Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009957.1 Kokia drynarioides strain JFW-HI SEQ_124703, 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: 2968
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.27
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:380 original size:216 final size:215
Alignment explanation
Indices: 1--519 Score: 698
Period size: 216 Copynumber: 2.4 Consensus size: 215
*
1 AATTCTCATGTAAATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTT
1 AATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAAC-TTTT
** * *
66 AGACCAAATGATGCGACTTTTCGACCATGTAATGTTCGAAATAATGCTCGAAGGATTGGATCGTC
65 AGACCAAATGATGCGACTTCCCAACCATGTAATGTTCGAAATAATGCTCGAAGGATTGGATCGAC
** * ** * **
131 TTGAATACTTTAAGGAACCGAAGCTACAAAAGAAGTCATAAAAGTTTGACAAGTTCGAAAGTTCA
130 TTGAATACTACAAGAAACAAAAGCTACAAAAGAACTCATAAAAGTTCAACAAGTTCGAAAGTTCA
*
196 TCCAACAACCAAGAGAGAAAC
195 TCCAACAACCAAGAAAGAAAC
*
217 AATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAACTTTGT
1 AATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTT-T
* * * * *
282 AGACCAAATGATGCGACTTCCCAAGCATGTACTGTTTGAAA-AATTGCTCGAATGATTGTATCGA
65 AGACCAAATGATGCGACTTCCCAACCATGTAATGTTCGAAATAA-TGCTCGAAGGATTGGATCGA
* * * * *
346 CTTGAATACTACAAGAAACAAAAGTTATAAAAGAACTCGTAAAAGTTCAACAAGTTCGGATGTTC
129 CTTGAATACTACAAGAAACAAAAGCTACAAAAGAACTCATAAAAGTTCAACAAGTTCGAAAGTTC
* * *
411 ATCCAAGACCCAAGAAAGACAC
194 ATCCAACAACCAAGAAAGAAAC
* ** *
433 AATTCTTACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTATTT
1 AATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACT-TTT
*
498 AGACCAAATGATGCGATTTCCC
65 AGACCAAATGATGCGACTTCCC
520 TAGGAAGGAT
Statistics
Matches: 266, Mismatches: 34, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
215 5 0.02
216 259 0.97
217 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (215 bp):
AATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTA
GACCAAATGATGCGACTTCCCAACCATGTAATGTTCGAAATAATGCTCGAAGGATTGGATCGACT
TGAATACTACAAGAAACAAAAGCTACAAAAGAACTCATAAAAGTTCAACAAGTTCGAAAGTTCAT
CCAACAACCAAGAAAGAAAC
Found at i:1595 original size:216 final size:216
Alignment explanation
Indices: 824--2968 Score: 2489
Period size: 216 Copynumber: 9.9 Consensus size: 216
814 GATCGTCTTA
** *
824 TGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCCGAA
1 TGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAA
* * * * * *
889 AATTACTCAAAGGAATGGATCGTGTTGAACACTTTAAGGAATCGGATTTAAAAAAGAACTCGTAA
66 AATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAA
** * *
954 AAGTTTGACAAGTTCGGAAGTTTGTCCAACAACCAAGAGAGAAACAATTCTCATGTAAATAAG-T
131 AAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
*
1018 TTTAATTCAAAGGCCAAAACT
196 TTTAATTCAAAGGTCAAAACT
* * * ** *
1039 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTTCCCGAAAATGTAATGTTCGGAA
1 TGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAA
* * * * * *
1104 AATTGCTCGAAGGATTGGATTGTCTTGAATACATTAAGGAACCGAAGCTATAAAAGAAGC-CGTA
66 AATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAA-CTCGTA
* * * *
1168 AAAGTTTGAAAAGCTT-GGAAGTTCATCCAAGAACCAAGAGAGACACAATTCTCACATAAATAAA
130 AAAGTTTGACAAG-TTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
** *
1232 TTTTTAAATTCAAATATCAAAATT
194 TTTTT-AATTCAAAGGTCAAAACT
* * * * ***
1256 TGTTTATAGAATGAAAAACTATTTAGACCAAATGATGCGGTTTCCCTCA-CATGGAATGTTAAAA
1 TGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCC-GAGCATGGAATGTTCGGA
* * * *
1320 AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAATCGAATTTAAAAAAGAACTCATA
65 AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTCGTA
* *
1385 AAAGTTTGACAAGTTCGGAAGTTCATTCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
130 AAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
* * *
1450 TTTTCATTCAAAGGCCGAAACT
195 TTTTAATTCAAAGGTCAAAACT
* * * * * *
1472 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTTCCCGAGCATGTAATGCTCGGAG
1 TGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAA
* * * * * * * *
1537 TATTGCTTGAAAGATTGGATCCTCTTGAATACTTTAAAGAACCGAAGTTATAAAAGAACTCGTAA
66 AATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAA
* * *
1602 AAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGACACAA-TCTCACGTAAATAAGTT
131 AAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
*
1666 TTTAATTCCAAA-ATCAAAACT
196 TTTAATT-CAAAGGTCAAAACT
* * *
1687 TGTTTACAAAATGAAAAGCTATTTAGACCAAATGATGCGATTT-CCGTTGCATGGAATGATCGGA
1 TGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCG-AGCATGGAATGTTCGGA
* * * * *
1751 AAATTACTAGAAGGAATGGATCGTCTAGAACACTTTAATGAACTGAAGCTATAAAAGAACTCGTA
65 AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTCGTA
** * ** * * *
1816 AAAGTTTGTTAATTTAAGAATTTCGTCCAAGAACCAAGAGAGAAACGATTCTCACGTAAATAAGT
130 AAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
* *
1881 TTTTAATTCAAAGGCCAAAACC
195 TTTTAATTCAAAGGTCAAAACT
* * * * *
1903 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTTCTCGACCATGGAATGTTC-GAA
1 TGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAA
* * * * * * * *
1967 ATATTGCTCGAAGGATTGGAACGTCTTAAATACTTTAAGGAACCGAAGCTATAAAAGAAGTCGTT
66 A-ATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTCGTA
* *
2032 AAAGTTTGACAAGTTTGGAAGTTCATCCAAGAGCCAAGAGA-AAACAATTCTCACGTAAATAAGT
130 AAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
* * * *
2096 TTTTAACTCAAAGTTCAGAACA
195 TTTTAATTCAAAGGTCAAAACT
* * *** *
2118 TGTTTACAAAATGAAAAACTATTTAGACCAAAAGATGTGATTTCCCTCTCATGGAATGTTCGAAA
1 TGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAA
* * * *
2183 AATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGGATTTAAAAAAGAACTTGTAA
66 AATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAA
* * *
2248 AAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAAAAACAACTCTCACGTAAATAAGTT
131 AAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
* *
2313 GTTAATTCAAAGG-CTGAAACT
196 TTTAATTCAAAGGTC-AAAACT
* * * * * * * *
2334 TGTTTACAAAATGACAAACTTTTTTAGATCAAATGATGCGACTTCCCGAGCGTGTAATGCTCAGA
1 TGTTTACAAAATGAAAAAC-TATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGA
** * * * * * * *
2399 GTATTGCTTG-AGAGATTGGATCTTCTTGAATACTTTAAGGAACC-AAATATATAAAATAACTCG
65 AAATTACTCGAAG-GAATGGATCGTCTTGAACACTTTAAGGAACCGAAGT-TATAAAAGAACTCG
* * * * *
2462 TAAAACTTCGACAAGTTCGAAAGTTCGTCCAGGAACCAAGAGAGAAACAATTCTCACGTAAATAA
128 TAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
* * *
2527 GGTTTTT-CTTCAAAGATCAAAACA
193 -GTTTTTAATTCAAAGGTCAAAACT
* ** *
2551 TGTTTAAAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTTGGAA
1 TGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAA
* ** *
2616 AATTACTCGAAGGAATGGATCGTCTTGAACACTTTAATGAACTAAAGCTATAAAAGAACTCGTAA
66 AATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAA
** * ** * * *
2681 AAGTTTGTTAATTTAAGAATTTCGTCCAAGAACCAAGAGAGAAACGATTCTCACGTAAATAAGTT
131 AAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
* * * *
2746 TTTAACTCAAAGTTCAGAACA
196 TTTAATTCAAAGGTCAAAACT
* * *** *
2767 TGTTTACAAAATGAAAAACTATTTAGACCAAAAGATGTGATTTCCCTCTCATGGAATGTTCGAAA
1 TGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAA
* * * *
2832 AATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGGATTTAAAAAAGAACTTGTAA
66 AATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAA
* * *
2897 AAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAAAAACAACTCTCACGTAAATAAGTT
131 AAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
*
2962 GTTAATT
196 TTTAATT
Statistics
Matches: 1603, Mismatches: 302, Indels: 49
0.82 0.15 0.03
Matches are distributed among these distances:
214 3 0.00
215 529 0.33
216 719 0.45
217 345 0.22
218 7 0.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.27
Consensus pattern (216 bp):
TGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAA
AATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAA
AAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
TTTAATTCAAAGGTCAAAACT
Found at i:1892 original size:431 final size:432
Alignment explanation
Indices: 823--2968 Score: 2822
Period size: 431 Copynumber: 5.0 Consensus size: 432
813 GGATCGTCTT
*
823 ATGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCCGA
1 ATGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGGA
* * *
888 AAATTACTCAAAGGAATGGATCGTGTTGAACACTTTAAGGAA-TCGGATTTAAAAAAGAACTCGT
66 AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACT-GAATTTAAAAAAGAACTCGT
*
952 AAAAGTTTGACAAGTTCGGAAGTTT-GTCCAACAACCAAGAGAGAAACAATTCTCATGTAAATAA
130 AAAAGTTTGACAAGTTCGGAA-TTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAA
1016 G-TTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGAC
194 GTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGAC
** * * *
1080 TTCCCGAAAATGTAATGTTCGGAAAATTGCTCGAAGGATTGGATTGTCTTGAATACATTAAGGAA
259 TTCCCGAGCATGTAATGTTCGGAATATTGCTCGAAGGATTGGATCGTCTTGAATACTTTAAGGAA
* *
1145 CCGAAGCTATAAAAGAAGC-CGTAAAAGTTTGAAAAGCTT-GGAAGTTCATCCAAGAACCAAGAG
324 CCGAAGTTATAAAAGAA-CTCGTAAAAGTTTGACAAG-TTCGGAAGTTCATCCAAGAACCAAGAG
* * * * *
1208 AGACACAATTCTCACATAAATAAATTTTTAAATTCAAATATCAAAAT
387 AGAAACAATTCTCACGTAAATAAGTTTTT-AATTCAAAGATCAAAAC
* * * * * ***
1255 TTGTTTATAGAATGAAAAACTATTTAGACCAAATGATGCGGTTTCCCTCACATGGAATGTTAAAA
1 ATGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGGA
*
1320 AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAA-TCGAATTTAAAAAAGAACTCAT
66 AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACT-GAATTTAAAAAAGAACTCGT
* * *
1384 AAAAGTTTGACAAGTTCGGAAGTTCATTCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAG
130 AAAAGTTTGACAAGTTCGGAATTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* *
1449 TTTTTCATTCAAAGGCCGAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACT
195 TTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACT
* * * * * *
1514 TCCCGAGCATGTAATGCTCGGAGTATTGCTTGAAAGATTGGATCCTCTTGAATACTTTAAAGAAC
260 TCCCGAGCATGTAATGTTCGGAATATTGCTCGAAGGATTGGATCGTCTTGAATACTTTAAGGAAC
* *
1579 CGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGA
325 CGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGA
*
1644 CACAA-TCTCACGTAAATAAGTTTTTAATTCCAAA-ATCAAAAC
390 AACAATTCTCACGTAAATAAGTTTTTAATT-CAAAGATCAAAAC
* * * * *
1686 TTGTTTACAAAATGAAAAGCTATTTAGACCAAATGATGCGATTTCCGTTGCATGGAATGATCGGA
1 ATGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGGA
* * * ** *
1751 AAATTACTAGAAGGAATGGATCGTCTAGAACACTTTAATGAACTGAAGCTATAAAAGAACTCGTA
66 AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACTGAATTTAAAAAAGAACTCGTA
** * ** * *
1816 AAAGTTTGTTAATTTAAGAATTTCGTCCAAGAACCAAGAGAGAAACGATTCTCACGTAAATAAGT
131 AAAGTTTGACAAGTTCGGAATTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
*
1881 TTTTAATTCAAAGGCCAAAACCTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTT
196 TTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTT
* * * * * *
1946 CTCGACCATGGAATGTTCGAAATATTGCTCGAAGGATTGGAACGTCTTAAATACTTTAAGGAACC
261 CCCGAGCATGTAATGTTCGGAATATTGCTCGAAGGATTGGATCGTCTTGAATACTTTAAGGAACC
* * * * *
2011 GAAGCTATAAAAGAAGTCGTTAAAGTTTGACAAGTTTGGAAGTTCATCCAAGAGCCAAGAGA-AA
326 GAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAA
* * *
2075 ACAATTCTCACGTAAATAAGTTTTTAACTCAAAGTTCAGAAC
391 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAAC
* * * *
2117 ATGTTTACAAAATGAAAAACTATTTAGACCAAAAGATGTGATTTCCCTCTCATGGAATGTTCGAA
1 ATGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGGA
* * *
2182 AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGGATTTAAAAAAGAACTTGTA
66 AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACTGAATTTAAAAAAGAACTCGTA
* * * *
2247 AAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAAAAACAACTCTCACGTAAATAAGT
131 AAAGTTTGACAAGTTCGGAATTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
* ** *
2312 TGTTAATTCAAAGGCTGAAACTTGTTTACAAAATGACAAACTTTTTTAGATCAAATGATGCGACT
196 TTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAAC-TTTTTAGACCAAATGATGCGACT
* * * * * *
2377 TCCCGAGCGTGTAATGCTCAGAGTATTGCTTG-AGAGATTGGATCTTCTTGAATACTTTAAGGAA
260 TCCCGAGCATGTAATGTTCGGAATATTGCTCGAAG-GATTGGATCGTCTTGAATACTTTAAGGAA
* * * * * * *
2441 CC-AAATATATAAAATAACTCGTAAAACTTCGACAAGTTCGAAAGTTCGTCCAGGAACCAAGAGA
324 CCGAAGT-TATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGA
*
2505 GAAACAATTCTCACGTAAATAAGGTTTTT-CTTCAAAGATCAAAAC
388 GAAACAATTCTCACGTAAATAA-GTTTTTAATTCAAAGATCAAAAC
* *
2550 ATGTTTAAAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTTGGA
1 ATGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGGA
* * ** *
2615 AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAATGAACTAAAGCTATAAAAGAACTCGTA
66 AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACTGAATTTAAAAAAGAACTCGTA
** * ** * *
2680 AAAGTTTGTTAATTTAAGAATTTCGTCCAAGAACCAAGAGAGAAACGATTCTCACGTAAATAAGT
131 AAAGTTTGACAAGTTCGGAATTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
* ** * * * * * * *
2745 TTTTAACTCAAAGTTCAGAACATGTTTACAAAATGAAAAACTATTTAGACCAAAAGATGTGATTT
196 TTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTT
*** * * * * * *
2810 CCCTCTCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACC
261 CCCGAGCATGTAATGTTCGGAATATTGCTCGAAGGATTGGATCGTCTTGAATACTTTAAGGAACC
* * * * * *
2875 GGATTTAAAAAAGAACTTGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAAAA
326 GAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAA
* *
2940 ACAACTCTCACGTAAATAAGTTGTTAATT
391 ACAATTCTCACGTAAATAAGTTTTTAATT
Statistics
Matches: 1477, Mismatches: 221, Indels: 32
0.85 0.13 0.02
Matches are distributed among these distances:
430 9 0.01
431 589 0.40
432 457 0.31
433 416 0.28
434 6 0.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.27
Consensus pattern (432 bp):
ATGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGGA
AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACTGAATTTAAAAAAGAACTCGTA
AAAGTTTGACAAGTTCGGAATTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
TTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTT
CCCGAGCATGTAATGTTCGGAATATTGCTCGAAGGATTGGATCGTCTTGAATACTTTAAGGAACC
GAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAA
ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAAC
Found at i:2606 original size:648 final size:645
Alignment explanation
Indices: 823--2968 Score: 2781
Period size: 648 Copynumber: 3.3 Consensus size: 645
813 GGATCGTCTT
*
823 ATGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCCG-
1 ATGTTTACAAAATGAAAAACTATTTAGACCAAAAGATGCGATTTCCCTCGCATGGAATGTT-CGA
* * *
887 AAAATTACTCAAAGGAATGGATCGTGTTGAACACTTTAAGGAATCGGATTTAAAAAAGAACTCGT
65 AAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGGATTTAAAAAAGAACTCGT
** * * *
952 AAAAGTTTGACAAGTTCGGAAGTTTGTCCAACAACCAAGAGAGAAACAATTCTCATGTAAATAAG
130 AAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAAAAACAACTCTCACGTAAATAAG
1017 TT-TTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACT
195 TTGTTAATTCAAAGG-CAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACT
** * * *
1081 TCCCGAAAATGTAATGTTCGGAAAATTGCTCGAAGGATTGGAT-TGTCTTGAATACATTAAGGAA
259 TCCCGAGCATGTAATGATCGGAAAATTGCTAGAAGGATTGGATCT-TCTTGAATACTTTAAGGAA
* *
1145 CCGAAGCTATAAAAGAAGC-CGTAAAAGTTTGAAAAGCTTGGAAGTTCATCCAAGAACCAAGAGA
323 CCGAAGCTATAAAAGAA-CTCGTAAAAGTTTGAAAAG-TTGAAAGTTCGTCCAAGAACCAAGAGA
* * * * ** * *
1209 GACACAATTCTCACATAAATAAATTTTTAAATTCAAATATCAAAATTTGTTTATAGAATGAAAAA
386 GAAACAATTCTCACGTAAATAAGTTTTT-AATTCAAAGATCAAAACATGTTTAAAAAATGAAAAA
* * *
1274 CTATTTAGACCAAATGATGCGGTTTCCCTCACATGGAATGTTAAAAAAATTACTCGAAGGAATGG
450 CTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTT-AGAAAATTACTCGAAGGAATGG
* ** * * *
1339 ATCGTCTTGAACACTTTAAGGAATCGAATTTAAAAAAGAACTCATAAAAGTTTGACAAGTTCGGA
514 ATCGTCTTGAACACTTTAAGGAACCGAAGCTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGGA
* * * * * *
1404 AGTTCATTCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTCATTCAAAG-GCCGA
579 AGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAACTCAAAGTTCAG-
1468 AAC
643 AAC
* * * * * ** * * *
1471 TTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTTCCCGAGCATGTAATGCTCGGA
1 ATGTTTACAAAATGAAAAACTATTTAGACCAAAAGATGCGATTTCCCTCGCATGGAATGTTCGAA
** * * * * * * * * * *
1536 GTATTGCTTGAAAGATTGGATCCTCTTGAATACTTTAAAGAACCGAAGTTATAAAAGAACTCGTA
66 AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGGATTTAAAAAAGAACTCGTA
* * * * *
1601 AAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGACACAA-TCTCACGTAAATAAGT
131 AAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAAAAACAACTCTCACGTAAATAAGT
* ** *
1665 TTTTAATTCCAAAATCAAAACTTGTTTACAAAATGA-AAAGCTATTTAGACCAAATGATGCGA-T
196 TGTTAATT-CAAAGGCAAAACTTGTTTACAAAATGACAAA-CTTTTTAGACCAAATGATGCGACT
* * * * * * * * *
1728 TTCCGTTGCATGGAATGATCGGAAAATTACTAGAAGGAATGGATCGTCTAGAACACTTTAATGAA
259 TCCCG-AGCATGTAATGATCGGAAAATTGCTAGAAGGATTGGATCTTCTTGAATACTTTAAGGAA
* ** * * *
1793 CTGAAGCTATAAAAGAACTCGTAAAAGTTTGTTAATTTAAGAATTTCGTCCAAGAACCAAGAGAG
323 CCGAAGCTATAAAAGAACTCGTAAAAGTTTGAAAAGTTGA-AAGTTCGTCCAAGAACCAAGAGAG
* ** * * *
1858 AAACGATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACCTGTTTACAAAATGACAAACT
387 AAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACATGTTTAAAAAATGAAAAACT
* * * * *
1923 TTTTAGACCAAATGATGCGACTT--CTCGACCATGGAATGTTCGAAATATTGCTCGAAGGATTGG
452 ATTTAGACCAAATGATGCGATTTCCCTCG--CATGGAATGTTAGAAA-ATTACTCGAAGGAATGG
* * * * *
1986 AACGTCTTAAATACTTTAAGGAACCGAAGCTATAAAAGAAGTCGTTAAAGTTTGACAAGTTTGGA
514 ATCGTCTTGAACACTTTAAGGAACCGAAGCTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGGA
*
2051 AGTTCATCCAAGAGCCAAGAGA-AAACAATTCTCACGTAAATAAGTTTTTAACTCAAAGTTCAGA
579 AGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAACTCAAAGTTCAGA
2115 AC
644 AC
* *
2117 ATGTTTACAAAATGAAAAACTATTTAGACCAAAAGATGTGATTTCCCTCTCATGGAATGTTCGAA
1 ATGTTTACAAAATGAAAAACTATTTAGACCAAAAGATGCGATTTCCCTCGCATGGAATGTTCGAA
*
2182 AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGGATTTAAAAAAGAACTTGTA
66 AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGGATTTAAAAAAGAACTCGTA
2247 AAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAAAAACAACTCTCACGTAAATAAGT
131 AAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAAAAACAACTCTCACGTAAATAAGT
* *
2312 TGTTAATTCAAAGGCTGAAACTTGTTTACAAAATGACAAACTTTTTTAGATCAAATGATGCGACT
196 TGTTAATTCAAAGGC-AAAACTTGTTTACAAAATGACAAAC-TTTTTAGACCAAATGATGCGACT
* * * ** *
2377 TCCCGAGCGTGTAATGCTCAGAGTATTGCTTG-AGAGATTGGATCTTCTTGAATACTTTAAGGAA
259 TCCCGAGCATGTAATGATCGGAAAATTGCTAGAAG-GATTGGATCTTCTTGAATACTTTAAGGAA
* ** * * * * *
2441 CCAAATATATAAAATAACTCGTAAAACTTCGACAAGTTCGAAAGTTCGTCCAGGAACCAAGAGAG
323 CCGAAGCTATAAAAGAACTCGTAAAAGTTTGAAAAGTT-GAAAGTTCGTCCAAGAACCAAGAGAG
*
2506 AAACAATTCTCACGTAAATAAGGTTTTT-CTTCAAAGATCAAAACATGTTTAAAAAATGAAAAAC
387 AAACAATTCTCACGTAAATAA-GTTTTTAATTCAAAGATCAAAACATGTTTAAAAAATGAAAAAC
*
2570 TATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTTGGAAAATTACTCGAAGGAATGGA
451 TATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATG-TTAGAAAATTACTCGAAGGAATGGA
* ** ** *
2635 TCGTCTTGAACACTTTAATGAACTAAAGCTATAAAAGAACTCGTAAAAGTTTGTTAA-TTTAAGA
515 TCGTCTTGAACACTTTAAGGAACCGAAGCTATAAAAGAACTCGTAAAAGTTTGACAAGTTT-GGA
* * *
2699 ATTTCGTCCAAGAACCAAGAGAGAAACGATTCTCACGTAAATAAGTTTTTAACTCAAAGTTCAGA
579 AGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAACTCAAAGTTCAGA
2764 AC
644 AC
* *
2766 ATGTTTACAAAATGAAAAACTATTTAGACCAAAAGATGTGATTTCCCTCTCATGGAATGTTCGAA
1 ATGTTTACAAAATGAAAAACTATTTAGACCAAAAGATGCGATTTCCCTCGCATGGAATGTTCGAA
*
2831 AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGGATTTAAAAAAGAACTTGTA
66 AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGGATTTAAAAAAGAACTCGTA
2896 AAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAAAAACAACTCTCACGTAAATAAGT
131 AAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAAAAACAACTCTCACGTAAATAAGT
2961 TGTTAATT
196 TGTTAATT
Statistics
Matches: 1291, Mismatches: 182, Indels: 49
0.85 0.12 0.03
Matches are distributed among these distances:
645 3 0.00
646 193 0.15
647 228 0.18
648 595 0.46
649 268 0.21
650 4 0.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.27
Consensus pattern (645 bp):
ATGTTTACAAAATGAAAAACTATTTAGACCAAAAGATGCGATTTCCCTCGCATGGAATGTTCGAA
AAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGGATTTAAAAAAGAACTCGTA
AAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAAAAACAACTCTCACGTAAATAAGT
TGTTAATTCAAAGGCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTTC
CCGAGCATGTAATGATCGGAAAATTGCTAGAAGGATTGGATCTTCTTGAATACTTTAAGGAACCG
AAGCTATAAAAGAACTCGTAAAAGTTTGAAAAGTTGAAAGTTCGTCCAAGAACCAAGAGAGAAAC
AATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACATGTTTAAAAAATGAAAAACTATTT
AGACCAAATGATGCGATTTCCCTCGCATGGAATGTTAGAAAATTACTCGAAGGAATGGATCGTCT
TGAACACTTTAAGGAACCGAAGCTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCAT
CCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAACTCAAAGTTCAGAAC
Done.