Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011642.1 Kokia drynarioides strain JFW-HI SEQ_126634, 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: 6425
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.29
Warning! 74 characters in sequence are not A, C, G, or T
Found at i:403 original size:18 final size:18
Alignment explanation
Indices: 380--418 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
370 ATTGCAGACT
*
380 TTTTGATA-CTTTGATGAA
1 TTTTGATATCTTAG-TGAA
398 TTTTGATATCTTAGTGAA
1 TTTTGATATCTTAGTGAA
416 TTT
1 TTT
419 ATTCAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.26, C:0.05, G:0.15, T:0.54
Consensus pattern (18 bp):
TTTTGATATCTTAGTGAA
Found at i:1525 original size:215 final size:213
Alignment explanation
Indices: 835--4804 Score: 3879
Period size: 215 Copynumber: 18.7 Consensus size: 213
825 GATTGTATTA
* *
835 TTTTTAATTCAAAAACCAAAAGTTGTTTACAAAATGAAAACTATTTAGACCT-AATGATGTGATT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGA-CTAAATGATGTGA-T
* * * *
899 TTCCAAGCATGGACTGTACAGAAAATTGCTCGAAGGAATGGATCGTCTAGAATACTTTAATGAAC
64 TTCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAC
* * **
964 AAAAGTTATAAAAGAACTTGTAAAAGTCTGTCAAGTT-TAAAGTTCGGCCGAGAACCAAGAA-AG
129 -AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAA-AAGAG
* * *
1027 AAACAATTCTCACATAAAGAAT
192 AAACAATTCTCACCTAAATAAG
* * *
1049 TTTTTCATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGAGATTT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACTAAATGATGTGATTT
* * **
1114 CCTAAGCTTGGAATGTTCAGAAAATTGCTCGAAGGAATGGTTTATCTTGAATACTTTAAGGAACC
66 CC-AAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-C
* * * * *
1179 GAAGTTATAAAAGAACTCATAATAAAAGTTTGTCAACTTCGGAAGTTCGGCCTAGAACCAACAGA
129 AAAGTTATAAAAGAACTC---GTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAAAGA
*
1244 GAAACTATTCTCACCTAAATAAG
191 GAAACAATTCTCACCTAAATAAG
* * * *
1267 TTTTTAATTCAAAGACCAAAAGCTGTTTACATAATGGCAACTATTTAGACTAAATGATGCGATTT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACTAAATGATGTGATTT
* * * * ** * * *
1332 CTAGAGTATGAAATTTTCTTAAAATTGCTCGAAGGAATGTATCGTCTTGAATAGTTTACGGAATC
66 CCA-AGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-C
* * * *
1397 AAAGTTATAAAAGAATTCGTAAAAGTTTTTAAAGTTCGGAAGTTCGACCGAGAACCAAAAGAGAA
129 AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAAAGAGAA
* **
1462 ACAATTCTCACTTAAATACC
194 ACAATTCTCACCTAAATAAG
* *
1482 TTTTTAATTCAAAGACCAAAAGTAGTTTAAAAAATGACAACTATTTAGACCTAAA-GATGTGATT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGA-CTAAATGATGTGATT
* * ** * * * *
1546 TCCCAAGCATAGACTAAT-GGAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAATGACC
65 T-CCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAC
* * * * ** * *
1610 AAAAGTTATAAAAGAACTCGTTAAATTTTGTCAAGTTCAGAAATTCAACAGAGTA-CAAGGAA-A
129 -AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAA--AAGA
* * * *
1673 GAAACAATTCTAACATAAATCAC
191 GAAACAATTCTCACCTAAATAAG
** * * **
1696 TTTTT--TT-----------TTTTTTTTACAAAATGACAATCTATTTAGAAC-AATTGATACGAT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA-CTATTTAG-ACTAAATGATGTGA-
** * * * *
1747 TTTCTGAGTATGGAATGTTC-GAAAAATTACTGGAAGGAATGGATCGTCTTGAATTCTTTAAGGA
63 TTTCCAAGCATGGAATGTTCAG-AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGA
* * * * * * * *
1811 AAAGAAGTTAAAAAAGAACTCGTAAAAGTTTGTCAAGTTTGGAAGTTCAGCTGAGAACGAATAGG
127 ACA-AAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAAAGA
1876 GAAACAATTCTCACCTAAATAAG
191 GAAACAATTCTCACCTAAATAAG
* * * * * * * *
1899 TTTTTAATTGAAAAACCAAAGGTAGTTTACAGAATGACAACAAATTAGACCT-AATAATGTGATT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGA-CTAAATGATGTGATT
* * * * *
1963 TCCCAACCATGGACTGTACAGAAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAATGAAC
65 T-CCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAC
** **
2028 AAAAGTTATAAAAGAACTTATAAAAGTTTGTCAAGTT-TAAAGTTCGGCCGAGAACCAAGAA-AG
129 -AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAA-AAGAG
* * *
2091 AAACAATTCTCACATAAAGAAT
192 AAACAATTCTCACCTAAATAAG
* * * *
2113 TTTTTAATGCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAAAGATGAGATTT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACTAAATGATGTGATTT
* * *
2178 CCTAAGCTTGGAATGTTCAGAAAATTGCTCGAAGGAAT-GATTCATCTTGAATA-TTTCAGGAAC
66 CC-AAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGA-TCGTCTTGAATACTTTAAGGAA-
* * * * * * *
2241 CGAAGTTATGAAAGAACTCGTAAAAGTTTGTCAAATTCGGATGTTCGGCCTAGAACCAAGAGAAA
128 CAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAAAGAGA
*
2306 AACTATTCTCACCTAAATAAG
193 AACAATTCTCACCTAAATAAG
* * * * * *
2327 TTTTTAATTTAAAGACCAAAAGTTGTTTACATAATGGCAACTATTAAGACTAAATTATGTAATTT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACTAAATGATGTGATTT
* ** * * * * *
2392 CTAGAGCATGGAATGTTCTTAAAATTGCTTGAAGGAATGAATCATCTTGAATAGTTTAAAGAATC
66 CCA-AGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-C
* * * **
2457 AAAGTTATAAAATAACTCGTAAAAGTTTTTCAAGTTCGTAAGTTCGATCGAGAACCAAAAGAGAA
129 AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAAAGAGAA
2522 ACAATTCTCACCTAAATAAG
194 ACAATTCTCACCTAAATAAG
* *
2542 TTTTTAATTCAAAGACCAAAAGTAGTTTAAAAAATGACAACTATTTAGACCT-AATGATGTGATC
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGA-CTAAATGATGTGAT-
* * * * * * * * *
2606 TCCCAAACATGGACTGTAT-GGGAAATAGCTCGAAAGAATGGATTGTCCTGAATACTTTAAGGAA
64 TTCCAAGCATGGAATGT-TCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA
* ** *
2670 CAAAAGTTATAAAAGAACTCGTTAAAGTTTGTCAAGTTCGGAAGTTCAACCGAGAA-CAAAGAAA
128 C-AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAA-AGA
* *
2734 GAAACAATTCTAACATAAATAA-
191 GAAACAATTCTCACCTAAATAAG
* * *
2756 --CTT--TT-------------TT-TTTACAAAATGACAATCTATTTAGAAC-AAGTGATGCGAT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA-CTATTTAG-ACTAAATGATGTGAT
* * * * * *
2802 TTCCCGAGCATGAAAAGTTCAAAAAATTGCTCGAAGGAATGGATCGTCCTGAATTCTTTAAGGAA
64 TT-CCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA
* * * * *
2867 CAGAAGTTAAAAAAGAACTCGCAAAAGTTTGTCAAGTTCGGAAGTTTGGCTGAGAACCAATAGAG
128 CA-AAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAAAGAG
2932 AAACAATTCTCACCTAAATAAG
192 AAACAATTCTCACCTAAATAAG
* * * * *
2954 TTTTTAATTGAAAAACCAAAAGTAGTTTACAGAAA-GACAAACAATTTAGACCT-AATAATGTGA
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACA-AAATGAC-AACTATTTAGA-CTAAATGATGTGA
* * * * *
3017 TTTCCCAAGCATGGACTGTACA-ATAAATTGCT-GAAGGAATGGATCATCTTGAACACTTTAATG
63 TTT-CCAAGCATGGAATGTTCAGA-AAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGG
* * * ** * **
3080 AACAAAATTTATAAAAGAACTTG-AAAATTTTGTCAAGTT-TAAAGTTTGGTAGAGAACCAAGAA
126 AAC-AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAA-AA
* *
3143 -AGAAACAATTCTCACATAAAGAA-
189 GAGAAACAATTCTCACCTAAATAAG
* * *
3166 TTTTTAAATTCAAAGACCAAAAGTTGTTTACAAAAAGACAACTATTTAGACCAAATGATGCGATT
1 TTTTT-AATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACTAAATGATGTGATT
* *
3231 TCCAAGCATGAAATGTTCAGAAAATTGCTCGAAGGAATGGATAC-TCTTAAATACTTTAAGGAAC
65 TCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGAT-CGTCTTGAATACTTTAAGGAA-
* * * * * *
3295 CAAAGTTATAAAAGAACTCGTAAAAGTTGGTCAACTTCGAAAGTTTGGCCCAGAACCAAGAGAGA
128 CAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAAAGAGA
** * *
3360 AATTATTGTCACCTAAATTAG
193 AACAATTCTCACCTAAATAAG
* * * * *
3381 TTTTTAATTCAAGGACCAAAAGTTGTTTACAAAATAAAAACTATTTAGACCAAATGATGCGATTT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACTAAATGATGTGATTT
* *
3446 CTCGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGATTACTTTAAGGAACC
66 C-CAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-C
* * * * *
3511 GAAGTTATAAAAGAACTCTTAAAAGTTAGTCAAGTTCGGAAGTTCGGTCGAGAACCAAGAGAGAA
129 AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAAAGAGAA
*
3576 ATAATTCTCACCTAAATAAG
194 ACAATTCTCACCTAAATAAG
* * *
3596 TTTTTAATTCAAAAACCAAAAGTTGTTTACAATATGACAACTATTTAGACCT-AATGATATGATT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGA-CTAAATGATGTGA-T
* * * * * *
3660 TTCCAAGCATGGACTGTACAGAAAATTACTTGAAGGAATGGATCGTCTTGAATACTATAATGAAC
64 TTCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAC
* * ** * *
3725 AAAAGTTATAAAAGAAGTTGTAAAAGTTTGTCAAGTT-TAAAGTTCGGCCAAAAACCAAGAA-AG
129 -AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAA-AAGAG
* * *
3788 AAACAATTCTCACATAAAGAAT
192 AAACAATTCTCACCTAAATAAG
* * * *
3810 TTTTTCATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGAGATTC
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACTAAATGATGTGATTT
* * * * *
3875 CCTGAGCTTGGAATGTTCAGAAAATTGCTCGAAGTAATGGTTTGTCTTGAATACTTTAAGGAACC
66 CC-AAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-C
* * * * * *
3940 AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAACTTCGAAAGTTCGGCCTAGAAACAAGACAGAA
129 AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAAAGAGAA
* * *
4005 ACTATTATCACCTAAAAAAG
194 ACAATTCTCACCTAAATAAG
* * * *
4025 TTTTTAATTCAAAGACCAAAAGTTGTTTACATAATGGCAATTATTTAGACTAAATGATGCGATTT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACTAAATGATGTGATTT
* ** * ** * * * * *
4090 CTAAAGCATTCAATTTTCTTAAATTTACTTGAAGGAATGGATCGTCTTAAATAGTTTAAGGAATC
66 C-CAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-C
* * * *
4155 AAAGTTAT-AAAGTAACTCATAAAAGTTTTTCAAGTTCAGAAGTTCGACCGAGAACCAAAAGAGA
129 AAAGTTATAAAAG-AACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAAAGAGA
4219 AACAATTCTCACCTAAATAAG
193 AACAATTCTCACCTAAATAAG
* * *
4240 TTTTTAATTTGAAA-ACCAAAAGTAGTTTAAAAAATGACAACTATTTAGACCT-AATGATGTGAT
1 TTTTTAA-TTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGA-CTAAATGATGTGAT
* * * *
4303 TTCCCAAGCATGGACTGTACAGAAAATTACTCGAAGGAATGGATCGTCTTG-A-ACTTTAATGAA
64 TT-CCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA
* * * *
4366 CAAAAGTTATAAAAGTACTCGTAAAA-CTT-T---G-TC--AAGTTCGGCTGAGAACGAATAA-A
128 C-AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAA-AAGA
4422 GAAACAATTCTCACCTAAATAAG
191 GAAACAATTCTCACCTAAATAAG
* * * *
4445 TTTTTAATTGAAAAACCAAAAGTAGTTTACAAAATAACAACTATTTAGACCT-AATGATGTGATT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGA-CTAAATGATGTGATT
* * * * * * **
4509 TCCCAAGCATGGACTGTACAAAAAATTACTCAAAGGAATGAATCGTCTTGAATACTTTATTGAAC
65 T-CCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAC
* ** * * *
4574 AAAAGTTATAAAAGAAGTTATAAAAGTTTGTCAGGTTC-AAAGTTCGACCGAGAACCAAGAA-AG
129 -AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAA-AAGAG
* * *
4637 AAACAATTCTCACATAAAGAAT
192 AAACAATTCTCACCTAAATAAG
* * * * *
4659 TTTTTAATTCAAAGACCAAAAGCTGTTT-CGAAATGACAACTATTTAGACCAAAAGATGAGATTT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACTAAATGATGTGATTT
* * * *
4723 CCTAAGCTTGGAATGTTCAGAAAATTGCTCGAAGGAATGGTTCATCTTGAATACTTTAATGAACC
66 CC-AAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-C
*
4788 GAAGTTATAAAAGAACT
129 AAAGTTATAAAAGAACT
4805 TGTATTTAGA
Statistics
Matches: 3090, Mismatches: 534, Indels: 265
0.79 0.14 0.07
Matches are distributed among these distances:
196 17 0.01
197 136 0.04
198 4 0.00
200 2 0.00
201 17 0.01
202 28 0.01
203 109 0.04
204 8 0.00
205 144 0.05
206 3 0.00
207 34 0.01
208 3 0.00
209 1 0.00
210 2 0.00
211 25 0.01
212 86 0.03
213 262 0.08
214 856 0.28
215 1076 0.35
216 93 0.03
217 22 0.01
218 162 0.05
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (213 bp):
TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACTAAATGATGTGATTT
CCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACAA
AGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAAAGAGAAAC
AATTCTCACCTAAATAAG
Found at i:3829 original size:429 final size:429
Alignment explanation
Indices: 835--4804 Score: 4078
Period size: 429 Copynumber: 9.3 Consensus size: 429
825 GATTGTATTA
* * *
835 TTTTTAATTCAAAAACCAAAAGTTGTTTACAAAATGAAAACTATTTAGACCTAATGATGTGATTT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGTGATTT
* * * * *
900 TCCAAGCATGGACTGTACAGAAAATTGCTCGAAGGAATGGATCGTCTAGAATACTTTAATGAACA
66 CCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACA
* * **
965 AAAGTTATAAAAGAACTTGTAAAAGTCTGTCAAGTT-TAAAGTTCGGCCGAGAACCAAGAAAGAA
131 AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAGAAAGAA
* * * *
1029 ACAATTCTCACATAAAGAATTTTTTCATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATT
196 ACAATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATT
* * * * **
1094 TAGACCAAATGATGAGA-TTTCCTAAGCTTGGAATGTTCAGAAAATTGCTCGAAGGAATGGTTTA
261 TAGACCTAATGATGTGATTTTCC-AAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCG
** * * *
1158 TCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATAATAAAAGTTTGTCAACTTCGGAA
325 TCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAACTC---GTAAAAGTTTGTCAAGTTC-AAA
* * * *
1223 GTTCGGCCTAGAACCAACAGAGAAACTATTCTCACCTAAATAAG
386 GTTCGGCCGAGAACCAAGAAAGAAACAATTCTCACCTAAATAAG
* * * * *
1267 TTTTTAATTCAAAGACCAAAAGCTGTTTACATAATGGCAACTATTTAGACTAAATGATGCGATTT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGTGATTT
* * * * ** * * *
1332 -CTAGAGTATGAAATTTTCTTAAAATTGCTCGAAGGAATGTATCGTCTTGAATAGTTTACGGAAT
66 CCCA-AGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-
* * * *
1396 C-AAAGTTATAAAAGAATTCGTAAAAGTTTTTAAAGTTCGGAAGTTCGACCGAGAACCAA-AAGA
129 CAAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAGAA-A
* ** * *
1459 GAAACAATTCTCACTTAAATACCTTTTTAATTCAAAGACCAAAAGTAGTTTAAAAAATGACAACT
193 GAAACAATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACT
* * * * ** * *
1524 ATTTAGACCTAAAGATGTGATTTCCCAAGCATAGACTAAT-GGAAAATTGCTCGAAAGAATGGAT
258 ATTTAGACCTAATGATGTGATTTTCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGAT
* * * * *
1588 CGTCTTGAATACTTTAATGACCAAAAGTTATAAAAGAACTCGTTAAATTTTGTCAAGTTCAGAAA
323 CGTCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCA-AAG
** * * * * * *
1653 TTCAACAGAGTA-CAAGGAAAGAAACAATTCTAACATAAATCAC
387 TTCGGCCGAGAACCAA-GAAAGAAACAATTCTCACCTAAATAAG
** * * * **
1696 TTTTT--TT-----------TTTTTTTTACAAAATGACAATCTATTTAGAACAATTGATACGATT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA-CTATTTAGACCAAATGATGTGATT
* ** * * * *
1748 TTCTGAGTATGGAATGTTC-GAAAAATTACTGGAAGGAATGGATCGTCTTGAATTCTTTAAGGAA
65 TCCCAAGCATGGAATGTTCAG-AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA
* * * * * * **
1812 -AAGAAGTTAAAAAAGAACTCGTAAAAGTTTGTCAAGTTTGGAAGTTCAGCTGAGAACGAATAGG
129 CAA-AAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAGAAA
* * * * * *
1876 GAAACAATTCTCACCTAAATAAGTTTTTAATTGAAAAACCAAAGGTAGTTTACAGAATGACAACA
193 GAAACAATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACT
* * * * * * *
1941 AATTAGACCTAATAATGTGATTTCCCAACCATGGACTGTACAGAAAATTACTCGAAGGAATGGAT
258 ATTTAGACCTAATGATGTGATTTTCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGAT
* ** *
2006 CGTCTTGAATACTTTAATGAACAAAAGTTATAAAAGAACTTATAAAAGTTTGTCAAGTTTAAAGT
323 CGTCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCAAAGT
* * *
2071 TCGGCCGAGAACCAAGAAAGAAACAATTCTCACATAAAGAAT
388 TCGGCCGAGAACCAAGAAAGAAACAATTCTCACCTAAATAAG
* * *
2113 TTTTTAATGCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAAAGATGAGATTT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGTGATTT
* * * *
2178 CCTAAGCTTGGAATGTTCAGAAAATTGCTCGAAGGAAT-GATTCATCTTGAATA-TTTCAGGAAC
66 CCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGA-TCGTCTTGAATACTTTAAGGAAC
** * * * *
2241 CGAAGTTATGAAAGAACTCGTAAAAGTTTGTCAAATTCGGATGTTCGGCCTAGAACCAAGAGAA-
130 AAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAGA-AAG
* * * *
2305 AAACTATTCTCACCTAAATAAGTTTTTAATTTAAAGACCAAAAGTTGTTTACATAATGGCAACTA
194 AAACAATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTA
* * * * ** * *
2370 TTAAGA-CTAAATTATGT-AATTTCTAGAGCATGGAATGTTCTTAAAATTGCTTGAAGGAATGAA
259 TTTAGACCT-AATGATGTGATTTTCCA-AGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGA
* * * * * *
2433 TCATCTTGAATAGTTTAAAGAATC-AAAGTTATAAAATAACTCGTAAAAGTTTTTCAAGTTCGTA
322 TCGTCTTGAATACTTTAAGGAA-CAAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTC-AA
**
2497 AGTTCGATCGAGAACCAA-AAGAGAAACAATTCTCACCTAAATAAG
385 AGTTCGGCCGAGAACCAAGAA-AGAAACAATTCTCACCTAAATAAG
* * * *
2542 TTTTTAATTCAAAGACCAAAAGTAGTTTAAAAAATGACAACTATTTAGACCTAATGATGTGATCT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGTGATTT
* * * * * * * *
2607 CCCAAACATGGACTGTAT-GGGAAATAGCTCGAAAGAATGGATTGTCCTGAATACTTTAAGGAAC
66 CCCAAGCATGGAATGT-TCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAC
* ** *
2671 AAAAGTTATAAAAGAACTCGTTAAAGTTTGTCAAGTTCGGAAGTTCAACCGAGAACAAAGAAAGA
130 AAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAGAAAGA
* * *
2736 AACAATTCTAACATAAATAA---CTT--TT-------------TT-TTTACAAAATGACAATCTA
195 AACAATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA-CTA
* * * * * * *
2782 TTTAGAAC-AAGTGATGCGATTTCCCGAGCATGAAAAGTTCAAAAAATTGCTCGAAGGAATGGAT
259 TTTAGACCTAA-TGATGTGATTTTCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGAT
* * * * * *
2846 CGTCCTGAATTCTTTAAGGAACAGAAGTTAAAAAAGAACTCGCAAAAGTTTGTCAAGTTCGGAAG
323 CGTCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTC-AAAG
* * * *
2911 TTTGGCTGAGAACCAATAGAGAAACAATTCTCACCTAAATAAG
387 TTCGGCCGAGAACCAAGAAAGAAACAATTCTCACCTAAATAAG
* * * * * *
2954 TTTTTAATTGAAAAACCAAAAGTAGTTTACAGAAA-GACAAACAATTTAGACCTAATAATGTGAT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACA-AAATGAC-AACTATTTAGACCAAATGATGTGAT
* * * * *
3018 TTCCCAAGCATGGACTGTACA-ATAAATTGCT-GAAGGAATGGATCATCTTGAACACTTTAATGA
64 TTCCCAAGCATGGAATGTTCAGA-AAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGA
* * * ** * **
3081 ACAAAATTTATAAAAGAACTTG-AAAATTTTGTCAAGTT-TAAAGTTTGGTAGAGAACCAAGAAA
128 ACAAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAGAAA
* * *
3144 GAAACAATTCTCACATAAAGAA-TTTTTAAATTCAAAGACCAAAAGTTGTTTACAAAAAGACAAC
193 GAAACAATTCTCACCTAAATAAGTTTTT-AATTCAAAGACCAAAAGTTGTTTACAAAATGACAAC
* * *
3208 TATTTAGACCAAATGATGCGA-TTTCCAAGCATGAAATGTTCAGAAAATTGCTCGAAGGAATGGA
257 TATTTAGACCTAATGATGTGATTTTCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGA
* * * *
3272 TAC-TCTTAAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTGGTCAACTTCGAA
322 T-CGTCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTC-AA
* * * ** * *
3336 AGTTTGGCCCAGAACCAAGAGAGAAATTATTGTCACCTAAATTAG
385 AGTTCGGCCGAGAACCAAGAAAGAAACAATTCTCACCTAAATAAG
* * * *
3381 TTTTTAATTCAAGGACCAAAAGTTGTTTACAAAATAAAAACTATTTAGACCAAATGATGCGATTT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGTGATTT
* * * *
3446 CTCGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGATTACTTTAAGGAACC
66 CCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACA
* * * * *
3511 GAAGTTATAAAAGAACTCTTAAAAGTTAGTCAAGTTCGGAAGTTCGGTCGAGAACCAAGAGAGAA
131 AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAGAAAGAA
* * *
3576 ATAATTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTACAATATGACAACTATT
196 ACAATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATT
* * * * *
3641 TAGACCTAATGATATGATTTTCCAAGCATGGACTGTACAGAAAATTACTTGAAGGAATGGATCGT
261 TAGACCTAATGATGTGATTTTCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGT
* * * * *
3706 CTTGAATACTATAATGAACAAAAGTTATAAAAGAAGTTGTAAAAGTTTGTCAAGTTTAAAGTTCG
326 CTTGAATACTTTAAGGAACAAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCAAAGTTCG
* * * * *
3771 GCCAAAAACCAAGAAAGAAACAATTCTCACATAAAGAAT
391 GCCGAGAACCAAGAAAGAAACAATTCTCACCTAAATAAG
* *
3810 TTTTTCATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGAGA-TT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGTGATTT
* * * * *
3874 CCCTGAGCTTGGAATGTTCAGAAAATTGCTCGAAGTAATGGTTTGTCTTGAATACTTTAAGGAAC
66 CCC-AAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAC
* * * * * *
3939 CAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAACTTCGAAAGTTCGGCCTAGAAACAAGACAGA
130 AAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAGAAAGA
* * * * * *
4004 AACTATTATCACCTAAAAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACATAATGGCAATTAT
195 AACAATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTAT
* * ** * ** * * *
4069 TTAGA-CTAAATGATGCGA-TTTCTAAAGCATTCAATTTTCTTAAATTTACTTGAAGGAATGGAT
260 TTAGACCT-AATGATGTGATTTTC-CAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGAT
* * * *
4132 CGTCTTAAATAGTTTAAGGAATC-AAAGTTAT-AAAGTAACTCATAAAAGTTTTTCAAGTTCAGA
323 CGTCTTGAATACTTTAAGGAA-CAAAAGTTATAAAAG-AACTCGTAAAAGTTTGTCAAGTTCA-A
*
4195 AGTTCGACCGAGAACCAA-AAGAGAAACAATTCTCACCTAAATAAG
385 AGTTCGGCCGAGAACCAAGAA-AGAAACAATTCTCACCTAAATAAG
* * * *
4240 TTTTTAATTTGAAA-ACCAAAAGTAGTTTAAAAAATGACAACTATTTAGACCTAATGATGTGATT
1 TTTTTAA-TTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGTGATT
* * * *
4304 TCCCAAGCATGGACTGTACAGAAAATTACTCGAAGGAATGGATCGTCTTG-A-ACTTTAATGAAC
65 TCCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAC
* * * * *
4367 AAAAGTTATAAAAGTACTCGTAAAA-CTT-T---G-TC--AAGTTCGGCTGAGAACGAATAAAGA
130 AAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAGAAAGA
* * * *
4424 AACAATTCTCACCTAAATAAGTTTTTAATTGAAAAACCAAAAGTAGTTTACAAAATAACAACTAT
195 AACAATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTAT
* * * * * * *
4489 TTAGACCTAATGATGTGATTTCCCAAGCATGGACTGTACAAAAAATTACTCAAAGGAATGAATCG
260 TTAGACCTAATGATGTGATTTTCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCG
** * ** *
4554 TCTTGAATACTTTATTGAACAAAAGTTATAAAAGAAGTTATAAAAGTTTGTCAGGTTCAAAGTTC
325 TCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCAAAGTTC
* * * *
4619 GACCGAGAACCAAGAAAGAAACAATTCTCACATAAAGAAT
390 GGCCGAGAACCAAGAAAGAAACAATTCTCACCTAAATAAG
* * * *
4659 TTTTTAATTCAAAGACCAAAAGCTGTTT-CGAAATGACAACTATTTAGACCAAAAGATGAGATTT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGTGATTT
* * * * * *
4723 CCTAAGCTTGGAATGTTCAGAAAATTGCTCGAAGGAATGGTTCATCTTGAATACTTTAATGAACC
66 CCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACA
*
4788 GAAGTTATAAAAGAACT
131 AAAGTTATAAAAGAACT
4805 TGTATTTAGA
Statistics
Matches: 2919, Mismatches: 522, Indels: 206
0.80 0.14 0.06
Matches are distributed among these distances:
410 37 0.01
411 30 0.01
412 213 0.07
413 55 0.02
415 2 0.00
416 15 0.01
417 244 0.08
418 160 0.05
419 62 0.02
420 191 0.07
421 9 0.00
422 2 0.00
425 2 0.00
426 50 0.02
427 216 0.07
428 295 0.10
429 705 0.24
430 318 0.11
431 12 0.00
432 193 0.07
433 104 0.04
434 4 0.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (429 bp):
TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGTGATTT
CCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACA
AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAACCAAGAAAGAA
ACAATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATT
TAGACCTAATGATGTGATTTTCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGT
CTTGAATACTTTAAGGAACAAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCAAAGTTCG
GCCGAGAACCAAGAAAGAAACAATTCTCACCTAAATAAG
Found at i:4133 original size:644 final size:638
Alignment explanation
Indices: 835--4804 Score: 3679
Period size: 644 Copynumber: 6.2 Consensus size: 638
825 GATTGTATTA
* * * *
835 TTTTTAATTCAAAAACCAAAAGTTGTTTACAAAATGAAAACTATTTAGACCTAATGATGTGATTT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTAC-AAATGACAACTATTTAGACCAAATGATGCGA-TT
* * * * * * *
900 TCCAAGCATGGACTGTACAGAAAATTGCTCGAAGGAATGGATCGTCTAGAATACTTTAATGAACA
64 TCTAAGCATTGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACC
* ** * **
965 AAAGTTATAAAAGAACTTGTAAAAGTCTGTCAAGTT-TAAAGTTCGGCCGAGAACCAAGAA-AGA
129 GAAGTTATAAAAGAACTCATAAAAGTTTGTCAAGTTCGGAAGTTCGG-CGAGAACCAA-AAGAGA
* * * * * *
1028 AACAATTCTCACATAAAGAATTTTTTCATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTAT
192 AACAATTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAAGTAGTTTAC-AAATGACAACTAT
* * * * * * * * * **
1093 TTAGACCAAATGATGAGATTTCCTAAGCTTGGAATGTTCAGAAAATTGCTCGAAGGAATGGTTTA
256 TTAGACCTAATGATGTGATTTCCCAAGCATGGACTGTACAGAAAATTACTTGAAGGAATGGATCG
* ** * * * **
1158 TCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATAATAAAAGTTTGTCAACTTCGGAA
321 TCTTGAA-ACTTTAATGAACAAAAGTTATAAAAGAACT--T-GTAAAACTTTGTCAAGTT-TAAA
* * * * * *
1223 GTTCGGCCT-AGAACCAACAGAGAAACTATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAA
381 GTTCGG-CTAAGAACCAAGAAAGAAACAATTCTCACATAAAGAATTTTTTAATTCAAAGACCAAA
* * * * * * * * * * **
1287 AGCTGTTTACATAATGGCAACTATTTAGACTAAATGATGCGATTTCTAGAGTATGAAATTTTCTT
445 AGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGAGATTCCCA-AGCATGGAATGTTCAG
* * * * * *
1352 AAAATTGCTCGAAGGAATGTATCGTCTTGAATAGTTTACGGAATCAAAGTTATAAAAGAATTCGT
509 AAAATTGCTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGT
* * * * * * * * * * *
1417 AAAAGTTTTTAAAGTTCGGAAGTTCGACCGAGAACCAA-AAGAGAAACAATTCTCACTTAAATAC
574 AAAAGTTTGTCAACTTCGAAAGTTCGGCCCAGAACCAAGAA-AGAAACTATTATCACCTAAAAAA
*
1481 C
638 G
* * *
1482 TTTTTAATTCAAAGACCAAAAGTAGTTTAAAAAATGACAACTATTTAGACCTAAA-GATGTGATT
1 TTTTTAATTCAAAGACCAAAAGTTGTTT-ACAAATGACAACTATTTAGACC-AAATGATGCGATT
* * * ** * * *
1546 TCCCAAGCATAGACTAAT-GGAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAATG-AC
64 T-CTAAGCATTGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAC
* * * * * * ** *
1609 CAAAAGTTATAAAAGAACTCGTTAAATTTTGTCAAGTTCAGAAATTCAACAGAGTA-CAAGGAA-
128 C-GAAGTTATAAAAGAACTCATAAAAGTTTGTCAAGTTCGGAAGTTCGGC-GAGAACCAA--AAG
* * * * ** **
1672 AGAAACAATTCTAACATAAATCACTTTTT--TT-----------TTTTTTTTACAAAATGACAAT
189 AGAAACAATTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAAGTAGTTTAC-AAATGACAA-
* ** * ** * * * *
1724 CTATTTAGAAC-AATTGATACGATTTTCTGAGTATGGAATGTTC-GAAAAATTACTGGAAGGAAT
252 CTATTTAGACCTAA-TGATGTGATTTCCCAAGCATGGACTGTACAG-AAAATTACTTGAAGGAAT
* * * * *
1787 GGATCGTCTTGAATTCTTTAAGGAA-AAGAAGTTAAAAAAGAACTCGTAAAAGTTTGTCAAGTTT
315 GGATCGTCTTGAA-ACTTTAATGAACAA-AAGTTATAAAAGAACTTGTAAAACTTTGTCAAGTTT
* * * * * ** * * * * *
1851 GGAAGTTCAGCTGAGAACGAATAGGGAAACAATTCTCACCTAAATAAGTTTTTAATTGAAAAACC
378 -AAAGTTCGGCTAAGAACCAAGAAAGAAACAATTCTCACATAAAGAATTTTTTAATTCAAAGACC
* * * * * * * * * * *
1916 AAAGGTAGTTTACAGAATGACAACAAATTAGACCTAATAATGTGATTTCCCAACCATGGACTGTA
442 AAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGAGA-TTCCCAAGCATGGAATGTT
* * * *
1981 CAGAAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAATGAACAAAAGTTATAAAAGAACT
506 CAGAAAATTGCTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACT
** * * * * * * *
2046 TATAAAAGTTTGTCAAGTT-TAAAGTTCGGCCGAGAACCAAGAAAGAAACAATTCTCACATAAAG
571 CGTAAAAGTTTGTCAACTTCGAAAGTTCGGCCCAGAACCAAGAAAGAAACTATTATCACCTAAAA
*
2110 AAT
636 AAG
* * *
2113 TTTTTAATGCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAAAGATGAGATTT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTAC-AAATGACAACTATTTAGACCAAATGATGCGATTT
* *
2178 CCTAAGC-TTGGAATGTTCAGAAAATTGCTCGAAGGAAT-GATTCATCTTGAATA-TTTCAGGAA
65 -CTAAGCATT-GAATGTTCAGAAAATTGCTCGAAGGAATGGA-TCGTCTTGAATACTTTAAGGAA
* * * * * * *
2240 CCGAAGTTATGAAAGAACTCGTAAAAGTTTGTCAAATTCGGATGTTCGGCCTAGAACCAAGAGAA
127 CCGAAGTTATAAAAGAACTCATAAAAGTTTGTCAAGTTCGGAAGTTCGG-CGAGAACCAAAAGAG
* * * * *
2305 AAACTATTCTCACCTAAATAAGTTTTTAATTTAAAGACCAAAAGTTGTTTACATAATGGCAACTA
191 AAACAATTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAAGTAGTTTACA-AATGACAACTA
* * * * * * ** * *
2370 TTAAGA-CTAAATTATGTAATTT-CTAGAGCATGGAATGTTCTTAAAATTGCTTGAAGGAATGAA
255 TTTAGACCT-AATGATGTGATTTCCCA-AGCATGGACTGTACAGAAAATTACTTGAAGGAATGGA
* * * * * * *
2433 TCATCTTGAATAGTTTAAAGAATC-AAAGTTATAAAATAACTCGTAAAAGTTTTTCAAGTTCGT-
318 TCGTCTTGAA-ACTTTAATGAA-CAAAAGTTATAAAAGAACTTGTAAAACTTTGTCAAGTT--TA
* * * * *
2496 AAGTTC-GATCGAGAACCAA-AAGAGAAACAATTCTCACCTAAATAAGTTTTTAATTCAAAGACC
379 AAGTTCGGCT-AAGAACCAAGAA-AGAAACAATTCTCACATAAAGAATTTTTTAATTCAAAGACC
* * * * * *
2559 AAAAGTAGTTTAAAAAATGACAACTATTTAGACCTAATGATGTGATCTCCCAAACATGGACTGTA
442 AAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGAGAT-TCCCAAGCATGGAATGT-
* * * * * * *
2624 T-GGGAAATAGCTCGAAAGAATGGATTGTCCTGAATACTTTAAGGAACAAAAGTTATAAAAGAAC
505 TCAGAAAATTGCTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAAC
* * * ** * * * * * *
2688 TCGTTAAAGTTTGTCAAGTTCGGAAGTTCAACCGAGAACAAAGAAAGAAACAATTCTAACATAAA
570 TCGTAAAAGTTTGTCAACTTCGAAAGTTCGGCCCAGAACCAAGAAAGAAACTATTATCACCTAAA
* *
2753 TAAC
635 AAAG
** * *
2757 TTTTT--TT---TTA-CAAAA--TG---AC-AAT-----CTATTTAGAACAAGTGATGCGATTTC
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAATGACAACTATTTAGACCAAATGATGCGATTT-
** * * * * *
2805 CCGAGCA-TGAAAAGTTCAAAAAATTGCTCGAAGGAATGGATCGTCCTGAATTCTTTAAGGAACA
65 CTAAGCATTG-AATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACC
* ** * *
2869 GAAGTTAAAAAAGAACTCGCAAAAGTTTGTCAAGTTCGGAAGTTTGGCTGAGAACCAATAGAGAA
129 GAAGTTATAAAAGAACTCATAAAAGTTTGTCAAGTTCGGAAGTTCGGC-GAGAACCAAAAGAGAA
* * *
2934 ACAATTCTCACCTAAATAAGTTTTTAATTGAAAAACCAAAAGTAGTTTACAGAAAGACAAACAAT
193 ACAATTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAAGTAGTTTACA-AATGAC-AACTAT
* *
2999 TTAGACCTAATAATGTGATTTCCCAAGCATGGACTGTACA-ATAAATTGC-TGAAGGAATGGATC
256 TTAGACCTAATGATGTGATTTCCCAAGCATGGACTGTACAGA-AAATTACTTGAAGGAATGGATC
* * *
3062 ATCTTGAACACTTTAATGAACAAAATTTATAAAAGAACTTG-AAAATTTTGTCAAGTTTAAAGTT
320 GTCTTGAA-ACTTTAATGAACAAAAGTTATAAAAGAACTTGTAAAACTTTGTCAAGTTTAAAGTT
* *
3126 TGG-TAGAGAACCAAGAAAGAAACAATTCTCACATAAAGAATTTTTAAATTCAAAGACCAAAAGT
384 CGGCTA-AGAACCAAGAAAGAAACAATTCTCACATAAAGAATTTTTTAATTCAAAGACCAAAAGT
* * * *
3190 TGTTTACAAAAAGACAACTATTTAGACCAAATGATGCGATTTCCAAGCATGAAATGTTCAGAAAA
448 TGTTTACAAAATGACAACTATTTAGACCAAATGATGAGATTCCCAAGCATGGAATGTTCAGAAAA
* *
3255 TTGCTCGAAGGAATGGATACTCTTAAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAA
513 TTGCTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAA
* * * * * **
3320 GTTGGTCAACTTCGAAAGTTTGGCCCAGAACCAAGAGAGAAATTATTGTCACCTAAATTAG
578 GTTTGTCAACTTCGAAAGTTCGGCCCAGAACCAAGAAAGAAACTATTATCACCTAAAAAAG
* * *
3381 TTTTTAATTCAAGGACCAAAAGTTGTTTACAAAATAAAAACTATTTAGACCAAATGATGCGATTT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTAC-AAATGACAACTATTTAGACCAAATGATGCGATTT
* * *
3446 CTCGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGATTACTTTAAGGAACC
65 CT-AAGCATTGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACC
* * *
3511 GAAGTTATAAAAGAACTCTTAAAAGTTAGTCAAGTTCGGAAGTTCGGTCGAGAACCAAGAGAGAA
129 GAAGTTATAAAAGAACTCATAAAAGTTTGTCAAGTTCGGAAGTTCGG-CGAGAACCAAAAGAGAA
* *
3576 ATAATTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTACAATATGACAACTATT
193 ACAATTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAAGTAGTTTACAA-ATGACAACTATT
* *
3641 TAGACCTAATGATATGATTTTCCAAGCATGGACTGTACAGAAAATTACTTGAAGGAATGGATCGT
257 TAGACCTAATGATGTGATTTCCCAAGCATGGACTGTACAGAAAATTACTTGAAGGAATGGATCGT
* * *
3706 CTTGAATACTATAATGAACAAAAGTTATAAAAGAAGTTGTAAAAGTTTGTCAAGTTTAAAGTTCG
322 CTTGAA-ACTTTAATGAACAAAAGTTATAAAAGAACTTGTAAAACTTTGTCAAGTTTAAAGTTCG
* * *
3771 GCCAAAAACCAAGAAAGAAACAATTCTCACATAAAGAATTTTTTCATTCAAAGACCAAAAGTTGT
386 GCTAAGAACCAAGAAAGAAACAATTCTCACATAAAGAATTTTTTAATTCAAAGACCAAAAGTTGT
* *
3836 TTACAAAATGACAACTATTTAGACCAAATGATGAGATTCCCTGAGCTTGGAATGTTCAGAAAATT
451 TTACAAAATGACAACTATTTAGACCAAATGATGAGATTCCC-AAGCATGGAATGTTCAGAAAATT
* * *
3901 GCTCGAAGTAATGGTTTGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGT
515 GCTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGT
* * *
3966 TTGTCAACTTCGAAAGTTCGGCCTAGAAACAAGACAGAAACTATTATCACCTAAAAAAG
580 TTGTCAACTTCGAAAGTTCGGCCCAGAACCAAGAAAGAAACTATTATCACCTAAAAAAG
* * *
4025 TTTTTAATTCAAAGACCAAAAGTTGTTTACATAATGGCAATTATTTAGACTAAATGATGCGATTT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTACA-AATGACAACTATTTAGACCAAATGATGCGATTT
* * ** * * * * * *
4090 CTAAAGCATTCAATTTTCTTAAATTTACTTGAAGGAATGGATCGTCTTAAATAGTTTAAGGAATC
65 CT-AAGCATTGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACC
* * * *
4155 AAAGTTAT-AAAGTAACTCATAAAAGTTTTTCAAGTTCAGAAGTTCGACCGAGAACCAAAAGAGA
129 GAAGTTATAAAAG-AACTCATAAAAGTTTGTCAAGTTCGGAAGTTCG-GCGAGAACCAAAAGAGA
** *
4219 AACAATTCTCACCTAAATAAGTTTTTAATTTGAAAACCAAAAGTAGTTTAAAAAATGACAACTAT
192 AACAATTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAAGTAGTTT-ACAAATGACAACTAT
*
4284 TTAGACCTAATGATGTGATTTCCCAAGCATGGACTGTACAGAAAATTACTCGAAGGAATGGATCG
256 TTAGACCTAATGATGTGATTTCCCAAGCATGGACTGTACAGAAAATTACTTGAAGGAATGGATCG
* *
4349 TCTTG-AACTTTAATGAACAAAAGTTATAAAAGTACTCGTAAAACTTTGTC-------AAGTTCG
321 TCTTGAAACTTTAATGAACAAAAGTTATAAAAGAACTTGTAAAACTTTGTCAAGTTTAAAGTTCG
* * * * * * * * *
4406 GCTGAGAACGAATAAAGAAACAATTCTCACCTAAATAAGTTTTTAATTGAAAAACCAAAAGTAGT
386 GCTAAGAACCAAGAAAGAAACAATTCTCACATAAAGAATTTTTTAATTCAAAGACCAAAAGTTGT
* * * * * *
4471 TTACAAAATAACAACTATTTAGACCTAATGATGTGATTTCCCAAGCATGGACTGTACAAAAAATT
451 TTACAAAATGACAACTATTTAGACCAAATGATGAGA-TTCCCAAGCATGGAATGTTCAGAAAATT
* * * * ** * * **
4536 ACTCAAAGGAATGAATCGTCTTGAATACTTTATTGAACAAAAGTTATAAAAGAAGTTATAAAAGT
515 GCTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGT
** * * * * * * *
4601 TTGTCAGGTTC-AAAGTTCGACCGAGAACCAAGAAAGAAACAATTCTCACATAAAGAAT
580 TTGTCAACTTCGAAAGTTCGGCCCAGAACCAAGAAAGAAACTATTATCACCTAAAAAAG
* * *
4659 TTTTTAATTCAAAGACCAAAAGCTGTTT-CGAAATGACAACTATTTAGACCAAAAGATGAGATTT
1 TTTTTAATTCAAAGACCAAAAGTTGTTTAC-AAATGACAACTATTTAGACCAAATGATGCGATTT
* * *
4723 CCTAAGC-TTGGAATGTTCAGAAAATTGCTCGAAGGAATGGTTCATCTTGAATACTTTAATGAAC
65 -CTAAGCATT-GAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAC
4787 CGAAGTTATAAAAGAACT
128 CGAAGTTATAAAAGAACT
4805 TGTATTTAGA
Statistics
Matches: 2785, Mismatches: 436, Indels: 218
0.81 0.13 0.06
Matches are distributed among these distances:
623 1 0.00
624 125 0.04
625 93 0.03
626 82 0.03
627 163 0.06
628 39 0.01
629 5 0.00
630 11 0.00
631 178 0.06
632 223 0.08
633 94 0.03
634 92 0.03
635 260 0.09
636 7 0.00
637 3 0.00
638 5 0.00
639 1 0.00
641 50 0.02
642 283 0.10
643 404 0.15
644 475 0.17
645 8 0.00
646 79 0.03
647 101 0.04
648 3 0.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (638 bp):
TTTTTAATTCAAAGACCAAAAGTTGTTTACAAATGACAACTATTTAGACCAAATGATGCGATTTC
TAAGCATTGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGA
AGTTATAAAAGAACTCATAAAAGTTTGTCAAGTTCGGAAGTTCGGCGAGAACCAAAAGAGAAACA
ATTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAAGTAGTTTACAAATGACAACTATTTAGA
CCTAATGATGTGATTTCCCAAGCATGGACTGTACAGAAAATTACTTGAAGGAATGGATCGTCTTG
AAACTTTAATGAACAAAAGTTATAAAAGAACTTGTAAAACTTTGTCAAGTTTAAAGTTCGGCTAA
GAACCAAGAAAGAAACAATTCTCACATAAAGAATTTTTTAATTCAAAGACCAAAAGTTGTTTACA
AAATGACAACTATTTAGACCAAATGATGAGATTCCCAAGCATGGAATGTTCAGAAAATTGCTCGA
AGGAATGGATAGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGTCA
ACTTCGAAAGTTCGGCCCAGAACCAAGAAAGAAACTATTATCACCTAAAAAAG
Found at i:6422 original size:215 final size:213
Alignment explanation
Indices: 5604--6425 Score: 820
Period size: 215 Copynumber: 3.8 Consensus size: 213
5594 ATAACTTTTT
* * * * * *
5604 TTTACAAAATGACAATGTATTTAGAAC-AAGTGATGCGATTTCCCGAGCATGGAATGTTCAAAAA
1 TTTACAAAATGACAA-CTATTTAGACCTAA-TGATGAGA-TTCCCAAACATGGAATGTT-AGAAA
* * * *
5668 ATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAATGAACAAAAGTTATAAAAGAACTTATAAA
62 ATAGCTCGAAAGAATGGATCGTCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAACTCATAAA
* * * * * * *
5733 AGTTTGTCAAGTT-TAAAGTTCGGCCGAGAACCAAGAAAGAAACAGTTCTCACATAAAGAATTTT
127 AGTTTGTCAAGTTCGAAAGTTCGACCGAGAACAAAGAAAGAAACAATTCTCACCTAAAAAAGTTT
5797 TTAATTCAAAGACCAAAAGTTG
192 TTAATTCAAAGACCAAAAGTTG
* * * *
5819 TTTACAAAATGACAACTATTTAGACCAAATGATGAGATTCCCTGAGCTTGGAATGTTCAGAAAAT
1 TTTACAAAATGACAACTATTTAGACCTAATGATGAGATTCCC-AAACATGGAATGTT-AGAAAAT
* * * * *
5884 TGCTCG-AAGTAATGGTTTGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAA
64 AGCTCGAAAG-AATGGATCGTCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAACTCATAAAA
* * * * * *
5948 GTTTGTCAACTTCGAAAGTTCGGCCTAGAA-ACAAGACAGAAACTATTATCACCTAAAAAAGTTT
128 GTTTGTCAAGTTCGAAAGTTCGACCGAGAACA-AAGAAAGAAACAATTCTCACCTAAAAAAGTTT
6012 TTAATTCAAAGACCAAAAGTTG
192 TTAATTCAAAGACCAAAAGTTG
* * * * * * ** * **
6034 TTTACATAATGGCAATTATTTAGA-CTAAATGATGCGATTTCTAAAGCATTCAATTTTCTTAAAT
1 TTTACAAAATGACAACTATTTAGACCT-AATGATGAGATTCCCAAA-CATGGAATGTT-AGAAA-
* * * * *
6098 TTA-CTTGAAGGAATGGATCGTCTTAAATAGTTTAAGGAATC-AAAGTTAT-AAAGTAACTCATA
62 ATAGCTCGAAAGAATGGATCGTCTTGAATACTTTAAGGAA-CAAAAGTTATAAAAG-AACTCATA
* * *
6160 AAAGTTTTTCAAGTTC-AGAAGTTCGACCGAGAACCAAA-AGAGAAACAATTCTCACCTAAATAA
125 AAAGTTTGTCAAGTTCGA-AAGTTCGACCGAGAA-CAAAGAAAGAAACAATTCTCACCTAAAAAA
* *
6223 GTTTTTAATTTGAAA-ACCAAAAGTAG
188 GTTTTTAA-TTCAAAGACCAAAAGTTG
* * * * *
6249 TTTAAAAAATGACAACTATTTAGACCTAATGATGTGATCTCCCAAACATGGACTGTATGGGAAAT
1 TTTACAAAATGACAACTATTTAGACCTAATGATGAGAT-TCCCAAACATGGAATGT-TAGAAAAT
* * * *
6314 AGCTCGAAAGAATGGATTGTCCTGAATACTTTAAGGAACAAAAGTTATAAAAGAACTCGTTAAAG
64 AGCTCGAAAGAATGGATCGTCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAACTCATAAAAG
* *
6379 TTTGTCAAGTTCGGAAGTTCAACCGAGAACAAAGAAAGAAACAATTC
129 TTTGTCAAGTTCGAAAGTTCGACCGAGAACAAAGAAAGAAACAATTC
Statistics
Matches: 500, Mismatches: 84, Indels: 46
0.79 0.13 0.07
Matches are distributed among these distances:
213 7 0.01
214 115 0.23
215 354 0.71
216 23 0.05
217 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (213 bp):
TTTACAAAATGACAACTATTTAGACCTAATGATGAGATTCCCAAACATGGAATGTTAGAAAATAG
CTCGAAAGAATGGATCGTCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAACTCATAAAAGTT
TGTCAAGTTCGAAAGTTCGACCGAGAACAAAGAAAGAAACAATTCTCACCTAAAAAAGTTTTTAA
TTCAAAGACCAAAAGTTG
Done.