Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015853.1 Corchorus olitorius cultivar O-4 contig15886, 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: 5904
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:2134 original size:761 final size:756
Alignment explanation
Indices: 677--2193 Score: 2501
Period size: 761 Copynumber: 2.0 Consensus size: 756
667 CCGAAAATCT
* * * *
677 TGTACTAACCCTTCATGGTTTTTGGGCTAAAAACGCGTTTCGGGGCCCTGGCTCAGTTTTGCATG
1 TGTACTAACCCATCATGGTTTTGGGGCTAAAAACCCGTTTCGGGGCCCCGGCTCAGTTTTGCATG
*
742 ATTTTTGGCAGATAGAATCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCCCTCAGCCAC
66 ATTTTTGGCAGAAAGAATCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCCCTCAGCCAC
807 ATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAAAATTGTTTCGATTTAATTAGAAATAGATT
131 ATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAAAATTGTTTCGATTTAATTAGAAATAGATT
872 AAGAATAAAAATAGAAAAATAATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTGCGTTGAAT
196 AAGAATAAAAATAGAAAAATAATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTGCGTTGAAT
* * *
937 TCTGTACTTTTTGCCGAAAATATAAATTTTTTGCATGATTTTTGATGTAAATACTCCTTGAAATA
261 TCTGTACTTTTTACCGAAAATATAAATTTTTTGCAAGATTTTTGACGTAAATACTCCTTGAAATA
* *
1002 TCTATATTCATCAAACAAACTCCCAGCGACGTACTATTTAAGAATTTGTTTTTACGAGCATCTTA
326 TCTATATTCATCAAACAAAATCCCAGCAACGTACTATTTAAGAATTTGTTTTTACGAGCATCTTA
*
1067 ATCTTGTTTCAATTTAATTAAAAATTAATTCGGAAAATAAATGGAAAAACGATATTAGAAGCATG
391 ATCTTGTTTCAATTTAATTAAAAATTAATTCAGAAAATAAATGGAAAAACGATATTAGAAGCATG
* *
1132 AAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTTGCAAAAAATTG
456 AAAAGCCCGTCAATCTTCTTGGCGTTGAATTATATATATTTTCTGAGTATTGTTGCAAAAAATTG
*
1197 AGAAAAAACTTTTCCGATCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGTCTAA
521 AGAAAAAACTTTTCCGATCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAA
1262 AAACGCGTTCCCAAGTCCCGACCCAATTTTGCATAATTTTTGGCCCAAAGACTCCTTGAAATATC
586 AAACGCGTTCCCAAGTCCCGACCCAATTTTGCATAATTTTTGGCCCAAAGACTCCTTGAAATATC
*
1327 TATATTCATCAAACCAAATGCCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAAT
651 TATATTCATCAAACCAAATGCCAGCCACAATGGATATAAGGATTTGTTTTTACGAGCATCTGAAT
1392 CTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAATTGG
716 CTTGTTTCAATTTAATTAGAAATTAATTCGG-AAAAAATTGG
*
1434 TGTACTAA-CCATCATGGTTTTGGGGCTAAAAACCCGTTTCGGGGGCCCCGGTTCAGTTTTGCAT
1 TGTACTAACCCATCATGGTTTTGGGGCTAAAAACCCGTTTC-GGGGCCCCGGCTCAGTTTTGCAT
* *
1498 GATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCTCTCAGCCA
65 GATTTTTGGCAGAAAGAATCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCCCTCAGCCA
* * *
1563 CATTAGATTTAAGGATTTGTTTTTACGAGCATTTGAAATTTTTTTCGATTTAATTAGAAATAGAT
130 CATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAAAATTGTTTCGATTTAATTAGAAATAGAT
**
1628 TCGGAA-AAAAATAGAAAAATAATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTGCGTTGAA
195 TAAGAATAAAAATAGAAAAATAATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTGCGTTGAA
* * ***
1692 TTCTGTATTTTTTACCTAAAATACTTTTTTTTGATTTTGCAAGATTTTTGACGTAAATACTCCTT
260 TTCTGTACTTTTTACCGAAAATA---TAAATT--TTTTGCAAGATTTTTGACGTAAATACTCCTT
* *
1757 GAAATATCTATATTCATCAAACAAAATCCCAGCAACGT-TTGATTTAAGTATTTGTTTTTACGAG
320 GAAATATCTATATTCATCAAACAAAATCCCAGCAACGTACT-ATTTAAGAATTTGTTTTTACGAG
1821 CATCTTAATCTTGTTTCAATTTAATTAAAAATTAATTCAGAAAATAAATGGAAAAGA-GATATTA
384 CATCTTAATCTTGTTTCAATTTAATTAAAAATTAATTCAGAAAATAAATGGAAAA-ACGATATTA
*
1885 GAAGCGTGAAAAGCCCGTCAATCTTCTTGGCGTTGAATTATATA-ATTTTCTGAGTATTGTTGCA
448 GAAGCATGAAAAGCCCGTCAATCTTCTTGGCGTTGAATTATATATATTTTCTGAGTATTGTTGCA
* * *
1949 AAAAATTGAGAAAAACCTTTTCCGATCAGTTTTTCGCCGAAATCGTGTACTAACCATCACTGTTT
513 AAAAATTGAGAAAAAACTTTTCCGATCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTT
* * * *
2014 TTGGC-AAAAATCGTGTTCCCGAG-CCTCGACTCAATTTTGCATGATATTTTT-GCGCAAAGACT
578 TTGGCTAAAAA-CGCGTTCCCAAGTCC-CGACCCAATTTTGCAT-A-ATTTTTGGCCCAAAGACT
*
2076 CCTTGAAATATCTATATTCATCAAACCAAATGTCAGCCACAATGGATATAAGGATTTGTTTTTAC
639 CCTTGAAATATCTATATTCATCAAACCAAATGCCAGCCACAATGGATATAAGGATTTGTTTTTAC
*
2141 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATTGG
704 GAGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAATTGG
2194 AAAAATCATA
Statistics
Matches: 708, Mismatches: 40, Indels: 21
0.92 0.05 0.03
Matches are distributed among these distances:
756 107 0.15
757 157 0.22
759 10 0.01
760 121 0.17
761 306 0.43
762 7 0.01
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (756 bp):
TGTACTAACCCATCATGGTTTTGGGGCTAAAAACCCGTTTCGGGGCCCCGGCTCAGTTTTGCATG
ATTTTTGGCAGAAAGAATCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCCCTCAGCCAC
ATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAAAATTGTTTCGATTTAATTAGAAATAGATT
AAGAATAAAAATAGAAAAATAATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTGCGTTGAAT
TCTGTACTTTTTACCGAAAATATAAATTTTTTGCAAGATTTTTGACGTAAATACTCCTTGAAATA
TCTATATTCATCAAACAAAATCCCAGCAACGTACTATTTAAGAATTTGTTTTTACGAGCATCTTA
ATCTTGTTTCAATTTAATTAAAAATTAATTCAGAAAATAAATGGAAAAACGATATTAGAAGCATG
AAAAGCCCGTCAATCTTCTTGGCGTTGAATTATATATATTTTCTGAGTATTGTTGCAAAAAATTG
AGAAAAAACTTTTCCGATCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAA
AAACGCGTTCCCAAGTCCCGACCCAATTTTGCATAATTTTTGGCCCAAAGACTCCTTGAAATATC
TATATTCATCAAACCAAATGCCAGCCACAATGGATATAAGGATTTGTTTTTACGAGCATCTGAAT
CTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAATTGG
Found at i:2313 original size:323 final size:325
Alignment explanation
Indices: 1735--2551 Score: 936
Period size: 323 Copynumber: 2.5 Consensus size: 325
1725 ATTTTGCAAG
* * * ** * * *
1735 ATTTTTGACGTAAATACTCCTTGAAATATCTATATTCATCAAACAAAATCCCAGCAACGTTTGAT
1 ATTTTTG-CGAAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCCACATTAGAT
* * * * *
1800 TTAAGTATTTGTTTTTACGAGCATCTTAATCTTGTTTCAATTTAATTAAAAATTAATTCAGAAAA
65 TTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAA
* * *
1865 TAAATGGAAAAGA-GATATTAGAAGCGTGAAAAGCCCGTCAATCTTCTTGGCGTTGAATTATATA
130 -AAATGGAAAA-ATGATATTAAAAGCGTGAAAAGACCATCAATCTTCTTGGCGTTGAATTATATA
* * * ** * * *
1929 ATTTTCTGAGTATTGTTGCAAAAAATTGAGAAAAACCTTTTCCGATCAGTTTTTCGCCG-AAATC
193 ATTTTCTGAGTATTGTGGCAAAAAAATCAGAAAAAAATTCTCCGATCAGATTTTAGCCGAAAATC
* *
1993 GTGTACTAACCATCACT-GTTTTT-GGC-AAAAATCGTG-TTCCCGAGCCTCGACTCAATTTTGC
258 GTGTACTAACCATCA-TGGTTTTTGGGCTAAAAA-CGTGTTTCCCGAGCCCCGACTCAATTTAGC
2054 ATGAT
321 ATGAT
* * * *
2059 ATTTTTGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCCACAATGGATA
1 ATTTTTGCGAAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCCACATTAGATT
2124 TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAA
66 TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAA
* * * *
2189 ATTGGAAAAATCATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGTTC-TTGAATTATAT-AT
131 AATGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTCTTG-GCGTTGAATTATATAAT
*
2252 TTCTCTGAGTATTGTGGCAAAAAAATCAGAAATAAAAATTCT-GGATCAGATTTTAGCCGAAAAT
195 TT-TCTGAGTATTGTGGCAAAAAAATCAG-AA-AAAAATTCTCCGATCAGATTTTAGCCGAAAAT
* ** * * *
2316 CGTGTACTAACCTTCATGGTTTTTGGGCTAAAAACGTGTTTCGGGGGCCCCGGCTCAGTTTAGCA
257 CGTGTACTAACCATCATGGTTTTTGGGCTAAAAACGTGTTTCCCGAGCCCCGACTCAATTTAGCA
2381 TGAT
322 TGAT
* * * *
2385 -TTTTGGCAAAAAGACTCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCCCTCAGCCACA
1 ATTTTTGCGAAAAGACTCCTTGAAATATCTATATTCATCAAACCAA----ATG---TCAGCCACA
* **
2449 TTAGATTTAAGGATTTGTTTTTACAAGCATCTGAAAATTGTTTCGATTTAATTAGAAA-TAGATT
59 TTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA-ATT
* * *
2513 CGGAATAAAAATAGAAAAATGATATTTAAAGCGAGAAAA
123 CGGAA-AAAAATGGAAAAATGATATTAAAAGCGTGAAAA
2552 TATTTCAATT
Statistics
Matches: 419, Mismatches: 55, Indels: 29
0.83 0.11 0.06
Matches are distributed among these distances:
321 5 0.01
322 74 0.18
323 125 0.30
324 38 0.09
325 48 0.11
326 28 0.07
329 2 0.00
331 2 0.00
332 69 0.16
333 28 0.07
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (325 bp):
ATTTTTGCGAAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCCACATTAGATT
TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAA
AATGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTCTTGGCGTTGAATTATATAATT
TTCTGAGTATTGTGGCAAAAAAATCAGAAAAAAATTCTCCGATCAGATTTTAGCCGAAAATCGTG
TACTAACCATCATGGTTTTTGGGCTAAAAACGTGTTTCCCGAGCCCCGACTCAATTTAGCATGAT
Found at i:2832 original size:209 final size:209
Alignment explanation
Indices: 2439--2898 Score: 669
Period size: 209 Copynumber: 2.2 Consensus size: 209
2429 ATCTCAGGCC
*
2439 CTCAGCCACATTA-GATTTAAGGATTTG-TTTTTACAAGCATCTGAAAATTGTTTCGATTTAATT
1 CTCAGCCAC-GTACGATTTAAGGATTTGTTTTTTACAAGCATCTGAAAATTGTTTCGATTTAATT
*
2502 AGAAATAGATTCGGAATAAAAATAGAAAAATGATATTTAAAGCGAGAAAATATTTCAATTTTTTT
65 AGAAATAGATTCGGAATAAAAATAGAAAAATGATATTTAAAACGAGAAAATATTTCAATTTTTTT
2567 TGGTTGAATTCTGTATTTTTTTGCCAATTTTTTTTTTGCATGATTTTTGACGTAAATACTCCTTG
130 TGGTTGAATTCTGTATTTTTTT-CC----------TTGCATGATTTTTGACGTAAATACTCCTTG
2632 AAATATCAATATTCATCAAACAAAAT
184 AAATATCAATATTCATCAAACAAAAT
* *
2658 CTCAGCCACGTACGATTTAAGGATTTGTTTTTTCCGAGCATCTGAAAATTGTTTCGATTTAATTA
1 CTCAGCCACGTACGATTTAAGGATTTGTTTTTTACAAGCATCTGAAAATTGTTTCGATTTAATTA
2723 GAAATAGATTCGGAATAAAAATAGAAAAATGATATTTAAAACGAGAAAAATATTTCAATTTTTTT
66 GAAATAGATTCGGAATAAAAATAGAAAAATGATATTTAAAACGAG-AAAATATTTCAATTTTTTT
* *
2788 TGCGTTGAATTCTGTATTTTTTT-C-TGCATGATTTTTGACGTAAATACTTCTTGAAATATCTAT
130 TG-GTTGAATTCTGTATTTTTTTCCTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCAAT
*
2851 ATTCATCAAACAAACT
194 ATTCATCAAACAAAAT
* *
2867 C-CTAACCACGTACGATTTAAGTATTTGTTTTT
1 CTC-AGCCACGTACGATTTAAGGATTTGTTTTT
2899 ACGTGAATCT
Statistics
Matches: 227, Mismatches: 9, Indels: 20
0.89 0.04 0.08
Matches are distributed among these distances:
208 1 0.00
209 80 0.35
218 2 0.01
219 23 0.10
220 80 0.35
221 21 0.09
222 20 0.09
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (209 bp):
CTCAGCCACGTACGATTTAAGGATTTGTTTTTTACAAGCATCTGAAAATTGTTTCGATTTAATTA
GAAATAGATTCGGAATAAAAATAGAAAAATGATATTTAAAACGAGAAAATATTTCAATTTTTTTT
GGTTGAATTCTGTATTTTTTTCCTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCAATAT
TCATCAAACAAAAT
Found at i:3406 original size:323 final size:325
Alignment explanation
Indices: 2812--3627 Score: 850
Period size: 323 Copynumber: 2.5 Consensus size: 325
2802 TATTTTTTTC
* * *
2812 TGCATGATTTTTGACGTAAATACTTCTTGAAATATCTATATTCATCAAA-CAAACTCCTAACCAC
1 TGCATGATTTTTGACGCAAAAACTCCTTGAAATATCTATATTCATCAAACCAAACTCCTAACCAC
* * * * * * *
2876 GTACGATTTAAGTATTTGTTTTTACGTGAATCTTAATCTTGTTTCAATTTAATTATAAATTAATT
66 ATACGATATAAGGATTTGATTTTACGAGAATCTGAATCTTGTTTCAATTTAATTAGAAATTAATT
* * * * *
2941 CGGAAAGTAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATTTTTTTGGCGTTGAAT
131 CGGAAAG-AAATGGAAAAACGATATTAAAAGCATGAAAAGACCATCAATCTTTTTGGCGTTGAAT
* * **
3006 TATATATTTTTCTGAGTATTGTTGCAAAAAATTGAGAAAAAAACTTTTCCGATCAATTTTTAGCC
195 TATATATTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAACAATTCCGATCAATTTTTAGCC
* *
3071 GAAATTGTGTACTAACCATCACGGTTTTTGG-CTAAAAACGCG-TTCCCGAGCGCCGACACAATT
260 GAAATCGTGTACTAACCATCACGGTTTTTGGACTAAAAACGCGTTTCCCGAGCCCCGACACAATT
3134 T
325 T
* * * *
3135 TGCATGATTTTTGACGCAAAGACTCCTTCAAATATCTATATTCATCAAACCAAA-T-GTCAGCCA
1 TGCATGATTTTTGACGCAAAAACTCCTTGAAATATCTATATTCATCAAACCAAACTCCT-AACCA
** * *
3198 CATTGGATATAAGGATTTGATTTTACGAGCATCTGAATCTTGTTTCAATTTTATTAGAAATTAAT
65 CATACGATATAAGGATTTGATTTTACGAGAATCTGAATCTTGTTTCAATTTAATTAGAAATTAAT
** **
3263 TCGGAAA-AAATTGGAAAATTGATATTAAAAGCATGAAAAGACCATCAATCTTTTTGTTGTTGAA
130 TCGGAAAGAAA-TGGAAAAACGATATTAAAAGCATGAAAAGACCATCAATCTTTTTGGCGTTGAA
* * *
3327 TTATATATTTTTCTGAGTATTGTGGCAAAAAATTCTGAAAAAAA-AATTCATGGTCAGATTTTT-
194 TTATATATTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAACAATTC-CGATCA-ATTTTTA
* * ** * * *
3390 GCCGAAAATCGTGTACTAATCATCATGGTTTTTGGACTAAAAACGCGTTTCGGGGGCCCCGGCTC
257 GCCG-AAATCGTGTACTAACCATCACGGTTTTTGGACTAAAAACGCGTTTCCCGAGCCCCGACAC
*
3455 AGTTT
321 AATTT
* * *
3460 TGCATGATTTTTG--GCAGATAAAATCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCCC
1 TGCATGATTTTTGACGCA-A-AAACTCCTTGAAATATCTATATTCATCAAACCAAACT-----CC
* * ** ** *
3523 TCAGCCACATTA-GATTTAATAATTTG-TATTTACGAGAATCTGAAAATTGTTTCGATTTAATTA
59 T-AACCACA-TACGATATAAGGATTTGAT-TTTACGAGAATCTGAATCTTGTTTCAATTTAATTA
* * *
3586 GAAA-TAGATTCGGAATA-ATAATAGAAAAATGATATTTAAAGC
121 GAAATTA-ATTCGGAA-AGA-AATGGAAAAACGATATTAAAAGC
3628 GAGAAAAATA
Statistics
Matches: 410, Mismatches: 61, Indels: 34
0.81 0.12 0.07
Matches are distributed among these distances:
321 6 0.01
322 94 0.23
323 147 0.36
324 16 0.04
325 58 0.14
326 1 0.00
331 3 0.01
332 62 0.15
333 21 0.05
334 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (325 bp):
TGCATGATTTTTGACGCAAAAACTCCTTGAAATATCTATATTCATCAAACCAAACTCCTAACCAC
ATACGATATAAGGATTTGATTTTACGAGAATCTGAATCTTGTTTCAATTTAATTAGAAATTAATT
CGGAAAGAAATGGAAAAACGATATTAAAAGCATGAAAAGACCATCAATCTTTTTGGCGTTGAATT
ATATATTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAACAATTCCGATCAATTTTTAGCCG
AAATCGTGTACTAACCATCACGGTTTTTGGACTAAAAACGCGTTTCCCGAGCCCCGACACAATTT
Found at i:4288 original size:324 final size:323
Alignment explanation
Indices: 3722--5167 Score: 1779
Period size: 324 Copynumber: 4.4 Consensus size: 323
3712 GTAAATACTT
* ** * * *
3722 CTTGAAATATCTATATTCATCAAACAAAATCCCAGCCACGTTCGATTTAAGTATTTGTTTTTACG
1 CTTGAAATATCTATATTCATCAAACCAAATGTCAGCCACATTAGATTTAAGGATTTGTTTTTACG
* * * ** * * *
3787 AGCATCTTAATCTTGTTTCAATTTAATTAAAAATTAATTCATAAAATAAATGTAAAAACGATATT
66 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAA-AATTGGAAAAATGATATT
* * * *
3852 AGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTTGAATTATATTTTTTTTCTGAGTATTGTGGC
130 AAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGC
** *
3917 AAAAAATTGGGAAAAAAACTTTTCTGATCAGTTTTTAGCCG-AAATCGTGTACTAACCATCACGG
195 AAAAAATTCAGAAAAAAA-TTTTCGGATCAGTTTTTAGCCGAAAATCGTGTACTAACCATCACGG
3981 TTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACTCAATTTTGCATGATTTTTGACACAAAGACTC
259 TTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACTCAATTTTGCATGATTTTTGACACAAAGACTC
* *
4046 CTTGAAATATCTATATTCATCAAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTACG
1 CTTGAAATATCTATATTCATCAAACCAAATGTCAGCCACATTAGATTTAAGGATTTGTTTTTACG
* *
4111 AACATCTGAATCTTGTTTCGATTTAATTAGAAATTAGTTCGGGAAAAAATTGGAAAAATGATATT
66 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GGAAAAAATTGGAAAAATGATATT
4176 AAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGC
130 AAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGC
* * *
4241 AAAAAATTCAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAAATCGTGTACTAACTATCATGGT
195 AAAAAATTCAGAAAAAAATTTTCGGATCAGTTTTTAGCCGAAAATCGTGTACTAACCATCACGGT
* * * * *
4306 TTTGGGGCTAAAAACGCGCTT--CGAGGTCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGA
260 TTT-TGGCTAAAAACGCG-TTCCCGA-G-CCCCGACTCAATTTTGCATGATTTTTGACACAAAGA
4369 CTC
321 CTC
* *
4372 CTTGAAATATCTATATTCATCTAACCAATCTCCGGCTCTCAGCCACATTAGATTTAAGGATTTGT
1 CTTGAAATATCTATATTCATCAAACCAA-AT---G---TCAGCCACATTAGATTTAAGGATTTGT
* *
4437 TTTTACGAGCATATGAATATTGTTTCGATTTAATTAGAAA-TAGATTCGGAAAAAAATT-GAAAA
59 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA-ATTCGG-AAAAAATTGGAAAA
* * * ** * * *
4500 ATGATATTTAAAGCGAGAATAATA-TTTCAATTTTTTTTTGCGTT-AATTATATATTTTTTCTGA
122 ATGATATTAAAAGCGTGAA-AAGACCATCAA-TCTTTTTGGTGTTGAATTATATATTTTTTCTGA
* * * *
4563 GTATTGTGGCAAAAAATTGAGAGAAAAACTTTTTGGATTAGTTTTTAGCC-AAAATCGTG---T-
185 GTATTGTGGCAAAAAATTCAGA-AAAAAATTTTCGGATCAGTTTTTAGCCGAAAATCGTGTACTA
*
4623 ACCATCACGGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACTCAATTTTGCATGATTTTTGGC
249 ACCATCACGGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACTCAATTTTGCATGATTTTTGAC
*
4688 GCAAAGACTC
314 ACAAAGACTC
* * *
4698 CTTGAAATATCTATACTCATCAAACCAAATGTCAGCCACATTGGATATAAGGATTTGGTTTTTAC
1 CTTGAAATATCTATATTCATCAAACCAAATGTCAGCCACATTAGATTTAAGGATTT-GTTTTTAC
*
4763 GAGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAATTTGGAAAAATGATAT
65 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA-TTGGAAAAATGATAT
4828 TAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGG
129 TAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGG
* * **
4893 CAAAAAATTTCAGAAAAAAAAATTAT-GGGTCAGAATTTAGCCGAAAATCGTGTACTAACCATCA
194 CAAAAAA-TTCAG--AAAAAAATTTTCGGATCAGTTTTTAGCCGAAAATCGTGTACTAACCATCA
* * * * * * * * *
4957 TGGTTTTTGGGCTAAAAACGCGTTTCGGGGCCCTC-AGCTCAGTTTTTCATGTTTTTTGACAGAT
256 CGGTTTTT-GGCTAAAAACGCGTTCCCGAGCCC-CGA-CTCAATTTTGCATGATTTTTGACACAA
*
5021 AGAATC
318 AGACTC
* *
5027 CTTGAAATATCTATATTCATCTAACCAATCTCAGGCCCTCAGCCACATTAGATTTAAGGATTTGT
1 CTTGAAATATCTATATTCATCAAACCAA----ATG---TCAGCCACATTAGATTTAAGGATTTGT
** * *
5092 TTTTACGAGCATCTGAAAATTGTTTCGATTTAATTAGAAA-TATATTCGGAATAAAAATAGAAAA
59 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA-ATTCGGAA-AAAATTGGAAAA
5156 ATGATACTTAAA
122 ATGATA-TTAAA
5168 TTGAGAAAAA
Statistics
Matches: 970, Mismatches: 105, Indels: 82
0.84 0.09 0.07
Matches are distributed among these distances:
319 29 0.03
320 60 0.06
321 63 0.06
322 17 0.02
323 37 0.04
324 214 0.22
325 19 0.02
326 128 0.13
327 29 0.03
328 37 0.04
329 53 0.05
330 1 0.00
332 79 0.08
333 111 0.11
334 2 0.00
335 59 0.06
336 32 0.03
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (323 bp):
CTTGAAATATCTATATTCATCAAACCAAATGTCAGCCACATTAGATTTAAGGATTTGTTTTTACG
AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATTGGAAAAATGATATTA
AAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCA
AAAAATTCAGAAAAAAATTTTCGGATCAGTTTTTAGCCGAAAATCGTGTACTAACCATCACGGTT
TTTGGCTAAAAACGCGTTCCCGAGCCCCGACTCAATTTTGCATGATTTTTGACACAAAGACTC
Found at i:4516 original size:886 final size:885
Alignment explanation
Indices: 2658--4558 Score: 2924
Period size: 886 Copynumber: 2.2 Consensus size: 885
2648 CAAACAAAAT
* * * * * *
2658 CTCAGCCAC-GTACGATTTAAGGATTTGTTTTTTCCGAGCATCTGAAAATTGTTTCGATTTAATT
1 CTCAGCCACATTA-GATTTAAGAATTTG-TATTTACGAGAATATGAAAATTGTTTCGATTTAATT
*
2722 AGAAATAGATTCGGAATAAAAATAGAAAAATGATATTTAAAACGAGAAAAATATTTCAA-TTTTT
64 AGAAATAGATTCGGAATAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTT
* * *
2786 TTTGCG----TT-GA-A----TT-CTG----TA-----TTT-TTTTCTGCATGATTTTTGACGTA
129 TTTGCGTTAATTATATATTTTTTGCCGAAAATATTTTTTTTGTTTTCTGCATAATTTTTGACGTA
* *
2830 AATACTTCTTGAAATATCTATATTCATCAAACAAACTCCTAACCACGTACGATTTAAGTATTTGT
194 AATACTTCTTGAAATATCTATATTCATCAAACAAAATCCCAACCACGTACGATTTAAGTATTTGT
* * * *
2895 TTTTACGTGAATCTTAATCTTGTTTCAATTTAATTATAAATTAATTCGGAAAGTAAATGGAAAAA
259 TTTTACGAGAATCTTAATCTTGTTTCAATTTAATTAAAAATTAATTCAGAAAATAAATGGAAAAA
*
2960 CGATATTAGAAGCGTGAAAAGCCCGTCAATTTTTTTGGCGTTGAATTATATATTTTTCTGAGTAT
324 CGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTCTGAGTAT
* *
3025 TGTTGCAAAAAATTGAGAAAAAAACTTTTCCGATCAATTTTTAGCCGAAATTGTGTACTAACCAT
389 TGTGGCAAAAAATTGAGAAAAAAACTTTTCCGATCAATTTTTAGCCGAAATCGTGTACTAACCAT
* *
3090 CACGGTTTTTGGCTAAAAACGCGTTCCCGAGCGCCGACACAATTTTGCATGATTTTTGACGCAAA
454 CACGGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACACAATTTTGCATGATTTTTGACACAAA
3155 GACTCCTTCAAATATCTATATTCATCAAACCAAATGTCAGCCACATTGGATATAAGGATTTGATT
519 GACTCCTTCAAATATCTATATTCATCAAACCAAATGTCAGCCACATTGGATATAAGGATTTGATT
* * *
3220 TTACGAGCATCTGAATCTTGTTTCAATTTTATTAGAAATTAATTCGGAAAAAATTGGAAAATTGA
584 TTACGAACATCTGAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAATTGGAAAAATGA
*
3285 TATTAAAAGCATGAAAAGACCATCAATCTTTTTGTTGTTGAATTATATATTTTTCTGAGTATTGT
649 TATTAAAAGCATGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTCTGAGTATTGT
* *
3350 GGCAAAAAATTCTGAAAAAAAAATTCATGGTCAGATTTTTGCCGAAAATCGTGTACTAATCATCA
714 GGCAAAAAATTCAGAAAAAAAAATTCAGGGTCAGATTTTTGCCGAAAATCGTGTACTAATCATCA
* * *
3415 TGGTTTTTGGACTAAAAACGCGTTTCGGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGATA
779 TGGTTTTGGGACTAAAAACGCGCTTCGAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGATA
3480 AAATCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCC
844 AAATCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCC
* *
3522 CTCAGCCACATTAGATTTAATAATTTGTATTTACGAGAATCTGAAAATTGTTTCGATTTAATTAG
1 CTCAGCCACATTAGATTTAAGAATTTGTATTTACGAGAATATGAAAATTGTTTCGATTTAATTAG
*
3587 AAATAGATTCGGAATAATAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTT
66 AAATAGATTCGGAATAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTT
* * * *
3652 TGCGTTGAATTCTGTATTTTTTGCCGAAAATATTTTTTTTGTTTT-TGCATAATTTTTTATGTAA
131 TGCGTT-AATTATATATTTTTTGCCGAAAATATTTTTTTTGTTTTCTGCATAATTTTTGACGTAA
* *
3716 ATACTTCTTGAAATATCTATATTCATCAAACAAAATCCCAGCCACGTTCGATTTAAGTATTTGTT
195 ATACTTCTTGAAATATCTATATTCATCAAACAAAATCCCAACCACGTACGATTTAAGTATTTGTT
* * *
3781 TTTACGAGCATCTTAATCTTGTTTCAATTTAATTAAAAATTAATTCATAAAATAAATGTAAAAAC
260 TTTACGAGAATCTTAATCTTGTTTCAATTTAATTAAAAATTAATTCAGAAAATAAATGGAAAAAC
* *
3846 GATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTTGAATTATATTTTTTTTCTGAGTAT
325 GATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATA-TATTTTTCTGAGTAT
* * *
3911 TGTGGCAAAAAATTGGGAAAAAAACTTTTCTGATCAGTTTTTAGCCGAAATCGTGTACTAACCAT
389 TGTGGCAAAAAATTGAGAAAAAAACTTTTCCGATCAATTTTTAGCCGAAATCGTGTACTAACCAT
*
3976 CACGGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACTCAATTTTGCATGATTTTTGACACAAA
454 CACGGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACACAATTTTGCATGATTTTTGACACAAA
* *
4041 GACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTT
519 GACTCCTTCAAATATCTATATTCATCAAACCAAATGTCAGCCACATTGGATATAAGGATTTGATT
* *
4106 TTACGAACATCTGAATCTTGTTTCGATTTAATTAGAAATTAGTTCGGGAAAAAATTGGAAAAATG
584 TTACGAACATCTGAATCTTGTTTCAATTTAATTAGAAATTAATTC-GGAAAAAATTGGAAAAATG
*
4171 ATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATT
648 ATATTAAAAGCATGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATA-TTTTTCTGAGTATT
**
4236 GTGGCAAAAAATTCAGAAAAAAATTTTC-GGGTCAG-TTTTTAGCCGAAAATCGTGTACTAA-CT
712 GTGGCAAAAAATTCAGAAAAAAAAATTCAGGGTCAGATTTTT-GCCGAAAATCGTGTACTAATC-
* *
4298 ATCATGGTTTTGGGGCTAAAAACGCGCTTCGAGGTCCCCGGCTCAGTTTTGCATGATTTTTGGCA
775 ATCATGGTTTTGGGACTAAAAACGCGCTTCGAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCA
* * *
4363 GA-AAGACTCCTTGAAATATCTATATTCATCTAACCAATCTCCGGCT
840 GATAA-AATCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCC
* * * *
4409 CTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATATGAATATTGTTTCGATTTAATTAG
1 CTCAGCCACATTAGATTTAAGAATTTGTATTTACGAGAATATGAAAATTGTTTCGATTTAATTAG
* *
4474 AAATAGATTCGGAA-AAAAATTGAAAAATGATATTTAAAGCGAGAATAATATTTCAATTTTTTTT
66 AAATAGATTCGGAATAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTT
4538 TGCGTTAATTATATATTTTTT
131 TGCGTTAATTATATATTTTTT
4559 CTGAGTATTG
Statistics
Matches: 939, Mismatches: 68, Indels: 39
0.90 0.07 0.04
Matches are distributed among these distances:
863 90 0.10
864 32 0.03
865 2 0.00
869 2 0.00
871 1 0.00
875 2 0.00
876 2 0.00
880 2 0.00
885 198 0.21
886 305 0.32
887 264 0.28
888 39 0.04
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (885 bp):
CTCAGCCACATTAGATTTAAGAATTTGTATTTACGAGAATATGAAAATTGTTTCGATTTAATTAG
AAATAGATTCGGAATAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTT
TGCGTTAATTATATATTTTTTGCCGAAAATATTTTTTTTGTTTTCTGCATAATTTTTGACGTAAA
TACTTCTTGAAATATCTATATTCATCAAACAAAATCCCAACCACGTACGATTTAAGTATTTGTTT
TTACGAGAATCTTAATCTTGTTTCAATTTAATTAAAAATTAATTCAGAAAATAAATGGAAAAACG
ATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTCTGAGTATTG
TGGCAAAAAATTGAGAAAAAAACTTTTCCGATCAATTTTTAGCCGAAATCGTGTACTAACCATCA
CGGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACACAATTTTGCATGATTTTTGACACAAAGA
CTCCTTCAAATATCTATATTCATCAAACCAAATGTCAGCCACATTGGATATAAGGATTTGATTTT
ACGAACATCTGAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAATTGGAAAAATGATA
TTAAAAGCATGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTCTGAGTATTGTGG
CAAAAAATTCAGAAAAAAAAATTCAGGGTCAGATTTTTGCCGAAAATCGTGTACTAATCATCATG
GTTTTGGGACTAAAAACGCGCTTCGAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGATAAA
ATCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCC
Found at i:5141 original size:655 final size:652
Alignment explanation
Indices: 3754--5213 Score: 2202
Period size: 655 Copynumber: 2.2 Consensus size: 652
3744 AACAAAATCC
* * * * * * *
3754 CAGCCACGTTCGATTTAAGTATTTGTTTTTACGAGCATCTTAATCTTGTTTCAATTTAATTAAAA
1 CAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAA
** * * **** * *
3819 AT-TAATTCATAAAATAAA-TGTAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTG
66 ATAT-ATTCGGAAAA-AAATTG-AAAAATGATATTA-AAGCGAGAAAA-TATTTCAATTTTTTTT
* * *
3882 GTGTTGAATTATATTTTTTTTCTGAGTATTGTGGCAAAAAATTGGGAAAAAAACTTTTCTGATCA
126 GCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAACTTTTCTGATCA
*
3947 GTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCG
191 GTTTTTAGCCAAAATCGTG-A-TAACCATCACGGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCG
*
4012 ACTCAATTTTGCATGATTTTTGACACAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATG
254 ACTCAATTTTGCATGATTTTTGACACAAAGACTCCTTGAAATATCTATACTCATCAAACCAAATG
*
4077 TCAGCCACATTGGATATAAGGATTTGTTTTTACGAACATCTGAATCTTGTTTCGATTTAATTAGA
319 TCAGCCACATTGGATATAAGGATTTGTTTTTACGAACATCTGAATCTTGTTTCAATTTAATTAGA
*
4142 AATTAGTTCGGGAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGG
384 AATTAATTCGGGAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGG
* *
4207 TGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAATTTTCGGGTCAGT
449 TGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAATTATCGGGTCAGA
* * *
4272 TTTTAGCCGAAAATCGTGTACTAACTATCATGGTTTTGGGGCTAAAAACGCGCTTCGAGGTCCCC
514 ATTTAGCCGAAAATCGTGTACTAACCATCATGGTTTTGGGGCTAAAAACGCGCTTCGAGGGCCCC
* * *
4337 GGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAATC
579 AGCTCAGTTTTGCATGATTTTTGACAGAAAGAATCCTTGAAATATCTATATTCATCTAACCAATC
* *
4402 TCCGGCTCT
644 TCAGGCCCT
*
4411 CAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATATGAATATTGTTTCGATTTAATTAGAA
1 CAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAA
*
4476 ATAGATTCGGAAAAAAATTGAAAAATGATATTTAAAGCGAGAATAATATTTCAATTTTTTTTTGC
66 ATATATTCGGAAAAAAATTGAAAAATGATA-TTAAAGCGAGAA-AATATTTCAA-TTTTTTTTGC
* *
4541 GTT-AATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAGAAAAACTTTT-TGGATTAG
128 GTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAACTTTTCT-GATCAG
4604 TTTTTAGCCAAAATCGTG-T-ACCATCACGGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACT
192 TTTTTAGCCAAAATCGTGATAACCATCACGGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACT
* *
4667 CAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATACTCATCAAACCAAATGTCA
257 CAATTTTGCATGATTTTTGACACAAAGACTCCTTGAAATATCTATACTCATCAAACCAAATGTCA
*
4732 GCCACATTGGATATAAGGATTTGGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAA
322 GCCACATTGGATATAAGGATTT-GTTTTTACGAACATCTGAATCTTGTTTCAATTTAATTAGAAA
4797 TTAATTC-GGAAAAAATTTGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGT
386 TTAATTCGGGAAAAAA-TTGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGT
4861 GTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTTCAGAAAAAAAAATTAT-GGGTCA
450 GTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAA-TTCAG--AAAAAAATTATCGGGTCA
* *
4925 GAATTTAGCCGAAAATCGTGTACTAACCATCATGGTTTTTGGGCTAAAAACGCGTTTCG-GGGCC
512 GAATTTAGCCGAAAATCGTGTACTAACCATCATGGTTTTGGGGCTAAAAACGCGCTTCGAGGGCC
* * *
4989 CTCAGCTCAGTTTTTCATGTTTTTTGACAGATAGAATCCTTGAAATATCTATATTCATCTAACCA
577 C-CAGCTCAGTTTTGCATGATTTTTGACAGAAAGAATCCTTGAAATATCTATATTCATCTAACCA
5054 ATCTCAGGCCCT
641 ATCTCAGGCCCT
*
5066 CAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAAAATTGTTTCGATTTAATTAGAA
1 CAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAA
* **
5131 ATATATTCGGAATAAAAATAGAAAAATGATACTTAAATTGAGAAAAATATTTCAA-TTTTTTTGC
66 ATATATTCGGAA-AAAAATTGAAAAATGATA-TTAAAGCGAG-AAAATATTTCAATTTTTTTTGC
* *
5195 GTTGAATTCTGTATTTTTT
128 GTTGAATTATATATTTTTT
5214 GCCGAATTTT
Statistics
Matches: 733, Mismatches: 55, Indels: 32
0.89 0.07 0.04
Matches are distributed among these distances:
652 136 0.19
653 134 0.18
654 22 0.03
655 215 0.29
656 140 0.19
657 86 0.12
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (652 bp):
CAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAA
ATATATTCGGAAAAAAATTGAAAAATGATATTAAAGCGAGAAAATATTTCAATTTTTTTTGCGTT
GAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAACTTTTCTGATCAGTTTT
TAGCCAAAATCGTGATAACCATCACGGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACTCAAT
TTTGCATGATTTTTGACACAAAGACTCCTTGAAATATCTATACTCATCAAACCAAATGTCAGCCA
CATTGGATATAAGGATTTGTTTTTACGAACATCTGAATCTTGTTTCAATTTAATTAGAAATTAAT
TCGGGAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAA
TTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAATTATCGGGTCAGAATTTAGC
CGAAAATCGTGTACTAACCATCATGGTTTTGGGGCTAAAAACGCGCTTCGAGGGCCCCAGCTCAG
TTTTGCATGATTTTTGACAGAAAGAATCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCC
CT
Found at i:5728 original size:552 final size:557
Alignment explanation
Indices: 4670--5904 Score: 1984
Period size: 552 Copynumber: 2.2 Consensus size: 557
4660 CCCGACTCAA
* * * *
4670 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATACTCATCAAACCAAATGTCAGCC
1 TTTTGCATGATTTTTGACGTAAACACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
*
4735 ACATTGGATATAAGGATTTGGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATTA
66 ACATTGGATATAAGGATTT-GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
*
4800 ATTCGGAAAAAATTTGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTG
130 ATTCGGAAAAAATTTGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTATTG
*
4865 AATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTTCAGAAAAAAAAATTATGGGTCAGAATT
195 AATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTTCAGAAAAAAAAATTACGGGTCAGAATT
* *
4930 TAGCCGAAAATCGTGTACTAACCATCATGGTTTTTGGGCTAAAAACGCGTTTCGGGGCCCTCAGC
260 TAGCCGAAAATCGTGTACTAACCATCATGGTTTTGGGGCTAAAAACGCGTTTCGGGGCCCTCACC
* * *
4995 TCAGTTTTTCATGTTTTTTGACAGATAGAATCCTTGAAATATCTATATTCATCTAACCAATCTCA
325 TCAGTTTTGCATGATTTTTGACAGAAAGAATCCTTGAAATATCTATATTCATCTAACCAATCTCA
5060 GGCCCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAAAATTGTTTCGATTTAA
390 GGCCCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAAAATTGTTTCGATTTAA
* **
5125 TTAGAAATATATTCGGAATAAAAATAGAAAAATGATACTTAAATTGAGAAAAATATTTCAA-TTT
455 TTAGAAATATATTCGAAATAAAAATAGAAAAATGATACTTAAAGCGAG-AAAATATTTCAATTTT
** **
5189 TTTTGCG-TTGAATTCTGTA-TTTTTTGC-CGAATTTTT
519 TTTTGCGTTTGAATTCTGTATTTTTTTGCAAAAAAATTT
5225 TTTTGCATGATTTTTGACGTAAACACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
1 TTTTGCATGATTTTTGACGTAAACACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
*
5290 ACATTGGATATAAGGATTTGTTTTTACGAGCATCTAAATCTT-TTTCGATTTAATTAGAAATTAA
66 ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
5354 TTCGGATAAAAA-TTGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTATTG
131 TTCGGA-AAAAATTTGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTATTG
* * *
5418 AATTATATTTTTTTTTCTGAGTATTGTGGCAAAAAA-TTCAG-AAAAAAAATTCCGGGTCAGATT
195 AATTATA-TATTTTTTCTGAGTATTGTGGCAAAAAATTTCAGAAAAAAAAATTACGGGTCAGAAT
*
5481 TTAGCCGAAAATCGTGTACTATCCATCATGGTTTTGGGGCTAAAAACGCGTTTCGGGGGCCC-CA
259 TTAGCCGAAAATCGTGTACTAACCATCATGGTTTTGGGGCTAAAAACGCGTTTC-GGGGCCCTCA
* * *
5545 CCTCAGTTTTGCATGATTTTTGGCAGAAAGACTTCTTGAAATATCTATATTCATCTAACCAATCT
323 CCTCAGTTTTGCATGATTTTTGACAGAAAGAATCCTTGAAATATCTATATTCATCTAACCAATCT
5610 CAGGCCCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAAAATTGTTTCGATTT
388 CAGGCCCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAAAATTGTTTCGATTT
*
5675 AATTAGAAATATATTCGAAATAAAAATAGAAAAATGATATTTAAAGCGAGAAAATATTTCAATTT
453 AATTAGAAATATATTCGAAATAAAAATAGAAAAATGATACTTAAAGCGAGAAAATATTTCAA-TT
5740 TTTTTTGCGTTTGAATTCTGTATTTTTTTGCAAAAAAAAATTT
517 TTTTTTGCGTTTGAATTCTGTATTTTTTTGC--AAAAAAATTT
* * * * * *
5783 TTTTGAATGATTTTTAACGTAAATACTCCTTAAAATATCTATATTCATCAAACAAAATCTCAGCC
1 TTTTGCATGATTTTTGACGTAAACACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
* ** * *
5848 ACGTACGATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
66 ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
Statistics
Matches: 629, Mismatches: 40, Indels: 18
0.92 0.06 0.03
Matches are distributed among these distances:
551 12 0.02
552 242 0.38
553 107 0.17
554 66 0.10
555 88 0.14
558 100 0.16
559 14 0.02
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (557 bp):
TTTTGCATGATTTTTGACGTAAACACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
TTCGGAAAAAATTTGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTATTGA
ATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTTCAGAAAAAAAAATTACGGGTCAGAATTT
AGCCGAAAATCGTGTACTAACCATCATGGTTTTGGGGCTAAAAACGCGTTTCGGGGCCCTCACCT
CAGTTTTGCATGATTTTTGACAGAAAGAATCCTTGAAATATCTATATTCATCTAACCAATCTCAG
GCCCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAAAATTGTTTCGATTTAAT
TAGAAATATATTCGAAATAAAAATAGAAAAATGATACTTAAAGCGAGAAAATATTTCAATTTTTT
TTGCGTTTGAATTCTGTATTTTTTTGCAAAAAAATTT
Done.