Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012379.1 Corchorus olitorius cultivar O-4 contig12412, 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: 11540
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Found at i:602 original size:2 final size:2
Alignment explanation
Indices: 595--619 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
585 CTTCATTTAT
595 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
620 TTTTCCTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2596 original size:171 final size:175
Alignment explanation
Indices: 2278--2598 Score: 388
Period size: 171 Copynumber: 1.9 Consensus size: 175
2268 CTGAATCTTA
2278 TTTCCATTTAATTAGAAATTAATTAAGAAAAAATACGAAAAACAATATTAGAAGCGTTAAAAGCC
1 TTTCCATTTAATTAGAAATTAATTAAGAAAAAATACGAAAAACAATATTAGAAGCGTTAAAAGCC
* * * * * * *
2343 CTTCAATATTTTTGATGCTGAGTTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAT
66 CTTCAATATTTTTGACGCTGAATTATATATTTTTTATGAATATTGTAGCAAAAAATTGAGAAAAA
2408 ATCTTTCGGGTCAATTTTTACAAAACTTTACCCGAAATCGTGTTG
131 ATCTTTCGGGTCAATTTTTACAAAACTTTACCCGAAATCGTGTTG
* * * * * *
2453 TTTCGATTTAATTAGAAATTAATT-CGTAAAATAA-ATGGAAAAACGATATTAGAAGTG-T-GAA
1 TTTCCATTTAATTAGAAATTAATTAAG-AAAA-AATA-CGAAAAACAATATTAGAAGCGTTAAAA
* * * *
2514 GCCCTTCAATCTTTTTGCCGTTGAATTATAT-TTTTTT-T-AATATTGTGGCAAAAAATTGAGAA
63 GCCCTTCAATATTTTTGACGCTGAATTATATATTTTTTATGAATATTGTAGCAAAAAATTGAGAA
*
2576 AAAA-CTTTTCGTGTCAATTTTTA
128 AAAATC-TTTCGGGTCAATTTTTA
2599 GCCGAAATCG
Statistics
Matches: 124, Mismatches: 18, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
170 1 0.01
171 38 0.31
172 1 0.01
173 6 0.05
174 29 0.23
175 29 0.23
176 20 0.16
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (175 bp):
TTTCCATTTAATTAGAAATTAATTAAGAAAAAATACGAAAAACAATATTAGAAGCGTTAAAAGCC
CTTCAATATTTTTGACGCTGAATTATATATTTTTTATGAATATTGTAGCAAAAAATTGAGAAAAA
ATCTTTCGGGTCAATTTTTACAAAACTTTACCCGAAATCGTGTTG
Found at i:4078 original size:332 final size:329
Alignment explanation
Indices: 2450--4964 Score: 2307
Period size: 332 Copynumber: 7.7 Consensus size: 329
2440 CGAAATCGTG
* * * *
2450 TTGTTTCGATTTAATTAGAAATTAATTCGTAAAATAAATGGAAAAACGATATTAGAAGTGTG--A
1 TTGTTTCGATTTAATTAGAAATAAATTTG-AAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
* * * *
2513 AGCCCTTCAATCTTTTTGCCGTTGAATTATAT-TTTTTT-T-AATATTGTGGCAAAAAATTGA-G
65 AACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGG
* * *
2574 AAAAAACTTTTCGTGTCAA---T------TTTTAGCCGAAATCGTGTACTAACTATCACTGTTTT
130 AAAAAA-TTTTCGGGTCAATTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTT
* ** *
2630 TGGCTAAAAACGCGTTTTGGG-CCTCCACTCAGTTTTGCATGGTTTTTGGC-ATACAGACTCCTT
194 TGGCTAAAAACGCGTTTCGGGTCC-CGGCTCAGTTTTGCATGATTTTTGGCGA-A-AGACTCCTT
* * *
2693 GAAAAATATATATTCATGTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
256 GAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
2758 ATCTGAATC
321 ATCTGAATC
* * * * * * * *
2767 TTGTTTTGATTTTATTAGAAATTAATTCAGAAAAAAAAAGGAAAAACGATATCATAAGTGTGAAA
1 TTGTTTCGATTTAATTAGAAATAAATT-TGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
* * *
2832 ACCCCTTCAATTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTAAGG
65 AACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGG
*
2897 -AAAAATGTTTCGGGTCAGTTTTTTTTTCCGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA
130 AAAAAAT-TTTCGGGTCA-----ATTTT--GCAAAATTTTAGCCGAAATCGTGTACTAACCATCA
* * * * * * *
2961 CGTTTTTTTGGTTAAAAACGCGTTTCGGAGTCACGGCTCAATTTTGCATTATTATTGGCTTAAAG
187 CG-GTTTTTGGCTAAAAACGCGTTTCGG-GTCCCGGCTCAGTTTTGCATGATTTTTGGC-GAAAG
* * * * *
3026 ACACCTTGAAATATCTATATTCATCGAAACAAATCTCAGCCACATCGGATTTAAGGATTTTTTTT
249 ACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTT
** *
3091 TACGAGTTTCTGAATT
314 TACGAGCATCTGAATC
** * * * * **
3107 TTGTTTTTATTTAATTAGAAATTAATTTGGAAAAAAATTCGAAAACCGATATTAGAAGCCCGAAA
1 TTGTTTCGATTTAATTAGAAATAAATTT-GAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
* * * * * *
3172 AGCCCGTCAATCTTTTTGGCTTTGAATTATATA-TTTTTATGAGTATTTTGGCCAAAAAAAATTG
65 AACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGG-C--AAAAAATTG
* ** *
3236 AGAAAAAAATTTT-GGG------TT---AGTTTTTAGCCGAAATCGTGTACGT-----T-ACGAT
127 AGGAAAAAATTTTCGGGTCAATTTTGCAAAATTTTAGCCGAAATCGTGTAC-TAACCATCACGGT
* * * * * *
3285 TTTTGGCAAAAAAACGTGTTTCGGGGGCCCGGTTCAGTTTTGCATGATTTTTGGTAGAAAGAATC
191 TTTTGGC-TAAAAACGCGTTTC-GGGTCCCGGCTCAGTTTTGCATGATTTTTGG-CGAAAGACTC
* * * * * *
3350 CTTGAAATATCTGTATTCATCTAACCAAATCTCAGCTACATTGGATTCACGAATTTGTTTTTACA
253 CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
* *
3415 AGTATCTAAATC
318 AGCATCTGAATC
* * * * * *
3427 TTGTTTTGATTTAATTATAAATAAATTTG-GAAAAAATGGGAAAATGATATTGGAAGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATAAATTTGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
** *
3491 ACCCTTCAATTTTTTTGGCGTTGTGTTATATATTTTTTCTTAGTATTGTGGCAAAAAATTGAGGA
66 ACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGA
* * * ** * *
3556 AAAATTTTTCGGGTCAATTTTTCGAAATTTTAATCGAAATC--GTA-T---CA-GA-GTTTTTTT
131 AAAAATTTTCGGGTCAATTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACG-GTTTTT
* * * * **
3613 GGCTAAAAATGCGCTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTAGGTCGAAAGACTTTTTGA
195 GGCTAAAAACGCGTTTC-GGGTCCCGGCTCAGTTTTGCATGATTTTTGG-CGAAAGACTCCTTGA
* * ** * * *
3678 AATATTTATATTCAACTAATTAAATTTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAACAT
258 AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
3743 CTGAATC
323 CTGAATC
* * *
3750 TTGTTTCGATTTAATTAGAAACAAATTTGGAAAAAAATGGAAAAACAATATTAGAAGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATAAATTTGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* * * *
3815 ACACTTCGATTTTTTTGGCATTGAATTATATATTCTTTCTGAGTATTGTGGCAAAAAATTGAGGA
66 ACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGA
* * * *
3880 AAAACTTTTCGGGTCAATCTTTGCAAAATTTTAACCAAAATCGTGTACCAACCATCACGGTTTTT
131 AAAAATTTTCGGGTCAAT-TTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT
* * * *
3945 GGCTAAAAACGCGTTCCGGAGTGCCAGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGA
195 GGCTAAAAACGCGTTTCGG-GTCCCGGCTCAGTTTTGCATGATTTTTGGCG-AAAGACTCCTTGA
* * *
4010 AATATCTATATTCATCGAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCAT
258 AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
4075 CTGAATC
323 CTGAATC
* * * * *
4082 TTGTTTTGATTTAATTAAAAATTAATTCAGAAAAAATAATGGGAAAACGATATTAGAAGCGTGAA
1 TTGTTTCGATTTAATTAGAAATAAATT-TGAAAAAA-AATGGAAAAACGATATTAGAAGCGTGAA
* * * * * **
4147 AAGCCCATCAA-TCTTTTGGCATTGAATTATATATTTTTTCTGAATATT-TCACAAAAAATTGAG
64 AAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG
* * * * *
4210 AAAAAAAATTTTCTGGTC-A----G----TTTTTAGTCGAAATCATGTACTAACCATCACGGTTT
129 -GAAAAAATTTTCGGGTCAATTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
** * * *
4266 TCAGCTAAAAACGCGTTTCGGGCCCCGACTAAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTG
193 TTGGCTAAAAACGCGTTTCGGGTCCCGGCTCAGTTTTGCATGATTTTTGGC-GAAAGACTCCTTG
* * * *
4331 AAATATCTATATTCATCTAACCAAGTCTAAGCCACAATGGATTTAAGGATTTATTTTTACGAGCA
257 AAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
*
4396 TTTGAATC
322 TCTGAATC
* * * *
4404 TTGTTTCAATTTAATAAAAAATAAA-TT--AAAAAAATGGAAAAATGATATTAGAAGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATAAATTTGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* * * *
4466 A-CCGTCAATTTTTTTGGCGTTGAATTACATATTTTTTCTGAGTATTGTTGCAAAGAATTGA-GA
66 ACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGA
* * * * * * * * *
4529 AAAAAATTTCGGGACAGTTTTAACAAAAGTTTAGTCGAAATCGTTTACT---CATTCATGTTTTT
131 AAAAATTTTCGGGTCAATTTT-GCAAAATTTTAGCCGAAATCGTGTACTAACCA-TCACGGTTTT
* * * * * * *
4591 TGGCTAAAAATGTGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTTGCATAAAGACT-TTTG
194 TGGCTAAAAACGCGTTTC-GGGTCCCGGCTCAGTTTTGCATGATTTTTGGC-GAAAGACTCCTTG
* *
4655 AAATATCTATATTCATCCTCATCTAACCAAATCTAAGCCACAATGGATTTAAGGATTTGTTTTTA
257 AAATATC--TA-T-AT--TCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA
4720 CGAGCATCTGAATC
316 CGAGCATCTGAATC
* * * ** *
4734 TTGTTTCAATTTAATAAGAAATAAA-TTCAAAAAAAAAAG-AAAACGATATTAGAAGCGTAAAAA
1 TTGTTTCGATTTAATTAGAAATAAATTTGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* * * * * *
4797 ACCCGTCAATTTTTTTGGCGTTGAATTACATA-TTTTTCTGAGTATTTTTGTAAAGAATTGAGGA
66 ACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGG-
* * * *
4861 AAAAAATTTCCGGGTCAGTTTTTGCAAAATTTTA----AAATCGTTTACT---CATTCATGGTTT
130 AAAAAATTTTCGGGTCA-ATTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCA-TCACGGTTT
* * *
4919 TTGGCTAAAAACGCGTTCTGGGGTCCCGACTCAGTTTTGGATGATT
193 TTGGCTAAAAACGCGTT-TCGGGTCCCGGCTCAGTTTTGCATGATT
4965 CTTGTTTCGA
Statistics
Matches: 1816, Mismatches: 286, Indels: 180
0.80 0.13 0.08
Matches are distributed among these distances:
316 39 0.02
317 117 0.06
318 70 0.04
319 52 0.03
320 139 0.08
321 6 0.00
322 156 0.09
323 191 0.11
324 148 0.08
325 77 0.04
326 34 0.02
327 5 0.00
328 2 0.00
329 61 0.03
330 87 0.05
331 56 0.03
332 194 0.11
333 78 0.04
334 37 0.02
338 29 0.02
339 38 0.02
340 175 0.10
341 5 0.00
342 14 0.01
343 6 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (329 bp):
TTGTTTCGATTTAATTAGAAATAAATTTGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
ACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGA
AAAAATTTTCGGGTCAATTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG
GCTAAAAACGCGTTTCGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCGAAAGACTCCTTGAAAT
ATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTG
AATC
Found at i:4438 original size:975 final size:965
Alignment explanation
Indices: 2450--4895 Score: 2784
Period size: 975 Copynumber: 2.5 Consensus size: 965
2440 CGAAATCGTG
* * * * * *
2450 TTGTTTCGATTTAATTAGAAATTAATTCGTAAAATAAATGGAAAAACGATATTAGAAGTGTG--A
1 TTGTTTCAATTTAATAAAAAATAAATT--TAAAA-AAATGGAAAAATGATATTAGAAGCGTGAAA
* * * * *
2513 AGCCCTTCAATCTTTTTGCCGTTGAAT-TATATTTTTT-TTAATATTGTGGCAAAAAATTGA-GA
63 AACCCTTCAATTTTTTTGGCGTTGATTATATATTTTTTCTTAGTATTGTGGCAAAAAATTGAGGA
* * * * *
2575 AAAAACTTTTCGTGTCAATTTTTAGCCGAAATCGTGT-A-C-TAA-C-TATCACTGTTTTTGGCT
128 AAAAA-TTTTCGGGTCAATTTTT---CGAAAT--TTTAATCGAAATCGTATCAATTTTTTTGGCT
* ** * * ** *
2635 AAAAACGCGTTTTGGGCCTCC-ACTCAGTTTTGCATGGTTTTTGGCATACAGACTCCTTGAAAAA
187 AAAAATGCGTTCGGGGCC-CCGGCTCAGTTTTGCATGATTTTTGGCA-A-AGACTTTTTGAAATA
* *
2699 TATATATTCATGTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGA
249 TTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGA
* * * * * * *
2764 ATCTTGTTTTGATTTTATTAGAAATTAATTCAGAAAAAAAAAGGAAAAACGATATCATAAGTGTG
314 ATCTTGTTTCGATTTAATTAGAAATAAATT-TGAAAAAAAAAGGAAAAACGATATTAGAAGCGTG
* *
2829 AAAACCCCTTCAATTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTA
378 AAAAACCCTTCAATTTTTTTGGCATTGAATTATATA-TTTTTCTGAGTATTGTGGCAAAAAATTG
* * * *
2894 AGGAAAAATGTTTCGGGTCAGTTTTTTTTTCCGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
442 AGGAAAAAT-TTTCGGGTCA----ATTTTT--GCAAAATTTTAACCAAAATCGTGTACCAACCAT
* * * * * **
2959 CACGTTTTTTTGGTTAAAAACGCGTTTCGGAGTCACGGCTCAATTTTGCATTATTATTGGCTTAA
500 CACGTGTTTTTGGCTAAAAACGCGTTCCGGAGTCACAGCTCAATTTTGCATGATTATTGGCGCAA
* *
3024 AGACACCTTGAAATATCTATATTCATCGAAACAAATCTCAGCCACATCGGATTTAAGGATTTTTT
565 AGACACCTTGAAATATCTATATTCATCGAAACAAATCTCAGCCACATCGGATATAAGGATTTGTT
** * * * * * *
3089 TTTACGAGTTTCTGAATTTTGTTTTTATTTAATTAGAAATTAATTTGGAAAAAAATTCGAAAACC
630 TTTACGAGCATCTGAATCTTGTTTTGATTTAATTAAAAATTAATTAGAAAAAAAATGCGAAAACC
* * *
3154 GATATTAGAAGCCCGAAAAGCCCGTCAATCTTTTTGGCTTTGAATTATATATTTTTATGAGTATT
695 GATATTAGAAGCCCGAAAAGCCCATCAATCTTTTTGGCATTGAATTATATATTTTTATGAATATT
* *
3219 TTGGCCAAAAAAAATTGAGAAAAAAATTTTGGGTTAGTTTTTAGCCGAAATCGTGTACGTTACGA
760 TT-G-CAAAAAAAATTGAGAAAAAAATTTTGGGTCAGTTTTTAGCCGAAATCATGTACGTTACGA
** * * ** * *
3284 TTTTTGGCAAAAAAACGTGTTTCGGGGGCCCGGTTCAGTTTTGCATGATTTTTGGTAGAAAGAAT
823 TTTTCAGCAAAAAAACGCGTTTCGGGGCCCCGACTAAGTTTTGCATGATTTTTGGCAGAAAGAAT
* * * * * *
3349 CCTTGAAATATCTGTATTCATCTAACCAAATCTCAGCTACATTGGATTCACGAATTTGTTTTTAC
888 CCTTGAAATATCTATATTCATCTAACCAAATCTAAGCCACAATGGATTCAAGAATTTATTTTTAC
*
3414 AAGTATCTAAATC
953 AAGCATCTAAATC
** * * * * *
3427 TTGTTTTGATTTAATTATAAATAAATTTGGAAAAAATGGGAAAATGATATTGGAAGCGTGAAAAA
1 TTGTTTCAATTTAATAAAAAATAAATTT-AAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAA
*
3492 CCCTTCAATTTTTTTGGCGTTGTGTTATATATTTTTTCTTAGTATTGTGGCAAAAAATTGAGGAA
65 CCCTTCAATTTTTTTGGCGTTG-ATTATATATTTTTTCTTAGTATTGTGGCAAAAAATTGAGGAA
*
3557 AAATTTTTCGGGTCAATTTTTCGAAATTTTAATCGAAATCGTATCAGAGTTTTTTTGGCTAAAAA
129 AAAATTTTCGGGTCAATTTTTCGAAATTTTAATCGAAATCGTATCA-A-TTTTTTTGGCTAAAAA
*
3622 TGCGCTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTAGGTCGAAAGACTTTTTGAAATATTTAT
192 TGCG-TTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGG-C-AAAGACTTTTTGAAATATTTAT
* ** * * *
3687 ATTCAACTAATTAAATTTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAACATCTGAATCTT
254 ATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTT
* * * *
3752 GTTTCGATTTAATTAGAAACAAATTTGGAAAAAAATGGAAAAACAATATTAGAAGCGTGAAAAAC
319 GTTTCGATTTAATTAGAAATAAATTTGAAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAAC
* *
3817 ACTTCGATTTTTTTGGCATTGAATTATATATTCTTTCTGAGTATTGTGGCAAAAAATTGAGGAAA
384 CCTTCAATTTTTTTGGCATTGAATTATATATT-TTTCTGAGTATTGTGGCAAAAAATTGAGGAAA
*
3882 AACTTTTCGGGTCAATCTTTGCAAAATTTTAACCAAAATCGTGTACCAACCATCACG-GTTTTTG
448 AA-TTTTCGGGTCAATTTTTGCAAAATTTTAACCAAAATCGTGTACCAACCATCACGTGTTTTTG
* *
3946 GCTAAAAACGCGTTCCGGAGTGC-CAGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGA
512 GCTAAAAACGCGTTCCGGAGT-CACAGCTCAATTTTGCATGATTATTGGCGCAAAGACACCTTGA
* * *
4010 AATATCTATATTCATCGAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCAT
576 AATATCTATATTCATCGAAACAAATCTCAGCCACATCGGATATAAGGATTTGTTTTTACGAGCAT
*
4075 CTGAATCTTGTTTTGATTTAATTAAAAATTAATTCAGAAAAAATAATGGGAAAA-CGATATTAGA
641 CTGAATCTTGTTTTGATTTAATTAAAAATTAATT-AGAAAAAA-AATGCGAAAACCGATATTAGA
** * *
4139 AGCGTGAAAAGCCCATCAATC-TTTTGGCATTGAATTATATATTTTTTCTGAATA-TTT-CACAA
704 AGCCCGAAAAGCCCATCAATCTTTTTGGCATTGAATTATATA-TTTTTATGAATATTTTGCAAAA
* * *
4201 AAAATTGAGAAAAAAAATTTTCTGGTCAGTTTTTAGTCGAAATCATGTAC-TAACCATCACGGTT
768 AAAATTGAG-AAAAAAATTTT-GGGTCAGTTTTTAGCCGAAATCATGTACGT-----T-ACGATT
* *
4265 TTCAGC-TAAAAACGCGTTTC-GGGCCCCGACTAAGTTTTGCATGATTTTTGGCAGAAAGACTCC
825 TTCAGCAAAAAAACGCGTTTCGGGGCCCCGACTAAGTTTTGCATGATTTTTGGCAGAAAGAATCC
* * * *
4328 TTGAAATATCTATATTCATCTAACCAAGTCTAAGCCACAATGGATTTAAGGATTTATTTTTACGA
890 TTGAAATATCTATATTCATCTAACCAAATCTAAGCCACAATGGATTCAAGAATTTATTTTTACAA
* *
4393 GCATTTGAATC
955 GCATCTAAATC
4404 TTGTTTCAATTTAATAAAAAATAAA-TTAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAA-
1 TTGTTTCAATTTAATAAAAAATAAATTTAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAAC
* * * * *
4467 CCGTCAATTTTTTTGGCGTTGAATTACATATTTTTTCTGAGTATTGTTGCAAAGAATTGA-GAAA
66 CCTTCAATTTTTTTGGCGTTG-ATTATATATTTTTTCTTAGTATTGTGGCAAAAAATTGAGGAAA
* * * * * * *
4531 AAAATTTCGGGACAGTTTTAACAAAAGTTTAGTCGAAATCGTTTACTCATTCATGTTTTTTGGCT
130 AAATTTTCGGGTCAATTTT-TCGAAATTTTAATCGAAATCG--TA-TCA---AT-TTTTTTGGCT
* *
4596 AAAAATGTGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTTGCATAAAGAC-TTTTGAAATA
187 AAAAATGCGTT-CGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGC--AAAGACTTTTTGAAATA
* *
4660 TCTATATTCATCCTCATCTAACCAAATCTAAGCCACAATGGATTTAAGGATTTGTTTTTACGAGC
249 T-T-TA-T-AT--TCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
* * * *
4725 ATCTGAATCTTGTTTCAATTTAATAAGAAATAAA-TTCAAAAAAAAAAG-AAAACGATATTAGAA
308 ATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTTGAAAAAAAAAGGAAAAACGATATTAGAA
* * * * * * * *
4788 GCGTAAAAAACCCGTCAATTTTTTTGGCGTTGAATTACATATTTTTCTGAGTATTTTTGTAAAGA
373 GCGTGAAAAACCCTTCAATTTTTTTGGCATTGAATTATATATTTTTCTGAGTATTGTGGCAAAAA
* *
4853 ATTGAGGAAAAAAATTTCCGGGTCAGTTTTTGCAAAATTTTAA
438 ATTGAGG--AAAAATTTTCGGGTCAATTTTTGCAAAATTTTAA
4896 AATCGTTTAC
Statistics
Matches: 1249, Mismatches: 171, Indels: 93
0.83 0.11 0.06
Matches are distributed among these distances:
972 13 0.01
973 31 0.02
974 94 0.08
975 230 0.18
976 87 0.07
977 185 0.15
978 35 0.03
979 77 0.06
980 45 0.04
981 34 0.03
982 202 0.16
983 138 0.11
984 77 0.06
985 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (965 bp):
TTGTTTCAATTTAATAAAAAATAAATTTAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAAC
CCTTCAATTTTTTTGGCGTTGATTATATATTTTTTCTTAGTATTGTGGCAAAAAATTGAGGAAAA
AATTTTCGGGTCAATTTTTCGAAATTTTAATCGAAATCGTATCAATTTTTTTGGCTAAAAATGCG
TTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAAAGACTTTTTGAAATATTTATATTCATC
TAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGA
TTTAATTAGAAATAAATTTGAAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAA
TTTTTTTGGCATTGAATTATATATTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAATTTTCG
GGTCAATTTTTGCAAAATTTTAACCAAAATCGTGTACCAACCATCACGTGTTTTTGGCTAAAAAC
GCGTTCCGGAGTCACAGCTCAATTTTGCATGATTATTGGCGCAAAGACACCTTGAAATATCTATA
TTCATCGAAACAAATCTCAGCCACATCGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTG
TTTTGATTTAATTAAAAATTAATTAGAAAAAAAATGCGAAAACCGATATTAGAAGCCCGAAAAGC
CCATCAATCTTTTTGGCATTGAATTATATATTTTTATGAATATTTTGCAAAAAAAATTGAGAAAA
AAATTTTGGGTCAGTTTTTAGCCGAAATCATGTACGTTACGATTTTCAGCAAAAAAACGCGTTTC
GGGGCCCCGACTAAGTTTTGCATGATTTTTGGCAGAAAGAATCCTTGAAATATCTATATTCATCT
AACCAAATCTAAGCCACAATGGATTCAAGAATTTATTTTTACAAGCATCTAAATC
Found at i:5624 original size:327 final size:326
Alignment explanation
Indices: 4964--6456 Score: 1350
Period size: 327 Copynumber: 4.6 Consensus size: 326
4954 TTTGGATGAT
* * * * * * *
4964 TCTTGTTTCGATTAAATTAGAAATTAATTCGGAAAAAAATGGAAAAATGATATTAGAAGCGTGAT
1 TCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATTGGAAAAACGATATTATAAGCATGAA
* * ** * * * *
5029 AAACCCTTCAATATTTTTAGCATTGAATTATATATTATTTTTATGAGTATTATGG-AAAAAAATT
66 AAACCCTTCAATTTTTTTGGTGTTAAATTATATA-T-TTTTTCTGAGTATTGTGGCAAAAAATTT
*** * * *
5093 GA-GAAAATTTTTTCGGGTCAGTTTTT--AACCA----A----AAATCATGTACTAACAATTACG
129 GAGGAAAAACCTTTCGGGTCAGTTTTTGCAA-AATTTTAGTGGAAATCGTGTACTAACCATTACG
* * * *** * * * **
5147 GTTTTTGGCTAAAAACGCGTTTCGGGGCCTCGACTCAGTTTTGTC-TGGTTTTTGTCATAAAGAC
193 ATTTTT-GCTAAGAACGC-ATTAAAGG--T---CTCAATTTTG-CATGATTTTTGGCGCAAAGAC
** * * * * * *
5211 TGTTTGAAATATATATATTAATCTAACCGAATCTCAGT-CACATTGGATTTAAGGATATGTTTTT
250 TCCTTGAAATATCTATATTCATCAAACCAAATCTCA-TCCACATTGGATATAAGGATTTGTTTTT
* *
5275 ACAAGCATTTGAA
314 ACGAGCATCTGAA
* *
5288 TCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATTGGAAAAATGATATTATAATCATGAA
1 TCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATTGGAAAAACGATATTATAAGCATG-A
* *
5353 AAAACCCTTCAATTTTTTTTAGTGTTAAATTATATACTTTTTCTGAGTATTGTGGC-AAAAATTT
65 AAAACCCTTCAA-TTTTTTTGGTGTTAAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTT
5417 GAGGAAAAACCTTTCGGGTCAGTTTTTGCAAAATTTTAGTGGAAATCGTGTACTAACCATTACGA
129 GAGGAAAAACCTTTCGGGTCAGTTTTTGCAAAATTTTAGTGGAAATCGTGTACTAACCATTACGA
*
5482 TTTTTGACTAAGAACACATT-AAGGTCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAA
194 TTTTTG-CTAAGAACGCATTAAAGGTCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAA
* *
5546 ATATCTATATTCATCAAACCAAATCTCATCCGCATTGGATAGAAGGATTTGTTTTTACGAGCATC
258 ATATCTATATTCATCAAACCAAATCTCATCCACATTGGATATAAGGATTTGTTTTTACGAGCATC
5611 TGAA
323 TGAA
* * * *
5615 TCTTGTTTCGATTTAATTAGAAATTAATTCGTGAAAAATAATGAAAAAACGATATTATAATCATG
1 TCTTGTTTCGATTTAATTAGAAATAAATTCG-GAAAAA-ATTGGAAAAACGATATTATAAGCATG
5680 AAAAAAACCCTTCAATTTTTTTGGTGTTAAATTATATATTTTTTCTGAGTATTGTGGC-AAAAAT
64 --AAAAACCCTTCAATTTTTTTGGTGTTAAATTATATATTTTTTCTGAGTATTGTGGCAAAAAAT
* *
5744 TTGAGGAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGTGGAAATAGTGTACTAACCATTAC
127 TTGAGGAAAAACCTTTCGGGTCAGTTTTTGCAAAATTTTAGTGGAAATCGTGTACTAACCATTAC
* * * *
5809 GGTTTTTGGGTAAGAACGCATTAAGGAGTCCTGTCTCAATTTTGCATGATTTTTGGTGCAAAAAC
192 GATTTTT-GCTAAGAACGCATTAA--AG----GTCTCAATTTTGCATGATTTTTGGCGCAAAGAC
*
5874 TCCTTGAAATATCTATATTCATCAAACCAAATCTCATCCGCATTGGATATAAGGATTTGTTTTTA
250 TCCTTGAAATATCTATATTCATCAAACCAAATCTCATCCACATTGGATATAAGGATTTGTTTTTA
5939 CGAGCATCTGAA
315 CGAGCATCTGAA
* * *
5951 TCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAATGGAAAAACGATATTAGAAGCGTG
1 TCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAT--TGGAAAAACGATATTATAAGCATG
** * * * * * * *
6016 -AAAGGCCGTCAATTGTTTTGGCGTTGAATTATATTTTTTTTTTTGCA-TATT-TTGCAAAAAAA
64 AAAAACCCTTCAATTTTTTTGGTGTTAAATTATA-TATTTTTTCTG-AGTATTGTGGC--AAAAA
* * * ** *** * *
6078 AATTGAGAAAAAACTTTTTTGGTCAGTTTTT-----A-CCCA----AAATCGTGTACTAACTATC
125 ATTTGAGGAAAAACCTTTCGGGTCAGTTTTTGCAAAATTTTAGTGGAAATCGTGTACTAACCATT
* * * * ** * *
6133 ACTGCTTTTTTTGTTAAAAACGCGTTTCGAGGT-TCCGACTCAGTTTCCATGATTTTTGGCAG-A
190 AC-G--ATTTTTGCTAAGAACGC-ATTAAAGGTCT-C-A---ATTTTGCATGATTTTTGGC-GCA
* * * * * *
6196 AAGACTCCTTGAAATATCTACATTCATCTAACCAAATCTCAGCCACAATAGATTTAAGGATTTGT
245 AAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCATCCACATTGGATATAAGGATTTGT
*
6261 TTTTATGAGCATCTGAA
310 TTTTACGAGCATCTGAA
*
6278 TCTCTGTTTCGATTTAATTAGAAATAAATTC--AAAAAA-TGGAAAAACGATACTTA-AAGCGTG
1 TCT-TGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATTGGAAAAACGATA-TTATAAGCATG
* * * * * *
6339 AAAAACCCTTC-AGTTTTTTGCTGTTGAATTATTTATTCTTTCTGAGTATTGTGGCAAAAAAGTT
64 AAAAACCCTTCAATTTTTTTGGTGTTAAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTT
* * * **
6403 GAGGAAAAACCCTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT
129 GAGGAAAAACCTTTCGGGTCAGTTTTTGCAAAATTTTAGTGGAAATCGTGTACT
6457 TTTTTTGCCA
Statistics
Matches: 985, Mismatches: 124, Indels: 113
0.81 0.10 0.09
Matches are distributed among these distances:
321 29 0.03
322 13 0.01
323 43 0.04
324 93 0.09
325 33 0.03
326 47 0.05
327 216 0.22
328 42 0.04
329 157 0.16
330 19 0.02
331 13 0.01
332 4 0.00
333 33 0.03
334 47 0.05
335 7 0.01
336 189 0.19
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (326 bp):
TCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATTGGAAAAACGATATTATAAGCATGAA
AAACCCTTCAATTTTTTTGGTGTTAAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTTGA
GGAAAAACCTTTCGGGTCAGTTTTTGCAAAATTTTAGTGGAAATCGTGTACTAACCATTACGATT
TTTGCTAAGAACGCATTAAAGGTCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATA
TCTATATTCATCAAACCAAATCTCATCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGA
A
Found at i:6646 original size:681 final size:669
Alignment explanation
Indices: 5787--8443 Score: 3026
Period size: 681 Copynumber: 3.9 Consensus size: 669
5777 AATTTTAGTG
* * * * * ** * *
5787 GAAATAGTGTACTAACCATTACGGTTTTTGGGTAAGAACGCATTAAGGAGTCCTGTCTCAATTTT
1 GAAATCGTGTACTAA-CATCACGGTTTTT-GCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTT
* * * * *
5852 GCATGATTTTTGGTGCAAAAACTCCTTGAAATATCTATATTCATCAAACCAAATCTCATCCGCAT
64 GCATGATTTTTAGCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACAT
* * * *
5917 TGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG
129 AGTATATAAGAATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCG
* *
5982 GAAAAAATAATGGAAAAACGATATTAGAAGCGTG-AAAGGCCGTCAATTGTTTTGGCGTTGAATT
194 GAAAAAA-AATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATTTTTTTGGCGTTGAATT
* * * ** *
6046 ATATTTTTTTTTTTGCATATTTTGCAAAAAAAAATTGAGAAAAAACTTTTTTGGTCAGTTTTTAC
258 ATA-TATTTTTTCTGAATATTTTGC---AAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAG
* * * * * * * *
6111 CCAAAATCGTGTACTAACTATCACTGCTTTTTTTGTTAAAAACGCGTTTCGAGGTTCCGACTCAG
319 CCGAAATCGTGTACTAACCATCAC-G-GTTTTTGGCTAAAAACGTGTTTC-AGGTCCCGGCTCAG
* *
6176 -TTTCCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTACATTCATCTAACCAAATCTCAGCC
381 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* *
6240 ACAATAGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTCTGTTTCGATTTAATTAGAAATAA
446 ACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCT-TGTTTCGATTTAATTAGAAATAA
*
6305 ATTC-AAAAAATGGAAAAACGATACTTAAAGCGTGAAAAACCCTTC-AGTTTTTTGCTGTTGAAT
510 ATTCGAAAAAATGGAAAAACGATA-TTAAAGCGTGAAAAACCCTTCAAATTTTTTGC-GTTGAAT
* * *
6368 TATTTATTCTTTCTGAGTATTGTGGCAAAAAAGTTGAGGAAAAACCCTTCGAGTCAATTTTTGCA
573 TATATATTTTTTCTGAGTATTGTGGCAAAAAA-TTGAGGAAAAACCTTTCGAGTCAATTTTTGCA
6433 AAATTTTAGCCGAAATCGTGTACTTTTTTTGCCAAC
637 AAATTTTA-CC-AAAT-GTGTACTTTTTTTGCCAAC
*
6469 GAAATCGTGTACTAATCATCACGGTTTTTGCCTAAAAACGCGTTCC-GAGTCTCGGCTCAATTTT
1 GAAATCGTGTACTAA-CATCACGGTTTTTG-CTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTT
* * * *
6533 GTATGATTTTTACCGCAAAGACTCCTTGAAATATCTATATTCATCGAATCAAATCTCAGCCACAT
64 GCATGATTTTTAGCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACAT
* *
6598 AGTATATAAGAATTTGTTTTTACGAGCATCTAAATCTTAATTCGATTTAATTAGAAATTAATTCA
129 AGTATATAAGAATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTC-
* * *** * * * *
6663 AGAAAAAAATAATGGAAAAACGATATGAGAAGCGTGAAAAGGTTGGCAATCTTTTTGACGTTGAC
193 -GGAAAAAA-AATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATTTTTTTGGCGTTGAA
* * * * *
6728 CTATATATTTTTTCCTGAATATTTTACAAAAAAATT--TATAAAACTTTTCGGGTCAGTTTTTTG
256 TTATATATTTTTT-CTGAATATTTTGC-AAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAG
* * *
6791 CCGAAATCATGTACTAACCATCACGGTTTTTGGCTAAAAACGTGTTTCATGGCCCCGGCTTAGTT
319 CCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGTGTTTCA-GGTCCCGGCTCAGTT
* * *
6856 TTGAATGATTTTTAGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCAGCCAC
383 TTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCAC
* * * *
6921 AATGGATTTAAGGATTT-TATTTTATGAGCATCTGAATCTTTTTTCAATTTAATTAGAAATTAAT
448 AATGGATTTAAGGATTTGT-TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAAT
* ** * *
6985 TCGGGAAAAAAATGGAAAAACGATATTAGATTGTGAAAAACCCTTCAATTTTTTTGGCATTGAAT
512 TC--G-AAAAAATGGAAAAACGATATTAAAGCGTGAAAAACCCTTCAAATTTTTT-GCGTTGAAT
* *
7050 TATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAACCTTTCGGGTCAATTTTTGCA
573 TATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG-GAAAAACCTTTCGAGTCAATTTTTGCA
7115 AAATTTTAACCAAAATTGTGTACTTTATTTTTTTGCCAAC
637 AAATTTT-ACC-AAA-TGTGTAC----TTTTTTTGCCAAC
*
7155 GAAATCGTGTACTAACTATCATGGTTTTTTTGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTT
1 GAAATCGTGTACTAAC-ATCACGG--TTTTTGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTT
* * *
7220 TGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACA
63 TGCATGATTTTTAGCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACA
*
7285 TTGTATATAAGAATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTTAATTAGAAATTAATT
128 TAGTATATAAGAATTTGTTTTTACGAGCATCTGAATCTTATTTCGA-TTTAATTAGAAATTAATT
* * *
7350 C--AAAAAAAA-AGAAAAACGATATTAAAAGCGTGAAATGCCCGTCAATTTTTTTGGCGTTGAAT
192 CGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATTTTTTTGGCGTTGAAT
* *
7412 TATATATTTTTTCTGAATATTTTGCAAAACATTGAG-AAAAACTTTTCGGGTTAGTTTTTAGCCG
257 TATATATTTTTTCTGAATATTTTGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCG
* *
7476 AAATCGTGTACTAACAATCACGGTTTTTGGCTAAAAACGTGTTTCAGGTCCCGGTTCAGTTTTGC
322 AAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGTGTTTCAGGTCCCGGCTCAGTTTTGC
*
7541 ATGATTTTGGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATG
387 ATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATG
* *
7606 GATTTAAGGATTTGTTTTTACGAGTATCTCAATCTTAGTTTCGATTTAATTAGAAATAAATTCGG
452 GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTT-GTTTCGATTTAATTAGAAATAAATTC-G
* * *
7671 AAAAAAAGGAAAAACGATATTAGAAGCGTG-AAAATCCTTCAAATTTTTTGACGTTAAATTATAT
515 AAAAAATGGAAAAACGATATTA-AAGCGTGAAAAACCCTTCAAATTTTTTG-CGTTGAATTATAT
* * *
7735 ATTTTTTCTGAGTATTGTGGCAAAAAATTG-GGAAAAAACTTTAC-AGGTCAGTTTTTGTAAAAT
578 ATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACCTTT-CGA-GTCAATTTTTGCAAAAT
7798 TTT-----A-----A----------C--C
641 TTTACCAAATGTGTACTTTTTTTGCCAAC
* * * * * *
7805 GAAATCGTGTACTACCATCACGGCTTTTGGCTAAAAACGCATTCCGGAGCCCCGACTCAATTTTT
1 GAAATCGTGTACTAACATCACGG-TTTTTGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTG
* * * * *
7870 CATAATTTTTAGCACAAAAAATCATTGAAATATCTATATTCATCGAAACAAATGC-CAGCCACAT
65 CATGATTTTTAGCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAAT-CTCAGCCACA-
* *
7934 TAG-ATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC
128 TAGTATATAAGAATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTC
* * * *
7998 AGAAAAAAAATGGAAAAACGATATTGGAAGCGTGAAAAGCCCATCAATTTTTTTGGCGTTGAATC
193 GGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATTTTTTTGGCGTTGAATT
* * * * * *
8063 ATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAATAGACGTTTCGGGTCAGCTTTTAGCCG
258 ATATATTTTTTCTGAATATT-TTGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCG
* * * * * **
8128 AAATTGTGTACTAACCATCACGGTTTTTGACTAAAAATGTGTTTTGAGG-CCACGGTTTTGTTTT
322 AAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGTG-TTTCAGGTCC-CGGCTCAGTTTT
** ** * * *
8192 GCATGATTTTTGGC-GTCGAGACTTTTTGAAATATCTTTATTTATCTAATCAAATCTCAGCCACA
385 GCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACA
* * * * *
8256 TTGGATTT-AGGAATTTGTTTTTACGTGCATCTGAATTTTGTTTCGATTTAATTAAAAATTAATT
449 ATGGATTTAAGG-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATT
* * * *** * *
8320 CAAAAAAAATATGAAAAATGATATTAAAAGCGTGAAAAGTTC-TCCAATCTTTTTGGCGTTAAAT
513 C-GAAAAAAT-GGAAAAACGATATT-AAAGCGTGAAAAACCCTTCAAAT-TTTTT-GCGTTGAAT
* * * * * * * *
8384 TATATATATTTTATGAGTATTTTTGCCAAAAATTGATGAAAAATCTTTCGGGTC-ATTTTT
573 TATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACCTTTCGAGTCAATTTTT
8444 ACCATCATTG
Statistics
Matches: 1718, Mismatches: 205, Indels: 133
0.84 0.10 0.06
Matches are distributed among these distances:
647 19 0.01
648 129 0.08
649 17 0.01
650 83 0.05
651 13 0.01
652 97 0.06
653 129 0.08
654 53 0.03
655 11 0.01
666 1 0.00
672 1 0.00
677 1 0.00
678 62 0.04
679 119 0.07
680 121 0.07
681 274 0.16
682 254 0.15
683 97 0.06
684 37 0.02
685 7 0.00
686 34 0.02
687 15 0.01
688 125 0.07
689 19 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (669 bp):
GAAATCGTGTACTAACATCACGGTTTTTGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGC
ATGATTTTTAGCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATAG
TATATAAGAATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCGGA
AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATTTTTTTGGCGTTGAATTATA
TATTTTTTCTGAATATTTTGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAAT
CGTGTACTAACCATCACGGTTTTTGGCTAAAAACGTGTTTCAGGTCCCGGCTCAGTTTTGCATGA
TTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATT
TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAA
TGGAAAAACGATATTAAAGCGTGAAAAACCCTTCAAATTTTTTGCGTTGAATTATATATTTTTTC
TGAGTATTGTGGCAAAAAATTGAGGAAAAACCTTTCGAGTCAATTTTTGCAAAATTTTACCAAAT
GTGTACTTTTTTTGCCAAC
Found at i:9775 original size:12 final size:12
Alignment explanation
Indices: 9760--9785 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9750 AATAGAAAAC
9760 AATTATAAATTT
1 AATTATAAATTT
9772 AATTATAAATTT
1 AATTATAAATTT
9784 AA
1 AA
9786 AGTCTTGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AATTATAAATTT
Found at i:10079 original size:22 final size:22
Alignment explanation
Indices: 10051--10239 Score: 98
Period size: 22 Copynumber: 8.5 Consensus size: 22
10041 TAGGTTATTG
*
10051 AAATTTCATAGTGTGGCTATCA
1 AAATTTCATAGTGTGGTTATCA
*
10073 AAATTTCATAATGTGGTTA-CAA
1 AAATTTCATAGTGTGGTTATC-A
** *
10095 AAATTTCATAG-AAGGTAATCA
1 AAATTTCATAGTGTGGTTATCA
* * * *
10116 AAGTTTCAAATTGTGTTTATCA
1 AAATTTCATAGTGTGGTTATCA
* *
10138 AAATTTCATAGTGAGATTGA-CA
1 AAATTTCATAGTGTGGTT-ATCA
* ** *
10160 CTAAA-TTCTATAGGGAAGTTATTA
1 --AAATTTC-ATAGTGTGGTTATCA
* * * * *
10184 ACATTCCATTGGGAGGTTATCA
1 AAATTTCATAGTGTGGTTATCA
* * *
10206 AAATTTCATAGTTTGATTATCC
1 AAATTTCATAGTGTGGTTATCA
10228 AAATTTCATAGT
1 AAATTTCATAGT
10240 TTACCAAATC
Statistics
Matches: 123, Mismatches: 35, Indels: 18
0.70 0.20 0.10
Matches are distributed among these distances:
21 14 0.11
22 90 0.73
23 7 0.06
24 12 0.10
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (22 bp):
AAATTTCATAGTGTGGTTATCA
Found at i:10493 original size:22 final size:21
Alignment explanation
Indices: 10308--10493 Score: 90
Period size: 22 Copynumber: 8.5 Consensus size: 21
10298 CATCAAAATT
*
10308 AATTTCATATAGAGGTTATCATA
1 AATTTCATA-GGAGGTTATCA-A
* *
10331 AATTT-ATACCGTGGTTATCAA
1 AATTTCATA-GGAGGTTATCAA
* * * * *
10352 AATTTCAGAGTGTGATGACCAA
1 AATTTCATAG-GAGGTTATCAA
*
10374 AATTTCATAGGATGGTTATCAG
1 AATTTCATAGGA-GGTTATCAA
*
10396 AATTTCATAGTGTA-GTTATTAA
1 AATTTCATAG-G-AGGTTATCAA
* * * * *
10418 AGTTCCACAGGGAGATTATCAC
1 AATTTCATA-GGAGGTTATCAA
*
10440 AATTTCTTAAGGAGGTTATCAA
1 AATTTCAT-AGGAGGTTATCAA
* *
10462 AATAAT-ATAGCGAGATTATCAA
1 AAT-TTCATAG-GAGGTTATCAA
10484 AATTTCATAG
1 AATTTCATAG
10494 TAAAACTATG
Statistics
Matches: 120, Mismatches: 32, Indels: 23
0.69 0.18 0.13
Matches are distributed among these distances:
21 11 0.09
22 99 0.82
23 9 0.08
24 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.34
Consensus pattern (21 bp):
AATTTCATAGGAGGTTATCAA
Found at i:10738 original size:22 final size:22
Alignment explanation
Indices: 10713--10754 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
10703 TCAGAATTTT
10713 ATAGGGTAATTATCAAAATTCC
1 ATAGGGTAATTATCAAAATTCC
* **
10735 ATAGTGTGGTTATCAAAATT
1 ATAGGGTAATTATCAAAATT
10755 TAATAAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
ATAGGGTAATTATCAAAATTCC
Done.