Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011778.1 Corchorus olitorius cultivar O-4 contig11811, 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: 3084
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Found at i:797 original size:153 final size:154
Alignment explanation
Indices: 1--1642 Score: 2434
Period size: 153 Copynumber: 10.7 Consensus size: 154
** *
1 GGGGCCCATTAGTTTCGTTTTCGAATCGTCTTCGATTTGG-AAACCTCAAAGCTTTTCTTTCCAT
1 GGGGCCCATTAGTGACGTTTT-GAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAT
65 TGTTTATGGCCTTAACTATAATC-TATTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
65 TGTTTATGGCC-TAACTATAATCAT-TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
129 TGGAACGACTTGTTATTTTGGGCCTATC
128 TGGAAC-ACTTGTTATTTTGGGCCTATC
* * *
157 GGGGACCATTAGTGACGTTTTGAGA-CGTCTTCGATTTGGC-AACCTTCGATGCCTTTCTTTCCA
1 GGGGCCCATTAGTGACGTTTTGA-ATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTCCA
* * *
220 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTTAGTCCACTTGTGAAATTTTTAGCTTAG
64 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGA-TTAGTCCAC-TGTGAAGTTTTTAGCTCAT
*
285 TTGGAACACGTTG-TATTTTGTG-CTATC
127 TTGGAACAC-TTGTTATTTTGGGCCTATC
312 GGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
1 GGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
377 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCTATTTG
66 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC-ATTTG
*
442 GAATACTTGTTATTTTGGGCCTATC
130 GAACACTTGTTATTTTGGGCCTATC
* * *
467 GGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGTCTTTTC-TTACGT
1 GGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG-CTTTTCTTTCCAT
* * * *
531 TGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCAGTATGTAGTTTTTAGCTCATTCG
65 TGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
596 GAACACTTGTTATTTTGGGCCTATC
130 GAACACTTGTTATTTTGGGCCTATC
621 GGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
1 GGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
* * * * * *
686 GTTTAGGGACTAACGATAATCCTTTTGGTAAGATTAGTCCACTGTGAAG-TTTTACCTCATTTGG
66 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
750 AACACTTGTTATTTTGGGCCTATC
131 AACACTTGTTATTTTGGGCCTATC
* *
774 GAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAAT
1 GGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
*
839 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACCGTGAAGTTTTTAGCTCATTTGG
66 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
*
904 AACCCTTGTTATTTTGGGCCTAT-
131 AACACTTGTTATTTTGGGCCTATC
* * * * *
927 TGGGCTCATTAGTAACGTTTTGAATCGTCTTCGATTTTGAAAACCTCAATGCTTTTCTTTCCATT
1 GGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
* * *
992 GTTTATTGCCTAACTATAATCATTTTGATGAGATTAGTCCAATGTGAAGTTTTTAGCTCATTTGG
66 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
*
1057 AACCCTTGTTATTTTGGGCCTATC
131 AACACTTGTTATTTTGGGCCTATC
* * *
1081 GGGGCCTATTAGTAACGTTTTGAATCGTCTTCGATTTGGAAAACCTCAATG-TTTT-TTTCCCAT
1 GGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTT-CCAT
* *
1144 TGTTTATTGCCTAACTATAATCATTTTGGTGAGATTAGTCTACTGTGAAGTTTTTAGCTCATTTG
65 TGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
*
1209 GAACCCTTGTTATTTTGGGCC--T-
130 GAACACTTGTTATTTTGGGCCTATC
* * *
1231 -------ATTAGTAACGTTTTGAATCGTGTTCGATTTGGAAAACCTCAATGC-TTT-TTTCCATT
1 GGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
* * * * * *
1287 GTTTATTGTCGAACTATAATCATTTTGATCAGATTAGTCCAATGTGAAGTTTTTAGCTCATTTGG
66 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
*
1352 AACACTTGTTATTTTGGGCCTTTC
131 AACACTTGTTATTTTGGGCCTATC
* *
1376 AGGGCCCATTCGT-ACCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAT
1 GGGGCCCATTAGTGA-CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAT
* *
1440 TGTTTAGGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
65 TGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
*
1505 GCACACTTG-TATTTTGGGCCTATC
130 GAACACTTGTTATTTTGGGCCTATC
* * * *
1529 GGGGCCCATTAGTGACATATTGAATCCTCTTCGATTTGGCAAACCTCAAGGCTTTTCTTTCCATT
1 GGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
1594 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
66 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
1643 ACTTGTTATT
Statistics
Matches: 1359, Mismatches: 95, Indels: 67
0.89 0.06 0.04
Matches are distributed among these distances:
142 83 0.06
143 49 0.04
144 1 0.00
151 2 0.00
152 43 0.03
153 521 0.38
154 308 0.23
155 250 0.18
156 76 0.06
157 26 0.02
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (154 bp):
GGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
AACACTTGTTATTTTGGGCCTATC
Found at i:1756 original size:135 final size:136
Alignment explanation
Indices: 1509--2981 Score: 661
Period size: 154 Copynumber: 10.0 Consensus size: 136
1499 CATTTGGCAC
** * * *
1509 ACTTG-TATTTTGGGCCTATCGGGGCCCATTAGTGACATATTGAATCCTCTTCGATTTGGCAAAC
1 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAC
* *
1573 CTCAAGGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
66 CTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTG
1638 TGAAG-
131 TGAAGT
*
1643 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTAGCAAAC
1 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAC
* * * *
1708 CTCAAAGCTTTTCTTTTCATTTTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTTCACCG
66 CTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTG
1773 TGAAGTTTTT
131 TGAAG----T
1783 AGCTCATTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
1 A---C--TTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
* *
1848 CAAACCTCAATGCTTTTCTTTCCATTGTTTACGGACTAACTATAATCATTTTGGTGAGATTAGTC
61 CAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTC
1913 CACTGTGAAGT
126 CACTGTGAAGT
** * ** ** *** * ** ** ** * * * *
1924 TTTTAGCTCGTTTGAAACACTTGTTATTTTTGGCCTATCGGGGCCCATTAG-TTCCGT-TTTGAA
1 ACTT-GTTATTTTG-GGC-C----TA-TCGGGGCCCATTAGTTCCGTTTTGAAT-CGTCTTCGAT
* * ** ** * * * *
1987 TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAA-T-TAGTCCAC
57 TTGGC--AAACCT--CAAAGCT---T--TTC--TTTCCATTGTTTATGGACTAACTATAAT-CAT
* ** *** * *
2050 TGTGAAGTTTTTAG-CTCA-TTTGGA-T
110 TTTGGTGAGATTAGTC-CACTGTGAAGT
* ** *
2075 CACTTGTTATTTTGGGCCTATCGGGGCCCATTACTGACATTTTGAATCGTCTTCGATTTGGCAAA
1 -ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAA
* *
2140 CCTCAATGCTTTTCTTACCATTGTTTATGG-CTTAACTATAATCATTTTGGTGAGATTAGTCCAC
65 CCTCAAAGCTTTTCTTTCCATTGTTTATGGAC-TAACTATAATCATTTTGGTGAGATTAGTCCAC
2204 TGTGAAGTTTTT
129 TGTGAAG----T
* * * * *** * *
2216 AGCTCATTTGGAACACTTCTTATTTTGGGCTTGTTGGGGTCCATTAGTGATGTATTGAATCGTAT
1 A---C--TT-G--------TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCT
** * * * *
2281 TCGATTTATCAGACCTCAATGCTTTTCATTCCATTGTTTATGGCCTAACTATAATCATTTTGGTG
52 TCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTG
2346 AGATTAGTCCACTGTGAAGTTTTTAACTCATTT
117 AGATTAGTCCACTGTGAAG-------------T
* *
2379 GGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGA
1 -----ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
* * *
2444 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTTGTC
61 CAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTC
*
2509 CACCGTG-AGT
126 CACTGTGAAGT
* * * * ** * * ** ** ** * * *
2519 -TTTAGTCTCTATTCGGAACACTTGTTATTTTGGGACTATCGGGGCCCATTAG-TTCCGT-TTTG
1 ACTT-GT-TAT-TTTGG-GC-C----TA-TCGGGGCCCATTAGTTCCGTTTTGAAT-CGTCTTCG
* * * ** ** * * *
2581 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
55 ATTTGGC--AAACCT--CAAAGCT---T--TTC--TTTCCATTGTTTATGGACTAACTATAATCA
2646 TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
109 TTTTGGTGAGATTAGTCCACTGTG-A------AG------T
**
2687 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGG
1 -----ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
* *
2752 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
61 CAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTC
2817 CACTGTGAAGTTTTTAGCTCATTT
126 CACTGTG-A------AG------T
** *
2841 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCTTCTTCGATTTGG
1 -----ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
* *
2906 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
61 CAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTC
2971 CACTGTGAAGT
126 CACTGTGAAGT
2982 TTTTAGCTCA
Statistics
Matches: 1028, Mismatches: 192, Indels: 231
0.71 0.13 0.16
Matches are distributed among these distances:
133 1 0.00
134 25 0.02
135 132 0.13
136 14 0.01
137 10 0.01
138 3 0.00
139 2 0.00
140 3 0.00
141 8 0.01
143 24 0.02
144 46 0.04
145 142 0.14
146 1 0.00
147 12 0.01
149 1 0.00
150 3 0.00
151 7 0.01
152 14 0.01
153 16 0.02
154 504 0.49
155 1 0.00
156 2 0.00
158 1 0.00
161 5 0.00
162 3 0.00
163 7 0.01
164 16 0.02
165 11 0.01
168 2 0.00
169 1 0.00
170 1 0.00
171 4 0.00
172 2 0.00
173 2 0.00
174 2 0.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (136 bp):
ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAC
CTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTG
TGAAGT
Found at i:2002 original size:154 final size:145
Alignment explanation
Indices: 1941--3084 Score: 1146
Period size: 154 Copynumber: 7.6 Consensus size: 145
1931 TCGTTTGAAA
*
1941 CACTTGTTATTTTTGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAA
1 CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAA
* * **
2006 CCTCAATGCTTTTCTTTCCATTGTTTATGGACTAA-T-TAGTCCA--CT-GTGA-AGTT--TTTA
66 CCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAAT-CATTTTGGTGAGA-TTAGTCCA
* * * *
2063 GC-T-CA---TTTGGAT
129 CCGTGAAGTTTTTAGCT
* ** *
2075 CACTTGTTATTTTGGGCCTATCGGGGCCCATTACTGACATTTTGAATCGTCTTCGATTTGGCAAA
1 CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAA
*
2140 CCTCAATGCTTTTCTTACCATTGTTTATGG-CTTAACTATAATCATTTTGGTGAGATTAGTCCAC
66 CCTCAATGCTTTTCTTTCCATTGTTTATGGAC-TAACTATAATCATTTTGGTGAGATTAGTCCAC
*
2204 TGTGAAGTTTTTAGCTCATTT
130 CGTGAAGTTTTTAG--C---T
* * * * * *** * * **
2225 GGAACACTTCTTATTTTGGGCTTGTTGGGGTCCATTAGTGATGTATTGAATCGTATTCGATTTAT
1 ----CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
* * *
2290 CAGACCTCAATGCTTTTCATTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
62 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTC
* *
2355 CACTGTGAAGTTTTTAACTCATTT
127 CACCGTGAAGTTTTT-A-GC---T
* *
2379 GGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGA
1 ----CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
* *
2444 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTTGTC
62 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTC
* **
2509 CACCGTGAGTTTTAGTCTCTATTCGGAA
127 CACCGTGA-----AGT-T-T-TT-AGCT
*
2537 CACTTGTTATTTTGGGACTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAA
1 CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAA
* *
2602 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
66 CCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACC
2667 GTGAAGTTTTTAGCTCATTT
131 GTGAAGTTTTTAG--C---T
**
2687 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGG
1 ----CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
*
2752 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
62 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTC
*
2817 CACTGTGAAGTTTTTAGCTCATTT
127 CACCGTGAAGTTTTTAG--C---T
** *
2841 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCTTCTTCGATTTGG
1 ----CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
*
2906 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
62 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTC
*
2971 CACTGTGAAGTTTTTAGCT
127 CACCGTGAAGTTTTTAGCT
* * * * **
2990 CATTGGAACAGATGTTATTTTGGACCTATCTGGGCCCATTGGTGACGTTTTGAATCGTCTTCGAT
1 C------AC--TTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAT
** *
3055 TTTACAAACCTCAAAGCTTTTCTTTCCATT
58 TTGGCAAACCTCAATGCTTTTCTTTCCATT
Statistics
Matches: 886, Mismatches: 73, Indels: 83
0.85 0.07 0.08
Matches are distributed among these distances:
133 1 0.00
134 92 0.10
135 3 0.00
136 3 0.00
137 1 0.00
138 6 0.01
139 1 0.00
140 2 0.00
141 1 0.00
142 1 0.00
145 6 0.01
146 2 0.00
147 1 0.00
148 1 0.00
149 4 0.00
150 1 0.00
151 2 0.00
152 1 0.00
153 76 0.09
154 672 0.76
155 2 0.00
159 3 0.00
160 1 0.00
161 1 0.00
162 2 0.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (145 bp):
CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAA
CCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACC
GTGAAGTTTTTAGCT
Found at i:2146 original size:134 final size:134
Alignment explanation
Indices: 1906--2169 Score: 447
Period size: 134 Copynumber: 2.0 Consensus size: 134
1896 TTTTGGTGAG
* *
1906 ATTAGTCCACTGTGAAGTTTTTAGCTCGTTTGAAACACTTGTTATTTTTGGCCTATCGGGGCCCA
1 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAAACACTTGTTATTTTGGGCCTATCGGGGCCCA
* ** * *
1971 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGG
66 TTACTGACATTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTACCATTGTTTATGG
2036 ACTA
131 ACTA
* *
2040 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGATCACTTGTTATTTTGGGCCTATCGGGGCCCA
1 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAAACACTTGTTATTTTGGGCCTATCGGGGCCCA
2105 TTACTGACATTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTACCATTGTTTATGG
66 TTACTGACATTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTACCATTGTTTATGG
2170 CTTAACTATA
Statistics
Matches: 121, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
134 121 1.00
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (134 bp):
ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAAACACTTGTTATTTTGGGCCTATCGGGGCCCA
TTACTGACATTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTACCATTGTTTATGG
ACTA
Found at i:2607 original size:308 final size:307
Alignment explanation
Indices: 2040--3084 Score: 1709
Period size: 308 Copynumber: 3.4 Consensus size: 307
2030 TTATGGACTA
*
2040 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGATCACTTGTTATTTTGGGCCTATCGGGGCCCA
1 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA
* * * *
2105 TTACTGACATTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTACCATTGTTTATGG
66 TTAGTGACGTTTTGAATCGTCTTCGATTTGACAAACCTCAATGCTTTTCTTTCCATTGTTTATGG
* *
2170 CTTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTC
131 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* * * * * * ** *
2235 TTATTTTGGGCTTGTTGGGGTCCATTAGTGATGTATTGAATCGTATTCGATTTATCAGACCTCAA
196 TTATTTTGGGC-TATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
*
2300 TGCTTTTCATTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
260 TGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
* *
2348 ATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCA
1 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA
**
2413 TTAGTTCCGTTTTGAATCGTCTTCGATTTGACAAACCTCAATGCTTTTCTTTCCATTGTTTATGG
66 TTAGTGACGTTTTGAATCGTCTTCGATTTGACAAACCTCAATGCTTTTCTTTCCATTGTTTATGG
* * *
2478 CCTAACTATAATCATTTTGGTGAGATTTGTCCACCGTG-AG-TTTTAGTCTCTATTCGGAACACT
131 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG-CTC-ATTTGGAACACT
**
2541 TGTTATTTTGGGACTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC
194 TGTTATTTTGGG-CTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTC
2606 AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
258 AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
2656 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA
1 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA
*
2721 TTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGG
66 TTAGTGACGTTTTGAATCGTCTTCGATTTGACAAACCTCAATGCTTTTCTTTCCATTGTTTATGG
2786 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
131 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
*
2851 TTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCTTCTTCGATTTGGCAAACCTCAA
196 TTATTTTGGG-CTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
2916 TGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
260 TGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
** * *
2964 ATTAGTCCACTGTGAAGTTTTTAGCTCA-TTGGAACAGATGTTATTTTGGACCTATCTGGGCCCA
1 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA
* * *
3028 TTGGTGACGTTTTGAATCGTCTTCGATTTTACAAACCTCAAAGCTTTTCTTTCCATT
66 TTAGTGACGTTTTGAATCGTCTTCGATTTGACAAACCTCAATGCTTTTCTTTCCATT
Statistics
Matches: 686, Mismatches: 46, Indels: 11
0.92 0.06 0.01
Matches are distributed among these distances:
306 6 0.01
307 90 0.13
308 578 0.84
309 6 0.01
310 6 0.01
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (307 bp):
ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA
TTAGTGACGTTTTGAATCGTCTTCGATTTGACAAACCTCAATGCTTTTCTTTCCATTGTTTATGG
CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
TTATTTTGGGCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAT
GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
Done.