Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011873.1 Corchorus olitorius cultivar O-4 contig11906, 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: 2774
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Found at i:286 original size:154 final size:154
Alignment explanation
Indices: 1--802 Score: 1193
Period size: 154 Copynumber: 5.2 Consensus size: 154
* * *
1 AGTTCCGTTTTAAATCGTCTTCGATTTAGG-AATCCTCGAA-GC-TTTCCTTTCCAATGTTTATG
1 AGTTCCGTTTTGAATCGTCTTCGATTT-GGCAAACCTC-AATGCATTT-CTTTCCATTGTTTATG
* **
63 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACGG
63 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCTTTTGGAACACTT
* * *
128 GTTATTTTGGGTCTATCGCGGCCCATT
128 GTTATTTTGGGCCTATCGAGGCCCAAT
* * *
155 AGTTCAGTTTTGAATCTTCTTCGATTTGGCAAACCTAAATGCATTTCTTTCCATTGTTTATGGCC
1 AGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCATTTCTTTCCATTGTTTATGGCC
* *
220 TAACTATAATCATTTTGGTGTGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTT
66 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCTTTTGGAACACTTGTT
*
285 ATTTTGGGCCTATCGAGGCCCACT
131 ATTTTGGGCCTATCGAGGCCCAAT
* * *
309 AGTTTCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGCC
1 AGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCATTTCTTTCCATTGTTTATGGCC
*
374 TAACTATAATCATTTTGGTGTGATTAGTCCACTGTGAAGTTTTTAACTCTTTTGGAACACTTGTT
66 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCTTTTGGAACACTTGTT
* * **
439 ATTTTGGGCGTAGCG-GGAACAATT
131 ATTTTGGGCCTATCGAGGCCCAA-T
* * * **
463 AGTTCTGTTTTGAATTGTCTACGATTTGGCAAACCTCAATGTTTTTCTTTCCATTGTTTATGGCC
1 AGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCATTTCTTTCCATTGTTTATGGCC
* * * *
528 TCACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT-A-TTTTTTGGACCAATTGTT
66 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCTTTTGGAACACTTGTT
*
591 ATTTTGGGACTATCGAGGCCCAAT
131 ATTTTGGGCCTATCGAGGCCCAAT
* * *
615 GGTTCCGTGTTGAATCGTCTTCGATTTGGCAAACCTCAATGCATTTCTTTCAATTGTTTATGGCC
1 AGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCATTTCTTTCCATTGTTTATGGCC
*
680 TAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAACTCTTTTGGAACACTTGTT
66 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCTTTTGGAACACTTGTT
745 ATTTTGGGCCTATCGAGGCCCAAT
131 ATTTTGGGCCTATCGAGGCCCAAT
769 AGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAC
1 AGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAC
803 TATAATAATT
Statistics
Matches: 585, Mismatches: 56, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
152 127 0.22
153 15 0.03
154 440 0.75
155 3 0.01
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (154 bp):
AGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCATTTCTTTCCATTGTTTATGGCC
TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCTTTTGGAACACTTGTT
ATTTTGGGCCTATCGAGGCCCAAT
Found at i:892 original size:119 final size:119
Alignment explanation
Indices: 681--921 Score: 410
Period size: 119 Copynumber: 2.0 Consensus size: 119
671 TTTATGGCCT
* * *
681 AACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAACTCTTTTGGAACACTTGTTA
1 AACTATAATAATTTTAGTGAGATTAGTCCACTCTGAAGTTTTTAACTCATTTGGAACACTTGTTA
*
746 TTTTGGGCCTATCGAGGCCCAATAGTTCCGTTTTGAATCGTCTTCGATTTGGCA
66 TTTTGGGCCTATCGAGGCCCAATAGTTCCGTTTTGAATCATCTTCGATTTGGCA
*
800 AACTATAATAATTTTGGTGAGATTAGTCCACTCTGAAGTTTTTAACTCATTTGGAACACTTGTTA
1 AACTATAATAATTTTAGTGAGATTAGTCCACTCTGAAGTTTTTAACTCATTTGGAACACTTGTTA
* * *
865 TTTTGGGCCTATCGGGGCCTATTAGTTCCGTTTTGAATCATCTTCGATTTGGCA
66 TTTTGGGCCTATCGAGGCCCAATAGTTCCGTTTTGAATCATCTTCGATTTGGCA
919 AAC
1 AAC
922 CTCAATTCTT
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
119 114 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.39
Consensus pattern (119 bp):
AACTATAATAATTTTAGTGAGATTAGTCCACTCTGAAGTTTTTAACTCATTTGGAACACTTGTTA
TTTTGGGCCTATCGAGGCCCAATAGTTCCGTTTTGAATCATCTTCGATTTGGCA
Found at i:1015 original size:273 final size:271
Alignment explanation
Indices: 530--1028 Score: 827
Period size: 273 Copynumber: 1.8 Consensus size: 271
520 TTATGGCCTC
* * ** *
530 ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTATTTTTTGGACCAATTGTTATTT
1 ACTATAATAATTTTGGTGAGATTAGTCCACTCTGAAGTTTTTATCATTTGGAACAATTGTTATTT
* *
595 TGGGACTATCGAGGCCCAATGGTTCCGTGTTGAATCGTCTTCGATTTGGCAAACCTCAATGCATT
66 TGGGACTATCGAGGCCCAATAGTTCCGTGTTGAATCATCTTCGATTTGGCAAACCTCAATGCATT
660 TCTTTCAATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTA
131 TCTTTCAATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTA
725 ACTCTTTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCAATAGTTCCGTTTTGAATCGTCTT
196 ACTCTTTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCAATAGTTCCGTTTTGAATCGTCTT
790 CGATTTGGCAA
261 CGATTTGGCAA
*
801 ACTATAATAATTTTGGTGAGATTAGTCCACTCTGAAGTTTTTAACTCATTTGGAACACTTGTTAT
1 ACTATAATAATTTTGGTGAGATTAGTCCACTCTGAAGTTTTT-A-TCATTTGGAACAATTGTTAT
* * * * * * *
866 TTTGGGCCTATCGGGGCCTATTAGTTCCGTTTTGAATCATCTTCGATTTGGCAAACCTCAATTCT
64 TTTGGGACTATCGAGGCCCAATAGTTCCGTGTTGAATCATCTTCGATTTGGCAAACCTCAATGCA
* *
931 TTTCTTTCAATTGTTTATGGCTTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
129 TTTCTTTCAATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTT
996 TAACTCTTTTGGAACACTTGTTATTTTGGGCCT
194 TAACTCTTTTGGAACACTTGTTATTTTGGGCCT
1029 GCTGTTTAGA
Statistics
Matches: 209, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
271 40 0.19
272 1 0.00
273 168 0.80
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (271 bp):
ACTATAATAATTTTGGTGAGATTAGTCCACTCTGAAGTTTTTATCATTTGGAACAATTGTTATTT
TGGGACTATCGAGGCCCAATAGTTCCGTGTTGAATCATCTTCGATTTGGCAAACCTCAATGCATT
TCTTTCAATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTA
ACTCTTTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCAATAGTTCCGTTTTGAATCGTCTT
CGATTTGGCAA
Found at i:1311 original size:154 final size:153
Alignment explanation
Indices: 1032--2774 Score: 2576
Period size: 154 Copynumber: 11.3 Consensus size: 153
1022 TGGGCCTGCT
* * * *
1032 GTTTAGAATTGTCTTCGATTTGGCAAACCTCAATTCTTTTCTTTCCTTTGTTTATGGCCTAACTA
1 GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
** * *
1097 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAATTCATTTGGACCACTAGTTATTTTG
66 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
1162 GGCCTATCGGGGCCCATTAGTTC
131 GGCCTATCGGGGCCCATTAGTTC
* * * * *
1185 TGTTTTAAATCCTCTTCGATTTGGCAAACCTAAATGCATTTCTTTCCTTTGTTTATGGCCTAACT
1 -GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
*
1250 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAAG-TCATTTGGACCACTTGTTATTT
65 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT-AGCTCATTTGGAACACTTGTTATTT
*
1314 TGGGCCTATCGGGGCCAATTAGTTC
129 TGGGCCTATCGGGGCCCATTAGTTC
* *
1339 TGTTTAGAATTGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
1 -GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
*
1404 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCACTTTGGAACACTTGTTATTT
65 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA-TTTGGAACACTTGTTATTT
* *
1469 TGGGCCTATCAGGGCCCATTAGTGAC
129 TGGGCCTATCGGGGCCCATTAGT-TC
* *
1495 GTTTTGAATCCTCTTCGATTTGGCAAACCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACTA
1 GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
* * * *
1560 TAATCATTTTAGTGAGATTAGTCCGCTGTAAAGTTTTTAACTCATTTGGAACACTTGTTATTTTG
66 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
* *
1625 GGCCTATCAGGGCCCATTAGTGAC
131 GGCCTATCGGGGCCCATTAGT-TC
* *
1649 GTTTTGAATCCTCTTCGATTTGGCAAACCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACTA
1 GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
* *
1714 CAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
66 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
* ** * *
1779 GACCTATCATGGCCCTTTAGTTTT
131 GGCCTATCGGGGCCCATTAG-TTC
* * * *
1803 GTTTTGAATCGTCTTCGATTTGCCAACCCTCGATGCTTTTTTTTCCATTGTTTATGGCCTAACTA
1 GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
* *
1868 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATCTTA
66 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
1933 GGCCT-TCCGGGGCCCATTAGTTCC
131 GGCCTAT-CGGGGCCCATTAGTT-C
* * *
1957 GTTTTGAATCGTCTTCGATTTGGCAACCCTCGACTGCTTTGCTTTCCATTGTTTATGGCCTAACT
1 GTTTTGAATCGTCTTCGATTTGGCAAACCTC-AATGCTTTTCTTTCCATTGTTTATGGCCTAACT
*
2022 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAAACACTTGTTATTTT
65 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
* * *
2087 AGGCCTTTCGGGGCCCATTAGCTC
130 GGGCCTATCGGGGCCCATTAGTTC
* * * * *
2111 GGTTTTGAATCGTTTTGGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGACTAACT
1 -GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
2176 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
65 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
2241 GGGCCTATCGGGGCCCATTAGTGTC
130 GGGCCTATCGGGGCCCATTAGT-TC
* * ** * *
2266 GTTTTGAATCGTCATCGATTTGGCAACCCTTGATGCTTTTATTTCCATTGTTTATGGGCTAACTA
1 GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
*
2331 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTA
66 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
*
2396 GGCCTTTCGGGGCCC-TTAGTTCC
131 GGCCTATCGGGGCCCATTAGTT-C
* * *
2419 GTTTTGAATCGTATTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
1 GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
* *
2484 TAATCATTTTTGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTA
66 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
* *
2549 GGCCTTTCGGGGCCCATTAGCTC
131 GGCCTATCGGGGCCCATTAGTTC
* * * *
2572 TGTTTTGAATCGTTTTGGATTTGGCAACCCTCGATGCGTTTTCTTTCCATTGTTTATGGCCTAAC
1 -GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGC-TTTTCTTTCCATTGTTTATGGCCTAAC
2637 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
64 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* * * *
2702 TAGGCCTTTCGGGGCCCATCAGGTGAC
129 TGGGCCTATCGGGGCCCATTA-GT-TC
* *
2729 GTTTTGAATCGTCTACGATTTGG-AAATCCTAAATGCTTTTCTTTCC
1 GTTTTGAATCGTCTTCGATTTGGCAAA-CCTCAATGCTTTTCTTTCC
Statistics
Matches: 1473, Mismatches: 98, Indels: 35
0.92 0.06 0.02
Matches are distributed among these distances:
152 1 0.00
153 150 0.10
154 882 0.60
155 409 0.28
156 30 0.02
157 1 0.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (153 bp):
GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
GGCCTATCGGGGCCCATTAGTTC
Found at i:2004 original size:463 final size:461
Alignment explanation
Indices: 800--2774 Score: 2827
Period size: 463 Copynumber: 4.3 Consensus size: 461
790 CGATTTGGCA
* * *
800 AACTATAATAATTTTGGTGAGATTAGTCCACTCTGAAGTTTTTAACTCATTTGGAACACTTGTTA
1 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
* ** * * * *
865 TTTTGGGCCTATCGGGGCCTATTAGTTCCGTTTTGAATCATCTTCGATTTGGCAAACCTCAATTC
66 TTTTGGGCCTATCGGGGCCCATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGC
* * *
930 TTTTCTTTCAATTGTTTATGGCTTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
131 TTTTATTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
* * * * *
995 TTAACTCTTTTGGAACACTTGTTA--TT-----TT--GGG-CC--T-G--CTGTTTAGAATTGTC
196 TTAGCTCATTTGGAACACTTGTTATTTTAGGCCTTCGGGGCCCATTAGTTCCGTTTTGAATCGTC
* *
1045 TTCGATTTGGCAAACCTCAATTCTTTTCTTTCCTTTGTTTATGGCCTAACTATAATCATTTTGGT
261 TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGT
* * * *
1110 GAGATTAGTCCACTGTGAAGTTTTTAATTCATTTGGACCACTAGTTATTTTGGGCCTATCGGGGC
326 GAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTAGGCCTATCGGGGC
* * * * *
1175 CCATTAGTTCTGTTTTAAATCCTCTTCGATTTGGCAAACCTAAATGCATTTCTTTCCTTTGTTTA
391 CCATTAGCTCTGTTTTGAATCCTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTA
1240 TGGCCT
456 TGGCCT
*
1246 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAAG-TCATTTGGACCACTTGTT
1 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT-AGCTCATTTGGAACACTTGTT
* * * * * *
1310 ATTTTGGGCCTATCGGGGCCAATTAGTTCTGTTTAGAATTGTCTTCGATTTGGCAAACCTCAATG
65 ATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATG
*
1375 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
130 CTTTTATTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
* * * **
1440 TTTAACTCACTTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATC
195 TTTAGCTCA-TTTGGAACACTTGTTATTTTAGGCCT-TCGGGGCCCATTAGTTCCGTTTTGAATC
* *
1505 CTCTTCGATTTGGCAAACCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
258 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
* * * * *
1570 AGTGAGATTAGTCCGCTGTAAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCAG
323 GGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTAGGCCTATCGG
*
1635 GGCCCATTAG-TGAC-GTTTTGAATCCTCTTCGATTTGGCAAACCTCAATGCCTTTCTTTCCATT
388 GGCCCATTAGCT--CTGTTTTGAATCCTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
1698 GTTTATGGCCT
451 GTTTATGGCCT
* *
1709 AACTACAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
1 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
* ** * *
1774 TTTTGGACCTATCATGGCCCTTTAGTTTTGTTTTGAATCGTCTTCGATTTGCCAACCCTCGATGC
66 TTTTGGGCCTATCGGGGCCCATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGC
*
1839 TTTTTTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
131 TTTTATTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
*
1904 TTAGCTCATTTGGAACACTTGTTATCTTAGGCCTTCCGGGGCCCATTAGTTCCGTTTTGAATCGT
196 TTAGCTCATTTGGAACACTTGTTATTTTAGGCCTT-CGGGGCCCATTAGTTCCGTTTTGAATCGT
* * *
1969 CTTCGATTTGGCAACCCTCGACTGCTTTGCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
260 CTTCGATTTGGCAAACCTC-AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
* * *
2034 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAAACACTTGTTATTTTAGGCCTTTCGGG
324 GTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTAGGCCTATCGGG
* * * * * *
2099 GCCCATTAGCTCGGTTTTGAATCGTTTTGGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTT
389 GCCCATTAGCTCTGTTTTGAATCCTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT
*
2164 TATGGACT
454 TATGGCCT
2172 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
1 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
* * * *
2237 TTTTGGGCCTATCGGGGCCCATTAGTGTCGTTTTGAATCGTCATCGATTTGGCAACCCTTGATGC
66 TTTTGGGCCTATCGGGGCCCATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGC
*
2302 TTTTATTTCCATTGTTTATGGGCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
131 TTTTATTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
2367 TTAGCTCATTTGGAACACTTGTTATTTTAGGCCTTTCGGGGCCC-TTAGTTCCGTTTTGAATCGT
196 TTAGCTCATTTGGAACACTTGTTATTTTAGGCC-TTCGGGGCCCATTAGTTCCGTTTTGAATCGT
* * * *
2431 ATTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTTG
260 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
* *
2496 TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGGCCTTTCGGGG
325 TGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTAGGCCTATCGGGG
* * * * *
2561 CCCATTAGCTCTGTTTTGAATCGTTTTGGATTTGGCAACCCTCGATGCGTTTTCTTTCCATTGTT
390 CCCATTAGCTCTGTTTTGAATCCTCTTCGATTTGGCAAACCTCAATGC-TTTTCTTTCCATTGTT
2626 TATGGCCT
454 TATGGCCT
2634 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
1 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
* * * *** * * * **
2699 TTTTAGGCCTTTCGGGGCCCATCAGGTGACGTTTTGAATCGTCTACGATTTGGAAATCCTAAATG
66 TTTTGGGCCTATCGGGGCCCATTA-GTTTTGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATG
*
2764 CTTTTCTTTCC
130 CTTTTATTTCC
Statistics
Matches: 1395, Mismatches: 106, Indels: 39
0.91 0.07 0.03
Matches are distributed among these distances:
446 188 0.13
447 17 0.01
449 2 0.00
454 1 0.00
455 1 0.00
457 3 0.00
458 2 0.00
460 1 0.00
461 155 0.11
462 218 0.16
463 803 0.58
464 4 0.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (461 bp):
AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
TTTTGGGCCTATCGGGGCCCATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGC
TTTTATTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
TTAGCTCATTTGGAACACTTGTTATTTTAGGCCTTCGGGGCCCATTAGTTCCGTTTTGAATCGTC
TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGT
GAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTAGGCCTATCGGGGC
CCATTAGCTCTGTTTTGAATCCTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTA
TGGCCT
Found at i:2078 original size:617 final size:611
Alignment explanation
Indices: 800--2774 Score: 2933
Period size: 617 Copynumber: 3.2 Consensus size: 611
790 CGATTTGGCA
* *
800 AACTATAATAATTTTGGTGAGATTAGTCCACTCTGAAGTTTTTAACTCATTTGGAACACTTGTTA
1 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTA
* * ** * *
865 TTTTGGGCCTATCGGGGCCTATTAGTTCCGTTTTGAATCATCTTCGATTTGGCAAACCTCAATTC
66 TTTTAGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGC
* *
930 TTTTCTTTCAATTGTTTATGGCTTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
131 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
* * *
995 TTAACTCTTTTGGAACACTTGTTATTTTGGGCC--T---G--C-----T--GTTTAGAATTGTCT
196 TTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATTAGTGCGTTTTGAATCGTCT
* *
1046 TCGATTTGGCAAACCTCAATTCTTTTCTTTCCTTTGTTTATGGCCTAACTATAATCATTTTGGTG
261 TCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTG
** * *
1111 AGATTAGTCCACTGTGAAGTTTTTAATTCATTTGGACCACTAGTTATTTTGGGCCTATCGGGGCC
326 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT-GGCCTATCGGGGCC
* * * ** * *
1176 CATTAGTTCTGTTTTAAATCCTCTTCGATTTGGCAAACCTAAATGCATTTCTTTCCTTTGTTTAT
390 C-TTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTAT
*
1241 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAAG-TCATTTGGACCAC
454 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT-AGCTCATTTGGAACAC
* * * * *
1305 TTGTTATTTTGGGCCTATCGGGGCCAATTAGTTCTGTTTAGAATTGTCTTCGATTTGGCAAACCT
518 TTGTTATTTTAGGCCT-TCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAACCCT
*
1370 CAATGCTTTTCTTTCCATTGTTTATGGCCT
582 CGATGCTTTTCTTTCCATTGTTTATGGCCT
1400 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCACTTTGGAACACTTGTT
1 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCA-TTTGGAACACTTGTT
* * *
1465 ATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCCTCTTCGATTTGGCAAACCTCAATG
65 ATTTTAGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
* * * *
1530 CCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCGCTGTAAAGTT
130 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
*
1595 TTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCC
195 TTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCATTAGTG-CGTTTTGAATCG
* * *
1660 TCTTCGATTTGGCAAACCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACTACAATCATTTTA
258 TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
**
1725 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGACCTATCATG
323 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG-CCTATCGGG
* * *
1790 GCCCTTTAGTTTTGTTTTGAATCGTCTTCGATTTGCCAACCCTCGATGCTTTTTTTTCCATTGTT
387 GCCC-TTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTT
1855 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
451 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
* *
1920 ACTTGTTATCTTAGGCCTTCCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
516 ACTTGTTATTTTAGGCCTT-CGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAACC
*
1985 CTCGACTGCTTTGCTTTCCATTGTTTATGGCCT
580 CTCGA-TGCTTTTCTTTCCATTGTTTATGGCCT
* *
2018 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAAACACTTGTTA
1 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTA
* * * * *
2083 TTTTAGGCCTTTCGGGGCCCATTAGCT--CGGTTTTGAATCGTTTTGGATTTGGCAACCCTCGAT
66 TTTTAGGCCTATCGGGGCCCATTAG-TGAC-GTTTTGAATCGTCTTCGATTTGGCAAACCTCAAT
*
2146 GCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGT
129 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGT
*
2211 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGTCGTTTTGAATC
194 TTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCATTAGTG-CGTTTTGAATC
* * ** * *
2276 GTCATCGATTTGGCAACCCTTGATGCTTTTATTTCCATTGTTTATGGGCTAACTATAATCATTTT
257 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
*
2341 GGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGGCCTTTCGG
322 GGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT-GGCCTATCGG
* *
2406 GGCCCTTAGTTCCGTTTTGAATCGTATTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTT
386 GGCCCTTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTT
*
2471 TATGGCCTAACTATAATCATTTTTGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
451 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
* * *
2536 ACTTGTTATTTTAGGCCTTTCGGGGCCCATTAGCTCTGTTTTGAATCGTTTTGGATTTGGCAACC
516 ACTTGTTATTTTAGGCC-TTCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAACC
2601 CTCGATGCGTTTTCTTTCCATTGTTTATGGCCT
580 CTCGATGC-TTTTCTTTCCATTGTTTATGGCCT
*
2634 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
1 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTA
* * * *
2699 TTTTAGGCCTTTCGGGGCCCATCAGGTGACGTTTTGAATCGTCTACGATTTGG-AAATCCTAAAT
66 TTTTAGGCCTATCGGGGCCCATTA-GTGACGTTTTGAATCGTCTTCGATTTGGCAAA-CCTCAAT
2763 GCTTTTCTTTCC
129 GCTTTTCTTTCC
Statistics
Matches: 1244, Mismatches: 101, Indels: 43
0.90 0.07 0.03
Matches are distributed among these distances:
600 47 0.04
601 166 0.13
603 1 0.00
607 1 0.00
609 1 0.00
614 1 0.00
615 3 0.00
616 300 0.24
617 646 0.52
618 78 0.06
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (611 bp):
AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTA
TTTTAGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGC
TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
TTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATTAGTGCGTTTTGAATCGTCT
TCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTG
AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGCCTATCGGGGCCC
TTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGG
CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
TTATTTTAGGCCTTCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAACCCTCGAT
GCTTTTCTTTCCATTGTTTATGGCCT
Done.