Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014192.1 Kokia drynarioides strain JFW-HI SEQ_129225, 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: 5425
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Found at i:384 original size:221 final size:221
Alignment explanation
Indices: 1--3612 Score: 5321
Period size: 221 Copynumber: 16.3 Consensus size: 221
* * * * ** *
1 TGAAAAATTAAAAGTAAAATTAAAATCCTGAAATTGAAAATGAAATTGTTGGTGTGGCATAAAAC
1 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
* * * *
66 TACTGGAAAGGGATAATATTCCTGTTTTATACAATCCTTTCTCTTCTTCAATGGAGAAGGATTGA
66 TAATGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGA
* * * *
131 ATGAAACAGTGACACGACGTCATCTGTGTCCCTCTTCTAATAGTTTTACGCCACATCAGTATTTT
131 ATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTT
* *
196 CATTCTTAATTTTAACATTTTCATCT
196 CATTCTTAATTTCAACATTTTCATCC
222 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
1 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
* * *
287 TAATGGAAAGGGATAATATCCCAGTTTCATAGAATCCTTTCTCTTCTTCAATGTAAAAGGATTGA
66 TAATGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGA
* * * *
352 ATGAAACAGTGACACCACATCATTTGTGTCCCTTTTACAATAGTTTTACGCCATATCAATATTTT
131 ATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTT
*
417 CATTCTTAATTTCAACATTTTCATCT
196 CATTCTTAATTTCAACATTTTCATCC
* * * *
443 TGAAAAAAAT-AAATTAAAATCAAAATCCTAAAATACAGGATGAAATTGTTGGTGTGGCATAAAA
1 TG-AAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAA
* * * *
507 CTATTGGAAAGGGATAATATCCCTGTTTTATACAATCCTTTCTCCTCTTCAATGGAAAAGAATTG
65 CTAATGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTG
* * *
572 AATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCATTAGTTTTATGCCACATCAGTAATT
130 AATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTT
637 TCATTCTTAATTTCAACATTTTCATCC
195 TCATTCTTAATTTCAACATTTTCATCC
* * * * **
664 TGAAAAAATAAAAATAAAATAAAAATCCTAAAATTCAATATGAAATTGTTGATGTGGCATAAAAC
1 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
* * *
729 -AATTGGAAAGGGATAATATCCCTATTCCATACAATCCTTTCTCTTCTTCAATGGAAAATGATTG
66 TAA-TGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTG
* *
793 AATGAAACAGTGACACAACGTCATTTGTGTCCCTTTTCCAATAGTTTTACACCACATCAGTATTT
130 AATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTT
858 TCATTCTTAATTTCAACATTTTCATCC
195 TCATTCTTAATTTCAACATTTTCATCC
* *
885 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATACAAGATGAAATTGTTGATGTGGCATAAAAC
1 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
* ** ** *
950 TGATGGAAAGGGATAATATCTTTGAGTCATACAATCCTTTCTCTTCTTCAATGGAAAAGAATTGA
66 TAATGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGA
* * ** * * *
1015 ATGAAACAGTGGCACCACGACATTTGTGTTTCTTTTCCAAAAGTTTTACGCCATATCAGTTTTTT
131 ATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTT
* *
1080 CATTCTTAATTTTAACATTTTCATCT
196 CATTCTTAATTTCAACATTTTCATCC
* *
1106 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGAAGTGACATAAAAC
1 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
* * ** * * *
1171 TAATGGAAAGGGATAATATACCAGTTTCATTGAATCCTTTCTCTTCTTCAATGTAAAAGGACTAA
66 TAATGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGA
* * * *
1236 ATGAAAAAGTGACGCCACGTCATTTGTGTCCCTTTTACAATAGTTTTACGCCATATCAGTATTTT
131 ATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTT
*
1301 CATTCTTAATTTCAACATTTTCATAC
196 CATTCTTAATTTCAACATTTTCATCC
* * * * *
1327 TGAAAAAAACAAATTAAAATCAAAATCCTAAAATACAGGATGAAATTGTTGATGTCGCATAAAAC
1 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
* * * *
1392 TATTGGAAAGGGATAATATCCCTGTTTTATACAATCCTTTCTCCTCTTCAATGGAAAAGAATTGA
66 TAATGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGA
* * *
1457 ATGAATCAGTAACACCACGTCATTTGTGTCCCTTTTCCATTAGTTTTACGCCACATCAGTATTTT
131 ATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTT
1522 CATTCTTAATTTCAACATTTTCATCC
196 CATTCTTAATTTCAACATTTTCATCC
* * ** *
1548 TGAAAAAATAAAATTAAAATTAAAATCCTAAAATTCAAAATGAAATTGTGGATGTGGCATAAAAC
1 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
* * *
1613 -AATTGGAAAGGGATAATATCCCTGTTTCATACAATTCTTTTTCCTCTTCAATGGAAAAGAATTG
66 TAA-TGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGG---A-AA---
*
1677 AGGAAAAGAATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCATTAGTTTTACGC
123 A-G----G-ATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGC
*
1742 CACATCAGTATTTTCATTCTTAATTTCAACATTTACATCC
182 CACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCC
* * **
1782 TGAAAAAATAAAATTAAAATTAAAATCCTAAAATTCAAAATGAAATTGTTGATGTGGCATAAAAC
1 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
* *
1847 -AATTGGAAAGGGATAATATCACTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAATGATTG
66 TAA-TGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTG
*
1911 AATGAAACAGTGACACAACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTT
130 AATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTT
*
1976 TCATTCTTAATTTCAAAATTTTCATCC
195 TCATTCTTAATTTCAACATTTTCATCC
* * *
2003 TG-AGAAATCAAATTAAAATTAAAGTCCTGAAATTCAGGATGAAATTGTTGGTGTGGCATAAAAC
1 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
* * *
2067 TATTGGAAAGGGATAATATCCCCGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAATGATTGA
66 TAATGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGA
* *
2132 ATGAAACAGTGACACAACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAATATTTT
131 ATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTT
* *
2197 CATTCTTAATTTTAACATTTTCATTC
196 CATTCTTAATTTCAACATTTTCATCC
* * *
2223 TGTAAAAATCAAATTAAAAATAAAATCCTAAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
1 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
* * * *
2288 TATTGGAATGGGATAATATCCCTGTTTTATACAATCCTTTCTCTTCTTCAATGGGAAAGGATTGA
66 TAATGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGA
* *
2353 ATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCTAATAGTTTTACGCCATATCAGTATTTT
131 ATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTT
*
2418 CATTCTTAATTTCAAAATTTTCATCC
196 CATTCTTAATTTCAACATTTTCATCC
*
2444 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATACAGGATGAAATTGTTGATGTGGCATAAAAC
1 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
** * ** * * *
2509 TGTTAGAAAGGGATAATATCTTTGTGTCATACAATCCTTTCTCTTCTTCAATGGAAAAGAATTGT
66 TAATGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGA
* ** *
2574 ATGAAACAGTGGCACCACGTCATTTGTGTTTCTTTTCCAAAAGTTTTACGCCACATCAGTATTTT
131 ATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTT
* *
2639 GATTCTTAATTTTAACATTTTCATCC
196 CATTCTTAATTTCAACATTTTCATCC
*
2665 TGAAAAAATCAAATTAAAATTAAAATCCTAAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
1 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
** * *
2730 TGTTGGAAAGGGATAAGATCCCTGTTTTATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGA
66 TAATGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGA
* * * * * * * *
2795 AAGAAATAGTGACACGATGTCATCTGTGTCCCTTTTCTAATAGTTTTACACCATATCAGTATTTT
131 ATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTT
*
2860 CATTCTTAATTTCAACATTTTCATTC
196 CATTCTTAATTTCAACATTTTCATCC
* *
2886 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATACAGGATGAAATTGTTGGTGTGGCATAAAAC
1 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
* * *
2951 TACTGGAAAGGGATAATATCCCTGTTTTATACAATCCTTTCTCCTCTTCAATGGAAAAGGATTGA
66 TAATGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGA
* * *
3016 ATGAAACAGTGACACCACGTAATTTGTGTTCCTTTT-CAATTAGTTTTACGCCACATCAATATTT
131 ATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAA-TAGTTTTACGCCACATCAGTATTT
*
3080 TCATTCTTAATTTTAACATTTTCATCC
195 TCATTCTTAATTTCAACATTTTCATCC
* *
3107 TGGAAAAATCAAATTAAAATTAAAATCATGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
1 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
* * *
3172 TAATGGAAAGGGATAATATCCCAGTTTCATAGAATCCTTTCTCCTCTTCAATGGAAAAGGATTGA
66 TAATGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGA
* * *
3237 ATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGTCATATAAGTATTTT
131 ATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTT
3302 CATTCTTAATTTCAACATTTTCATCC
196 CATTCTTAATTTCAACATTTTCATCC
* * **
3328 TGAAAAATTAAAATTAAAATTAAAATCCTGAAATTCAAAATGAAATTGTTGATGTGGCATAAAAC
1 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
*
3393 -AATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAATGATTG
66 TAA-TGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTG
* * *
3457 AATGAAACAGTGACACAACATCATTTGTGTCCCTTTTCCAATAGTTTTATGCCACATCAGTATTT
130 AATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTT
3522 TCATTCTTAATTTCAACATTTTCATCC
195 TCATTCTTAATTTCAACATTTTCATCC
** * * *
3549 TGGGAAAATCGAATTAAAATTAAAAACCTGAAATTCAGGATGAAATTGTTGGTGTGGCATAAAA
1 TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAA
3613 AATTATTGAA
Statistics
Matches: 3062, Mismatches: 306, Indels: 46
0.90 0.09 0.01
Matches are distributed among these distances:
220 217 0.07
221 2617 0.85
222 12 0.00
224 1 0.00
225 2 0.00
227 1 0.00
228 1 0.00
229 1 0.00
230 2 0.00
231 1 0.00
234 207 0.07
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (221 bp):
TGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAAC
TAATGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGA
ATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTT
CATTCTTAATTTCAACATTTTCATCC
Found at i:1683 original size:13 final size:13
Alignment explanation
Indices: 1665--1690 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1655 CCTCTTCAAT
1665 GGAAAAGAATTGA
1 GGAAAAGAATTGA
1678 GGAAAAGAATTGA
1 GGAAAAGAATTGA
1691 ATGAAACAGT
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:0.54, C:0.00, G:0.31, T:0.15
Consensus pattern (13 bp):
GGAAAAGAATTGA
Found at i:3733 original size:164 final size:164
Alignment explanation
Indices: 3447--3781 Score: 485
Period size: 164 Copynumber: 2.0 Consensus size: 164
3437 TCTTCAATGG
* * *
3447 AAAATGATTGAATGAAACAGTGACACAACATCATTTGTGTCCCTTTTCCAATAGTTTTATGCCAC
1 AAAATTATTGAATGAAACAGCGACACAACATCATTTGTGTCCCTTTTCCAATAGTTTTACGCCAC
* ** ** *
3512 ATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGGGAAAATCGAATTAAAATTAAAAACC
66 ATCAGTATTTTCATTCTTAATTTCAACATTTACATCCTGAAAAAATAAAAATAAAATTAAAAACC
** **
3577 TGAAATTCAGGATGAAA-TTGTTGGTGTGGCATAA
131 TGAAATTCAAAAT-AAAGTTGTTGACGTGGCATAA
*
3611 AAAATTATTGAATGAAACAGCGACACAACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCAC
1 AAAATTATTGAATGAAACAGCGACACAACATCATTTGTGTCCCTTTTCCAATAGTTTTACGCCAC
* *
3676 A-CAAGTATTTTCATTCTTAATTTTAACATTTACATCCTGAAAAAATAAAAATAAAATTAAAATC
66 ATC-AGTATTTTCATTCTTAATTTCAACATTTACATCCTGAAAAAATAAAAATAAAATTAAAAAC
3740 CTGAAATTCAAAATAAAGTTGTTGACGTGGCATAA
130 CTGAAATTCAAAATAAAGTTGTTGACGTGGCATAA
3775 AACAATT
1 AA-AATT
3782 GGAAAGGGAT
Statistics
Matches: 152, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
163 4 0.03
164 144 0.95
165 4 0.03
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (164 bp):
AAAATTATTGAATGAAACAGCGACACAACATCATTTGTGTCCCTTTTCCAATAGTTTTACGCCAC
ATCAGTATTTTCATTCTTAATTTCAACATTTACATCCTGAAAAAATAAAAATAAAATTAAAAACC
TGAAATTCAAAATAAAGTTGTTGACGTGGCATAA
Found at i:4006 original size:221 final size:221
Alignment explanation
Indices: 3611--5418 Score: 2030
Period size: 221 Copynumber: 8.1 Consensus size: 221
3601 TGTGGCATAA
* * *
3611 AAAATTATTGAATGAAACAGCGACACAACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCAC
1 AAAATGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCAC
* * *
3676 A-CAAGTATTTTCATTCTTAATTTTAACATTTACATCCTGAAAAAATAAAAATAAAATTAAAATC
66 ATC-AGTATTTTCATTCTTAATTTCAACATTTACATCCTGAAAAAATCAAATTAAAATTAAAATC
* ** ** *
3740 CTGAAATTCAAAAT-AAAGTTGTTGACGTGGCATAAAACAATTGGAAAGGGATAATATCCCTGTT
130 CTGAAATTTAGGATGAAA-TTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTT
*
3804 TCACACAATCCTTTCTCTTCTTCAATGG
194 TCATACAATCCTTTCTCTTCTTCAATGG
* *
3832 AAAATGACTGAATGAAACAGTGACACAACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCAC
1 AAAATGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCAC
* * * * *
3897 ATCAGTATTTTCGTTCTTAATTTCAACATTTTCATCATGAGAAAATCAAATTAAAATTAAAATCT
66 ATCAGTATTTTCATTCTTAATTTCAACATTTACATCCTGAAAAAATCAAATTAAAATTAAAATCC
*
3962 TGAAATATAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTC
131 TGAAATTTAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTC
*
4027 ATACAATCCTTTCTGTTCTTCAATGG
196 ATACAATCCTTTCTCTTCTTCAATGG
* * *
4053 AAAATGATTGAATGAAACACTGATACAACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCAC
1 AAAATGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCAC
* * * *
4118 ATCGGTA-TTTCATTCTTAATTTCATCATTTTCATCCTG-AAAAATCAAATTAAAATTAAAATAC
66 ATCAGTATTTTCATTCTTAATTTCAACATTTACATCCTGAAAAAATCAAATTAAAATTAAAATCC
* *
4181 TGAAATTCAGGATGAAATTGTTGATGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTC
131 TGAAATTTAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTC
*
4246 ATAGAATCCTTTCTCTTCTTCAATGG
196 ATACAATCCTTTCTCTTCTTCAATGG
* * *
4272 AAAATGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCTATTGGTTTTACGCCAC
1 AAAATGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCAC
* * * *
4337 ATCAGTATTTTCATTC-TAATGTCAACATTTTCATCTTGAGAAAATCAAATTAAAATTAAAATCC
66 ATCAGTATTTTCATTCTTAATTTCAACATTTACATCCTGAAAAAATCAAATTAAAATTAAAATCC
* *
4401 TGAAATTTAGGATGAAATTGTTGGTGTGGCAAAAAACTATTGGAAAGGGATAATATCCTTGTTTC
131 TGAAATTTAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTC
*
4466 ATACAATCCTTTCTCTTCTTCAGTGG
196 ATACAATCCTTTCTCTTCTTCAATGG
*
4492 AAAATGATTTAATAAAATGGAAAAGGATTGAATAAAACAGTGAAACCACGTCATTTGTGTCCCTT
1 AAAATG-----AT----T-G---A--A-TG----AAACAGTGACACCACGTCATTTGTGTCCCTT
* * * *
4557 TTTCAATAATTTTACGCTACATCAGTATTTTCATTCTTAATTTCAACATTTACATCCTG--AAAT
46 TTCCAATAGTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACATTTACATCCTGAAAAAA
* * * * * * * * *** * *
4620 TCAGGA-TGAAATT---GT-TTG---TGT-GGCAT-ATAACTATCGGAAAGGGATAATATCCCTA
111 TCA-AATTAAAATTAAAATCCTGAAATTTAGG-ATGA-AATTGTTGGTGTGGCATAA-A--ACTA
* * ** *** * * * **** *** ** *
4675 CTT-CATA-CCACCCTTTCCCTTCTTTAATGGA-AAAGGATT-GAATGAT--ACGG
170 -TTGGAAAGGGATAATATCCC-TGTTTCAT--ACAATCCTTTCTCTTCTTCAATGG
* * *
4725 AAAAGGATGGAATGAAACAATGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCAC
1 AAAATGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCAC
4790 ATCAGTATTTTCATTCTTAATTTCAACATTTACATCCTGAAAAAATCAAATTAAAATTAAAATCC
66 ATCAGTATTTTCATTCTTAATTTCAACATTTACATCCTGAAAAAATCAAATTAAAATTAAAATCC
* * *
4855 TGAAATTTAGGATGAAATTGTTGGTAT-GCATAAAACCATTGGAAAAGGATAATATCCCTGTTTC
131 TGAAATTTAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTC
4919 ATACAATCCTTTCTCTTCTTCAATGG
196 ATACAATCCTTTCTCTTCTTCAATGG
* *
4945 AAAATGATTGAATAAAATGGAAAAGGATTGAATAAAACAGTGACACCACGTCATTTGCGCCCCTT
1 -AAA--A-TG-AT----T-G---A--A-TG----AAACAGTGACACCACGTCATTTGTGTCCCTT
* * * * *
5010 TTCCAATAATTTTACGCCACATCAATATTTTAATTCTTAATTTCAACATTTTCATCCTTAAAAAA
46 TTCCAATAGTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACATTTACATCCTGAAAAAA
**
5075 TCAAATTAAAATTAAAATCCTGAAATACAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAA
111 TCAAATTAAAATTAAAATCCTGAAATTTAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAA
* *
5140 AGGGATAATATCCCTGTTTTATACAAT-CTTTACTCCTCTTCAATGG
176 AGGGATAATATCCCTGTTTCATACAATCCTTT-CTCTTCTTCAATGG
* *
5186 AAAATGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCATTAGTTTCACGCCAC
1 AAAATGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCAC
* *
5251 ATCAATATTTTCATTCTTAATTTCAACATTTACACCCTGAAAAAATCAAATTAAAATTAAAATCC
66 ATCAGTATTTTCATTCTTAATTTCAACATTTACATCCTGAAAAAATCAAATTAAAATTAAAATCC
* *
5316 TGAAATTTAGGATGAAATTGTTGGTGT-GCATAAAACCATTGGAAAAGGATAATATCCCTGTTTC
131 TGAAATTTAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTC
5380 ATACAATCCTTTCTCTTCTTCAATGG
196 ATACAATCCTTTCTCTTCTTCAATGG
5406 AAAATGATTGAAT
1 AAAATGATTGAAT
5419 AAAATGG
Statistics
Matches: 1338, Mismatches: 173, Indels: 153
0.80 0.10 0.09
Matches are distributed among these distances:
213 85 0.06
214 1 0.00
215 12 0.01
216 1 0.00
217 8 0.01
218 14 0.01
219 200 0.15
220 222 0.17
221 407 0.30
222 15 0.01
223 5 0.00
224 1 0.00
225 6 0.00
226 1 0.00
228 3 0.00
229 1 0.00
230 2 0.00
231 4 0.00
232 16 0.01
233 10 0.01
234 5 0.00
235 17 0.01
236 13 0.01
237 3 0.00
238 1 0.00
239 12 0.01
240 200 0.15
241 73 0.05
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (221 bp):
AAAATGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCAC
ATCAGTATTTTCATTCTTAATTTCAACATTTACATCCTGAAAAAATCAAATTAAAATTAAAATCC
TGAAATTTAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTC
ATACAATCCTTTCTCTTCTTCAATGG
Found at i:4514 original size:20 final size:20
Alignment explanation
Indices: 4489--4528 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4479 TCTTCTTCAG
* *
4489 TGGAAAATGATTTAATAAAA
1 TGGAAAAGGATTGAATAAAA
4509 TGGAAAAGGATTGAATAAAA
1 TGGAAAAGGATTGAATAAAA
4529 CAGTGAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (20 bp):
TGGAAAAGGATTGAATAAAA
Found at i:4682 original size:213 final size:213
Alignment explanation
Indices: 4397--4831 Score: 645
Period size: 213 Copynumber: 2.0 Consensus size: 213
4387 TAAAATTAAA
* * * * *
4397 ATCCTGAAATTTAGGATGAAATTGTTGGTGTGGCAAAAAACTATTGGAAAGGGATAATATCCTTG
1 ATCCTGAAATTTAGGATGAAATTGTTTGTGTGGCATATAACTATCGGAAAGGGATAATATCCCTG
* *
4462 TTTCATACAATCCTTTCTCTTCTTCAGTGGAAAATGATTTAATAAAATGGAAAAGGATTGAATAA
66 TTTCATACAATCCTTTCTCTTCTTCAATGGAAAATGATTGAATAAAATGGAAAAGGATTGAATAA
* * *
4527 AACAGTGAAACCACGTCATTTGTGTCCCTTTTTCAATAATTTTACGCTACATCAGTATTTTCATT
131 AACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAATTTTACGCCACATCAGTATTTTCATT
4592 CTTAATTTCAACATTTAC
196 CTTAATTTCAACATTTAC
* *
4610 ATCCTGAAATTCAGGATGAAATTGTTTGTGTGGCATATAACTATCGGAAAGGGATAATATCCCTA
1 ATCCTGAAATTTAGGATGAAATTGTTTGTGTGGCATATAACTATCGGAAAGGGATAATATCCCTG
* * * * * * * * * * *
4675 CTTCATACCACCCTTTCCCTTCTTTAATGGAAAAGGATTGAATGATACGGAAAAGGATGGAATGA
66 TTTCATACAATCCTTTCTCTTCTTCAATGGAAAATGATTGAATAAAATGGAAAAGGATTGAATAA
* *
4740 AACAATGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTTCATT
131 AACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAATTTTACGCCACATCAGTATTTTCATT
4805 CTTAATTTCAACATTTAC
196 CTTAATTTCAACATTTAC
4823 ATCCTGAAA
1 ATCCTGAAA
4832 AAATCAAATT
Statistics
Matches: 197, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
213 197 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Consensus pattern (213 bp):
ATCCTGAAATTTAGGATGAAATTGTTTGTGTGGCATATAACTATCGGAAAGGGATAATATCCCTG
TTTCATACAATCCTTTCTCTTCTTCAATGGAAAATGATTGAATAAAATGGAAAAGGATTGAATAA
AACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAATTTTACGCCACATCAGTATTTTCATT
CTTAATTTCAACATTTAC
Found at i:4898 original size:453 final size:448
Alignment explanation
Indices: 4180--5425 Score: 1592
Period size: 453 Copynumber: 2.8 Consensus size: 448
4170 AATTAAAATA
* * * **
4180 CTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTT
1 CTGAAATACAGGATGAAATTGTTGGTGTGGCATAAAACTATCGGAAAGGGATAATATCCCTACTT
* *
4245 CATAGAATCCTTT-CTCTTCTTCAATGGAAAATGAT--------TGAATGAAACAGTGACACCAC
66 CATACAA-CCTTTACTCCTCTTCAATGGAAAATGATGGAAAAGATGAATGAAACAGTGACACCAC
* * *
4301 GTCATTTGTGTCCCTTTTCTATTGGTTTTACGCCACATCAGTATTTTCATTC-TAATGTCAACAT
130 GTCATTTGTGTCCCTTTTCCATTAGTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACAT
* * *
4365 TTTCATCTTGAGAAAATCAAATTAAAATTAAAATCCTGAAATTTAGGATGAAATTGTTGGTGTGG
195 TTACATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTTAGGATGAAATTGTTGGTGT-G
* * * * *
4430 CAAAAAACTATTGGAAAGGGATAATATCCTTGTTTCATACAATCCTTTCTCTTCTTCAGTGGAAA
259 CATAAAACCATTGGAAAAGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAA
* * * *
4495 ATGATTTAATAAAATGGAAAAGGATTGAATAAAACAGTGAAACCACGTCATTTGTGTCCCTTTTT
324 ATGATTGAATAAAATGGAAAAGGATTGAATAAAACAGTGAAACCACGTCATTTGCGCCCCTTTTC
* * *
4560 CAATAATTTTACGCTACATCAGTATTTTCATTCTTAATTTC-A-A-CAT-TT-A-C-ATC
389 CAATAATTTTACGCCACATCAATATTTTAATTCTTAATTTCAACATCATCTTAATCAATC
* * *
4613 CTGAAATTCAGGATGAAATTGTTTGTGTGGCATATAACTATCGGAAAGGGATAATATCCCTACTT
1 CTGAAATACAGGATGAAATTGTTGGTGTGGCATAAAACTATCGGAAAGGGATAATATCCCTACTT
* *
4678 CATACCACCCTTT-C-CCTTCTTTAATGGAAAAGGATTGAATGATACGGAAAAGGATGGAATGAA
66 CATA-CAACCTTTACTCC-TCTTCAATGG---A--A---AATGAT--GGAAAA-GAT-GAATGAA
* *
4741 ACAATGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTTCATTC
117 ACAGTGACACCACGTCATTTGTGTCCCTTTTCCATTAGTTTTACGCCACATCAGTATTTTCATTC
4806 TTAATTTCAACATTTACATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTTAGGATGAA
182 TTAATTTCAACATTTACATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTTAGGATGAA
*
4871 ATTGTTGGTATGCATAAAACCATTGGAAAAGGATAATATCCCTGTTTCATACAATCCTTTCTCTT
247 ATTGTTGGTGTGCATAAAACCATTGGAAAAGGATAATATCCCTGTTTCATACAATCCTTTCTCTT
*
4936 CTTCAATGGAAAATGATTGAATAAAATGGAAAAGGATTGAATAAAACAGTGACACCACGTCATTT
312 CTTCAATGGAAAATGATTGAATAAAATGGAAAAGGATTGAATAAAACAGTGAAACCACGTCATTT
5001 GCGCCCCTTTTCCAATAATTTTACGCCACATCAATATTTTAATTCTTAATTTCAACATTTTCATC
377 GCGCCCCTTTTCCAATAATTTTACGCCACATCAATATTTTAATTCTTAATTTCAACA---TCAT-
5066 CTTAAAAAATCAAATTAAAATTAAAATC
438 CTT----AATC-------------AATC
* **
5094 CTGAAATACAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTT
1 CTGAAATACAGGATGAAATTGTTGGTGTGGCATAAAACTATCGGAAAGGGATAATATCCCTACTT
* *
5159 TATACAATCTTTACTCCTCTTCAATGGAAAATGAT--------TGAATGAAACAGTGACACCACG
66 CATACAACCTTTACTCCTCTTCAATGGAAAATGATGGAAAAGATGAATGAAACAGTGACACCACG
* *
5216 TCATTTGTGTCCCTTTTCCATTAGTTTCACGCCACATCAATATTTTCATTCTTAATTTCAACATT
131 TCATTTGTGTCCCTTTTCCATTAGTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACATT
*
5281 TACACCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTTAGGATGAAATTGTTGGTGTGCA
196 TACATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTTAGGATGAAATTGTTGGTGTGCA
5346 TAAAACCATTGGAAAAGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAT
261 TAAAACCATTGGAAAAGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAT
5411 GATTGAATAAAATGG
326 GATTGAATAAAATGG
Statistics
Matches: 712, Mismatches: 48, Indels: 78
0.85 0.06 0.09
Matches are distributed among these distances:
432 1 0.00
433 78 0.11
434 1 0.00
436 1 0.00
438 1 0.00
441 6 0.01
452 1 0.00
453 227 0.32
454 71 0.10
455 1 0.00
459 3 0.00
461 227 0.32
462 1 0.00
466 1 0.00
467 1 0.00
473 6 0.01
476 1 0.00
478 1 0.00
480 6 0.01
481 75 0.11
482 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (448 bp):
CTGAAATACAGGATGAAATTGTTGGTGTGGCATAAAACTATCGGAAAGGGATAATATCCCTACTT
CATACAACCTTTACTCCTCTTCAATGGAAAATGATGGAAAAGATGAATGAAACAGTGACACCACG
TCATTTGTGTCCCTTTTCCATTAGTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACATT
TACATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTTAGGATGAAATTGTTGGTGTGCA
TAAAACCATTGGAAAAGGATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAT
GATTGAATAAAATGGAAAAGGATTGAATAAAACAGTGAAACCACGTCATTTGCGCCCCTTTTCCA
ATAATTTTACGCCACATCAATATTTTAATTCTTAATTTCAACATCATCTTAATCAATC
Found at i:4965 original size:20 final size:20
Alignment explanation
Indices: 4940--4981 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
4930 TCTCTTCTTC
*
4940 AATGGAAAATGATTGAATAA
1 AATGGAAAAGGATTGAATAA
4960 AATGGAAAAGGATTGAATAA
1 AATGGAAAAGGATTGAATAA
4980 AA
1 AA
4982 CAGTGACACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.21, T:0.21
Consensus pattern (20 bp):
AATGGAAAAGGATTGAATAA
Found at i:5048 original size:240 final size:240
Alignment explanation
Indices: 4610--5425 Score: 1136
Period size: 240 Copynumber: 3.5 Consensus size: 240
4600 CAACATTTAC
* * * * * *
4610 ATCCTGAAATTCAGGATGAAATTGTTTGTGTGGCATATAACTATCGGAAAGGGATAATATCCCTA
1 ATCCTGAAATTCAGGATGAAATTGTTGGTGTGGCATAAAACCATTGGAAAAGGATAATATCCCTG
* * * * * * * * * *
4675 CTTCATACCACCCTTTCCCTTCTTTAATGGAAAAGGATTGAATGATACGGAAAAGGATGGAATGA
66 TTTCATACAATCCTTTCTCTTCTTCAATGGAAAATGATTGAATAAAATGGAAAAGGATTGAAT-A
* *
4740 AACAATGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTTCATT
130 AACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAATATTTTCATT
4805 CTTAATTTCAACATTTACATCCTGAAAAAATCAAATTAAAATTAAA
195 CTTAATTTCAACATTTACATCCTGAAAAAATCAAATTAAAATTAAA
* *
4851 ATCCTGAAATTTAGGATGAAATTGTTGGTAT-GCATAAAACCATTGGAAAAGGATAATATCCCTG
1 ATCCTGAAATTCAGGATGAAATTGTTGGTGTGGCATAAAACCATTGGAAAAGGATAATATCCCTG
4915 TTTCATACAATCCTTTCTCTTCTTCAATGGAAAATGATTGAATAAAATGGAAAAGGATTGAATAA
66 TTTCATACAATCCTTTCTCTTCTTCAATGGAAAATGATTGAATAAAATGGAAAAGGATTGAAT-A
* * * *
4980 AACAGTGACACCACGTCATTTGCGCCCCTTTTCCAATAATTTTACGCCACATCAATATTTTAATT
130 AACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAATATTTTCATT
* *
5045 CTTAATTTCAACATTTTCATCCTTAAAAAATCAAATTAAAATTAAA
195 CTTAATTTCAACATTTACATCCTGAAAAAATCAAATTAAAATTAAA
* * *
5091 ATCCTGAAATACAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTG
1 ATCCTGAAATTCAGGATGAAATTGTTGGTGTGGCATAAAACCATTGGAAAAGGATAATATCCCTG
* *
5156 TTTTATACAAT-CTTTACTCCTCTTCAATGG-AAA--A-TG-AT----T-G---A--A-TG---A
66 TTTCATACAATCCTTT-CTCTTCTTCAATGGAAAATGATTGAATAAAATGGAAAAGGATTGAATA
* *
5201 AACAGTGACACCACGTCATTTGTGTCCCTTTTCCATTAGTTTCACGCCACATCAATATTTTCATT
130 AACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAATATTTTCATT
*
5266 CTTAATTTCAACATTTACACCCTGAAAAAATCAAATTAAAATTAAA
195 CTTAATTTCAACATTTACATCCTGAAAAAATCAAATTAAAATTAAA
*
5312 ATCCTGAAATTTAGGATGAAATTGTTGGTGT-GCATAAAACCATTGGAAAAGGATAATATCCCTG
1 ATCCTGAAATTCAGGATGAAATTGTTGGTGTGGCATAAAACCATTGGAAAAGGATAATATCCCTG
5376 TTTCATACAATCCTTTCTCTTCTTCAATGGAAAATGATTGAATAAAATGG
66 TTTCATACAATCCTTTCTCTTCTTCAATGGAAAATGATTGAATAAAATGG
Statistics
Matches: 513, Mismatches: 49, Indels: 37
0.86 0.08 0.06
Matches are distributed among these distances:
220 54 0.11
221 139 0.27
223 1 0.00
224 2 0.00
225 4 0.01
226 1 0.00
228 1 0.00
229 1 0.00
230 1 0.00
231 1 0.00
232 1 0.00
236 2 0.00
237 2 0.00
238 1 0.00
240 220 0.43
241 82 0.16
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.33
Consensus pattern (240 bp):
ATCCTGAAATTCAGGATGAAATTGTTGGTGTGGCATAAAACCATTGGAAAAGGATAATATCCCTG
TTTCATACAATCCTTTCTCTTCTTCAATGGAAAATGATTGAATAAAATGGAAAAGGATTGAATAA
ACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAATATTTTCATTC
TTAATTTCAACATTTACATCCTGAAAAAATCAAATTAAAATTAAA
Found at i:5060 original size:21 final size:21
Alignment explanation
Indices: 5031--5070 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5021 TTACGCCACA
* *
5031 TCAATATTTTAATTCTTAATT
1 TCAACATTTTAATCCTTAATT
*
5052 TCAACATTTTCATCCTTAA
1 TCAACATTTTAATCCTTAA
5071 AAAATCAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (21 bp):
TCAACATTTTAATCCTTAATT
Done.