Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009811.1 Kokia drynarioides strain JFW-HI SEQ_124532, 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: 195968
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 105 characters in sequence are not A, C, G, or T
Found at i:15898 original size:21 final size:20
Alignment explanation
Indices: 15872--15919 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 20
15862 AACAAAATTA
15872 CAAAAATAATCAAAATAATTTT
1 CAAAAATAA--AAAATAATTTT
15894 CAAAAATTAAAAAATAATTTT
1 CAAAAA-TAAAAAATAATTTT
*
15915 TAAAA
1 CAAAA
15920 TTTAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 15 0.62
22 6 0.25
23 3 0.12
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (20 bp):
CAAAAATAAAAAATAATTTT
Found at i:15924 original size:21 final size:21
Alignment explanation
Indices: 15883--15925 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
15873 AAAAATAATC
15883 AAAATAATTTTCAAAAATTAA
1 AAAATAATTTTCAAAAATTAA
* *
15904 AAAATAATTTTTAAAATTTAA
1 AAAATAATTTTCAAAAATTAA
15925 A
1 A
15926 TTATTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATAATTTTCAAAAATTAA
Found at i:16204 original size:22 final size:22
Alignment explanation
Indices: 16161--16205 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
16151 TGTAACAAGA
* *
16161 TTTTAATTTAACATTATTAATT
1 TTTTAATTTAACATGATCAATT
16183 TTTTAATTTAAC-TCGATCAATT
1 TTTTAATTTAACAT-GATCAATT
16205 T
1 T
16206 CACTTGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTTAATTTAACATGATCAATT
Found at i:20145 original size:2 final size:2
Alignment explanation
Indices: 20138--20162 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20128 AATGCAAGTA
20138 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 A
20163 AAGTACCACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23547 original size:4 final size:4
Alignment explanation
Indices: 23540--23568 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
23530 GGTATATATA
23540 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
23569 TTTTTTAATT
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:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:27636 original size:12 final size:11
Alignment explanation
Indices: 27613--27646 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
27603 TTGTCGGACT
27613 AAAAGCAAAAA
1 AAAAGCAAAAA
27624 AAAAGCAAAAA
1 AAAAGCAAAAA
27635 AAAA--AAAAA
1 AAAAGCAAAAA
27644 AAA
1 AAA
27647 GAGTTTATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 8 0.35
11 15 0.65
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAGCAAAAA
Found at i:29590 original size:2 final size:2
Alignment explanation
Indices: 29585--29620 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
29575 TTAAAAAAAA
*
29585 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29621 GGAGTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:52043 original size:3 final size:3
Alignment explanation
Indices: 52035--52061 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
52025 GATAATGAAG
52035 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
52062 AGGATAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:61491 original size:3 final size:3
Alignment explanation
Indices: 61465--61516 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
61455 TGGGAATCTT
* * *
61465 CAC CAT CAC CAT CAC CAT CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
61513 CAC C
1 CAC C
61517 TTTGGAACTC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.62, G:0.00, T:0.06
Consensus pattern (3 bp):
CAC
Found at i:79869 original size:22 final size:22
Alignment explanation
Indices: 79838--79895 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
79828 TGCTGTTGTG
79838 TTTTGTTATTGTTTTAC-TACTA
1 TTTTGTTATTGTTTT-CTTACTA
* * *
79860 TTTTGCTATTATATTCTTACTA
1 TTTTGTTATTGTTTTCTTACTA
*
79882 TTTTGTTGTTGTTT
1 TTTTGTTATTGTTT
79896 GGATATTATA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.16, C:0.09, G:0.10, T:0.66
Consensus pattern (22 bp):
TTTTGTTATTGTTTTCTTACTA
Found at i:84511 original size:32 final size:31
Alignment explanation
Indices: 84437--84514 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 31
84427 GGTTAAATTA
* * *
84437 TTATTTGAAG-TTTGAATTTGATAATTATTT
1 TTATTTTAAGATTTGAATTTGACAAATATTT
** *
84467 TTATACTGAGATTTGAACTTTGACAAATATTT
1 TTATTTTAAGATTTGAA-TTTGACAAATATTT
84499 TTATTTTAAGATTTGA
1 TTATTTTAAGATTTGA
84515 GTTTAGGGTT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
30 6 0.16
31 6 0.16
32 25 0.68
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.51
Consensus pattern (31 bp):
TTATTTTAAGATTTGAATTTGACAAATATTT
Found at i:85387 original size:3 final size:3
Alignment explanation
Indices: 85379--85408 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
85369 GTTTGATCAA
85379 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
85409 GATGTTATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:86299 original size:2 final size:2
Alignment explanation
Indices: 86292--86316 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
86282 CTTTATTACG
86292 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 A
86317 ATTTTTACAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:99351 original size:30 final size:31
Alignment explanation
Indices: 99230--99356 Score: 86
Period size: 30 Copynumber: 4.2 Consensus size: 31
99220 GATCTAATTC
* * * *
99230 AAATTTTCAAAAACTTTAACA-GTTTAATTA
1 AAATTTTCAAAAATTTTAAGAGGCTTAACTA
* * *
99260 AACTTTTTAAAACTTTTAAG-GGCTTAA-TA
1 AAATTTTCAAAAATTTTAAGAGGCTTAACTA
* * * *
99289 AGAA-TTTCTAAAA-TTTATGAGTCCTAACTA
1 A-AATTTTCAAAAATTTTAAGAGGCTTAACTA
*
99319 AAATTTTCAAAAATTTTTAGAGGCTTAA-TAA
1 AAATTTTCAAAAATTTTAAGAGGCTTAACT-A
99350 AAATTTT
1 AAATTTT
99357 AATTAAACCG
Statistics
Matches: 72, Mismatches: 18, Indels: 13
0.70 0.17 0.13
Matches are distributed among these distances:
28 5 0.07
29 16 0.22
30 33 0.46
31 18 0.25
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (31 bp):
AAATTTTCAAAAATTTTAAGAGGCTTAACTA
Found at i:102076 original size:19 final size:18
Alignment explanation
Indices: 102054--102101 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
102044 ATTGCTGCTC
* *
102054 AAAAATTAAATGAAATATA
1 AAAAATTAAATCAAAT-CA
*
102073 AAAAATCAAATCAAATCA
1 AAAAATTAAATCAAATCA
*
102091 AATAATTAAAT
1 AAAAATTAAAT
102102 TCATGCCCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (18 bp):
AAAAATTAAATCAAATCA
Found at i:105282 original size:132 final size:132
Alignment explanation
Indices: 105045--105313 Score: 502
Period size: 132 Copynumber: 2.0 Consensus size: 132
105035 TTTCTACAAA
105045 ATTTGGAGTTCCGCTTTGGGTTTTGCATTAAAGAACCAACCTTTCACCCTCCATTTTCCCTTTTG
1 ATTTGGAGTTCCGCTTTGGGTTTTGCATTAAAGAACCAACCTTTCACCCTCCATTTTCCCTTTTG
*
105110 CATTTCTGAAGTGAAAACTCTCATGGCACAAAGGGTATACTAGCTTCATTCTCCTGTGTTTTATT
66 CATTTCTGAAGTGAAAAATCTCATGGCACAAAGGGTATACTAGCTTCATTCTCCTGTGTTTTATT
105175 TC
131 TC
*
105177 ATTTGGAGTTCCTCTTTGGGTTTTGCATTAAAGAACCAACCTTTCACCCTCCATTTTCCCTTTTG
1 ATTTGGAGTTCCGCTTTGGGTTTTGCATTAAAGAACCAACCTTTCACCCTCCATTTTCCCTTTTG
* *
105242 CATTTCTGAAGTGAAAAATCTCATGGCACGAAGGGTATACTAGCTTCATTCTTCTGTGTTTTATT
66 CATTTCTGAAGTGAAAAATCTCATGGCACAAAGGGTATACTAGCTTCATTCTCCTGTGTTTTATT
105307 TC
131 TC
105309 ATTTG
1 ATTTG
105314 TTTTGACAAT
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 133 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (132 bp):
ATTTGGAGTTCCGCTTTGGGTTTTGCATTAAAGAACCAACCTTTCACCCTCCATTTTCCCTTTTG
CATTTCTGAAGTGAAAAATCTCATGGCACAAAGGGTATACTAGCTTCATTCTCCTGTGTTTTATT
TC
Found at i:112259 original size:61 final size:60
Alignment explanation
Indices: 112148--112264 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 60
112138 ATTCAGGAAC
* ** * *
112148 TAACTTGGACAAAAAAAAAATTCAAGCCCCGTTGTGAGAACAATTGCCAAGTTAAAAACT
1 TAACTTGGACAAAAAAAAAATTCAAACCCCAATGTGAAAACAATTACCAAGTTAAAAACT
* * *
112208 TAACTTGGACCAAAAAAAAAGTTCAAACCCCAATGTGAAAATAGTTACCAAGTTAAA
1 TAACTTGGA-CAAAAAAAAAATTCAAACCCCAATGTGAAAACAATTACCAAGTTAAA
112265 GCCCCAAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
60 9 0.19
61 39 0.81
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.21
Consensus pattern (60 bp):
TAACTTGGACAAAAAAAAAATTCAAACCCCAATGTGAAAACAATTACCAAGTTAAAAACT
Found at i:126910 original size:32 final size:32
Alignment explanation
Indices: 126874--126946 Score: 146
Period size: 32 Copynumber: 2.3 Consensus size: 32
126864 AACAAATTAG
126874 CAAAAATCAATGGTTCAAGTTCATATATTTAC
1 CAAAAATCAATGGTTCAAGTTCATATATTTAC
126906 CAAAAATCAATGGTTCAAGTTCATATATTTAC
1 CAAAAATCAATGGTTCAAGTTCATATATTTAC
126938 CAAAAATCA
1 CAAAAATCA
126947 GACTAATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (32 bp):
CAAAAATCAATGGTTCAAGTTCATATATTTAC
Found at i:127053 original size:86 final size:87
Alignment explanation
Indices: 126906--127142 Score: 300
Period size: 86 Copynumber: 2.7 Consensus size: 87
126896 ATATATTTAC
* * *
126906 CAAAAATCAATGGTTCAAGTTCATATATTTACCAAAAATCAGACTAATTTTTCAATATTTATAAC
1 CAAAAATCAATGGTTCAAGTTCATGTATTTACCAAAAACCAGACTAAATTTTCAATATTTATAAC
*
126971 AATTTATATGCAACAAATTAG-
66 AACTTATATGCAACAAATTAGA
* *
126992 CAAAAATAAATGGTTC-A-TTGACATGTATTTACCAAAAACCAGACTAAATTTTCAATGTTTATA
1 CAAAAATCAATGGTTCAAGTT--CATGTATTTACCAAAAACCAGACTAAATTTTCAATATTTATA
*
127055 ACAACTTATGTGCAACAAATTAGA
64 ACAACTTATATGCAACAAATTAGA
* ** * * * * *
127079 AAAAAATCAACAGTTCAAGTTCATGCATTTGCCAACAACCAGACAAAATTTTCAATTTTTATAA
1 CAAAAATCAATGGTTCAAGTTCATGTATTTACCAAAAACCAGACTAAATTTTCAATATTTATAA
127143 AGTAGAAGGA
Statistics
Matches: 130, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
84 2 0.02
85 1 0.01
86 74 0.57
87 50 0.38
88 1 0.01
89 2 0.02
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (87 bp):
CAAAAATCAATGGTTCAAGTTCATGTATTTACCAAAAACCAGACTAAATTTTCAATATTTATAAC
AACTTATATGCAACAAATTAGA
Found at i:127527 original size:86 final size:86
Alignment explanation
Indices: 127376--127537 Score: 211
Period size: 86 Copynumber: 1.9 Consensus size: 86
127366 TCAACAATTT
* * * * * *
127376 ATATACAACAAATTAGCAAAAATCAATGGTTCAAGTTCATGTATTTACCAACAACGGGACTAAAT
1 ATATACAACAAATTAACAAAAATCAATGGTTCAAGTGCATGTATTCACCAAAAACGAGACCAAAT
*
127441 TTTCAATTTTTATAACAAATC
66 TTTCAAATTTTATAACAAATC
* *
127462 ATATGCAACAAATTAACAAAAATCGACT-GTTCAAGTGCATGTATTCACCAAAAAAC-AGACCAA
1 ATATACAACAAATTAACAAAAATC-AATGGTTCAAGTGCATGTATTCACC-AAAAACGAGACCAA
127525 ATTTTCAAATTTT
64 ATTTTCAAATTTT
127538 GTAAAGCAAG
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
86 58 0.89
87 7 0.11
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (86 bp):
ATATACAACAAATTAACAAAAATCAATGGTTCAAGTGCATGTATTCACCAAAAACGAGACCAAAT
TTTCAAATTTTATAACAAATC
Found at i:128096 original size:168 final size:169
Alignment explanation
Indices: 127818--128156 Score: 468
Period size: 168 Copynumber: 2.0 Consensus size: 169
127808 TTTTACATGC
* ** * * **
127818 AACAAATTAGCACAAATTAACAATTCAAGTTCATATATTCACCAAAAACCAGACTAAATTTTGAA
1 AACAAATTAGCAAAAACCAACAATTCAAGTGCATATATGCACCAAAAACCAGACTAAATTTCAAA
***
127883 TTTTTGTAAAATAAGAGGATCAAAGTCTAACAAATTAAAGTTTCCAATGAAATTCAGTCTTACAC
66 TTTTTGTAAAATAAGAGGATCAAAGTCTAACAAATTAAAGTTTCCAATGAAATTCAAAATTACAC
*
127948 CA-TTAAGTAAATAAGAGTTTTAAACTATCGGAGATCAA
131 CATTTAAGTAAATAAGAGTTTTAAACTACCGGAGATCAA
** *
127986 AACAAATTAGCAAAAACCAACTGTTCAAGTGCATGTATGCACCAAAAA-CAGGA-TCAAATTTCA
1 AACAAATTAGCAAAAACCAACAATTCAAGTGCATATATGCACCAAAAACCA-GACT-AAATTTCA
* *
128049 AATTTTTGTAAATTAAGAGGATCAAATTCTAACAAATTAAAGTTTCCAATGAAATTCAAAATTAC
64 AATTTTTGTAAAATAAGAGGATCAAAGTCTAACAAATTAAAGTTTCCAATGAAATTCAAAATTAC
* * *
128114 ATCATTTAAGTAAATAAGAGTTTTAAATTACCTGAGATCAA
129 ACCATTTAAGTAAATAAGAGTTTTAAACTACCGGAGATCAA
128155 AA
1 AA
128157 ACCCATTTTG
Statistics
Matches: 149, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
167 3 0.02
168 111 0.74
169 35 0.23
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (169 bp):
AACAAATTAGCAAAAACCAACAATTCAAGTGCATATATGCACCAAAAACCAGACTAAATTTCAAA
TTTTTGTAAAATAAGAGGATCAAAGTCTAACAAATTAAAGTTTCCAATGAAATTCAAAATTACAC
CATTTAAGTAAATAAGAGTTTTAAACTACCGGAGATCAA
Found at i:129780 original size:29 final size:30
Alignment explanation
Indices: 129727--129862 Score: 143
Period size: 30 Copynumber: 4.6 Consensus size: 30
129717 AGTTTATTTT
*
129727 AAAATTCGAATTTAACCCCTAAATTTTCCA
1 AAAATTCTAATTTAACCCCTAAATTTTCCA
* *
129757 AAAATTCTAATTTGACCCC-AAATTTTTCA
1 AAAATTCTAATTTAACCCCTAAATTTTCCA
* ** * *
129786 AAGATTCCCATTTGA-CCCTCAAACTTTCC-
1 AAAATTCTAATTTAACCCCT-AAATTTTCCA
* *
129815 AAAATTCTGATTTAACCCCTAAAGTTTCCA
1 AAAATTCTAATTTAACCCCTAAATTTTCCA
*
129845 AAAATTCAAATTTAACCC
1 AAAATTCTAATTTAACCC
129863 AATTTTAATG
Statistics
Matches: 87, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
28 3 0.03
29 40 0.46
30 44 0.51
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAATTCTAATTTAACCCCTAAATTTTCCA
Found at i:133707 original size:207 final size:199
Alignment explanation
Indices: 133340--134018 Score: 644
Period size: 207 Copynumber: 3.4 Consensus size: 199
133330 GTGAAACAAG
* * **
133340 TTAACAAACCAAGTTTACATGGCTTGATCATCTCACCATTCTAGCTTAACTTGAATCGTTACATT
1 TTAACAAACCAAG-TTACATGGCATGATCATCT-ACCATTGTAGCTTAACTCAAATCGTTACATT
* * *
133405 TAACCTGACCCAATGCCATACCCCATTCATCGGTTACATGCAACTATTCAAGTTAAACTCTAGTG
64 TAACCCGACCCAATGTCATACCCCATTCA-C-GTTACATGTAACTATTCAAGTTAAACTCTAGTG
* * * *
133470 TGTCAAATGAATA-CGACACATTATATTATATTTTAAACTAATGCGACATCATTAAATTAAGCTC
127 -GTCAAGTGAATATC-ACA-ATTACATTATATTTTAAACTAATGCCACATCATTTAATTAAGCTC
133534 AACTCATAAAA
189 AACTCATAAAA
* * *
133545 TTAAGAAACCAAGTTACATGGTATGATCATCTGACCATTGTAGCTTATTAACTCAAATCATTACA
1 TTAACAAACCAAGTTACATGGCATGATCATCT-ACCATTGTAGC---TTAACTCAAATCGTTACA
133610 TTTAACCCGACCCAATGTCATACCCCATTCACCGATTACATGTAACTATTCAAGTTAAACTCTAG
62 TTTAACCCGACCCAATGTCATACCCCATTCA-CG-TTACATGTAACTATTCAAGTTAAACTCTAG
* * ** * * *
133675 TGGGTCGAGTGAATATCACAAGTTACATTATATTTTAAACTAATGCCAAATTGTTTTATT-TGTT
125 T-GGTCAAGTGAATATCACAA-TTACATTATATTTTAAACTAATGCCACATCATTTAATTAAGCT
*
133739 GAACTCATAAAA
188 CAACTCATAAAA
* * * * * *
133751 TTGACAAACCAAGCTACATGGCATGATCATCTAGTCATTGTAGCTTAATTCGAGTCGTTACATTT
1 TTAACAAACCAAGTTACATGGCATGATCATCTA-CCATTGTAGCTTAACTCAAATCGTTACATTT
* ** * *
133816 GACCCGACCTGAT-TCATACTCCATTCAC-TT--AT-T-AC-A--C--G--CAA--CTA-T--TC
65 AACCCGACCCAATGTCATACCCCATTCACGTTACATGTAACTATTCAAGTTAAACTCTAGTGGTC
* * * *
133863 AAGTGAATATGACACCTTACATTATATTTTAAACTAATGCTACATCATTTAATTAAGCTCATCTC
130 AAGTGAATATCACA-ATTACATTATATTTTAAACTAATGCCACATCATTTAATTAAGCTCAACTC
*
133928 ATAAAG
194 ATAAAA
* **
133934 TTAATAAACCAAGTTACATGGCATGATCATCTAACCATTAAAGCTTAACTCAAATC-TATACATT
1 TTAACAAACCAAGTTACATGGCATGATCATCT-ACCATTGTAGCTTAACTCAAATCGT-TACATT
* * *
133998 TAACTCGACCCGATGTTATAC
64 TAACCCGACCCAATGTCATAC
134019 ACCACTCATA
Statistics
Matches: 397, Mismatches: 64, Indels: 47
0.78 0.13 0.09
Matches are distributed among these distances:
182 48 0.12
183 73 0.18
184 6 0.02
185 1 0.00
186 3 0.01
188 2 0.01
190 1 0.00
192 1 0.00
194 1 0.00
195 2 0.01
196 1 0.00
197 2 0.01
199 2 0.01
201 1 0.00
202 13 0.03
203 27 0.07
204 27 0.07
205 13 0.03
206 52 0.13
207 119 0.30
208 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (199 bp):
TTAACAAACCAAGTTACATGGCATGATCATCTACCATTGTAGCTTAACTCAAATCGTTACATTTA
ACCCGACCCAATGTCATACCCCATTCACGTTACATGTAACTATTCAAGTTAAACTCTAGTGGTCA
AGTGAATATCACAATTACATTATATTTTAAACTAATGCCACATCATTTAATTAAGCTCAACTCAT
AAAA
Found at i:135861 original size:31 final size:31
Alignment explanation
Indices: 135826--135886 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
135816 ATGGTCACTC
135826 AATTA-TTCAATACTGTTTATTTAAGTCATTG
1 AATTATTTCAA-ACTGTTTATTTAAGTCATTG
* * *
135857 AATTATTTGAAAGTGTTTGTTTAAGTCATT
1 AATTATTTCAAACTGTTTATTTAAGTCATT
135887 AGATTGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (31 bp):
AATTATTTCAAACTGTTTATTTAAGTCATTG
Found at i:137081 original size:12 final size:11
Alignment explanation
Indices: 137050--137082 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
137040 AAACTTTCAT
137050 AAAATATTAAA
1 AAAATATTAAA
137061 AAAA-ATTAAA
1 AAAATATTAAA
137071 AAAATACTTAAA
1 AAAATA-TTAAA
137083 TTTGTTCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 5 0.25
12 5 0.25
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAATATTAAA
Found at i:137684 original size:23 final size:23
Alignment explanation
Indices: 137632--137684 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
137622 AAAGAGATCG
* * *
137632 AAGTTAAATTGTAATTTTTACAA
1 AAGTAAAAATGTAATTTTTAAAA
*
137655 TAGTAAAAATGTAATTTTTAAAA
1 AAGTAAAAATGTAATTTTTAAAA
*
137678 AATTAAA
1 AAGTAAA
137685 TTAAAATTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40
Consensus pattern (23 bp):
AAGTAAAAATGTAATTTTTAAAA
Found at i:139671 original size:28 final size:28
Alignment explanation
Indices: 139628--139685 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
139618 AATTTAAACA
139628 AATGAGTTTAACTGCTACTACTCGAGTC
1 AATGAGTTTAACTGCTACTACTCGAGTC
* * *
139656 AATGAGTTTAATTGCTACTATTTGAGTC
1 AATGAGTTTAACTGCTACTACTCGAGTC
139684 AA
1 AA
139686 GACTGGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (28 bp):
AATGAGTTTAACTGCTACTACTCGAGTC
Found at i:141950 original size:31 final size:31
Alignment explanation
Indices: 141915--141975 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
141905 TATGCCTTTT
*
141915 TTCATGTATTCATATTATTATTATTTTCATG
1 TTCATGTATTCATATTATTATTATATTCATG
141946 TTCATGTATTCATATTATTATTATATTCAT
1 TTCATGTATTCATATTATTATTATATTCAT
141976 AATAGATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.57
Consensus pattern (31 bp):
TTCATGTATTCATATTATTATTATATTCATG
Found at i:144866 original size:21 final size:24
Alignment explanation
Indices: 144822--144876 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 24
144812 TGCATAGTAG
*
144822 GTATCGGTAGTTCTGTGTATGCTT
1 GTATCGGTAGTTCAGTGTATGCTT
144846 GTATCGGTAGTT-AG-G-ATGCTT
1 GTATCGGTAGTTCAGTGTATGCTT
144867 GTATCGGTAG
1 GTATCGGTAG
144877 AAGTTGCAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 16 0.53
22 1 0.03
23 1 0.03
24 12 0.40
ACGTcount: A:0.16, C:0.11, G:0.33, T:0.40
Consensus pattern (24 bp):
GTATCGGTAGTTCAGTGTATGCTT
Found at i:144966 original size:21 final size:21
Alignment explanation
Indices: 144942--144989 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
144932 AGACATATAT
*
144942 CGGTAGAACTGTCACTTGTAC
1 CGGTAGAACTATCACTTGTAC
* * *
144963 CGGTAAAACTATCATTTGTAT
1 CGGTAGAACTATCACTTGTAC
144984 CGGTAG
1 CGGTAG
144990 TAATCTACAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (21 bp):
CGGTAGAACTATCACTTGTAC
Found at i:146979 original size:31 final size:29
Alignment explanation
Indices: 146944--147013 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 29
146934 ACTACAAAAA
*
146944 TAGTCACTTTTATTTGACTCAG-ATTACATTT
1 TAGTCACTTATATTTGA---AGTATTACATTT
*
146975 TAGTCACTTATATTTGAAGTGTTACATTT
1 TAGTCACTTATATTTGAAGTATTACATTT
147004 TAGTCACTTA
1 TAGTCACTTA
147014 GGTTAAGGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 2 0.06
29 18 0.50
31 16 0.44
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.47
Consensus pattern (29 bp):
TAGTCACTTATATTTGAAGTATTACATTT
Found at i:162618 original size:21 final size:21
Alignment explanation
Indices: 162592--162632 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
162582 CAAAATTAAT
162592 TGAACCAAATA-AAGGCTTTCG
1 TGAACCAAA-AGAAGGCTTTCG
162613 TGAACCAAAAGAAGGCTTTC
1 TGAACCAAAAGAAGGCTTTC
162633 TTGCCAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (21 bp):
TGAACCAAAAGAAGGCTTTCG
Found at i:168742 original size:21 final size:22
Alignment explanation
Indices: 168700--168748 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
168690 ACCATATTTC
168700 AATATTAAAATATTTTAAGTTA
1 AATATTAAAATATTTTAAGTTA
* *
168722 AATATTAATAT-TTTTATGTTA
1 AATATTAAAATATTTTAAGTTA
*
168743 ATTATT
1 AATATT
168749 TTTTATAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
AATATTAAAATATTTTAAGTTA
Found at i:176357 original size:16 final size:16
Alignment explanation
Indices: 176319--176367 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
176309 TTTTTATAAA
*
176319 TTTTTTTGAAATTTGTT
1 TTTTTTTTAAATTT-TT
**
176336 GATTTTTTAAATTTTT
1 TTTTTTTTAAATTTTT
*
176352 TTTTTTTTCAATTTTT
1 TTTTTTTTAAATTTTT
176368 ATGAATTATG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.73
Consensus pattern (16 bp):
TTTTTTTTAAATTTTT
Found at i:176838 original size:48 final size:48
Alignment explanation
Indices: 176786--176880 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
176776 TGGTGGAGGA
*
176786 CCAAGATTTCTAAATTAGAAAAAAATTTAAGAACTTAATGTCTCAAAT
1 CCAAGATTTCTAAATTAGAAAAAAATTCAAGAACTTAATGTCTCAAAT
*
176834 CCAAGATTTCTAAATTAGAAAAAAGTTCAAGAACTTAATGTCTCAAA
1 CCAAGATTTCTAAATTAGAAAAAAATTCAAGAACTTAATGTCTCAAA
176881 AATTAACAGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.29
Consensus pattern (48 bp):
CCAAGATTTCTAAATTAGAAAAAAATTCAAGAACTTAATGTCTCAAAT
Found at i:189883 original size:22 final size:22
Alignment explanation
Indices: 189855--189898 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
189845 CCATCAATAT
189855 ATACATTAAATGTGATTTTGAA
1 ATACATTAAATGTGATTTTGAA
189877 ATACATTAAATGTGATTTTGAA
1 ATACATTAAATGTGATTTTGAA
189899 TAAGATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (22 bp):
ATACATTAAATGTGATTTTGAA
Found at i:191078 original size:2 final size:2
Alignment explanation
Indices: 191073--191104 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
191063 AAAATCCAAA
191073 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
191105 GGAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:193705 original size:35 final size:35
Alignment explanation
Indices: 193659--193738 Score: 151
Period size: 35 Copynumber: 2.3 Consensus size: 35
193649 TAACCTTTGT
193659 TCATGTTTGTTTGTGTTTGTTAAGGGTTTCAATGC
1 TCATGTTTGTTTGTGTTTGTTAAGGGTTTCAATGC
*
193694 TCATGTTTGTTTGTGTTTGTTAAGGGTTTCAATGT
1 TCATGTTTGTTTGTGTTTGTTAAGGGTTTCAATGC
193729 TCATGTTTGT
1 TCATGTTTGT
193739 GTATTTAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.14, C:0.07, G:0.25, T:0.54
Consensus pattern (35 bp):
TCATGTTTGTTTGTGTTTGTTAAGGGTTTCAATGC
Found at i:194756 original size:14 final size:15
Alignment explanation
Indices: 194734--194764 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
194724 TCTAATAATG
194734 TAACTAAAATAAATT
1 TAACTAAAATAAATT
194749 TAAC-AAAATAAATT
1 TAACTAAAATAAATT
194763 TA
1 TA
194765 TCATTGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (15 bp):
TAACTAAAATAAATT
Found at i:195758 original size:233 final size:233
Alignment explanation
Indices: 195351--195823 Score: 732
Period size: 233 Copynumber: 2.0 Consensus size: 233
195341 TTAAAATTGT
** *
195351 TACATCTCATACAAGTAGTAGTATACATCTATTACAAAATTGTCCGATAAATGCAGGTAAGATTA
1 TACATCTCATACAAGTAGTAGTATACATCTATTACAAAATCATCCGATAAATGCAGGAAAGATTA
* * *
195416 CCCGGACACACTCGAACTCGGAGTATGGATTCTTACCCTATTATGCCTAAAATTAGGCTGAGAAG
66 CCCGGACACACTCGAAATCAGAGTATGGATTCTTACCCTATTATGCCTAAAATTAGGCCGAGAAG
195481 CAATAGTCCGAGCACTTACTCAAACAAGATACCTACTAGAACTACCACAACAAAGGTACTAAATG
131 CAATAGTCCGAGCACTTACTCAAACAAGATACCTACTAGAACTACCACAACAAAGGTACTAAATG
* * * * *
195546 CTTTGAGGAACCCGAAAATAAACACTGAAGTAGTAGTA
196 CATCGAGAAACCCAAAAATAAAAACTGAAGTAGTAGTA
* * ** *
195584 TACATCTCATACGATTAGTAGTATATTTCTATTACAAAATCATTCGATAAATGCAGGAAAGATTA
1 TACATCTCATACAAGTAGTAGTATACATCTATTACAAAATCATCCGATAAATGCAGGAAAGATTA
* *
195649 CCCGGAGACACTCGAAATCAGAGTATGGATTCTTACGCTATTATGCCTAAAATT-GGACCGAGAA
66 CCCGGACACACTCGAAATCAGAGTATGGATTCTTACCCTATTATGCCTAAAATTAGG-CCGAGAA
* * *
195713 GCAGTAGTCCGAGCGCTTACTCAAACAAGATACCTACTAGAACTACTACAACAAAGGTACTAAAT
130 GCAATAGTCCGAGCACTTACTCAAACAAGATACCTACTAGAACTACCACAACAAAGGTACTAAAT
*
195778 GCATCGAGAAACCCAAAAATAAAAACTGAAGTGGTAGTA
195 GCATCGAGAAACCCAAAAATAAAAACTGAAGTAGTAGTA
195817 TACATCT
1 TACATCT
195824 ATTACAAAAT
Statistics
Matches: 217, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
232 2 0.01
233 215 0.99
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (233 bp):
TACATCTCATACAAGTAGTAGTATACATCTATTACAAAATCATCCGATAAATGCAGGAAAGATTA
CCCGGACACACTCGAAATCAGAGTATGGATTCTTACCCTATTATGCCTAAAATTAGGCCGAGAAG
CAATAGTCCGAGCACTTACTCAAACAAGATACCTACTAGAACTACCACAACAAAGGTACTAAATG
CATCGAGAAACCCAAAAATAAAAACTGAAGTAGTAGTA
Done.