Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012068.1 Kokia drynarioides strain JFW-HI SEQ_127066, 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: 165466
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Warning! 215 characters in sequence are not A, C, G, or T
Found at i:800 original size:13 final size:13
Alignment explanation
Indices: 784--839 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
774 TCTTTTTCTT
784 TTTTATTATTTAA
1 TTTTATTATTTAA
797 TTTTATTA-TTATA
1 TTTTATTATTTA-A
* **
810 TTTTATAATAAAA
1 TTTTATTATTTAA
* *
823 TATTAGTATTTAA
1 TTTTATTATTTAA
836 TTTT
1 TTTT
840 TAAACTTTAA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
12 3 0.09
13 28 0.88
14 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (13 bp):
TTTTATTATTTAA
Found at i:1005 original size:95 final size:87
Alignment explanation
Indices: 896--1130 Score: 253
Period size: 83 Copynumber: 2.7 Consensus size: 87
886 GTATTTTGTT
* * * *
896 TTAAAAAATATATTTAATTCAAGTGGTGGCCCCATTTAATGTGGCACCACCAAAAAAAATTTTAA
1 TTAAAAAATTTATTTAATTAAAGTGGTGGCACCATTTAATATGGCACCACCAAAAAAAA--TT-A
*
961 TTTATTTTAAAAATATAAATAAAAAATTAT
63 --T-TTTT-AAAATATAAATAAAAAA-TAA
*** * *
991 TTAAATTTTTTATTTAATTAAAGGGGTGGGACCATTTAATAT-G-ACC-CC-AAAAAAATTATTT
1 TTAAAAAATTTATTTAATTAAAGTGGTGGCACCATTTAATATGGCACCACCAAAAAAAATTATTT
1052 TTAAAATATAAATAAAAAATAA
66 TTAAAATATAAATAAAAAATAA
** *
1074 TTAAAAAATTTATTTAATTAAAGTGGTGGCGTCATCTAATATGGCACCACCAAAAAA
1 TTAAAAAATTTATTTAATTAAAGTGGTGGCACCATTTAATATGGCACCACCAAAAAA
1131 TTTAAATTTT
Statistics
Matches: 118, Mismatches: 18, Indels: 16
0.78 0.12 0.11
Matches are distributed among these distances:
83 36 0.31
84 18 0.15
85 7 0.06
86 3 0.03
87 5 0.04
88 1 0.01
89 2 0.02
91 7 0.06
92 2 0.02
93 3 0.03
94 1 0.01
95 33 0.28
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (87 bp):
TTAAAAAATTTATTTAATTAAAGTGGTGGCACCATTTAATATGGCACCACCAAAAAAAATTATTT
TTAAAATATAAATAAAAAATAA
Found at i:1114 original size:83 final size:87
Alignment explanation
Indices: 962--1154 Score: 225
Period size: 83 Copynumber: 2.2 Consensus size: 87
952 AAATTTTAAT
* *** *
962 TTATTTTAAAAATATAAATAAAAAATTATTTAAATTTTTTATTTAATTAAAGGGGTGGGACCATT
1 TTATTTTAAAAATATAAATAAAAAATTAATTAAAAAATTTATTTAATTAAAGGGGTGGGACCATC
1027 TAATAT-G-ACC-CCAAAAAAA
66 TAATATGGCACCACCAAAAAAA
* * *
1046 TTATTTTTAAAATATAAATAAAAAA-TAATTAAAAAATTTATTTAATTAAAGTGGTGGCG-TCAT
1 TTATTTTAAAAATATAAATAAAAAATTAATTAAAAAATTTATTTAATTAAAGGGGTGG-GACCAT
*
1109 CTAATATGGCACCACCAAAAAAT
65 CTAATATGGCACCACCAAAAAAA
*
1132 TTAAATTTTCAAAAAAATAAATA
1 TT--ATTTT-AAAAATATAAATA
1155 TTAAATAATA
Statistics
Matches: 91, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
83 36 0.40
84 26 0.29
85 3 0.03
86 10 0.11
88 5 0.05
89 11 0.12
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (87 bp):
TTATTTTAAAAATATAAATAAAAAATTAATTAAAAAATTTATTTAATTAAAGGGGTGGGACCATC
TAATATGGCACCACCAAAAAAA
Found at i:3226 original size:92 final size:92
Alignment explanation
Indices: 3119--3372 Score: 339
Period size: 92 Copynumber: 2.7 Consensus size: 92
3109 ATTTTTTTGA
* * *
3119 AAATTTTAAATTTTTTGGTCGTGCCATATTAGATGGCGTCACCACTTTAATTAAATAAATTTTTT
1 AAATTTTAATTTTTTTGGTGGTGCCATATTAAATGGC-TCACCACTTTAATTAAATAAATTTTTT
*
3184 AATTATTTTTTATTTATATTTTAAAAAT
65 AATAATTTTTTATTTATATTTTAAAAAT
* *
3212 -AATTTTAATTTTTTTGGTGGTGCCATATTAAATGGTCTCATCTCTTTAATTAAATAAATTTTTT
1 AAATTTTAATTTTTTTGGTGGTGCCATATTAAATGG-CTCACCACTTTAATTAAATAAATTTTTT
*
3276 AAATAATTTTTTATTTATATTTTTAAAAT
65 -AATAATTTTTTATTTATATTTTAAAAAT
* * ** * *
3305 AAATTTAAATTTTTTTTTGTGGTGATATATTAAATGGCCTCACCATTTTAATTAAATAAAATTTT
1 AAATTTTAA-TTTTTTTGGTGGTGCCATATTAAATGG-CTCACCACTTTAATTAAATAAATTTTT
3370 TAA
64 TAA
3373 ACAAAATACT
Statistics
Matches: 141, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
92 57 0.40
93 27 0.19
94 9 0.06
95 48 0.34
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.50
Consensus pattern (92 bp):
AAATTTTAATTTTTTTGGTGGTGCCATATTAAATGGCTCACCACTTTAATTAAATAAATTTTTTA
ATAATTTTTTATTTATATTTTAAAAAT
Found at i:3285 original size:12 final size:13
Alignment explanation
Indices: 3261--3310 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
3251 ATCTCTTTAA
3261 TTAAATAAATTTT
1 TTAAATAAATTTT
3274 TTAAAT-AATTTT
1 TTAAATAAATTTT
** *
3286 TTATTTATATTTT
1 TTAAATAAATTTT
*
3299 TAAAATAAATTT
1 TTAAATAAATTT
3311 AAATTTTTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TTAAATAAATTTT
Found at i:3316 original size:25 final size:25
Alignment explanation
Indices: 3269--3316 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
3259 AATTAAATAA
* * **
3269 ATTTTTTAAATAATTTTTTATTTAT
1 ATTTTTAAAATAAATTTAAATTTAT
3294 ATTTTTAAAATAAATTTAAATTT
1 ATTTTTAAAATAAATTTAAATTT
3317 TTTTTTGTGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTTTAAAATAAATTTAAATTTAT
Found at i:3370 original size:95 final size:93
Alignment explanation
Indices: 3123--3373 Score: 319
Period size: 95 Copynumber: 2.7 Consensus size: 93
3113 TTTTGAAAAT
* * * * * *
3123 TTTAAA-TTTTTTGGTCGTGCCATATTAGATGGCGTCACCACTTTAATTAAAT-AAATTTTTTAA
1 TTTAAATTTTTTTGGTGGTGACATATTAAATGGCCTCACCATTTTAATTAAATAAAATTTTTAAA
*
3186 TTATTTTTTATTTATATTTTAAAAATAA
66 TAATTTTTTATTTATATTTTAAAAATAA
* * * * *
3214 TTTTAATTTTTTTGGTGGTGCCATATTAAATGGTCTCATC-TCTTTAATTAAATAAATTTTTTAA
1 TTTAAATTTTTTTGGTGGTGACATATTAAATGGCCTCACCAT-TTTAATTAAATAAAATTTTTAA
*
3278 ATAATTTTTTATTTATATTTTTAAAATAAA
65 ATAATTTTTTATTTATATTTTAAAAAT-AA
* *
3308 TTTAAATTTTTTTTTGTGGTGATATATTAAATGGCCTCACCATTTTAATTAAATAAAATTTTTAA
1 TTTAAA-TTTTTTTGGTGGTGACATATTAAATGGCCTCACCATTTTAATTAAATAAAATTTTTAA
3373 A
65 A
3374 CAAAATACTA
Statistics
Matches: 136, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
91 5 0.04
92 39 0.29
93 33 0.24
94 7 0.05
95 51 0.38
96 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (93 bp):
TTTAAATTTTTTTGGTGGTGACATATTAAATGGCCTCACCATTTTAATTAAATAAAATTTTTAAA
TAATTTTTTATTTATATTTTAAAAATAA
Found at i:3470 original size:13 final size:13
Alignment explanation
Indices: 3428--3483 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
3418 TTAAAGTTTA
*
3428 AAAATTAAATACT
1 AAAATTAAATAAT
* ** *
3441 AATATTTTATTAT
1 AAAATTAAATAAT
3454 AAAA-TATAATAAT
1 AAAATTA-AATAAT
3467 AAAATTAAATAAT
1 AAAATTAAATAAT
3480 AAAA
1 AAAA
3484 AACAAAAAGA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
12 1 0.03
13 29 0.91
14 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATTAAATAAT
Found at i:3733 original size:28 final size:28
Alignment explanation
Indices: 3700--3764 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
3690 TAAATTTTAG
* *
3700 GTTATTTTTGTATTTAA-TAAAAAAATA
1 GTTATTTTTGTAATTAATTAAAAAAAAA
*
3727 GATTATTTATGTAATTAATTAAAAAAAAA
1 G-TTATTTTTGTAATTAATTAAAAAAAAA
3756 GTTATTTTT
1 GTTATTTTT
3765 ATAAAAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 1 0.03
28 21 0.66
29 10 0.31
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.48
Consensus pattern (28 bp):
GTTATTTTTGTAATTAATTAAAAAAAAA
Found at i:8880 original size:32 final size:30
Alignment explanation
Indices: 8817--8883 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 30
8807 GTCTAATTGC
* *
8817 AATTTTATGAGATTAATAAGAATTTTCAAA
1 AATTTTAAGAGATTAATAAAAATTTTCAAA
*
8847 AATTTTAAGAGAGTTTAATTAAAAATTTTAAAA
1 AATTTTAAGAGA--TTAA-TAAAAATTTTCAAA
8880 AATT
1 AATT
8884 AAAAAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 11 0.35
32 4 0.13
33 16 0.52
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.40
Consensus pattern (30 bp):
AATTTTAAGAGATTAATAAAAATTTTCAAA
Found at i:9962 original size:23 final size:22
Alignment explanation
Indices: 9927--9979 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
9917 AAGAAATTCA
**
9927 ATAAATAAAAAAATATAAA-ATT
1 ATAAATATTAAAATA-AAATATT
9949 ATTAAATATTAAAATAAAATATT
1 A-TAAATATTAAAATAAAATATT
9972 ATAAATAT
1 ATAAATAT
9980 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
ATAAATATTAAAATAAAATATT
Found at i:19661 original size:137 final size:138
Alignment explanation
Indices: 19415--19691 Score: 502
Period size: 137 Copynumber: 2.0 Consensus size: 138
19405 TAACATGTAC
*
19415 ATAATGATTTATATGGATTATCTTTTAACAATAGAAATAAATAAAAATTTCAATAGAATAATTAA
1 ATAATGATTTATATGGATTACCTTTTAACAATAGAAATAAATAAAAATTTCAATAGAATAATTAA
*
19480 TTTACTCTTCAATTTAATATATTTAGATTAATTTATTCGTTCTTTGAGTAAAGAT-AAAAAAAAT
66 TTTACTCTTCAATCTAATATATTTAGATTAATTTATTCGTTCTTTGAGTAAAGATAAAAAAAAAT
19544 ACAATCCA
131 ACAATCCA
* * *
19552 ATAATGATTTATATGGATTACCTTTTAACAATAGAAATAAATGAAATTTTCAATAGAATAATTAG
1 ATAATGATTTATATGGATTACCTTTTAACAATAGAAATAAATAAAAATTTCAATAGAATAATTAA
19617 TTTACTCTTCAATCTAATATATTTAGATTAATTTATTCGTTCTTTGAGTAAAGATAAAAAAAAAT
66 TTTACTCTTCAATCTAATATATTTAGATTAATTTATTCGTTCTTTGAGTAAAGATAAAAAAAAAT
19682 ACAATCCA
131 ACAATCCA
19690 AT
1 AT
19692 TTTTAGTATA
Statistics
Matches: 134, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
137 115 0.86
138 19 0.14
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.39
Consensus pattern (138 bp):
ATAATGATTTATATGGATTACCTTTTAACAATAGAAATAAATAAAAATTTCAATAGAATAATTAA
TTTACTCTTCAATCTAATATATTTAGATTAATTTATTCGTTCTTTGAGTAAAGATAAAAAAAAAT
ACAATCCA
Found at i:22813 original size:61 final size:62
Alignment explanation
Indices: 22737--22862 Score: 175
Period size: 61 Copynumber: 2.0 Consensus size: 62
22727 AAATCAAAAC
** *
22737 TTTGCATCCAATCAATTTGAA-TTTAACATTATTTTGGGGTTTT-TTTTCGGAAAGTAATGAT
1 TTTGCATCCAATCAATTT-AACTTTAACATTATTTTGGGGTTTTCTTTTCAAAAAATAATGAT
* * *
22798 TTTGCATCGAATCAATTTAACTTTACCATTATTTTGGGTTTTTCTTTTCAAAAAATAATGAT
1 TTTGCATCCAATCAATTTAACTTTAACATTATTTTGGGGTTTTCTTTTCAAAAAATAATGAT
22860 TTT
1 TTT
22863 ATTGGTGAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 2 0.04
61 37 0.65
62 18 0.32
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.48
Consensus pattern (62 bp):
TTTGCATCCAATCAATTTAACTTTAACATTATTTTGGGGTTTTCTTTTCAAAAAATAATGAT
Found at i:27183 original size:14 final size:14
Alignment explanation
Indices: 27152--27182 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
27142 GGCATCTCCA
27152 TTTTCTTCTTCTTC
1 TTTTCTTCTTCTTC
27166 TTTTCTTC-TCTTC
1 TTTTCTTCTTCTTC
27179 TTTT
1 TTTT
27183 TTTATTTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTCTTCTTCTTC
Found at i:27629 original size:20 final size:21
Alignment explanation
Indices: 27606--27655 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
27596 AACTGTTTTT
*
27606 TAATTATTTTAATTTA-ATTA
1 TAATTATTTTAAATTATATTA
* *
27626 TAATT-TTTTAAATTATGTTT
1 TAATTATTTTAAATTATATTA
27646 TAATTATTTT
1 TAATTATTTT
27656 TAAAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 9 0.36
20 12 0.48
21 4 0.16
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TAATTATTTTAAATTATATTA
Found at i:27635 original size:14 final size:12
Alignment explanation
Indices: 27601--27656 Score: 51
Period size: 14 Copynumber: 4.3 Consensus size: 12
27591 ATTTAAACTG
27601 TTTTTTAATTAT
1 TTTTTTAATTAT
27613 TTTAATTTAATTAT
1 TTT--TTTAATTAT
27627 AATTTTTTAAATTA-
1 --TTTTTT-AATTAT
*
27641 TGTTTTAATTAT
1 TTTTTTAATTAT
27653 TTTT
1 TTTT
27657 AAAATTTTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
11 5 0.14
12 11 0.31
14 12 0.33
15 5 0.14
16 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (12 bp):
TTTTTTAATTAT
Found at i:27650 original size:11 final size:10
Alignment explanation
Indices: 27602--27658 Score: 55
Period size: 11 Copynumber: 5.7 Consensus size: 10
27592 TTTAAACTGT
27602 TTTTTAATTA
1 TTTTTAATTA
27612 -TTTTAATTTA
1 TTTTTAA-TTA
* *
27622 ATTATAATT-
1 TTTTTAATTA
*
27631 TTTTAAATTA
1 TTTTTAATTA
27641 TGTTTTAATTA
1 T-TTTTAATTA
27652 TTTTTAA
1 TTTTTAA
27659 AATTTTTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
9 12 0.32
10 12 0.32
11 14 0.37
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTTAATTA
Found at i:28381 original size:47 final size:47
Alignment explanation
Indices: 28312--28402 Score: 128
Period size: 47 Copynumber: 1.9 Consensus size: 47
28302 GTAAAGATAA
* * *
28312 AAGGCCACGTGATGTAAAAACACTGATGCGGAGGATTTTTAGGGCAC
1 AAGGCCACGTGACGTAAAAACACTGATGCAGAGGATTTTAAGGGCAC
* * *
28359 AAGGCCACGTGACGTAATAACACTGGTGTAGAGGATTTTAAGGG
1 AAGGCCACGTGACGTAAAAACACTGATGCAGAGGATTTTAAGGG
28403 GACAGAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 38 1.00
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (47 bp):
AAGGCCACGTGACGTAAAAACACTGATGCAGAGGATTTTAAGGGCAC
Found at i:28772 original size:16 final size:18
Alignment explanation
Indices: 28733--28766 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28723 TAAATTTATA
28733 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
28750 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
28767 AATTTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:28944 original size:24 final size:24
Alignment explanation
Indices: 28902--28949 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
28892 ATATTAAATA
* *
28902 TTAAAATAATATAATATAAATATTT
1 TTAAAATAATAAAAAAT-AATATTT
28927 TTAAAA-AATAAAAAATAATATTT
1 TTAAAATAATAAAAAATAATATTT
28950 ACGGACTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 8 0.38
25 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TTAAAATAATAAAAAATAATATTT
Found at i:40680 original size:28 final size:26
Alignment explanation
Indices: 40625--40694 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 26
40615 TATTTGTAAA
40625 AAAATATTTATATTATTTTTAAAATATTT
1 AAAAT-TTTATA-TATTTTTAAAATA-TT
* **
40654 AATAATTTTATATATTTTTCATTTATT
1 AA-AATTTTATATATTTTTAAAATATT
*
40681 AAAATTTTTTATAT
1 AAAATTTTATATAT
40695 AGTCATCTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 11 0.31
27 4 0.11
28 10 0.28
29 8 0.22
30 3 0.08
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (26 bp):
AAAATTTTATATATTTTTAAAATATT
Found at i:45546 original size:9 final size:9
Alignment explanation
Indices: 45518--45553 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
45508 AAATGAGTTG
45518 TTTTTATTAA
1 TTTTT-TTAA
45528 TTTATTTTAA
1 TTT-TTTTAA
45538 TTTTTTTAA
1 TTTTTTTAA
45547 TTTTTTT
1 TTTTTTT
45554 CATATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 13 0.52
10 10 0.40
11 2 0.08
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:46430 original size:23 final size:23
Alignment explanation
Indices: 46400--46443 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
46390 TAGAGAAAAC
46400 ACCAAATAAACCTGGCCAGGTAT
1 ACCAAATAAACCTGGCCAGGTAT
46423 ACCAAATAAACCTGGCCAGGT
1 ACCAAATAAACCTGGCCAGGT
46444 GCACCCAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.16
Consensus pattern (23 bp):
ACCAAATAAACCTGGCCAGGTAT
Found at i:46864 original size:26 final size:26
Alignment explanation
Indices: 46828--46885 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
46818 TTAAAGCTGA
46828 CTCATTCAAGTCAATCATTTACCTGC
1 CTCATTCAAGTCAATCATTTACCTGC
46854 CTCATTCAAGTCAATCATTTACCTGC
1 CTCATTCAAGTCAATCATTTACCTGC
46880 CTCATT
1 CTCATT
46886 TCAATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.26, C:0.31, G:0.07, T:0.36
Consensus pattern (26 bp):
CTCATTCAAGTCAATCATTTACCTGC
Found at i:46945 original size:18 final size:18
Alignment explanation
Indices: 46901--46946 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
46891 TTTTTTATTT
46901 TAAAATTT-AATATTAAA
1 TAAAATTTAAATATTAAA
46918 TAAAATTTTAAATA-TATAA
1 TAAAA-TTTAAATATTA-AA
46937 TAAAATTTAA
1 TAAAATTTAA
46947 GTAAAAGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.19
18 10 0.38
19 11 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAAATTTAAATATTAAA
Found at i:50029 original size:12 final size:12
Alignment explanation
Indices: 50012--50087 Score: 59
Period size: 12 Copynumber: 6.5 Consensus size: 12
50002 TGATTATATC
50012 TGTTTTGATTGT
1 TGTTTTGATTGT
*
50024 TGTTTT-AATGT
1 TGTTTTGATTGT
* *
50035 TGTTTTTAATGT
1 TGTTTTGATTGT
50047 TGTTTT-ATTGT
1 TGTTTTGATTGT
* *
50058 TATTTTTG-TTGC
1 T-GTTTTGATTGT
*
50070 TGTTTTGGTTGT
1 TGTTTTGATTGT
*
50082 TATTTT
1 TGTTTT
50088 TGTTGTTTGG
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
11 20 0.38
12 33 0.62
ACGTcount: A:0.11, C:0.01, G:0.20, T:0.68
Consensus pattern (12 bp):
TGTTTTGATTGT
Found at i:50037 original size:11 final size:11
Alignment explanation
Indices: 50021--50063 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
50011 CTGTTTTGAT
50021 TGTTGTTTTAA
1 TGTTGTTTTAA
50032 TGTTGTTTTTAA
1 TGTTG-TTTTAA
*
50044 TGTTGTTTTAT
1 TGTTGTTTTAA
*
50055 TGTTATTTT
1 TGTTGTTTT
50064 TGTTGCTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.14, C:0.00, G:0.16, T:0.70
Consensus pattern (11 bp):
TGTTGTTTTAA
Found at i:50038 original size:23 final size:23
Alignment explanation
Indices: 50012--50063 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
50002 TGATTATATC
*
50012 TGTTTTGATTGTTGTTTTAATGT
1 TGTTTTGAATGTTGTTTTAATGT
* *
50035 TGTTTTTAATGTTGTTTTATTGT
1 TGTTTTGAATGTTGTTTTAATGT
*
50058 TATTTT
1 TGTTTT
50064 TGTTGCTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.13, C:0.00, G:0.17, T:0.69
Consensus pattern (23 bp):
TGTTTTGAATGTTGTTTTAATGT
Found at i:50064 original size:23 final size:23
Alignment explanation
Indices: 50021--50088 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
50011 CTGTTTTGAT
* *
50021 TGTTGTTTTAATGTTGTTTTTAA
1 TGTTGTTTTATTGTTATTTTTAA
**
50044 TGTTGTTTTATTGTTATTTTTGT
1 TGTTGTTTTATTGTTATTTTTAA
* *
50067 TGCTGTTTTGGTTGTTATTTTT
1 TGTTGTTTT-ATTGTTATTTTT
50089 GTTGTTTGGA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
23 27 0.71
24 11 0.29
ACGTcount: A:0.10, C:0.01, G:0.19, T:0.69
Consensus pattern (23 bp):
TGTTGTTTTATTGTTATTTTTAA
Found at i:50067 original size:20 final size:20
Alignment explanation
Indices: 50020--50108 Score: 63
Period size: 23 Copynumber: 4.1 Consensus size: 20
50010 TCTGTTTTGA
* *
50020 TTGTTGTTTTAATGTTGTTTT
1 TTGTTGTTTTATTGTT-ATTT
50041 TAATGTTGTTTTATTGTTATTT
1 T--TGTTGTTTTATTGTTATTT
*
50063 TTGTTGCTGTTTTGGTTGTTATTT
1 TTG-T--TGTTTT-ATTGTTATTT
*
50087 TTGTTGTTTGGA-TGTTATTT
1 TTGTTGTTT-TATTGTTATTT
50107 TT
1 TT
50109 ATGAATTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 15
0.74 0.07 0.20
Matches are distributed among these distances:
20 12 0.21
21 7 0.12
22 4 0.07
23 21 0.38
24 12 0.21
ACGTcount: A:0.10, C:0.01, G:0.20, T:0.69
Consensus pattern (20 bp):
TTGTTGTTTTATTGTTATTT
Found at i:50092 original size:12 final size:12
Alignment explanation
Indices: 50049--50094 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
50039 TTTAATGTTG
*
50049 TTTTATTGTTAT
1 TTTTGTTGTTAT
* *
50061 TTTTGTTGCTGT
1 TTTTGTTGTTAT
*
50073 TTTGGTTGTTAT
1 TTTTGTTGTTAT
50085 TTTTGTTGTT
1 TTTTGTTGTT
50095 TGGATGTTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.07, C:0.02, G:0.20, T:0.72
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:50896 original size:15 final size:15
Alignment explanation
Indices: 50859--50899 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
50849 ATTAAATTAT
50859 ATTTTTATAA--TAA
1 ATTTTTATAATTTAA
* *
50872 AATTTAATAATTTAA
1 ATTTTTATAATTTAA
50887 ATTTTTATAATTT
1 ATTTTTATAATTT
50900 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 8 0.36
15 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTTATAATTTAA
Found at i:55305 original size:35 final size:35
Alignment explanation
Indices: 55261--55345 Score: 170
Period size: 35 Copynumber: 2.4 Consensus size: 35
55251 CGAATAAAAG
55261 AATATTCGTCCTTTTTTCTGTGAAAAAAAAACATA
1 AATATTCGTCCTTTTTTCTGTGAAAAAAAAACATA
55296 AATATTCGTCCTTTTTTCTGTGAAAAAAAAACATA
1 AATATTCGTCCTTTTTTCTGTGAAAAAAAAACATA
55331 AATATTCGTCCTTTT
1 AATATTCGTCCTTTT
55346 GTTAAATTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.40
Consensus pattern (35 bp):
AATATTCGTCCTTTTTTCTGTGAAAAAAAAACATA
Found at i:56625 original size:29 final size:29
Alignment explanation
Indices: 56591--56653 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
56581 ATAAAAAAAA
* *
56591 ATAATTGAATAAATATTTTACAATTTTTT
1 ATAATTAAATAAATATATTACAATTTTTT
* * *
56620 ATAATTAAATTATTATATTATAATTTTTT
1 ATAATTAAATAAATATATTACAATTTTTT
56649 ATAAT
1 ATAAT
56654 CGAGTGATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (29 bp):
ATAATTAAATAAATATATTACAATTTTTT
Found at i:57393 original size:22 final size:22
Alignment explanation
Indices: 57368--57418 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
57358 TTATTATTAA
57368 AATATAAATTAAT-AAAAATAAT
1 AATATAAA-TAATAAAAAATAAT
*
57390 AATATATAATATTAAAAAATAAT
1 AATATA-AATAATAAAAAATAAT
57413 -ATATAA
1 AATATAA
57419 CCTACTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.04
22 14 0.54
23 11 0.42
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AATATAAATAATAAAAAATAAT
Found at i:57393 original size:62 final size:62
Alignment explanation
Indices: 57285--57404 Score: 172
Period size: 62 Copynumber: 1.9 Consensus size: 62
57275 TTGTTATTAA
* * *
57285 ATTTTAATAAGATTATTATTAAATATTATTTAATAAAAATAGTAATAAATAAT-TTAATCAT
1 ATTTTAATAAGATTATTATTAAATATAAATTAATAAAAATAATAATAAATAATATTAATCAT
*
57346 ATTTTAATATA-ATTATTATTAAAATATAAATTAATAAAAATAATAATATATAATATTAA
1 ATTTTAATA-AGATTATTATT-AAATATAAATTAATAAAAATAATAATAAATAATATTAA
57405 AAAATAATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
61 18 0.35
62 30 0.58
63 4 0.08
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (62 bp):
ATTTTAATAAGATTATTATTAAATATAAATTAATAAAAATAATAATAAATAATATTAATCAT
Found at i:57412 original size:20 final size:20
Alignment explanation
Indices: 57362--57418 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
57352 ATATAATTAT
*
57362 TATTAAAATATAA-AT-TAA
1 TATTAAAAAATAATATATAA
57380 TA--AAAATAATAATATATAA
1 TATTAAAA-AATAATATATAA
57399 TATTAAAAAATAATATATAA
1 TATTAAAAAATAATATATAA
57419 CCTACTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 4 0.12
17 4 0.12
18 4 0.12
19 5 0.15
20 12 0.36
21 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TATTAAAAAATAATATATAA
Found at i:66125 original size:25 final size:25
Alignment explanation
Indices: 66077--66126 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
66067 GTGTTAGTTT
* *
66077 AAAACATTAATATATATTTTTATTA
1 AAAACATTAATATATAATTATATTA
* *
66102 AAAATATTAATATTTAATTATATTA
1 AAAACATTAATATATAATTATATTA
66127 TTGCAATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
AAAACATTAATATATAATTATATTA
Found at i:66157 original size:17 final size:17
Alignment explanation
Indices: 66116--66159 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
66106 TATTAATATT
*
66116 TAATTATATTATTGCAA
1 TAATAATATTATTGCAA
* * *
66133 TAAAAATATTATTGTAG
1 TAATAATATTATTGCAA
66150 TAATAATATT
1 TAATAATATT
66160 TTTTGAATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (17 bp):
TAATAATATTATTGCAA
Found at i:66691 original size:22 final size:23
Alignment explanation
Indices: 66645--66687 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
66635 CTAATGTTTT
66645 ATTTAATTTTTTATTAAAAAATA
1 ATTTAATTTTTTATTAAAAAATA
*
66668 ATTT-ATTTTTT-TTGAAAAAT
1 ATTTAATTTTTTATTAAAAAAT
66688 TAATGGCCAA
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:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTAATTTTTTATTAAAAAATA
Found at i:69684 original size:9 final size:9
Alignment explanation
Indices: 69604--69711 Score: 59
Period size: 9 Copynumber: 11.9 Consensus size: 9
69594 AAATAAATTT
69604 TTATAAAAA
1 TTATAAAAA
69613 -TATAAAAA
1 TTATAAAAA
69621 -TATAAAGAAA
1 TTAT-AA-AAA
69631 TGTATAAAAA
1 T-TATAAAAA
*
69641 TGT-TGAAAAT
1 T-TAT-AAAAA
*
69651 TTTTAACAAA
1 TTATAA-AAA
*
69661 -TATATAAA
1 TTATAAAAA
69669 TCT-TAAAAA
1 T-TATAAAAA
69678 TTATAAAAA
1 TTATAAAAA
*
69687 -TAAAAAAA
1 TTATAAAAA
69695 TT-TATAAAA
1 TTATA-AAAA
69704 TTATAAAA
1 TTATAAAA
69712 GCCTGTAATT
Statistics
Matches: 79, Mismatches: 7, Indels: 26
0.71 0.06 0.23
Matches are distributed among these distances:
8 23 0.29
9 31 0.39
10 20 0.25
11 2 0.03
12 3 0.04
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (9 bp):
TTATAAAAA
Found at i:71020 original size:23 final size:23
Alignment explanation
Indices: 70994--71050 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
70984 TTAAAACCTA
70994 AAAAGTAAAAAGATTAAATTTGT
1 AAAAGTAAAAAGATTAAATTTGT
71017 AAAAGTAAAAAGATTAAATTTGT
1 AAAAGTAAAAAGATTAAATTTGT
*
71040 AAAAATAAAAA
1 AAAAGTAAAAA
71051 TATAAGGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (23 bp):
AAAAGTAAAAAGATTAAATTTGT
Found at i:81009 original size:35 final size:35
Alignment explanation
Indices: 80970--81036 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
80960 ACATGAGAGA
80970 AAAAATAAATTAATCGCACCACACCGTATTCCATT
1 AAAAATAAATTAATCGCACCACACCGTATTCCATT
* *
81005 AAAAATAAATTAATCGTATCACACCGTATTCC
1 AAAAATAAATTAATCGCACCACACCGTATTCC
81037 GATCATCCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.43, C:0.24, G:0.06, T:0.27
Consensus pattern (35 bp):
AAAAATAAATTAATCGCACCACACCGTATTCCATT
Found at i:86155 original size:132 final size:131
Alignment explanation
Indices: 85799--86124 Score: 307
Period size: 131 Copynumber: 2.5 Consensus size: 131
85789 AACATTGGGG
* * * * * * *
85799 TTTTTCGTTCACAATACTCGAACTTAAAATC-TTACTTAAAAGAAATCAAA-TTTTTACCACAT-
1 TTTTTCGTTCACAAAACTCAAACTCAAAA-CATTACTCAAAAGATATCAAACTCTTTATCAC-TC
* ** * * * * * * **
85861 GATTTAGTAGACGCTATATCAAGTTAAGTCAAGCCCTTAAATAAAATGTAAAGTTCTTCCTGCAT
64 GATCTAACAAACGCTATTTCAAATTAAATCAAACCCTTAAATAAAAAGTAAAACTCTTCCTGCAT
85926 TAT
129 TAT
* * * ** * * * * *
85929 TTTTTCGTTCACGAAACTCAAACTCGAGATTTTACTTAAAAGATATCGAATTTTTTATCACTTGA
1 TTTTTCGTTCACAAAACTCAAACTCAAAACATTACTCAAAAGATATCAAACTCTTTATCACTCGA
* * *
85994 TCTAACAAACGCTGTTTCAAATTGAATCAAACCCTTAAATAAAAAGTAAAACTCTTCGTGCATTA
66 TCTAACAAACGCTATTTCAAATTAAATCAAACCCTTAAATAAAAAGTAAAACTCTTCCTGCATTA
86059 T
131 T
* *
86060 TTTGTTCGTTCACAAAACTCAAACTCAAAACATTGCTCAAAAGATATCAAACTCTTTATCCCTCG
1 TTT-TTCGTTCACAAAACTCAAACTCAAAACATTACTCAAAAGATATCAAACTCTTTATCACTCG
86125 TTTTAATAAA
Statistics
Matches: 156, Mismatches: 36, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
130 41 0.26
131 66 0.42
132 49 0.31
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.34
Consensus pattern (131 bp):
TTTTTCGTTCACAAAACTCAAACTCAAAACATTACTCAAAAGATATCAAACTCTTTATCACTCGA
TCTAACAAACGCTATTTCAAATTAAATCAAACCCTTAAATAAAAAGTAAAACTCTTCCTGCATTA
T
Found at i:88070 original size:31 final size:28
Alignment explanation
Indices: 88018--88088 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
88008 AGGATTTGTG
* *
88018 AAAATTGAATCAAATTCAAATTTTCATGTAT
1 AAAATTGCAT-AAAATCAAA-TTT-ATGTAT
88049 AAAATTGCATAAAATCAAAATTTATGTAT
1 AAAATTGCATAAAATC-AAATTTATGTAT
* *
88078 GATATTGCATA
1 AAAATTGCATA
88089 TTGAACTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 15 0.43
30 8 0.23
31 12 0.34
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.37
Consensus pattern (28 bp):
AAAATTGCATAAAATCAAATTTATGTAT
Found at i:88856 original size:3 final size:3
Alignment explanation
Indices: 88848--88900 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
88838 GCACTTTTGA
88848 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
88896 ATT AT
1 ATT AT
88901 AGTTTCTATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:90934 original size:184 final size:184
Alignment explanation
Indices: 90625--90992 Score: 700
Period size: 184 Copynumber: 2.0 Consensus size: 184
90615 TAATGCATTC
90625 AATGTATTGGTACATTAAGCTTGAATATGACTAAGACCTCAGCACTCGTGACAATATATTCATTT
1 AATGTATTGGTACATTAAGCTTGAATATGACTAAGACCTCAGCACTCGTGACAATATATTCATTT
*
90690 GTTTCTCATTGGTTGCATCTTCATTGATCACTACTCTTTGCCCTTGGCCTTGTTAGAGTCGCAAT
66 GTTTCTCATTGGTTGCATCTTCATTGATCACTACTATTTGCCCTTGGCCTTGTTAGAGTCGCAAT
90755 TTGCATCAAGCTTCCTGTTTCTCCTCATCAGCTTCTTGAATGCTCTATTGAAGT
131 TTGCATCAAGCTTCCTGTTTCTCCTCATCAGCTTCTTGAATGCTCTATTGAAGT
90809 AATGTATTGGTACATTAAGCTTGAATATGACTAAGACCTCAGCACTCGTGACAATATATTCATTT
1 AATGTATTGGTACATTAAGCTTGAATATGACTAAGACCTCAGCACTCGTGACAATATATTCATTT
* * *
90874 GTTTCTCATTGGTTGCATCTTCTTTGATCACTACTATTTTCCCTTGGCCTTGTTAGAGTCGCGAT
66 GTTTCTCATTGGTTGCATCTTCATTGATCACTACTATTTGCCCTTGGCCTTGTTAGAGTCGCAAT
90939 TTGCATCAAGCTTCCTGTTTCTCCTCATCAGCTTCTTGAATGCTCTATTGAAGT
131 TTGCATCAAGCTTCCTGTTTCTCCTCATCAGCTTCTTGAATGCTCTATTGAAGT
90993 TTTGAGTGAG
Statistics
Matches: 180, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
184 180 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (184 bp):
AATGTATTGGTACATTAAGCTTGAATATGACTAAGACCTCAGCACTCGTGACAATATATTCATTT
GTTTCTCATTGGTTGCATCTTCATTGATCACTACTATTTGCCCTTGGCCTTGTTAGAGTCGCAAT
TTGCATCAAGCTTCCTGTTTCTCCTCATCAGCTTCTTGAATGCTCTATTGAAGT
Found at i:92665 original size:20 final size:21
Alignment explanation
Indices: 92632--92684 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
92622 ATTTAATTTA
92632 ATAA-TAATTAAAATATTT-TT
1 ATAATTAATT-AAATATTTATT
*
92652 ATAATTAATTAAATTTTTATT
1 ATAATTAATTAAATATTTATT
*
92673 AT-TTTAATTAAA
1 ATAATTAATTAAA
92685 AAATAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 20 0.69
21 9 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATAATTAATTAAATATTTATT
Found at i:101265 original size:126 final size:126
Alignment explanation
Indices: 101065--101308 Score: 357
Period size: 126 Copynumber: 1.9 Consensus size: 126
101055 ATTATCGAGA
* *
101065 AGAAGAAACTTAGTGTACGGTATGCCTCTCCCTTTTTCCCCTATAACGGAGGTGAAAAAGTCCAA
1 AGAAGAAACTTAGTGTACCGTATGCCTCTCCCTTTTTCCCCTATAACAGAGGTGAAAAAGTCCAA
* *
101130 CCCAATCCCTGCTCCGACTCAAGATAGTGATGATCATGATCCATCACGTGATGAATTATCG
66 CCCAATCCCTGCTCCGACTCAAGATAATGATGATCATGATCCATCACATGATGAATTATCG
* * * *
101191 AGAAGAAACTTAGTGTTCCGTATGCCTTTCCC-TTTTCCTCCTATAACAGAGGTGAAAACGTTC-
1 AGAAGAAACTTAGTGTACCGTATGCCTCTCCCTTTTTCC-CCTATAACAGAGGTGAAAAAGTCCA
** *
101254 ACCGCGTTCCCTGCTCCGATTCAAGATAATGATGATCATGATCCATCACATGATG
65 ACC-CAATCCCTGCTCCGACTCAAGATAATGATGATCATGATCCATCACATGATG
101309 GATCTGATGA
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
125 9 0.09
126 96 0.91
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (126 bp):
AGAAGAAACTTAGTGTACCGTATGCCTCTCCCTTTTTCCCCTATAACAGAGGTGAAAAAGTCCAA
CCCAATCCCTGCTCCGACTCAAGATAATGATGATCATGATCCATCACATGATGAATTATCG
Found at i:104968 original size:40 final size:40
Alignment explanation
Indices: 104913--104994 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
104903 ACATAATTTT
104913 TGTTGGTATAGTAACAGATTTAGCCTTCGATGTTTACTGG
1 TGTTGGTATAGTAACAGATTTAGCCTTCGATGTTTACTGG
104953 TGTTGGTATAGTAACAGATTTAGCCTTCGATGTTTACTGG
1 TGTTGGTATAGTAACAGATTTAGCCTTCGATGTTTACTGG
104993 TG
1 TG
104995 CGATTACATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.22, C:0.12, G:0.26, T:0.40
Consensus pattern (40 bp):
TGTTGGTATAGTAACAGATTTAGCCTTCGATGTTTACTGG
Found at i:105727 original size:58 final size:58
Alignment explanation
Indices: 105637--105754 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
105627 ACAGAAGATC
105637 TTAATTTCCTTGTCCATTCAAAAGGAACTTATTGCATGTCAAGAGCTTGAAAACCATT
1 TTAATTTCCTTGTCCATTCAAAAGGAACTTATTGCATGTCAAGAGCTTGAAAACCATT
105695 TTAATTTCCTTGTCCATTCAAAAGGAACTTATTGCATGTCAAGAGCTTGAAAACCATT
1 TTAATTTCCTTGTCCATTCAAAAGGAACTTATTGCATGTCAAGAGCTTGAAAACCATT
105753 TT
1 TT
105755 TTAAGTAGGC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (58 bp):
TTAATTTCCTTGTCCATTCAAAAGGAACTTATTGCATGTCAAGAGCTTGAAAACCATT
Found at i:110388 original size:30 final size:30
Alignment explanation
Indices: 110348--110424 Score: 127
Period size: 30 Copynumber: 2.6 Consensus size: 30
110338 GACATAAATG
* *
110348 GGGTTACCGTGTTCGTCAGTGAGTTGAACC
1 GGGTTGCCGTGTTCGTCAGTGAGTTGAACA
*
110378 GGGTTGCCGTGTTCGTCAGTGAGTTGAATA
1 GGGTTGCCGTGTTCGTCAGTGAGTTGAACA
110408 GGGTTGCCGTGTTCGTC
1 GGGTTGCCGTGTTCGTC
110425 TCTCAAATCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.13, C:0.18, G:0.36, T:0.32
Consensus pattern (30 bp):
GGGTTGCCGTGTTCGTCAGTGAGTTGAACA
Found at i:111650 original size:17 final size:19
Alignment explanation
Indices: 111623--111657 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
111613 TTAGATAATA
111623 ATAATCAAAT-AATTTGAG
1 ATAATCAAATAAATTTGAG
111641 ATAA-CAAATAAATTTGA
1 ATAATCAAATAAATTTGA
111658 AATTTTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.31
Consensus pattern (19 bp):
ATAATCAAATAAATTTGAG
Found at i:122614 original size:30 final size:31
Alignment explanation
Indices: 122580--122642 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
122570 CAACTCAGTA
122580 ACTTAAATAAAAA-TCTCGAATAATTCAATG
1 ACTTAAATAAAAATTCTCGAATAATTCAATG
* *
122610 ACTTAAGTAAAAATTTTCGAATAATTCAATG
1 ACTTAAATAAAAATTCTCGAATAATTCAATG
122641 AC
1 AC
122643 CATTTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 12 0.40
31 18 0.60
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.32
Consensus pattern (31 bp):
ACTTAAATAAAAATTCTCGAATAATTCAATG
Found at i:127468 original size:4 final size:4
Alignment explanation
Indices: 127459--127487 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
127449 AAATGTACGA
127459 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
127488 CCCTTTTAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:142617 original size:21 final size:20
Alignment explanation
Indices: 142592--142630 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
142582 TGCAATAAAA
142592 ATAAAATAATAGAAAAGAGTG
1 ATAAAATAAT-GAAAAGAGTG
* *
142613 ATAAATTGATGAAAAGAG
1 ATAAAATAATGAAAAGAG
142631 AAGAGAAGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (20 bp):
ATAAAATAATGAAAAGAGTG
Found at i:143770 original size:18 final size:17
Alignment explanation
Indices: 143747--143782 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
143737 TTTCTCTCAC
*
143747 AAAAAAAGGAAAGTTAA
1 AAAAAAAAGAAAGTTAA
143764 AAAAAAAAGAAAGTTAA
1 AAAAAAAAGAAAGTTAA
143781 AA
1 AA
143783 TATTCAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (17 bp):
AAAAAAAAGAAAGTTAA
Found at i:145602 original size:2 final size:2
Alignment explanation
Indices: 145595--145623 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
145585 TGCTATTTAA
145595 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
145624 AACTTAGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:147956 original size:2 final size:2
Alignment explanation
Indices: 147949--147973 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
147939 ATTATACGTG
147949 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
147974 GCATAAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:148621 original size:17 final size:18
Alignment explanation
Indices: 148599--148632 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
148589 ACATGTATAA
148599 ATAAATATA-AAAAATGC
1 ATAAATATATAAAAATGC
*
148616 ATAAATGTATAAAAATG
1 ATAAATATATAAAAATG
148633 TAAAAAGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAATATATAAAAATGC
Found at i:154106 original size:15 final size:15
Alignment explanation
Indices: 154086--154118 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
154076 CTCAATTATT
*
154086 AATTTTTTTAAATTA
1 AATTTTTTGAAATTA
154101 AATTTTTTGAAATTA
1 AATTTTTTGAAATTA
154116 AAT
1 AAT
154119 GTTGTTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
AATTTTTTGAAATTA
Found at i:155376 original size:15 final size:16
Alignment explanation
Indices: 155346--155379 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
155336 GTTTGTAACA
*
155346 ATGGAGAATTCTCTCT
1 ATGGAGAATCCTCTCT
155362 ATGGA-AATCCTCTCT
1 ATGGAGAATCCTCTCT
155377 ATG
1 ATG
155380 AGAGTCTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (16 bp):
ATGGAGAATCCTCTCT
Found at i:161069 original size:24 final size:24
Alignment explanation
Indices: 161037--161115 Score: 131
Period size: 24 Copynumber: 3.3 Consensus size: 24
161027 ACTCTGTCTG
161037 GGCTCGTAAGAGCTAATCATTCTA
1 GGCTCGTAAGAGCTAATCATTCTA
*
161061 GGCTCGTAAGAGCTAATTATTCTA
1 GGCTCGTAAGAGCTAATCATTCTA
* *
161085 GGCTCGTAAGAGCTAATCATTTTG
1 GGCTCGTAAGAGCTAATCATTCTA
161109 GGCTCGT
1 GGCTCGT
161116 GCTGGCTAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (24 bp):
GGCTCGTAAGAGCTAATCATTCTA
Found at i:164219 original size:52 final size:50
Alignment explanation
Indices: 164153--164278 Score: 125
Period size: 48 Copynumber: 2.5 Consensus size: 50
164143 AGAACTCTAA
*
164153 AATTAATTATGATTACGAAAAATATATCTTATAAATATATATATTAGT-TAG
1 AATTAATTAGGATTACGAAAAATATAT-TTATAAATATATATATTA-TATAG
* * *
164204 AATTGAATTAGGATTATG-AAAAT-TA-TTATATATATATATCTTATATAG
1 AATT-AATTAGGATTACGAAAAATATATTTATAAATATATATATTATATAG
* * * *
164252 AACTAATTAGGATCACCAAAATTATAT
1 AATTAATTAGGATTACGAAAAATATAT
164279 ATAGAGTTCA
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
47 11 0.18
48 26 0.43
49 2 0.03
50 2 0.03
51 9 0.15
52 11 0.18
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (50 bp):
AATTAATTAGGATTACGAAAAATATATTTATAAATATATATATTATATAG
Found at i:165097 original size:237 final size:235
Alignment explanation
Indices: 164684--165148 Score: 693
Period size: 237 Copynumber: 2.0 Consensus size: 235
164674 TATGATAAAG
* * * * *
164684 AGTCTATTGAGCTAATTAAACAACAAGGCATAGATTTTATGAGGAATAAGGATAGAGGTATTTAT
1 AGTCTATTGAGCTAATTAAACAACAAGGCATAGATTTTACGAGGAATAAAGAAAAAGGTATCTAT
* * * * *
164749 TCGAGATTTTGGCATGATGGTTTTGATTTACGGGTTGGGTTTTAGCGAATTGACTTGGGTAATTT
66 TCGAGATTTTGGCATCATAGTTTTGATTTACGGGTTGGGTTTCAGAGAATTGACTTGGGTAACTT
* *
164814 TTTATAGTGCTTATGATTTCGGGTTTTTGTTGAAGATTTTGACTCAACATCCACTACTGTCTGAT
131 TTCATAGTGCTTATGATTTCGGGTTTTTGTTGAAGATTTTGACTCAACATCCACTACCGTCTGAT
164879 CTCAAGTCTTTCATGCGACATTTAACTTATTACGATGAAA
196 CTCAAGTCTTTCATGCGACATTTAACTTATTACGATGAAA
* * * *
164919 AGTCTATTG-GACTACTTAAACAACAAGGTATAGATTTTGCGAGGAATAAAGAAAAATGTATCTA
1 AGTCTATTGAG-CTAATTAAACAACAAGGCATAGATTTTACGAGGAATAAAGAAAAAGGTATCTA
*
164983 TTCGAGAGATTTTGGCATCATAGTTTTGATTT-CTGGGTAT-GGTTTCGGAGAATTGACTTGGGT
65 TTC--GAGATTTTGGCATCATAGTTTTGATTTAC-GGGT-TGGGTTTCAGAGAATTGACTTGGGT
*
165046 AACTTTTCATAGTGCTTATGATTTCGGGTTTTTGTTGAAGATTTTGACTCAACATCTACTACCGT
126 AACTTTTCATAGTGCTTATGATTTCGGGTTTTTGTTGAAGATTTTGACTCAACATCCACTACCGT
*
165111 CTGATCTCAAGTCTTTCATGCGACATTTGACTTATTAC
191 CTGATCTCAAGTCTTTCATGCGACATTTAACTTATTAC
165149 TTCCGTTGCA
Statistics
Matches: 206, Mismatches: 19, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
234 1 0.00
235 56 0.27
236 1 0.00
237 147 0.71
238 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (235 bp):
AGTCTATTGAGCTAATTAAACAACAAGGCATAGATTTTACGAGGAATAAAGAAAAAGGTATCTAT
TCGAGATTTTGGCATCATAGTTTTGATTTACGGGTTGGGTTTCAGAGAATTGACTTGGGTAACTT
TTCATAGTGCTTATGATTTCGGGTTTTTGTTGAAGATTTTGACTCAACATCCACTACCGTCTGAT
CTCAAGTCTTTCATGCGACATTTAACTTATTACGATGAAA
Done.