Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008288.1 Kokia drynarioides strain JFW-HI SEQ_122953, 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: 103805
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:2300 original size:15 final size:14
Alignment explanation
Indices: 2276--2312 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
2266 TTGTTTAATT
2276 AAAAAT-AATTTTCG
1 AAAAATGAATTTT-G
2290 AAAAATGAATTTTG
1 AAAAATGAATTTTG
2304 AAAAATGAA
1 AAAAATGAA
2313 AAAACTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.57, C:0.03, G:0.11, T:0.30
Consensus pattern (14 bp):
AAAAATGAATTTTG
Found at i:22617 original size:106 final size:106
Alignment explanation
Indices: 22432--22642 Score: 422
Period size: 106 Copynumber: 2.0 Consensus size: 106
22422 CTAGTTTGGT
22432 TCAGTTTAAACAGCATTGCAAAAAACAAAAAAACATTGTTGAAACTTAACCCCACTTAGTCACTT
1 TCAGTTTAAACAGCATTGCAAAAAACAAAAAAACATTGTTGAAACTTAACCCCACTTAGTCACTT
22497 CAGGTGTCATATATCAAACCTTAAATCTGCATTTAAATCCG
66 CAGGTGTCATATATCAAACCTTAAATCTGCATTTAAATCCG
22538 TCAGTTTAAACAGCATTGCAAAAAACAAAAAAACATTGTTGAAACTTAACCCCACTTAGTCACTT
1 TCAGTTTAAACAGCATTGCAAAAAACAAAAAAACATTGTTGAAACTTAACCCCACTTAGTCACTT
22603 CAGGTGTCATATATCAAACCTTAAATCTGCATTTAAATCC
66 CAGGTGTCATATATCAAACCTTAAATCTGCATTTAAATCC
22643 CAAATCAAGT
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 105 1.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (106 bp):
TCAGTTTAAACAGCATTGCAAAAAACAAAAAAACATTGTTGAAACTTAACCCCACTTAGTCACTT
CAGGTGTCATATATCAAACCTTAAATCTGCATTTAAATCCG
Found at i:24432 original size:15 final size:15
Alignment explanation
Indices: 24412--24443 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
24402 AAAACTTCTT
*
24412 AAAAAACAAAACCAA
1 AAAAAAAAAAACCAA
24427 AAAAAAAAAAACCAA
1 AAAAAAAAAAACCAA
24442 AA
1 AA
24444 CTTTACTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAACCAA
Found at i:25282 original size:235 final size:235
Alignment explanation
Indices: 24871--25708 Score: 1053
Period size: 235 Copynumber: 3.7 Consensus size: 235
24861 ACAAAGATAT
* * * * *
24871 ATTTTAAATTACAACCAGCAACTTTAGGCCTCAGATTTGTAACTTTTAATTTCATCAGACTGAAG
1 ATTTTAAGTTACGACCAGAAACTTTAGGCCTCAGATTTGTAAGTTTTAATCTCATCAGACTGAAG
* * *
24936 GTCTGACAATGTAGGCAATTCTTAATCATCATGAGCCTCTTAAATCCGTAGATTCATTAATAGTT
66 GTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCTTAAATCAGTAGATTCATTAATAATT
** ** *
25001 ACATCACTCAAAACAAAGCCATATACAGGCTACTCACAAGTTTTAACATAGGGAGAAAACAGTTG
131 ACATCACTCAAAACAAAGCCATATACAAACTACTTGCATGTTTTAACATAGGGAGAAAACAGTTG
*
25066 GTCCATGCCCAACAAGCATGACCACCACCATCACAATTAA
196 GTCCATGCCCAACAAGCATGACCACCACCATCACAAATAA
*
25106 ATTTTAAGTTAGGACCAGAAACTTTAGGCCTCAGATTTGTAAGTTTTAATCTCATCAGACTGAAG
1 ATTTTAAGTTACGACCAGAAACTTTAGGCCTCAGATTTGTAAGTTTTAATCTCATCAGACTGAAG
* * *
25171 GTCTGACAATGTAGGCAATTCTTAATCATCATGAGCCTCTTATATCAGTAGATTCATTAATAGTT
66 GTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCTTAAATCAGTAGATTCATTAATAATT
*
25236 ACATCACTCAAAACAAAGCCATATACAAACCACTTGCATGTTTTAACA-A-GGAGAAAACAGTTG
131 ACATCACTCAAAACAAAGCCATATACAAACTACTTGCATGTTTTAACATAGGGAGAAAACAGTTG
*
25299 GACCATGCCCAACAAGCATGACCACCACCATCACAAATAA
196 GTCCATGCCCAACAAGCATGACCACCACCATCACAAATAA
* *
25339 CTTTTAAGTTACAACCAGAAACTTTAGGCCTCAGATTTGTAAGTTTTAATCTCATCAGACTGAAG
1 ATTTTAAGTTACGACCAGAAACTTTAGGCCTCAGATTTGTAAGTTTTAATCTCATCAGACTGAAG
* * * *
25404 ATCTGACAATGTAAGCAATTCTTAATCATCATAAGCCTCTAAAAGCA-TAGATTCATTAATAATT
66 GTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCTTAAATCAGTAGATTCATTAATAATT
* * ** * *
25468 ACATCACTCAAAACAAAGCTATATACAGAA-TACATGCATGTTTTAATGTAGGGAGAAAATGAAA
131 ACATCACTCAAAACAAAGCCATATACA-AACTACTTGCATGTTTTAACATAGGGAGAAAA--CAG
25532 TTGGT---TG--------G--T-----CCACCATCACAAATAA
193 TTGGTCCATGCCCAACAAGCATGACCACCACCATCACAAATAA
* * * * * *
25557 GTTTTAAGTTATGATCAGCAACTTTAGGCCTCAGATTTGTAA-TTTCTATTTTCATCAGACT-AT
1 ATTTTAAGTTACGACCAGAAACTTTAGGCCTCAGATTTGTAAGTTT-TAATCTCATCAGACTGA-
** * * *
25620 AGGTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTC-TAAAAGAATAG-GTCCTTCAATA
64 AGGTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCTTAAATCAGTAGATTCATT-AATA
25683 ATTACATCACTCAAAACAAAGCCATA
128 ATTACATCACTCAAAACAAAGCCATA
25709 CACAGAGTAC
Statistics
Matches: 545, Mismatches: 49, Indels: 35
0.87 0.08 0.06
Matches are distributed among these distances:
217 12 0.02
218 137 0.25
223 1 0.00
225 1 0.00
232 56 0.10
233 160 0.29
234 9 0.02
235 164 0.30
236 5 0.01
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (235 bp):
ATTTTAAGTTACGACCAGAAACTTTAGGCCTCAGATTTGTAAGTTTTAATCTCATCAGACTGAAG
GTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCTTAAATCAGTAGATTCATTAATAATT
ACATCACTCAAAACAAAGCCATATACAAACTACTTGCATGTTTTAACATAGGGAGAAAACAGTTG
GTCCATGCCCAACAAGCATGACCACCACCATCACAAATAA
Found at i:25701 original size:218 final size:211
Alignment explanation
Indices: 25323--25926 Score: 762
Period size: 218 Copynumber: 2.8 Consensus size: 211
25313 AGCATGACCA
* * * *
25323 CCACCATCACAAATAACTTTTAAGTTACAACCAGAAACTTTAGGCCTCAGATTTGTAAGTTTTAA
1 CCACCATCACAAATAAGTTTTAAGTTACGATCAGAAACTTTAGGCCTCAGATTTGTAA-TTTTAT
* *
25388 TCTCATCAGACTGAAGATCTGACAATGTAAGCAATTCTTAATCATCATAAGCCTCTAAAAGCATA
65 TCTCATCAGACTGAAGGTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCTAAAAGCATA
* *
25453 GATTCATTAATAATTACATCACTCAAAACAAAGCTATATACAGAATACATGCATGTTTTAATGTA
130 GA-TCCTTAATAATTACATCACTCAAAACAAAGCTATATACAGAATACATGCATG-----ATATA
* * *
25518 GGGAGAAAATGAAATTGGTTGGT
189 AGGAGAAAAAGAAATTAGTTGGT
* *
25541 CCACCATCACAAATAAGTTTTAAGTTATGATCAGCAACTTTAGGCCTCAGATTTGTAATTTCTAT
1 CCACCATCACAAATAAGTTTTAAGTTACGATCAGAAACTTTAGGCCTCAGATTTGTAATTT-TAT
* *
25606 TTTCATCAGACT-ATAGGTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCTAAAAGAAT
65 TCTCATCAGACTGA-AGGTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCTAAAAGCAT
* * * *
25670 AGGTCCTTCAATAATTACATCACTCAAAACAAAGCCATACACAGAGTACATGCATGATATAAGGA
129 AGATCCTT-AATAATTACATCACTCAAAACAAAGCTATATACAGAATACATGCATGATATAAGGA
25735 GAAAAAGAAATTAGTTGGT
193 GAAAAAGAAATTAGTTGGT
* * *** * *
25754 CCACCAACAAAAAATAAGTTTTTAAGTTACGATCATTGATTTTAGGCCTCAGATTTGTAGTTTTT
1 CCACCATC-ACAAATAAG-TTTTAAGTTACGATCAGAAACTTTAGGCCTCAGATTTGTA-ATTTT
* * *
25819 GTTGTCATCAAACTGAAGGTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCTAAAAAGC
63 ATTCTCATCAGACTGAAGGTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCT-AAAAGC
* * *
25884 ATAGATTCTTTACA-AATTACATCACTCAAAACAATGATATATA
127 ATAGA-TCCTTA-ATAATTACATCACTCAAAACAAAGCTATATA
25927 TAAGCACCCA
Statistics
Matches: 339, Mismatches: 37, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
213 31 0.09
214 8 0.02
215 89 0.26
216 39 0.12
217 13 0.04
218 159 0.47
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (211 bp):
CCACCATCACAAATAAGTTTTAAGTTACGATCAGAAACTTTAGGCCTCAGATTTGTAATTTTATT
CTCATCAGACTGAAGGTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCTAAAAGCATAG
ATCCTTAATAATTACATCACTCAAAACAAAGCTATATACAGAATACATGCATGATATAAGGAGAA
AAAGAAATTAGTTGGT
Found at i:28669 original size:14 final size:14
Alignment explanation
Indices: 28650--28676 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28640 CATGACTCAA
28650 ATTTTGTTGTTATT
1 ATTTTGTTGTTATT
28664 ATTTTGTTGTTAT
1 ATTTTGTTGTTAT
28677 CGTTTGGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (14 bp):
ATTTTGTTGTTATT
Found at i:29209 original size:29 final size:31
Alignment explanation
Indices: 29148--29232 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 31
29138 AGATAAATCT
*
29148 TAAAATTATATATG-AA-TTTAATTTTGTATA
1 TAAATTTATATATGAAATTTTAATTTTG-ATA
29178 TAAATTTATATA-GAAATTTTAATTTTG-TA
1 TAAATTTATATATGAAATTTTAATTTTGATA
* * *
29207 TAATTTTATATATAAAATTTTGATTT
1 TAAATTTATATATGAAATTTTAATTT
29233 AATTCAATTC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.29
30 24 0.50
31 10 0.21
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (31 bp):
TAAATTTATATATGAAATTTTAATTTTGATA
Found at i:29219 original size:31 final size:32
Alignment explanation
Indices: 29150--29232 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 32
29140 ATAAATCTTA
29150 AAATTATATAT-G-AA-TTTAATTTTGTATAT
1 AAATTATATATAGAAATTTTAATTTTGTATAT
29179 AAATT-TATATAGAAATTTTAATTTTGTATA-
1 AAATTATATATAGAAATTTTAATTTTGTATAT
** *
29209 ATTTTATATATA-AAATTTTGATTT
1 AAATTATATATAGAAATTTTAATTT
29233 AATTCAATTC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
28 5 0.11
29 6 0.13
30 16 0.34
31 20 0.43
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (32 bp):
AAATTATATATAGAAATTTTAATTTTGTATAT
Found at i:31334 original size:3 final size:3
Alignment explanation
Indices: 31321--31350 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
31311 TAATCATGCT
31321 TGA TGGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA T-GA TGA TGA TGA TGA TGA TGA TGA TG
31351 GATTATTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:33884 original size:22 final size:23
Alignment explanation
Indices: 33856--33899 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
33846 TTTCTAAAAT
*
33856 TTAAAATATT-TTACTTAAGTTC
1 TTAAAATATTATTAATTAAGTTC
33878 TTAAAATATTATTAATTAAGTT
1 TTAAAATATTATTAATTAAGTT
33900 TTTTCCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (23 bp):
TTAAAATATTATTAATTAAGTTC
Found at i:37380 original size:35 final size:35
Alignment explanation
Indices: 37316--37383 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
37306 GGTAAAGTTA
*
37316 GTATATTCTCTTATTTTGTGCACTGTGATCCTACT
1 GTATATTCTCTTATTCTGTGCACTGTGATCCTACT
* * * *
37351 GTATATTGTCTTCTTCTGTTCACTTTGATCCTA
1 GTATATTCTCTTATTCTGTGCACTGTGATCCTA
37384 GCGCTATAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.16, C:0.21, G:0.13, T:0.50
Consensus pattern (35 bp):
GTATATTCTCTTATTCTGTGCACTGTGATCCTACT
Found at i:42769 original size:27 final size:26
Alignment explanation
Indices: 42720--42770 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
42710 TTTTTAAATT
* *
42720 AAAAATAAAATTATACTTTAATCCCC
1 AAAAATAAAATTATAATTAAATCCCC
*
42746 AAAATATAAAATTTTAATTAAATCC
1 AAAA-ATAAAATTATAATTAAATCC
42771 TTTTAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAAATAAAATTATAATTAAATCCCC
Found at i:48581 original size:228 final size:230
Alignment explanation
Indices: 48070--48581 Score: 631
Period size: 228 Copynumber: 2.2 Consensus size: 230
48060 ATTCACTCTC
*
48070 AATTTTTCATCAATAATTTAACAGCAAAATTATAAAATAAGAAAAAGAATTTAACTTGGCAGACA
1 AATTTTTCATCAATAATTTAACAGCAAAATTATAAAATAAGAAAAA-AATTTAA----GCAAACA
* * * **
48135 AGAACTTGATTATATGATCATGCAAGCACAAGATTAGATTAAAACAAGAGATTAAGTTGCCTCAA
61 AGAACTTAATTATATGATCATGCAAACACAAGATTAGATTAAAACAAGAGATTAAATCACCTCAA
* ** *
48200 AGTCCTCTAATTTCATCTAACACTACAAGTTTAAAGCAGTGATCAACATGAAACAATATAACAAA
126 AGTCATCTAATTTCATAAAACACTACAAGTTTAAAGCAGTGATCAACATGAAACAACATAACAAA
* * * * *
48265 GAATTCTCAACAACTGTTCATCTTTTCTTTTCCCTGATCA
191 AAATTCTCAACAACTATTCAGCTTCTCTTTTCACTGATCA
* * * *
48305 AA-TTTTCATCAATAATTTAACATCAAAACTATCAAACAAAAAAAAAAAATTT-A-CAAACAA-A
1 AATTTTTCATCAATAATTTAACAGCAAAATTAT-AAA-ATAAGAAAAAAATTTAAGCAAACAAGA
* *
48366 ACTTAATTATTTGATCATGCAAACACAAGATTCA-ATTAAAACAATAGATTAAATCACCTCAAAG
64 ACTTAATTATATGATCATGCAAACACAAGATT-AGATTAAAACAAGAGATTAAATCACCTCAAAG
* * * *
48430 TCATTTAATTTCATAAAACACTACGAGTTTAAAGCAGTGATCCACATGAAACAACATAATTAAAA
128 TCATCTAATTTCATAAAACACTACAAGTTTAAAGCAGTGATCAACATGAAACAACATAA-CAAAA
* * *
48495 AATTTTCAACAATTATTCAGCTTCTCTTTTTACTGAT-A
192 AATTCTCAACAACTATTCAGCTTCTCTTTTCACTGATCA
*
48533 AATTTTTCATCAATAATTTAACAGCAAAATTATTAAATAAGGAAAAAAA
1 AATTTTTCATCAATAATTTAACAGCAAAATTATAAAATAA-GAAAAAAA
48582 ATAACTTGAC
Statistics
Matches: 238, Mismatches: 33, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
227 3 0.01
228 120 0.50
229 68 0.29
234 29 0.12
235 10 0.04
236 8 0.03
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (230 bp):
AATTTTTCATCAATAATTTAACAGCAAAATTATAAAATAAGAAAAAAATTTAAGCAAACAAGAAC
TTAATTATATGATCATGCAAACACAAGATTAGATTAAAACAAGAGATTAAATCACCTCAAAGTCA
TCTAATTTCATAAAACACTACAAGTTTAAAGCAGTGATCAACATGAAACAACATAACAAAAAATT
CTCAACAACTATTCAGCTTCTCTTTTCACTGATCA
Found at i:48802 original size:210 final size:210
Alignment explanation
Indices: 48400--49040 Score: 600
Period size: 210 Copynumber: 2.9 Consensus size: 210
48390 ACAAGATTCA
* ** * ** * * *
48400 ATTAAAACAATAGATTAAATCACCTCAAAGTCATTTAATTTCATAAAACACTACGAGTTTAAAGC
1 ATTAAAACAAGAGATTAAATTGCCTCAAAGTCATCTAATTTCATCTAGCACTACTAATTTAAAGC
* * * * * *
48465 AGTGATCCA-CATGAAACAACATAATTAAAAAATTTTCAACAATTATTCAGCTTCTCTTTTTACT
66 AGTGAT-CAGCATGAAACAACGTAATT-AAAAATTTTCTACAATTATTCATCTTTTCATTTTCCT
* ** * * ** *
48529 GATAAATTTTTCATCAATAATTTAACAGCAAAATTATT-AAATAA-GGAAAAAAAATAACTTGAC
129 -AT-CATTTTTTTTCAATAA-TAAACAGC-AAATTTTTCAAATAAGGGGGAAAAAA-ACCTTGAC
*
48592 AAACAAAACTT-GGGT-T-C-G
189 AAACAAAACTTAGGATATACAG
* *
48610 ATTAAAATAAGAGATTAAATTGCCTCAAAGTTATCTAATTTCATCTAGCACTACTAATTTAAAGC
1 ATTAAAACAAGAGATTAAATTGCCTCAAAGTCATCTAATTTCATCTAGCACTACTAATTTAAAGC
* *
48675 AGTGATCAGCATGAAACAACGTAATTGAAAATTTTTCTACAATTATTAATCTTTTCATTTTCCTA
66 AGTGATCAGCATGAAACAACGTAATT-AAAAATTTTCTACAATTATTCATCTTTTCATTTTCCT-
*
48740 ATCATTTTTTTTCAATAATGGAACCA-CAAATTTTTCAAATAAGGGGGAAAAAGAACCTTGACAA
129 ATCATTTTTTTTCAATAAT--AAACAGCAAATTTTTCAAATAAGGGGGAAAAA-AACCTTGACAA
*
48804 ACAAAACTCGATTACATGATAATACAAACACAAG
191 ACAAAA--C--TT--AGGAT-AT------AC-AG
48838 ATTAGATCAAAACAAGAGATTAAATTGCCTCAAAGTCATCTAATTTCATCTAGCACTACTAATTT
1 A-T---T-AAAACAAGAGATTAAATTGCCTCAAAGTCATCTAATTTCATCTAGCACTACTAATTT
*
48903 AAAGCAGTGATCTGCATGAAACAACGTAATTAAAGAATTTTCTACAATTATTCATC-TTTCATTT
61 AAAGCAGTGATCAGCATGAAACAACGTAATTAAA-AATTTTCTACAATTATTCATCTTTTCATTT
* * * *
48967 TCCTATCATTTTTTTCCAATAATAAAACATCAAATTTATCAAATAAGGGGG-AAAAAACTTTGAC
125 TCCTATCATTTTTTTTCAATAAT-AAACAGCAAATTTTTCAAATAAGGGGGAAAAAAACCTTGAC
49031 AAACAAAACT
189 AAACAAAACT
49041 CGATTACATG
Statistics
Matches: 358, Mismatches: 42, Indels: 47
0.80 0.09 0.11
Matches are distributed among these distances:
208 8 0.02
209 22 0.06
210 133 0.37
211 1 0.00
212 1 0.00
214 2 0.01
217 2 0.01
219 1 0.00
225 1 0.00
226 1 0.00
227 1 0.00
228 2 0.01
229 17 0.05
230 8 0.02
231 38 0.11
232 16 0.04
233 104 0.29
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (210 bp):
ATTAAAACAAGAGATTAAATTGCCTCAAAGTCATCTAATTTCATCTAGCACTACTAATTTAAAGC
AGTGATCAGCATGAAACAACGTAATTAAAAATTTTCTACAATTATTCATCTTTTCATTTTCCTAT
CATTTTTTTTCAATAATAAACAGCAAATTTTTCAAATAAGGGGGAAAAAAACCTTGACAAACAAA
ACTTAGGATATACAG
Found at i:49084 original size:233 final size:233
Alignment explanation
Indices: 48613--49113 Score: 773
Period size: 233 Copynumber: 2.2 Consensus size: 233
48603 GGGTTCGATT
* *
48613 AAAATAAGAGATTAAATTGCCTCAAAGTTATCTAATTTCATCTAGCACTACTAATTTAAAGCAGT
1 AAAACAAGAGATTAAATTGCCTCAAAGTCATCTAATTTCATCTAGCACTACTAATTTAAAGCAGT
*
48678 GATCAGCATGAAACAACGTAATTGAAAATTTTTCTACAATTATTAATCTTTTCATTTTCCTAATC
66 GATCAGCATGAAACAACGTAATTGAAAAATTTTCTACAATTATTAATCTTTTCATTTTCCTAATC
* * * *
48743 ATTTTTTTTCAATAATGGAACCACAAATTTTTCAAATAAGGGGGAAAAAGAACCTTGACAAACAA
131 ATTTTTTTCCAATAATGAAAACACAAATTTATCAAATAAGGGGGAAAAAGAACCTTGACAAACAA
48808 AACTCGATTACATGATAATACAAACACAAGATTAGATC
196 AACTCGATTACATGATAATACAAACACAAGATTAGATC
48846 AAAACAAGAGATTAAATTGCCTCAAAGTCATCTAATTTCATCTAGCACTACTAATTTAAAGCAGT
1 AAAACAAGAGATTAAATTGCCTCAAAGTCATCTAATTTCATCTAGCACTACTAATTTAAAGCAGT
* *
48911 GATCTGCATGAAACAACGTAATT-AAAGAATTTTCTACAATTATTCATC-TTTCATTTTCCT-AT
66 GATCAGCATGAAACAACGTAATTGAAA-AATTTTCTACAATTATTAATCTTTTCATTTTCCTAAT
*
48973 CATTTTTTTCCAATAAT-AAAACATCAAATTTATCAAATAAGGGGG-AAAA-AACTTTGACAAAC
130 CATTTTTTTCCAATAATGAAAACA-CAAATTTATCAAATAAGGGGGAAAAAGAACCTTGACAAAC
* * *
49035 AAAACTCGATTACATGATCATGCAAACACAAGATTCGAT-
194 AAAACTCGATTACATGATAATACAAACACAAGATTAGATC
* * * * *
49074 TAAACAAAACATTAAACTGCCTCAAATTCATCTAATTTCA
1 AAAACAAGAGATTAAATTGCCTCAAAGTCATCTAATTTCA
49114 CCGAATACAA
Statistics
Matches: 248, Mismatches: 18, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
228 35 0.14
229 48 0.19
230 8 0.03
231 38 0.15
232 15 0.06
233 104 0.42
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (233 bp):
AAAACAAGAGATTAAATTGCCTCAAAGTCATCTAATTTCATCTAGCACTACTAATTTAAAGCAGT
GATCAGCATGAAACAACGTAATTGAAAAATTTTCTACAATTATTAATCTTTTCATTTTCCTAATC
ATTTTTTTCCAATAATGAAAACACAAATTTATCAAATAAGGGGGAAAAAGAACCTTGACAAACAA
AACTCGATTACATGATAATACAAACACAAGATTAGATC
Found at i:50101 original size:29 final size:30
Alignment explanation
Indices: 50037--50103 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
50027 ATTTGACTTT
*
50037 ATTTGATTCATTTTAATAGTATAAGGACTA
1 ATTTGATCCATTTTAATAGTATAAGGACTA
* *
50067 AATTGATCCA-TTTAATGGTA-AAGGGACTA
1 ATTTGATCCATTTTAATAGTATAA-GGACTA
*
50096 GTTTGATC
1 ATTTGATC
50104 AGATCTTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 2 0.06
29 21 0.68
30 8 0.26
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (30 bp):
ATTTGATCCATTTTAATAGTATAAGGACTA
Found at i:50857 original size:13 final size:13
Alignment explanation
Indices: 50839--50864 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50829 TGTTTTAACC
50839 AAAAACAAATAAA
1 AAAAACAAATAAA
50852 AAAAACAAATAAA
1 AAAAACAAATAAA
50865 TTTAAATCCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAAACAAATAAA
Found at i:63700 original size:11 final size:11
Alignment explanation
Indices: 63686--63756 Score: 63
Period size: 11 Copynumber: 6.1 Consensus size: 11
63676 TAAATACTTC
*
63686 TAAAATAATAG
1 TAAAATAATAA
63697 TAAAATTAATAA
1 TAAAA-TAATAA
63709 TAAAATAATAA
1 TAAAATAATAA
*
63720 TTATACAATATTCAA
1 -TA-A-AATAAT-AA
*
63735 -ATAATAATAA
1 TAAAATAATAA
63745 TAAAATAATAA
1 TAAAATAATAA
63756 T
1 T
63757 TTTATGATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
10 2 0.04
11 26 0.53
12 12 0.24
13 2 0.04
14 5 0.10
15 2 0.04
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:70294 original size:29 final size:30
Alignment explanation
Indices: 70257--70316 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
70247 TTATCGTTTT
70257 AAATAAAAAATAAAA-TAATTAAATTAATAA
1 AAATAAAAAATAAAAGTAATTAAATT-ATAA
*
70287 AAAT-AAAAATAAAAGTGATTAAATTATAA
1 AAATAAAAAATAAAAGTAATTAAATTATAA
70316 A
1 A
70317 TGTAGGAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (30 bp):
AAATAAAAAATAAAAGTAATTAAATTATAA
Found at i:73847 original size:17 final size:16
Alignment explanation
Indices: 73814--73862 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
73804 TACATTTGTG
*
73814 AATAAATAATTTTAAAA
1 AATAAA-AATTTCAAAA
73831 ATATAAAAATTTCAAAA
1 A-ATAAAAATTTCAAAA
*
73848 AATTAAAATTTCAAA
1 AATAAAAATTTCAAA
73863 TCAAATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 13 0.45
17 11 0.38
18 5 0.17
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAAAATTTCAAAA
Found at i:73881 original size:21 final size:21
Alignment explanation
Indices: 73842--73881 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
73832 TATAAAAATT
73842 TCAAAAAATTAAAATTTCAAA
1 TCAAAAAATTAAAATTTCAAA
*
73863 TCAAATAA-TAAAATATTCA
1 TCAAAAAATTAAAAT-TTCA
73882 TAAAAATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (21 bp):
TCAAAAAATTAAAATTTCAAA
Found at i:77471 original size:17 final size:18
Alignment explanation
Indices: 77435--77488 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 18
77425 TTGTGTATTT
* *
77435 AAAAGTTATTTTTAAAAC
1 AAAAGTAATATTTAAAAC
77453 AAAAGTAATATTTAAACAAC
1 AAAAGTAATATTT-AA-AAC
*
77473 AAAAATAATATTTAAA
1 AAAAGTAATATTTAAA
77489 CTATCGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 12 0.39
19 4 0.13
20 15 0.48
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (18 bp):
AAAAGTAATATTTAAAAC
Found at i:77473 original size:20 final size:20
Alignment explanation
Indices: 77450--77489 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
77440 TTATTTTTAA
*
77450 AACAAAAGTAATATTTAAAC
1 AACAAAAATAATATTTAAAC
77470 AACAAAAATAATATTTAAAC
1 AACAAAAATAATATTTAAAC
77490 TATCGATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.25
Consensus pattern (20 bp):
AACAAAAATAATATTTAAAC
Found at i:78075 original size:2 final size:2
Alignment explanation
Indices: 78068--78103 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
78058 TTCTTGCTGC
78068 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78104 GCATGCATGC
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):
AT
Found at i:80090 original size:29 final size:30
Alignment explanation
Indices: 80009--80097 Score: 83
Period size: 31 Copynumber: 3.0 Consensus size: 30
79999 GATTAAATCA
* * *
80009 AAATTAAAGTTTCA-AGTATACATTTGAACT
1 AAATTAAAGTTTCATA-TATACAATTGCACC
* * * *
80039 ACAATTAGAGTTTCATGTGTACAGTTGCACC
1 A-AATTAAAGTTTCATATATACAATTGCACC
80070 AAATTAAAG-TTCATATATACAATTGCAC
1 AAATTAAAGTTTCATATATACAATTGCAC
80098 GTTAAATCAA
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
29 16 0.34
30 8 0.17
31 23 0.49
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (30 bp):
AAATTAAAGTTTCATATATACAATTGCACC
Found at i:88605 original size:24 final size:24
Alignment explanation
Indices: 88571--88627 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
88561 AAACAAGATG
88571 AAGATTGTAAGGCTAGTGTATTGC
1 AAGATTGTAAGGCTAGTGTATTGC
* *
88595 ACGATTGTAAGGCTAGTGTATTGG
1 AAGATTGTAAGGCTAGTGTATTGC
88619 AAGATTGTA
1 AAGATTGTA
88628 CTCTTCCTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (24 bp):
AAGATTGTAAGGCTAGTGTATTGC
Found at i:95743 original size:223 final size:223
Alignment explanation
Indices: 95348--95789 Score: 699
Period size: 223 Copynumber: 2.0 Consensus size: 223
95338 AGGAACTAGT
** *
95348 ATTTATTTCTTAGAGACTGAAAAGTTTATTTCATTCTTTGCAGATTCTTCAAAATCAAGTTCTGG
1 ATTTATTTCTTAGAGACTGAAAAGTTTATTTCATTCTTTGCAGAAACTTCAAAATCAACTTCTGG
* * *
95413 ACATTTCAACAGAAAGGGATGAACTAAAGACACAAATCGAGGAACTGACTAGCAAATTATCCTTC
66 ACATATCAACAGAAAGGGATAAACTAAAGACACAAATCGAGGAACTGACTAGCAAATTATCCTGC
*
95478 CTCGAAAAGGAAAATCTTAAAAACGATTCTAATGATATGGTTGGCTGTTTATAAAAATGAC-CCT
131 CTCGAAAAGGAAAATCTTAAAAACGATTCTAATGACATGGTTGGCTGTTTA-AAAAATGACTCCT
95542 TTTTAGCTAACAATCTAACTAGGTTGAGA
195 TTTTAGCTAACAATCTAACTAGGTTGAGA
95571 ATTTATTTCTTAGAGACTGAAAAGTTTATTTCATTCTTTGCAGAAACTT-AAAGATCAACTTCTG
1 ATTTATTTCTTAGAGACTGAAAAGTTTATTTCATTCTTTGCAGAAACTTCAAA-ATCAACTTCTG
*
95635 GACATATCAACAGAAAGGGATAAACTAAAGACACAAATCGAGGAACTGACTAGCAGATTATCCTG
65 GACATATCAACAGAAAGGGATAAACTAAAGACACAAATCGAGGAACTGACTAGCAAATTATCCTG
* ** * * **
95700 CTTCGAAGCGGAAAATCTTAAAAATGATTCTAATGACATGGTTGGTTGTTTAAAAAATGACTTTT
130 CCTCGAAAAGGAAAATCTTAAAAACGATTCTAATGACATGGTTGGCTGTTTAAAAAATGACTCCT
* *
95765 TTTTGGCTAGCAATCTAACTAGGTT
195 TTTTAGCTAACAATCTAACTAGGTT
95790 AGGAATTATC
Statistics
Matches: 200, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
222 12 0.06
223 188 0.94
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (223 bp):
ATTTATTTCTTAGAGACTGAAAAGTTTATTTCATTCTTTGCAGAAACTTCAAAATCAACTTCTGG
ACATATCAACAGAAAGGGATAAACTAAAGACACAAATCGAGGAACTGACTAGCAAATTATCCTGC
CTCGAAAAGGAAAATCTTAAAAACGATTCTAATGACATGGTTGGCTGTTTAAAAAATGACTCCTT
TTTAGCTAACAATCTAACTAGGTTGAGA
Found at i:98189 original size:21 final size:22
Alignment explanation
Indices: 98142--98189 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
98132 TCATTAAAAA
98142 ATATATAAAAAAATTTTACATC
1 ATATATAAAAAAATTTTACATC
*
98164 A-ATATAAATAAATCTTT-CAT-
1 ATATATAAAAAAAT-TTTACATC
98184 ATATAT
1 ATATAT
98190 TTCAATCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 18 0.78
22 4 0.17
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATATAAAAAAATTTTACATC
Found at i:100546 original size:31 final size:30
Alignment explanation
Indices: 100450--100548 Score: 92
Period size: 31 Copynumber: 3.1 Consensus size: 30
100440 ACGTTTTGGG
* * *
100450 AAATTTTGAGAGGATTAATTAGAATTTCCAA
1 AAATTTTG-GAAGATTAATTAAAATTTCTAA
100481 AAATTTTGGAAGATCTAATTTTAAAAATTT-TAA
1 AAATTTTGGAAGAT-TAA--TT-AAAATTTCTAA
* *
100514 AACTTTTGGAAGGCTTAATTAAAATTTCTAA
1 AAATTTTGGAA-GATTAATTAAAATTTCTAA
100545 AAAT
1 AAAT
100549 CTTAGGGGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
30 12 0.21
31 19 0.34
33 17 0.30
34 8 0.14
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.38
Consensus pattern (30 bp):
AAATTTTGGAAGATTAATTAAAATTTCTAA
Done.