Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009624.1 Kokia drynarioides strain JFW-HI SEQ_124340, 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: 7115
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Found at i:1803 original size:215 final size:216
Alignment explanation
Indices: 465--5740 Score: 5938
Period size: 216 Copynumber: 24.5 Consensus size: 216
455 TTCGTATCAT
* * * * * * *
465 GATCCATTCCTTCAATCAATTTTCTGAATATTCCATGCTCTTGAAATCTCATTATTTGGTCTAAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCACATCATTTGGTCTAAA
** **
530 TAGTTTCACATTATT-TAAACAAGTTTTGGTCTTTGGGTTAAAAACTTATTTACGTGAGAATTAT
66 TAGTTTGTCATT-TTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTAT
* * * * * *
594 TTCTGTCATGGTTCTTGGACAAACTTTCGAACTCGTCAAACTTTTACAAGTTCTTTTATAACTTT
130 TTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC
659 GGTTCCTTAAAGTATT-AGAGAC
195 GGTTCCTTAAAGTATTCA-AGAC
* * * * ** * * * * *
681 AATCAATTCCTTCTATCAATTTTCCGAATATTCCATTCCCGTGAAATCGCATCATTTGGTCTTAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCACATCATTTGGTCTAAA
* * * * *
746 TAGTTTGTCATTTTTTAAACAAGTTTTGGGCTTTGGATTAAAAACTTATTTACGTAAGAATTGTT
66 TAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATT
* * * * * *
811 TCTCTCTTGGTTCTTTGACGAACTTCCAAACTTGTCAAACTATTACGATTTCTTTTATAACTTTG
131 TCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCG
876 GTTCCTTAAAGTAGTT-AAGAC
196 GTTCCTTAAAGTA-TTCAAGAC
* * * * ** * * * * * *
897 GATACTTTCCCTCAAGCAATTTTTCAAACAATACTTGCTCGGGAAATCGCATCATTTGATCTAAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCACATCATTTGGTCTAAA
* * *
962 TAG-TTATCATTTTGTAAACAAGTTTTGGTCTTTAAATT-AAAACTTATTTACGTGAGAATTGTT
66 TAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATT
* * * * *
1025 TCTCTCTTGGTTCTTAGACGCACTTGCGAACTTGTTAAACTTTTACGAGTTCTTTTATAACTTCA
131 TCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCG
* * *
1090 GTTCCTTAAAGTAATGAAGAT
196 GTTCCTTAAAGTATTCAAGAC
* * * *
1111 GATGCATTCCTTCGAACAATATTTTGAACATTCCATGCTCGGGAAATCACATCATTTGGTCTAAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCACATCATTTGGTCTAAA
** * * * *
1176 TAGTTTGTCATTTTGTAAACAACCTTCGGTGTTTGAATTAAAAACTTATTTACGTGAGTATTGTT
66 TAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATT
* * *
1241 TCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGGGTTCTTTTATAACTTCT
131 TCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCG
*
1306 GTTCGTTAAAGTA-T-AAGAC
196 GTTCCTTAAAGTATTCAAGAC
* ** ** * ** *
1325 GATCCATTCCTTCAAGCAATTTTTCAAACATTTGATGCTCGAGAAATCGTATCATTTGTTCTAAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCACATCATTTGGTCTAAA
** ** * *
1390 TCTTTTGTCATTTTGTAAACAACATTTGGTCTTTGAATTAAAATCTTACTTACGT--G----ATT
66 TAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATT
* * * *
1449 TCTCTCTTCGTTCTTGGACTAAC-TTCCAATCTTATCAAACTTTTACGAGTTCTTTTATAACTTC
131 TCTCTCTTGGTTCTTGGACGAACTTTCGAA-CTTGTCAAACTTTTACGAGTTCTTTTATAACTTC
*
1513 GGAT--TTAAAGTATTCAAGAC
195 GGTTCCTTAAAGTATTCAAGAC
* * * *
1533 GATCCATTCCTTTGATCAATTTTTCGAATATTCCATGCTCGTGAAAT-AGCATCATTTGGTCTAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCA-CATCATTTGGTCTAA
* * *
1597 ATAGTTTGTCATTTTTTAAACAAGTTTTGGTCTTTGGATTAAAAACTTATTTACGTGAGAATTGT
65 ATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTAT
** * * * *
1662 TTCTCTCTTGGTTCTTGGATAAAC-TCCCAATCTTGTCCAACTTTT-CTAGTTCTTTTATAACTT
130 TTCTCTCTTGGTTCTTGGACGAACTTTCGAA-CTTGTCAAACTTTTACGAGTTCTTTTATAACTT
*
1725 CGGTTCATTAAAGTATTCAAGAC
194 CGGTTCCTTAAAGTATTCAAGAC
* * *
1748 GATCCATTCCTTCCAGCAATTTTTTGAACATTCCATGCTCGGGAAATCACATCATTTGGTTTAAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCACATCATTTGGTCTAAA
* * * * * * *
1813 TAGTTTGTCAATTTGTAAAAAAAACTTTTGGTCTTTCAATTAAAATCTTATTTACATGAGAATTG
66 TAGTTTGTCATTTTGT--AAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTA
* * * * * *
1878 CTTATCTTTTGGTTTTTGGATGAACTTTCGAA-TTGGTCAAAC-TTTATGAGTTCTTTTATAACT
129 TTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTT-GTCAAACTTTTACGAGTTCTTTTATAACT
*
1941 TTGGTTCCTTAAAGTATTCAAGAC
193 TCGGTTCCTTAAAGTATTCAAGAC
* * * * * * * *
1965 CATCCATTTCTTCTAGCAA-TTTTTCAAGTATTCCATGCACGGGAAATCGCATCATTTGGTCTAA
1 GATCCATTCCTTCGAGCAATTTTTTGAA-CATTCCATGCTCGTGAAATCACATCATTTGGTCTAA
** *
2029 ATAGTTTGTCATTTTGTAAACAAAATTTGGTCTTTGAATTAAAATCTTATTTACGTGAGAATTAT
65 ATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTAT
*
2094 TTCTCTCTTGGTTCTTGGACGAAC-TTCGATCTTGTCAAACTTTTACGAGTTCTTTTATAACTTC
130 TTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC
*
2158 GATTCCTTAAAGTATTCAAGAC
195 GGTTCCTTAAAGTATTCAAGAC
* * *
2180 GATCCATTCCTTCGAGTAATTTTTTGAACATTCCATGCTCGAGAAATCACATCATTCGGTCTAAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCACATCATTTGGTCTAAA
* * * * * * * * **
2245 TAGTTTGTTATTTTGTGAAAAAACTTTTTGTGTTTAAATCAAAAACTTATTTACGTGGGAATCGT
66 TAGTTTGTCATTTTGT-AAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTAT
* * * *
2310 TTCTCTTTTGGTTCTTGGACGAACTTCCGATCTTGTCAAACTTTTATGAGTTCTTTTATAACTTC
130 TTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC
* * *
2375 GGTTCATTAAATTATTCAAGGC
195 GGTTCCTTAAAGTATTCAAGAC
* * * * * * *
2397 GATCCATTCCTTTGATCAATTTTTCGAATATTCCATGCTCTTGAAATCTCATTATTTGGTCTAAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCACATCATTTGGTCTAAA
* ** * * * *
2462 TAGTTTCTCATTATT-TAAACAAGTTTTGGTCTTTGGGTTAAAAACATGTTTACATGAAAATTAT
66 TAGTTTGTCATT-TTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTAT
* * * * *
2526 TTCTGTCATGGTTCTTGGACAAACTTTCGAACTCGTCAAACTTTTACGAGTTCTTTTATAACTTT
130 TTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC
*
2591 GGTTCCTTAAAGTATTAAAGAC
195 GGTTCCTTAAAGTATTCAAGAC
* * * * * * * *
2613 AATCCATTCCTTCTATCAATTTTCTGAATATTCCATTCCCGTGAAATCGCATCATTTGGTCTAAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCACATCATTTGGTCTAAA
* * * * *
2678 TAGATTGTCATATTT-TAAA-AATGTTTTGGTCTTTGGATTAAAAACTCATTTATGTCAGAATTA
66 TAGTTTGTCAT-TTTGTAAACAA-GTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTA
* * * * *
2741 TTTCTCTCTTGATTCTAT-GATGAACTTCCAAACTTGT-AAACCTTTTACAAGTTCTTTTATAAC
129 TTTCTCTCTTGGTTCT-TGGACGAACTTTCGAACTTGTCAAA-CTTTTACGAGTTCTTTTATAAC
* * * * *
2804 TTC-CTTCGTTAAAATATTCCAGAT
192 TTCGGTTCCTTAAAGTATTCAAGAC
* * ** * *
2828 GATCCATTCCTTTGAGAAATTTTCCGAACATTCCATGCTCGGGAAATCACAT-ATTTGGTATAAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCACATCATTTGGTCTAAA
* * * *
2892 TAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAATATCTTATTTACATGAGAATTA-T
66 TAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATT
* * * * * * *
2956 T-TCACATGGTTTTTCGACAAACTTTCGATCTTGTCAAACTTTTATGAGTTCTTTTATAACTTCG
131 TCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCG
* *
3020 GTTCCTTAAAGTAATGAAGAC
196 GTTCCTTAAAGTATTCAAGAC
* * *
3041 GATGCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCACATCATTTGGTCTAAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCACATCATTTGGTCTAAA
* * * * *
3106 TAGTTTGTCATTTTGTACACAACTTTTGGTGTTTGAATTAAAAACTTATTTACGTGAGTATTGTT
66 TAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATT
* * *
3171 TCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGGGTTCTTTTATAACTTCT
131 TCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCG
* *
3236 GTTCGTTAAAGTA-T-AAGAT
196 GTTCCTTAAAGTATTCAAGAC
* ** * *
3255 GATCCATTCCTTCAAGCAATTTTTTGAACATTTGATGCTCGAGAAATCGCATCATTTGGTCTAAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCACATCATTTGGTCTAAA
** *
3320 TCA-TTTGTCATTTTGTAAACAACATTTGGTCTTTGAATTAAAATCTTATTTACGTGAGAATTAT
66 T-AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTAT
* * *
3384 TTCTCTCTTGGTTCTTGGACGAACTTTTGATCTTATCAAACTTTTACGAGTTCTTTTATAACTTC
130 TTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC
* *
3449 GGATCATTAAAGTATTCAAGA-
195 GGTTCCTTAAAGTATTCAAGAC
* ** * *
3470 GATCCATTCCTTCGATCAATTTTTCAAATATTCCATGCTCGTGAAAT-AGCACCATTTGGTCTAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCA-CATCATTTGGTCTAA
* * *
3534 ATAGTTTCTCATTTTTTAAACAA-TGTTTGGTCTTTGGATTAAAAACTTATTTACGTGAGAATTA
65 ATAGTTTGTCATTTTGTAAACAAGT-TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTA
* * *
3598 TTTCTCTCTTGGTTCTTGGATGAACTTTCGATCTTATCAAACTTTTACGAGTTCTTTTATAACTT
129 TTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT
* * * *
3663 TGGATCATTATAGTATTCAAGAC
194 CGGTTCCTTAAAGTATTCAAGAC
* * * *
3686 GATCCATTCCTTCGATCAATTTTTCGAATATTCCATGCTCGTGAAAT-AGTATCATTTGGTCTAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCA-CATCATTTGGTCTAA
* * * *
3750 ATAGTTTCTCATTTTTTAAACAAGGTTTGGTCTTTGGATTAAAAACTTATTTACGTGAGAATTAT
65 ATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTAT
* * *
3815 TTCTCTCTTAGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTT
130 TTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC
3880 GGTTCCTTAAAGTATT-AGAGAC
195 GGTTCCTTAAAGTATTCA-AGAC
* * * **
3902 AATTCATTCCTTCGATCAATTTTTTG-ACTATTCCATGCTCGTGAAATTGCATCATTTGGTCTAA
1 GATCCATTCCTTCGAGCAATTTTTTGAAC-ATTCCATGCTCGTGAAATCACATCATTTGGTCTAA
* *
3966 AGAGTTTGTCATATTT-TCAAA-AAGTTTTGGTCTTTGGATTAAAAACTTATTTACGTGAGAATT
65 ATAGTTTGTCAT-TTTGT-AAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATT
* * * * *
4029 GTTTCTCTCTTGATTCTTTGACGAAC-TTCTGAACTTGTCAAGCTTTTACTAGTTCTTTTATAAC
128 ATTTCTCTCTTGGTTCTTGGACGAACTTTC-GAACTTGTCAAACTTTTACGAGTTCTTTTATAAC
* * *
4093 TTC-GTTCCATAAAGTATTCATGAT
192 TTCGGTTCCTTAAAGTATTCAAGAC
* * * * * *
4117 GATCCATTCATTCCAGCAATTTTTCGAACATTCCATGGTCAG-GAAAACACATCATTTGGTTTAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTC-GTGAAATCACATCATTTGGTCTAA
* * * * *
4181 ATAGTTTGTCATTTTGTAAACAAGTTTTTGTGTTTGAATTAAAATCTTATTTACGTGAAAATTGT
65 ATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTAT
* * * *
4246 TTCTCTCTTGGTTGTTGGACGAACTTCCGAACTTGTCAAACTTTTACAAGTTTTTTTATAACTTC
130 TTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC
* * * *
4311 GGTTTCATAAAATATTAAAGAC
195 GGTTCCTTAAAGTATTCAAGAC
* * * * * * * *
4333 AATCCATTCATTCCAGTAA-TTTCTCAAGCATTCCATACTCGGGAAAT-AGCATCATTTGGTCTA
1 GATCCATTCCTTCGAGCAATTTTTTGAA-CATTCCATGCTCGTGAAATCA-CATCATTTGGTCTA
* * * *
4396 AATAGTTTGTCATTTTGTAAACAAGTTTTGGTGTTTGAATTAAAATCTTATTTATGTGAGAATTG
64 AATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTA
** * * * *
4461 TTTCTCTCCCGGTTCTTGGACAAACTTCCAAACTTATCAAACTTTTACGAGTTCTTTTATAACTT
129 TTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT
*
4526 CGGTTCCGTAAAGTATTCAAGAC
194 CGGTTCCTTAAAGTATTCAAGAC
* * * *
4549 GATCTATTCCTTTGAGCAA-TTTTTGAACATTCCACGCTCGGGAAATCACATCATTTGGTCTAAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCACATCATTTGGTCTAAA
* * * * * *
4613 TAGTTTGTCATTTTGTAAACAACTTTTGGTGTTCGAATTAAAAACTTATTTACATGAGTATTTTT
66 TAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATT
* * **
4678 TCTCTCTTGGTTCTTGGACGAACTTTCAAACTTGTCAAACTTTTACGAGTTCTTGTATAACTTTT
131 TCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCG
* *
4743 GTTCGTTAAAGTA-T-AAGAT
196 GTTCCTTAAAGTATTCAAGAC
* * * * *
4762 GATCCATTCCTTCCAGCAATTTTTTGAGCATTCCATGCACGAGAAATCGCATCATTTGGTCTAAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCACATCATTTGGTCTAAA
* * * * * *
4827 TCGTTTGACATTTTGTAAACAACATTTT-GTCTTTGAATTAAAATCTTATTTAAGTAAGAATTAT
66 TAGTTTGTCATTTTGTAAACAA-GTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTAT
* * * * *
4891 TTCTCTCTTGGTTCTTGGAAGAACTTTGGATCTTATCAAACTTTTATGAGTTCTTTTATAACTTC
130 TTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC
* *
4956 GGATCATTAAAGTATTCAAGAC
195 GGTTCCTTAAAGTATTCAAGAC
* ** * *
4978 GATCCATTCCTTCGATCAATTTTCCGAATATTCCATGCTCGTGAAAT-AGCATCATTTGGTCTAT
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCA-CATCATTTGGTCTAA
* * * * * *
5042 ATAGTTTCTCATTTTTTAAACAAGGTTTGGTCATTGGATTAAAAACTTATTTATGTGAGAATTAT
65 ATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTAT
* * * * * * *
5107 TTCTCTCCTGGCTCTTGGACGAACATCCGATCTTATCAAACTTTTACGAGTTCTTTTATAACTTT
130 TTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC
* * * *
5172 GGATCATTAAAGTAATCAAGAT
195 GGTTCCTTAAAGTATTCAAGAC
* ** * *
5194 GATCCATTCCTTCGATCAATTTTCCGAATATTCCATGCTCGTGAAAT-AGCATCATTTGGTGTAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCA-CATCATTTGGTCTAA
* * * * *
5258 ATAGTTTCTCATTTTTTAAACAAGGTTTGGTCTTTGGATTAAAAACTTATTTACGTGAAAATTAT
65 ATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTAT
* * * * *
5323 GTCTCTCTAGGTTCTTGGAAGAAC-TTCTGAACTTGCCAAACTATTACGAGTTCTTTTATAACTT
130 TTCTCTCTTGGTTCTTGGACGAACTTTC-GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT
* *
5387 TGGCTCCTTAAAGTATT-AGAGAC
194 CGGTTCCTTAAAGTATTCA-AGAC
* * * * **
5410 AATCCATTCCTTCGATCAACTTTTTG-ACTATTCCATGCTCATGAAATTGCATCATTTGGTCTAA
1 GATCCATTCCTTCGAGCAATTTTTTGAAC-ATTCCATGCTCGTGAAATCACATCATTTGGTCTAA
* * * * *
5474 ATAGTTTGTCATATTT-TCAATAAGTTTTGGTCTTTGTATTAAAAACTTGTTTAAGTGAGAATTA
65 ATAGTTTGTCAT-TTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTA
* * * * * *
5538 TTTCTCTCTTGATTCTTTGAAGAACTTCCGAACTTGTCAAGCTTTTACAAGTTCTTTTATAACTT
129 TTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT
* * *
5603 C-GTTCCTTAGAGTATTCATGAT
194 CGGTTCCTTAAAGTATTCAAGAC
* * * * *
5625 GATCCATTCATTCCAGCAATTTTTTGAACATTCCATGGTCAG-GAAAACACATCATTTGGTTTAA
1 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTC-GTGAAATCACATCATTTGGTCTAA
* * * *
5689 ATAGTCTATCATTTTGTAAACAAGTTTTTGTGTTTGAATTAAAAATCTTATT
65 ATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAA-CTTATT
5741 ATCATTTTAT
Statistics
Matches: 4329, Mismatches: 647, Indels: 168
0.84 0.13 0.03
Matches are distributed among these distances:
206 8 0.00
207 5 0.00
208 162 0.04
210 1 0.00
211 1 0.00
212 46 0.01
213 112 0.03
214 790 0.18
215 1025 0.24
216 1867 0.43
217 306 0.07
218 6 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (216 bp):
GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGTGAAATCACATCATTTGGTCTAAA
TAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATT
TCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCG
GTTCCTTAAAGTATTCAAGAC
Found at i:5746 original size:45 final size:44
Alignment explanation
Indices: 5695--5784 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 44
5685 TTAAATAGTC
* *
5695 TATCATTTTGTAAACAAGTTTTTGTGTTTGAATTAAAAATCTTAT
1 TATCATTTTATAAACAAATTTTTGTGTTTGAATT-AAAATCTTAT
5740 TATCATTTTATAAACAAATTTTTGTGTTTGAATTAAAATCTTAT
1 TATCATTTTATAAACAAATTTTTGTGTTTGAATTAAAATCTTAT
5784 T
1 T
5785 TACGTGAGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
44 11 0.26
45 32 0.74
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (44 bp):
TATCATTTTATAAACAAATTTTTGTGTTTGAATTAAAATCTTAT
Found at i:5996 original size:260 final size:260
Alignment explanation
Indices: 5506--6000 Score: 690
Period size: 260 Copynumber: 1.9 Consensus size: 260
5496 AGTTTTGGTC
* * **
5506 TTTGTATTAAAAACTTGTTTAAGTGAGAATTATTTCTCTCTTGATTCTTTGAAGAACTTCCGAAC
1 TTTGAATTAAAAACTTATTTAAGTGAGAATTATTTCTCTCTTGATTCTCGGAAGAACTTCCGAAC
* * * * * **
5571 TTGTCAAGCTTTTACAAGTTCTTTTATAACTTCGTTCCTTAGAGTATTCATGATGATCCATTCAT
66 TTGTCAAACTTTTACAAGTTCTTTTATAACTTCGTTCCGTAAAGTATTAAAGACAATCCATTCAT
* * ** *
5636 TCCAGCAATTTTTTGAACATTCCATGGTCAGGAAAACACATCATTTGGTTTAAATAGTCTATCAT
131 TCCAACAATTTTTTCAACATTCCATACTCAGGAAAACACATCATTTGGTCTAAATAGTCTATCAT
*
5701 TTTGTAAACAAGTTTTTGTGTTTGAATTAAAAATCTTATTATCATTTTATAAACAAATTTTTGTG
196 TTTGTAAACAAGTTTTGGTGTTTGAATTAAAAATCTTATTATCATTTTATAAACAAATTTTTGTG
* * * * *
5766 TTTGAATTAAAATCTTATTTACGTGAGAATTATTTCTCTCTTGGTTGTCGGACGAACTTCCGAAC
1 TTTGAATTAAAAACTTATTTAAGTGAGAATTATTTCTCTCTTGATTCTCGGAAGAACTTCCGAAC
*
5831 TTGTCAAACTTTTACAAGTTCTTTTATAACTTCGATTCCGTAAAGTATTAAAGACAATCCATTCC
66 TTGTCAAACTTTTACAAGTTCTTTTATAACTTCG-TTCCGTAAAGTATTAAAGACAATCCATTCA
* * * * *
5896 TTCCAATAA-TTTTTCAAGCATTCCATACTCGGGAAATA-GCATCATTTGGTCTAAATAGTTTGT
130 TTCCAACAATTTTTTCAA-CATTCCATACTCAGGAAA-ACACATCATTTGGTCTAAATAGTCTAT
5959 CATTTTGTAAACAAGTTTTGGTGTTTGAATT-AAAATCTTATT
193 CATTTTGTAAACAAGTTTTGGTGTTTGAATTAAAAATCTTATT
6001 TACGTGAGAA
Statistics
Matches: 204, Mismatches: 28, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
260 107 0.52
261 96 0.47
262 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (260 bp):
TTTGAATTAAAAACTTATTTAAGTGAGAATTATTTCTCTCTTGATTCTCGGAAGAACTTCCGAAC
TTGTCAAACTTTTACAAGTTCTTTTATAACTTCGTTCCGTAAAGTATTAAAGACAATCCATTCAT
TCCAACAATTTTTTCAACATTCCATACTCAGGAAAACACATCATTTGGTCTAAATAGTCTATCAT
TTTGTAAACAAGTTTTGGTGTTTGAATTAAAAATCTTATTATCATTTTATAAACAAATTTTTGTG
Found at i:6530 original size:216 final size:215
Alignment explanation
Indices: 6148--6609 Score: 608
Period size: 216 Copynumber: 2.1 Consensus size: 215
6138 GGGAAGTCAC
* * *
6148 ACTTTTACGAGTTCTGTTATAACTTTGGTTCCGTAAAGTATTAAAGACGATCCATTCCTTCAATC
1 ACTTTTACGAGTTCTTTTATAAC-TTCGTTCCGTAAAGTATTAAAGACGATCCATTCCTTCAAGC
* * * *
6213 AATTTTTGAGCATTCCATGCTTGGGAAATCGCATCATTAGGTCTAAATAGTTTGTCATTTTGTAA
65 AATTTTTGAACATTCCATGCTCGAGAAATCACATCATTAGGTCTAAATAGTTTGTCATTTTGTAA
* * * *
6278 AACACATTTGGTCTTTGAATTAAAATCTCATTTACGTGATAATTTTTTCTCTCTTGGTTCTTGGA
130 AACACATTTGGTCTTTGAATTAAAAACTCATTTACGTGAGAATTGTTTCTCTCTTGATTCTTGGA
* *
6343 CAAAC-TTCTGATCTTTTCAA-
195 CAAACTTTC-GAACTTGTCAAG
* * **
6363 ACTTTTCCGAGTTCTTTTATAACTTCAGTTCCGTAAAGTATTCAAGACGATCCATTCCTTTGAGC
1 ACTTTTACGAGTTCTTTTATAACTTC-GTTCCGTAAAGTATTAAAGACGATCCATTCCTTCAAGC
* *
6428 AATTTTTTGAACATTCCATGGTCGAGAAATCACATCATTTGGTCTAAATAGTTTGTCATTTTGT-
65 AA-TTTTTGAACATTCCATGCTCGAGAAATCACATCATTAGGTCTAAATAGTTTGTCATTTTGTA
* * ** *
6492 AAACAACTTTTGGTCTTTGGATTAAAAACTTGTTTACGTGAGAATTGTTTCTCTCTTGATTCTTT
129 AAAC-ACATTTGGTCTTTGAATTAAAAACTCATTTACGTGAGAATTGTTTCTCTCTTGATTCTTG
**
6557 GATGAACTTTCGAACTTGTCAAG
193 GACAAACTTTCGAACTTGTCAAG
*
6580 A-TTTTACAAGTTCTTTTATAACTTCGTTCC
1 ACTTTTACGAGTTCTTTTATAACTTCGTTCC
6610 TCAAAGCATT
Statistics
Matches: 214, Mismatches: 28, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
214 2 0.01
215 66 0.31
216 142 0.66
217 4 0.02
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (215 bp):
ACTTTTACGAGTTCTTTTATAACTTCGTTCCGTAAAGTATTAAAGACGATCCATTCCTTCAAGCA
ATTTTTGAACATTCCATGCTCGAGAAATCACATCATTAGGTCTAAATAGTTTGTCATTTTGTAAA
ACACATTTGGTCTTTGAATTAAAAACTCATTTACGTGAGAATTGTTTCTCTCTTGATTCTTGGAC
AAACTTTCGAACTTGTCAAG
Found at i:6645 original size:21 final size:21
Alignment explanation
Indices: 6619--6666 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
6609 CTCAAAGCAT
6619 TCATTTGGTCTAAATAGTTTG
1 TCATTTGGTCTAAATAGTTTG
*
6640 TCATTTGGTCTAAATCGTTTG
1 TCATTTGGTCTAAATAGTTTG
6661 TCATTT
1 TCATTT
6667 TGTAAACAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (21 bp):
TCATTTGGTCTAAATAGTTTG
Found at i:6772 original size:178 final size:178
Alignment explanation
Indices: 6462--6783 Score: 520
Period size: 178 Copynumber: 1.8 Consensus size: 178
6452 AGAAATCACA
* * *
6462 TCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGGATTAAAAACTTGTTT
1 TCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACATTTGGTCTTTGAATTAAAAACTTATTT
* * * *
6527 ACGTGAGAATTGTTTCTCTCTTGATTCTTTGATGAACTTTCGAACTTGTCAAGATTTTACAAGTT
66 ACGTGAGAATTATTTCTCTCTTGATTCTTGGATGAACTTCCGAACTTATCAAGATTTTACAAGTT
6592 CTTTTATAACTTCGTTCCTCAAAGCATTCATTTGGTCTAAATAGTTTG
131 CTTTTATAACTTCGTTCCTCAAAGCATTCATTTGGTCTAAATAGTTTG
* *
6640 TCATTTGGTCTAAATCGTTTGTCATTTTGTAAACAACATTTGGTCTTTGAATTAAAATCTTATTT
1 TCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACATTTGGTCTTTGAATTAAAAACTTATTT
* * *
6705 ACGTGAGAATTATTTCTCTCTTGGTTCTTGGATGAACTTCCGATCTTATCAA-ACTTTTACGAGT
66 ACGTGAGAATTATTTCTCTCTTGATTCTTGGATGAACTTCCGAACTTATCAAGA-TTTTACAAGT
6769 TCTTTTATAACTTCG
130 TCTTTTATAACTTCG
6784 GATCATTAAA
Statistics
Matches: 131, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
177 1 0.01
178 130 0.99
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (178 bp):
TCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACATTTGGTCTTTGAATTAAAAACTTATTT
ACGTGAGAATTATTTCTCTCTTGATTCTTGGATGAACTTCCGAACTTATCAAGATTTTACAAGTT
CTTTTATAACTTCGTTCCTCAAAGCATTCATTTGGTCTAAATAGTTTG
Found at i:6988 original size:394 final size:395
Alignment explanation
Indices: 6246--7003 Score: 1171
Period size: 394 Copynumber: 1.9 Consensus size: 395
6236 GGAAATCGCA
6246 TCATTAGGTCTAAATAGTTTGTCATTTTGTAAAACACATTTGGTCTTTGAATTAAAATCTCATTT
1 TCATTAGGTCTAAATAGTTTGTCATTTTGTAAAACACATTTGGTCTTTGAATTAAAATCTCATTT
* * * * *
6311 ACGTGATAATTTTTTCTCTCTTGGTTCTTGGACAAACTTCTGATCTTTTCAAACTTTTCCGAGTT
66 ACGTGAGAATTATTTCTCTCTTGGTTCTTGGACAAACTTCCGATCTTATCAAACTTTTACGAGTT
* * *
6376 CTTTTATAACTTCAGTTCCGTAAAGTATTCAAGACGATCCATTCCTTTGAGCAATTTTTTGAACA
131 CTTTTATAACTTCAGATCAGTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTTGAACA
* * * *
6441 TTCCATGGTCGAGAAATCACATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGT
196 TTCCATGCTCGAGAAATAACATCATTTGGTCTAAATAGTTTCTCATTTTGTAAACAACGTTTGGT
* * * * * *
6506 CTTTGGATTAAAAACTTGTTTACGTGAGAATTGTTTCTCTCTTGATTCTTTGATGAACTTTCGAA
261 CTTTGGAGTAAAAACCTATTTACGTGAGAATTATTTCTCTCTTGATTCTTAGACGAACTTTCGAA
*
6571 CTTGTCAAGATTTTACAAGTTCTTTTATAACTTC-GTTCCTCAAAGCATTCATTTGGTCTAAATA
326 CTTGTCAAGATTTCACAAGTTCTTTTATAACTTCTGTTCCTCAAAGCATTCATTTGGTCTAAATA
6635 GTTTG
391 GTTTG
* * *
6640 TCATTTGGTCTAAATCGTTTGTCATTTTGT-AAACAACATTTGGTCTTTGAATTAAAATCTTATT
1 TCATTAGGTCTAAATAGTTTGTCATTTTGTAAAAC-ACATTTGGTCTTTGAATTAAAATCTCATT
**
6704 TACGTGAGAATTATTTCTCTCTTGGTTCTTGGATGAACTTCCGATCTTATCAAACTTTTACGAGT
65 TACGTGAGAATTATTTCTCTCTTGGTTCTTGGACAAACTTCCGATCTTATCAAACTTTTACGAGT
* * * *
6769 TCTTTTATAACTTCGGATCATTAAAGTATTCAAGACGATCCATTCCTTCGATCAATTTTTTGAAT
130 TCTTTTATAACTTCAGATCAGTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTTGAAC
* * *
6834 ATTCCATGCTCGTGAAATAACATCATTTGGTCTAAATAGTTTCTCATTTTTTAAACAAGGTTTGG
195 ATTCCATGCTCGAGAAATAACATCATTTGGTCTAAATAGTTTCTCATTTTGTAAACAACGTTTGG
* *
6899 TCTTTGGAGTAAAAACCTATTTACGTGAGAATTATTTCTCTCTTGGTTCTTAGGCGAACTTTCGA
260 TCTTTGGAGTAAAAACCTATTTACGTGAGAATTATTTCTCTCTTGATTCTTAGACGAACTTTCGA
*
6964 ACTTGTCAA-ACTTTCACGAGTTCTTTTATAACTTCTGTTC
325 ACTTGTCAAGA-TTTCACAAGTTCTTTTATAACTTCTGTTC
7004 GTTAAGGTAT
Statistics
Matches: 327, Mismatches: 34, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
393 5 0.02
394 318 0.97
395 4 0.01
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (395 bp):
TCATTAGGTCTAAATAGTTTGTCATTTTGTAAAACACATTTGGTCTTTGAATTAAAATCTCATTT
ACGTGAGAATTATTTCTCTCTTGGTTCTTGGACAAACTTCCGATCTTATCAAACTTTTACGAGTT
CTTTTATAACTTCAGATCAGTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTTGAACA
TTCCATGCTCGAGAAATAACATCATTTGGTCTAAATAGTTTCTCATTTTGTAAACAACGTTTGGT
CTTTGGAGTAAAAACCTATTTACGTGAGAATTATTTCTCTCTTGATTCTTAGACGAACTTTCGAA
CTTGTCAAGATTTCACAAGTTCTTTTATAACTTCTGTTCCTCAAAGCATTCATTTGGTCTAAATA
GTTTG
Found at i:7114 original size:214 final size:216
Alignment explanation
Indices: 6640--7115 Score: 661
Period size: 216 Copynumber: 2.2 Consensus size: 216
6630 AAATAGTTTG
* * * *
6640 TCATTTGGTCTAAATCGTTTGTCATTTTGTAAACAACATTTGGTCTTTGAATTAAAATCTTATTT
1 TCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACATTTGGTCTTTGAAGTAAAAACCTATTT
* * *
6705 ACGTGAGAATTATTTCTCTCTTGGTTCTTGGATGAACTTCCGATCTTATCAAACTTTTACGAGTT
66 ACGTGAGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTATCAAACTTTCACGAGTT
* * * *
6770 CTTTTATAACTTCGGATCATTAAAGTATTCAAGACGATCCATTCCTTCGATCAATTTTTTGAATA
131 CTTTTATAACTTCGGATCATTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTCGAACA
*
6835 TTCCATGCTCGTGAAATAACA
196 TTCCATGCTCGAGAAATAACA
* * ** *
6856 TCATTTGGTCTAAATAGTTTCTCATTTTTTAAACAAGGTTTGGTCTTTGGAGTAAAAACCTATTT
1 TCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACATTTGGTCTTTGAAGTAAAAACCTATTT
* *
6921 ACGTGAGAATTATTTCTCTCTTGGTTCTTAGG-CGAACTTTCGAACTTGTCAAACTTTCACGAGT
66 ACGTGAGAATTATTTCTCTCTTGGTTCTT-GGACGAACTTCCGAACTTATCAAACTTTCACGAGT
* * * * *
6985 TCTTTTATAACTTCTGTTCGTTAAGGTA-T-AAGACGATTCATTCCTTCAAGCAATTTTTCGAAC
130 TCTTTTATAACTTCGGATCATTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTCGAAC
** **
7048 ATTTGATGCTCGAGAAATCGCA
195 ATTCCATGCTCGAGAAATAACA
*
7070 TCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCT
1 TCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACATTTGGTCT
Statistics
Matches: 227, Mismatches: 32, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
214 88 0.39
215 1 0.00
216 136 0.60
217 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (216 bp):
TCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACATTTGGTCTTTGAAGTAAAAACCTATTT
ACGTGAGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTATCAAACTTTCACGAGTT
CTTTTATAACTTCGGATCATTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTCGAACA
TTCCATGCTCGAGAAATAACA
Done.