Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007228.1 Corchorus capsularis cultivar CVL-1 contig07249, 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: 14688
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:844 original size:320 final size:320
Alignment explanation
Indices: 1--3201 Score: 3009
Period size: 320 Copynumber: 10.1 Consensus size: 320
* * *
1 AAATCGAAACAAGATTAAGATACTCGAAAAAACAAATCTTTATATTCAATATTGCTGATATTTGC
1 AAATCGAAACAAGATTGAGATACTCGAAAAAACAAATCCTTATATTCAATATTGCTGAGATTTGC
* * * * * * *
66 TTCGATGATTATAGATATTTAAAGGAGTTTTTGCGCCAAAAATCATGCAGAATTGAGCCGGCGTT
66 TTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCT
* ** ** *
131 CAAGAATTTGTTTTTAGCCAAAAACAATGATGGTTAGTACACGATTTCGGCTAAAAAACTGACCC
131 CCAGAATGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCT-AAAAACTGACCC
*
196 GAAAAATTTTCTCTCAATTTTTTGCCACAATACAAAGAAGAAAATATATAATTCAACTCCAAAAA
195 GAAAAATTTTCTCTCAATTTTTTGCCACAATACAAAGAAAAAAATATATAATTCAACTCCAAAAA
*
261 GATTAAGGGCTTTTCACGCTTCAAATATCGTTTTTCGTTCTTTTTTCCAAATTAATTTCTAATT
260 GATTGAGGGCTTTTCACGCTTCAAATATCGTTTTTCG---TTTTTTCCAAATTAATTTCTAATT
* * *
325 AAATCGAAATAAGATTGAGATACTCGAAAAAACAAATCCTTATATTCCATATTGCTGATATTTGC
1 AAATCGAAACAAGATTGAGATACTCGAAAAAACAAATCCTTATATTCAATATTGCTGAGATTTGC
* * * *
390 TTCGATGAATTTAGATATTTCAAGGAGTCTTTGCACCAAAAATCATACAGAATTGAG-CAGGGGC
66 TTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTC-GGGGC
* * * * *
454 TCCAGAATTCGTTTTTAGCTAGAAACAGTGATGATTAGTACACGATTTCGGCTAAAAAACAT-AT
130 TCCAGAATGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCT-AAAAAC-TGAC
*
518 CCGAAAAATTTTCTCTCAA-TTTTTACCACAATACAAAGAAAAAAAATATATAATTCAACTCCAA
193 CCGAAAAATTTTCTCTCAATTTTTTGCCACAATACAAAG-AAAAAAATATATAATTCAACTCCAA
* *
582 AAAGATTGAGGGCTTTTCACGCTTGAAATATCGTTTTTCGTTTTTTCCAAATTAATTTCTAGTT
257 AAAGATTGAGGGCTTTTCACGCTTCAAATATCGTTTTTCGTTTTTTCCAAATTAATTTCTAATT
* *
646 AAATCGAAACAAGATTGAGATACTTGAAAAAAC-AATCCTTATATTCAATATTGCTGAGATTTGA
1 AAATCGAAACAAGATTGAGATACTCGAAAAAACAAATCCTTATATTCAATATTGCTGAGATTTGC
* * * * * * * **
710 TTCAATGAATATAAATATATT-AAAGAGTCTTTGCACCAAAATTCATGCAGAATTCAGTAAGGGC
66 TTCGATGAATATAGATAT-TTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGC
* * * *
774 TCCAGAATTCGATTTCAGCCAGAAACCGTGATGATTAGTACACGATTTCGGCTAAAAACCTGACC
130 TCCAGAATGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAAA-CTGACC
*
839 CGAAAAATTTTCTCTCAA-TTTTTACCACAATACAAAG-AAAAAATATATAATTCAACTCCAAAA
194 CGAAAAATTTTCTCTCAATTTTTTGCCACAATACAAAGAAAAAAATATATAATTCAACTCCAAAA
* * * *
902 AGATTGAGGGCTTTTCACGCTTGAAATATCGTTTTTGGTTTTTTTCCGAATTAATTTCTAATG
259 AGATTGAGGGCTTTTCACGCTTCAAATATCGTTTTTCG-TTTTTTCCAAATTAATTTCTAATT
*
965 AAATCGAAACAAGATTGAGATTCTCGAAAAAACAAAAT-CTTATATTCAATATTGCTGAGATTTG
1 AAATCGAAACAAGATTGAGATACTCGAAAAAAC-AAATCCTTATATTCAATATTGCTGAGATTTG
* * * * ** * *
1029 CTTCGATGATTATATATATTTCAAGGAGTTTTTGCACCAAAAATCATGCAGTATTGAGCCGGGGT
65 CTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGC
* * *
1094 TCAAGAATTCGTTTTTAGCCAAAAACCGTGACTG-TTAGTACACGATTTCGGCTAAAAAACTAAC
130 TCCAGAATGCGTTTTTAGCCAAAAACCGTGA-TGATTAGTACACGATTTCGGCT-AAAAACTGAC
*
1158 CTGAAAAATTTTCTCTCAATTTTTTGCCACAATACAAAGAAAAAAATA-ATAATTCAACTCCAAA
193 CCGAAAAATTTTCTCTCAATTTTTTGCCACAATACAAAGAAAAAAATATATAATTCAACTCCAAA
* * * *
1222 AAGATTGAGGGCTTTTCACGCTTCCAATATCGTTTGTCGTTTTTTTTCCGAATTAATTTCTATTT
258 AAGATTGAGGGCTTTTCACGCTTCAAATATCGTTTTTCG--TTTTTTCCAAATTAATTTCTAATT
* *
1287 AAATCGAAACAAGATTGAGATACTCGAAAAAACAAATCCTTATATTCAATATTTCTGAGATTTGG
1 AAATCGAAACAAGATTGAGATACTCGAAAAAACAAATCCTTATATTCAATATTGCTGAGATTTGC
* * *
1352 TTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCGAAAATCATGCAAAATCGAGTCGGGTCT
66 TTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCT
* *
1417 CCAGAATGCGTTTTTAG-CAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAAACTGACCCG
131 CCAGAATGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAAACTGACCCG
* * ** *** **** * * *
1481 AAAATTTTTTTCTCAA--------CAC-CGA-AAAGATTTAGGGCT-T--TTCACGCTTC---TA
196 AAAAATTTTCTCTCAATTTTTTGCCACAATACAAAGAAAAAAATATATAATTCA-ACTCCAAAAA
** * *** * ** * ** ** * * *
1530 -A-T-ATCGTTTTTCATTTTTTTCTGAAT-TAATTTCTAATTTAAT-CAAAATAAGATT-GAGA-
260 GATTGAGGGCTTTTCA--CGCTTC-AAATATCGTTTTTCGTTTTTTCCAAATTAA-TTTCTA-AT
1588 T
320 T
* * *
1589 -ACTCG----AA-A---A------------AACAAATGCTTATATTCAATATTGCTGAGATTTGG
1 AAATCGAAACAAGATTGAGATACTCGAAAAAACAAATCCTTATATTCAATATTGCTGAGATTTGC
* *
1633 TTCGATGAATATAGATATTTCAAAGAGTCTTTGCGCCAAAAATCATGCAAAATTAAGTCGGGGCT
66 TTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCT
* * * * * * *
1698 CCGGAATGCGTTTTTAG-CGAAAACAGTGATCG-TTAGTACACGAATTCAGCTAAAAACCGATCC
131 CCAGAATGCGTTTTTAGCCAAAAACCGTGAT-GATTAGTACACGATTTCGGCTAAAAACTGACCC
** * * * * * * * *
1761 GAAATTTTTTTTCTCAACTTCTTGCCACAATACATACAAAAAGATATATTATTC-ATTGCCAAAA
195 GAAAAATTTTCTCTCAATTTTTTGCCACAATACAAAGAAAAAAATATATAATTCAACT-CCAAAA
* * * * * *
1825 AGATTGACGAGCTTTTAACTCTTCAAATATCGTTTTTCCATTTTTTCCGAACTAATTTCTAATT
259 AGATTGA-GGGCTTTTCACGCTTCAAATATCGTTTTT-CGTTTTTTCCAAATTAATTTCTAATT
* ** * * *
1889 AAATCCAAACAAGATTGAGATGA-TAAAAAAAAACAAATCCTTATATCCAATATGGCTAAGATTT
1 AAATCGAAACAAGATTGAGAT-ACT-CGAAAAAACAAATCCTTATATTCAATATTGCTGAGA-TT
* * * *
1953 TG-TTCGATGAATATATATATTTCAAGGAGTATTTGCGCCAAAATTCTTGCAAAATTGAGTCGGG
63 TGCTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGG
*** ** * * *
2017 GCTTTGGAACACGTCTTTAGCTAAAAACCGTG-T--TAACGTACACGATTTCGGCTAAAAACTGA
128 GCTCCAGAATGCGTTTTTAGCCAAAAACCGTGATGATTA-GTACACGATTTCGGCTAAAAACTGA
* * ** *
2079 CCC-AAAAAGTTTTTTCTCAAGTTTTTTGCCATAATACTCAG-AAAAAATATATAATTCAACACC
192 CCCGAAAAA-TTTTCTCTCAA-TTTTTTGCCACAATACAAAGAAAAAAATATATAATTCAACTCC
* *** * *
2142 AAAAAGACTGACGGGCTTTTCATATTTCTAATATCGTTTTTCCATTTTTT--ATAATTAATTTCT
255 AAAAAGATTGA-GGGCTTTTCACGCTTCAAATATCGTTTTT-CGTTTTTTCCA-AATTAATTTCT
2205 AATT
317 AATT
* * * * * * * *
2209 AAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAAT-CTGACTGACATATG
1 AAATCGAAACAAGATTGAGATACTCGAAAAAACAAATCCTTATATTCAATATTG-CTGAGATTTG
* * * ** * * * * *
2273 GTTCGAAGAATATAGATATTTCAAGGTGTCTTTGCATCAAAAACCCTGTAAAATCGAGGCGGGGC
65 CTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGC
** * *
2338 TCCAGAATGCGGATTTAGCCAAAAACCGTGATGA--CGTACATGATTTCGGCTAAAAACTGACCC
130 TCCAGAATGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAAACTGACCC
* * * ** * **
2401 GAAAACTATTT-TCTCAATTTTTTGTCATAATACTCAGAAAAAATTATATAATTCAAAGCCAAAA
195 GAAAAAT-TTTCTCTCAATTTTTTGCCACAATACAAAGAAAAAAATATATAATTCAACTCCAAAA
* *
2465 AGATTGACGGG-TTTTCCACGCTTCTAATATCGTTTTTCCAATTTTTTCCAAATTAATTTCTAAT
259 AGATTGA-GGGCTTTT-CACGCTTCAAATATCGTTTTT-C-GTTTTTTCCAAATTAATTTCTAAT
2529 T
320 T
* * * * * *
2530 AAATCAAAACAAGATTGAGATGCT-TAAAAAATCAAATCCTTTTATTCAATATGGCTAAGATTTT
1 AAATCGAAACAAGATTGAGATACTCGAAAAAA-CAAATCCTTATATTCAATATTGCTGAGA---T
** ** * * *
2594 TTTTTTTTATGAATATAGATATTTCAAGGAGTTTTTGCGGCAAAAATCATTCAAAATTGAGTCGG
62 TTGCTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGG
* * * * * * * * ** *
2659 GACT-CTGAACGAGGTTTTAACTAAAAACTGTGAT-AACA-TAAACGATTTCGGCTAAAAACTGA
127 GGCTCCAGAATGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAAACTGA
** * ** * *
2721 CCCGATAAGGTTTT-TCTCAATCTTTTGCCACAATACTTAG-AAGAAATATATAATTCAACGCCA
192 CCCGA-AAAATTTTCTCTCAATTTTTTGCCACAATACAAAGAAAAAAATATATAATTCAACTCCA
* * * * * *
2784 AAAAGATTGACGGGCTTTTCACACTTCTAAGATCATTTTTTCATTTTTTTTCCGAATTAATTTCT
256 AAAAGATTGA-GGGCTTTTCACGCTTCAAATATC-GTTTTTC--GTTTTTTCCAAATTAATTTCT
2849 AATT
317 AATT
* * * * * * *
2853 AAATCGAAACAAGATTGAGATGCTC-ATAAAAACAAATCATTATATCCAATGTGGCTAACATTTG
1 AAATCGAAACAAGATTGAGATACTCGA-AAAAACAAATCCTTATATTCAATATTGCTGAGATTTG
** * *
2917 GATCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATCCAAAATTGAG-CTTGGG
65 CTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTC-GGGG
* * * * * *
2981 TTCCAGAAAGCATTTTTAGCCAAAAACAGTGATGGTTAGTACACGATTTCGACTAAAAACTGACC
129 CTCCAGAATGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAAACTGACC
* * * *
3046 CGAAAAATTTTTTCTTAATTTTTTGCCACAATACACAG-AAAAAATATATAATTCAACGCCAAAA
194 CGAAAAATTTTCTCTCAATTTTTTGCCACAATACAAAGAAAAAAATATATAATTCAACTCCAAAA
* *
3110 AGATTGAGGGCTTTTCACGCTTCTAATATCGTTTTTCGTTTTGTTTTCCGAATTAATTTCTAATT
259 AGATTGAGGGCTTTTCACGCTTCAAATATCGTTTTTCG--TT-TTTTCCAAATTAATTTCTAATT
* *
3175 AAATCGAAATAAGATTGAGATGCTCGA
1 AAATCGAAACAAGATTGAGATACTCGA
3202 GAGAGAGAGA
Statistics
Matches: 2402, Mismatches: 359, Indels: 233
0.80 0.12 0.08
Matches are distributed among these distances:
281 162 0.07
282 1 0.00
289 3 0.00
290 1 0.00
291 6 0.00
292 2 0.00
293 2 0.00
294 3 0.00
296 2 0.00
297 6 0.00
298 10 0.00
299 9 0.00
300 14 0.01
301 7 0.00
302 8 0.00
303 14 0.01
304 1 0.00
305 11 0.00
306 5 0.00
308 4 0.00
309 4 0.00
310 7 0.00
311 1 0.00
312 3 0.00
318 90 0.04
319 249 0.10
320 453 0.19
321 349 0.15
322 395 0.16
323 267 0.11
324 312 0.13
325 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (320 bp):
AAATCGAAACAAGATTGAGATACTCGAAAAAACAAATCCTTATATTCAATATTGCTGAGATTTGC
TTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCT
CCAGAATGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAAACTGACCCG
AAAAATTTTCTCTCAATTTTTTGCCACAATACAAAGAAAAAAATATATAATTCAACTCCAAAAAG
ATTGAGGGCTTTTCACGCTTCAAATATCGTTTTTCGTTTTTTCCAAATTAATTTCTAATT
Found at i:2181 original size:321 final size:320
Alignment explanation
Indices: 1493--3199 Score: 1853
Period size: 323 Copynumber: 5.3 Consensus size: 320
1483 AATTTTTTTC
* * * * *
1493 TCAACACCGAAAAGATTTA-GGGCTTTTCACGCTTCTAATATCGTTTTT-CATTTTTTTCTGAAT
1 TCAACGCCAAAAAGATTGACGGGCTTTTCACACTTCTAATATCGTTTTTCCA-TTTTTTCCGAAT
* * * * * * * *
1556 TAATTTCTAATTTAATCAAAATAAGATTGAGATACTCGAAAAAACAAATGCTTATATTCAATATT
65 TAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCAAAAAAACAAATCCTTATATCCAATATG
*
1621 GCTGAGATTTGGTTCGATGAATATAGATATTTCAAAGAGTCTTTGCGCCAAAAATCATGCAAAAT
130 GCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAAT
* ** * * * *
1686 TAAGTCGGGGCTCCGGAATGCGTTTTTAG-CGAAAACAGTGATCGTTAGTACACGAATTCAGCTA
195 TGAGTCGGGGCTCCGGAACACGTTTTTAGCCAAAAACCGTGAT-GTTAGTACACGATTTCGGCTA
* * ** * * * *
1750 AAAACCGATCCGAAATTTTTTTTCTCAACTTCTTGCCACAATACATACA-AAAAGATATATTAT
259 AAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATAC-T-CAGAAAAAATATATAAT
** * * * * *
1813 TCATTGCCAAAAAGATTGACGAGCTTTTAACTCTTCAAATATCGTTTTTCCATTTTTTCCGAACT
1 TCAACGCCAAAAAGATTGACGGGCTTTTCACACTTCTAATATCGTTTTTCCATTTTTTCCGAATT
* * *
1878 AATTTCTAATTAAATCCAAACAAGATTGAGATGATAAAAAAAAACAAATCCTTATATCCAATATG
66 AATTTCTAATTAAATCGAAACAAGATTGAGATGCT-CAAAAAAACAAATCCTTATATCCAATATG
* * * * * *
1943 GCTAAGATTTTGTTCGATGAATATATATATTTCAAGGAGTATTTGCGCCAAAATTCTTGCAAAAT
130 GCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAAT
** * * *
2008 TGAGTCGGGGCTTTGGAACACGTCTTTAGCTAAAAACCGTG-T-TAACGTACACGATTTCGGCTA
195 TGAGTCGGGGCTCCGGAACACGTTTTTAGCCAAAAACCGTGATGTTA-GTACACGATTTCGGCTA
* *
2071 AAAACTGACCCAAAAAGTTTTTTCTCAAGTTTTTTGCCATAATACTCAGAAAAAATATATAAT
259 AAAACTGACCCGAAAAGTTTTTTCTCAA-TTTTTTGCCACAATACTCAGAAAAAATATATAAT
* * * * **
2134 TCAACACCAAAAAGACTGACGGGCTTTTCATATTTCTAATATCGTTTTTCCATTTTTT-ATAATT
1 TCAACGCCAAAAAGATTGACGGGCTTTTCACACTTCTAATATCGTTTTTCCATTTTTTCCGAATT
* * ** * *
2198 AATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATCTGA
66 AATTTCTAATTAAATCGAAACAAGATTGAGATGCTCAAAAAAACAAATCCTTATATCCAATATGG
* * * * ** * * * *
2263 CTGACATATGGTTCGAAGAATATAGATATTTCAAGGTGTCTTTGCATCAAAAACCCTGTAAAATC
131 CTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATT
* * ** ** *
2328 GAGGCGGGGCTCCAGAATGCGGATTTAGCCAAAAACCGTGATG--ACGTACATGATTTCGGCTAA
196 GAGTCGGGGCTCCGGAACACGTTTTTAGCCAAAAACCGTGATGTTA-GTACACGATTTCGGCTAA
* * * *
2391 AAACTGACCCGAAAACTATTTTCTCAATTTTTTGTCATAATACTCAGAAAAAATTATATAAT
260 AAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAA-TATATAAT
* * *
2453 TCAAAGCCAAAAAGATTGACGGG-TTTTCCACGCTTCTAATATCGTTTTTCCAATTTTTTCCAAA
1 TCAACGCCAAAAAGATTGACGGGCTTTT-CACACTTCTAATATCGTTTTTCC-ATTTTTTCCGAA
* * * * *
2517 TTAATTTCTAATTAAATCAAAACAAGATTGAGATGCTTAAAAAATCAAATCCTTTTATTCAATAT
64 TTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCAAAAAAACAAATCCTTATATCCAATAT
* ** ** * * *
2582 GGCTAAGATTTTTTTTTTTTATGAATATAGATATTTCAAGGAGTTTTTGCGGCAAAAATCATTCA
129 GGCTGAGA---TTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCA
* * * * * * *** *
2647 AAATTGAGTCGGGACT-CTGAACGA-GGTTTTAACTAAAAACTGTGATAACA-TAAACGATTTCG
191 AAATTGAGTCGGGGCTCCGGAAC-ACGTTTTTAGCCAAAAACCGTGATGTTAGTACACGATTTCG
* * * * *
2709 GCTAAAAACTGACCCGATAAGGTTTTTCTCAATCTTTTGCCACAATACTTAGAAGAAATATATAA
255 GCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAA
2774 T
320 T
* * *
2775 TCAACGCCAAAAAGATTGACGGGCTTTTCACACTTCTAAGATCATTTTTTCATTTTTTTTCCGAA
1 TCAACGCCAAAAAGATTGACGGGCTTTTCACACTTCTAATATCGTTTTTCCA--TTTTTTCCGAA
* * *
2840 TTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCATAAAAACAAATCATTATATCCAATGT
64 TTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCAAAAAAACAAATCCTTATATCCAATAT
* * * *
2905 GGCTAACATTTGGATCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATCCAAAA
129 GGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAA
* * * * * *
2970 TTGAG-CTTGGGTTCCAGAA-AGCATTTTTAGCCAAAAACAGTGATGGTTAGTACACGATTTCGA
194 TTGAGTC-GGGGCTCCGGAACA-CGTTTTTAGCCAAAAACCGTGAT-GTTAGTACACGATTTCGG
* * *
3033 CTAAAAACTGACCCGAAAAATTTTTTCTTAATTTTTTGCCACAATACACAGAAAAAATATATAAT
256 CTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
* **
3098 TCAACGCCAAAAAGATTGA-GGGCTTTTCACGCTTCTAATATCGTTTTTCGTTTTGTTTTCCGAA
1 TCAACGCCAAAAAGATTGACGGGCTTTTCACACTTCTAATATCGTTTTTC-CATT-TTTTCCGAA
*
3162 TTAATTTCTAATTAAATCGAAATAAGATTGAGATGCTC
64 TTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTC
3200 GAGAGAGAGA
Statistics
Matches: 1147, Mismatches: 210, Indels: 58
0.81 0.15 0.04
Matches are distributed among these distances:
318 29 0.03
319 199 0.17
320 117 0.10
321 251 0.22
322 243 0.21
323 254 0.22
324 53 0.05
325 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (320 bp):
TCAACGCCAAAAAGATTGACGGGCTTTTCACACTTCTAATATCGTTTTTCCATTTTTTCCGAATT
AATTTCTAATTAAATCGAAACAAGATTGAGATGCTCAAAAAAACAAATCCTTATATCCAATATGG
CTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATT
GAGTCGGGGCTCCGGAACACGTTTTTAGCCAAAAACCGTGATGTTAGTACACGATTTCGGCTAAA
AACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
Found at i:2749 original size:641 final size:638
Alignment explanation
Indices: 1493--3644 Score: 2191
Period size: 641 Copynumber: 3.3 Consensus size: 638
1483 AATTTTTTTC
* * *
1493 TCAACACCGAAAAGATTTA-GGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTT-TCTGAAT
1 TCAACACCAAAAAGATTGACGGGCTTTTCACACTTCTAATATCGTTTTTCATTTTTTATC--AAT
* * * * * * * *
1556 TAATTTCTAATTTAATCAAAATAAGATTGAGATACTCGAAAAAACAAATGCTTATATTCAATATT
64 TAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGTAAAAACAAATCCTTATATCCAAT-CT
* *
1621 GCTGAGATTTGGTTCGATGAATATAGATATTTCAAAGAGTCTTTGCGCCAAAAATCATGCAAAAT
128 GCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAAT
* * * * * *
1686 TAAGTCGGGGCTCCGGAATGCGTTTTTAG-CGAAAACAGTGATCGTTAGTACACGAATTCAGCTA
193 TGAGGCGGGGCTCCAGAATGCGTTTTTAGCCAAAAACAGTGATCG-TAGTACACGATTTCGGCTA
* * ** * * * *
1750 AAAACCGATCCGAAATTTTTTTTCTCAACTTCTTGCCACAATACATACA-AAAAGATATATTATT
257 AAAACTGACCCGAAAAATTTTTTCTCAATTTTTTGCCACAATAC-T-CAGAAAAAATATATAATT
** * * * * *
1814 CATTGCCAAAAAGATTGACGAGCTTTTAACTCTTCAAATATCGTTTTTCCATTTTTTCCGAACTA
320 CAAAGCCAAAAAGATTGACG-GGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTA
* *
1879 ATTTCTAATTAAATCCAAACAAGATTGAGATGATAAAAAAAAACAAATCCTTATATCCAATATGG
384 ATTTCTAATTAAATCAAAACAAGATTGAGATGCTAAAAAAAAACAAATCCTTATATCCAATATGG
* *
1944 CTAAGATTTTGTTCGATGAATATATATATTTCAAGGAGTATTTGCGCCAAAATTCTTGCAAAATT
449 CTAAGATTTTGTTCGATGAATATAGATATTTCAAGGAGTATTTGCGCCAAAAATCTTGCAAAATT
* * * * * *
2009 GAGTCGGGGCTTTGGAACACGTCTTTAGCTAAAAACCGTGTTAACGTACACGATTTCGGCTAAAA
514 GAGTCGGGACTCTGGAACACGTCTTTAACTAAAAACCGTGATAACATAAACGATTTCGGCTAAAA
* * *
2074 ACTGACCCAAAAAGTTTTTTCTCAAGTTTTTTGCCATAATACTCAGAAAAAATATATAAT
579 ACTGACCCAAAAAGGTTTTTCTCAAGTCTTTTGCCACAATACTCAGAAAAAATATATAAT
* * *
2134 TCAACACCAAAAAGACTGACGGGCTTTTCATATTTCTAATATCGTTTTTCCATTTTTTAT-AATT
1 TCAACACCAAAAAGATTGACGGGCTTTTCACACTTCTAATATCGTTTTT-CATTTTTTATCAATT
* *
2198 AATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATCTGA
65 AATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATCTG-
* * * ** * * * *
2263 CTGACATATGGTTCGAAGAATATAGATATTTCAAGGTGTCTTTGCATCAAAAACCCTGTAAAATC
129 CTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATT
** * *
2328 GAGGCGGGGCTCCAGAATGCGGATTTAGCCAAAAACCGTGAT-G-ACGTACATGATTTCGGCTAA
194 GAGGCGGGGCTCCAGAATGCGTTTTTAGCCAAAAACAGTGATCGTA-GTACACGATTTCGGCTAA
* * * *
2391 AAACTGACCCGAAAACTATTTTCTCAATTTTTTGTCATAATACTCAGAAAAAATTATATAATTCA
258 AAACTGACCCGAAAAATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAA-TATATAATTCA
*
2456 AAGCCAAAAAGATTGACGGGTTTTCCACGCTTCTAATATCGTTTTTCCAATTTTTTCCAAATTAA
322 AAGCCAAAAAGATTGACGGGTTTT-CACGCTTCTAATATCGTTTTTCC-ATTTTTTCCGAATTAA
* * * *
2521 TTTCTAATTAAATCAAAACAAGATTGAGATGCT-TAAAAAATCAAATCCTTTTATTCAATATGGC
385 TTTCTAATTAAATCAAAACAAGATTGAGATGCTAAAAAAAAACAAATCCTTATATCCAATATGGC
* ** * *
2585 TAAGATTTTTTTTTTTTATGAATATAGATATTTCAAGGAGTTTTTGCGGCAAAAATCATT-CAAA
450 TAAGA---TTTTGTTCGATGAATATAGATATTTCAAGGAGTATTTGCGCCAAAAATC-TTGCAAA
* *
2649 ATTGAGTCGGGACTCT-GAACGAGGT-TTTAACTAAAAACTGTGATAACATAAACGATTTCGGCT
511 ATTGAGTCGGGACTCTGGAAC-ACGTCTTTAACTAAAAACCGTGATAACATAAACGATTTCGGCT
* * * *
2712 AAAAACTGACCCGATAAGGTTTTTCTCAA-TCTTTTGCCACAATACTTAGAAGAAATATATAAT
575 AAAAACTGACCCAAAAAGGTTTTTCTCAAGTCTTTTGCCACAATACTCAGAAAAAATATATAAT
* * * *
2775 TCAACGCCAAAAAGATTGACGGGCTTTTCACACTTCTAAGATCATTTTTTCATTTTTTTTCCGAA
1 TCAACACCAAAAAGATTGACGGGCTTTTCACACTTCTAATATC-GTTTTTCATTTTTTAT-C-AA
* * *
2840 TTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCATAAAAACAAATCATTATATCCAATGT
63 TTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATCT
* * *
2905 GGCTAACATTTGGATCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATCCAAAA
128 -GCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAA
* * * * * *
2970 TTGA-GCTTGGGTTCCAGAAAGCATTTTTAGCCAAAAACAGTGATGGTTAGTACACGATTTCGAC
192 TTGAGGC-GGGGCTCCAGAATGCGTTTTTAGCCAAAAACAGTGATCG-TAGTACACGATTTCGGC
* *
3034 TAAAAACTGACCCGAAAAATTTTTTCTTAATTTTTTGCCACAATACACAGAAAAAATATATAATT
255 TAAAAACTGACCCGAAAAATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATT
* **
3099 CAACGCCAAAAAGATTGA-GGGCTTTTCACGCTTCTAATATCGTTTTTCGTTTTGTTTTCCGAAT
320 CAAAGCCAAAAAGATTGACGGG-TTTTCACGCTTCTAATATCGTTTTTC-CATT-TTTTCCGAAT
* *
3163 TAATTTCTAATTAAATCGAAATAAGATTGAGATGCTCGAGAGAGAGAGAAAAAAAAAACAACACA
382 TAATTTCTAATTAAATCAAAACAAGATTGAGATGCT--------------------------A-A
* * * *
3228 CACACACACACAACAAATCCTTATATCCAATGTTGCTGAGATTTGGTTTC-ATGAATATAGATAT
420 -A-A-A-A-A-AACAAATCCTTATATCCAATATGGCTAAGATTTTG-TTCGATGAATATAGATAT
* * * * * * * * *
3292 TTCAA-GAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGC
478 TTCAAGGAGTATTTGCGCCAAAAATCTTGCAAAATTGAGTCGGGACTCTGGAACACGTCTTTAAC
* ** * * *
3356 GAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAAACTAACCCGAAAA-GTTTTTCCTCAA-
543 TAAAAACCGTGAT-AACA-TAAACGATTTCGGCTAAAAACTGACCCAAAAAGGTTTTT-CTCAAG
* *
3419 TGTTTTGCCACAATACTCATAAAAAA-ATATAAT
605 TCTTTTGCCACAATACTCAGAAAAAATATATAAT
** * * ** * * *
3452 TCAATGCCAAAAAAATTAAATGGTTTTTCACACTTCTAATATCGTTTTTCCTTTTTTTTCGAATT
1 TCAACACCAAAAAGATTGACGGGCTTTTCACACTTCTAATATCGTTTTTCATTTTTTATC-AATT
* * * * * ** *
3517 AATTTTTAATTAAATCGGAACAAGATTTAGATGCTCGTAAAAACAAATACTTAAATTGAATGTGG
65 AATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATCT-G
* ** * * * * *
3582 TTGGGATTTTGTTCGATGAATATAGATATTTCAATGAGTATTTACGCCAAAAATCATGTAAAA
129 CTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAA
3645 CTCAGCCGTA
Statistics
Matches: 1254, Mismatches: 189, Indels: 102
0.81 0.12 0.07
Matches are distributed among these distances:
638 2 0.00
639 12 0.01
640 129 0.10
641 272 0.22
642 105 0.08
643 73 0.06
644 177 0.14
645 75 0.06
646 63 0.05
647 1 0.00
674 2 0.00
675 151 0.12
676 57 0.05
677 54 0.04
678 57 0.05
679 24 0.02
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (638 bp):
TCAACACCAAAAAGATTGACGGGCTTTTCACACTTCTAATATCGTTTTTCATTTTTTATCAATTA
ATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATCTGCT
GACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGA
GGCGGGGCTCCAGAATGCGTTTTTAGCCAAAAACAGTGATCGTAGTACACGATTTCGGCTAAAAA
CTGACCCGAAAAATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAAGC
CAAAAAGATTGACGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTA
ATTAAATCAAAACAAGATTGAGATGCTAAAAAAAAACAAATCCTTATATCCAATATGGCTAAGAT
TTTGTTCGATGAATATAGATATTTCAAGGAGTATTTGCGCCAAAAATCTTGCAAAATTGAGTCGG
GACTCTGGAACACGTCTTTAACTAAAAACCGTGATAACATAAACGATTTCGGCTAAAAACTGACC
CAAAAAGGTTTTTCTCAAGTCTTTTGCCACAATACTCAGAAAAAATATATAAT
Found at i:12667 original size:2 final size:2
Alignment explanation
Indices: 12660--12684 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12650 GATACTCATA
12660 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12685 ATTCAACACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13397 original size:314 final size:314
Alignment explanation
Indices: 12819--14087 Score: 1363
Period size: 315 Copynumber: 4.0 Consensus size: 314
12809 ATGTGGCCGA
* * **
12819 GATTTTATTAGATGAATAAAGATATTTCAAGGAGTTTCAGTGCCAAAAATCATGCAAAACAGAGT
1 GATTTGATTAGATGAATAAAGATATTTCAAGGAGTTTCAGCGCCAAAAATCATGCAAAACAGAAC
* * * * *
12884 CGTAGCCCAGGAAA-ACATTTTTAGCCAAAAACTGTGATGGTTAGCACACGATTTCGGCTA-ATA
66 CGGAGCCCA--AAACGCATTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTATA-A
* * * *
12947 TTTTACAAAAATTGACCCGAAAGTTATTTCCTCAATTTTTAGCCACGATACTCATAAAAAATATA
128 TTTTGCAAAAATTGACCCGAAAGATATTTCCTAAATTTTTAGCCACAATACTCATAAAAAATATA
* *
13012 TAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTCCG
193 TAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTTATTTTCTG
* * * *
13077 AATTAATTTTTAATTAAATCGAAACATGATTGAGATGCTTGTAAAAACAATGGCTGG
258 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAATGGCTGG
** * **
13134 GATTTGATTAGATGAATATTGATATTTCAAGGAGTTTTAGCGCCAAAAATCATGCAAAATTGAAC
1 GATTTGATTAGATGAATAAAGATATTTCAAGGAGTTTCAGCGCCAAAAATCATGCAAAACAGAAC
* * * * * * *
13199 CGGGATCCCAAAACGCGTTTTTAGCAAAAAACCGTGACGATT-TTACACGATTTTGGTTATAATT
66 C-GGAGCCCAAAACGCATTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTATAATT
* * * *
13263 TTGCAAAAATTGACCCGAAAGATATTTTCAAAATTTTTAGCTACAATACTCTTAAAAAATATATA
130 TTGCAAAAATTGACCCGAAAGATATTTCCTAAATTTTTAGCCACAATACTCATAAAAAATATATA
* * * * * * *
13328 ATTCAACGCTAAAAATATTCG-AGGGCTTTTCACGTTTTTAATATCGTATTT-CTTATTTTCCTA
195 ATTCAATGCCAAAAAGATT-GAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTTATTTT-CTG
* *
13391 AATTAATTTCTAATTAAATCGAAACAAGATTCATATGCACGTAAAAACAAATCCTTAAATCCAAT
258 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-------AA-----AAA--C-A-
* *
13456 ATAGCTGA
307 ATGGCTGG
* **
13464 GATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTCAGCGCCAAAAATCATGCAAAACAGAGT
1 GATTTGATTAGATGAATAAAGATATTTCAAGGAGTTTCAGCGCCAAAAATCATGCAAAACAGAAC
* ** * * * * *
13529 CGTAGCACCGGAACGCATTTTTAGCCAAAAACCGTAATGGTTAGTATATGATTTCGACTAGT-AT
66 CGGAGC-CCAAAACGCATTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTA-TAAT
* *
13593 TTTGCAAAAATTGACCCGAAAGTTATTTCCTCAATTTTTAGCCACGAA-ACTCATAAAAAATATA
129 TTTGCAAAAATTGACCCGAAAGATATTTCCTAAATTTTTAGCCAC-AATACTCATAAAAAATATA
** *
13657 TAATTCAATGCCAAAAAGATTGAAGGAATTTTCACGCTTCTAATATCGTTTTTCCTT-TTTTTTG
193 TAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTTATTTTCTG
* * ** * *
13721 AATTAATTTTTAATTAAATCGAAACATGATAAAGAAT-ATTGTAAAAACAATGGCTGG
258 AATTAATTTCTAATTAAATCGAAACAAGATTCAG-ATGCTCGTAAAAACAATGGCTGG
* * ** * * **
13778 AATTTGGTTAGATGAATATTGATATTTCAAGGA-TTCTCGGTGCCAAAAAATCATGCAAAATTGA
1 GATTTGATTAGATGAATAAAGATATTTCAAGGAGTT-TCAGCGCC-AAAAATCATGCAAAACAGA
** * * *
13842 ACCGG-GCCCCGGAATGCGTTTTTAGCCAAAAACCTGTGATGATTAATACACGATTTCGGCTATA
64 ACCGGAG-CCCAAAACGCATTTTTAGCCAAAAACC-GTGATGATTAGTACACGATTTCGGCTATA
* * * * *
13906 ATTTTGCAAAATTTGACCAGAAAGATATTTTCTAAATTTTTAGCCACAATACTCTTAAAATATAT
127 ATTTTGCAAAAATTGACCCGAAAGATATTTCCTAAATTTTTAGCCACAATACTCATAAAAAATAT
* * * *
13971 ATAATTCAATGCCAAAAAGATTGATGGGCTTTTCATGCTTTTAATATCGTTTTTCATATATTTTC
192 ATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCT-TATTTTC
*
14036 TGAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATGCTCGTAAAAACAA
256 TGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
14088 ATCCTTAAAT
Statistics
Matches: 781, Mismatches: 136, Indels: 72
0.79 0.14 0.07
Matches are distributed among these distances:
313 8 0.01
314 225 0.29
315 229 0.29
316 10 0.01
317 46 0.06
318 3 0.00
321 2 0.00
323 2 0.00
326 3 0.00
328 1 0.00
329 4 0.01
330 125 0.16
331 117 0.15
332 6 0.01
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (314 bp):
GATTTGATTAGATGAATAAAGATATTTCAAGGAGTTTCAGCGCCAAAAATCATGCAAAACAGAAC
CGGAGCCCAAAACGCATTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTATAATTT
TGCAAAAATTGACCCGAAAGATATTTCCTAAATTTTTAGCCACAATACTCATAAAAAATATATAA
TTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTTATTTTCTGAAT
TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAATGGCTGG
Done.