Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011814.1 Corchorus capsularis cultivar CVL-1 contig11835, 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: 6138
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Found at i:592 original size:326 final size:323
Alignment explanation
Indices: 1--5174 Score: 5760
Period size: 324 Copynumber: 16.1 Consensus size: 323
* * **
1 CAAAAAAACTGTGATGGTTAGTACACGATTTTGACTAAAAACTG-ACCCGAATTTTTTTTCCTCA
1 CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGAACCAAAATTTTTTTT-CTCA
* * * *
65 AGTTT-TTGCGACAATAAACAGAAAAAATATAAAATTCAATGCCAAAAAGATTGATGGGCTTTTC
65 A-TTTCTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTC
* * * * * *
129 ACGCGTCTAATGTCGTTTTCCCTTTTTTTTTTCCGATTTAGTTTCAAATTAAATCGAAACAAGAT
129 ACGCTTCTAATATCGTTTTTCC-ATTTTTTTTCCGATATAGTTTCTAATTAAATCGAAACAAGAT
* * * *
194 TGAGATGCTCAAAAAAA-AAATCCTTATAACCAACATTGCTGAGATTTAGTCCCATGAGTATAGA
193 TGAGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGGTTCGATGAATATAGA
* * * *
258 TATTTCAAGCAGTTTTTGAGCAAAAAATCATGCAAAATTGAGCCGGTGTTCCAGAACCCCTTTTT
258 TATTTCAAGCAGTCTTTGAGCCAAAAATCATGCAAAATTGAGCCGG-GCTCCGGAACCCCTTTTT
323 AG
322 AG
* * * *
325 CAAAAAAATCGTGATGGTTAGTAAACAATTTTAGCTAAAAACTGAACCAAAATTTGTTTTTTCTC
1 CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGAACCAAAA-TT-TTTTTTCTC
* * * *
390 AATTTCTTGCAACAATACACAGAAAACATATATAATCCAATGCCAAAAAGATTGATGGGCTTTTC
64 AATTTCTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTC
455 ACGCTTCTAATGA-CGTTTTTCCATTTTTTTTCCGATATAGTTTCTAATTAAATCGAAACAAGAT
129 ACGCTTCTAAT-ATCGTTTTTCCATTTTTTTTCCGATATAGTTTCTAATTAAATCGAAACAAGAT
519 TGAGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGGTTCGATGAATATAGA
193 TGAGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGGTTCGATGAATATAGA
* *
584 TATTTCAAGCAGAT-TTTGAGCCAAAAATCATGCAAAATTTAGTCGGGGCTCCGGAACCCCTTTT
258 TATTTCAAGCAG-TCTTTGAGCCAAAAATCATGCAAAATTGAG-CCGGGCTCCGGAACCCCTTTT
648 TAG
321 TAG
* * *
651 CAAAAAAACCGTGATGGTTTGTATACGATTTTGGCTAAAAACTGAACCAAATTTTTTTTTTCTCA
1 CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGAACCAAA-ATTTTTTTTCTCA
* * *
716 ATTTCTTGCCACAATACACAGAAAATATATATAATCCAATACCAAAAAGATTGACGGGCTTTTCA
65 ATTTCTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCA
* * * *
781 CGCTTCTAATATCGTTTTTTTTTTCATTTTGTTTT-CGA-ATTAATTTTTAATTAAATCGAAAAA
130 CGCTTCTAATATCG----TTTTTCCATTTT-TTTTCCGATA-TAGTTTCTAATTAAATCGAAACA
* * * * * *
844 AGATTCAGATGTTCATAAAAAGAAATCCTTA-AATCC-A-A-TG-AGACAGATTTGTTTCGATGA
189 AGATTGAGATGCTCAAAAAAACAAATCCTTATAA-CCAACATTGCTG--AGATTTGGTTCGATGA
* * ** * * * *
904 ATATAGATATTTCAAGAATTCTTTGATTCAAAAATCATGCGAAATTGAGCTGGGCTCCGAAACGT
251 ATATAGATATTTCAAGCAGTCTTTGAGCCAAAAATCATGCAAAATTGAGCCGGGCTCCGGAAC-C
**
969 GTTTTTTAGG
315 CCTTTTTA-G
** * * * *
979 C--AAAAACCGTGATGGTTAGTATGCGATTTCGGTTAAAAACT-AACCCGAAAA-TTGTTTTCTT
1 CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGAA-CC-AAAATTTTTTTTCTC
* * *
1040 AATTTTTTTGCCACAATACACAG-AAAAATATATAATTCAATGCCAAAAAGATTGACAGGCATTT
64 AA-TTTCTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTT
* ** *
1104 CAAGCTTCTAATATCGTTTTTCTTTTTTTTTTTCCGATTTAGTTTCTAATTAAATCGAAACAAGA
128 CACGCTTCTAATATCGTTTTTC-CATTTTTTTTCCGATATAGTTTCTAATTAAATCGAAACAAGA
* * *
1169 TTGAGGTACTC-AAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGATTCGATGAATATAG
192 TTGAGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGGTTCGATGAATATAG
* *
1233 ATATTTCAAGCAGTCTTTGAGCCAAAAATCATGCAAAATTGAGTCGGGACTCTGGAACCCCTTTT
257 ATATTTCAAGCAGTCTTTGAGCCAAAAATCATGCAAAATTGAGCCGGG-CTCCGGAACCCCTTTT
1298 TAG
321 TAG
* * *
1301 C---AAAA-----A-----AGTACACGATTTGGGCTAAAAACTGACCCGAAATTTTTTTTCTCAA
1 CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGAACCAAAATTTTTTTTCTC-A
* * *
1353 ATTT-TTTCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGATGGCCTTTTCA
65 ATTTCTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCA
* * * * *
1417 CGCTTCTAATGTTG-TTTTCCCTTTTGTTTTCCGATTTAGTTTCAAATTAAATCGAAACAAGATT
130 CGCTTCTAATATCGTTTTTCCATTTT-TTTTCCGATATAGTTTCTAATTAAATCGAAACAAGATT
* * *
1481 GAGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTAGTTTGATGAGTATAGAT
194 GAGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGGTTCGATGAATATAGAT
* * *
1546 ATTTCAAGCAGTTTTTGAGCCAAAAATCATGCAAAATT-A------AT--TGAA---------AG
259 ATTTCAAGCAGTCTTTGAGCCAAAAATCATGCAAAATTGAGCCGGGCTCCGGAACCCCTTTTTAG
* * * * *
1593 CAAAAAAATCGTGATGGTTAGTAAACAATTTTAGCTAAAAACTGAACCAAATTTTTTTTTTCTCA
1 CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGAACCAAA-ATTTTTTTTCTCA
* * *
1658 ATTTCTTGCCACAATACACAGAAAATATATATAATCCAATGCCAAAAAGATTGATGGGCTTTTCA
65 ATTTCTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCA
1723 CGCTTCTAATGA-CGTTTTTCCATTTTTTTTTCCGATATAGTTTCTAATTAAATCGAAACAAGAT
130 CGCTTCTAAT-ATCGTTTTTCCA-TTTTTTTTCCGATATAGTTTCTAATTAAATCGAAACAAGAT
*
1787 TGAGATGCTCGAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGGTTCGATGAATATAGA
193 TGAGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGGTTCGATGAATATAGA
* *
1852 TATTTCAAGCAGTTTTTGAGCCAAAAATCATGCAAAATTGAGTCGGGACTCCGGAACCCCTTTTT
258 TATTTCAAGCAGTCTTTGAGCCAAAAATCATGCAAAATTGAGCCGGG-CTCCGGAACCCCTTTTT
1917 AG
322 AG
**
1919 CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTG-ACCCGAATTTTTTTTCCTCA
1 CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGAACCAAAATTTTTTTT-CTCA
* * *
1983 AGTTT-TTGCGACAATTCACAGAAAAAATATATAATTCAATGCCAAAAAGATTGATGGGCTTTTC
65 A-TTTCTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTC
* * * * *
2047 ACGCGTCTAATGTCG-TTTTCCTTTTTTTTTTCCGATTTAGTTTCAAATTAAATCGAAACAAGAT
129 ACGCTTCTAATATCGTTTTTCC-ATTTTTTTTCCGATATAGTTTCTAATTAAATCGAAACAAGAT
*
2111 TGAGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTAGTTCGATGAATATAGA
193 TGAGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGGTTCGATGAATATAGA
* * *
2176 TATTTCAAGCAGTCTTTGAGGCAAAAATCATGCAAACTTGAGTCGGGGCTCCGGAACCCCTTTTT
258 TATTTCAAGCAGTCTTTGAGCCAAAAATCATGCAAAATTGAG-CCGGGCTCCGGAACCCCTTTTT
2241 AG
322 AG
* * *
2243 GAAAAAAACCGTGATGGTTAGTATACGATTTTGGCTAAAAACTGAACCAAATTTTTTTTTCTCAA
1 CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGAACCAAAATTTTTTTTCTCAA
* * *
2308 TTTCTTGCCACAATACACAGAAAATATATATAA-TCGTATACCAAAAAGATTGACGGGCTTTTCA
66 TTTCTTGCCACAATACACAGAAAAAATATATAATTC-AATGCCAAAAAGATTGACGGGCTTTTCA
* * * * *
2372 CGCTTCTAATATCATTTTTTCCATTTTTTTTCCGA-ATTAATTTTTAGTTAAATCGAAAAAAGAT
130 CGCTTCTAATATC-GTTTTTCCATTTTTTTTCCGATA-TAGTTTCTAATTAAATCGAAACAAGAT
* * * * * *
2436 TTAGATGCTCATAAAAACAAATCATTATATCC-A-A-TG-AGACAGATTTGTTTCGATGAATATA
193 TGAGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTG--AGATTTGGTTCGATGAATATA
* * * ***
2497 GATATTTCAAGAAGTCTTTGAGTCC-AAAATCATGCAAAATTGAGCTGGGCTCCGAAACGTATTT
256 GATATTTCAAGCAGTCTTTGAG-CCAAAAATCATGCAAAATTGAGCCGGGCTCCGGAAC-CCCTT
2561 TTTAG
319 TTTAG
* * *
2566 TC--AAAAACCGTGATGGTTAGTATACGATTTCGACTAAAAACT-AACCCGAAAA--TTTTTTCT
1 -CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGAA-CC-AAAATTTTTTTTCT
* * * * *
2626 TAATTTTTTGTCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGA-AGGCATTT
63 CAATTTCTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTT
* **
2690 CAAGCTTCTAATATCGTTTTT-C--TTTTTTT----T-T--TTTCCGATT---T-------A-AT
128 CACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGATATAGTTTCTAATTAAATCGAAACAAGAT
* * * * *
2734 TGAGATGCTCGAAAAAACAAATTCTTATATCCAATATTACTGAGATTTGGTTCGATGAATATAGA
193 TGAGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGGTTCGATGAATATAGA
* * ** * *
2799 TAGTTCAAGCAGTCTTTGAGCCAAAAATCACGCAAAATTGAGACAAGGCTCCGAAACGCCTTTTT
258 TATTTCAAGCAGTCTTTGAGCCAAAAATCATGCAAAATTGAG-CCGGGCTCCGGAACCCCTTTTT
2864 AG
322 AG
* * * * * * *
2866 C-AAAAAATCGTGATGGTTAGTACATGAATTTGGCTAAGAACTTACCCGGAAAA--TTTTTTCAC
1 CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGAACC--AAAATTTTTTTTCTC
* * * * **
2928 AATTT-TTTCCACAAAACACAGAAAAAATATGTAATTCAATGTCAAAAAGATTGATAGGCTTTTC
64 AATTTCTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTC
* * * * * *
2992 ATGCTTCTAATGTCG-TTTTCCCTTTTTTTTCCGATTTAGTTTCTAATTAAATTGAAACAAGACT
129 ACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGATATAGTTTCTAATTAAATCGAAACAAGATT
* *
3056 GAGATGCTCAAAAAAACAAATCCTTATAACCAATATTGCTGAGATTTGGTTCGATGAATATAGAA
194 GAGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGGTTCGATGAATATAGAT
* * *
3121 ATTTCAAGCAGTCTTTGAGACAAAAATCACGCAAAATTGAGCCGGGGCTCCGGAACGCCTTTTTA
259 ATTTCAAGCAGTCTTTGAGCCAAAAATCATGCAAAATTGAGCC-GGGCTCCGGAACCCCTTTTTA
3186 G
323 G
* * * *
3187 C-AAAAAACCGTGATTGTTAGTACATGATTTTGGCTAAAAATTGACCCGAAAA-TTTTTTTCTCA
1 CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGAACC-AAAATTTTTTTTCTC-
* *
3250 AATTT-TTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGATGGGTTTTTC
64 AATTTCTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTC
* * * *
3314 ACGCTTCTAATGTCGTTTTTCCATTTTTTTTTCTGATTTAGTTTCTAATCAAATCGAAACAAGAT
129 ACGCTTCTAATATCGTTTTTCCA-TTTTTTTTCCGATATAGTTTCTAATTAAATCGAAACAAGAT
* * *
3379 TGAGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGTTTCGATAAATGTAGA
193 TGAGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGGTTCGATGAATATAGA
* **
3444 TATTTCAAGCAATCTTTGAGTAAAAAATCATGC-AAATTGAGCCGGGGCTCCGGAACCCCTTTTT
258 TATTTCAAGCAGTCTTTGAGCCAAAAATCATGCAAAATTGAGCC-GGGCTCCGGAACCCCTTTTT
3508 AG
322 AG
* * *
3510 CAAAAAAATCGTGATGGTTAGTACACAATTTTAGCTAAAAACTGAACCAAAATTTTTTTTTTCTC
1 CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGAACCAAAA--TTTTTTTTCTC
* * *
3575 AATTTCTTGCCACAATACACAGAAAATATATATAATCCAATGCCAAAAATATTGACGGGCTTTTC
64 AATTTCTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTC
* ** * *
3640 ACACTTCTAATATCGTTTCTT-TTTTTTCATTTTCTTCTGA-ATTAATTTTTAATTAAATCGAAA
129 ACGCTTCTAATATCGTTT-TTCCATTTT--TTTTC--C-GATA-TAGTTTCTAATTAAATCGAAA
* * * * * * ** *
3703 AAAAATTCAGATGCTCATAAAAACAAATCATTATATCC-A-A-TGACACAGATTTGTTTCGATGA
187 CAAGATTGAGATGCTCAAAAAAACAAATCCTTATAACCAACATTG-CTGAGATTTGGTTCGATGA
* * * * * *
3765 ATATAAATATTTCAAGAAGTCTTTGAGCCAAAAACCATGCAAAATTTAGTCGGGGCTCCGGAACG
251 ATATAGATATTTCAAGCAGTCTTTGAGCCAAAAATCATGCAAAATTGAG-CCGGGCTCCGGAACC
3830 CCTTTTTAG
315 CCTTTTTAG
* * * *
3839 C-AAAAAACCGTGATTGTTAATACACGATTTTGGCTAAAAACTGATCCGAAATTTTTTTTCAT-A
1 CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGAACCAAAATTTTTTTTC-TCA
* ** * *
3902 ATTTTTTGCCACAATACAC--ATTAAA-ATATAATTCAATGCCAGAAAGATTGACGGGCATTTCA
65 ATTTCTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCA
* * *
3964 CGCTTCTAATATCGTTTTTCCA--TTTTTTCCGA-ATTAATTTCTAATTAAATCGAAAGAAAATT
130 CGCTTCTAATATCGTTTTTCCATTTTTTTTCCGATA-TAGTTTCTAATTAAATCGAAACAAGATT
* * * * * *
4026 GAGATGCTCGACAAAACAAATCCTTATATA-AAATATTGCTGAGATTTGGTTAGAAGAATATAGA
194 GAGATGCTCAAAAAAACAAATCCTTATA-ACCAACATTGCTGAGATTTGGTTCGATGAATATAGA
* * * * *
4090 TATTTCAAGTAATCTTTGAGGCAAAAATCACGCAAAATTGAGCCGGGGCTCCGGAACGCCTTTTT
258 TATTTCAAGCAGTCTTTGAGCCAAAAATCATGCAAAATTGAGCC-GGGCTCCGGAACCCCTTTTT
4155 AG
322 AG
* * * * * *
4157 C-AAAAACCCGTAATGG-TAGTATATGATTTTGGCTAAAAACTGACCCGATAATTTTTTTTCTCA
1 CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGAACC-AAAATTTTTTTTCTCA
* * * * **
4220 ATTTTTTGCCACAATACTCAAAAAAAATATATAATTCAATGCCAAAAAGATTGACAGATTTTTCA
65 ATTTCTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCA
* * * * *
4285 CGCTTCTAATGTCGTTTTTCCA-TTTCTTTCTGATTTAATTTCTAATTAAATCGAAACAAGATTG
130 CGCTTCTAATATCGTTTTTCCATTTTTTTTCCGATATAGTTTCTAATTAAATCGAAACAAGATTG
* * * *
4349 AGATGCTCAAAAAATCAAATCCTTATAACCAACATTGCTGAGATTTGATTTGATGAATATAGAAA
195 AGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGGTTCGATGAATATAGATA
* *
4414 TTTCAAGCAGTCTTTGAGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAATCTCTTTTTAG
260 TTTCAAGCAGTCTTTGAGCCAAAAATCATGCAAAATTGAGCC-GGGCTCCGGAACCCCTTTTTAG
* *
4479 CAAAAAAAAAGCCGTGATGGTTAGTACACGATTTTGCCTAAAAAGTGAACCAAAAATTTTTTTTC
1 C--AAAAAAA-CCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGAACC-AAAATTTTTTTTC
* * * * *
4544 TCTATTGCTTGCCACAATACACAGAATATATATATAATTCAATGGCAAAAAGATTGACGGGCTTT
62 TCAATTTCTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTT
* * *
4609 TCACGCTTCTAATATCGTTTTTTTTTTCA-TTTTTTTCC-AAATTAATTTCTAATTAAATCGAAA
127 TCACGCTTCTAATATCG----TTTTTCCATTTTTTTTCCGATA-TAGTTTCTAATTAAATCGAAA
* * * * * ** *
4672 CAAGATTCAGATGCT-AATAAAACCAAATCCTTATATCCAATGA-TCCTGAGATTTAATTCTATG
187 CAAGATTGAGATGCTCAA-AAAAACAAATCCTTATAACCAA-CATTGCTGAGATTTGGTTCGATG
* * * *
4735 AATATAGATATTTCAAGTAGTCTTTGCA-CCAAAAATCATGCAAAATTGAGCTGGGCTCTGTAAC
250 AATATAGATATTTCAAGCAGTCTTTG-AGCCAAAAATCATGCAAAATTGAGCCGGGCTCCGGAAC
*
4799 GCCTTTTTTAG
314 -CCCTTTTTAG
* * *
4810 CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTTACCCGAAATTTTTTTTCAT-A
1 CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGAACCAAAATTTTTTTTC-TCA
* * * *
4874 ATTTTTTGCCAAAATACACATAAAAAATATATAATTCAATGCCAAAAAGATTGACGGACTTTTCA
65 ATTTCTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCA
* * * *
4939 TGCTTCTAATATCGTTTTTCCA---TTTTTCTG-TATTAATTTTTAATTAAATCGAAACAAGATT
130 CGCTTCTAATATCGTTTTTCCATTTTTTTTCCGATA-TAGTTTCTAATTAAATCGAAACAAGATT
* * * * *
5000 GAGATACTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATTTGGTTCGATAAATATAGAT
194 GAGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGGTTCGATGAATATAGAT
** * ** ***
5065 ATTTCAAGCAGTCTTTGAGCCAAAAATCACCCAAAACTGAGCCGAGGCTCTTGAATGTCTTTTTA
259 ATTTCAAGCAGTCTTTGAGCCAAAAATCATGCAAAATTGAGCCG-GGCTCCGGAACCCCTTTTTA
5130 G
323 G
*
5131 C-AAAAAACCGTGATGGTTAGT-CTATGATTTTGGCTAAAAACTGA
1 CAAAAAAACCGTGATGGTTAGTAC-ACGATTTTGGCTAAAAACTGA
5175 CACGAAAAAT
Statistics
Matches: 4160, Mismatches: 506, Indels: 372
0.83 0.10 0.07
Matches are distributed among these distances:
292 3 0.00
295 4 0.00
298 29 0.01
299 5 0.00
300 150 0.04
301 56 0.01
302 1 0.00
303 8 0.00
305 31 0.01
306 79 0.02
307 142 0.03
308 6 0.00
309 9 0.00
310 75 0.02
311 172 0.04
312 3 0.00
313 1 0.00
315 1 0.00
316 61 0.01
317 33 0.01
318 123 0.03
319 13 0.00
320 72 0.02
321 444 0.11
322 329 0.08
323 242 0.06
324 501 0.12
325 379 0.09
326 465 0.11
327 275 0.07
328 136 0.03
329 100 0.02
330 69 0.02
331 141 0.03
332 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (323 bp):
CAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGAACCAAAATTTTTTTTCTCAA
TTTCTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAC
GCTTCTAATATCGTTTTTCCATTTTTTTTCCGATATAGTTTCTAATTAAATCGAAACAAGATTGA
GATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGGTTCGATGAATATAGATAT
TTCAAGCAGTCTTTGAGCCAAAAATCATGCAAAATTGAGCCGGGCTCCGGAACCCCTTTTTAG
Found at i:4541 original size:970 final size:966
Alignment explanation
Indices: 2731--5182 Score: 3449
Period size: 970 Copynumber: 2.5 Consensus size: 966
2721 TTTCCGATTT
* * *
2731 AATTGAGATGCTCGA-AAAAACAAATTCTTATATCCAAT-ATTACTGAGATTTGGTTCGATGAAT
1 AATTCAGATGCTC-ATAAAAACAAA-TCTTATATCCAATGATCAC-GAGATTTGATTCGATGAAT
* * * *
2794 ATAGATAGTTCAAGCAGTCTTTGAGCCAAAAATCACGCAAAATTGAGACAAGGCTCCGAAACGCC
63 ATAGATATTTCAAGAAGTCTTTGAGCCAAAAATCATGCAAAATTGAG-CAGGGCTCCGAAACGCC
* * * * *
2859 TTTTTAGCAAAAAATCGTGATGGTTAGTACATGAATTTGGCTAAGAACTTACCCGGAAA-ATTTT
127 TTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTTACCC-GAAATTTTTT
* * * * **
2923 TTCACAATTTTTT-CCACAAAACACAGAAAAAATATGTAATTCAATGTCAAAAAGATTGATAGGC
191 TTCATAATTTTTTGCCACAATACACA-TAAAAATA--TAATTCAATGCCAAAAAGATTGACGGGC
* * * * * *
2987 TTTTCATGCTTCTAATGTCGTTTTCCCTTTTTTTTCCGATTTAGTTTCTAATTAAATTGAAACAA
253 TTTTCATGCTTCTAATATCGTTTTTCC-ATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAA
* * *
3052 GACTGAGATGCTCAAAAAAACAAATCCTTATA-ACCAATATTGCTGAGATTTGGTTCGATGAATA
317 GATTGAGATGCTCGAAAAAACAAATCCTTATATA-CAATATTGCTGAGATTTGGTTCGAAGAATA
*
3116 TAGAAATTTCAAGCAGTCTTTGAGACAAAAATCACGCAAAATTGAGCCGGGGCTCCGGAACGCCT
381 TAGATATTTCAAGCAGTCTTTGAGACAAAAATCACGCAAAATTGAGCCGGGGCTCCGGAACGCCT
* * * *
3181 TTTTAGCAAAAAACCGTGATTGTTAGTACATGATTTTGGCTAAAAATTGACCCGAAAATTTTTTT
446 TTTTAGCAAAAAACCGT-AATGGTAGTATATGATTTTGGCTAAAAACTGACCCGAAAATTTTTTT
* ** *
3246 CTCAAATTTTTGCCACAATACACAGAAAAAATATATAATTCAATGCCAAAAAGATTGATGGGTTT
510 CTCAAATTTTTGCCACAATACACAAAAAAAATATATAATTCAATGCCAAAAAGATTGACAGATTT
* *
3311 TTCACGCTTCTAATGTCGTTTTTCCATTTTTTTTTCTGATTTAGTTTCTAATCAAATCGAAACAA
575 TTCACGCTTCTAATGTCGTTTTTCCA-TTTTCTTTCTGATTTAATTTCTAATCAAATCGAAACAA
*
3376 GATTGAGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGTTTCGATAAATGT
639 GATTGAGATGCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGTTTCGATAAATAT
* *
3441 AGATATTTCAAGCAATCTTTGAGTAAAAAATCATGCAAATTGAGCCGGGGCTCCGGAACCCCTTT
704 AGAAATTTCAAGCAATCTTTGAGCAAAAAATCATGCAAATTGAGCCGGGGCTCCGGAACCCCTTT
* *
3506 TTAGCAAAAAAATCGTGATGGTTAGTACACAATTTTAGCTAAAAACTGAACCAAAATTTTTTTTT
769 TTAGCAAAAAAACCGTGATGGTTAGTACACAATTTTAGCTAAAAACTGAACCAAAATATTTTTTT
* *
3571 TCTCAATTTCTTGCCACAATACACAGAAAATATATATAATCCAATGCCAAAAATATTGACGGGCT
834 TCTCAATTGCTTGCCACAATACACAGAAAATATATATAATCCAATGCCAAAAAGATTGACGGGCT
** *
3636 TTTCACACTTCTAATATCGTTTCTTTTTTTTCATTTTCTTCTGAATTAATTTTTAATTAAATCGA
899 TTTCACACTTCTAATATCG-TT-TTTTTTTTCATTTTCTTCCAAATTAATTTCTAATTAAATCGA
3701 AAAAA
962 AAAAA
*
3706 AATTCAGATGCTCATAAAAACAAATCATTATATCCAATGA-CAC-AGATTTGTTTCGATGAATAT
1 AATTCAGATGCTCATAAAAACAAATC-TTATATCCAATGATCACGAGATTTGATTCGATGAATAT
* * * * *
3769 AAATATTTCAAGAAGTCTTTGAGCCAAAAACCATGCAAAATTTAGTCGGGGCTCCGGAACGCCTT
65 AGATATTTCAAGAAGTCTTTGAGCCAAAAATCATGCAAAATTGAG-CAGGGCTCCGAAACGCCTT
* * * *
3834 TTTAGCAAAAAACCGTGATTGTTAATACACGATTTTGGCTAAAAACTGATCCGAAATTTTTTTTC
129 TTTAGCAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTTACCCGAAATTTTTTTTC
* * *
3899 ATAATTTTTTGCCACAATACACATTAAAATATAATTCAATGCCAGAAAGATTGACGGGCATTTCA
194 ATAATTTTTTGCCACAATACACATAAAAATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCA
* * *
3964 CGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAAGAAAATTGAG
259 TGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAG
* * *
4029 ATGCTCGACAAAACAAATCCTTATATAAAATATTGCTGAGATTTGGTTAGAAGAATATAGATATT
324 ATGCTCGAAAAAACAAATCCTTATATACAATATTGCTGAGATTTGGTTCGAAGAATATAGATATT
* * *
4094 TCAAGTAATCTTTGAGGCAAAAATCACGCAAAATTGAGCCGGGGCTCCGGAACGCCTTTTTAGCA
389 TCAAGCAGTCTTTGAGACAAAAATCACGCAAAATTGAGCCGGGGCTCCGGAACGCCTTTTTAGCA
* * *
4159 AAAACCCGTAATGGTAGTATATGATTTTGGCTAAAAACTGACCCGATAATTTTTTTTCTCAATTT
454 AAAAACCGTAATGGTAGTATATGATTTTGGCTAAAAACTGACCCGA-AAATTTTTTTCTCAAATT
*
4224 TTTGCCACAATACTCAAAAAAAATATATAATTCAATGCCAAAAAGATTGACAGATTTTTCACGCT
518 TTTGCCACAATACACAAAAAAAATATATAATTCAATGCCAAAAAGATTGACAGATTTTTCACGCT
*
4289 TCTAATGTCGTTTTTCCA-TTTCTTTCTGATTTAATTTCTAATTAAATCGAAACAAGATTGAGAT
583 TCTAATGTCGTTTTTCCATTTTCTTTCTGATTTAATTTCTAATCAAATCGAAACAAGATTGAGAT
* *
4353 GCTCAAAAAATCAAATCCTTATAACCAACATTGCTGAGATTTGATTT-GATGAATATAGAAATTT
648 GCTCAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTG-TTTCGATAAATATAGAAATTT
* * * *
4417 CAAGCAGTCTTTGAGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAATCTCTTTTTAGCAA
712 CAAGCAATCTTTGAGCAAAAAATCATGC-AAATTGAGCCGGGGCTCCGGAACCCCTTTTTAGC--
* *
4482 AAAAAAAGCCGTGATGGTTAGTACACGATTTT-GCCTAAAAAGTGAACCAAAA-ATTTTTTTTCT
774 AAAAAAA-CCGTGATGGTTAGTACACAATTTTAG-CTAAAAACTGAACCAAAATATTTTTTTTCT
* * * *
4545 CTATTGCTTGCCACAATACACAGAATATATATATAATTCAATGGCAAAAAGATTGACGGGCTTTT
837 CAATTGCTTGCCACAATACACAGAAAATATATATAATCCAATGCCAAAAAGATTGACGGGCTTTT
* * *
4610 CACGCTTCTAATATCGTTTTTTTTTTCATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAA
902 CACACTTCTAATATCGTTTTTTTTTTCATTTTCTTCCAAATTAATTTCTAATTAAATCGAAAAAA
* * * * *
4675 GATTCAGATGCTAATAAAACCAAATCCTTATATCCAATGATC-CTGAGATTTAATTCTATGAATA
1 AATTCAGATGCTCATAAAAACAAAT-CTTATATCCAATGATCAC-GAGATTTGATTCGATGAATA
* * * *
4739 TAGATATTTCAAGTAGTCTTTGCA-CCAAAAATCATGCAAAATTGAGCTGGGCTCTGTAACGCCT
64 TAGATATTTCAAGAAGTCTTTG-AGCCAAAAATCATGCAAAATTGAGCAGGGCTCCGAAACGCC-
4803 TTTTTAGCAAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTTACCCGAAATTTTTT
127 TTTTTAGC-AAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTTACCCGAAATTTTTT
* *
4868 TTCATAATTTTTTGCCAAAATACACATAAAAAATATATAATTCAATGCCAAAAAGATTGACGGAC
191 TTCATAATTTTTTGCCACAATACACAT--AAAA-ATATAATTCAATGCCAAAAAGATTGACGGGC
* * *
4933 TTTTCATGCTTCTAATATCGTTTTTCCA-TTTTTCTGTATTAATTTTTAATTAAATCGAAACAAG
253 TTTTCATGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG
* *
4997 ATTGAGATACTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGATTTGGTTCGATA-AATAT
318 ATTGAGATGCTCGAAAAAACAAATCCTTATATACAATATTGCTGAGATTTGGTTCGA-AGAATAT
* * * * ** * *
5061 AGATATTTCAAGCAGTCTTTGAGCCAAAAATCACCCAAAACTGAGCCGAGGCTCTTGAATGTCTT
382 AGATATTTCAAGCAGTCTTTGAGACAAAAATCACGCAAAATTGAGCCGGGGCTCCGGAACGCCTT
* * *
5126 TTTAGCAAAAAACCGTGATGGTTAGTCTATGATTTTGGCTAAAAACTGACACGAAAA
447 TTTAGCAAAAAACCGTAATGG-TAGTATATGATTTTGGCTAAAAACTGACCCGAAAA
5183 ATTATCGGGC
Statistics
Matches: 1314, Mismatches: 138, Indels: 51
0.87 0.09 0.03
Matches are distributed among these distances:
968 124 0.09
969 146 0.11
970 276 0.21
971 204 0.16
972 122 0.09
973 140 0.11
974 181 0.14
975 120 0.09
976 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (966 bp):
AATTCAGATGCTCATAAAAACAAATCTTATATCCAATGATCACGAGATTTGATTCGATGAATATA
GATATTTCAAGAAGTCTTTGAGCCAAAAATCATGCAAAATTGAGCAGGGCTCCGAAACGCCTTTT
TAGCAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTTACCCGAAATTTTTTTTCAT
AATTTTTTGCCACAATACACATAAAAATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCATG
CTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGAT
GCTCGAAAAAACAAATCCTTATATACAATATTGCTGAGATTTGGTTCGAAGAATATAGATATTTC
AAGCAGTCTTTGAGACAAAAATCACGCAAAATTGAGCCGGGGCTCCGGAACGCCTTTTTAGCAAA
AAACCGTAATGGTAGTATATGATTTTGGCTAAAAACTGACCCGAAAATTTTTTTCTCAAATTTTT
GCCACAATACACAAAAAAAATATATAATTCAATGCCAAAAAGATTGACAGATTTTTCACGCTTCT
AATGTCGTTTTTCCATTTTCTTTCTGATTTAATTTCTAATCAAATCGAAACAAGATTGAGATGCT
CAAAAAAACAAATCCTTATAACCAACATTGCTGAGATTTGTTTCGATAAATATAGAAATTTCAAG
CAATCTTTGAGCAAAAAATCATGCAAATTGAGCCGGGGCTCCGGAACCCCTTTTTAGCAAAAAAA
CCGTGATGGTTAGTACACAATTTTAGCTAAAAACTGAACCAAAATATTTTTTTTCTCAATTGCTT
GCCACAATACACAGAAAATATATATAATCCAATGCCAAAAAGATTGACGGGCTTTTCACACTTCT
AATATCGTTTTTTTTTTCATTTTCTTCCAAATTAATTTCTAATTAAATCGAAAAAA
Found at i:5450 original size:267 final size:267
Alignment explanation
Indices: 4970--5451 Score: 638
Period size: 267 Copynumber: 1.8 Consensus size: 267
4960 ATTTTTCTGT
* *
4970 ATTAATTTTTAATTAAATCGAAACAAGATTGAGATACTCGAAAAAACAAATCCTTATATCCAATA
1 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGAAAAAACAAATCCTTATATCCAATA
* *
5035 TTGCTGAGATTTGGTTCGATAAATATAGATATTTCAAGCAGTCTTTGAGCCAAAAATCACCCAAA
66 TGGCTGAGATTTGGTTCGATAAATATAGATATTTCAAGCAGTCTTTGAGCCAAAAACCACCCAAA
* * * * **
5100 ACTGAGCCGAGGCTCTTGAATGTCTTTTTAGCAAAAAACCGTGATGGTTAGTCTATGATTTTGGC
131 ACTGAGCCGAGGCTCTCGAACGTCTTTTTAGCAAAAAACAGTGATGGTTAGTCTACGATTACGGC
5165 TAAAAACTGACACGAAAAATTATCGGGCTTTTCACGCGCATAATATCGTTTTTTTTTCCACTTCT
196 TAAAAACTGACACGAAAAATTATCGGGCTTTTCACGCGCATAATATCGTTTTTTTTTCCACTTCT
5230 TTTCCGA
261 TTTCCGA
* *
5237 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC-ATGAAAACAAATCCTTATATCCAAT
1 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGA-AAAAACAAATCCTTATATCCAAT
* * * **
5301 GA-GGCTGAGATTTGGTTCGATTAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAACCATGC-
65 -ATGGCTGAGATTTGGTTCGATAAATATAGATATTTCAAGCAGTCTTTGAGCCAAAAACCACCCA
* * *
5364 AAACTTGAGCTGGGGCTC-CGAAACG-CGTTTTTAGC-CAAAACGAGTGATGGTTAG-C-ACGCA
129 AAAC-TGAGCCGAGGCTCTCG-AACGTC-TTTTTAGCAAAAAAC-AGTGATGGTTAGTCTACG--
* *
5424 ATTACGGCTAAAAACTTACTCGAAAAAT
188 ATTACGGCTAAAAACTGACACGAAAAAT
5452 ATATAATTCA
Statistics
Matches: 185, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
265 2 0.01
266 13 0.07
267 169 0.91
268 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (267 bp):
ATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGAAAAAACAAATCCTTATATCCAATA
TGGCTGAGATTTGGTTCGATAAATATAGATATTTCAAGCAGTCTTTGAGCCAAAAACCACCCAAA
ACTGAGCCGAGGCTCTCGAACGTCTTTTTAGCAAAAAACAGTGATGGTTAGTCTACGATTACGGC
TAAAAACTGACACGAAAAATTATCGGGCTTTTCACGCGCATAATATCGTTTTTTTTTCCACTTCT
TTTCCGA
Found at i:6060 original size:320 final size:318
Alignment explanation
Indices: 5445--6138 Score: 921
Period size: 320 Copynumber: 2.2 Consensus size: 318
5435 AAACTTACTC
* **
5445 GAAAAATATATAATTCAATGCTAAAAAAGATTGACGGGCTTTTCACGCTTAAAATATCGTTTTTC
1 GAAAAATATATAATTCAATGC-CAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTC
* * * *
5510 CATTTTTTTTGAATTAATTTTTAATTAAATCGAAGCAAGATTGAGATGCTCGAATAAACAAATTC
65 CATTTTTTTTAAATTAATTTTTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCC
* * * * * * * *
5575 TTATTTCCAATGTGCCTGACTTTTGGTTCAATGAATATAGATATTTCCAGGAGACTTTGCGCCAA
130 TTATATCCAATATGCCTGACGTTTGGTTCAATGAATATAGATATTTCAAGCAGACTTGGAGCAAA
* * *
5640 AAATCATGTAAAATCGAGTCGGGGCTCCAGAACGCGTTTTTAGCCAAAAACCGTGTTGGTTAATA
195 AAATCATGCAAAATCGAGTCGGGGCTCCAGAACGCCTTTTTAGCCAAAAACCGTGATGGTTAATA
*
5705 CACAATTTCGGCTAAAAACTGACCCAAAATTTTTTCTCAATTTTTTACCACAATACACA
260 CACAATTTCGGCTAAAAACTGACCCAAAATTTTTTCTCAATTTTTTACCACAATACAAA
* * *
5764 GAAAAATATATAATTCATTGCCAAAAAGATTGACGGGCTTTTCACGTTTCTAATGTCGTTTTTCC
1 GAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCC
*
5829 ATTTTTTTTCCAAATT-ATTTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAATAAAT
66 ATTTTTTTT--AAATTAATTTT-TAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAAT
* * * *
5893 CCTTATATCCAATAT-CGTTGAGGTTTGGTTCGATGAATATAGATATTTCAAGCAGTCTTGGAGC
128 CCTTATATCCAATATGC-CTGACGTTTGGTTCAATGAATATAGATATTTCAAGCAGACTTGGAGC
*
5957 AAAAAATCATGCAAAATTGAGTCGGGGCTCCAGAACGCCTTTTTAG-CAAAAAGCCGTGATGGTT
192 AAAAAATCATGCAAAATCGAGTCGGGGCTCCAGAACGCCTTTTTAGCCAAAAA-CCGTGATGGTT
* * ** * * *
6021 AGTA-A-ATTTTTTTGCTAAAAATTGACCCGAAATTTTTTTCTCAATTTTTTGCCACAATACAAA
256 AATACACA-ATTTCGGCTAAAAACTGACCC-AAAATTTTTTCTCAATTTTTTACCACAATACAAA
* * * *
6084 AAAAGAATATATACTTCAATGCCAAAAAGGTTGACGGGCTTTTCACACTTCTAAT
1 GAAA-AATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAAT
Statistics
Matches: 326, Mismatches: 41, Indels: 14
0.86 0.11 0.04
Matches are distributed among these distances:
318 49 0.15
319 50 0.15
320 182 0.56
321 45 0.14
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (318 bp):
GAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCC
ATTTTTTTTAAATTAATTTTTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCT
TATATCCAATATGCCTGACGTTTGGTTCAATGAATATAGATATTTCAAGCAGACTTGGAGCAAAA
AATCATGCAAAATCGAGTCGGGGCTCCAGAACGCCTTTTTAGCCAAAAACCGTGATGGTTAATAC
ACAATTTCGGCTAAAAACTGACCCAAAATTTTTTCTCAATTTTTTACCACAATACAAA
Done.