Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012442.1 Corchorus capsularis cultivar CVL-1 contig12463, 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: 5274
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Found at i:843 original size:333 final size:333
Alignment explanation
Indices: 1--1278 Score: 1951
Period size: 333 Copynumber: 3.8 Consensus size: 333
* *
1 AATTAATGGCAAAAATAATCATAAAAAATATATAATTCAATGGCAAAAAGATTGAATGGCTTTTC
1 AATTAATGGCAAAAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAATGGCTTATC
* *
66 ACGCTTCTAATATCATTTTTCCTTTATTTTTCAAATTAATTTCAAATCAAAACGAAACAAGATTT
66 ACGCTTCTAATATCGTTTTTCCTTTTTTTTTCAAATTAATTTCAAATCAAAACGAAACAAGATTT
* *
131 AGATGTTTGTAAAAAAAAAAAAAAAATCCTTAAATGCAATTTGACTGAGATTCAGATAGAT-AAG
131 AGATGTTTGT-------AAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGATAGATGAA-
*
195 TACAAAAATTTCTAGGATTCTATGCGCAAAAAATCATGAAAAACTGAGTC-GGGTCCCCGGAACG
188 TACAAAAATTTCTAGGAGTCTATGCGCAAAAAATCATGAAAAACTGAGTCTGGGTCCCCGGAACG
* *
259 CGATTTTAGCAAAGAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACC
253 CGATTTTAGCAAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
*
324 CGAAAGATTTTTCCTG
318 CGAAAGATTTTTCCTC
*
340 AATTAATGGCAAAAATAAACATAAAAAATATATAATTCAATGCCAAAAAGATTGAATGGCTTATC
1 AATTAATGGCAAAAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAATGGCTTATC
* ** * * *
405 ACGCTTCTAATATCGTTTTTCCTTTTTTTTTCGAATTAATTTTTACTTAAATCGAAACAAGATTT
66 ACGCTTCTAATATCGTTTTTCCTTTTTTTTTCAAATTAATTTCAAATCAAAACGAAACAAGATTT
* * **
470 AGATGTTCGTAAAAACAAATCCTTAAA-GCCAATGTGGCTGAGATTTGGATAGATGAATACAAAA
131 AGATGTTTGTAAAAACAAATCCTTAAATG-CAATTTGGCTGAGATTCAGATAGATGAATACAAAA
* * * *
534 ATTTCTAGGAGCCT-TGGCGCAAAAAATCATGCAAAACTGAG-CTGGGACCTCGGAACGCGATTT
195 ATTTCTAGGAGTCTAT-GCGCAAAAAATCATGAAAAACTGAGTCTGGGTCCCCGGAACGCGATTT
* ** * * * *
597 TAGTAAAAAATTGTAATAGTTAGTACACGATTTCGACTGAAATTTTGCAAAAATTGAACCGAAAG
259 TAGCAAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAG
*
662 ATTTTTTGCTC
324 A-TTTTTCCTC
* * *
673 AATTTATGGCAATAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTATC
1 AATTAATGGCAAAAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAATGGCTTATC
*
738 ACGCTTCTAATATCGTTTTTCTTTTTTTTTTCAAATTAATTTCAAATCAAAACGAAACAAGATTT
66 ACGCTTCTAATATCGTTTTTCCTTTTTTTTTCAAATTAATTTCAAATCAAAACGAAACAAGATTT
* *
803 AGATGTTTGTAAGAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGATAGATGAGTACAAAAA
131 AGATGTTTGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGATAGATGAATACAAAAA
*
868 TTTCTAGGAGTCTATGCGCAAAAAATCATGAAAAACTGAGTCAGGG-CCCCGGAACGCGATTTTA
196 TTTCTAGGAGTCTATGCGCAAAAAATCATGAAAAACTGAGTCTGGGTCCCCGGAACGCGATTTTA
*
932 GCAAAAAACCGTGATAGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGAT
261 GCAAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGAT
997 TTTTCCTC
326 TTTTCCTC
* *
1005 AATTAATGGAAAAAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAATGGCTTTTC
1 AATTAATGGCAAAAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAATGGCTTATC
* *
1070 ACGCTTCTAATATCG-TTTTCTTTTTTTTTTCAAATTAATTTCAAATCAAAACGAATCAAGATTT
66 ACGCTTCTAATATCGTTTTTCCTTTTTTTTTCAAATTAATTTCAAATCAAAACGAAACAAGATTT
*
1134 AGATGTTTGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGATAGATGAGTACAAAAA
131 AGATGTTTGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGATAGATGAATACAAAAA
* *
1199 TTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAACTGAGTCGGGGT-CCCGGAACGCGATTTTA
196 TTTCTAGGAGTCTATGCGCAAAAAATCATGAAAAACTGAGTCTGGGTCCCCGGAACGCGATTTTA
* *
1263 GCCAAAAATCGTGATA
261 GCAAAAAACCGTGATA
1279 ATTCAATGGC
Statistics
Matches: 856, Mismatches: 74, Indels: 26
0.90 0.08 0.03
Matches are distributed among these distances:
331 190 0.22
332 238 0.28
333 294 0.34
334 6 0.01
339 128 0.15
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (333 bp):
AATTAATGGCAAAAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAATGGCTTATC
ACGCTTCTAATATCGTTTTTCCTTTTTTTTTCAAATTAATTTCAAATCAAAACGAAACAAGATTT
AGATGTTTGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGATAGATGAATACAAAAA
TTTCTAGGAGTCTATGCGCAAAAAATCATGAAAAACTGAGTCTGGGTCCCCGGAACGCGATTTTA
GCAAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGAT
TTTTCCTC
Found at i:1408 original size:251 final size:253
Alignment explanation
Indices: 1051--1529 Score: 854
Period size: 251 Copynumber: 1.9 Consensus size: 253
1041 TCAATGCCAA
*
1051 AAAGATTGAATGGCTTTTCACGCTTCTAATATCGTTTTCTTTTTTTTTTCAAATTAATTTCAAAT
1 AAAGATTGAATGGCTTTTCACGCTTCTAATA-C-TTGTCTTTTTTTTTTCAAATTAATTTCAAAT
*
1116 CAAAACGAATCAAGATTTAGATGTTTGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCA
64 CAAAACGAAACAAGATTTAGATGTTTGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCA
** *
1181 GATAGATGAGTACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAACTGAGTCGGGGT
129 GATAGATGAGTACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAACTGAACCGGGGC
*
1246 CCCGGAACGCGATTTTAGCCAAAAATCGTGATAATTCAATGGCTTTTCACGCTTTTAGCC
194 CCCGGAACGCGATTTTAGCCAAAAACCGTGATAATTCAATGGCTTTTCACGCTTTTAGCC
1306 AAAGATTGAATGGCTTTTCACGCTTCTAATA-TTGT-TTTTTTTTTTCAAATTAATTTCAAATCA
1 AAAGATTGAATGGCTTTTCACGCTTCTAATACTTGTCTTTTTTTTTTCAAATTAATTTCAAATCA
*
1369 AAACGAAACAAGATTTAGATGTTTGTAAAAACAAATCCTTAAATGCAATTTGGTTGAGATTCAGA
66 AAACGAAACAAGATTTAGATGTTTGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGA
*
1434 TAGATGAGTACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAGCTGAACCGGGGCCC
131 TAGATGAGTACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAACTGAACCGGGGCCC
1499 CGGAACGCGATTTTAGCCAAAAACCGTGATA
196 CGGAACGCGATTTTAGCCAAAAACCGTGATA
1530 GTTAGTATAC
Statistics
Matches: 216, Mismatches: 8, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
251 182 0.84
252 3 0.01
255 31 0.14
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (253 bp):
AAAGATTGAATGGCTTTTCACGCTTCTAATACTTGTCTTTTTTTTTTCAAATTAATTTCAAATCA
AAACGAAACAAGATTTAGATGTTTGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGA
TAGATGAGTACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAACTGAACCGGGGCCC
CGGAACGCGATTTTAGCCAAAAACCGTGATAATTCAATGGCTTTTCACGCTTTTAGCC
Found at i:2466 original size:335 final size:330
Alignment explanation
Indices: 1306--2526 Score: 1897
Period size: 333 Copynumber: 3.7 Consensus size: 330
1296 GCTTTTAGCC
*
1306 AAAGATTGAATGGCTTTTCACGCTTCTAATA----TTGT--TTTTTTTTTTCAAATTAATTTCAA
1 AAAGATTGAATGGCTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTTTTCAAATTAATTTCAA
* *
1365 ATCAAAACGAAACAAGATTTAGATGTTTGTAAAAACAAATCCTTAAATGCAATTTGGTTGAGATT
66 ATCAAAACGAAACAAGATTTAGATGTTTGTAAAAAAAAATCCTTAAATGCAATTTGGCTGAGATT
* *
1430 CAGATAGATGAGTACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAGCTGAACCGGG
131 CAGATAGATAAGTACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAA-CTGAGCCGGG
1495 GCCCCGGAACGCGATTTTAGCCAAAAACCGTGATAGTTAGTATACGATTTCGGCTAAAATTTTGC
195 GCCCCGGAACGCGATTTTAGCCAAAAACCGTGATAGTTAGTATACGATTTCGGCTAAAATTTTGC
1560 AAAAATTGACCCGAAAGATTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAATTC
260 -AAAATTGACCCGAAAGATTTTTCCTCAATTAATGG-AAAAATAATCATAAAAAATATATAATTC
1625 AATGCCAA
323 AATGCCAA
* *
1633 AAAGATTGAATGGCTTTTCGCGCTTCTAATATCGTTTTTCC-TTTATTTTTCAAATTAATTTCAA
1 AAAGATTGAATGGCTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTTTTCAAATTAATTTCAA
1697 ATCAAAACGAAACAAGATTTAGATGTTTGTAAAAAAAAAAAAGAAATCCTTAAATGCAATTTGGC
66 ATCAAAACGAAACAAGATTTAGATGTTTGT------AAAAAA-AAATCCTTAAATGCAATTTGGC
*
1762 TGAGATTCAGATAGATAAGTA-AAGAAATTTCTAGGATTCTCTGCGCAAAAAATCATGAAAACTG
124 TGAGATTCAGATAGATAAGTACAA-AAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAACTG
* *
1826 AGTCGGGACCCCGGAACGCGATTTTAGCCAAAAACCGTGATAGTTAGT-TCACGATTTCGGCTAA
188 AGCCGGGGCCCCGGAACGCGATTTTAGCCAAAAACCGTGATAGTTAGTAT-ACGATTTCGGCTAA
* * *
1890 AATTTTGCAAAATTGACGCGAAAGATTTTTCCTCAATTAATGGAAAAAATAATCATATAAGATAT
252 AATTTTGCAAAATTGACCCGAAAGATTTTTCCTCAATTAATGG-AAAAATAATCATAAAAAATAT
1955 ATAATTCAATGCCAA
316 ATAATTCAATGCCAA
* *
1970 AAAGATTCAATGGCTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTATTTTCAAATTAATTTG
1 AAAGATTGAATGGCTTTTCACGCTTCTAATATCGTTTTTCC-TTTTTT-TTTTCAAATTAATTTC
* * *
2035 AAATCAAAACGAAACAAGATTTAGATGTTTGTAAAAACAAATCCTTAAATGCAATTTCGCTGAAA
64 AAATCAAAACGAAACAAGATTTAGATGTTTGTAAAAAAAAATCCTTAAATGCAATTTGGCTGAGA
2100 TTCAGATAGATAAGTACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAACTGAGCCG
129 TTCAGATAGATAAGTACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATG-AAAACTGAGCCG
* *
2165 GGGCCCCGGAACGCGATGTTAGCCAAAAACCGTGATAGTTAGTATACGATTTCGACTAAAATTTT
193 GGGCCCCGGAACGCGATTTTAGCCAAAAACCGTGATAGTTAGTATACGATTTCGGCTAAAATTTT
*
2230 GCAAATGTTGACCCGAAAGATTTTTCCTCAATTAATGG-AAAATAATCATAAAAAATATATTAA-
258 GCAAA-ATTGACCCGAAAGATTTTTCCTCAATTAATGGAAAAATAATCATAAAAAATATA-TAAT
2293 TCAATGCCAA
321 TCAATGCCAA
* *
2303 AAAGATTGAATGGCTTTTCACACTTCTCATATCGTTTTTCCTTTTTTTTTTCCAAATTAATTTCA
1 AAAGATTGAATGGCTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTTTT-CAAATTAATTTCA
* * *
2368 AATCAATACGAAACAAGATTTAGATGTTTGTTTAAAAAAAAAATCCTTAATTGCAATTTGACTGA
65 AATCAAAACGAAACAAGATTTAGATGTTTG--T-AAAAAAAAATCCTTAAATGCAATTTGGCTGA
* *
2433 GATTCAGATAGATAAGTACAGAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAACTGAGTC
127 GATTCAGATAGATAAGTACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAACTGAGCC
* *
2498 GGGGCTCCGGAACGCGATTTTAGACAAAA
192 GGGGCCCCGGAACGCGATTTTAGCCAAAA
2527 CGAAACAAGA
Statistics
Matches: 822, Mismatches: 45, Indels: 47
0.90 0.05 0.05
Matches are distributed among these distances:
327 30 0.04
331 7 0.01
332 99 0.12
333 140 0.17
334 123 0.15
335 110 0.13
337 108 0.13
338 77 0.09
339 81 0.10
340 47 0.06
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (330 bp):
AAAGATTGAATGGCTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTTTTCAAATTAATTTCAA
ATCAAAACGAAACAAGATTTAGATGTTTGTAAAAAAAAATCCTTAAATGCAATTTGGCTGAGATT
CAGATAGATAAGTACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAACTGAGCCGGGG
CCCCGGAACGCGATTTTAGCCAAAAACCGTGATAGTTAGTATACGATTTCGGCTAAAATTTTGCA
AAATTGACCCGAAAGATTTTTCCTCAATTAATGGAAAAATAATCATAAAAAATATATAATTCAAT
GCCAA
Found at i:2656 original size:148 final size:150
Alignment explanation
Indices: 2375--2668 Score: 452
Period size: 148 Copynumber: 2.0 Consensus size: 150
2365 TCAAATCAAT
*
2375 ACGAAACAAGATTTAGATGTTTGTTTAAAAAAAAAATCCTTAATTGCAATTTGACTGAGATTCAG
1 ACGAAACAAGATTTAGATGTTTG-TTAAAAAAAAAATCCTTAAATGCAATTTGACTGAGATTCAG
* * * ** *
2440 ATAGATAAGTACAGAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAACTGAGTCGGGGCTC
65 ACAGATAAGTACAAAAAATTCTAGGAGTCTCTGCGCAAAAAATCATGAAAACTGAACCGGGACTC
2505 CGGAACGCGATTTTAGACAAA
130 CGGAACGCGATTTTAGACAAA
* *
2526 ACGAAACAAGATTTAGATGTTTG-T-AAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGA
1 ACGAAACAAGATTTAGATGTTTGTTAAAAAAAAAATCCTTAAATGCAATTTGACTGAGATTCAGA
2589 CAGATAAGTA-AAAAAATTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAACTGAACCGGGAAC-
66 CAGATAAGTACAAAAAATTCTAGGAGTCTCTGCGCAAAAAATCATG-AAAACTGAACCGGG-ACT
2652 CCGGAACGCGATTTTAG
129 CCGGAACGCGATTTTAG
2669 CCCAAAACTG
Statistics
Matches: 132, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
147 33 0.25
148 74 0.56
149 2 0.02
151 23 0.17
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (150 bp):
ACGAAACAAGATTTAGATGTTTGTTAAAAAAAAAATCCTTAAATGCAATTTGACTGAGATTCAGA
CAGATAAGTACAAAAAATTCTAGGAGTCTCTGCGCAAAAAATCATGAAAACTGAACCGGGACTCC
GGAACGCGATTTTAGACAAA
Found at i:3167 original size:332 final size:332
Alignment explanation
Indices: 2522--5274 Score: 3240
Period size: 331 Copynumber: 8.5 Consensus size: 332
2512 CGATTTTAGA
* *
2522 CAAAACGAAACAAGATTTAGATGTTTGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCA
1 CAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCA
* * * * *
2587 GACAGATAAGTA-AAAAAATTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAACTGAACCGGGAA
66 GATAGATAAGTACAAAAATTTCTAGGAGCCTCTGCGCAAAAAATCATGCAAAACTGAGCCGGG-A
** * *
2651 CC-CGGAACGCGATTTTAGCCCAAAA-CTGTGATAGTTAGTATACGATTTCGACTAAAATTTTGC
130 CCTCGGAACGCGATTTTAGCAAAAAATC-GTGATAGTTAGTACACGATTTCGGCTAAAATTTTGC
* *
2714 AAAAATTGATCCGAAATA-TTTTTCCTCAATTAATGGAAAAAATAATCATAAAAAATATATAATT
194 AAAAATTGATCCGAAAGATTTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAATT
* * *
2778 CAATGCCAAAAAGATTGAATGGCTTATCACGTTTCTAATATCGTTTTTCTTTTTTTTTTCGAATT
259 CAATGCCAAAAAGATTGAATGGCTTATCACGCTTCTAATATCGTTTTTC-CTTTTTTTTCAAATT
2843 AATTTTTACT
323 AATTTTTACT
* * *
2853 TAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAA-GCCAATGTGGCTGAGATTT
1 CAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAATG-CAATTTGGCTGAGATTC
* * **
2917 GGATAGATGAA-TACAAAAATTTCTAGGAGCCT-TGGCGCAAAAAATAATTTAAAACTGAGCCGG
65 AGATAGAT-AAGTACAAAAATTTCTAGGAGCCTCT-GCGCAAAAAATCATGCAAAACTGAGCCGG
* * * * * *
2980 GACCTCGGAACTCGATTTTAGTAAAAAATTGTAATAGTTAGTACACGATTTCGACTGAAATTTTG
128 GACCTCGGAACGCGATTTTAGCAAAAAATCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTG
* * *
3045 TAAAAATTGATCCGAAAGATTTTTTGCTCAATTTATGGCAAAAATAATCATAAAAAATATATAAT
193 CAAAAATTGATCCGAAAGATTTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAAT
*
3110 TCAATGCCAAAAAGATTGAATGGCTTATCACGCTTCTAATATCATTTTTCCTTTTTTTTCCAAAT
258 TCAATGCCAAAAAGATTGAATGGCTTATCACGCTTCTAATATCGTTTTTCCTTTTTTTT-CAAAT
** *
3175 TAATTTCAAAT
322 TAATTTTTACT
* * * * *
3186 CAAAACGAAACAAGATTTAGATGTTTGTAAAAAAAAAATCCTTAATTGCAATTTGACTGAGATTC
1 CAAATCGAAACAAGATTTAGATGTTCGT-AAAAACAAATCCTTAAATGCAATTTGGCTGAGATTC
* * * * * **
3251 AGATAGATAAGTACAGAAATTTCTTGGAGTCTCTGTGCAAAAAATCATG-AAAACTAAATCGGG-
65 AGATAGATAAGTACAAAAATTTCTAGGAGCCTCTGCGCAAAAAATCATGCAAAACTGAGCCGGGA
* *
3314 GCTCCGGAACGCGATTTTAG-ACAAAAATCGTGATAGTTAGTACACGTTTTCGGCTAAAATTTTG
130 CCT-CGGAACGCGATTTTAGCA-AAAAATCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTG
**
3378 CAAAAATTGATCCGAAAGA-TTTTTCGACAATTAATGGCAAAAATAATCAT-AAAAATATATAAT
193 CAAAAATTGATCCGAAAGATTTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAAT
* * *
3441 TCAATGCCAAAATGATTGAATGGCTTTTCACGCTTATAATATCGTTTTTCCTTTTTTTTTCAAAT
258 TCAATGCCAAAAAGATTGAATGGCTTATCACGCTTCTAATATCGTTTTTCC-TTTTTTTTCAAAT
*
3506 TAATTTCATA-T
322 TAATTT-TTACT
* * *
3517 CAAAACGAAACAAGATTTAGATGTTTGTAAAAAAAAAAAATCCTTAAATGCAATTTGGCTGAGAT
1 CAAATCGAAACAAGATTTAGATGTTCGT---AAAAACAAATCCTTAAATGCAATTTGGCTGAGAT
* * * ** *
3582 TCAGATAGATATGTACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATAATAAAAAACTGAACCGG
63 TCAGATAGATAAGTACAAAAATTTCTAGGAGCCTCTGCGCAAAAAATCATGCAAAACTGAGCCGG
* * ** *
3647 GGCCCCATAACGCGATTTTAGCAAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTG
128 GACCTCGGAACGCGATTTTAGCAAAAAATCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTG
*
3712 CAAAAATTGATCCGAAAGA-TTTTTCCTGAATTAATGGCAAAAATAATCATAAAAAATATATAAT
193 CAAAAATTGATCCGAAAGATTTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAAT
* *
3776 TCAATGCCAAAAAGATTGAATGGCTTATCACGTTTCTAATATCGTTTTTCCTTTTTTTTCGAATT
258 TCAATGCCAAAAAGATTGAATGGCTTATCACGCTTCTAATATCGTTTTTCCTTTTTTTTCAAATT
3841 AATTTTTACT
323 AATTTTTACT
* * *
3851 TAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAA-GCCAATGTGGCTGAGATTT
1 CAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAATG-CAATTTGGCTGAGATTC
* *
3915 GGATAGATGAA-TACAAAAATTTCTAGGAGCCT-TGGCGCAAAAAATCATGCAAAACTGAGTCGG
65 AGATAGAT-AAGTACAAAAATTTCTAGGAGCCTCT-GCGCAAAAAATCATGCAAAACTGAGCCGG
** * * * * * * *
3978 GACCTCTAAACTCGATTTTAGTAAAAAATTGTTATAGTTAGAACACGATTTCGTCTAAAATATTG
128 GACCTCGGAACGCGATTTTAGCAAAAAATCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTG
* *
4043 CAAAAATTGATCCGAAAGAATTTTTTCCTCATTTTATGGCAAAAATAATCAT-AAAAATATATAA
193 CAAAAATTGATCCGAAAG-ATTTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAA
* * * *
4107 TTTAATGCCAAAAAGATTGAAGGGCTTATCACGCTTCTAATATCGTTTTTCCTTTGTTTTCGAAT
257 TTCAATGCCAAAAAGATTGAATGGCTTATCACGCTTCTAATATCGTTTTTCCTTTTTTTTCAAAT
*
4172 TAATTTTTAGT
322 TAATTTTTACT
* * * *
4183 TAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCTTTAAA-GCCAATGTGGCTGAGATTT
1 CAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAATG-CAATTTGGCTGAGATTC
* * * *
4247 GGATAGATGAA-TACAAAAATTTCTAGGAGCCT-TGGCGCAAAAAATCAGGCAAAATTGAGCCAG
65 AGATAGAT-AAGTACAAAAATTTCTAGGAGCCTCT-GCGCAAAAAATCATGCAAAACTGAGCCGG
* * * ** * * *
4310 GACCTCGGAACGCGATATTAGTAAAAAATTGAAATAATTAGTACACGATTTCGACTGAAATTTTG
128 GACCTCGGAACGCGATTTTAGCAAAAAATCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTG
*
4375 CAAAAATTGATCCGAAAGATTTTTTGCTCAATTAATGGCAAAAATAATCAT-AAAAATATATAAT
193 CAAAAATTGATCCGAAAGATTTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAAT
* *
4439 TCAATGCCAAAAAGATTGAATAGCTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTTCAAATT
258 TCAATGCCAAAAAGATTGAATGGCTTATCACGCTTCTAATATCGTTTTTCCTTTTTTTTCAAATT
** *
4504 AATTTCAAAT
323 AATTTTTACT
* * * *
4514 CAAAACGAAACAAGATTTAGATGTTTGTAAAACCAAATCCTTAAATGCAATTTGGCTGAGATTTA
1 CAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCA
* * * * *
4579 GATAGATAAGTACAGAAATTTCTAGGAGTCTCTGTGC-AAAAATCATGCAAAACTGAGTCGGGGC
66 GATAGATAAGTACAAAAATTTCTAGGAGCCTCTGCGCAAAAAATCATGCAAAACTGAGCCGGGAC
* * *
4643 CCCGGAACGCGATTTTAGCCAAAAACCGTGATA---AGTACACGATTTCGGCTAAAATTTTGCAA
131 CTCGGAACGCGATTTTAGCAAAAAATCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAA
* * *
4705 AAATTGACCCGAAAGA-TTTTTCCTCAATTAATTGC-AAAATAATCATAAAAAATATACAATTCA
196 AAATTGATCCGAAAGATTTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAATTCA
* *
4768 ATACCAAAAAGATTGAATGGCTTTTCACGCTTCTAATATCG------CTTTTTTTTCAAATTAA-
261 ATGCCAAAAAGATTGAATGGCTTATCACGCTTCTAATATCGTTTTTCCTTTTTTTTCAAATTAAT
4826 --TT--T
326 TTTTACT
4829 CAAAT-----C-A-A---A-A----C---AAAACAAATCCTTAAATGCAATTTGGCTGAGATTCA
1 CAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCA
* * * * *
4876 GATAGATAAGTACAGAAATTTCTTGGAGTCC-CTGTGCAAAAAATCATG-AAAACTAAGTCGGG-
66 GATAGATAAGTACAAAAATTTCTAGGAG-CCTCTGCGCAAAAAATCATGCAAAACTGAGCCGGGA
*
4938 GCTACGGAACGCGATTTTAG-ACAAAAATCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTG
130 CCT-CGGAACGCGATTTTAGCA-AAAAATCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTG
* ** *
5002 CAAAAATTGACCCGAAAGA-TTTTTCGACAATTAATGGCAAAAATAATCATAAAGAATATATAAT
193 CAAAAATTGATCCGAAAGATTTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAAT
* *
5066 TCAATGCCAAAAAGATTGAATGGCTTTTCACGCTTCTAATATCG-----CTTTTTTTTTCAAATT
258 TCAATGCCAAAAAGATTGAATGGCTTATCACGCTTCTAATATCGTTTTTCCTTTTTTTTCAAATT
5126 AA---TT--T
323 AATTTTTACT
5131 CAAAT-----C-A-A---A-A----C---AAAACAAATCCTTAAATGCAATTTGGCTGAGATTCA
1 CAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCA
* * * *
5178 GATAGATAAGTACAAAAATTTCTATGAGTCTCTGCACAAAAAATCATGAAAAACTGAGCCTGGG-
66 GATAGATAAGTACAAAAATTTCTAGGAGCCTCTGCGCAAAAAATCATGCAAAACTGAGCC-GGGA
* ** * * *
5242 CCCCGGAACGAAAATTTAGCCAAAAACCGTGAT
130 CCTCGGAACGCGATTTTAGCAAAAAATCGTGAT
Statistics
Matches: 2155, Mismatches: 222, Indels: 118
0.86 0.09 0.05
Matches are distributed among these distances:
296 1 0.00
297 108 0.05
298 11 0.01
300 61 0.03
301 67 0.03
302 106 0.05
303 33 0.02
304 5 0.00
305 1 0.00
308 1 0.00
309 1 0.00
310 1 0.00
315 5 0.00
320 17 0.01
325 11 0.01
326 71 0.03
327 42 0.02
330 52 0.02
331 516 0.24
332 440 0.20
333 318 0.15
334 223 0.10
335 64 0.03
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (332 bp):
CAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCA
GATAGATAAGTACAAAAATTTCTAGGAGCCTCTGCGCAAAAAATCATGCAAAACTGAGCCGGGAC
CTCGGAACGCGATTTTAGCAAAAAATCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAA
AAATTGATCCGAAAGATTTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAATTCA
ATGCCAAAAAGATTGAATGGCTTATCACGCTTCTAATATCGTTTTTCCTTTTTTTTCAAATTAAT
TTTTACT
Found at i:4490 original size:998 final size:992
Alignment explanation
Indices: 2522--5148 Score: 3697
Period size: 998 Copynumber: 2.7 Consensus size: 992
2512 CGATTTTAGA
2522 CAAAACGAAACAAGATTTAGATGTTTGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCA
1 CAAAACGAAACAAGATTTAGATGTTTGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCA
* * **
2587 GACAGATAAGTA-AAAAAATTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAACTGAACCGGGAA
66 GATAGATAAGTACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAACTGAACCGGGGC
* * * *
2651 CCCGGAACGCGATTTTAGCCCAAAACTGTGATAGTTAGTATACGATTTCGACTAAAATTTTGCAA
131 CCCGGAACGCGATTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAA
* *
2716 AAATTGATCCGAAATATTTTTCCTCAATTAATGGAAAAAATAATCATAAAAAATATATAATTCAA
196 AAATTGATCCGAAAGATTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAATTCAA
*
2781 TGCCAAAAAGATTGAATGGCTTATCACGTTTCTAATATCGTTTTTCTTTTTTTTTTCGAATTAAT
261 TGCCAAAAAGATTGAATGGCTTATCACGTTTCTAATATCGTTTTTC-CTTTTTTTTCGAATTAAT
2846 TTTTACTTAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAAGCCAATGTGGCTG
325 TTTTACTTAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAAGCCAATGTGGCTG
* *
2911 AGATTTGGATAGATGAATACAAAAATTTCTAGGAGCCTTGGCGCAAAAAATAATTTAAAACTGAG
390 AGATTTGGATAGATGAATACAAAAATTTCTAGGAGCCTTGGCGCAAAAAATCA-TGAAAACTGAG
* *
2976 CCGGGACCTCGGAACTCGATTTTAGTAAAAAATTGTAATAGTTAGTACACGATTTCGACTGAAAT
454 TCGGGACCTCGGAACTCGATTTTAGTAAAAAATTGTAATAGTTAGTACACGATTTCGACTAAAAT
* *
3041 TTTGTAAAAATTGATCCGAAAGATTTTTTGCTCAATTTATGGCAAAAATAATCATAAAAAATATA
519 TTTGCAAAAATTGATCCGAAAGATTTTTTCCTCAATTTATGGCAAAAATAATCAT-AAAAATATA
* *
3106 TAATTCAATGCCAAAAAGATTGAATGGCTTATCACGCTTCTAATATCATTTTTCCTTTTTTTTCC
583 TAATTCAATGCCAAAAAGATTGAATGGCTTATCACGCTTCTAATATCGTTTTTCCTTTGTTTTCC
* *
3171 AAATTAATTTCAAATCAAAACGAAACAAGATTTAGATGTTTGTAAAAAAAAAATCCTTAATTGCA
648 AAATTAATTTCAAATCAAAACGAAACAAGATTTAGATGTTCGTAAAAAAAAAATCCTTAATAGCA
* * * * * *
3236 ATTTGACTGAGATTCAGATAGATAAGTACAGAAATTTCTTGGAGTCTCTGTGCAAAAAATCATGA
713 ATGTGACTGAGATTCAGATAGATAAGTACAAAAATTTCTAGGAGCCTCTGCGCAAAAAATCAGGA
* ** * ** * *
3301 AAACTAAATCGGGGCTCCGGAACGCGATTTTAGACAAAAATCGTGATAGTTAGTACACGTTTTCG
778 AAACTAAACCGGACCTCCGGAACGCGATATTAGACAAAAATCGAAATAATTAGTACACGATTTCG
*
3366 GCTAAAATTTTGCAAAAATTGATCCGAAAGATTTTTCGACAATTAATGGCAAAAATAATCATAAA
843 ACTAAAATTTTGCAAAAATTGATCCGAAAGATTTTTCGACAATTAATGGCAAAAATAATCATAAA
* *
3431 AATATATAATTCAATGCCAAAATGATTGAATGGCTTTTCACGCTTATAATATCGTTTTTCCTTTT
908 AATATATAATTCAATGCCAAAAAGATTGAATAGCTTTTCACGCTTATAATATCGTTTTTCC-TTT
*
3496 TTTTTCAAATTAATTTCATAT
972 TTTTTCAAATTAATTTCAAAT
*
3517 CAAAACGAAACAAGATTTAGATGTTTGTAAAAAAAAAAAATCCTTAAATGCAATTTGGCTGAGAT
1 CAAAACGAAACAAGATTTAGATGTTTGT---AAAAACAAATCCTTAAATGCAATTTGGCTGAGAT
* * *
3582 TCAGATAGATATGTACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATAATAAAAAACTGAACCGG
63 TCAGATAGATAAGTACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAACTGAACCGG
** *
3647 GGCCCCATAACGCGATTTTAGCAAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTG
128 GGCCCCGGAACGCGATTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTG
*
3712 CAAAAATTGATCCGAAAGATTTTTCCTGAATTAATGGCAAAAATAATCATAAAAAATATATAATT
193 CAAAAATTGATCCGAAAGATTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAATT
3777 CAATGCCAAAAAGATTGAATGGCTTATCACGTTTCTAATATCGTTTTTCCTTTTTTTTCGAATTA
258 CAATGCCAAAAAGATTGAATGGCTTATCACGTTTCTAATATCGTTTTTCCTTTTTTTTCGAATTA
3842 ATTTTTACTTAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAAGCCAATGTGGC
323 ATTTTTACTTAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAAGCCAATGTGGC
3907 TGAGATTTGGATAGATGAATACAAAAATTTCTAGGAGCCTTGGCGCAAAAAATCATGCAAAACTG
388 TGAGATTTGGATAGATGAATACAAAAATTTCTAGGAGCCTTGGCGCAAAAAATCATG-AAAACTG
** * * *
3972 AGTCGGGACCTCTAAACTCGATTTTAGTAAAAAATTGTTATAGTTAGAACACGATTTCGTCTAAA
452 AGTCGGGACCTCGGAACTCGATTTTAGTAAAAAATTGTAATAGTTAGTACACGATTTCGACTAAA
* *
4037 ATATTGCAAAAATTGATCCGAAAGAATTTTTTCCTCATTTTATGGCAAAAATAATCATAAAAATA
517 ATTTTGCAAAAATTGATCCGAAAG-ATTTTTTCCTCAATTTATGGCAAAAATAATCATAAAAATA
* *
4102 TATAATTTAATGCCAAAAAGATTGAAGGGCTTATCACGCTTCTAATATCGTTTTTCCTTTGTTTT
581 TATAATTCAATGCCAAAAAGATTGAATGGCTTATCACGCTTCTAATATCGTTTTTCCTTTGTTTT
* ** * * * * *
4167 -CGAATTAATTTTTAGTTAAATCGAAACAAGATTTAGATGTTCGT-AAAAACAAATCTTTAA-AG
646 CCAAATTAATTTCAAATCAAAACGAAACAAGATTTAGATGTTCGTAAAAAAAAAATCCTTAATAG
* **
4229 CCAATGTGGCTGAGATTTGGATAGATGAA-TACAAAAATTTCTAGGAGCCT-TGGCGCAAAAAAT
711 -CAATGTGACTGAGATTCAGATAGAT-AAGTACAAAAATTTCTAGGAGCCTCT-GCGCAAAAAAT
* * * *
4292 CAGGCAAAATTGAGCCAGGACCT-CGGAACGCGATATTAGTA-AAAAATTGAAATAATTAGTACA
773 CAGG-AAAACTAAACC-GGACCTCCGGAACGCGATATTAG-ACAAAAATCGAAATAATTAGTACA
* * *
4355 CGATTTCGACTGAAATTTTGCAAAAATTGATCCGAAAGATTTTTTGCTCAATTAATGGCAAAAAT
835 CGATTTCGACTAAAATTTTGCAAAAATTGATCCGAAAGATTTTTCG-ACAATTAATGGCAAAAAT
*
4420 AATCATAAAAATATATAATTCAATGCCAAAAAGATTGAATAGCTTTTCACGCTTCTAATATCGTT
899 AATCATAAAAATATATAATTCAATGCCAAAAAGATTGAATAGCTTTTCACGCTTATAATATCGTT
4485 TTTCCTTTTTTTTCAAATTAATTTCAAAT
964 TTTCCTTTTTTTTCAAATTAATTTCAAAT
* *
4514 CAAAACGAAACAAGATTTAGATGTTTGTAAAACCAAATCCTTAAATGCAATTTGGCTGAGATTTA
1 CAAAACGAAACAAGATTTAGATGTTTGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCA
* * * **
4579 GATAGATAAGTACAGAAATTTCTAGGAGTCTCTGTGC-AAAAATCATGCAAAACTGAGTCGGGGC
66 GATAGATAAGTACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAACTGAACCGGGGC
4643 CCCGGAACGCGATTTTAGCCAAAAACCGTGATA---AGTACACGATTTCGGCTAAAATTTTGCAA
131 CCCGGAACGCGATTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAA
* * *
4705 AAATTGACCCGAAAGATTTTTCCTCAATTAATTGC-AAAATAATCATAAAAAATATACAATTCAA
196 AAATTGATCCGAAAGATTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAATTCAA
* * * *
4769 TACCAAAAAGATTGAATGGCTTTTCACGCTTCTAATATCG------CTTTTTTTTCAAATTAA--
261 TGCCAAAAAGATTGAATGGCTTATCACGTTTCTAATATCGTTTTTCCTTTTTTTTCGAATTAATT
*
4826 TTT-C--AAAT-----C-A-A---A-A----C---AAAACAAATCCTTAAATG-CAATTTGGCTG
326 TTTACTTAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAA-GCCAATGTGGCTG
** * * * * *
4869 AGATTCAGATAGAT-AAGTACAGAAATTTCTTGGAGTCCCT-GTGCAAAAAATCATGAAAACTAA
390 AGATTTGGATAGATGAA-TACAAAAATTTCTAGGAG-CCTTGGCGCAAAAAATCATGAAAACTGA
* * * * *
4932 GTCGGG-GCTACGGAACGCGATTTTAG-ACAAAAATCGTGATAGTTAGTACACGATTTCGGCTAA
453 GTCGGGACCT-CGGAACTCGATTTTAGTA-AAAAATTGTAATAGTTAGTACACGATTTCGACTAA
* ** *
4995 AATTTTGCAAAAATTGACCCGAAAGA-TTTTTCGACAATTAATGGCAAAAATAATCATAAAGAAT
516 AATTTTGCAAAAATTGATCCGAAAGATTTTTTCCTCAATTTATGGCAAAAATAATCATAAA-AAT
* *
5059 ATATAATTCAATGCCAAAAAGATTGAATGGCTTTTCACGCTTCTAATATCG--CTT--TTT-TTT
580 ATATAATTCAATGCCAAAAAGATTGAATGGCTTATCACGCTTCTAATATCGTTTTTCCTTTGTTT
*
5119 T-CAAATTAATTTCAAATCAAAACAAAACAA
645 TCCAAATTAATTTCAAATCAAAACGAAACAA
5149 ATCCTTAAAT
Statistics
Matches: 1483, Mismatches: 130, Indels: 80
0.88 0.08 0.05
Matches are distributed among these distances:
953 26 0.02
954 3 0.00
956 2 0.00
957 30 0.02
958 55 0.04
959 82 0.06
960 68 0.05
961 4 0.00
963 1 0.00
967 1 0.00
968 1 0.00
971 1 0.00
972 1 0.00
973 1 0.00
978 4 0.00
980 1 0.00
981 3 0.00
983 16 0.01
989 65 0.04
990 61 0.04
993 52 0.04
994 68 0.05
995 30 0.02
996 66 0.04
997 173 0.12
998 424 0.29
999 244 0.16
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (992 bp):
CAAAACGAAACAAGATTTAGATGTTTGTAAAAACAAATCCTTAAATGCAATTTGGCTGAGATTCA
GATAGATAAGTACAAAAATTTCTAGGAGTCTCTGCGCAAAAAATCATGAAAAACTGAACCGGGGC
CCCGGAACGCGATTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAA
AAATTGATCCGAAAGATTTTTCCTCAATTAATGGCAAAAATAATCATAAAAAATATATAATTCAA
TGCCAAAAAGATTGAATGGCTTATCACGTTTCTAATATCGTTTTTCCTTTTTTTTCGAATTAATT
TTTACTTAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAAGCCAATGTGGCTGA
GATTTGGATAGATGAATACAAAAATTTCTAGGAGCCTTGGCGCAAAAAATCATGAAAACTGAGTC
GGGACCTCGGAACTCGATTTTAGTAAAAAATTGTAATAGTTAGTACACGATTTCGACTAAAATTT
TGCAAAAATTGATCCGAAAGATTTTTTCCTCAATTTATGGCAAAAATAATCATAAAAATATATAA
TTCAATGCCAAAAAGATTGAATGGCTTATCACGCTTCTAATATCGTTTTTCCTTTGTTTTCCAAA
TTAATTTCAAATCAAAACGAAACAAGATTTAGATGTTCGTAAAAAAAAAATCCTTAATAGCAATG
TGACTGAGATTCAGATAGATAAGTACAAAAATTTCTAGGAGCCTCTGCGCAAAAAATCAGGAAAA
CTAAACCGGACCTCCGGAACGCGATATTAGACAAAAATCGAAATAATTAGTACACGATTTCGACT
AAAATTTTGCAAAAATTGATCCGAAAGATTTTTCGACAATTAATGGCAAAAATAATCATAAAAAT
ATATAATTCAATGCCAAAAAGATTGAATAGCTTTTCACGCTTATAATATCGTTTTTCCTTTTTTT
TCAAATTAATTTCAAAT
Found at i:5187 original size:302 final size:297
Alignment explanation
Indices: 4542--5274 Score: 1146
Period size: 297 Copynumber: 2.4 Consensus size: 297
4532 AGATGTTTGT
* *
4542 AAAACCAAATCCTTAAATGCAATTTGGCTGAGATTTAGATAGATAAGTACAGAAATTTCTAGGAG
1 AAAA-CAAATCCTTAAATGCAATTTGGCTGAGATTCAGATAGATAAGTACAGAAATTTCTTGGAG
* * *
4607 TCTCTGTGC-AAAAATCATGCAAAACTGAGTCGGGGCCCCGGAACGCGATTTTAGCCAAAAACCG
65 TCTCTGTGCAAAAAATCATG-AAAACTAAGTCGGGGCCACGGAACGCGATTTTAGACAAAAACCG
*
4671 TGATAAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTAA
129 TGATAAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCACAATTAA
*
4736 TTGCAAAATAATCATAAAAAATATACAATTCAATACCAAAAAGATTGAATGGCTTTTCACGCTTC
194 TGGCAAAATAATCATAAAAAATATACAATTCAATACCAAAAAGATTGAATGGCTTTTCACGCTTC
4801 TAATATCGCTTTTTTTTCAAATTAATTTCAAATCAAAAC
259 TAATATCGCTTTTTTTTCAAATTAATTTCAAATCAAAAC
4840 AAAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGATAGATAAGTACAGAAATTTCTTGGAGT
1 AAAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGATAGATAAGTACAGAAATTTCTTGGAGT
* * *
4905 CCCTGTGCAAAAAATCATGAAAACTAAGTCGGGGCTACGGAACGCGATTTTAGACAAAAATCGTG
66 CTCTGTGCAAAAAATCATGAAAACTAAGTCGGGGCCACGGAACGCGATTTTAGACAAAAACCGTG
*
4970 ATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCGACAATTA
131 ATA---AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCACAATTA
* * *
5035 ATGGCAAAAATAATCATAAAGAATATATAATTCAATGCCAAAAAGATTGAATGGCTTTTCACGCT
193 ATGGC-AAAATAATCATAAAAAATATACAATTCAATACCAAAAAGATTGAATGGCTTTTCACGCT
5100 TCTAATATCGCTTTTTTTTTCAAATTAATTTCAAATCAAAAC
257 TCTAATATCGC-TTTTTTTTCAAATTAATTTCAAATCAAAAC
*
5142 AAAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGATAGATAAGTACAAAAATTTCTAT-GAG
1 AAAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGATAGATAAGTACAGAAATTTCT-TGGAG
** * * * * ** * *
5206 TCTCTGCACAAAAAATCATGAAAAACTGAGCCTGGGCCCCGGAACGAAAATTTAGCCAAAAACCG
65 TCTCTGTGCAAAAAATCATG-AAAACTAAGTCGGGGCCACGGAACGCGATTTTAGACAAAAACCG
5271 TGAT
129 TGAT
Statistics
Matches: 399, Mismatches: 28, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
297 110 0.28
298 14 0.04
300 61 0.15
301 67 0.17
302 108 0.27
303 39 0.10
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.28
Consensus pattern (297 bp):
AAAACAAATCCTTAAATGCAATTTGGCTGAGATTCAGATAGATAAGTACAGAAATTTCTTGGAGT
CTCTGTGCAAAAAATCATGAAAACTAAGTCGGGGCCACGGAACGCGATTTTAGACAAAAACCGTG
ATAAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCACAATTAATG
GCAAAATAATCATAAAAAATATACAATTCAATACCAAAAAGATTGAATGGCTTTTCACGCTTCTA
ATATCGCTTTTTTTTCAAATTAATTTCAAATCAAAAC
Done.