Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011647.1 Corchorus olitorius cultivar O-4 contig11680, 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: 2597
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.42
Found at i:315 original size:154 final size:154
Alignment explanation
Indices: 1--2594 Score: 2938
Period size: 154 Copynumber: 16.5 Consensus size: 154
* * ***
1 TGAAGTTTTTAGCTCATTTGGAACACTCT-TTATTTTGGGCCTATTGGGGCTCATTAGTGACGTT
1 TGAAGTTTTTAGCTCATTTGGAACACT-TGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTT
*
65 TTGAATCGTCTTCGATTT-GCAACCCTCAATGCTTTTCTTTCCATTGTTTATGACCTAACTATAA
65 TTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAA
129 TCATTTTGGTGAGATTAGTCCACTG
130 TCATTTTGGTGAGATTAGTCCACTG
* *
154 TGAAGTTTTTAGATCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTCGTTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTT
*
219 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTATTTATGGCCTAACTATAAT
66 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
*
284 CATTTTGGTGAGTTTAGTCCACTG
131 CATTTTGGTGAGATTAGTCCACTG
* * *
308 TGAAGTTTTTAGCCCATTTGGAACACTTGTTATTAT-GGCATATCGGGGCCCATTAGTTTTGTTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTT
* * *
372 TGAATCGTCTTCGATTTGGAAACCCTCAATGCTTTTCTTTCCATAGTTTATGGCCTAACAATAAT
66 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
* * *
437 CATTTTGTTGACATCAGTCCACTG
131 CATTTTGGTGAGATTAGTCCACTG
**
461 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTT
* * * * * * *
526 GGAATCATCTTCGATTTGGCTACACTCAATGCGTTTCTTTTCATTGTTTATGTCCTAACTATAAT
66 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
591 CATTTTGGTGAGATTAGTCCACTG
131 CATTTTGGTGAGATTAGTCCACTG
* * *
615 TGAAGTTTTTAGCTTATTTGGAACACTAGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTAT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTT
* * *
680 TGAATCGTCTTCGATTTGGCAACCTTTAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATTAT
66 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
*
745 CAATTTGGTGAGATTAGTCCACTG
131 CATTTTGGTGAGATTAGTCCACTG
*
769 TGAAGTTTTTAGTCTCATTTGGAACACTTGTTGTTTTGGGCCTATCGGGG-CCATTAGTTTTGTT
1 TGAAGTTTTTAG-CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTT
833 TTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAA
65 TTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAA
898 TCATTTTGGTGAGATTAGTCCACTG
130 TCATTTTGGTGAGATTAGTCCACTG
* *
923 TGAAGTTTTTAGCTCATTCGGAACACTTGTTATTTTGGGTCCTATCGGGGACCAATTAGTTTTGT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG-CCTATCGGGG-CCCATTAGTTTTGT
* *
988 TTTGAATTGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGCCCTAACTATA
64 TTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
1053 ATCATTTTGGTGAGATTAGTCCACTG
129 ATCATTTTGGTGAGATTAGTCCACTG
* *
1079 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGTCCGTATCGAGGCCAATTAGTTTTGT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG-CC-TATCGGGGCCCATTAGTTTTGT
* *
1144 TTTGAATTGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGCCCTAACTATA
64 TTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
* *
1209 ATCATTTCGGTTGAGATTAGTCCAATG
129 ATCATTTTGG-TGAGATTAGTCCACTG
* * **
1236 TGAAGTTTTTAGCTCATTTTGAACACTTGTTA-----AGCCTATCGGGGCCCATTAGTTCCGTTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTT
* * * * * *
1296 TGAATCGTCATCGATTTGGCAACACTCAATGATTTTCTTTCCATTGTTTATTGCCTAACAAAAAT
66 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
*
1361 CATTTTGGTGAGATTAGTCCACTA
131 CATTTTGGTGAGATTAGTCCACTG
* ** *
1385 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGAG---AT--TAGTCCACTGTGAAGTTTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA-T-T--AG-TTT
* * *** * **
1445 TAGCTCATTTGGAA-C-ACTT-GTTATTTTGGGCCTAACTGGGC-CAATTAGTTCCATTTTGAAT
61 T-G-T--TTT-GAATCGTCTTCG--A-TTT-GG-C-AAC---CCTCAATGCTTTTC--TTTCCAT
* ** ** * * *
1506 CGTCTTCGATTTGG-C-AACCCTCAATGC-TTTTCTTTCCATTGTTTATGTCCTAACTA
110 TGT-TT--A--TGGCCTAACTAT-AAT-CATTTT-GGT-GA--GATTA-GTCC--ACTG
* * * * * * * * ** *
1562 TAATCATTTTTGTGAGATTAGTCCACTAT-GAAGTATTTAGCTCA-ATTGAAACACTTTTTATTT
1 TGA--AGTTTT-T-AG----CT-CA-TTTGGAA-CACTT-G-TTATTTTG-GGC-C----TA-TC
* * * **** ** * * *
1625 TGGGCCTATCAGGTCCCATTAGTTCCAT-TTGGAATCATCTTCGATTTGGCAAACCTCAATGCTT
46 GGGGCCCATTA-GTTTTGTT--TTGAATCGT-C-------TTCGATTTGGCAACCCTCAATGCTT
* * * *
1689 TTCTTTCCAATGTTTATGACCTAACTATAATCATTTTGGTAAGATTAGTCCACTT
100 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
* * * *
1744 TGAAGTTTTTAGCTCATTTGGAACACTTTTTATTTTGGCCCTATTGGGGCCCATTAGTGATT-TT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-TTTGTT
* * * * *
1808 TTGAATCATCTTCTATTT-GCAACCTTCAATGCGTTTCTTTCCATTGTTTATGCCCTAACTATAA
65 TTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAA
*
1872 TCATTTTGGTGAGATTAGTGCACTG
130 TCATTTTGGTGAGATTAGTCCACTG
* * * * * ***
1897 TGAAGTTTTTAGCTTAATTGGAATACTTGTTATTTTGGCCCTATCGGGGACCATTAGTTCCATTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTT
*
1962 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGTCCTAACTATAAT
66 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
2027 CATTTTGGTGAGATTAGTCCACTG
131 CATTTTGGTGAGATTAGTCCACTG
* **
2051 TGAAGTTTTTAGCTCGTTTCAAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTT
*
2116 TGAATCGTCTTCGATTTGGCAACCGTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
66 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
2181 CATTTTGGTGAGATTAGTCCACTG
131 CATTTTGGTGAGATTAGTCCACTG
***
2205 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCATTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTT
*
2270 CGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
66 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
*
2335 CATTTTGGTAAGATTAGTCCACT-
131 CATTTTGGTGAGATTAGTCCACTG
* * * * * * **
2358 TGGAAGTTTTTAGCTCAATTGGAACACTCGGTATTTTGGGCATATCGAGGACCATTAGTTCCGTT
1 T-GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTT
* *
2423 TTGAATCGTCTTCGATTTGGCAACCTTTAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAA
65 TTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAA
* * *
2488 TCATTTCGGTAAGATTAGTCCACTA
130 TCATTTTGGTGAGATTAGTCCACTG
* * * * ***
2513 TGAAGTTTTTAGCTCAATTGAAACACTTTTTATTTTGGGCCTATCAGGGCCCATTAGTTCCATTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTT
* *
2578 CGAATCATCTTCGATTT
66 TGAATCGTCTTCGATTT
2595 TGC
Statistics
Matches: 2100, Mismatches: 241, Indels: 199
0.83 0.09 0.08
Matches are distributed among these distances:
149 49 0.02
150 85 0.04
151 5 0.00
152 2 0.00
153 377 0.18
154 1047 0.50
155 36 0.02
156 232 0.11
157 55 0.03
158 5 0.00
159 6 0.00
160 2 0.00
161 5 0.00
162 4 0.00
163 4 0.00
164 18 0.01
165 3 0.00
166 7 0.00
167 2 0.00
169 5 0.00
170 11 0.01
171 7 0.00
172 6 0.00
173 5 0.00
174 5 0.00
175 4 0.00
177 6 0.00
178 2 0.00
179 6 0.00
180 6 0.00
181 2 0.00
182 5 0.00
184 4 0.00
185 5 0.00
186 5 0.00
187 6 0.00
188 8 0.00
189 11 0.01
190 5 0.00
192 3 0.00
193 7 0.00
194 4 0.00
195 7 0.00
196 2 0.00
197 4 0.00
198 2 0.00
199 3 0.00
200 6 0.00
201 1 0.00
202 2 0.00
203 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.42
Consensus pattern (154 bp):
TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTT
TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
CATTTTGGTGAGATTAGTCCACTG
Found at i:1406 original size:615 final size:612
Alignment explanation
Indices: 1--2594 Score: 3120
Period size: 615 Copynumber: 4.1 Consensus size: 612
* * **
1 TGAAGTTTTTAGCTCATTTGGAACACTCT-TTATTTTGGGCCTATTGGGGCTCATTAGTGACGTT
1 TGAAGTTTTTAGCTCATTTGGAACACT-TGTTA---T-GGCCTATCGGGGCCCATTAGTTCCGTT
65 TTGAATCGTCTTCGATTT-GCAACCCTCAATGCTTTTCTTTCCATTGTTTATGACCTAACTATAA
61 TTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGACCTAACTATAA
*
129 TCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGATCATTTGGAACACTTGTTATTTTGGGC
126 TCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGC
*
194 CTATCGGGGCCCATTAGTTTCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTT
191 CTATCGGGGCCCATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTT
* * *
259 CCATTATTTATGGCCTAACTATAATCATTTTGGTGAGTTTAGTCCACTGTGAAGTTTTTAGCCCA
256 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA
* * ***
324 TTTGGAACACTTGTTATTAT-GGCATATCGGGGCCCATTAGTTTTGTTTTGAATCGTCTTCGATT
321 TTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCGTCTTCGATT
* * * * * * *
388 TGGAAACCCTCAATGCTTTTCTTTCCATAGTTTATGGCCTAACAATAATCATTTTGTTGACATCA
386 TGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTA
*
453 GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAG
451 GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAG
* * * * *
518 TTCCGTTTGGAATCATCTTCGATTTGGCTACACTCAATGCGTTTCTTTTCATTGTTTATGTCCTA
516 TTCCGTTTTGAATCATCTTCGATTTGGCAACCCTCAATGCGTTTCTTTCCATTGTTTATGCCCTA
*
583 ACTATAATCATTTTGGTGAGATTAGTCCACTG
581 ACTATAATCATTTCGGTGAGATTAGTCCACTG
* * ** *
615 TGAAGTTTTTAGCTTATTTGGAACACTAGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTAT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTTA---T-GGCCTATCGGGGCCCATTAGTTCCGTTT
* * * *
680 TGAATCGTCTTCGATTTGGCAACCTTTAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATTAT
62 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGACCTAACTATAAT
* *
745 CAATTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGTCTCATTTGGAACACTTGTTGTTTTGGGC
127 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG-CTCATTTGGAACACTTGTTATTTTGGGC
810 CTATCGGGG-CCATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTT
191 CTATCGGGGCCCATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTT
874 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA
256 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA
* * *** *
939 TTCGGAACACTTGTTATTTTGGGTCCTATCGGGGACCAATTAGTTTTGTTTTGAATTGTCTTCGA
321 TTTGGAACACTTGTTATTTTGGG-CCTATCGGGG-CCCATTAGTTCCATTTTGAATCGTCTTCGA
* *
1004 TTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGCCCTAACTATAATCATTTTGGTGAGAT
384 TTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGAT
*
1069 TAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGTCCGTATCGAGGCCAA
449 TAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG-CC-TATCGAGGCCCA
** ** *
1134 TTAGTTTTGTTTTGAATTGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGC
512 TTAGTTCCGTTTTGAATCATCTTCGATTTGGCAACCCTCAATGCGTTTCTTTCCATTGTTTATGC
*
1199 CCTAACTATAATCATTTCGGTTGAGATTAGTCCAATG
577 CCTAACTATAATCATTTCGG-TGAGATTAGTCCACTG
* *
1236 TGAAGTTTTTAGCTCATTTTGAACACTTGTTA-AGCCTATCGGGGCCCATTAGTTCCGTTTTGAA
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATGGCCTATCGGGGCCCATTAGTTCCGTTTTGAA
* * * * *
1300 TCGTCATCGATTTGGCAACACTCAATGATTTTCTTTCCATTGTTTATTG-CCTAACAAAAATCAT
66 TCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTA-TGACCTAACTATAATCAT
* *
1364 TTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGAG---AT
130 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
** * * *
1426 --TAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA-C-ACTT-GTTATTTTGGGCCTAACTGGGC
195 CGGGGCCCA-T-T--AG-TTTT-G-T--TTT-GAATCGTCTTCG--A-TTT-GG-C-AAC---CC
* **
1486 -CAATTAGTTCCATTTTGAATCGTCTTCGATTTGGCAACCCTCAAT-GCTTTTCTTTCCATTGTT
241 TCAA-T-G---C--TTT---TC-T-TTCCA-TT-G------TTTATGGC----C--T--A-----
* * * * * *
1549 TATGTCCTA-ACTATAATCATTTTTGTGAGATTAGTCCACTATGAAGTATTTAGCTCAATTGAAA
273 -A----CTATA--ATCAT--TTTG-GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
* * * * * *
1613 CACTTTTTATTTTGGGCCTATCAGGTCCCATTAGTTCCATTTGGAATCATCTTCGATTTGGCAAA
328 CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCGTCTTCGATTTGGCAAC
* *
1678 CCTCAATGCTTTTCTTTCCAATGTTTATGACCTAACTATAATCATTTTGGTAAGATTAGTCCACT
393 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACT
* * * * * ****
1743 TTGAAGTTTTTAGCTCATTTGGAACACTTTTTATTTTGGCCCTATTGGGGCCCATTAGTGATTTT
458 GTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTT
* *
1808 TTGAATCATCTTCTATTT-GCAACCTTCAATGCGTTTCTTTCCATTGTTTATGCCCTAACTATAA
523 TTGAATCATCTTCGATTTGGCAACCCTCAATGCGTTTCTTTCCATTGTTTATGCCCTAACTATAA
* *
1872 TCATTTTGGTGAGATTAGTGCACTG
588 TCATTTCGGTGAGATTAGTCCACTG
* * * * *
1897 TGAAGTTTTTAGCTTAATTGGAATACTTGTTATTTTGGCCCTATCGGGGACCATTAGTTCCATTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTTA---TGG-CCTATCGGGGCCCATTAGTTCCGTTT
*
1962 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGTCCTAACTATAAT
62 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGACCTAACTATAAT
* **
2027 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCGTTTCAAACACTTGTTATTTTGGGCC
127 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
*
2092 TATCGGGGCCCATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCGTCAATGCTTTTCTTTC
192 TATCGGGGCCCATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTC
2157 CATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCAT
257 CATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCAT
*
2222 TTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTCGAATCGTCTTCGATTT
322 TTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCGTCTTCGATTT
2287 GGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAG
387 GGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAG
* * * * *
2352 TCCACT-TGGAAGTTTTTAGCTCAATTGGAACACTCGGTATTTTGGGCATATCGAGGACCATTAG
452 TCCACTGT-GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAG
* * * * *
2416 TTCCGTTTTGAATCGTCTTCGATTTGGCAACCTTTAATGCTTTTCTTTCCATTGTTTATGGCCTA
516 TTCCGTTTTGAATCATCTTCGATTTGGCAACCCTCAATGCGTTTCTTTCCATTGTTTATGCCCTA
* *
2481 ACTATAATCATTTCGGTAAGATTAGTCCACTA
581 ACTATAATCATTTCGGTGAGATTAGTCCACTG
* * * * *
2513 TGAAGTTTTTAGCTCAATTGAAACACTTTTTATTTTGGGCCTATCAGGGCCCATTAGTTCCATTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTTA---T-GGCCTATCGGGGCCCATTAGTTCCGTTT
* *
2578 CGAATCATCTTCGATTT
62 TGAATCGTCTTCGATTT
2595 TGC
Statistics
Matches: 1708, Mismatches: 179, Indels: 184
0.82 0.09 0.09
Matches are distributed among these distances:
610 1 0.00
611 3 0.00
612 3 0.00
613 1 0.00
614 74 0.04
615 463 0.27
616 291 0.17
617 14 0.01
618 141 0.08
619 8 0.00
620 90 0.05
621 50 0.03
622 2 0.00
623 2 0.00
624 3 0.00
626 3 0.00
627 2 0.00
628 1 0.00
629 1 0.00
631 2 0.00
633 4 0.00
636 5 0.00
637 3 0.00
638 4 0.00
639 2 0.00
640 1 0.00
642 1 0.00
643 2 0.00
644 4 0.00
645 3 0.00
646 5 0.00
649 4 0.00
651 2 0.00
653 1 0.00
654 1 0.00
655 1 0.00
656 3 0.00
658 3 0.00
659 2 0.00
660 2 0.00
661 48 0.03
662 58 0.03
663 38 0.02
664 8 0.00
665 134 0.08
666 154 0.09
667 52 0.03
669 3 0.00
670 1 0.00
671 4 0.00
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.42
Consensus pattern (612 bp):
TGAAGTTTTTAGCTCATTTGGAACACTTGTTATGGCCTATCGGGGCCCATTAGTTCCGTTTTGAA
TCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGACCTAACTATAATCATT
TTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
GGGGCCCATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATT
GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
AACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCGTCTTCGATTTGGCA
ACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCA
CTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCG
TTTTGAATCATCTTCGATTTGGCAACCCTCAATGCGTTTCTTTCCATTGTTTATGCCCTAACTAT
AATCATTTCGGTGAGATTAGTCCACTG
Found at i:1441 original size:51 final size:51
Alignment explanation
Indices: 1369--1472 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
1359 ATCATTTTGG
1369 TGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
1 TGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
*
1420 TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
1 TGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
1471 TG
1 TG
1473 GGCCTAACTG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.43
Consensus pattern (51 bp):
TGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
Found at i:1471 original size:27 final size:27
Alignment explanation
Indices: 1390--1471 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
1380 CACTATGAAG
1390 TTTTTAGCTCATTTGGAACACTTGTTA
1 TTTTTAGCTCATTTGGAACACTTGTTA
* * ** *
1417 TTTTGAG---A-TTAGTCCAC-TGTGAA
1 TTTTTAGCTCATTTGGAACACTTGT-TA
1440 GTTTTTAGCTCATTTGGAACACTTGTTA
1 -TTTTTAGCTCATTTGGAACACTTGTTA
1468 TTTT
1 TTTT
1472 GGGCCTAACT
Statistics
Matches: 38, Mismatches: 10, Indels: 14
0.61 0.16 0.23
Matches are distributed among these distances:
22 3 0.08
23 7 0.18
24 7 0.18
27 11 0.29
28 7 0.18
29 3 0.08
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (27 bp):
TTTTTAGCTCATTTGGAACACTTGTTA
Found at i:1569 original size:205 final size:200
Alignment explanation
Indices: 1219--1626 Score: 602
Period size: 205 Copynumber: 2.0 Consensus size: 200
1209 ATCATTTCGG
* * *
1219 TTGAGATTAGTCCAATGTGAAGTTTTTAGCTCATTTTGAACACTTGTTAAGCCTATCGGGGCCCA
1 TTGAGATTAGTCCAATGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAAGCCTAACGGGGCCAA
*
1284 TTAGTTCCGTTTTGAATCGTCATCGATTTGGCAACACTCAATGATTTTCTTTCCATTGTTTATTG
66 TTAGTTCCATTTTGAATCGTCATCGATTTGGCAACACTCAATGATTTTCTTTCCATTGTTTATTG
* * *
1349 CCTAACAAAAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTGGAACACTTG
131 CCTAACAAAAATCATTTTGGTGAGATTAGTCCACTATGAAGTATTTAGCTCAATTGAAACACTTG
1414 TTATT
196 TTATT
* * *
1419 TTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAACTGG
1 TTGAGATTAGTCCAATGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA-----AGCCTAACGGG
* * *
1484 GCCAATTAGTTCCATTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTT
61 GCCAATTAGTTCCATTTTGAATCGTCATCGATTTGGCAACACTCAATGATTTTCTTTCCATTGTT
* * *
1549 TA-TGTCCTAACTATAATCATTTTTGTGAGATTAGTCCACTATGAAGTATTTAGCTCAATTGAAA
126 TATTG-CCTAACAAAAATCATTTTGGTGAGATTAGTCCACTATGAAGTATTTAGCTCAATTGAAA
*
1613 CACTTTTTATT
190 CACTTGTTATT
1624 TTG
1 TTG
1627 GGCCTATCAG
Statistics
Matches: 185, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
200 47 0.25
204 2 0.01
205 136 0.74
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (200 bp):
TTGAGATTAGTCCAATGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAAGCCTAACGGGGCCAA
TTAGTTCCATTTTGAATCGTCATCGATTTGGCAACACTCAATGATTTTCTTTCCATTGTTTATTG
CCTAACAAAAATCATTTTGGTGAGATTAGTCCACTATGAAGTATTTAGCTCAATTGAAACACTTG
TTATT
Done.