Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009474.1 Kokia drynarioides strain JFW-HI SEQ_124182, 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: 229112
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 19 characters in sequence are not A, C, G, or T
Found at i:171 original size:56 final size:56
Alignment explanation
Indices: 96--210 Score: 203
Period size: 56 Copynumber: 2.1 Consensus size: 56
86 TAAAAATAAT
*
96 AATAAATAAATAAATAATAATAAGAAAAATAGAATTGAGTTTCGAGGCCCGAACGA
1 AATAAATAAATAAAAAATAATAAGAAAAATAGAATTGAGTTTCGAGGCCCGAACGA
* *
152 AATAAATAAATAAAAAATAATAAGAAAAATAGAATTGAGTTTCGAGGGCCGGACGA
1 AATAAATAAATAAAAAATAATAAGAAAAATAGAATTGAGTTTCGAGGCCCGAACGA
208 AAT
1 AAT
211 TGGGCTTGTA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.54, C:0.08, G:0.17, T:0.21
Consensus pattern (56 bp):
AATAAATAAATAAAAAATAATAAGAAAAATAGAATTGAGTTTCGAGGCCCGAACGA
Found at i:1130 original size:25 final size:27
Alignment explanation
Indices: 1102--1154 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 27
1092 AAAAAAATAT
1102 TATTAGA-AACAATT-TTT-TATTTAAA
1 TATTAGACAAC-ATTGTTTATATTTAAA
1127 TATTAGACAACATTGTTTATATTTAAA
1 TATTAGACAACATTGTTTATATTTAAA
1154 T
1 T
1155 CGCATTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 10 0.40
26 6 0.24
27 9 0.36
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (27 bp):
TATTAGACAACATTGTTTATATTTAAA
Found at i:1150 original size:79 final size:80
Alignment explanation
Indices: 1066--1227 Score: 265
Period size: 79 Copynumber: 2.0 Consensus size: 80
1056 AGTTGGAACA
* *
1066 ATATTTATATCGTATTGAAAGAAA-ATAAAAAAATATTATTAGAAACAA-TTTTTTATTTAAATA
1 ATATTTAAATCGCATTGAAAGAAATA-AAAAAAATATTATTAGAAACAATTTTTTTATTTAAATA
*
1129 TTAGACAACATTGTTT
65 TTAGACAACAATGTTT
1145 ATATTTAAATCGCATTGAAAGAAATAAAAAAAATATTATTAGAAACAATTTTTTTATTTAAATAT
1 ATATTTAAATCGCATTGAAAGAAATAAAAAAAATATTATTAGAAACAATTTTTTTATTTAAATAT
*
1210 TAGAGAACAATGTTT
66 TAGACAACAATGTTT
1225 ATA
1 ATA
1228 AGAAACTGAA
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
79 44 0.57
80 33 0.43
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.39
Consensus pattern (80 bp):
ATATTTAAATCGCATTGAAAGAAATAAAAAAAATATTATTAGAAACAATTTTTTTATTTAAATAT
TAGACAACAATGTTT
Found at i:3468 original size:14 final size:14
Alignment explanation
Indices: 3449--3487 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3439 TTTGTTCACT
*
3449 GAAAATGGTTTCTA
1 GAAAATGATTTCTA
* *
3463 GAAAATGATTTTTG
1 GAAAATGATTTCTA
3477 GAAAATGATTT
1 GAAAATGATTT
3488 ACTTTTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (14 bp):
GAAAATGATTTCTA
Found at i:3967 original size:15 final size:15
Alignment explanation
Indices: 3947--4000 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
3937 ATACTACAAA
3947 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
3962 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
3979 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
3996 ATATT
1 ATATT
4001 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:4064 original size:16 final size:16
Alignment explanation
Indices: 4033--4069 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
4023 ATGTGAAGTA
4033 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
4049 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
4065 TATTA
1 TATTA
4070 AAATAAAATT
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:4195 original size:9 final size:9
Alignment explanation
Indices: 4175--4209 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
4165 TATTAAAAAA
4175 TAAAATATTT
1 TAAAA-ATTT
4185 TAAAAATTT
1 TAAAAATTT
4194 TAAAAATTT
1 TAAAAATTT
4203 TAAAAAT
1 TAAAAAT
4210 AAAAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 20 0.80
10 5 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
TAAAAATTT
Found at i:4768 original size:54 final size:54
Alignment explanation
Indices: 4686--4800 Score: 230
Period size: 54 Copynumber: 2.1 Consensus size: 54
4676 AAAAATTTCA
4686 AATCATTTCCATGTTTATTGCTTTGAGTTATGCTGAGAAAAACTACATATATAT
1 AATCATTTCCATGTTTATTGCTTTGAGTTATGCTGAGAAAAACTACATATATAT
4740 AATCATTTCCATGTTTATTGCTTTGAGTTATGCTGAGAAAAACTACATATATAT
1 AATCATTTCCATGTTTATTGCTTTGAGTTATGCTGAGAAAAACTACATATATAT
4794 AATCATT
1 AATCATT
4801 GCTTCGATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (54 bp):
AATCATTTCCATGTTTATTGCTTTGAGTTATGCTGAGAAAAACTACATATATAT
Found at i:8301 original size:17 final size:19
Alignment explanation
Indices: 8269--8306 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
8259 GTTAAAGTAC
*
8269 AATTTTATTATTAATT-TA
1 AATTTTATTATAAATTATA
8287 AATTTT-TTATAAATTATA
1 AATTTTATTATAAATTATA
8305 AA
1 AA
8307 AAATCTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATTTTATTATAAATTATA
Found at i:9555 original size:14 final size:14
Alignment explanation
Indices: 9536--9565 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9526 GTTTGGTAAT
9536 TTGTTGATAATTGA
1 TTGTTGATAATTGA
*
9550 TTGTTGATTATTGA
1 TTGTTGATAATTGA
9564 TT
1 TT
9566 ACAGTGATCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (14 bp):
TTGTTGATAATTGA
Found at i:27353 original size:13 final size:13
Alignment explanation
Indices: 27332--27364 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
27322 AATATAAAAC
*
27332 AAAAGTAATATTA
1 AAAACTAATATTA
27345 AAAACTAATATTA
1 AAAACTAATATTA
27358 AAAACTA
1 AAAACTA
27365 TTAACAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (13 bp):
AAAACTAATATTA
Found at i:27928 original size:16 final size:18
Alignment explanation
Indices: 27907--27953 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 18
27897 ACTTAACATG
27907 AAATAATTTAAAT-T-CA
1 AAATAATTTAAATCTACA
27923 AAATAATTTAAATCTAACA
1 AAATAATTTAAATCT-ACA
27942 AAAT-ATTTAAAT
1 AAATAATTTAAAT
27954 GTAAATTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 13 0.46
17 1 0.04
18 8 0.29
19 6 0.21
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATAATTTAAATCTACA
Found at i:35552 original size:15 final size:15
Alignment explanation
Indices: 35529--35570 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
35519 GTAACACGTG
*
35529 TATAAATAAATAATT
1 TATATATAAATAATT
35544 TATATATAAATTAATT
1 TATATATAAA-TAATT
35560 TA-ATA-AAATAA
1 TATATATAAATAA
35571 AATATCTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 3 0.12
14 3 0.12
15 12 0.48
16 7 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TATATATAAATAATT
Found at i:35597 original size:17 final size:17
Alignment explanation
Indices: 35551--35597 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
35541 ATTTATATAT
*
35551 AAATTAATTTAATAAAATA
1 AAATT-ATTTAA-AAAAAA
*
35570 AAA-TATCTAAAAAAAA
1 AAATTATTTAAAAAAAA
35586 AAATTATTTAAA
1 AAATTATTTAAA
35598 TTATTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 8 0.33
17 12 0.50
18 1 0.04
19 3 0.12
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATTATTTAAAAAAAA
Found at i:38036 original size:20 final size:20
Alignment explanation
Indices: 38011--38049 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38001 AGAGTTTAGA
38011 GTTCAAAGTTCGAGATTCAT
1 GTTCAAAGTTCGAGATTCAT
* *
38031 GTTCAAGGTTCGAGGTTCA
1 GTTCAAAGTTCGAGATTCA
38050 AAATAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (20 bp):
GTTCAAAGTTCGAGATTCAT
Found at i:41204 original size:233 final size:233
Alignment explanation
Indices: 40797--41257 Score: 922
Period size: 233 Copynumber: 2.0 Consensus size: 233
40787 ATGAAAGGGA
40797 GGGTTAATGTAATCAGCGAAATGCTTTCGAGTAGGGGGAGAGTGTATTGAAGGTGTGACAGTTCA
1 GGGTTAATGTAATCAGCGAAATGCTTTCGAGTAGGGGGAGAGTGTATTGAAGGTGTGACAGTTCA
40862 AAGAGAAACTGTTTTGCTCCTAGCCATTAAGAACAGCCAGTTTGAGGCCATCAAAGTTATGGTTG
66 AAGAGAAACTGTTTTGCTCCTAGCCATTAAGAACAGCCAGTTTGAGGCCATCAAAGTTATGGTTG
40927 AATGGATTCTAGAGATGGAGAAAGAAGACAGCTTAAATCTCAAGGACGAGCTAGGCAAATACCAT
131 AATGGATTCTAGAGATGGAGAAAGAAGACAGCTTAAATCTCAAGGACGAGCTAGGCAAATACCAT
40992 TCTGCACCTAGCAATACTCATTAGGTTTTTCGAGTAGG
196 TCTGCACCTAGCAATACTCATTAGGTTTTTCGAGTAGG
41030 GGGTTAATGTAATCAGCGAAATGCTTTCGAGTAGGGGGAGAGTGTATTGAAGGTGTGACAGTTCA
1 GGGTTAATGTAATCAGCGAAATGCTTTCGAGTAGGGGGAGAGTGTATTGAAGGTGTGACAGTTCA
41095 AAGAGAAACTGTTTTGCTCCTAGCCATTAAGAACAGCCAGTTTGAGGCCATCAAAGTTATGGTTG
66 AAGAGAAACTGTTTTGCTCCTAGCCATTAAGAACAGCCAGTTTGAGGCCATCAAAGTTATGGTTG
41160 AATGGATTCTAGAGATGGAGAAAGAAGACAGCTTAAATCTCAAGGACGAGCTAGGCAAATACCAT
131 AATGGATTCTAGAGATGGAGAAAGAAGACAGCTTAAATCTCAAGGACGAGCTAGGCAAATACCAT
41225 TCTGCACCTAGCAATACTCATTAGGTTTTTCGA
196 TCTGCACCTAGCAATACTCATTAGGTTTTTCGA
41258 TTTCGCAGTT
Statistics
Matches: 228, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
233 228 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (233 bp):
GGGTTAATGTAATCAGCGAAATGCTTTCGAGTAGGGGGAGAGTGTATTGAAGGTGTGACAGTTCA
AAGAGAAACTGTTTTGCTCCTAGCCATTAAGAACAGCCAGTTTGAGGCCATCAAAGTTATGGTTG
AATGGATTCTAGAGATGGAGAAAGAAGACAGCTTAAATCTCAAGGACGAGCTAGGCAAATACCAT
TCTGCACCTAGCAATACTCATTAGGTTTTTCGAGTAGG
Found at i:43106 original size:20 final size:20
Alignment explanation
Indices: 43072--43115 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
43062 CCTTCTTTCA
43072 TTTTTTTTAATTTCTGA-TTG
1 TTTTTTTTAATTTCT-ATTTG
43092 TTTTGTTTTAA-TTCTATTTG
1 TTTT-TTTTAATTTCTATTTG
43112 TTTT
1 TTTT
43116 CATCGGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.05
20 15 0.68
21 6 0.27
ACGTcount: A:0.14, C:0.05, G:0.09, T:0.73
Consensus pattern (20 bp):
TTTTTTTTAATTTCTATTTG
Found at i:48210 original size:25 final size:23
Alignment explanation
Indices: 48175--48222 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
48165 TACTAATTTT
*
48175 AAAAAAATAAATAAATCGTAATA
1 AAAAAAATAAAAAAATCGTAATA
*
48198 AAAAATAATTAAAAAAATCTTAATA
1 AAAAA-AA-TAAAAAAATCGTAATA
48223 CAATTTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 14 0.67
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAAAAATAAAAAAATCGTAATA
Found at i:59635 original size:11 final size:11
Alignment explanation
Indices: 59609--59649 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
59599 AATGTCCTAT
*
59609 AAAATA-TAAT
1 AAAATATTAAA
59619 AAAATATTAAA
1 AAAATATTAAA
59630 AAAATATTTAAA
1 AAAATA-TTAAA
59642 AAAATATT
1 AAAATATT
59650 TTTAAGACTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 6 0.21
11 11 0.39
12 11 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAATATTAAA
Found at i:59654 original size:14 final size:12
Alignment explanation
Indices: 59619--59650 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
59609 AAAATATAAT
59619 AAAATA-TTAAA
1 AAAATATTTAAA
59630 AAAATATTTAAA
1 AAAATATTTAAA
59642 AAAATATTT
1 AAAATATTT
59651 TTAAGACTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAAATATTTAAA
Found at i:60355 original size:5 final size:5
Alignment explanation
Indices: 60345--60383 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
60335 AAAAACTTAG
60345 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
60384 TTAAAATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:60428 original size:19 final size:19
Alignment explanation
Indices: 60402--60450 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
60392 TATTTTATAT
60402 TATG-ATTTAATATTTAAGA
1 TATGTATTTAATATTTAA-A
*
60421 TAT-TATTTATTATTTAAA
1 TATGTATTTAATATTTAAA
*
60439 TTTGTATTTAAT
1 TATGTATTTAAT
60451 TTATGTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (19 bp):
TATGTATTTAATATTTAAA
Found at i:61268 original size:21 final size:21
Alignment explanation
Indices: 61243--61298 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
61233 TTATTTTCTA
*
61243 TTTCTTTTCTTTTTAATTTTG
1 TTTCTTTTATTTTTAATTTTG
61264 TTTCTTTTATTTTTAATTTTG
1 TTTCTTTTATTTTTAATTTTG
61285 TTTCTTTTATTTTT
1 TTTCTTTTATTTTT
61299 CTTCATATCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.11, C:0.07, G:0.04, T:0.79
Consensus pattern (21 bp):
TTTCTTTTATTTTTAATTTTG
Found at i:64120 original size:16 final size:16
Alignment explanation
Indices: 64099--64129 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
64089 AATGATAGCA
64099 AAAAAAAAAAAGAAAG
1 AAAAAAAAAAAGAAAG
*
64115 AAAAAACAAAAGAAA
1 AAAAAAAAAAAGAAA
64130 TAATAACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAGAAAG
Found at i:82795 original size:31 final size:31
Alignment explanation
Indices: 82760--82818 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
82750 ATTATTAAAC
** *
82760 TATTTCAATGTTTTTATTTAAATCACTGGAT
1 TATTTCAAAATTTTTATTTAAAGCACTGGAT
*
82791 TATTTGAAAATTTTTATTTAAAGCACTG
1 TATTTCAAAATTTTTATTTAAAGCACTG
82819 AGCTATTAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.49
Consensus pattern (31 bp):
TATTTCAAAATTTTTATTTAAAGCACTGGAT
Found at i:84778 original size:14 final size:15
Alignment explanation
Indices: 84748--84779 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
84738 ATTTTAAGTT
84748 AATTTTATTTTTCAA
1 AATTTTATTTTTCAA
84763 AATTTTATTTTT-AA
1 AATTTTATTTTTCAA
84777 AAT
1 AAT
84780 AAACCGTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTTTATTTTTCAA
Found at i:86408 original size:2 final size:2
Alignment explanation
Indices: 86403--86438 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
86393 TCCAGGTAAT
86403 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
86439 AGACCTCAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:92639 original size:22 final size:21
Alignment explanation
Indices: 92596--92647 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
92586 ATTTGTATTT
*
92596 TTTTTATTTTATTTTGTTTTAA
1 TTTTT-TTATATTTTGTTTTAA
92618 GTTTTTTTATATTTT-TTATTAA
1 -TTTTTTTATATTTTGTT-TTAA
*
92640 TATTTTTA
1 TTTTTTTA
92648 ACATATCAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 9 0.35
22 12 0.46
23 5 0.19
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (21 bp):
TTTTTTTATATTTTGTTTTAA
Found at i:93797 original size:19 final size:19
Alignment explanation
Indices: 93760--93812 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
93750 CTTTTTATTC
93760 AAGATC-TC-AATGATTTCT
1 AAGATCTTCGAATG-TTTCT
*
93778 AAGATCTTTGAATGTTTCT
1 AAGATCTTCGAATGTTTCT
93797 AAGATCTTCGAATGTT
1 AAGATCTTCGAATGTT
93813 GCTGTCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 6 0.19
19 21 0.68
20 4 0.13
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (19 bp):
AAGATCTTCGAATGTTTCT
Found at i:94410 original size:31 final size:31
Alignment explanation
Indices: 94368--94432 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
94358 TTAACAGTCC
94368 AATGACTTAAATAAAATCTTTCGAATAATTT
1 AATGACTTAAATAAAATCTTTCGAATAATTT
* *
94399 AATGCCTTAAATAAAATCTTTTGAATAATTT
1 AATGACTTAAATAAAATCTTTCGAATAATTT
94430 AAT
1 AAT
94433 AACCAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (31 bp):
AATGACTTAAATAAAATCTTTCGAATAATTT
Found at i:99458 original size:23 final size:23
Alignment explanation
Indices: 99428--99475 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
99418 GTGTAAAAAC
99428 TTGTGACTCTAAATAGCTCATGG
1 TTGTGACTCTAAATAGCTCATGG
99451 TTGTGACTCTAAATAGCTCATGG
1 TTGTGACTCTAAATAGCTCATGG
99474 TT
1 TT
99476 CTAGTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.38
Consensus pattern (23 bp):
TTGTGACTCTAAATAGCTCATGG
Found at i:104539 original size:13 final size:13
Alignment explanation
Indices: 104521--104551 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
104511 GGGGTAAAAG
104521 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
*
104534 TTTTCTTTTTTTT
1 TTTTCTTTTTTCT
104547 TTTTC
1 TTTTC
104552 AATTTTGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:111893 original size:17 final size:17
Alignment explanation
Indices: 111868--111900 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
111858 TAAAAATTCT
*
111868 AAAATTTATATTTTTTA
1 AAAAATTATATTTTTTA
111885 AAAAATTATATTTTTT
1 AAAAATTATATTTTTT
111901 TAAATCCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AAAAATTATATTTTTTA
Found at i:115462 original size:234 final size:234
Alignment explanation
Indices: 115049--115516 Score: 927
Period size: 234 Copynumber: 2.0 Consensus size: 234
115039 CCACTTAATG
115049 CATCTAAGTTCTCATTACATATTTAACGAAGGAATGATAGAAGTCAAATTTTATAATCTTAATGA
1 CATCTAAGTTCTCATTACATATTTAACGAAGGAATGATAGAAGTCAAATTTTATAATCTTAATGA
115114 TAAAAAACTAATAAATTTTATGATTGAGTCGCTAAAACAAGAACACACTATAATTAAATTATCTT
66 TAAAAAACTAATAAATTTTATGATTGAGTCGCTAAAACAAGAACACACTATAATTAAATTATCTT
*
115179 TGATTTAATAATTTTGATATTTTTCTTTAGAAAATAATTTTAGTACGGTATATTTTCATTGATTG
131 TGATTTAATAATTTTGATATTTTTCTTTAGAAAATAATTTTAATACGGTATATTTTCATTGATTG
115244 AGTTTAATTTAATATGCAACAATAAACGTAATAAATTTT
196 AGTTTAATTTAATATGCAACAATAAACGTAATAAATTTT
115283 CATCTAAGTTCTCATTACATATTTAACGAAGGAATGATAGAAGTCAAATTTTATAATCTTAATGA
1 CATCTAAGTTCTCATTACATATTTAACGAAGGAATGATAGAAGTCAAATTTTATAATCTTAATGA
115348 TAAAAAACTAATAAATTTTATGATTGAGTCGCTAAAACAAGAACACACTATAATTAAATTATCTT
66 TAAAAAACTAATAAATTTTATGATTGAGTCGCTAAAACAAGAACACACTATAATTAAATTATCTT
115413 TGATTTAATAATTTTGATATTTTTCTTTAGAAAATAATTTTAATACGGTATATTTTCATTGATTG
131 TGATTTAATAATTTTGATATTTTTCTTTAGAAAATAATTTTAATACGGTATATTTTCATTGATTG
115478 AGTTTAATTTAATATGCAACAATAAACGTAATAAATTTT
196 AGTTTAATTTAATATGCAACAATAAACGTAATAAATTTT
115517 TATCATAATA
Statistics
Matches: 233, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
234 233 1.00
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (234 bp):
CATCTAAGTTCTCATTACATATTTAACGAAGGAATGATAGAAGTCAAATTTTATAATCTTAATGA
TAAAAAACTAATAAATTTTATGATTGAGTCGCTAAAACAAGAACACACTATAATTAAATTATCTT
TGATTTAATAATTTTGATATTTTTCTTTAGAAAATAATTTTAATACGGTATATTTTCATTGATTG
AGTTTAATTTAATATGCAACAATAAACGTAATAAATTTT
Found at i:124504 original size:6 final size:6
Alignment explanation
Indices: 124493--124522 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
124483 TAGTGAGAGT
124493 AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG
1 AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG
124523 GGGAGAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
AGGAAG
Found at i:124968 original size:75 final size:76
Alignment explanation
Indices: 124845--124999 Score: 276
Period size: 75 Copynumber: 2.0 Consensus size: 76
124835 ATTGGATAAT
* *
124845 AATTAACATTTAAAGTTTATTTCATTTAGTGAACAGTTAGATTATGATG-AGAAAAAAAAATGAG
1 AATTAACATTTAAAGTTTATTCCATTTAGTGAACAGTTAGATTATGATGAAAAAAAAAAAATGAG
124909 AAGTTTGAAAC
66 AAGTTTGAAAC
124920 AATTAACATTTAAAGTTTATTCCATTTAGTGAACAGTTAGATTATGATGAAAAAAAAAAAAATGA
1 AATTAACATTTAAAGTTTATTCCATTTAGTGAACAGTTAGATTATGATG-AAAAAAAAAAAATGA
124985 GAAGTTTGAAAC
65 GAAGTTTGAAAC
124997 AAT
1 AAT
125000 CTAGTGTGGT
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
75 48 0.63
77 28 0.37
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (76 bp):
AATTAACATTTAAAGTTTATTCCATTTAGTGAACAGTTAGATTATGATGAAAAAAAAAAAATGAG
AAGTTTGAAAC
Found at i:129586 original size:15 final size:14
Alignment explanation
Indices: 129565--129593 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
129555 TTATCATGTG
129565 TTATATATA-TATT
1 TTATATATATTATT
129578 TTATATATATTATT
1 TTATATATATTATT
129592 TT
1 TT
129594 CACTAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTATATATATTATT
Found at i:130017 original size:15 final size:14
Alignment explanation
Indices: 129989--130036 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 14
129979 TGCATTAGCT
129989 AATTTTTTAT-GTA
1 AATTTTTTATAGTA
130002 AATTTTTTATAAGTA
1 AATTTTTTAT-AGTA
*
130017 AATTTGTTATA-T-
1 AATTTTTTATAGTA
130029 AATTTTTT
1 AATTTTTT
130037 TTTTATTCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 7 0.23
13 11 0.35
14 1 0.03
15 12 0.39
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (14 bp):
AATTTTTTATAGTA
Found at i:138400 original size:56 final size:54
Alignment explanation
Indices: 138284--138407 Score: 153
Period size: 56 Copynumber: 2.2 Consensus size: 54
138274 ACACTAATAA
*
138284 TCACTCAATTATTAGTATTTTTTTTGTCATCTAACAATGAAAAGTTATAAAACGG
1 TCACTCAATTATTAGTATTTTTTTTGTCATC-AACAATGAAAAGTTACAAAACGG
* *
138339 TCACTCAATTATTAGTAATTTTTTTTTGTCATC-A-AATTATAAAGATTACAAAATGG
1 TCACTCAATTATTAGT-A-TTTTTTTTGTCATCAACAATGA-AAAG-TTACAAAACGG
*
138395 TCACTCAAATATT
1 TCACTCAATTATT
138408 GAAACACCAA
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
54 4 0.07
55 21 0.34
56 22 0.36
57 14 0.23
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (54 bp):
TCACTCAATTATTAGTATTTTTTTTGTCATCAACAATGAAAAGTTACAAAACGG
Found at i:139038 original size:6 final size:6
Alignment explanation
Indices: 139024--139053 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
139014 TAAAACAAGA
*
139024 CCAACG CCAATG CCAATG CCAATG CCAATG
1 CCAATG CCAATG CCAATG CCAATG CCAATG
139054 GATGAATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.33, C:0.37, G:0.17, T:0.13
Consensus pattern (6 bp):
CCAATG
Found at i:148265 original size:13 final size:11
Alignment explanation
Indices: 148186--148272 Score: 56
Period size: 11 Copynumber: 7.7 Consensus size: 11
148176 AAAAAAATTA
148186 AATATTTATTT
1 AATATTTATTT
148197 -ATATTATATTT
1 AATATT-TATTT
148208 AATTTATTTA-TT
1 AA--TATTTATTT
* *
148220 AAAATTT-TAT
1 AATATTTATTT
*
148230 ATATAATTATCTT
1 A-ATATTTAT-TT
148243 AATATTTATTT
1 AATATTTATTT
*
148254 AATATATATATT
1 AATATTTAT-TT
148266 AA-ATTTA
1 AATATTTA
148273 AATTTATGTG
Statistics
Matches: 59, Mismatches: 8, Indels: 18
0.69 0.09 0.21
Matches are distributed among these distances:
10 11 0.19
11 23 0.39
12 17 0.29
13 4 0.07
14 4 0.07
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (11 bp):
AATATTTATTT
Found at i:149550 original size:23 final size:26
Alignment explanation
Indices: 149520--149570 Score: 81
Period size: 23 Copynumber: 2.1 Consensus size: 26
149510 TTTAAAATAT
149520 TTATATTTTTT-AAAA-ATTTAT-TA
1 TTATATTTTTTGAAAATATTTATGTA
149543 TTATATTTTTTGAAAATATTTATGTA
1 TTATATTTTTTGAAAATATTTATGTA
149569 TT
1 TT
149571 TTTATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 11 0.44
24 4 0.16
25 6 0.24
26 4 0.16
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (26 bp):
TTATATTTTTTGAAAATATTTATGTA
Found at i:149570 original size:21 final size:19
Alignment explanation
Indices: 149509--149573 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 19
149499 TATTCTTTAA
149509 TTTTAAAATATTTA-TATT
1 TTTTAAAATATTTATTATT
*
149527 TTTTAAAAATTTATTATTATATT
1 TTTT-AAAATAT-TTA-T-TATT
149550 TTTTGAAAATATTTATGTATT
1 TTTT-AAAATATTTAT-TATT
149571 TTT
1 TTT
149574 ATATATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 4 0.11
19 6 0.16
20 3 0.08
21 8 0.21
22 3 0.08
23 14 0.37
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTTAAAATATTTATTATT
Found at i:151366 original size:79 final size:79
Alignment explanation
Indices: 151233--151407 Score: 278
Period size: 79 Copynumber: 2.2 Consensus size: 79
151223 TAATGGGAAG
*
151233 AAGATATTGGAACCAAAGATATTGAATCTTTTGGTTAATGGATTTTAAAGATTCAAGCTTTGAGA
1 AAGATATTGGAACCAAAGATATTGAATCTTTTGATTAATGGATTTTAAAGATTCAAGCTTTGAGA
151298 CAAATTTATAACTA
66 CAAATTTATAACTA
* * * *
151312 AAGATATTGGAACCAAATATATTGAATCTTTTGATTAATGGGTTTTAAATATTCAAGTTTTGAGA
1 AAGATATTGGAACCAAAGATATTGAATCTTTTGATTAATGGATTTTAAAGATTCAAGCTTTGAGA
* *
151377 CAGATTTGTAACTA
66 CAAATTTATAACTA
*
151391 AAGATATTGGAATCAAA
1 AAGATATTGGAACCAAA
151408 AGAGAAGAAG
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 88 1.00
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (79 bp):
AAGATATTGGAACCAAAGATATTGAATCTTTTGATTAATGGATTTTAAAGATTCAAGCTTTGAGA
CAAATTTATAACTA
Found at i:151697 original size:31 final size:29
Alignment explanation
Indices: 151628--151701 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
151618 ACAAAATAAT
**
151628 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATGGCA
*
151657 AACATAAGTGACTAAAATGTAACCTGAGGCA
1 AACATAAGTGACTAAAATGTAACAT--GGCA
*
151688 AACAAAAGTGACTA
1 AACATAAGTGACTA
151702 TTTTTGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.22
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACATGGCA
Found at i:163280 original size:55 final size:55
Alignment explanation
Indices: 163235--163341 Score: 134
Period size: 56 Copynumber: 2.0 Consensus size: 55
163225 ATAATTTTTT
*
163235 CATT-TTT-TTTTATAAAAATACTT-AATCTATCAAAATGATTG-AAAAAATGTTA
1 CATTATTTATTTTAGAAAAA-ACTTAAATCTATCAAAATGATTGAAAAAAATGTTA
*
163287 CATTATTTCATTTTAGAAAAAATTTAAAATCTATCAAAATGATTG-AAAAAATGTT
1 CATTATTT-ATTTTAGAAAAAACTT-AAATCTATCAAAATGATTGAAAAAAATGTT
163342 TCAATCAACA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
52 4 0.08
53 3 0.06
54 3 0.06
55 10 0.21
56 28 0.58
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (55 bp):
CATTATTTATTTTAGAAAAAACTTAAATCTATCAAAATGATTGAAAAAAATGTTA
Found at i:165375 original size:23 final size:22
Alignment explanation
Indices: 165345--165446 Score: 116
Period size: 23 Copynumber: 4.5 Consensus size: 22
165335 ACGCTAGCGC
165345 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTT-GTGT
*
165368 GCTTACTGTTTCACACTTTGTGT
1 GCTTACTGTTTCGCAC-TTGTGT
165391 GCTTACTGTTTCGCACCTTGTGT
1 GCTTACTGTTTCGCA-CTTGTGT
* *
165414 GCCTACTGGATT-GCACTATGTGT
1 GCTTACT-GTTTCGCACT-TGTGT
*
165437 TCTTACTGTT
1 GCTTACTGTT
165447 AAGTACTTCG
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
22 4 0.06
23 58 0.85
24 6 0.09
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.44
Consensus pattern (22 bp):
GCTTACTGTTTCGCACTTGTGT
Found at i:166267 original size:14 final size:14
Alignment explanation
Indices: 166248--166275 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
166238 TTAAATAAAA
166248 ATAATATAAAATTT
1 ATAATATAAAATTT
166262 ATAATATAAAATTT
1 ATAATATAAAATTT
166276 TTGTAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAATATAAAATTT
Found at i:169626 original size:6 final size:6
Alignment explanation
Indices: 169560--169622 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
169550 CATCTTTAAG
* *
169560 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACGTAC ACACAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* *
169608 ACACAC ACACAC ACA
1 ACATAC ACATAC ACA
169623 CACAGTGCCT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.49, C:0.38, G:0.02, T:0.11
Consensus pattern (6 bp):
ACATAC
Found at i:172614 original size:76 final size:76
Alignment explanation
Indices: 172524--172677 Score: 263
Period size: 76 Copynumber: 2.0 Consensus size: 76
172514 AAGAAAGAAT
* *
172524 TCAAGTACTTAAATAGAAAAATTCTAAAAATTAAATGGTGATTTATGTCTATTATTTTTTCCCAA
1 TCAAGTACTAAAATAGAAAAATTCTAAAAATTAAATGGTGATTGATGTCTATTATTTTTTCCCAA
172589 AAAAGTTCACA
66 AAAAGTTCACA
* *
172600 TCAAGTACTAAAATAGAAAATTTCTAAAAATTAAATGGTGATTGATGTCTATTGTTTTTTCCCAA
1 TCAAGTACTAAAATAGAAAAATTCTAAAAATTAAATGGTGATTGATGTCTATTATTTTTTCCCAA
*
172665 AAGAGTTCACA
66 AAAAGTTCACA
172676 TC
1 TC
172678 TTAGTTTTTA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36
Consensus pattern (76 bp):
TCAAGTACTAAAATAGAAAAATTCTAAAAATTAAATGGTGATTGATGTCTATTATTTTTTCCCAA
AAAAGTTCACA
Found at i:186057 original size:45 final size:45
Alignment explanation
Indices: 186000--186092 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 45
185990 TTATTTATTT
* *
186000 AAAAAATATATTCTCATCCAATTTGGAA-ATCTAAGTTGACACTTA
1 AAAAAATATATTCTCATCCAATTT-AAAGATCCAAGTTGACACTTA
* * *
186045 AAAAAATCTATTCTCATCCCATTTAAAGATCCAAGTTGATACTTA
1 AAAAAATATATTCTCATCCAATTTAAAGATCCAAGTTGACACTTA
186090 AAA
1 AAA
186093 TTTTGTTGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 2 0.05
45 40 0.95
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (45 bp):
AAAAAATATATTCTCATCCAATTTAAAGATCCAAGTTGACACTTA
Found at i:188676 original size:17 final size:18
Alignment explanation
Indices: 188656--188701 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
188646 TTACAGACAT
*
188656 TTAATAAAAAAT-ATATA
1 TTAATAAAAAATGATAAA
188673 TTAATAATTAAAATGATAAA
1 TTAATAA--AAAATGATAAA
188693 TT-ATAAAAA
1 TTAATAAAAA
188702 TAATCATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 10 0.40
19 9 0.36
20 6 0.24
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
TTAATAAAAAATGATAAA
Found at i:196646 original size:18 final size:19
Alignment explanation
Indices: 196593--196649 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
196583 ACAAAAATTA
*
196593 AAAAATTAAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
196612 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
196631 AAAAATTCTAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
196649 A
1 A
196650 TCTTTAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 11 0.33
19 22 0.67
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:197467 original size:26 final size:24
Alignment explanation
Indices: 197428--197493 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 24
197418 CTCTGTCAAC
197428 AAAAATTAAAAAATATATATATTTAT
1 AAAAATTAAAAAAT-T-TATATTTAT
197454 AAAAAGTT-AAAAATTTATATTTA-
1 AAAAA-TTAAAAAATTTATATTTAT
*
197477 AAATATATATAAAAATT
1 AAAAAT-TA-AAAAATT
197494 AAAAATTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
22 1 0.03
23 5 0.14
24 8 0.23
25 8 0.23
26 11 0.31
27 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAAATTAAAAAATTTATATTTAT
Found at i:197499 original size:32 final size:32
Alignment explanation
Indices: 197446--197506 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
197436 AAAAATATAT
*
197446 ATATTTATAAAAAGTTAAAAATTTATATTTAAA
1 ATATATATAAAAAGTTAAAAATTTA-ATTTAAA
197479 ATATATATAAAAA-TTAAAAATTTAATTT
1 ATATATATAAAAAGTTAAAAATTTAATTT
197507 TTTCTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 4 0.15
32 11 0.41
33 12 0.44
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (32 bp):
ATATATATAAAAAGTTAAAAATTTAATTTAAA
Found at i:204531 original size:31 final size:29
Alignment explanation
Indices: 204489--204546 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
204479 AAAATATAAT
*
204489 TTTTAAAAAATTAAATTAAAATTTTATCG
1 TTTTAAAAAATTAAAGTAAAATTTTATCG
* *
204518 TTTTACAAGAAATTAGAGTATAATTTTAT
1 TTTTA-AA-AAATTAAAGTAAAATTTTAT
204547 ATTTATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.21
30 2 0.08
31 17 0.71
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (29 bp):
TTTTAAAAAATTAAAGTAAAATTTTATCG
Found at i:213531 original size:33 final size:33
Alignment explanation
Indices: 213435--213531 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 33
213425 TTTTATTTAA
213435 ATTTTTTAAAATTTTTAGTAAATATA-AAATTATATTT
1 ATTTTTTAAAA---TTA-TAAATATATAAATTAT-TTT
* *
213472 -TTATCTTAAAATAATAAATAT-T---TTATTTT
1 ATT-TTTTAAAATTATAAATATATAAATTATTTT
213501 ATTTTTTAAAATTATAAATATATAAATTATT
1 ATTTTTTAAAATTATAAATATATAAATTATT
213532 AAAAAGATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
29 19 0.39
30 7 0.14
33 12 0.24
34 2 0.04
36 2 0.04
37 7 0.14
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (33 bp):
ATTTTTTAAAATTATAAATATATAAATTATTTT
Found at i:218683 original size:20 final size:20
Alignment explanation
Indices: 218649--218686 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
218639 TGATCATTTT
218649 GTAACAAAACGATAACATAA
1 GTAACAAAACGATAACATAA
218669 GTAACTAAAAC-ATAACAT
1 GTAAC-AAAACGATAACAT
218687 TTCAAACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.58, C:0.16, G:0.08, T:0.18
Consensus pattern (20 bp):
GTAACAAAACGATAACATAA
Found at i:219720 original size:42 final size:42
Alignment explanation
Indices: 219657--219740 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
219647 GCCCGGCCCG
*
219657 AATCAGTTTATACTTATTCTTTTTGCTGCTGTTTAGCTGCTA
1 AATCAGTTTATACTTACTCTTTTTGCTGCTGTTTAGCTGCTA
*
219699 AATCAGTTTATGCTTACTCTTTTTGCTGCTGTTTAGCTGCTA
1 AATCAGTTTATACTTACTCTTTTTGCTGCTGTTTAGCTGCTA
219741 TTTAGGCATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (42 bp):
AATCAGTTTATACTTACTCTTTTTGCTGCTGTTTAGCTGCTA
Found at i:220576 original size:12 final size:12
Alignment explanation
Indices: 220559--220593 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
220549 CCATGAATGC
220559 TTCTTCTTCATT
1 TTCTTCTTCATT
220571 TTCTTCTTCATT
1 TTCTTCTTCATT
220583 TTCTTCTTCAT
1 TTCTTCTTCAT
220594 CAATCTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.66
Consensus pattern (12 bp):
TTCTTCTTCATT
Found at i:229046 original size:23 final size:23
Alignment explanation
Indices: 229020--229075 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
229010 ATTTAATCTT
*
229020 TTATAATTTTTAAAATGATAAAA
1 TTATAATTTTTAAAATAATAAAA
***
229043 TTAT-ATTTTTGTTATAATAAAA
1 TTATAATTTTTAAAATAATAAAA
*
229065 TTTTAATTTTT
1 TTATAATTTTT
229076 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (23 bp):
TTATAATTTTTAAAATAATAAAA
Done.