Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016486.1 Corchorus olitorius cultivar O-4 contig16519, 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: 4562
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Found at i:631 original size:324 final size:323
Alignment explanation
Indices: 1--2398 Score: 3196
Period size: 324 Copynumber: 7.4 Consensus size: 323
* * * *
1 AGAAATAAATTCCG-AAAAAATTGAAAAAACAATATTCGAAGCGTGAAAAACCTTTAAAATTTTA
1 AGAAATAAATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTT--AATTTTT
*
65 TTTGGTGTTGAATCATATATTTTTTGAGAGTAGTGTGGC--AAAAATGAGAAAATAAGTTTTCGG
64 TTTGGCGTTGAATCATATATTTTTTGAGAGTAGTGTGGCAAAAAAATGAGAAAATAAGTTTTCGG
* *
128 GTCAATTTTTAACCAAAATCGTGTACGTTAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGG
129 GTCAATTTTTAGCCGAAATCGTGTAC--TAACCATCACGGTTTTTTGCTAAAAACGCGTTTC-GG
* * *
193 GCCTCGGCTCAGTTTTGCATGATTTTTGGCATAAACACTCCTTGAAATATCTATATTCATATAAC
191 GCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAAC
* * * * * *
258 CAAATCTCAACAAATTTGGATTTAAGGATTTATTATTACGGGTATCTGAATTATGTTTCGATCTA
256 CAAATCTCAGCCAATTTGGATTTAAGGATTTATTTTTACGAGTATCTGAATTTTGTTTCGATTTA
323 ATT
321 ATT
* *
326 AGAAATAAGTTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGCGAAAAACCCTTAAATTTTTT
1 AGAAATAAATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTT-AA-TTTTT
*
391 TTTGGCGTTGAATCATATATTTTTTGAGAGTAGTGTGG-AAAAAAATGAGAAAATAAGTTTTCGT
64 TTTGGCGTTGAATCATATATTTTTTGAGAGTAGTGTGGCAAAAAAATGAGAAAATAAGTTTTCGG
* * * **
455 GTCAATTTTTAACCGAAATTGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGAGTT
129 GTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGGCC
* * * *
520 CCGGCTCAATTTTGCATTATTTTTGGCAAAAAGACTCCTTGAAATATCTATATAT-ATATAACGA
194 CCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATAT-TCATATAACCA
* * * * *
584 AATCCCAGACAATTTGGATTTATGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAAT
258 AATCTCAGCCAATTTGGATTTAAGGATTTATTTTTACGAGTATCTGAATTTTGTTTCGATTTAAT
649 T
323 T
** * * *
650 AGAAATAAACTTC--AAAAAAA-TGGAAAAACGTTATTGGAAGCATGAAAACCCCTTCAATTTTT
1 AGAAATAAA-TTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTT-AATTTTT
* * * * * *
712 TTTGACGTTGAATTATATATTTTAT-AGAGTATTGTGGCAAAAAAAAAGAGAAGA-AAGTTTTCG
64 TTTGGCGTTGAATCATATATTTTTTGAGAGTAGTGTGGC-AAAAAAATGAGAAAATAAGTTTTCG
* * * *
775 GGTCAACTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACACGTTTCGAGG
128 GGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTCG-GG
** *
840 CCCTAGCTCAGTTTTGCATGACTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACC
192 CCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACC
** *
905 AAATCTCAGCCAATTTAAATTTAGGGATTTATTTTTACGAGTATCTGAATTTTGTTTCGATTTAA
257 AAATCTCAGCCAATTTGGATTTAAGGATTTATTTTTACGAGTATCTGAATTTTGTTTCGATTTAA
970 TT
322 TT
*
972 AGAAATAAATTCGGAAAAAAATTGGAAACACAATATTCGAAGCGTGAAAAACCCTTAATTTTTTT
1 AGAAATAAATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTAATTTTTTT
* * *
1037 TGG-GTTTGAATCATAT-TTTTTT-AGAGTTGTGTAGC-AAAAAATGAGAAAAGAAGTTTTCGGG
66 TGGCG-TTGAATCATATATTTTTTGAGAGTAGTGTGGCAAAAAAATGAGAAAATAAGTTTTCGGG
1098 TCAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGGCCC
130 TCAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGG-CC
* * * * * *
1163 CCGGCTCAGTTTTACATTATTTTTGGCA-AAAAACTCCTTGAAATATCTATATTTATATCACAAA
194 CCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAA
*
1227 ATCTCAGCCAATTTGGATTTAA-GA-TT-TTTTTACGAGAATCTGAATTTTGTTTCGATTTAATT
259 ATCTCAGCCAATTTGGATTTAAGGATTTATTTTTACGAGTATCTGAATTTTGTTTCGATTTAATT
* * * * *
1289 AGAAATAAATTCAGAAAAAAA-TGGAAAAACGATATTTGGAAGCATGAAAACCCCTTTAA-TTTT
1 AGAAATAAATTCGGAAAAAAATTGGAAAAACAATA-TTCGAAGCGTGAAAAACCC-TTAATTTTT
* * * * *
1352 TTTGGCGTTGAATTATATATTTTGT-AGAATTGTGTGGCAAAAAAAT--G-AAATAAGTTTTTGG
64 TTTGGCGTTGAATCATATATTTTTTGAGAGTAGTGTGGCAAAAAAATGAGAAAATAAGTTTTCGG
* *
1413 GTAAACTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTTGCTAAAAACGCGTTTCGGGG
129 GTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTTTTGCTAAAAACGCGTTTC-GGG
*
1478 CCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCGTTGAAATATCTATATTCATATAACC
192 CCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACC
* *
1543 AAATCTCAGCCAATTTGGATTTAAGGATTTATTTTTACGGGTATCTGAATTTTGTTTCGATCTAA
257 AAATCTCAGCCAATTTGGATTTAAGGATTTATTTTTACGAGTATCTGAATTTTGTTTCGATTTAA
1608 TT
322 TT
* * *
1610 AAAAATAAATTCGGAAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAACCCTT--TCTTTTT
1 AGAAATAAATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTAAT-TTTTT
* * *
1673 TTGGGGTTGAATCATATATTTTTTTG-GAGTTGTGTGGCAAACAAAATGAGAAAATAAGTTTTCA
65 TTGGCGTTGAATCATATA-TTTTTTGAGAGTAGTGTGGCAAA-AAAATGAGAAAATAAGTTTTCG
*
1737 GGTCAATTTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTCAGGG
128 GGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTC-GGG
** * * * * * *
1802 CTTCGGCTCAGTTTTGCTTGATTTTTGGCACAAACAATCCTTGAAATATCTATATTCACATAACT
192 CCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACC
* * * *
1867 AAATCTCAGCCAATTTGGATATAAGGATTTATTTTTACGGGTAGT-TTAATTTTGTTTCGATCTA
257 AAATCTCAGCCAATTTGGATTTAAGGATTTATTTTTACGAGTA-TCTGAATTTTGTTTCGATTTA
1931 ATT
321 ATT
*
1934 GGAAATAAATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTAAATTTTTT
1 AGAAATAAATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTT-AATTTTTT
* * * * *
1999 TTGGCGTTGAATCATATATTTTTTGCGAGTACTGTGGCAAATAAATGAGAAAAAAAGTTTTCGAG
65 TTGGCGTTGAATCATATATTTTTTGAGAGTAGTGTGGCAAAAAAATGAGAAAATAAGTTTTCGGG
* * * *
2064 TCAATTTTTAGCCGAAATTGTGTACAAACCATCACAGTTTTTTGCTAAAAACGCGTTTCAGAGCC
130 TCAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTC-GGGCC
* * * *
2129 TCGTCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCCTGAAATATCTATATTCATATAACTAA
194 CCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAA
* * * * * *
2194 ATCTCAGCAAATTTGGATTTAAAGATTTCTTTTTACGAGCATCTTAAATTTGTTTCGATTTAATT
259 ATCTCAGCCAATTTGGATTTAAGGATTTATTTTTACGAGTATCTGAATTTTGTTTCGATTTAATT
* * * * * **
2259 AGAAATAAATTCGGAAAATAATTGGAAAAACGATATTGGAAGCGTGATACACCCTTTCTTTTTTT
1 AGAAATAAATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTAATTTTTTT
* * * **
2324 TGGGGTTCAATCATATATTTTTTTAGAGTTCTGTGGCAAAAAAATGAGAAAATAAGTTTTCGGGT
66 TGGCGTTGAATCATATATTTTTTGAGAGTAGTGTGGCAAAAAAATGAGAAAATAAGTTTTCGGGT
2389 CAATTTTTAG
131 CAATTTTTAG
2399 TTTTGCATGA
Statistics
Matches: 1834, Mismatches: 197, Indels: 85
0.87 0.09 0.04
Matches are distributed among these distances:
316 59 0.03
317 141 0.08
318 79 0.04
319 11 0.01
320 101 0.06
321 274 0.15
322 201 0.11
323 35 0.02
324 421 0.23
325 350 0.19
326 114 0.06
327 48 0.03
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (323 bp):
AGAAATAAATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTAATTTTTTT
TGGCGTTGAATCATATATTTTTTGAGAGTAGTGTGGCAAAAAAATGAGAAAATAAGTTTTCGGGT
CAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGGCCCC
GGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAAT
CTCAGCCAATTTGGATTTAAGGATTTATTTTTACGAGTATCTGAATTTTGTTTCGATTTAATT
Found at i:1960 original size:11 final size:11
Alignment explanation
Indices: 1930--1963 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1920 GTTTCGATCT
*
1930 AATTGGAAATA
1 AATTGGAAAAA
1941 AATTCGGAAAAA
1 AATT-GGAAAAA
1953 AATTGGAAAAA
1 AATTGGAAAAA
1964 CAATATTCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.59, C:0.03, G:0.18, T:0.21
Consensus pattern (11 bp):
AATTGGAAAAA
Found at i:2629 original size:261 final size:261
Alignment explanation
Indices: 2136--2659 Score: 771
Period size: 261 Copynumber: 2.0 Consensus size: 261
2126 GCCTCGTCTC
* * * *
2136 AGTTTTGCATGATTTTTGGCAGAAAGACTCCCTGAAATATCTATATTCATATAACTAAATCTCAG
1 AGTTTTGCATGATTTTTGGCAGAAACACTCACTGAAATATCTATATTCATAAAACCAAATCTCAG
* * *
2201 CAAATTTGGATTTAAAGATTTCTTTTTACGAGCATCTTAAATTTGTTTCGATTTAATTAGAAATA
66 CAAATTTGGATTTAAAGATTTATTTTTACGAGCATCTGAAATTTGTTTCGATCTAATTAGAAATA
* * * * * ** *
2266 AATTCGGAAAATAATTGGAAAAACGATATTGGAAGCGTGATACACCCTTTCTTTTTTTTGGGGTT
131 AATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTAATTTTTTTTGGCGTT
* * * * *
2331 CAATCATATATTTTTTTAGAGTTCTGTGGCAAAAAAATGAGAAAATAAGTTTTCGGGTCAATTTT
196 CAATCATATATTTTTTGAGAGTACTGTGGCAAAAAAATGAGAAAAAAAGTTTTCGAGTCAATCTT
2396 T
261 T
*
2397 AGTTTTGCATGATTTTTGGCAGAAACACTCATTGAAATATCTATATTCATAAAACCAAATCTCAG
1 AGTTTTGCATGATTTTTGGCAGAAACACTCACTGAAATATCTATATTCATAAAACCAAATCTCAG
* * * * *
2462 CCAATTTGGATTTAAGGATTTATTTTTACGGGTATCTGAATTTTGTTTCGATCTAATTAGAAATA
66 CAAATTTGGATTTAAAGATTTATTTTTACGAGCATCTGAAATTTGTTTCGATCTAATTAGAAATA
*
2527 AATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTTAAAAACCCTTAAATTTTTTTTGGCGT
131 AATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTT-AATTTTTTTTGGCGT
* *
2592 TGAATCATATATTTTTTGAGAGTAGTGTGGC-AAAAAATGAGAAAAAAAGTTTTCGAGTCAATCT
195 TCAATCATATATTTTTTGAGAGTACTGTGGCAAAAAAATGAGAAAAAAAGTTTTCGAGTCAATCT
2656 TT
260 TT
2658 AG
1 AG
2660 CCGAAATCGT
Statistics
Matches: 233, Mismatches: 29, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
261 194 0.83
262 39 0.17
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (261 bp):
AGTTTTGCATGATTTTTGGCAGAAACACTCACTGAAATATCTATATTCATAAAACCAAATCTCAG
CAAATTTGGATTTAAAGATTTATTTTTACGAGCATCTGAAATTTGTTTCGATCTAATTAGAAATA
AATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTAATTTTTTTTGGCGTT
CAATCATATATTTTTTGAGAGTACTGTGGCAAAAAAATGAGAAAAAAAGTTTTCGAGTCAATCTT
T
Found at i:3017 original size:324 final size:322
Alignment explanation
Indices: 2397--4562 Score: 3070
Period size: 324 Copynumber: 6.7 Consensus size: 322
2387 GTCAATTTTT
* * *
2397 AGTTTTGCATGATTTTTGGCAGAAACACTCATTGAAATATCTATATTCATAAAACCAAATCTCAG
1 AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAG
* * * * *
2462 CCAATTTGGATTTAAGGATTTATTTTTACGGGTATCTGAATTTTGTTTCGATCTAATTAGAAATA
66 CAAATTTGGATTTAAGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATA
* *
2527 AATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTTAAAAACCCTTAAATTTTTTTTGGCGT
131 AATTCGG-AAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTT-TATTTTTTTTGGCGT
* *
2592 TGAATCATATATTTTTTGAGAGTAGTGTGGC-AAAAAATGAGAAAAAAAGTTTTCGAGTCAATCT
194 TGAATCATATATTTTTTGAGAGTTGTGTGGCAAAAAAATGAG-AAAAAAGTTTTCGAGTCAATTT
* * *
2656 TTAGCCGAAATCGTGTACAAACCATCACGGATTTTTGCTAAAAACGCATTTCGGGACCCCGGCTC
258 TTAGCCGAAATCGTGTACAAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGCTC
* *
2721 AGTTTTGCATGATTTTTTGGCAGAAAGACTCCCTGAAATATCTATATTCATATAACCAAGTCTCA
1 AGTTTTGCATGA-TTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCA
* *
2786 GCAAATTTGGATTTAAGGATTTCTTTTTACGAGCATCTGAAATTTGTTTCGATCTAATTAGAAAT
65 GCAAATTTGGATTTAAGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAAT
* * * *
2851 AAATTCGGAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAACCCTTTCTTTTTTTTGGGGTT
130 AAATTCGGAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTTATTTTTTTTGGCGTT
*
2916 GAATCATATATTTTTTGAGAGTTGTGTGGCAAAAAAATGAGAAAATAAGTTTTCGGGTCAATTTT
195 GAATCATATATTTTTTGAGAGTTGTGTGGCAAAAAAATGAGAAAA-AAGTTTTCGAGTCAATTTT
* * *
2981 TAACCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGGGCCTCGGCTC
259 TAGCCGAAATCGTGTACAAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGCTC
*
3045 AGTTTTGCATGATTTTTGGCAGAAACACTCCTTGAAATATCTATATTCATATAACCAAATCTCAG
1 AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAG
* * * * * *
3110 CCAATTTGGATTTAAGGATTTATTTTTACGGGTATTTGAATTTTGTTTCGATCTAATTAGAAATA
66 CAAATTTGGATTTAAGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATA
*
3175 AATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTAAATTTTTTTTGGCGT
131 AATTCGG-AAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTT-TATTTTTTTTGGCGT
** *
3240 TGAATCATATATTTTTTGAGAGTACTGTGGCAAATAAATGAGTAAAAAAGTTTTCGAGTCAATTT
194 TGAATCATATATTTTTTGAGAGTTGTGTGGCAAAAAAATGAG-AAAAAAGTTTTCGAGTCAATTT
3305 TTAGCCGAAATCGTGTACAAACCATCACGGTTTTTTGCTAAAAACGCGTTTC-GGGCCCCTGGCT
258 TTAGCCGAAATCGTGTACAAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGGGCCCC-GGCT
3369 C
322 C
*
3370 AGTTTTGCATGATTTTTGGCAGAAAAACTCCTTGAAATATCTATATTCATATAACCAAATCTCAG
1 AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAG
* * *
3435 CAAATTTCGATTTAAGGAATTC-TTTTACGAGCATCTTAATTTTGTTTCGATTTAATTAGAAATA
66 CAAATTTGGATTTAAGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATA
* * *
3499 AATTCGGAAAACAATTGGAAAAACAATATTCGAAGAGTGAAAAAACCCTTCA-TTTTTTTGGCAT
131 AATTCGGAAAA-AATTGGAAAAACAATATTCGAAGCGTG-AAAAACCCTTTATTTTTTTTGGCGT
* ** * * * * *
3563 TGAATTATATATTTCGT-AGAGTTGTGTGGAAAAAAAAATTAGAATAAAGTTTTCGGGTCAACTT
194 TGAATCATATATTTTTTGAGAGTTGTGTGG-CAAAAAAATGAGAAAAAAGTTTTCGAGTCAATTT
*** * *
3627 TTAGCCGAAATCGTGTATGCACCATCACGGTTTTTGGCTAAAAAAC-CGTTTCGGGGCTCCGGCT
258 TTAGCCGAAATCGTGTACAAACCATCACGGTTTTTTGCT-AAAAACGCGTTTCGGGGCCCCGGCT
3691 C
322 C
* * *
3692 AATATTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATACATATAACCAAATCTCAG
1 AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAG
* * *
3757 CAAATTTCGATTTAAGGATTTCTTTTTACGAGCATCTTAATTTTGTTTCGATTTAATTAGAAAGA
66 CAAATTTGGATTTAAGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATA
* *
3822 AATTCGGAAAAAATTGGAAAAACAATATTCGAAGCATGAAAAACCCTTAAATTTTTTTTGGCGTT
131 AATTCGGAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTT-TATTTTTTTTGGCGTT
* * * *
3887 GAATCATATATGTTTTAAGAGTAGTGTGGC-AAAAAATGAGAAAAAAAGTTTTCGAGACAATTTT
195 GAATCATATATTTTTTGAGAGTTGTGTGGCAAAAAAATGAG-AAAAAAGTTTTCGAGTCAATTTT
* *
3951 TAGCCGAAATCGTGTATAAACCATCACGGTTTTTTGCTAAAAACGCGTTTC-GGG---AGGCTC
259 TAGCCGAAATCGTGTACAAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGCTC
*
4011 AATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAG
1 AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAG
* * *
4076 CAAATTTGGATTTAATGATTTCTTTTTACGAGCATCTTAAATTTGTTTCGATTTAATTAGAAATA
66 CAAATTTGGATTTAAGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATA
** * * *
4141 AATTCGGAAAAAAAATTGGAAAAACTTTATTAGAAGCGTGAAAAA-CCTTTATTTTTTTGGGGGT
131 AATTCGG--AAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTTATTTTTTTTGGCGT
* *
4205 TGAATCATATATTTTTTTAGAGTTGTGTGGCAAAAAAATGAGAAAAGAAGTTTTCGGGTCAATTT
194 TGAATCATATATTTTTTGAGAGTTGTGTGGCAAAAAAATGAGAAAA-AAGTTTTCGAGTCAATTT
** *
4270 TTATTCGAAATCGTGTACAAACCATCACTGTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGCTC
258 TTAGCCGAAATCGTGTACAAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGCTC
* * * *
4335 AGTTTTGCATTATTTTTGGCA-AAAGGACTCCTTGAAATATATATATTTATATAACAAAATCTCA
1 AGTTTTGCATGATTTTTGGCAGAAA-GACTCCTTGAAATATCTATATTCATATAACCAAATCTCA
* * * *
4399 ACCAATTTGGATTTAAGGATTTCTTTTTACGAGAATCTGAATTTTGTTTCAATTTAATTAGAAAT
65 GCAAATTTGGATTTAAGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAAT
*** * * * * *
4464 AAATTC--AAAAAAAAAGAGAAAACGATATTGGAAGCTTG-AAAACACTTTCAATTTTTTTTTAG
130 AAATTCGGAAAAAATTGGA-AAAACAATATTCGAAGCGTGAAAAACCCTTT--A-TTTTTTTTGG
* *
4526 CGTTGAATTATATATTTTAT-AGAGTTGTGTGGCAAAA
191 CGTTGAATCATATATTTTTTGAGAGTTGTGTGGCAAAA
Statistics
Matches: 1662, Mismatches: 148, Indels: 65
0.89 0.08 0.03
Matches are distributed among these distances:
319 180 0.11
320 90 0.05
321 65 0.04
322 201 0.12
323 369 0.22
324 423 0.25
325 330 0.20
326 4 0.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (322 bp):
AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAG
CAAATTTGGATTTAAGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATA
AATTCGGAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTTATTTTTTTTGGCGTTG
AATCATATATTTTTTGAGAGTTGTGTGGCAAAAAAATGAGAAAAAAGTTTTCGAGTCAATTTTTA
GCCGAAATCGTGTACAAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGCTC
Found at i:3233 original size:910 final size:910
Alignment explanation
Indices: 1487--3308 Score: 2802
Period size: 910 Copynumber: 2.0 Consensus size: 910
1477 GCCCCGGCTC
* * *
1487 AGTTTTGCATGATTTTTGGCAGAAAGACTCGTTGAAATATCTATATTCATATAACCAAATCTCAG
1 AGTTTTGCATGATTTTTGGCAGAAACACTCATTGAAATATCTATATTCATAAAACCAAATCTCAG
1552 CCAATTTGGATTTAAGGATTTATTTTTACGGGTATCTGAATTTTGTTTCGATCTAATTAAAAATA
66 CCAATTTGGATTTAAGGATTTATTTTTACGGGTATCTGAATTTTGTTTCGATCTAATTAAAAATA
* *
1617 AATTCGGAAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAACCCTTTCTTTTTTTGGGGTTG
131 AATTCGGAAAAAAATTGGAAAAACAATATTAGAAGCGTGAAAAACCCTTTCTTTTTTTGGCGTTG
* * *
1682 AATCATATATTTTTTTGGAGTTGTGTGGCAAACAAAATGAGAAAATAAGTTTTCAGGTCAATTTT
196 AATCATATATTTTTTTGGAGTAGTGTGGCAAACAAAATGAGAAAAAAAGTTTTCAGGTCAATCTT
* * * **
1747 TAACCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTCAGGGCTTCGGCTCA
261 TAACCGAAATCGTGTACAAACCATCACGGATTTTTGCTAAAAACGCATTTCAGGGCCCCGGCTCA
* * *
1812 GTTTTGCTTGATTTTTGGCACAAACAATCCTTGAAATATCTATATTCACATAACTAAATCTCAGC
326 GTTTTGCATGATTTTTGGCACAAACAATCCCTGAAATATCTATATTCACATAACCAAATCTCAGC
* * * * * *
1877 CAATTTGGATATAAGGATTTATTTTTACGGGTAGTTTAATTTTGTTTCGATCTAATTGGAAATAA
391 AAATTTGGATATAAGGATTTATTTTTACGAGCAGTTGAAATTTGTTTCGATCTAATTAGAAATAA
*
1942 ATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTAAATTTTTTTTGGCGTT
456 ATTCGGAAAAAAATTGGAAAAACAATATTAGAAGCGTGAAAAACCCTTAAATTTTTTTTGGCGTT
* *
2007 GAATCATATATTTTTTGCGAGTACTGTGGCAAATAAATGAGAAAAAAAGTTTTCGAGTCAATTTT
521 GAATCATATATTTTTTGAGAGTACTGTGGCAAAAAAATGAGAAAAAAAGTTTTCGAGTCAATTTT
* * *
2072 TAGCCGAAATTGTGTACAAACCATCACAGTTTTTTGCTAAAAACGCGTTTCAGAGCCTCGTCTCA
586 TAACCGAAATCGTGTACAAACCATCACAGTTTTTTGCTAAAAACGCGTTTCAGAGCCTCGGCTCA
* *
2137 GTTTTGCATGATTTTTGGCAGAAAGACTCCCTGAAATATCTATATTCATATAACTAAATCTCAGC
651 GTTTTGCATGATTTTTGGCAGAAACACTCCCTGAAATATCTATATTCATATAACCAAATCTCAGC
* *
2202 AAATTTGGATTTAAAGATTTCTTTTTACGAGCATCTTAAATTTGTTTCGATTTAATTAGAAATAA
716 AAATTTGGATTTAAAGATTTATTTTTACGAGCATCTTAAATTTGTTTCGATCTAATTAGAAATAA
* * * * * ** *
2267 ATTCGGAAAATAATTGGAAAAACGATATTGGAAGCGTGATACACCCTTTCTTTTTTTTGGGGTTC
781 ATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTAATTTTTTTTGGCGTTC
* * *
2332 AATCATATATTTTTTTAGAGTTCTGTGGCAAAAAAATGAG-AAAATAAGTTTTCGGGTCAATTTT
846 AATCATATATTTTTTGAGAGTACTGTGGCAAAAAAATGAGTAAAA-AAGTTTTCGAGTCAATTTT
2396 T
910 T
2397 AGTTTTGCATGATTTTTGGCAGAAACACTCATTGAAATATCTATATTCATAAAACCAAATCTCAG
1 AGTTTTGCATGATTTTTGGCAGAAACACTCATTGAAATATCTATATTCATAAAACCAAATCTCAG
*
2462 CCAATTTGGATTTAAGGATTTATTTTTACGGGTATCTGAATTTTGTTTCGATCTAATTAGAAATA
66 CCAATTTGGATTTAAGGATTTATTTTTACGGGTATCTGAATTTTGTTTCGATCTAATTAAAAATA
* *
2527 AATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTTAAAAACCCTTAAAT-TTTTTTTGGCG
131 AATTCGGAAAAAAATTGGAAAAACAATATTAGAAGCGTGAAAAACCCTT---TCTTTTTTTGGCG
2591 TTGAATCATATA-TTTTTTGAGAGTAGTGTGGC-AA-AAAATGAGAAAAAAAGTTTTC-GAGTCA
193 TTGAATCATATATTTTTTTG-GAGTAGTGTGGCAAACAAAATGAGAAAAAAAGTTTTCAG-GTCA
*
2652 ATCTTTAGCCGAAATCGTGTACAAACCATCACGGATTTTTGCTAAAAACGCATTTC-GGGACCCC
256 ATCTTTAACCGAAATCGTGTACAAACCATCACGGATTTTTGCTAAAAACGCATTTCAGGG-CCCC
* * * * *
2716 GGCTCAGTTTTGCATGATTTTTTGGCAGAAAGACTCCCTGAAATATCTATATTCATATAACCAAG
320 GGCTCAGTTTTGCATGA-TTTTTGGCACAAACAATCCCTGAAATATCTATATTCACATAACCAAA
* *
2781 TCTCAGCAAATTTGGATTTAAGGATTTCTTTTTACGAGCA-TCTGAAATTTGTTTCGATCTAATT
384 TCTCAGCAAATTTGGATATAAGGATTTATTTTTACGAGCAGT-TGAAATTTGTTTCGATCTAATT
* **
2845 AGAAATAAATTCGG-AAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAACCCTT-TCTTTTTT
448 AGAAATAAATTCGGAAAAAAATTGGAAAAACAATATTAGAAGCGTGAAAAACCCTTAAATTTTTT
* ** * *
2908 TTGGGGTTGAATCATATATTTTTTGAGAGTTGTGTGGCAAAAAAATGAGAAAATAAGTTTTCGGG
513 TTGGCGTTGAATCATATATTTTTTGAGAGTACTGTGGCAAAAAAATGAGAAAAAAAGTTTTCGAG
* * * *
2973 TCAATTTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGGGCC
578 TCAATTTTTAACCGAAATCGTGTACAAACCATCACAGTTTTTTGCTAAAAACGCGTTTCAGAGCC
*
3038 TCGGCTCAGTTTTGCATGATTTTTGGCAGAAACACTCCTTGAAATATCTATATTCATATAACCAA
643 TCGGCTCAGTTTTGCATGATTTTTGGCAGAAACACTCCCTGAAATATCTATATTCATATAACCAA
* * * * *
3103 ATCTCAGCCAATTTGGATTTAAGGATTTATTTTTACGGGTAT-TTGAATTTTGTTTCGATCTAAT
708 ATCTCAGCAAATTTGGATTTAAAGATTTATTTTTACGAGCATCTT-AAATTTGTTTCGATCTAAT
3167 TAGAAATAAATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTAAATTTTT
772 TAGAAATAAATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTT-AATTTTT
* *
3232 TTTGGCGTTGAATCATATATTTTTTGAGAGTACTGTGGCAAATAAATGAGTAAAAAAGTTTTCGA
836 TTTGGCGTTCAATCATATATTTTTTGAGAGTACTGTGGCAAAAAAATGAGTAAAAAAGTTTTCGA
3297 GTCAATTTTT
901 GTCAATTTTT
3307 AG
1 AG
3309 CCGAAATCGT
Statistics
Matches: 827, Mismatches: 74, Indels: 22
0.90 0.08 0.02
Matches are distributed among these distances:
908 2 0.00
909 294 0.36
910 376 0.45
911 121 0.15
912 33 0.04
913 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (910 bp):
AGTTTTGCATGATTTTTGGCAGAAACACTCATTGAAATATCTATATTCATAAAACCAAATCTCAG
CCAATTTGGATTTAAGGATTTATTTTTACGGGTATCTGAATTTTGTTTCGATCTAATTAAAAATA
AATTCGGAAAAAAATTGGAAAAACAATATTAGAAGCGTGAAAAACCCTTTCTTTTTTTGGCGTTG
AATCATATATTTTTTTGGAGTAGTGTGGCAAACAAAATGAGAAAAAAAGTTTTCAGGTCAATCTT
TAACCGAAATCGTGTACAAACCATCACGGATTTTTGCTAAAAACGCATTTCAGGGCCCCGGCTCA
GTTTTGCATGATTTTTGGCACAAACAATCCCTGAAATATCTATATTCACATAACCAAATCTCAGC
AAATTTGGATATAAGGATTTATTTTTACGAGCAGTTGAAATTTGTTTCGATCTAATTAGAAATAA
ATTCGGAAAAAAATTGGAAAAACAATATTAGAAGCGTGAAAAACCCTTAAATTTTTTTTGGCGTT
GAATCATATATTTTTTGAGAGTACTGTGGCAAAAAAATGAGAAAAAAAGTTTTCGAGTCAATTTT
TAACCGAAATCGTGTACAAACCATCACAGTTTTTTGCTAAAAACGCGTTTCAGAGCCTCGGCTCA
GTTTTGCATGATTTTTGGCAGAAACACTCCCTGAAATATCTATATTCATATAACCAAATCTCAGC
AAATTTGGATTTAAAGATTTATTTTTACGAGCATCTTAAATTTGTTTCGATCTAATTAGAAATAA
ATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTAATTTTTTTTGGCGTTC
AATCATATATTTTTTGAGAGTACTGTGGCAAAAAAATGAGTAAAAAAGTTTTCGAGTCAATTTTT
Done.