Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011783.1 Corchorus olitorius cultivar O-4 contig11816, 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: 3384
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Found at i:390 original size:154 final size:154
Alignment explanation
Indices: 1--969 Score: 1510
Period size: 154 Copynumber: 6.3 Consensus size: 154
* *
1 CCAAATGAGCTAAAAAACTTTACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAA
1 CCAAATGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* *
66 CAATGGAAAGAAACGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACAAATGGGCCC
65 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC
* ** *
131 TGATAGGGCCCAAAATATTAGGTGTT
130 CGATA-GGCCCAAAATAACAAGTGTT
* * * *
157 CCAAATGAGCTAAAAACTTTCACAATGGACTGATCTCACTAAAATGATTATACTTAGGCCATAAA
1 CCAAATGAGCTAAAAAC-TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
*
222 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCATTAATGGGCCC
65 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC
* * *
287 TGGTAGGCCCAAAATAACAGGTGTT
130 CGATAGGCCCAAAATAACAAGTGTT
* * *
312 CCAAATGAGCTAAAAACTTCACAGTGGACTGATCTCACTAAAATGATTATACTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
377 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCC
66 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCC
* *
442 AATAGGCCCAACATAACAAGTGTT
131 GATAGGCCCAAAATAACAAGTGTT
* *
466 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGGTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* * * *
531 AATGGAAACAAAAGCATTGAGGCTTGCCAAATCGAAGAAGATTCAAAACGTCACTGATGGGCCCC
66 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCC
596 GATAGGCCCAAAATAACAAGTGTT
131 GATAGGCCCAAAATAACAAGTGTT
*
620 CCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* * * * *
685 AATGGAAACAAAAGCATTGAGGCTTGCCAATTC-ATAGAAGATTCAATACGTCACTAATGGGCCC
66 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA-AGACGATTCAAAACGTCACTAATGGGCCC
**
749 CGATAGGCCCAAAATAACAAGTAAT
130 CGATAGGCCCAAAATAACAAGTGTT
* * *
774 CCAAATTAGCT-AAAAGTTCACAGTGGACTAATCTCACCAAAATCATTATAGTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* *
838 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCTC
66 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCC
*
903 GATAGGCCCAAAATAACAAGTATT
131 GATAGGCCCAAAATAACAAGTGTT
*
927 CCAAATGAGCTAAAAACTTCACAGTCGACTAATCTCACCAAAA
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
970 ACAATGGAAA
Statistics
Matches: 760, Mismatches: 49, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
153 144 0.19
154 457 0.60
155 41 0.05
156 118 0.16
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (154 bp):
CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCC
GATAGGCCCAAAATAACAAGTGTT
Found at i:621 original size:308 final size:308
Alignment explanation
Indices: 1--3384 Score: 4990
Period size: 308 Copynumber: 11.0 Consensus size: 308
* *
1 CCAAATGAGCTAAAAAACTTTACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAA
1 CCAAATGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * *
66 CAATGGAAAGAAACGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACAAATGGGCCC
65 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCC
* ** * * *
131 TGATAGGGCCCAAAATATTAGGTGTTCCAAATGAGCTAAAAACTTTCACAATGGACTGATCTCAC
130 CGATA-GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAC-TTCACAGTGGACTAATCTCAC
* *
196 TAAAATGATTATACTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGA
193 CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGA
* * * *
261 CGATTCAAAACGTCATTAATGGGCCCTGGTAGGCCCAAAATAACAGGTGTT
258 CGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
* * *
312 CCAAATGAGCTAAAAACTTCACAGTGGACTGATCTCACTAAAATGATTATACTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
*
377 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCC
66 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCC
* * *
442 AATAGGCCCAACATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAA
131 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
* * * *
507 AATGATTATAGGTAGGCCATAAACAATGGAAACAAAAGCATTGAGGCTTGCCAAATCGAAGAAGA
196 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
*
572 TTCAAAACGTCACTGATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
261 TTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
*
620 CCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* * * *
685 AATGGAAACAAAAGCATTGAGGCTTGCCAATTC-ATAGAAGATTCAATACGTCACTAATGGGCCC
66 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA-AGACGATTCAATACGTCACTAATGGGCCC
** * *
749 CGATAGGCCCAAAATAACAAGTAATCCAAATTAGCT-AAAAGTTCACAGTGGACTAATCTCACCA
130 CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
*
813 AAATCATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG
195 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG
* * *
878 ATTCAATACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTATT
260 ATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
*
927 CCAAATGAGCTAAAAACTTCACAGTCGACTAATCTCACC---------------A----A-AAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* * **
972 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGGTTCAAAACGGAACTAATGGGCCCC
66 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCC
* * * *
1037 GATAGGCCCAAAATAACAAGTGTTCCAACTGAGCTATAAAGTTCACAGTGTACTAATCTCACCAA
131 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
*
1102 AATGATTATAGTTAGGCCTTAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
196 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
** * *
1167 TTCAAAACGGAACTAATGAGCCCCGATAGGCCAAAAATAACAAGTGTT
261 TTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
* * * * *
1215 CAAAATGAGCTAAAAACTTCAAAGTGGACTAATCTAAACAAAATGATTATAGGTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* * * ** *
1280 AATGGAAACAAAAGCATTGAGGCTTGCCAATTCGAAGAAAATTCAATACGTCACTAATGGGCCAC
66 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCC
*
1345 GATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
131 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
1410 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
196 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
* **
1475 TTCAAAACAG-AACTAATGGGCGTCGATAGGCCCAAAATAACAAGTGTT
261 TTCAAAAC-GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
1523 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* * * ** * *
1588 AATGGAATGAAAATCATTGAGGTCTGATAAATCGAATACGATTCAATACGTCACTAATGGACCCC
66 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCC
* * *
1653 AATAAGCCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
131 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
* * ** *
1718 AATGATTATAGTTAGGCCATAAACAATGGAATGAAAAGCATTGAGGTCTGATAAATCGAATACGA
196 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
* * * * *
1783 TTCAATACGTCACTAATGGACCCCAATAAGCCCAAAATAAGAAGTGTT
261 TTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
*
1831 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGACCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
** * * * *
1896 AAT-GAAATGAAAAGCATTGAGGTTTGATAAATCGAATACGATTCAATACGTCCCTAATGGACGC
66 AATGGAAA-GAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCC
* * *
1960 CAATAAGCCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
130 CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
* * *
2025 AAATTATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATGGAGATTTGCCAAATCGAAGACG
195 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG
*
2090 ATTCAAAACAG-AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
260 ATTCAAAAC-GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
*
2139 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATAATTATAGTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
*
2204 AATGGAAAGAAAAGCATTGAGGTTTGCCAGATCGAAGACGATTCAATACGTCACTAATGGGCCCC
66 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCC
* * * * *
2269 GATAGGCCCAAAATAACAAGTGTTCGAAATGAGATAAAAACTTCAAAGTGGACTAATCTAAACAA
131 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
* * * * * *
2334 AATGATTATAGGTAGGCCATAAACAATGGAAACAAAAACATTGAGGCTTGCCAATTCGAAGAAGA
196 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
*
2399 TTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
261 TTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
*
2447 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* * * *
2512 AATGGAAAGAAAACCATTAAGGTTTGCCAAATCGAAGACGATTTAAAACGTCACTAATGGG-CCC
66 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCC
* * * * *
2576 GACAGGCCCAAAATAACAAGTGTTCGAAATGAGCTAAAAACTTCAAAGTGGACTAATCTAAACAA
131 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
* * * * * *
2641 AATGATTATAGGTAGGCCATAAACAATGGAAA-AAAAACATTAAGGCTTGCCAATTCGAAGAAGA
196 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
*
2705 TTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
261 TTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
* *
2753 CCAAATTAAGCTAAAAAGTTCACAGTGGACTAATACTCACCAAAATGATTATAGTTAGGCCATAA
1 CCAAA-TGAGCTAAAAACTTCACAGTGGACTAAT-CTCACCAAAATGATTATAGTTAGGCCATAA
* * *
2818 ACAATGGAAAGAAAAGCATTAGAGGTTTTGCCTAATCGAAGACGATTCAATACGTTAGTAATGGG
64 ACAATGGAAAGAAAAGCATT-GAGG-TTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGG
* *
2883 CCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCA
127 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
** * *
2948 CCAAAATGATTATAAATAGGCCATAAAGAATGGAAAGAAAAGCATTGAGGTTTGCCATATCGAAG
192 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
* * *
3013 ACGATTCAATACGTCACTAATGGGCCCCAATAGGCCCAAAATAAGAAGTGTT
257 ACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
*
3065 CCGAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* *
3130 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGTCTCC
66 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCC
* * *
3195 GATAGGCCCAAAATAACAAGTGTTCCATATGAGCCAAAAACTTCACAGTGGACAAATCTCACCAA
131 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
* * * *
3260 AATGATTATAGTTAGGCAAT-AACAATGGAAAGAAAAGCATTGAGGTTCGCCAAACCGAAGACAA
196 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
* * *
3324 TTCAAAA-GTGAACTAATGGGCCTCGATAGGCACAAAATAACAAGTGTT
261 TTCAAAACGT-CACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
3372 CCAAATGAGCTAA
1 CCAAATGAGCTAA
Statistics
Matches: 2786, Mismatches: 251, Indels: 76
0.89 0.08 0.02
Matches are distributed among these distances:
287 90 0.03
288 167 0.06
292 1 0.00
303 1 0.00
306 86 0.03
307 389 0.14
308 1605 0.58
309 46 0.02
310 198 0.07
311 127 0.05
312 76 0.03
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (308 bp):
CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCC
GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
TTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
Found at i:1082 original size:134 final size:134
Alignment explanation
Indices: 834--1103 Score: 443
Period size: 134 Copynumber: 2.0 Consensus size: 134
824 GTTAGGCCAT
* **
834 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGG
1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGG
*
899 CCTCGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTCG-ACTAATCTC
66 CCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGT-GTACTAATCTC
963 ACCAA
130 ACCAA
*
968 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGGTTCAAAACGGAACTAATGGG
1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGG
* * * *
1033 CCCCGATAGGCCCAAAATAACAAGTGTTCCAACTGAGCTATAAAGTTCACAGTGTACTAATCTCA
66 CCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGTACTAATCTCA
1098 CCAA
131 CCAA
1102 AA
1 AA
1104 TGATTATAGT
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
133 1 0.01
134 125 0.99
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.20
Consensus pattern (134 bp):
AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGG
CCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGTACTAATCTCA
CCAA
Found at i:1248 original size:154 final size:154
Alignment explanation
Indices: 968--3384 Score: 3633
Period size: 154 Copynumber: 15.7 Consensus size: 154
958 ATCTCACCAA
* * **
968 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGGTTCAAAACGGAACTAATGGG
1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGG
* * * *
1033 CCCCGATAGGCCCAAAATAACAAGTGTTCCAACTGAGCTATAAAGTTCACAGTGTACTAATCTCA
66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
*
1098 CCAAAATGATTATAGTTAGGCCTT
131 CCAAAATGATTATAGTTAGGCCAT
* ** *
1122 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAG
1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGG
* * * *
1187 CCCCGATAGGCCAAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCAAAGTGGACTAATCTAA
66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
* *
1252 ACAAAATGATTATAGGTAGGCCAT
131 CCAAAATGATTATAGTTAGGCCAT
* * * **
1276 AAACAATGGAAACAAAAGCATTGAGGCTTGCCAATTCGAAGAAAATTCAATACGTCACTAATGGG
1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGG
* *
1341 CCACGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
1406 CCAAAATGATTATAGTTAGGCCAT
131 CCAAAATGATTATAGTTAGGCCAT
* *
1430 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGG
1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATAC-GTCACTAATGG
**
1494 GCGTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
65 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
1559 ACCAAAATGATTATAGTTAGGCCAT
130 ACCAAAATGATTATAGTTAGGCCAT
* * * ** * *
1584 AAACAATGGAATGAAAATCATTGAGGTCTGATAAATCGAATACGATTCAATACGTCACTAATGGA
1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGG
* * *
1649 CCCCAATAAGCCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
1714 CCAAAATGATTATAGTTAGGCCAT
131 CCAAAATGATTATAGTTAGGCCAT
* * ** * *
1738 AAACAATGGAATGAAAAGCATTGAGGTCTGATAAATCGAATACGATTCAATACGTCACTAATGGA
1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGG
* * *
1803 CCCCAATAAGCCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
*
1868 CCAAAATGATTATAGTTAGACCAT
131 CCAAAATGATTATAGTTAGGCCAT
** * *
1892 AAACAAT-GAAATGAAAAGCATTGAGGTTTGATAAATCGAATACGATTCAATACGTCCCTAATGG
1 AAACAATGGAAA-GAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGG
* * * * *
1956 ACGCCAATAAGCCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
65 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
*
2021 ACCAAAATTATTATAGTTAGGCCAT
130 ACCAAAATGATTATAGTTAGGCCAT
* * * *
2046 AAACAATGGAAAGAAAAGCATGGAGATTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGG
1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATAC-GTCACTAATGG
2110 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
65 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
*
2175 ACCAAAATAATTATAGTTAGGCCAT
130 ACCAAAATGATTATAGTTAGGCCAT
*
2200 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAGATCGAAGACGATTCAATACGTCACTAATGGG
1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGG
* * * *
2265 CCCCGATAGGCCCAAAATAACAAGTGTTCGAAATGAGATAAAAACTTCAAAGTGGACTAATCTAA
66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
* *
2330 ACAAAATGATTATAGGTAGGCCAT
131 CCAAAATGATTATAGTTAGGCCAT
* * * * *
2354 AAACAATGGAAACAAAAACATTGAGGCTTGCCAATTCGAAGAAGATTCAATACGTCACTAATGGG
1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGG
2419 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
*
2484 CTAAAATGATTATAGTTAGGCCAT
131 CCAAAATGATTATAGTTAGGCCAT
* * * *
2508 AAACAATGGAAAGAAAACCATTAAGGTTTGCCAAATCGAAGACGATTTAAAACGTCACTAATGGG
1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGG
* * * *
2573 -CCCGACAGGCCCAAAATAACAAGTGTTCGAAATGAGCTAAAAACTTCAAAGTGGACTAATCTAA
66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
* *
2637 ACAAAATGATTATAGGTAGGCCAT
131 CCAAAATGATTATAGTTAGGCCAT
* * * * *
2661 AAACAATGGAAA-AAAAACATTAAGGCTTGCCAATTCGAAGAAGATTCAATACGTCACTAATGGG
1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGG
* *
2725 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATTAAGCTAAAAAGTTCACAGTGGACTAATACT
66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAA-TGAGCTAAAAACTTCACAGTGGACTAAT-CT
2790 CACCAAAATGATTATAGTTAGGCCAT
129 CACCAAAATGATTATAGTTAGGCCAT
* * *
2816 AAACAATGGAAAGAAAAGCATTAGAGGTTTTGCCTAATCGAAGACGATTCAATACGTTAGTAATG
1 AAACAATGGAAAGAAAAGCATT-GAGG-TTTGCCAAATCGAAGACGATTCAATACGTCACTAATG
* *
2881 GGCCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAATGGACTAATCT
64 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
**
2946 CACCAAAATGATTATAAATAGGCCAT
129 CACCAAAATGATTATAGTTAGGCCAT
* *
2972 AAAGAATGGAAAGAAAAGCATTGAGGTTTGCCATATCGAAGACGATTCAATACGTCACTAATGGG
1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGG
* * *
3037 CCCCAATAGGCCCAAAATAAGAAGTGTTCCGAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
3102 CCAAAATGATTATAGTTAGGCCAT
131 CCAAAATGATTATAGTTAGGCCAT
*
3126 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGT
1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGG
* * * *
3191 CTCCGATAGGCCCAAAATAACAAGTGTTCCATATGAGCCAAAAACTTCACAGTGGACAAATCTCA
66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
*
3256 CCAAAATGATTATAGTTAGGCAAT
131 CCAAAATGATTATAGTTAGGCCAT
* * * * *
3280 -AACAATGGAAAGAAAAGCATTGAGGTTCGCCAAACCGAAGACAATTCAA-AAGTGAACTAATGG
1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGT-CACTAATGG
* *
3343 GCCTCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAA
65 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
Statistics
Matches: 2072, Mismatches: 178, Indels: 27
0.91 0.08 0.01
Matches are distributed among these distances:
152 49 0.02
153 218 0.11
154 1610 0.78
155 47 0.02
156 55 0.03
157 28 0.01
158 65 0.03
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (154 bp):
AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGG
CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
CCAAAATGATTATAGTTAGGCCAT
Done.