Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006633.1 Kokia drynarioides strain JFW-HI SEQ_121223, 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: 3200
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Found at i:402 original size:216 final size:216
Alignment explanation
Indices: 18--1227 Score: 1422
Period size: 216 Copynumber: 5.6 Consensus size: 216
8 ATTTGTACTG
* *
18 GTAAAACTTTTACGAGTTCTTTTATAACTTAGGATCCTTAAAGTATTCAAAACGA-CACATTCCT
1 GTAAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAAACGATC-CATTCCT
* * * * *
82 TCGAGAAATTTTCTGAACATTCCATTCTCGGGAAATCGTATCATTTGGTCAAAATAGTTTGTCAT
65 TCGAGGAATTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCAT
* *
147 TTTGTAAA-ACACTTTTTATCTTTGAGTTAAAAACTTATTTTGGTAAGAATTGTTTGTCTATTGG
130 TTTGTAAACA-ACTTTTTATCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCTATTGG
* *
211 TCCTTGGTCGAACTTCTTAACTT
194 TTCTTGGTCGAACTTCTGAACTT
* * *
234 GTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT
1 GTAAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAAACGATCCATTCCTT
* * * * * *
299 TGAGGAATTTCCCGAACATTTCATGCTCGAGAAATTGCATCATTTGGTCCAATTAGTTTGTCATT
66 CGAGGAATTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATT
* * * * *
364 TTGTAAACAACTTTTTATCTTTGAATTAAAATCTTATTTTTGTGAGAATTGTTTGGCTCTTAGTT
131 TTGTAAACAACTTTTTATCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCTATTGGTT
*
429 CTTGGAT--ATACGTCTGAAC-T
196 CTTGG-TCGA-ACTTCTGAACTT
* * * *
449 ATAAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAATGTATTCAAAACGATTCATTCCTT
1 GTAAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAAACGATCCATTCCTT
* * * * *
514 CGAGAAATTTTTTGAACATTTCATTCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTTTCATT
66 CGAGGAATTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATT
579 TTGTAAA-ACACTTTTTATCTTTGAATTAAAAACTTATTTTGGTGAGAATAT-TTTGTCTATTGG
131 TTGTAAACA-ACTTTTTATCTTTGAATTAAAAACTTATTTTGGTGAGAAT-TGTTTGTCTATTGG
* * *
642 TCCTTGGCCGAACATCTGAACTT
194 TTCTTGGTCGAACTTCTGAACTT
* * ** * * *
665 GTCAAACTATTATTAGTTCTTTTATAACTTTGGATCCTTAAAGTATTCAAGACGATCCATTCTTT
1 GTAAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAAACGATCCATTCCTT
* * * ** *
730 TGAGCAATTTTTTTGAATGTTCCATGCTCGAGAAATCGCATCATTTGGTCCATATAGTTTGTCAT
66 CGAGGAA-TTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCAT
* * * * * * *
795 TTTGTAAACAACTTTCTATCTTTAAATTAAAAACATATTTAGGTTAGAATTGGTTGTCTCTTGGT
130 TTTGTAAACAACTTTTTATCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCTATTGGT
* * *
860 TCTTGGACGAATATTC-GAACTG
195 TCTTGGTCGAA-CTTCTGAACTT
** *
882 GTAAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTTAAAGTATTCAAAACGGTCCATTCCTT
1 GTAAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAAACGATCCATTCCTT
* * * * * * **
947 TGAGGAATTTTCTGAACAATCCATGCTTGGGAAATCACATCATTAGGTCCAAATAGTTTAACATT
66 CGAGGAATTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATT
** ** * *
1012 TTGTAAACAACTTTTGGTCTTTGAATTTAAAAA-TTATTTACGTGAGAATTATTTTTCTATTGGT
131 TTGTAAACAACTTTTTATCTTTGAA-TTAAAAACTTATTTTGGTGAGAATTGTTTGTCTATTGGT
*
1076 TCTTGGTCGAACTTCTAAACTT
195 TCTTGGTCGAACTTCTGAACTT
* * * * * *
1098 GTATAACCTTTACGAGTTATTTTATTACTTTGGTTCCTTAAAGTATTCAAGATGATCCATTCCTT
1 GTAAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAAACGATCCATTCCTT
* ** * * *
1163 CGAGGAACTTTCCAAACATTCCATGCTCGGGAAATCG--T-A--TCGTGCAAATAGTTTGTCATT
66 CGAGGAATTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATT
1223 TTGTA
131 TTGTA
1228 CATTCCATGC
Statistics
Matches: 840, Mismatches: 139, Indels: 35
0.83 0.14 0.03
Matches are distributed among these distances:
211 21 0.03
213 1 0.00
214 2 0.00
215 188 0.22
216 435 0.52
217 190 0.23
218 3 0.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.41
Consensus pattern (216 bp):
GTAAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAAACGATCCATTCCTT
CGAGGAATTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATT
TTGTAAACAACTTTTTATCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCTATTGGTT
CTTGGTCGAACTTCTGAACTT
Found at i:1757 original size:216 final size:216
Alignment explanation
Indices: 1264--3001 Score: 1894
Period size: 216 Copynumber: 8.1 Consensus size: 216
1254 TGCAAATCGT
* * * * * * * *
1264 ATCCATTCCTTAGAGCAATTTTT-GAACGTTCGATGCTCGAGAAATAGCGTCATTTGGTCCAAAA
1 ATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCAAGAAATCGCATCATTTGGTCCAAAT
**
1328 AGTTTGTCATTTTGTAAACAACTTTTTTGTCTTTGAATTAAAAACTTATTTAAATGAGAATTATT
66 AGTTTGTCATTTTGTAAACAAC-TTTTTGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATT
** * * *
1393 TACCTATTGGTCCTTTGCCGAACTTCAGAACTTGTCAAACTTTCT-CGAGTACTTTTATAACTTC
130 TGTCTATTGGTCCTTGGCCGAACTTCCGAACTTGTCAAACTTT-TACGAGTTCTTTTATAACTTC
** * *
1457 GGTTCCCGAAGGTATTCAAAACG
194 GGTTCCTTAAAGTATTCAAGACG
* * * *** *
1480 ATCCATTCCTTCAAG-AATTTTTCGAACAATCCATGCTTGGGAAATCGCATCATTAGGTCCAAAT
1 ATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCAAGAAATCGCATCATTTGGTCCAAAT
* * * * *
1544 AGTTTATCATTTTGTAAACAACTTTTGGTCTTTGAGTTTAAAACATATTTACGTGAGAATTATTT
66 AGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATTT
* * * ** * * * * * *
1609 TTCTCTTGGTTCTTGGTTGAACTTCTGAAATTGT-ATATCCTTTATGAGTTCTTTTATAACTTTG
131 GTCTATTGGTCCTTGGCCGAACTTCCGAACTTGTCA-AACTTTTACGAGTTCTTTTATAACTTCG
* *
1673 GTTCCTTAAAGTATACAAGATG
195 GTTCCTTAAAGTATTCAAGACG
* * * ***
1695 ATCCATTCCTTCGAGGAATTTCTCAAACATTCCATTCTTGGGAAATCGCATCATTTGGTCCAAAT
1 ATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCAAGAAATCGCATCATTTGGTCCAAAT
* *
1760 AGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAA-TAAAAACTTATTTACATGAGAATTGTTT
66 AGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATTT
* * **
1824 ATCTATTGGTCCTTGGCCGAACTTCCGAACTAGTCAAACTTTTACGAGTTCTTTTATAACTTCAA
131 GTCTATTGGTCCTTGGCCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGG
1889 TTCCTTAAAGTATTCAAGACG
196 TTCCTTAAAGTATTCAAGACG
* ** * * * * *
1910 ATCCATTGCTTCGAGCAATTTTTTTAA-ATTTCCATTCTCAAGAATTTGCATCATGTGGACCAAT
1 ATCCATTCCTTCGAGCAATTTTTCGAACA-TTCCATTCTCAAGAAATCGCATCATTTGGTCCAAA
* * * * *
1974 TAGTTTGTCGTTTTGTAAAAAACTTTTTATCTTTGAATTAAAAATTTATTTAGGTGAGAA-TAGT
65 TAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTACGTGAGAATTA-T
* ** * * * *
2038 TTGTCTCTTGGTTTTTGGACGAA-TATCCGAACTGGTAAAAATTTTACGAGTTCTTTTATAACTT
129 TTGTCTATTGGTCCTTGGCCGAACT-TCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT
* *
2102 AGGTTCCTTAAAGTATTCAA-AGGG
193 CGGTTCCTTAAAGTATTCAAGA-CG
* * * ** *
2126 ATGCATTCCTTCGAGAAATTTTTCGAAC-TTCCATTCTCAGGAAATCATATCATTTGGTCAAAAT
1 ATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCAAGAAATCGCATCATTTGGTCCAAAT
* ** * *
2190 AGTTTGTCATTTTGTAAA-ACACTTTTTATCTTTGAATTAAAAACTTATTTTGGTAAGAATTGTT
66 AGTTTGTCATTTTGTAAACA-ACTTTTTGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATT
* * * *
2254 TGTTTATTGGTCCTTAGTCGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCG
130 TGTCTATTGGTCCTTGGCCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCG
*
2319 GTTCCTTAAAGTATTCAAGATG
195 GTTCCTTAAAGTATTCAAGACG
* * * ** * * * * *
2341 ATGCC-TTACTTCAAGGAATTTCCCGAACATTCCATGCTCGAGAAGTCGCATCATTTAGTCTAAA
1 AT-CCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCAAGAAATCGCATCATTTGGTCCAAA
* * * *
2405 CAGTTTCTCATTTTGTAAATAACTTTTTGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTT
65 TAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATT
* * ** * *
2470 TGTCTCA-TGGTCCTTGGCTGAACTTCCGAACTTGTCAAAGTTTTACGAGTTCTTGAATAACATA
130 TGTCT-ATTGGTCCTTGGCCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC
*
2534 TGTTCCTTAAAGTATTCAAGACG
194 GGTTCCTTAAAGTATTCAAGACG
* *** * *
2557 ATCCATTCCTTCGAGCAATTTTTCGAATATTCCATTCTCAAGAAATTAAAACATTTGGTCAAAAT
1 ATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCAAGAAATCGCATCATTTGGTCCAAAT
* * **
2622 AGTTTGTCGTTTTGTAAA-ATACATTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTATT
66 AGTTTGTCATTTTGTAAACA-ACTTTTTGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATT
** *
2686 TGTCTATTGGTCCTTATCCGAACATT-CGAACTTGTCGAACTTTTACGAGTTCTTTTATAACTTC
130 TGTCTATTGGTCCTTGGCCGAAC-TTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC
*
2750 GGTTCCTTAAAGCATTCAAGACG
194 GGTTCCTTAAAGTATTCAAGACG
* * * * *
2773 ATCCACTCCTTCGAGCAATTTTTCAAACATTCCATGCTCAAGAAATCACATCATTTGGTCCAATT
1 ATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCAAGAAATCGCATCATTTGGTCCAAAT
* *
2838 AGTTTGTCATTTTGTAAACAGCTTTTTGTATTTGAATTAAAAACTTATTGT--GATGAGAA-TAG
66 AGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATT-TACG-TGAGAATTA-
* * * * *
2900 TTTGTCT-TTCGGTTCTTGGACGAACATCCGAACTGGTAAAACTTTTACGAGTTCTTTTATAACT
128 TTTGTCTATT-GGTCCTTGGCCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACT
* * *
2964 TAGGTTCCTTAAAGTATTCAAAACA
192 TCGGTTCCTTAAAGTATTCAAGACG
*
2989 ATGCATTCCTTCG
1 ATCCATTCCTTCG
3002 GGAAATCGCA
Statistics
Matches: 1271, Mismatches: 222, Indels: 58
0.82 0.14 0.04
Matches are distributed among these distances:
214 4 0.00
215 481 0.38
216 780 0.61
217 6 0.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (216 bp):
ATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCAAGAAATCGCATCATTTGGTCCAAAT
AGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATTT
GTCTATTGGTCCTTGGCCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGG
TTCCTTAAAGTATTCAAGACG
Found at i:2091 original size:431 final size:432
Alignment explanation
Indices: 1264--3007 Score: 2034
Period size: 431 Copynumber: 4.0 Consensus size: 432
1254 TGCAAATCGT
* * * * * *
1264 ATCCATTCCTTAGAGCAATTTTT-GAACGTTCGATGCTC-GAGAAAT-AGCGTCATTTGGTCCAA
1 ATCCATTCCTTCGAGAAATTTTTCGAACATTCCATTCTCAG-GAAATCA-CATCATTTGGT-CAA
*
1326 AA-AGTTTGTCATTTTGT-AAACAACTTTTTTGTCTTTGAATTAAAAACTTATTTAAATGAGAAT
63 AATAGTTTGTCATTTTGTAAAAC-AC-TTTTTGTCTTTGAATTAAAAACTTATTTAGATGAGAAT
* * * *
1389 TATTTACCTATTGGTCCTTTGCCGAACTTCAGAACTTGTCAAACTTTCT-CGAGTACTTTTATAA
126 TATTTATCTATTGGTCCTTAGCCGAACTTCCGAACTTGTCAAACTTT-TACGAGTTCTTTTATAA
** * * *
1453 CTTCGGTTCCCGAAGGTATTCAAAACGATCCATTCCTTCAAG-AATTTTTCGAACAATCCATGCT
190 CTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCT
*** * * * *
1517 TGGGAAATCGCATCATTAGGTCCAAATAGTTTATCATTTTGTAAACAACTTTTGGTCTTTGAGTT
255 CAAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATT
* * * ** * * * *
1582 TAAAACATATTTACGTGAGAATTA-TTTTTCTCTTGGTTCTTGGTTGAACTTCTGAAATTGTATA
320 AAAAACTTATTTACGTGAGAA-TAGTTTGTCTCTTGGTTCTTGGACGAACTTCCGAACTGGTAAA
* * * * * *
1646 TCCTTTATGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATACAAGATG
384 ACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGACG
* * * ** * *
1695 ATCCATTCCTTCGAGGAATTTCTCAAACATTCCATTCTTGGGAAATCGCATCATTTGGTCCAAAT
1 ATCCATTCCTTCGAGAAATTTTTCGAACATTCCATTCTCAGGAAATCACATCATTTGGTCAAAAT
* *
1760 AGTTTGTCATTTTGT-AAACAACTTTTTGTCTTTGAA-TAAAAACTTATTTACATGAGAATTGTT
66 AGTTTGTCATTTTGTAAAAC-ACTTTTTGTCTTTGAATTAAAAACTTATTTAGATGAGAATTATT
* * *
1823 TATCTATTGGTCCTTGGCCGAACTTCCGAACTAGTCAAACTTTTACGAGTTCTTTTATAACTTCA
130 TATCTATTGGTCCTTAGCCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCG
* * * ** *
1888 ATTCCTTAAAGTATTCAAGACGATCCATTGCTTCGAGCAATTTTTTTAA-ATTTCCATTCTCAAG
195 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTCGAACA-TTCCATGCTCAAG
* * * * * * * *
1952 AATTTGCATCATGTGGACCAATTAGTTTGTCGTTTTGTAAAAAACTTTTTATCTTTGAATTAAAA
259 AAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAA
* * * *
2017 ATTTATTTAGGTGAGAATAGTTTGTCTCTTGGTTTTTGGACGAA-TATCCGAACTGGTAAAAATT
324 ACTTATTTACGTGAGAATAGTTTGTCTCTTGGTTCTTGGACGAACT-TCCGAACTGGTAAAACTT
*
2081 TTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA-AGGG
388 TTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGA-CG
* *
2126 ATGCATTCCTTCGAGAAATTTTTCGAAC-TTCCATTCTCAGGAAATCATATCATTTGGTCAAAAT
1 ATCCATTCCTTCGAGAAATTTTTCGAACATTCCATTCTCAGGAAATCACATCATTTGGTCAAAAT
* * * * *
2190 AGTTTGTCATTTTGTAAAACACTTTTTATCTTTGAATTAAAAACTTATTTTGGTAAGAATTGTTT
66 AGTTTGTCATTTTGTAAAACACTTTTTGTCTTTGAATTAAAAACTTATTTAGATGAGAATTATTT
* * * *
2255 GTTTATTGGTCCTTAGTCGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGG
131 ATCTATTGGTCCTTAGCCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGG
* * * ** *
2320 TTCCTTAAAGTATTCAAGATGATGCC-TTACTTCAAGGAATTTCCCGAACATTCCATGCTCGAGA
196 TTCCTTAAAGTATTCAAGACGAT-CCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTCAAGA
* * * * * *
2384 AGTCGCATCATTTAGTCTAAACAGTTTCTCATTTTGTAAATAACTTTTTGTCTTTGAATTAAAAA
260 AATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAA
* * * * * *
2449 CTTATTTACGTGAGAATTGTTTGTCTCATGGTCCTTGG-CTGAACTTCCGAACTTGTCAAAGTTT
325 CTTATTTACGTGAGAATAGTTTGTCTCTTGGTTCTTGGAC-GAACTTCCGAACTGGTAAAACTTT
** * *
2513 TACGAGTTCTTGAATAACATATGTTCCTTAAAGTATTCAAGACG
389 TACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGACG
* * * * * *
2557 ATCCATTCCTTCGAGCAATTTTTCGAATATTCCATTCTCAAGAAATTAAAACATTTGGTCAAAAT
1 ATCCATTCCTTCGAGAAATTTTTCGAACATTCCATTCTCAGGAAATCACATCATTTGGTCAAAAT
* * * * *
2622 AGTTTGTCGTTTTGTAAAATACATTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTATTT
66 AGTTTGTCATTTTGTAAAACACTTTTTGTCTTTGAATTAAAAACTTATTTAGATGAGAATTATTT
* * *
2687 GTCTATTGGTCCTTATCCGAACATT-CGAACTTGTCGAACTTTTACGAGTTCTTTTATAACTTCG
131 ATCTATTGGTCCTTAGCCGAAC-TTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCG
* * * *
2751 GTTCCTTAAAGCATTCAAGACGATCCACTCCTTCGAGCAATTTTTCAAACATTCCATGCTCAAGA
195 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTCAAGA
* * * *
2816 AATCACATCATTTGGTCCAATTAGTTTGTCATTTTGTAAACAGCTTTTTGTATTTGAATTAAAAA
260 AATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAA
*
2881 CTTATTGT--GATGAGAATAGTTTGTCT-TTCGGTTCTTGGACGAACATCCGAACTGGTAAAACT
325 CTTATT-TACG-TGAGAATAGTTTGTCTCTT-GGTTCTTGGACGAACTTCCGAACTGGTAAAACT
* *
2943 TTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAAACA
387 TTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGACG
* *
2989 ATGCATTCCTTCGGGAAAT
1 ATCCATTCCTTCGAGAAAT
3008 CGCATCATTT
Statistics
Matches: 1113, Mismatches: 176, Indels: 47
0.83 0.13 0.04
Matches are distributed among these distances:
429 1 0.00
430 179 0.16
431 519 0.47
432 409 0.37
433 5 0.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (432 bp):
ATCCATTCCTTCGAGAAATTTTTCGAACATTCCATTCTCAGGAAATCACATCATTTGGTCAAAAT
AGTTTGTCATTTTGTAAAACACTTTTTGTCTTTGAATTAAAAACTTATTTAGATGAGAATTATTT
ATCTATTGGTCCTTAGCCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGG
TTCCTTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTCAAGAA
ATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAAC
TTATTTACGTGAGAATAGTTTGTCTCTTGGTTCTTGGACGAACTTCCGAACTGGTAAAACTTTTA
CGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGACG
Found at i:3149 original size:189 final size:189
Alignment explanation
Indices: 2814--3188 Score: 590
Period size: 189 Copynumber: 2.0 Consensus size: 189
2804 CCATGCTCAA
* * *
2814 GAAATCACATCATTTGGTCCAATTAGTTTGTCATTTTGTAAACAGCTTTTTGTATTTGAATTAAA
1 GAAATCACATCATTTGGACCAATTAGTTTGTCAATTTGTAAACAACTTTTTGTATTTGAATTAAA
* *
2879 AACTTATTGTGATGAGAATAGTTTGTCTTTCGGTTCTTGGACGAACATCCGAACTGGTAAAACTT
66 AACTTATTCTGATGAGAATAGTTTGTCTTTCGGTTCTTGGACGAACATCAGAACTGGTAAAACTT
*
2944 TTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAAACAATGCATTCCTTCGG
131 TTACGAGTTCTTTTATAACTTAGGATCCTTAAAGTATTCAAAACAATGCATTCCTTCGG
* *
3003 GAAATCGCATCATTTGGACCGATTAGTTTGTCAATTTGTAAACAACTTTTTGTATTTGAATTAAA
1 GAAATCACATCATTTGGACCAATTAGTTTGTCAATTTGTAAACAACTTTTTGTATTTGAATTAAA
* * * *
3068 AACTTATTCTGGTGAGAATTGTTTGTCTCTT-GGTTCTTGGACGAACATTAGAACTTGTAAAACT
66 AACTTATTCTGATGAGAATAGTTTGTCT-TTCGGTTCTTGGACGAACATCAGAACTGGTAAAACT
* * * *
3132 TTTTCGAGTTTTTTTATAACTTAGGATGCTTAAAGTATTCAAAACAATTCATTCCTT
130 TTTACGAGTTCTTTTATAACTTAGGATCCTTAAAGTATTCAAAACAATGCATTCCTT
3189 TGAGAAATTT
Statistics
Matches: 169, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
189 167 0.99
190 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.40
Consensus pattern (189 bp):
GAAATCACATCATTTGGACCAATTAGTTTGTCAATTTGTAAACAACTTTTTGTATTTGAATTAAA
AACTTATTCTGATGAGAATAGTTTGTCTTTCGGTTCTTGGACGAACATCAGAACTGGTAAAACTT
TTACGAGTTCTTTTATAACTTAGGATCCTTAAAGTATTCAAAACAATGCATTCCTTCGG
Done.