Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006808.1 Corchorus capsularis cultivar CVL-1 contig06829, 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: 4615
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Found at i:551 original size:111 final size:111
Alignment explanation
Indices: 354--562 Score: 251
Period size: 111 Copynumber: 1.9 Consensus size: 111
344 AAAAGTCGTG
* *
354 TGTCGGAATGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAA
1 TGTCGGAATGAGATGAACTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTAGAAGTCCAAA
* * * *
419 GCATCAACTTTGCGAGTTTGTATGCAACACATCGTTCTTAGAGGCT
66 ACATCAACTTTGAGAGGTTGTATGCAAAACATCGTTCTTAGAGGCT
* * * * * * *
465 TGTCGGAGTGAGATGAACTTTTTGGACAGC-CTTGTGCAGAAACAAAGCTTTCCTAGATG-CCTA
1 TGTCGGAATGAGATGAACTTGTTAGACAGCGC-TATGCACAAACAAAGCTCTCCTAGAAGTCC-A
* *
528 AAACCTCAACTTTGAGCGGTTGTATGCAAAACATC
64 AAACATCAACTTTGAGAGGTTGTATGCAAAACATC
563 ATTTTTAGCG
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
110 3 0.04
111 78 0.96
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (111 bp):
TGTCGGAATGAGATGAACTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTAGAAGTCCAAA
ACATCAACTTTGAGAGGTTGTATGCAAAACATCGTTCTTAGAGGCT
Found at i:1401 original size:111 final size:111
Alignment explanation
Indices: 1226--1433 Score: 265
Period size: 111 Copynumber: 1.9 Consensus size: 111
1216 AAAAGTCGTG
* * *
1226 TGTCGGAATGAGATGATCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAA
1 TGTCGGAATGAGATGAACTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAA
* * * *
1291 GCATCAACTTTGCGAGTTTGTATGCAACACATCGTTCTTAGCGGTT
66 ACATCAACTTTGAGAGGTTGTATGCAAAACATCGTTCTTAGCGGTT
* * * * * *
1337 TGTCGGAGTGAGATGAACTTTTTGGACAGC-CTTGTGCAGAAACAAAGCTTTCCTAGAAGCCCAA
1 TGTCGGAATGAGATGAACTTGTTAGACAGCGC-TATGCACAAACAAAGCTCTCCTAGAAGCCCAA
* *
1401 AACCTCAACTTTGAGCGGTTGTATGCAAAACAT
65 AACATCAACTTTGAGAGGTTGTATGCAAAACAT
1434 TTATTTTTAG
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
110 1 0.01
111 80 0.99
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (111 bp):
TGTCGGAATGAGATGAACTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAA
ACATCAACTTTGAGAGGTTGTATGCAAAACATCGTTCTTAGCGGTT
Found at i:2204 original size:885 final size:887
Alignment explanation
Indices: 1030--2917 Score: 3110
Period size: 886 Copynumber: 2.1 Consensus size: 887
1020 GGCTCATTCC
* * * * * *
1030 AGATGCATTTTTT-GCGCTACGAGTGCGCAAATGTCGTGCGTCGAAGTGCA-ATGAGATTGTTCG
1 AGATGCATTTTTTCGCGCAACGAGTGCCCAAAAGTCGTGTGTCGAA-TG-AGATGAGCTTGTTAG
* * * * * *
1093 ACAGCCCTATGCACAAACAAAGCTTT-CACGAAGTCCAAAGCCTCAACTTTGCGCGTTTTTGTGC
64 ACAGCGCTATGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCATCAACTTTGCACATTTCTGTGC
** * * *
1157 TATTCATAGTTCTTAGCAAAACTCTTTCTGGATGCGTCTTTTTCGCGCAACGAGTGCTCAAAAGT
129 TAAACATAGTTCTTAGCAAAACTCTTTCTAGATGCATCTTTTTCGCGCAACGAGTGCCCAAAAGT
*
1222 CGTGTGTCGGAATGAGATGATCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTC
194 CGTGTGTCGGAATGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTC
*
1287 CAAAGCATCAACTTTGCGAGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAGTGAGATG
259 CAAAGCATCAACTTTGCGAGTTTGTATGCAACACATCGTTCTGAGCGGTTTGTCGGAGTGAGATG
* *
1352 AACTTTTTGGACAGCCTTGTGCAGAAACAAAGCTTTCCTAGAAGCCCAAAACCTC-AACTTTGAG
324 AACTTTTTGGACAGCCCTGTACAGAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAAACTTTGAG
*
1416 CGG-TTGTATGCAAAACATTTATTTTTAGCGAAAGGCTCATTCCAAGTGCATTTGTTGCGCAAG-
389 CGGTTTGTATGCAAAACA-TCATTTTTAGCGAAAGGCTCATTCCAAGTGCATTTGTTGCGC-AGC
1479 GAGTGCTCAAATGTCGGGCGTCGAAGTGCGATGAGATTGTTTCACAGCCCTATGCACAAACAAAG
452 GAGTGCTCAAATGTCGGGCGTCGAAGTGCGATGAGATTGTTTCACAGCCCTATGCACAAACAAAG
*
1544 CTTGTTAGGCAGCGCTATGCACAAACAAAGCTCTGCTCGATGTCCAAAGCATCAACTATGTGCAT
517 CTTGTTAGGCAGCGCTATGCACAAACAAAGCTCTGCTCGATGTCCAAAGCATCAACTATGCGCAT
1609 TCGTATGCAAAACATCGTTCTTAGCAGTTTGTCGGAGTGAGATGAACTTTTTGGATAGCCATGTG
582 TCGTATGCAAAACATCGTTCTTAGCAGTTTGTCGGAGTGAGATGAACTTTTTGGATAGCC-TGTG
*
1674 CACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCACT
646 CACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACCTTGAGCGGTTGTATGCAAAACATCACT
1739 TTTAGCGAAAGG-TCATTCTAGATGCATTTTTTGCGCTACGAGTGCTCAAATGTCGTGCGTCGAA
711 TTTAGCGAAAGGCTCATTCTAGATGCATTTTTTGCGCTACGAGTGCTCAAATGTCGTGCGTCGAA
1803 GTGCAATGAGATTGTTCGACAGCCCTATGCACAAACAAAGC-TTCCACGAAGTCCAAAGCCTCAA
776 GTGCAATGAGATTGTTCGACAGCCCTATGCACAAACAAAGCTTTCCACGAAGTCCAAAGCCTCAA
*
1867 CTTTGCACATTTCTGTGCTAAACATAGTTCTTAGCATAACTCTTTCT
841 CTTTGCACATTTCTGTGCTAAACATAGTTCTTAGCAGAACTCTTTCT
* * *
1914 AGATGTATTTTTTCGCGCAATGAGTGCCCAAAAGTCGTGTGTCGGAATGAGATGAGCTTTTTAGA
1 AGATGCATTTTTTCGCGCAACGAGTGCCCAAAAGTCGTGTGTC-GAATGAGATGAGCTTGTTAGA
* *
1979 CAGCGCTATGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCGTCAATTTTGCACATTTCTGTGCT
65 CAGCGCTATGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCATCAACTTTGCACATTTCTGTGCT
* * *
2044 AAACATAGTTCTTAGCATAACTCTTTCTAGATGTAT-TTTTTCGCGCAATGAGTGCCCAAAAGTC
130 AAACATAGTTCTTAGCAAAACTCTTTCTAGATGCATCTTTTTCGCGCAACGAGTGCCCAAAAGTC
*
2108 GTGTGTCGGAATGAGATGAGCTTTTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCC
195 GTGTGTCGGAATGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCC
* * *
2173 AAAGCATCAATTTTGCGAGTTTGTGTGCAACACATCGTTCTGAGCTGTTTGTCGGAGTGAGATGA
260 AAAGCATCAACTTTGCGAGTTTGTATGCAACACATCGTTCTGAGCGGTTTGTCGGAGTGAGATGA
* *
2238 GCTTTTTGGACAGCCCTGTACAGAAACAAAGCTTTCGTAGAAGCCCAAAACCTCAAACTTTGAGC
325 ACTTTTTGGACAGCCCTGTACAGAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAAACTTTGAGC
* *
2303 GGTTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGGTGCATTTTTTGCGCAGCGAG
390 GGTTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAAGTGCATTTGTTGCGCAGCGAG
*
2368 TGCTCAAATGTCGGGCGTCGAAGTGCGATGAGATTGTTTCACAGCCCTGTGCACAAACAAAGCTT
455 TGCTCAAATGTCGGGCGTCGAAGTGCGATGAGATTGTTTCACAGCCCTATGCACAAACAAAGCTT
*
2433 GTTAGGCAGCGCTATGCACAAACAAAGCTTTGCTCGATGTCCAAAGCATCAACTATGCGCATTCG
520 GTTAGGCAGCGCTATGCACAAACAAAGCTCTGCTCGATGTCCAAAGCATCAACTATGCGCATTCG
2498 TATGCAAAACATCGTTCTTAGCAGTTTGTCGGAGTGAGATGAACTTTTTGGATAGCCTGTGCACA
585 TATGCAAAACATCGTTCTTAGCAGTTTGTCGGAGTGAGATGAACTTTTTGGATAGCCTGTGCACA
*
2563 AACAAAGCTTTCCTAGAAGCCCAAAACCTCAACCTTGAGCGGTTGTATGCAAAACATCATTTTTA
650 AACAAAGCTTTCCTAGAAGCCCAAAACCTCAACCTTGAGCGGTTGTATGCAAAACATCACTTTTA
* *
2628 GCGAAAGGCTCATTCTAGATGCATTTTTTGCGCTTCGAGTGCTCAAATGTCGTGCGTTGAAGTGC
715 GCGAAAGGCTCATTCTAGATGCATTTTTTGCGCTACGAGTGCTCAAATGTCGTGCGTCGAAGTGC
* ** * *
2693 AATGAGATTGTTCGACAGCCCTGTGCACAAACAAAGCTTTCCTTGAAGTCCAAAGCGTCAATTTT
780 AATGAGATTGTTCGACAGCCCTATGCACAAACAAAGCTTTCCACGAAGTCCAAAGCCTCAACTTT
* *
2758 GCACATTTTTGTGCTAAACATAGTTCTTAGCAGAACTCTTTTT
845 GCACATTTCTGTGCTAAACATAGTTCTTAGCAGAACTCTTTCT
* * * *
2801 GGATGCGTTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTGTCAGAGTGAGATGAGCTTGTTAGA
1 AGATGCATTTTTTCGCGCAACGAGTGCCCAAAAGTCGTGTGTC-GAATGAGATGAGCTTGTTAGA
* * *
2866 CAGCGCTATGCATAAACAAAGCTCTCCTCAAAGTCCAAAGCATCAACTTTGC
65 CAGCGCTATGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCATCAACTTTGC
2918 GCGTTTGTTT
Statistics
Matches: 930, Mismatches: 65, Indels: 15
0.92 0.06 0.01
Matches are distributed among these distances:
884 13 0.01
885 342 0.37
886 394 0.42
887 181 0.19
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (887 bp):
AGATGCATTTTTTCGCGCAACGAGTGCCCAAAAGTCGTGTGTCGAATGAGATGAGCTTGTTAGAC
AGCGCTATGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCATCAACTTTGCACATTTCTGTGCTA
AACATAGTTCTTAGCAAAACTCTTTCTAGATGCATCTTTTTCGCGCAACGAGTGCCCAAAAGTCG
TGTGTCGGAATGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCA
AAGCATCAACTTTGCGAGTTTGTATGCAACACATCGTTCTGAGCGGTTTGTCGGAGTGAGATGAA
CTTTTTGGACAGCCCTGTACAGAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAAACTTTGAGCG
GTTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAAGTGCATTTGTTGCGCAGCGAGT
GCTCAAATGTCGGGCGTCGAAGTGCGATGAGATTGTTTCACAGCCCTATGCACAAACAAAGCTTG
TTAGGCAGCGCTATGCACAAACAAAGCTCTGCTCGATGTCCAAAGCATCAACTATGCGCATTCGT
ATGCAAAACATCGTTCTTAGCAGTTTGTCGGAGTGAGATGAACTTTTTGGATAGCCTGTGCACAA
ACAAAGCTTTCCTAGAAGCCCAAAACCTCAACCTTGAGCGGTTGTATGCAAAACATCACTTTTAG
CGAAAGGCTCATTCTAGATGCATTTTTTGCGCTACGAGTGCTCAAATGTCGTGCGTCGAAGTGCA
ATGAGATTGTTCGACAGCCCTATGCACAAACAAAGCTTTCCACGAAGTCCAAAGCCTCAACTTTG
CACATTTCTGTGCTAAACATAGTTCTTAGCAGAACTCTTTCT
Found at i:2213 original size:158 final size:158
Alignment explanation
Indices: 1638--2188 Score: 695
Period size: 158 Copynumber: 3.5 Consensus size: 158
1628 CTTAGCAGTT
* * * * * * *
1638 TGTCGGAGTGAGATGAACTTTTTGGATAGC-CATGTGCACAAACAAAGCTTTCCTAGAAGCCCAA
1 TGTCGGAATGAGATGAGCTTTTTAGACAGCGC-TATGCACAAACAAAGCTTTCCTCGAAGTCCAA
* ** * * * * * * *
1702 AACCTCAACTTTG-AGCGGTTGTATGCAAAACATCACTT-TTAGCGA-AAGGTCATTCTAGATGC
65 AGCCTCAACTTTGCA-CATTTCTGTGCTAAACAT-AGTTCTTAGC-ATAA-CTCTTTCTAGATGT
* * * *
1764 ATTTTTT-GCGCTACGAGTGCTCAAATGTCGTG
126 ATTTTTTCGCGCAATGAGTGCCCAAAAGTCGTG
* * * * * *
1796 CGTC-GAAGTGCA-ATGAGATTGTTCGACAGCCCTATGCACAAACAAAGC-TTCCACGAAGTCCA
1 TGTCGGAA-TG-AGATGAGCTTTTTAGACAGCGCTATGCACAAACAAAGCTTTCCTCGAAGTCCA
1858 AAGCCTCAACTTTGCACATTTCTGTGCTAAACATAGTTCTTAGCATAACTCTTTCTAGATGTATT
64 AAGCCTCAACTTTGCACATTTCTGTGCTAAACATAGTTCTTAGCATAACTCTTTCTAGATGTATT
1923 TTTTCGCGCAATGAGTGCCCAAAAGTCGTG
129 TTTTCGCGCAATGAGTGCCCAAAAGTCGTG
1953 TGTCGGAATGAGATGAGCTTTTTAGACAGCGCTATGCACAAACAAAGCTTTCCTCGAAGTCCAAA
1 TGTCGGAATGAGATGAGCTTTTTAGACAGCGCTATGCACAAACAAAGCTTTCCTCGAAGTCCAAA
* *
2018 GCGTCAATTTTGCACATTTCTGTGCTAAACATAGTTCTTAGCATAACTCTTTCTAGATGTATTTT
66 GCCTCAACTTTGCACATTTCTGTGCTAAACATAGTTCTTAGCATAACTCTTTCTAGATGTATTTT
2083 TTCGCGCAATGAGTGCCCAAAAGTCGTG
131 TTCGCGCAATGAGTGCCCAAAAGTCGTG
*
2111 TGTCGGAATGAGATGAGCTTTTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAA
1 TGTCGGAATGAGATGAGCTTTTTAGACAGCGCTATGCACAAACAAAGCTTTCCTCGAAGTCCAAA
* *
2176 GCATCAATTTTGC
66 GCCTCAACTTTGC
2189 GAGTTTGTGT
Statistics
Matches: 348, Mismatches: 35, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
156 23 0.07
157 104 0.30
158 219 0.63
159 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (158 bp):
TGTCGGAATGAGATGAGCTTTTTAGACAGCGCTATGCACAAACAAAGCTTTCCTCGAAGTCCAAA
GCCTCAACTTTGCACATTTCTGTGCTAAACATAGTTCTTAGCATAACTCTTTCTAGATGTATTTT
TTCGCGCAATGAGTGCCCAAAAGTCGTG
Found at i:3469 original size:111 final size:111
Alignment explanation
Indices: 3276--3486 Score: 246
Period size: 111 Copynumber: 1.9 Consensus size: 111
3266 TGTGTCGGAA
* * * * * *
3276 TGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCTAAAGCATCAAC
1 TGAGATGAACTTGTTAGACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAAACATCAAC
* *
3341 TTTGCGAGTTTGAATGCAACACATCGTTCTTAGCGGTTTGTCGTAG
66 TTTGCGAGTTTGAATGCAAAACATCATTCTTAGCGGTTTGTCGTAG
* * * * * *
3387 TGAGATGAACTTTTTGGACAGCCCTGTGCAGAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAAC
1 TGAGATGAACTTGTTAGACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAAACATCAAC
* *
3452 TTTGATCG-G-TTGTATGCAAAACATCATTTTTAGCG
66 TTTG--CGAGTTTGAATGCAAAACATCATTCTTAGCG
3487 AAAGGCTCAT
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
111 79 0.96
112 1 0.01
113 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (111 bp):
TGAGATGAACTTGTTAGACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAAACATCAAC
TTTGCGAGTTTGAATGCAAAACATCATTCTTAGCGGTTTGTCGTAG
Found at i:3796 original size:427 final size:428
Alignment explanation
Indices: 2428--4014 Score: 2351
Period size: 428 Copynumber: 3.7 Consensus size: 428
2418 GCACAAACAA
* * * * *
2428 AGCTTGTTAGGCAGCGCTATGCACAAACAAAGCTTTGCTCGATGTCCAAAGCATCAACTATGCGC
1 AGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCG-
* * *
2493 A-TTCGTATGCAA-AACATCGTTCTTAGCAGTTTGTCGGAGTGAGATGAACTTTTTGGATAG-CC
65 AGTTTGTATGCAACAA-ATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCC
* *
2555 TGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACCTTGAGCGGTTGTATGCAAAACAT
129 TATGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACAT
* * **
2620 CATTTTTAGCGAAAGGCTCATTCTAGATGCATTTTTTGCGCTTCGAGTGCTCAAATGTCGTGCGT
194 CATTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCCCAACGAGTGCTCAAATGTCGTGCGT
* * * *
2685 TGAAGTGCAATGAGATTGTTCGACAGCCCTGTGCACAAACAAAGCTTTCCTTGAAGTCCAAAGCG
259 CGAAGTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGTCCAAAGCG
2750 TCAATTTTGCACATTTTTGTGCTAAACATAGTTCTTAGCAGAACTCTTTTTGGATGCGTTTTTTC
324 TCAATTTTGCACATTTTTGTGCTAAACATAGTTCTTAGCAGAACTCTTTTTGGATGCGTTTTTTC
* * *
2815 GCGCAACGAGTGCTCAAAAGTCGTGTGTCAGAGTGAGATG
389 GCGAAACGAGTGCTCAAAAGTCGTGTGTCGGAATGAGATG
* * *
2855 AGCTTGTTAGACAGCGCTATGCATAAACAAAGCTCTCCTCAAAGTCCAAAGCATCAACTTTGCGC
1 AGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGA
* * * * * * * *
2920 GTTTGTTTGCAACACATCGTTCTTAGAGGTGTGTTGGAGTGAGATGAGCTTTTTGAACCGCCCTA
66 GTTTGTATGCAACAAATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTA
* * * * * * * *
2985 TGCACAAACAAAACTTCCCTGGAAGCCCAAAATCTAAAGTTTGAGCAGTTCTATGCAAAACATCA
131 TGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCA
* * * * * *
3050 TTTTTAGTGACAA-GCTCATTCCAGGTCCACTTTTTGCGCAACGAGTGCTCAAATGTCGGGCGTC
196 TTTTTAGCGA-AAGGCTCATTCCAGATGCATTTTTTGCCCAACGAGTGCTCAAATGTCGTGCGTC
* * * *
3114 GAAGTGTGATGAGATTGATT-CACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGGCCAAAGCG
260 GAAGTGCGATGAGATTG-TTGGACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGTCCAAAGCG
* * *
3178 TCAATTTTGCACATTTCTGTGCTAAACATAGTTCTAAGCAGAACTCTTTTTTGATGCGTTTTTTC
324 TCAATTTTGCACATTTTTGTGCTAAACATAGTTCTTAGCAGAACTCTTTTTGGATGCGTTTTTTC
*
3243 GCGAAACGAGTGCTAAAAAGTCGTGTGTCGGAATGAGATG
389 GCGAAACGAGTGCTCAAAAGTCGTGTGTCGGAATGAGATG
*
3283 AGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCTAAAGCATCAACTTTGCGA
1 AGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGA
* * * *
3348 GTTTGAATGCAACACATCGTTCTTAGCGGTTTGTCGTAGTGAGATGAACTTTTTGGACAGCCCTG
66 GTTTGTATGCAACAAATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTA
* *
3413 TGCAGAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGATCGGTTGTATGCAAAACATCA
131 TGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCA
* *
3478 TTTTTAGCGAAAGGCTCATTCCATATGCATTTTTTGCCCAACGAGTGCTCAAATGTGGTGCGTCG
196 TTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCCCAACGAGTGCTCAAATGTCGTGCGTCG
* * * *
3543 AATTGCGATGAGATTGTTGGAAAGCCCTGTGCACAAACAAAGCTTT-CAAGAAGTCAAAAGTC-T
261 AAGTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGTCCAAAG-CGT
* * * * * *
3606 CAACTTTGCGCGTTTTTGTGCTAAACATAATTCTTAGCAAAACTCTTTCTGGATGCGTTTTTTCG
325 CAATTTTGCACATTTTTGTGCTAAACATAGTTCTTAGCAGAACTCTTTTTGGATGCGTTTTTTCG
3671 CGAAACGAGTGCTCAAAAGTCGTGTGTCGGAATGAGATG
390 CGAAACGAGTGCTCAAAAGTCGTGTGTCGGAATGAGATG
* *
3710 AGTTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGACCAAAGCATCAACTTTGCGA
1 AGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGA
*
3775 GTTTGTATGCAACAAATCGTTCTTAGCGGTTTGTCGGAGTGAGCTGAACTTTTTGGACAGCCCTA
66 GTTTGTATGCAACAAATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTA
*
3840 TGCAGAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCA
131 TGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCA
* * *
3905 TTTTTAGCGAAAGGCTCATTCGAGATGCTTTTTTTGCCCAACGAGTCCTCAAATGTCGTGCGTCG
196 TTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCCCAACGAGTGCTCAAATGTCGTGCGTCG
*
3970 AATTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTT
261 AAGTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTT
4015 GGTAGGCAGC
Statistics
Matches: 1037, Mismatches: 115, Indels: 16
0.89 0.10 0.01
Matches are distributed among these distances:
427 502 0.48
428 531 0.51
429 4 0.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (428 bp):
AGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGA
GTTTGTATGCAACAAATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTA
TGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCA
TTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCCCAACGAGTGCTCAAATGTCGTGCGTCG
AAGTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGTCCAAAGCGTC
AATTTTGCACATTTTTGTGCTAAACATAGTTCTTAGCAGAACTCTTTTTGGATGCGTTTTTTCGC
GAAACGAGTGCTCAAAAGTCGTGTGTCGGAATGAGATG
Found at i:4263 original size:300 final size:300
Alignment explanation
Indices: 3721--4310 Score: 966
Period size: 300 Copynumber: 2.0 Consensus size: 300
3711 GTTTGTTAGA
* *
3721 CAGCGCTATGCACAAACAAAGCTCTCCTCGAAGACCAAAGCATCAACTTTGCGAGTTTGTATGCA
1 CAGCGCTATGAACAAACAAAGCTCTCCTCGAAGACCAAAGCATCAACTTTGCGAGTTCGTATGCA
* * * *
3786 ACAAATCGTTCTTAGCGGTTTGTCGGAGTGAGCTGAACTTTTTGGACAGCCCTATGCAGAAACAA
66 ACAAATCGTTCTTAGCAGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCATATGCACAAACAA
*
3851 AGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTTAGCGAA
131 AGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTCTATGCAAAACATCATTTTTAGCGAA
* * * *
3916 AGGCTCATTCGAGATGCTTTTTTTGCCCAACGAGTCCTCAAATGTCGTGCGTCGAATTGCGATGA
196 AGGCTCATTCCAGAAGCTTTTTTTGCCCAACGAGTACTCAAATGTCGTGCATCGAATTGCGATGA
*
3981 GATTGTTGGACAGCCCTGTGCACAAACAAAGCTTGGTAGG
261 GATTGTTGGAAAGCCCTGTGCACAAACAAAGCTTGGTAGG
* *
4021 CAGCGCTATGAACAAACAAAGCTCTCCTCGATGTCCAAAGCATCAACTTTGCGCA-TTCGTATGC
1 CAGCGCTATGAACAAACAAAGCTCTCCTCGAAGACCAAAGCATCAACTTTGCG-AGTTCGTATGC
* * *
4085 AACACATCGTTCTTAGCAGTTTGTCGGAGTGAGATGAACTTTTTGGATAGCCATGTGCACAAACA
65 AACAAATCGTTCTTAGCAGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCATATGCACAAACA
** *
4150 AAGCTTTCCTAGAAGTTCAAAAGCTCAACTTTGAGCGGTTCTATGCAAAACATCATTTTTAGCGA
130 AAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTCTATGCAAAACATCATTTTTAGCGA
* *
4215 AAGGCTCATTCCAGAAGCTTTTTTTGCGCAACGAGTACTCAAATGTCGTGTATCGAATTGCGATG
195 AAGGCTCATTCCAGAAGCTTTTTTTGCCCAACGAGTACTCAAATGTCGTGCATCGAATTGCGATG
4280 AGATTGTTGGAAAGCCCTGTGCACAAACAAA
260 AGATTGTTGGAAAGCCCTGTGCACAAACAAA
4311 TCTTTCACGA
Statistics
Matches: 267, Mismatches: 22, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
300 266 1.00
301 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (300 bp):
CAGCGCTATGAACAAACAAAGCTCTCCTCGAAGACCAAAGCATCAACTTTGCGAGTTCGTATGCA
ACAAATCGTTCTTAGCAGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCATATGCACAAACAA
AGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTCTATGCAAAACATCATTTTTAGCGAA
AGGCTCATTCCAGAAGCTTTTTTTGCCCAACGAGTACTCAAATGTCGTGCATCGAATTGCGATGA
GATTGTTGGAAAGCCCTGTGCACAAACAAAGCTTGGTAGG
Done.