Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016394.1 Corchorus olitorius cultivar O-4 contig16427, 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: 3523
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1171 original size:332 final size:331
Alignment explanation
Indices: 1--3523 Score: 4566
Period size: 334 Copynumber: 10.6 Consensus size: 331
* * *
1 ATCGTTTTTCTTTTTTTTTCCCGGAATTTATTTCTAATTAAATCGAAACAAGATTTTGATGCTCG
1 ATCGTTTTTCCTTTTTTTTCCC-GAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCG
* * ** * * * **
66 TTAAAACAAATTCTTAAATCCGATGTGGCTGGGATTTGGTTACA-TGAATATAGATATTTTGGGG
65 TAAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACT-AATATAGATATTTTAAGG
* * ** *
130 AGTTTTTTTTGTTAAAAATCATTCAAAACTGAGCCGGGGCTTCGAAACACGTTTTTAGCCCGTAA
129 AG-TCTTTTTGTTAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCG-AA
* * * *
195 ATCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGAAAAATATTTCCT
192 AAC--CATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCT
* *
260 CATTGTTTTGCCACAACGATCAG-AAAAATATATAATTCAACGCAAAAAGCATAGAAGGGTTTTT
255 CATTGTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTT
*
324 CACGCCTCTAAT
320 CACGCTTCTAAT
* * * *
336 ATCGTTTTTCCTTTTATTT-CTGAATATATTTCTAATTAAATCGAAGCAAGAATTAGATGCTCGT
1 ATCGTTTTTCCTTTTTTTTCCCGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT
*
400 -AAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAACATAGATATTTTAAGGAG
66 AAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAG
** * * * *****
464 TCTTTTTGTTAAAAATCATGCAGTACTGAGAC-GGGACCCGAAACGCATTTTTAGCCCGATCGTG
131 TCTTTTTGTTAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAAACC
* * * * *
528 AAGGTTAGTACACGATTTCGGCAAAAATTTTGCAAAAACTAACCTGAAAAATTTTTCCTCATTCT
196 ATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCATTGT
* *
593 TTAGCCACAACGGTCAGAATAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCACGCT
261 TTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCACGCT
658 TCTAAT
326 TCTAAT
* * *
664 ATCGTTTTTCCTTTTTTTT-CTGAATATATTTCTAATTAAATCGAAACAAGATTTAAATGCTTGT
1 ATCGTTTTTCCTTTTTTTTCCCGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT
728 AAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAG
66 AAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAG
* * *
793 TCTTTCTGTTAAAAATCATGCAAAACTGAGCCGGTGCCCAGAAACGCGTTTTTAGCCCGAAAACC
131 TCTTTTTGTTAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAAACC
** *
858 AT-GAAAGTACACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCATTGT
196 ATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCATTGT
* *
922 TTTGCCACAATGGTCAGAAAAAATATATAATTGAACGCAAAAAGCATTGAAGGGTTTTTCACGCT
261 TTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCACGCT
987 TCTAAT
326 TCTAAT
*
993 ATCGTTTTTCCTTCTTTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTC
1 ATCGTTTTTCC-T-TTTTTTTCCCGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTC
* * * * *
1058 GTAAAAACAAATCCTTAAATCCAATGTGGCTGGGATTTGGTCACA-TGAATATAGATATTTTAAG
64 GTAAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACT-AATATAGATATTTTAAG
1122 GAGTCTTTTTGTTAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAA
128 GAGTCTTTTTGTTAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAA
* * *
1187 ATCGTGATGGTT-GTACACGATTTCGGCTAAAATTTTGCAAAAACTGACACGATAAATTTTTCCT
193 A-C--CATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCT
1251 CATTGTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTT
255 CATTGTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTT
1316 CACGCTTCTAAT
320 CACGCTTCTAAT
* *
1328 ATCGTTTTTCCTTTTATTT-CTGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT
1 ATCGTTTTTCCTTTTTTTTCCCGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT
*
1392 CAAAACAAATCCATTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGA
66 AAAAACAAATCC-TTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGA
* * * *
1457 GTCTTTCTGTAAAAAATCATGCAAAACTGAGACAGGGCCCCGAAACGCGTTTTTAGCCCGAAAAC
130 GTCTTTTTGTTAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAAAC
*
1522 CGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCA
195 C---ATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCA
*
1587 TTGTTTTGCCACAACGGTCACAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCA
257 TTGTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCA
1652 CGCTTCTAAT
322 CGCTTCTAAT
* * * *
1662 ATTGTTTTTCCTTTTATTT-CTGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGT
1 ATCGTTTTTCCTTTTTTTTCCCGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT
* ***
1726 AAAAACAAATTCTTAAATCAAATTTGGCTGAGATTTGACCAGACTAATATAGATATTTTAAAGGA
66 AAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTT-AAGGA
** *** **
1791 GTCTTTCAGTTAAAAATCATGCAAAACTGAGTAAGGGCCCCGAAAAACGTTTTTAGCCCGAAAAC
130 GTCTTTTTGTTAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAAAC
* * *
1856 CGTGATGGTCAGTACACGATTTCGGCTAAAAATTTGCAAAAATTGACCCGAAAAATTTTTCCCTC
195 C---ATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTT-CCTC
* *
1921 AATGTTTTTGCCACAACGGTCA-AAAAAATATATAATTCAACGCAAAAAG-AGTTGAAGGGTTTA
256 ATTG-TTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCA-TTGAAGGGTTTT
*
1984 TGACGCTTCTAAT
319 TCACGCTTCTAAT
* * * *
1997 ATCGTTTTTGCTTTTATTTT--TGAATATATTTCTAATTAAATCGAAACAACATTTAAATGCTCG
1 ATCGTTTTTCCTTTT-TTTTCCCGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCG
*
2060 TAAAAACAAAACCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGA
65 TAAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGA
* * * * *
2125 GTCTTTTTGTTAAAAATCATGCAAAACTAAGACGGGACCCCGGAACGCATTTTTAGCCCGAAAAT
130 GTCTTTTTGTTAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAAA-
* * *
2190 CGTGAAGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTAACCCGAAAAATTTTTCCTCA
194 C--CATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCA
* *
2255 TTCTTTAGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCA
257 TTGTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCA
* *
2320 TGCTTCGCAAAAAGCATT
322 CGCTT--C---TA--A-T
** ** ** * *
2338 GAAGGGTTTTTCACGCTTCTAATATTGTTTTTC-TTTTTATTTCTGAATATATTTCTAAT-TAAA
1 --ATCGTTTTT--C-C-T-T--T-TT-TTTCCCGAATATATTTCT-AAT-TA-----AATCGAAA
* * * * * *
2401 TCGAAAAAAGATTTAGATGCTAGTAAAAACAAAACCTTAAATCAAATTTGGCTAAGATTTAGTTA
48 -C-AAGAT----TTAGATGCTCGTAAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTA
* *
2466 GACTAACATTGATATTTTAAGGAGT-TTTTCTGTTAAAAATCATGCAAAACTGAGCCGGGGCCCC
107 GACTAATATAGATATTTTAAGGAGTCTTTT-TGTTAAAAATCATGCAAAACTGAGCCGGGGCCCC
* * *
2530 GAAAAGCGTTTTTAGCCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAA
171 GAAACGCGTTTTTAGCCCGAAAA-C--CATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAA
* * * *
2595 ATTGACCTGAAAAATTTTTCCTCATTGTTTTGCCACAACGGTTAGAAAAAATTTATAATTCAACG
233 ACTGACCCGAAAAATTTTTCCTCATTGTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACG
2660 CAAAAAGCATTGAAGGGTTTTTCACGCTTCTAAT
298 CAAAAAGCATTGAAGGGTTTTTCACGCTTCTAAT
* * * *
2694 ATTGTTTTTCCTTTTATTTCTC-AATATATTTCTAATTAAATCGAACCAAGATTTAGATGCTCGT
1 ATCGTTTTTCCTTTTTTTTCCCGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT
* *
2758 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAG
66 AAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAG
* * * ** *
2823 CCTTTCTGTTAAAAATCTTGCAAAACTGAGTTGGGGCCCCGAAACGCGTTTTTAGCTCGAAAACC
131 TCTTTTTGTTAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAAACC
* *
2888 GTGATGGTTAGTACACGATTTCGGCTAAAATTTCGCAAAAACTGACCCG-AAAATTCTTCCTCAT
196 ---ATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCAT
* * *
2952 TGTTTTGCCCCAACGATCAGAAATAATATATAATTCAACGC-AAAAGCATTGAAGGGTTTTTCAC
258 TGTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCAC
3016 GCTTCTAAT
323 GCTTCTAAT
* * *
3025 ATCGTTTTTCC--TTTTTTCCCGAATTTATTTCTAATTAAATCCAAACAAGATTTAAATGCTCGT
1 ATCGTTTTTCCTTTTTTTTCCCGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT
3088 AAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAG
66 AAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAG
* ** * ** *
3153 TCTTTCTGTTAAAAAATCATTTAAAACTGAGCCGAGGCCCCGAAACTTGTTTTTAGCCCGAAATC
131 TCTTTTTGTT-AAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAAAC
* * *
3218 C---GTGA-TACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCAAAAAATGTTTCCTCATTG
195 CATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCATTG
*
3279 TTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATCGAAGGGTTTTTCACGC
260 TTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCACGC
3344 TTCTAAT
325 TTCTAAT
* * * * *
3351 ATCG-TTTTCC-TTTTTTTCCTGAATTTATTTCTAATTTAATCGAAACATGATTTAGATGCTCCT
1 ATCGTTTTTCCTTTTTTTTCCCGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT
* * *
3414 AAAAACAAAT-C------C-AATGTGGCTGGGATTTGGTTACA-TGAATATAGATATTTTAAGGA
66 AAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACT-AATATAGATATTTTAAGGA
* * *
3470 GTCTTTTTGTTAAAAATCATGCAAAACTGAGACGGGGCCCTGGAACGCGTTTTT
130 GTCTTTTTGTTAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTT
Statistics
Matches: 2831, Mismatches: 283, Indels: 166
0.86 0.09 0.05
Matches are distributed among these distances:
317 36 0.01
318 49 0.02
319 1 0.00
324 36 0.01
325 61 0.02
326 91 0.03
327 74 0.03
328 109 0.04
329 232 0.08
330 156 0.06
331 122 0.04
332 334 0.12
333 415 0.15
334 434 0.15
335 321 0.11
336 21 0.01
337 3 0.00
338 5 0.00
339 2 0.00
340 1 0.00
341 1 0.00
343 9 0.00
344 3 0.00
345 13 0.00
346 2 0.00
347 2 0.00
348 1 0.00
349 1 0.00
350 3 0.00
351 5 0.00
352 9 0.00
353 3 0.00
354 9 0.00
356 1 0.00
357 1 0.00
358 3 0.00
359 5 0.00
360 3 0.00
362 1 0.00
363 4 0.00
364 249 0.09
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (331 bp):
ATCGTTTTTCCTTTTTTTTCCCGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT
AAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAG
TCTTTTTGTTAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAAACC
ATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCATTGT
TTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCACGCT
TCTAAT
Found at i:1753 original size:333 final size:333
Alignment explanation
Indices: 1--3523 Score: 4888
Period size: 333 Copynumber: 10.5 Consensus size: 333
* * * * *
1 ATCGTTTTTCTTTTTTTTTCCCGGAATTTATTTCTAATTAAATCGAAACAAGATTTTGATGCTCG
1 ATCGTTTTTCCTTTTATTT--CTGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCG
* * ** * * * **
66 TTAAAACAAATTCTTAAATCCGATGTGGCTGGGATTTGGTTACA-TGAATATAGATATTTTGGGG
64 TAAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACT-AATATAGATATTTTAAGG
* * * * ** * *
130 AGTTTTTTTTGTTAAAAATCATTCAAAACTGAGCCGGGGCTTCGAAACACGTTTTTAGCCCGTAA
128 AG-TCTTTCTGTTAAAAATCATGCAAAACTGAGACGGGGCCCCGAAACGCGTTTTTAGCCCGAAA
* * *
195 ATCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGAAAAATATTTCCT
192 ACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCT
* *
260 CATTGTTTTGCCACAACGATCAG-AAAAATATATAATTCAACGCAAAAAGCATAGAAGGGTTTTT
257 CATTGTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTT
*
324 CACGCCTCTAAT
322 CACGCTTCTAAT
* *
336 ATCGTTTTTCCTTTTATTTCTGAATATATTTCTAATTAAATCGAAGCAAGAATTAGATGCTCGT-
1 ATCGTTTTTCCTTTTATTTCTGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTA
*
400 AAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAACATAGATATTTTAAGGAGT
66 AAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAGT
* ** * * *
465 CTTTTTGTTAAAAATCATGCAGTACTGAGAC-GGGACCCGAAACGCATTTTTAGCCCG---ATCG
131 CTTTCTGTTAAAAATCATGCAAAACTGAGACGGGGCCCCGAAACGCGTTTTTAGCCCGAAAACCG
* * * *
526 TGAAGGTTAGTACACGATTTCGGCAAAAATTTTGCAAAAACTAACCTGAAAAATTTTTCCTCATT
196 TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCATT
* * *
591 CTTTAGCCACAACGGTCAGAATAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCACG
261 GTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCACG
656 CTTCTAAT
326 CTTCTAAT
* * *
664 ATCGTTTTTCCTTTTTTTTCTGAATATATTTCTAATTAAATCGAAACAAGATTTAAATGCTTGTA
1 ATCGTTTTTCCTTTTATTTCTGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTA
729 AAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAGT
66 AAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAGT
* * *
794 CTTTCTGTTAAAAATCATGCAAAACTGAGCCGGTGCCCAGAAACGCGTTTTTAGCCCGAAAACC-
131 CTTTCTGTTAAAAATCATGCAAAACTGAGACGGGGCCCCGAAACGCGTTTTTAGCCCGAAAACCG
** *
858 --AT-GAAAGTACACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCATT
196 TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCATT
* *
920 GTTTTGCCACAATGGTCAGAAAAAATATATAATTGAACGCAAAAAGCATTGAAGGGTTTTTCACG
261 GTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCACG
985 CTTCTAAT
326 CTTCTAAT
* * *
993 ATCGTTTTTCCTTCTTTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTC
1 ATCGTTTTTCC-T-TTTATTT-CTGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTC
* * * * *
1058 GTAAAAACAAATCCTTAAATCCAATGTGGCTGGGATTTGGTCACA-TGAATATAGATATTTTAAG
63 GTAAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACT-AATATAGATATTTTAAG
* *
1122 GAGTCTTTTTGTTAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAA
127 GAGTCTTTCTGTTAAAAATCATGCAAAACTGAGACGGGGCCCCGAAACGCGTTTTTAGCCCGAAA
* * *
1187 ATCGTGATGGTT-GTACACGATTTCGGCTAAAATTTTGCAAAAACTGACACGATAAATTTTTCCT
192 ACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCT
1251 CATTGTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTT
257 CATTGTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTT
1316 CACGCTTCTAAT
322 CACGCTTCTAAT
*
1328 ATCGTTTTTCCTTTTATTTCTGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTC
1 ATCGTTTTTCCTTTTATTTCTGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTA
1393 AAAACAAATCCATTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAG
66 AAAACAAATCC-TTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAG
* *
1458 TCTTTCTGTAAAAAATCATGCAAAACTGAGACAGGGCCCCGAAACGCGTTTTTAGCCCGAAAACC
130 TCTTTCTGTTAAAAATCATGCAAAACTGAGACGGGGCCCCGAAACGCGTTTTTAGCCCGAAAACC
*
1523 GTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCAT
195 GTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCAT
*
1588 TGTTTTGCCACAACGGTCACAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCAC
260 TGTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCAC
1653 GCTTCTAAT
325 GCTTCTAAT
* *
1662 ATTGTTTTTCCTTTTATTTCTGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGTA
1 ATCGTTTTTCCTTTTATTTCTGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTA
* ***
1727 AAAACAAATTCTTAAATCAAATTTGGCTGAGATTTGACCAGACTAATATAGATATTTTAAAGGAG
66 AAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTT-AAGGAG
* * **
1792 TCTTTCAGTTAAAAATCATGCAAAACTGAGTA-AGGGCCCCGAAAAACGTTTTTAGCCCGAAAAC
130 TCTTTCTGTTAAAAATCATGCAAAACTGAG-ACGGGGCCCCGAAACGCGTTTTTAGCCCGAAAAC
* * *
1856 CGTGATGGTCAGTACACGATTTCGGCTAAAAATTTGCAAAAATTGACCCGAAAAATTTTTCCCTC
194 CGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTT-CCTC
* *
1921 AATGTTTTTGCCACAACGGTCA-AAAAAATATATAATTCAACGCAAAAAG-AGTTGAAGGGTTTA
258 ATTG-TTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCA-TTGAAGGGTTTT
*
1984 TGACGCTTCTAAT
321 TCACGCTTCTAAT
* * * *
1997 ATCGTTTTTGCTTTTATTTTTGAATATATTTCTAATTAAATCGAAACAACATTTAAATGCTCGTA
1 ATCGTTTTTCCTTTTATTTCTGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTA
*
2062 AAAACAAAACCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAGT
66 AAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAGT
* * * * * *
2127 CTTTTTGTTAAAAATCATGCAAAACTAAGACGGGACCCCGGAACGCATTTTTAGCCCGAAAATCG
131 CTTTCTGTTAAAAATCATGCAAAACTGAGACGGGGCCCCGAAACGCGTTTTTAGCCCGAAAACCG
* *
2192 TGAAGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTAACCCGAAAAATTTTTCCTCATT
196 TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCATT
* * *
2257 CTTTAGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCATG
261 GTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCACG
2322 CTTCGCAAAAAGCATTGAAGGGTTT
326 CTT---------C--T-AA-----T
* * *
2347 TTCACGCTTCTAATATTGTTTTTCTTTTTATTTCTGAATATATTTCTAATTAAATCGAAAAAAGA
1 AT--CG----T--T-T-----TTCCTTTTATTTCTGAATATATTTCTAATTAAATCGAAACAAGA
* * * * * *
2412 TTTAGATGCTAGTAAAAACAAAACCTTAAATCAAATTTGGCTAAGATTTAGTTAGACTAACATTG
52 TTTAGATGCTCGTAAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAG
* * *
2477 ATATTTTAAGGAGTTTTTCTGTTAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAAAGCGTTTT
117 ATATTTTAAGGAGTCTTTCTGTTAAAAATCATGCAAAACTGAGACGGGGCCCCGAAACGCGTTTT
* * * *
2542 TAGCCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAA
182 TAGCCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAA
* *
2607 AATTTTTCCTCATTGTTTTGCCACAACGGTTAGAAAAAATTTATAATTCAACGCAAAAAGCATTG
247 AATTTTTCCTCATTGTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTG
2672 AAGGGTTTTTCACGCTTCTAAT
312 AAGGGTTTTTCACGCTTCTAAT
* * *
2694 ATTGTTTTTCCTTTTATTTCTCAATATATTTCTAATTAAATCGAACCAAGATTTAGATGCTCGTA
1 ATCGTTTTTCCTTTTATTTCTGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTA
* * *
2759 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAGC
66 AAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAGT
* ** *
2824 CTTTCTGTTAAAAATCTTGCAAAACTGAGTTGGGGCCCCGAAACGCGTTTTTAGCTCGAAAACCG
131 CTTTCTGTTAAAAATCATGCAAAACTGAGACGGGGCCCCGAAACGCGTTTTTAGCCCGAAAACCG
* *
2889 TGATGGTTAGTACACGATTTCGGCTAAAATTTCGCAAAAACTGACCCG-AAAATTCTTCCTCATT
196 TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCATT
* * *
2953 GTTTTGCCCCAACGATCAGAAATAATATATAATTCAACGC-AAAAGCATTGAAGGGTTTTTCACG
261 GTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCACG
3017 CTTCTAAT
326 CTTCTAAT
* * * * *
3025 ATCGTTTTTCCTTTT-TTCCCGAATTTATTTCTAATTAAATCCAAACAAGATTTAAATGCTCGTA
1 ATCGTTTTTCCTTTTATTTCTGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTA
3089 AAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAGT
66 AAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAGT
** * * ** *
3154 CTTTCTGTTAAAAAATCATTTAAAACTGAGCCGAGGCCCCGAAACTTGTTTTTAGCCCGAAATCC
131 CTTTCTGTT-AAAAATCATGCAAAACTGAGACGGGGCCCCGAAACGCGTTTTTAGCCCGAAAACC
* *
3219 --G-T-G--A-TACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCAAAAAATGTTTCCTCAT
195 GTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCAT
*
3277 TGTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATCGAAGGGTTTTTCAC
260 TGTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCAC
3342 GCTTCTAAT
325 GCTTCTAAT
* * * *
3351 ATCG-TTTTCCTTTT-TTTCCTGAATTTATTTCTAATTTAATCGAAACATGATTTAGATGCTCCT
1 ATCGTTTTTCCTTTTATTT-CTGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT
* * *
3414 AAAAACAAAT-C------C-AATGTGGCTGGGATTTGGTTACA-TGAATATAGATATTTTAAGGA
65 AAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACT-AATATAGATATTTTAAGGA
* * *
3470 GTCTTTTTGTTAAAAATCATGCAAAACTGAGACGGGGCCCTGGAACGCGTTTTT
129 GTCTTTCTGTTAAAAATCATGCAAAACTGAGACGGGGCCCCGAAACGCGTTTTT
Statistics
Matches: 2863, Mismatches: 263, Indels: 142
0.88 0.08 0.04
Matches are distributed among these distances:
317 36 0.01
318 49 0.02
319 1 0.00
324 36 0.01
325 65 0.02
326 84 0.03
327 80 0.03
328 110 0.04
329 225 0.08
330 158 0.06
331 126 0.04
332 333 0.12
333 471 0.16
334 434 0.15
335 324 0.11
336 18 0.01
338 1 0.00
339 1 0.00
341 1 0.00
342 1 0.00
344 1 0.00
345 3 0.00
347 2 0.00
350 2 0.00
352 4 0.00
353 1 0.00
355 1 0.00
356 1 0.00
358 1 0.00
359 1 0.00
364 292 0.10
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (333 bp):
ATCGTTTTTCCTTTTATTTCTGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTA
AAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAGT
CTTTCTGTTAAAAATCATGCAAAACTGAGACGGGGCCCCGAAACGCGTTTTTAGCCCGAAAACCG
TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCATT
GTTTTGCCACAACGGTCAGAAAAAATATATAATTCAACGCAAAAAGCATTGAAGGGTTTTTCACG
CTTCTAAT
Found at i:2329 original size:31 final size:31
Alignment explanation
Indices: 2294--2356 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
2284 TATAATTCAA
*
2294 CGCAAAAAGCATTGAAGGGTTTTTCATGCTT
1 CGCAAAAAGCATTGAAGGGTTTTTCACGCTT
2325 CGCAAAAAGCATTGAAGGGTTTTTCACGCTT
1 CGCAAAAAGCATTGAAGGGTTTTTCACGCTT
2356 C
1 C
2357 TAATATTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (31 bp):
CGCAAAAAGCATTGAAGGGTTTTTCACGCTT
Done.