 ATTTAAAAATAATTATATTTAA
148704 ATTTAAAAATTAATTATATTTA
1 ATTTAAAAA-TAATTATATTTA
148726 TTAGTTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 7 0.37
23 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTAAAAATAATTATATTTAA
Found at i:156937 original size:2 final size:2
Alignment explanation
Indices: 156925--156959 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
156915 ATTTTTGTTT
*
156925 AG AG CG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
156960 TACCCGATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:159457 original size:26 final size:25
Alignment explanation
Indices: 159397--159458 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
159387 TTAATATTAT
*
159397 TTTTGAAAAGTGCTTTTAAAAGGTG
1 TTTTGAAAAATGCTTTTAAAAGGTG
* * * *
159422 CTATGAAAAAATGTTTTTGAAAGGTAG
1 TTTTG-AAAAATGCTTTTAAAAGGT-G
159449 TTTTGAAAAA
1 TTTTGAAAAA
159459 ACTTGATTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
25 3 0.11
26 21 0.75
27 4 0.14
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37
Consensus pattern (25 bp):
TTTTGAAAAATGCTTTTAAAAGGTG
Found at i:159805 original size:15 final size:15
Alignment explanation
Indices: 159785--159828 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
159775 AACTTCTCCA
159785 TTTGAAAAAAATATT
1 TTTGAAAAAAATATT
*
159800 TTTGAAAAACTAATTTT
1 TTTGAAAAA--AATATT
*
159817 TTTTAAAAAAAT
1 TTTGAAAAAAAT
159829 TACTTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 12 0.48
17 13 0.52
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTGAAAAAAATATT
Found at i:159829 original size:15 final size:15
Alignment explanation
Indices: 159785--159829 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
159775 AACTTCTCCA
*
159785 TTTGAAAAAAATATT
1 TTTGAAAAAAATTTT
159800 TTTGAAAAACTAATTTT
1 TTTGAAAAA--AATTTT
*
159817 TTTTAAAAAAATT
1 TTTGAAAAAAATT
159830 ACTTATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 13 0.50
17 13 0.50
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (15 bp):
TTTGAAAAAAATTTT
Found at i:160135 original size:13 final size:14
Alignment explanation
Indices: 160108--160139 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
160098 AACATATCGA
160108 TAATT-TTTAGTAT
1 TAATTATTTAGTAT
160121 TAATTATTTAG-AT
1 TAATTATTTAGTAT
160134 TAATTA
1 TAATTA
160140 ATAATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (14 bp):
TAATTATTTAGTAT
Found at i:171710 original size:30 final size:30
Alignment explanation
Indices: 171669--171737 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
171659 GGTGTCCAAT
* ** * *
171669 TCCACCACCTCCACCAGCCCCTCCGCCAGC
1 TCCACCTCCTCCACCAAACCCACCACCAGC
* *
171699 TCCACCTCCTCCTCCAAATCCACCACCAGC
1 TCCACCTCCTCCACCAAACCCACCACCAGC
171729 TCCACCTCC
1 TCCACCTCC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.61, G:0.06, T:0.14
Consensus pattern (30 bp):
TCCACCTCCTCCACCAAACCCACCACCAGC
Done.