Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012054.1 Corchorus olitorius cultivar O-4 contig12087, 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: 3444
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Found at i:1394 original size:154 final size:154
Alignment explanation
Indices: 1019--2646 Score: 2300
Period size: 154 Copynumber: 10.6 Consensus size: 154
1009 TCAAAACGGA
* * *
1019 AAGTGTTCCAAATGAGTTAAAAACTTCACCGTGGACTAATATCACCAAAATGATTATAGTTAGGC
1 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* * ** *
1084 CATAAACAGTTGAAAG-AAA-CATTGAGGGTTG-CAAATCGAAGACGATTCAAAACGTCACTAGT
66 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* *
1146 GGGCCCCGATAGGCTCAAAATAAC
131 GGGCCCAGATAGGCCCAAAATAAC
1170 AAGTGTTCCAAATGAGCTAAAAATCTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
1 AAGTGTTCCAAATGAGCTAAAAA-CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* *
1235 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATAGAAGACGATTCAAAACGGAAATAA
65 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
1300 TGGGCCCAGATAGGCCCAAAATAA-
130 TGGGCCCAGATAGGCCCAAAATAAC
* *
1324 AATGTGTTCCAAATGAGCTAAAATCTTCACAGTCGACTAATCTCACCAAAATGATTATAGTTAGG
1 AA-GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* * *
1389 CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAAACTGAACTAA
65 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
* * *
1454 TGGGCCCCGATTGGCCCAAAATAGC
130 TGGGCCCAGATAGGCCCAAAATAAC
* * *
1479 AAGTGTTCCAAATGAGTTAACAACTTCACAGTGGACTAATCTCACCAAAATGATTAGAGTTAGGC
1 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* *
1544 CATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAAT
66 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
*
1609 GGGCCCAGATAGGCCCAAAATAAA
131 GGGCCCAGATAGGCCCAAAATAAC
* *
1633 AAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGC
1 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* * **
1698 CATAAACAATTGAAAGAAAGGCATTGAGGGTTG-CAAATCGAAGACGATTCAAAACGTCACTAAT
66 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
*
1762 GGGCCTC-GATAGGCTCAAAATAAC
131 GGGCC-CAGATAGGCCCAAAATAAC
*
1786 AAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
1 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* * * **
1851 CATTAACAATGGAAAGAAAGGCCAAT-AGGGTTG-CAAATCGAAGTA-GATTCAAAACGTCACTA
66 CATAAACAATGGAAAGAAAAG-CATTGAGGGTTGCCAAATCGAAG-ACGATTCAAAACGGAACTA
* ** *
1913 ATGGGTCCC-GATTGGTTCGAAATAAC
129 ATGGG-CCCAGATAGGCCCAAAATAAC
*
1939 AAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
1 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* * * * **
2004 CATTAACAATGGAAGGAAAGGCATTGAGGGTTG-CAAATGGAAGTA-GATTCAAAACGTCACTAA
66 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAG-ACGATTCAAAACGGAACTAA
* * *
2067 TGGGGCCC-GATTGGCTCGAAATAAC
130 T-GGGCCCAGATAGGCCCAAAATAAC
*
2092 AAGTGTTCCAAATGAGCTAAAAAACTTCACAGTGGACTAATCTCACCAAAATGATCATAGTTAGG
1 AAGTGTTCCAAATGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* * * * * *
2157 CCATAAACAAT-GTAAG-GAAGCATTAAGGTTTGCCTAATCGAAGACGATTCAAATCGGAACTAA
65 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
*
2220 TGGGCCTAGATAGGCCCAAAATAA-
130 TGGGCCCAGATAGGCCCAAAATAAC
*
2244 AATGTGTTCCAAATGAGCTAAAATCTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
1 AA-GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* * * * ** *
2309 CAATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCTAATCGAAGTCGATTCAAAACGTCATTAA
65 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
2374 TGGGCCCAGATAGGCCCAAAATAA-
130 TGGGCCCAGATAGGCCCAAAATAAC
* * * *
2398 AATGTTTTCCAAATGAGCTAAAAACTTCATAGTGGAATAATCTCACCAAAATGATTTTAGTTAGG
1 AA-GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* * * * *
2463 TCATAAACAATGGAATGAAAAGCATTGAGGGTTTCCAAATCGAAGGCGAATCAAAACGGAACTAA
65 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
*
2528 TGGGCCCTGATAGGCCCAAAATAAC
130 TGGGCCCAGATAGGCCCAAAATAAC
*
2553 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGC
1 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* *
2618 TATAAACAATGGAAAGAAAAACATTGAGG
66 CATAAACAATGGAAAGAAAAGCATTGAGG
2647 TTTAGTTAGG
Statistics
Matches: 1343, Mismatches: 114, Indels: 37
0.90 0.08 0.02
Matches are distributed among these distances:
151 22 0.02
152 131 0.10
153 405 0.30
154 714 0.53
155 71 0.05
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (154 bp):
AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
GGGCCCAGATAGGCCCAAAATAAC
Found at i:1944 original size:460 final size:459
Alignment explanation
Indices: 1019--2646 Score: 2357
Period size: 460 Copynumber: 3.5 Consensus size: 459
1009 TCAAAACGGA
* * *
1019 AAGTGTTCCAAATGAGTTAAAAACTTCACCGTGGACTAATATCACCAAAATGATTATAGTTAGGC
1 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* * ** *
1084 CATAAACAGTTGAAAG-AAA-CATTGAGGGTTGCAAATCGAAGACGATTCAAAACGTCACTAGTG
66 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCAAATCGAAGACGATTCAAAACGGAACTAATG
*
1147 GGCCCCGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAATCTTCACAGTGGACTAATC
131 GG-CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA-CTTCACAGTGGACTAATC
*
1212 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATAG
194 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCG
*
1277 AAGACGATTCAAAACGGAAATAATGGGCC-CAGATAGGCCCAAAATAAAATGTGTTCCAAATGAG
259 AAGACGATTCAAAACGGAACTAATGGGCCTC-GATAGGCCCAAAATAAAATGTGTTCCAAATGAG
*
1341 CTAAAATCTTCACAGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
323 CTAAAATCTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* *
1406 AAAAGCATTGAGGTTTGCCAAATCGAAG-ACAATTCAAAAC-TGAACTAATGGGCCCCGATTGGC
388 AAAAGCATTGAGGTTTGCCAAATCGAAGTA-GATTCAAAACGT-CACTAATGGG-CCCGATTGGC
*
1469 CCAAAATAGC
450 CCAAAATAAC
* * *
1479 AAGTGTTCCAAATGAGTTAACAACTTCACAGTGGACTAATCTCACCAAAATGATTAGAGTTAGGC
1 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* *
1544 CATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAAT
66 CATAAACAATGGAAAGAAAAGCATTGAGGGTTG-CAAATCGAAGACGATTCAAAACGGAACTAAT
* *
1609 GGGCCCAGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATC
130 GGGCCC-GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * *
1674 TTACCAAAATGATTATAGTTAGGCCATAAACAATTGAAAGAAAGGCATTGAGGGTTG-CAAATCG
194 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCG
** *
1738 AAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCTCAAAATAACAA-GTGTTCCAAATGAG
259 AAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAA-AATGTGTTCCAAATGAG
*
1802 CTAAAAAT-TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATTAACAATGGAAA
323 CT-AAAATCTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* * * *
1866 GAAAGGCCAAT-AGGGTTG-CAAATCGAAGTAGATTCAAAACGTCACTAATGGGTCCCGATTGGT
387 GAAAAG-CATTGAGGTTTGCCAAATCGAAGTAGATTCAAAACGTCACTAATGGG-CCCGATTGGC
* *
1929 TCGAAATAAC
450 CCAAAATAAC
*
1939 AAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
1 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* * * * **
2004 CATTAACAATGGAAGGAAAGGCATTGAGGGTTGCAAATGGAAGTA-GATTCAAAACGTCACTAAT
66 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCAAATCGAAG-ACGATTCAAAACGGAACTAAT
* * *
2068 GGGGCCCGATTGGCTCGAAATAACAAGTGTTCCAAATGAGCTAAAAAACTTCACAGTGGACTAAT
130 -GGGCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAAACTTCACAGTGGACTAAT
* * * * * *
2133 CTCACCAAAATGATCATAGTTAGGCCATAAACAAT-GTAAG-GAAGCATTAAGGTTTGCCTAATC
193 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATC
* *
2196 GAAGACGATTCAAATCGGAACTAATGGGCCTAGATAGGCCCAAAATAAAATGTGTTCCAAATGAG
258 GAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAAAATGTGTTCCAAATGAG
*
2261 CTAAAATCTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCAATAAACAATGGAAAG
323 CTAAAATCTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * * *
2326 AAAAGCATTGAGGTTTGCCTAATCGAAGTCGATTCAAAACGTCATTAATGGGCCCAGATAGGCCC
388 AAAAGCATTGAGGTTTGCCAAATCGAAGTAGATTCAAAACGTCACTAATGGGCCC-GATTGGCCC
2391 AAAATAA-
452 AAAATAAC
* * * *
2398 AATGTTTTCCAAATGAGCTAAAAACTTCATAGTGGAATAATCTCACCAAAATGATTTTAGTTAGG
1 AA-GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* * * * *
2463 TCATAAACAATGGAATGAAAAGCATTGAGGGTTTCCAAATCGAAGGCGAATCAAAACGGAACTAA
65 CCATAAACAATGGAAAGAAAAGCATTGAGGG-TTGCAAATCGAAGACGATTCAAAACGGAACTAA
2528 TGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
129 TGGGCCC-GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
* * *
2593 CTCACTAAAATGATTATAGTTAGGCTATAAACAATGGAAAGAAAAACATTGAGG
193 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
2647 TTTAGTTAGG
Statistics
Matches: 1042, Mismatches: 101, Indels: 48
0.87 0.08 0.04
Matches are distributed among these distances:
458 22 0.02
459 193 0.19
460 458 0.44
461 196 0.19
462 106 0.10
463 67 0.06
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (459 bp):
AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCAAATCGAAGACGATTCAAAACGGAACTAATG
GGCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
ACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAA
GACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAAAATGTGTTCCAAATGAGCTA
AAATCTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
AGCATTGAGGTTTGCCAAATCGAAGTAGATTCAAAACGTCACTAATGGGCCCGATTGGCCCAAAA
TAAC
Found at i:2751 original size:103 final size:103
Alignment explanation
Indices: 2566--2752 Score: 302
Period size: 103 Copynumber: 1.8 Consensus size: 103
2556 TGTTCCAAAT
* * *
2566 GAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCTATAAACAATGGA
1 GAGCTAAAAACTTCACAGTGGACTAATCCCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
*
2631 AAGAAAAACATTGAGGTTTAGTTAGGCCATAAACAATG
66 AAGAAAAACATTAAGGTTTAGTTAGGCCATAAACAATG
* *
2669 GAGCTAAAAATTTCACAGTGGACTAATCCCACCAAAATGATTATAGTTAGGCCATTAACAATGGA
1 GAGCTAAAAACTTCACAGTGGACTAATCCCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
* *
2734 AAGAGAAGCATTAAGGTTT
66 AAGAAAAACATTAAGGTTT
2753 GCCTAATCGA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
103 76 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (103 bp):
GAGCTAAAAACTTCACAGTGGACTAATCCCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
AAGAAAAACATTAAGGTTTAGTTAGGCCATAAACAATG
Found at i:2868 original size:257 final size:257
Alignment explanation
Indices: 2412--2906 Score: 796
Period size: 257 Copynumber: 1.9 Consensus size: 257
2402 TTTTCCAAAT
* * * *
2412 GAGCTAAAAACTTCATAGTGGAATAATCTCACCAAAATGATTTTAGTTAGGTCATAAACAATGGA
1 GAGCTAAAAACTTCACAGTGGAATAATCCCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
* * * *
2477 ATGAAAAGCATTGAGGGTTTCCAAATCGAAGGCGAATCAAAACGGAACTAATGGGCCCTGATAGG
66 AAGAAAAGCATTGAAGGTTTCCAAATCGAAGACGAATCAAAACGGAACTAATGGGCCCAGATAGG
*
2542 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGAT
131 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* *
2607 TATAGTTAGGCTATAAACAATGGAAAGAAAAACATTGAGGTTTAGTTAGGCCATAAACAATG
196 TATAGTTAGGCCATAAACAAGGGAAAGAAAAACATTGAGGTTTAGTTAGGCCATAAACAATG
* * *
2669 GAGCTAAAAATTTCACAGTGGACTAATCCCACCAAAATGATTATAGTTAGGCCATTAACAATGGA
1 GAGCTAAAAACTTCACAGTGGAATAATCCCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
* * *
2734 AAGAGAAGCATT-AAGGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAG
66 AAGAAAAGCATTGAAGGTTT-CCAAATCGAAGACGAATCAAAACGGAACTAATGGGCCCAGATAG
*
2798 GCCCAAAATAA-AATGTGTTCCAAATGAGCTAAAATCTTCACAGTGGACTAATCTCACCAAAATG
130 GCCCAAAATAACAA-GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG
2862 ATTATAGTTAGGCCATAAACAAGGGAAAGAAAAACATTGAGGTTT
194 ATTATAGTTAGGCCATAAACAAGGGAAAGAAAAACATTGAGGTTT
2907 GCCTAATCGA
Statistics
Matches: 218, Mismatches: 18, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
256 8 0.04
257 210 0.96
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.23
Consensus pattern (257 bp):
GAGCTAAAAACTTCACAGTGGAATAATCCCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
AAGAAAAGCATTGAAGGTTTCCAAATCGAAGACGAATCAAAACGGAACTAATGGGCCCAGATAGG
CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
TATAGTTAGGCCATAAACAAGGGAAAGAAAAACATTGAGGTTTAGTTAGGCCATAAACAATG
Found at i:2949 original size:154 final size:153
Alignment explanation
Indices: 2669--3444 Score: 1116
Period size: 154 Copynumber: 5.0 Consensus size: 153
2659 ATAAACAATG
* * *
2669 GAGCTAAAAATTTCACAGTGGACTAATCCCACCAAAATGATTATAGTTAGGCCATTAACAATGGA
1 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
* *
2734 AAGAGAAGCATTAAGGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGG
66 AAGAAAAGCATTGAGGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGG
2799 CCCAAAATAAAATGTGTTCCAAAT
131 CCCAAAATAAAA-GTGTTCCAAAT
* *
2823 GAGCTAAAATCTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAGGGA
1 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
*
2888 AAGAAAAACATTGAGGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGG
66 AAGAAAAGCATTGAGGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGG
*
2953 CCCAAAATATAATGTGTTCCAAAT
131 CCCAAAATA-AAAGTGTTCCAAAT
* *
2977 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTGTAGTTAGGCTATAAACAATGGA
1 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
* *
3042 AAGAAAAGCATTGACGTTTGCCTAATCGAAGAAGATTCAAAACGGAACTAATGGGCCCAGATAGG
66 AAGAAAAGCATTGAGGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGG
3107 CCCAAAATAAAAAGTGTTCCAAAT
131 CCCAAAAT-AAAAGTGTTCCAAAT
* * *
3131 GAGTTAAAAACTTCACAGTGGACTAATCTTACCAAAAATGATTATAGTTAGGCCATAAACAATTG
1 GAGCTAAAAACTTCACAGTGGACTAATCTCACC-AAAATGATTATAGTTAGGCCATAAACAATGG
* * * * *
3196 AAAGAAAGGCATTGAGGGTTG-CAAATCGAAGACGATTCAAAACGTCAA-TAATGGGCCTC-GGT
65 AAAGAAAAGCATTGAGGTTTGCCTAATCGAAGACGATTCAAAACG-GAACTAATGGGCC-CAGAT
*
3258 AGGCTCAAAATAACAAGTGTTCCAAAT
128 AGGCCCAAAATAA-AAGTGTTCCAAAT
* *
3285 GTGCTAAAAACTTCACATTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
1 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
* * * * * *
3350 AAGAAAAGCCATTCCGAGGGTTG-C-AACTCG-ACATGA-TCAAAACGGAACTAACGAGCCCCGA
66 AAGAAAAG-CATT--GAGGTTTGCCTAA-TCGAAGACGATTCAAAACGGAACTAATGGGCCCAGA
*
3411 TAGGCCCAAAATAGCAAGTGTTCCAAAT
127 TAGGCCCAAAATA-AAAGTGTTCCAAAT
3439 GAGCTA
1 GAGCTA
Statistics
Matches: 564, Mismatches: 45, Indels: 26
0.89 0.07 0.04
Matches are distributed among these distances:
153 43 0.08
154 451 0.80
155 58 0.10
156 12 0.02
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (153 bp):
GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
AAGAAAAGCATTGAGGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGG
CCCAAAATAAAAGTGTTCCAAAT
Found at i:3026 original size:411 final size:411
Alignment explanation
Indices: 2258--3060 Score: 1315
Period size: 411 Copynumber: 2.0 Consensus size: 411
2248 TGTTCCAAAT
*
2258 GAGCTAAAATCTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCAATAAACAATGGA
1 GAGCTAAAATCTTCACAGTGGACTAATCCCACCAAAATGATTATAGTTAGGCAATAAACAATGGA
* * ** *
2323 AAGAAAAGCATTGAGGTTTGCCTAATCGAAGTCGATTCAAAACGTCATTAATGGGCCCAGATAGG
66 AAGAAAAGCATTAAGGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGG
* *
2388 CCCAAAATAAAATGTTTTCCAAATGAGCTAAAAACTTCATAGTGGAATAATCTCACCAAAATGAT
131 CCCAAAATAAAATGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAATAATCTCACCAAAATGAT
* * * * * *
2453 TTTAGTTAGGTCATAAACAATGGAATGAAAAGCATTGAGGGTTTCCAAATCGAAGGCGAATCAAA
196 TATAGTTAGGCCATAAACAAGGGAAAGAAAAACATTGAGGGTTTCCAAATCGAAGACGAATCAAA
*
2518 ACGGAACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
261 ACGGAACTAATGGGCCCAGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
* *
2583 GTGGACTAATCTCACTAAAATGATTATAGTTAGGCTATAAACAATGGAAAGAAAAACATTGAGGT
326 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCTATAAACAATGGAAAGAAAAACATTGACGT
2648 TTAGTTAGGCCATAAACAATG
391 TTAGTTAGGCCATAAACAATG
* *
2669 GAGCTAAAAAT-TTCACAGTGGACTAATCCCACCAAAATGATTATAGTTAGGCCATTAACAATGG
1 GAGCT-AAAATCTTCACAGTGGACTAATCCCACCAAAATGATTATAGTTAGGCAATAAACAATGG
*
2733 AAAGAGAAGCATTAAGGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAG
65 AAAGAAAAGCATTAAGGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAG
* *
2798 GCCCAAAATAAAATGTGTTCCAAATGAGCTAAAATCTTCACAGTGGACTAATCTCACCAAAATGA
130 GCCCAAAATAAAATGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAATAATCTCACCAAAATGA
* *
2863 TTATAGTTAGGCCATAAACAAGGGAAAGAAAAACATTGA-GGTTTGCCTAATCGAAGACGATTCA
195 TTATAGTTAGGCCATAAACAAGGGAAAGAAAAACATTGAGGGTTT-CCAAATCGAAGACGAATCA
*
2927 AAACGGAACTAATGGGCCCAGATAGGCCCAAAATATA-ATGTGTTCCAAATGAGCTAAAAACTTC
259 AAACGGAACTAATGGGCCCAGATAGGCCCAAAATA-ACAAGTGTTCCAAATGAGCTAAAAACTTC
* *
2991 ACAGTGGACTAATCTCACCAAAATGATTGTAGTTAGGCTATAAACAATGGAAAGAAAAGCATTGA
323 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCTATAAACAATGGAAAGAAAAACATTGA
3056 CGTTT
388 CGTTT
3061 GCCTAATCGA
Statistics
Matches: 362, Mismatches: 27, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
410 5 0.01
411 351 0.97
412 6 0.02
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.23
Consensus pattern (411 bp):
GAGCTAAAATCTTCACAGTGGACTAATCCCACCAAAATGATTATAGTTAGGCAATAAACAATGGA
AAGAAAAGCATTAAGGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGG
CCCAAAATAAAATGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAATAATCTCACCAAAATGAT
TATAGTTAGGCCATAAACAAGGGAAAGAAAAACATTGAGGGTTTCCAAATCGAAGACGAATCAAA
ACGGAACTAATGGGCCCAGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
GTGGACTAATCTCACCAAAATGATTATAGTTAGGCTATAAACAATGGAAAGAAAAACATTGACGT
TTAGTTAGGCCATAAACAATG
Done.