Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1204
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: 12508
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Found at i:3316 original size:157 final size:157
Alignment explanation
Indices: 2649--3680 Score: 489
Period size: 157 Copynumber: 6.7 Consensus size: 157
2639 CTTTCTTACG
* * * * * *
2649 AAAGCATCACTATC--GTGTCCTAATGAGGAA-AAG-TGTTTATGGTGCCCAATCTTGAAAATAA
1 AAAGCATCAATATCATGTATCCTAACGA-GAAGAAGATGTTTATGGTGCCTAATCATGAAAAGAA
* *
2710 TGAAGATCATTACTAGAATCCATGTTTGTCTTATTTAAGGCATAAACTTAAACTCTACA--AAAA
65 TGAAG-TCATTACTAGAATCCATGTTTGTCTTATTTGAGGCATAAACTTAGA-TCT-CATGAAAA
* *
2773 CTAGTGGAAGAAAAGCCTTTCTTGA-GAAA--
127 ATAGTGGAAGAAAAGGCTTTCTT-ATGAAACC
* * * * * * *
2802 AAAGCATAAATACCATGTATCCTCATGAGAAAAATG-TGTTTATGGTGCCTATTC-TTAAAAGGA
1 AAAGCATCAATATCATGTATCCTAACGAGAAGAA-GATGTTTATGGTGCCTAATCATGAAAA-GA
** * * * * *
2865 ATG--GGGATTATCATGAGAATCCATGTTTGTTTTATTTAAGAGG--TGAACTTTGATTTTATGA
64 ATGAAGTCATTA-C-T-AGAATCCATGTTTGTCTTATTT--GAGGCATAAACTTAGATCTCATGA
**
2926 AAAATAGTGGTAA-AAAAGGC-TT-TTACCCCAAAGCC
124 AAAATAGTGG-AAGAAAAGGCTTTCTTA--TGAAA-CC
* * *
2961 AAACCATCAATGTCATGTATCC---C-A-AAGAAGAT-TTT-TGGTGTCTAATCATGAAAAGAAT
1 AAAGCATCAATATCATGTATCCTAACGAGAAGAAGATGTTTATGGTGCCTAATCATGAAAAGAAT
* * * * * * * *
3019 -AGAGACTATTACAAAAATCCATGTTTGTCTCATTTGAGGAATAAACTTTA-ATTTTAAGAAAAA
66 GA-AGTC-ATTACTAGAATCCATGTTTGTCTTATTTGAGGCATAAAC-TTAGATCTCATGAAAAA
* * **
3082 TGAG-GCAAAGAAAA-GCTTTCCT-TGCAAAAA
128 T-AGTG-GAAGAAAAGGCTTTCTTATG-AAACC
* * * * * *
3112 AAATCATCAATATCATGTATCCTAAAGAGGAGAACATATTTATGGTGCCCAATCATGAAAAGAAT
1 AAAGCATCAATATCATGTATCCTAACGAGAAGAAGATGTTTATGGTGCCTAATCATGAAAAGAAT
* * *
3177 GAAAGTCACTACTAGAATCCATGTTTGTCTTATTTGAGGCACAAACTTAGA-CTCATGAAAAATG
66 G-AAGTCATTACTAGAATCCATGTTTGTCTTATTTGAGGCATAAACTTAGATCTCATGAAAAATA
3241 GTGGAAGAAAAGGCTTTCTTATGAAACC
130 GTGGAAGAAAAGGCTTTCTTATGAAACC
* *
3269 AAAGCATCAATATCATGTATCCTAACGAGAAGAAGGTGCTTATGGTGCCTAATCATGAAAAGAAT
1 AAAGCATCAATATCATGTATCCTAACGAGAAGAAGATGTTTATGGTGCCTAATCATGAAAAGAAT
* * * * * * * * * *
3334 GGGAA-TTATTA-TGAAAATCCATGTTTGCCTCATTTCAAG-ATGAACTTTGATTTTATGAAAAA
66 --GAAGTCATTACT-AGAATCCATGTTTGTCTTATTTGAGGCATAAACTTAGATCTCATGAAAAA
* * *
3396 TAGTGTTAA-AAAA-GCTTTCCT-TGCAAAGTC
128 TAGTG-GAAGAAAAGGCTTTCTTATG-AAA-CC
* * * * * *
3426 AAACCTTCAATGTCATGTATCC---C-A-ATGAGGAT-TTT-TGGTGCCTAATCTTGAAAAGAAT
1 AAAGCATCAATATCATGTATCCTAACGAGAAGAAGATGTTTATGGTGCCTAATCATGAAAAGAAT
* * * * * * ** * * * *
3484 GGA-TACTGTTACAAGAATCCAT-TCTTGTCTCATTTAAGGGAGGAACTTTGATTTCAAGGAAAA
66 GAAGT-C-ATTACTAGAATCCATGT-TTGTCTTATTTGAGGCATAAACTTAGATCTCATGAAAAA
* * *
3547 T-GGGGTAAAGAAAA-GCTTTCTTGTGAAAGC
128 TAGTGG--AAGAAAAGGCTTTCTTATGAAACC
* * *
3577 AAATCATTAATATCATGTAT-CT-A-GA-ATAGAACG-TGTTTATAGG-GCCTAATCATGACAAG
1 AAAGCATCAATATCATGTATCCTAACGAGA-AGAA-GATGTTTAT-GGTGCCTAATCATGAAAAG
*** * * *
3636 AGCAAAGATCGTTACTAGAATCCTTGTTTGTCTCATTTGAGGCAT
63 AATGAAG-TCATTACTAGAATCCATGTTTGTCTTATTTGAGGCAT
3681 GGGCTTATAC
Statistics
Matches: 673, Mismatches: 132, Indels: 146
0.71 0.14 0.15
Matches are distributed among these distances:
148 3 0.00
149 1 0.00
150 52 0.08
151 61 0.09
152 79 0.12
153 41 0.06
154 21 0.03
155 75 0.11
156 105 0.16
157 148 0.22
158 64 0.10
159 22 0.03
160 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (157 bp):
AAAGCATCAATATCATGTATCCTAACGAGAAGAAGATGTTTATGGTGCCTAATCATGAAAAGAAT
GAAGTCATTACTAGAATCCATGTTTGTCTTATTTGAGGCATAAACTTAGATCTCATGAAAAATAG
TGGAAGAAAAGGCTTTCTTATGAAACC
Found at i:3559 original size:465 final size:459
Alignment explanation
Indices: 2543--4104 Score: 1537
Period size: 465 Copynumber: 3.4 Consensus size: 459
2533 ATTTTTTATT
* ** * * *
2543 CCTAATCTCGAAAAGAATAGAGACTATTATGAGAATCTATGTTTGTCTCATTTAAGTAATGAACT
1 CCTAATCACGAAAAGAATAGAGACTATTACAAGAATCCATGTTTGTCTCATTTAAGGAAGGAACT
*
2608 TTGATTTTAAGGAAAAT-AGGACAAAGAAAAGCTTTC-T-T----ACGAAAGCATCACTATC--G
66 TTGATTTTAAGGAAAATGAGG-CAAAGAAAAGCTTTCTTGTGAAAAC-AAAGCATCAATATCATG
* * * *
2664 TGTCCTAATGAGGA-AA-AGTGTTTATGGTGCCCAATCTTGAAAATAATG-AAGATCATTACTAG
129 TATCCTAAAGAGGAGAACA-TGTTTATGGTGCCCAATCATGAAAAGAATGAAAGATCATTACTAG
* * *
2726 AATCCATGTTTGTCTTATTTAAGGCATAAACTTAAACTCTACAAAAACTAGTGGAAGAAAAGCCT
193 AATCCATGTTTGTCTTATTTGAGGCATAAACTTAAACTCT--AAAAA-TGGTGGAAGAAAAGACT
* * * * *
2791 TTCTTGAGAAA--AAAGCATAAATACCATGTATCCTCATGAGAAAAATGTGTTTATGGTGCCTAT
255 TTCTT-AGAAACCAAAGCATCAATATCATGTATCCTAATGAGAAGAATGTG-TTATGGTGCCTAA
* * *
2854 TCTTAAAAGGAATGGGGATTATCATGAGAATCCATGTTTGTTTTATTTAAGAGGTGAACTTTGAT
318 TCTTAAAA-GAATGGGGATTATTATGAGAATCCATGTTTGTCTCATTTAAGA--TGAACTTTGAT
* *
2919 TTTATGAAAAATAGTGGTAAAAAAGGCTTTTACC-CCAAAGCCAAACCATCAATGTCATGTATCC
380 TTTATGAAAAATAGTGTTAAAAAA-GC-TTT-CCTACAAAGCCAAACCATCAATGTCATGTATCC
* *
2983 CAAAGAAGATTTTTGGTG
442 CAATGAGGATTTTTGGTG
* * * * **
3001 TCTAATCATGAAAAGAATAGAGACTATTACAAAAATCCATGTTTGTCTCATTTGAGGAATAAACT
1 CCTAATCACGAAAAGAATAGAGACTATTACAAGAATCCATGTTTGTCTCATTTAAGGAAGGAACT
* * * * *
3066 TTAATTTTAAGAAAAATGAGGCAAAGAAAAGCTTTCCTTG-CAAAAAAAATCATCAATATCATGT
66 TTGATTTTAAGGAAAATGAGGCAAAGAAAAGCTTT-CTTGTGAAAACAAAGCATCAATATCATGT
* *
3130 ATCCTAAAGAGGAGAACATATTTATGGTGCCCAATCATGAAAAGAATGAAAG-TCACTACTAGAA
130 ATCCTAAAGAGGAGAACATGTTTATGGTGCCCAATCATGAAAAGAATGAAAGATCATTACTAGAA
* * *
3194 TCCATGTTTGTCTTATTTGAGGCACAAACTTAGACTCATGAAAAATGGTGGAAGAAAAGGCTTTC
195 TCCATGTTTGTCTTATTTGAGGCATAAACTTAAACTC-T-AAAAATGGTGGAAGAAAAGACTTTC
* *
3259 TTATGAAACCAAAGCATCAATATCATGTATCCTAACGAGAAGAAGGTGCTTATGGTGCCTAATCA
258 TTA-GAAACCAAAGCATCAATATCATGTATCCTAATGAGAAGAATGTG-TTATGGTGCCTAATC-
* * * *
3324 TGAAAAGAATGGGAATTATTATGAAAATCCATGTTTGCCTCATTTCAAGATGAACTTTGATTTTA
320 TTAAAAGAATGGGGATTATTATGAGAATCCATGTTTGTCTCATTT-AAGATGAACTTTGATTTTA
* * *
3389 TGAAAAATAGTGTTAAAAAAGCTTTCCTTGCAAAGTCAAACCTTCAATGTCATGTATCCCAATGA
384 TGAAAAATAGTGTTAAAAAAGCTTTCC-TACAAAGCCAAACCATCAATGTCATGTATCCCAATGA
3454 GGATTTTTGGTG
448 GGATTTTTGGTG
** * * * *
3466 CCTAATCTTGAAAAGAATGGATACTGTTACAAGAATCCAT-TCTTGTCTCATTTAAGGGAGGAAC
1 CCTAATCACGAAAAGAATAGAGACTATTACAAGAATCCATGT-TTGTCTCATTTAAGGAAGGAAC
* * * * * *
3530 TTTGATTTCAAGGAAAATGGGGTAAAGAAAAGCTTTCTTGTGAAAGCAAATCATTAATATCATGT
65 TTTGATTTTAAGGAAAATGAGGCAAAGAAAAGCTTTCTTGTGAAAACAAAGCATCAATATCATGT
** * * * *
3595 AT-CT--AGAATAGAACGTGTTTATAGG-GCCTAATCATGACAAG-A-GCAAAGATCGTTACTAG
130 ATCCTAAAGAGGAGAACATGTTTAT-GGTGCCCAATCATGAAAAGAATG-AAAGATCATTACTAG
* * *** * ** * *
3654 AATCCTTGTTTGTCTCATTTGAGGCATGGGCTTATACTCTACAGAAATGGTATATGAAAAGAATT
193 AATCCATGTTTGTCTTATTTGAGGCATAAACTTAAACTCTA-A-AAATGGTGGAAGAAAAGACTT
* * ** * * *
3719 TCTTGCGAAGCCAAAGCATCAATATTTTATATCCTAATAAGAAGAATATGTCTATGGTGCCTAAT
256 TCTT-AGAAACCAAAGCATCAATATCATGTATCCTAATGAGAAGAATGTGT-TATGGTGCCTAA-
* * * * *
3784 TTTTTTTAAAA-AGTGGGGATTATTATGAGAATCAATGTTTGTCTCATTTTGGAGATGAACTTTA
318 ---TCTTAAAAGAATGGGGATTATTATGAGAATCCATGTTTGTCTCA-TTT-AAGATGAACTTTG
* * * ** * * *
3848 ATTCTATGAAAAATAGTTGTAAAAAAAGCTTTCCCTATAAAGCCAATTCATAAATGTCATGGATT
378 ATTTTATGAAAAATAG-TGTTAAAAAAGCTTT-CCTACAAAGCCAAACCATCAATGTCATGTATC
3913 CCAATGAGGATTTTTGGTG
441 CCAATGAGGATTTTTGGTG
* * * * * * *
3932 CCTAATCACCAAAAGAATGGAGACTACTGCAAGAATCCATGTTTGTTTCATTTGA-G-TGG-ACT
1 CCTAATCACGAAAAGAATAGAGACTATTACAAGAATCCATGTTTGTCTCATTTAAGGAAGGAACT
** *
3994 TTGATTTTAAGGAAAAT-AGGTCAAAGAAAAGCTCTTCTTGTGAAGTCAAAGCATTAATATCATG
66 TTGATTTTAAGGAAAATGAGG-CAAAGAAAAGCT-TTCTTGTGAAAACAAAGCATCAATATCATG
* * * *
4058 TATCCCAATA-AGGAGAACGTGTTTGTAGTGCCCAATCATGAAAAGAA
129 TATCCTAA-AGAGGAGAACATGTTTATGGTGCCCAATCATGAAAAGAA
4105 AGAGATTGTT
Statistics
Matches: 918, Mismatches: 140, Indels: 82
0.81 0.12 0.07
Matches are distributed among these distances:
458 84 0.09
459 4 0.00
460 3 0.00
461 8 0.01
462 138 0.15
463 46 0.05
464 74 0.08
465 223 0.24
466 213 0.23
467 114 0.12
468 11 0.01
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (459 bp):
CCTAATCACGAAAAGAATAGAGACTATTACAAGAATCCATGTTTGTCTCATTTAAGGAAGGAACT
TTGATTTTAAGGAAAATGAGGCAAAGAAAAGCTTTCTTGTGAAAACAAAGCATCAATATCATGTA
TCCTAAAGAGGAGAACATGTTTATGGTGCCCAATCATGAAAAGAATGAAAGATCATTACTAGAAT
CCATGTTTGTCTTATTTGAGGCATAAACTTAAACTCTAAAAATGGTGGAAGAAAAGACTTTCTTA
GAAACCAAAGCATCAATATCATGTATCCTAATGAGAAGAATGTGTTATGGTGCCTAATCTTAAAA
GAATGGGGATTATTATGAGAATCCATGTTTGTCTCATTTAAGATGAACTTTGATTTTATGAAAAA
TAGTGTTAAAAAAGCTTTCCTACAAAGCCAAACCATCAATGTCATGTATCCCAATGAGGATTTTT
GGTG
Found at i:4132 original size:466 final size:461
Alignment explanation
Indices: 2543--4193 Score: 1447
Period size: 466 Copynumber: 3.6 Consensus size: 461
2533 ATTTTTTATT
* ** * * *
2543 CCTAATC-TCGAAAAGAATAGAGACTATTATGAGAATCTATGTTTGTCTCATTTAAGTAATGAAC
1 CCTAATCAT-GAAAAGAATGGAGACTATTACAAGAATCCATGTTTGTCTCATTT--G-AGTGGAC
* * * * *
2607 TTTGATTTTAAGGAAAAT-AGGACAAAGAAAAGCTTTC-T-T-ACG-AAAGCATCACTATC--GT
62 TTTGATTTTAAGGAAAATGAGGTCAAAGAAAAGCTTTCTTGTGAAGCAAATCATTAATATCATGT
* * * * * * * * *
2665 GTCCTAATGAGGA-AAAGTGTTTATGGTGCCCAATCTTGAAAATAATGAAGATCATTACTAGAAT
127 ATCCCAA-AAGGAGAACGTGTTTATAGTGCCCAATCATGAAAAGAAAG-AGATCGTTACTAGAAT
* * * * * * * **
2729 CCATGTTTGTCTTATTTAAGGCATAAACTTAAACTC-TACAAAAACTAGTGGAAGAAAAGCCTTT
190 CCATGTTTGTCTCATTTGAGGCACAAACTTAGACTCAT-GAAAAA-TGGTAGAAGAAAAGAATTT
* * * * ** * * *
2793 CTTGA-GAAA--AAAGCATAAATACCATGTATCCTCATGAGAAAAATG-TGTTTATGGTGCCTAT
253 CTT-ACGAAACCAAAGCATCAATATCATATATCCTAACAAGAAGAA-GATGCTTATGGTGCCTAA
* * * * * *
2854 TC-TTAAAAGGAATGGGGATTATCATGAGAATCCATGTTTGTTTTATTTAAGAGGTGAACTTTGA
316 TCATGAAAA-GAATGGGGATTATTATGAGAATCCATGTTTGTCTCATTTTAGAGATGAACTTTGA
* *
2918 TTTTATGAAAAATAGTGGTAAAAAAGGCTTTTACCC-CAAAGCCAAACCATCAATGTCATGTATC
380 TTTTATGAAAAATAGTTGTAAAAAAAGC-TTT-CCCTCAAAGCCAAACCATCAATGTCATGTATC
* *
2982 CCAAAGAAGATTTTTGGTG
443 CCAATGAGGATTTTTGGTG
* * * **
3001 TCTAATCATGAAAAGAATAGAGACTATTACAAAAATCCATGTTTGTCTCATTTGAGGAATAAACT
1 CCTAATCATGAAAAGAATGGAGACTATTACAAGAATCCATGTTTGTCTCATTTGA-G--TGGACT
* * ** ** *
3066 TTAATTTTAAGAAAAATGAGG-CAAAGAAAAGCTTTCCTTGCAAAAAAAATCATCAATATCATGT
63 TTGATTTTAAGGAAAATGAGGTCAAAGAAAAGCTTT-CTTGTGAAGCAAATCATTAATATCATGT
* * * * * * **
3130 ATCCTAAAGAGGAGAACATATTTATGGTGCCCAATCATGAAAAGAATGAAAGTCACTACTAGAAT
127 ATCCCAAA-AGGAGAACGTGTTTATAGTGCCCAATCATGAAAAGAAAGAGA-TCGTTACTAGAAT
* * **
3195 CCATGTTTGTCTTATTTGAGGCACAAACTTAGACTCATGAAAAATGGTGGAAGAAAAGGCTTTCT
190 CCATGTTTGTCTCATTTGAGGCACAAACTTAGACTCATGAAAAATGGTAGAAGAAAAGAATTTCT
* * * *
3260 TATGAAACCAAAGCATCAATATCATGTATCCTAACGAGAAGAAGGTGCTTATGGTGCCTAATCAT
255 TACGAAACCAAAGCATCAATATCATATATCCTAACAAGAAGAAGATGCTTATGGTGCCTAATCAT
* * * *
3325 GAAAAGAATGGGAATTATTATGAAAATCCATGTTTGCCTCATTTCA-AGATGAACTTTGATTTTA
320 GAAAAGAATGGGGATTATTATGAGAATCCATGTTTGTCTCATTTTAGAGATGAACTTTGATTTTA
* * * *
3389 TGAAAAATAG-TGTTAAAAAAGCTTTCCTTGCAAAGTCAAACCTTCAATGTCATGTATCCCAATG
385 TGAAAAATAGTTGTAAAAAAAGCTTTCCCT-CAAAGCCAAACCATCAATGTCATGTATCCCAATG
3453 AGGATTTTTGGTG
449 AGGATTTTTGGTG
* * * * *
3466 CCTAATCTTGAAAAGAATGGATACTGTTACAAGAATCCAT-TCTTGTCTCATTTAAGGGAGGAAC
1 CCTAATCATGAAAAGAATGGAGACTATTACAAGAATCCATGT-TTGTCTCATTT--GAGTGG-AC
* *
3530 TTTGATTTCAAGGAAAATGGGGT-AAAGAAAAGCTTTCTTGTGAAAGCAAATCATTAATATCATG
62 TTTGATTTTAAGGAAAATGAGGTCAAAGAAAAGCTTTCTTGTG-AAGCAAATCATTAATATCATG
* * * * * *
3594 TAT-CTAGAA-TAGAACGTGTTTATAGGGCCTAATCATGACAAGAGCAA-AGATCGTTACTAGAA
126 TATCCCAAAAGGAGAACGTGTTTATAGTGCCCAATCATGA-AA-AGAAAGAGATCGTTACTAGAA
* **** * * *
3656 TCCTTGTTTGTCTCATTTGAGGCATGGGCTTATACTC-T-ACAGAAATGGTATATGAAAAGAATT
189 TCCATGTTTGTCTCATTTGAGGCACAAACTTAGACTCATGA-A-AAATGGTAGAAGAAAAGAATT
* * ** * *
3719 TCTTGCGAAGCCAAAGCATCAATATTTTATATCCTAATAAGAAGAATATG-TCTATGGTGCCTAA
252 TCTTACGAAACCAAAGCATCAATATCATATATCCTAACAAGAAGAAGATGCT-TATGGTGCCTAA
** * * * *
3783 TTTTTTTTAAAA-AGTGGGGATTATTATGAGAATCAATGTTTGTCTCATTTTGGAGATGAACTTT
316 ---TCATGAAAAGAATGGGGATTATTATGAGAATCCATGTTTGTCTCATTTTAGAGATGAACTTT
* * * ** * *
3847 AATTCTATGAAAAATAGTTGTAAAAAAAGCTTTCCCTATAAAGCCAATTCATAAATGTCATGGAT
378 GATTTTATGAAAAATAGTTGTAAAAAAAGCTTTCCCT-CAAAGCCAAACCATCAATGTCATGTAT
*
3912 TCCAATGAGGATTTTTGGTG
442 CCCAATGAGGATTTTTGGTG
** * * *
3932 CCTAATCACCAAAAGAATGGAGACTACTGCAAGAATCCATGTTTGTTTCATTTGAGTGGACTTTG
1 CCTAATCATGAAAAGAATGGAGACTATTACAAGAATCCATGTTTGTCTCATTTGAGTGGACTTTG
*
3997 ATTTTAAGGAAAAT-AGGTCAAAGAAAAGCTCTTCTTGTGAAGTCAAAGCATTAATATCATGTAT
66 ATTTTAAGGAAAATGAGGTCAAAGAAAAGCT-TTCTTGTGAAG-CAAATCATTAATATCATGTAT
* * *
4061 CCCAATAAGGAGAACGTGTTTGTAGTGCCCAATCATGAAAAGAAAGAGATTGTTA-TGACAATCC
129 CCCAA-AAGGAGAACGTGTTTATAGTGCCCAATCATGAAAAGAAAGAGATCGTTACT-AGAATCC
* * * * * **
4125 ATGTTTGTCTCATTTG-TGCAACAAACTTTGATTCTATAAAAAATGGTGAAAAGAAAAGCTTTTC
192 ATGTTTGTCTCATTTGAGGC-ACAAACTTAGACTC-ATGAAAAATGGT-AGAAGAAAAGAATTTC
4189 TTACG
254 TTACG
4194 GCATCAAAGA
Statistics
Matches: 975, Mismatches: 165, Indels: 96
0.79 0.13 0.08
Matches are distributed among these distances:
455 1 0.00
456 1 0.00
458 80 0.08
459 5 0.01
460 2 0.00
461 3 0.00
462 135 0.14
463 52 0.05
464 81 0.08
465 230 0.24
466 247 0.25
467 114 0.12
468 23 0.02
469 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (461 bp):
CCTAATCATGAAAAGAATGGAGACTATTACAAGAATCCATGTTTGTCTCATTTGAGTGGACTTTG
ATTTTAAGGAAAATGAGGTCAAAGAAAAGCTTTCTTGTGAAGCAAATCATTAATATCATGTATCC
CAAAAGGAGAACGTGTTTATAGTGCCCAATCATGAAAAGAAAGAGATCGTTACTAGAATCCATGT
TTGTCTCATTTGAGGCACAAACTTAGACTCATGAAAAATGGTAGAAGAAAAGAATTTCTTACGAA
ACCAAAGCATCAATATCATATATCCTAACAAGAAGAAGATGCTTATGGTGCCTAATCATGAAAAG
AATGGGGATTATTATGAGAATCCATGTTTGTCTCATTTTAGAGATGAACTTTGATTTTATGAAAA
ATAGTTGTAAAAAAAGCTTTCCCTCAAAGCCAAACCATCAATGTCATGTATCCCAATGAGGATTT
TTGGTG
Found at i:5086 original size:466 final size:466
Alignment explanation
Indices: 4148--5105 Score: 1175
Period size: 466 Copynumber: 2.1 Consensus size: 466
4138 TTGTGCAACA
* * * *
4148 AACTTTGATTCTATAAAAAAT-GGTGAAAAGAAAAGCTTTTCTTACGGCATCAAAGATCACTATA
1 AACTTTGATTCTATGAAAAATAGG-GGAAAGAAAAACTTTTCTTACGACATCAAAGATCACTATA
* ** * *** **
4212 ATGTATCCCAATGAAGGGAACGTATTTTTGGTTCTCAATCTTGAAAAGAATGGAACTAATATGAG
65 ATGTATCCCAATGAAGGGAACATATTTTTCATTCTCAATCTCGAAAAGAAAAAAACTAATACAAG
* * * *
4277 AATCCATATTTGTCTCATTTGAGGCACGAACTAAACTCTATTGAAAATAGTGAGAGGAAAAGTCT
130 AATCAATATTCGTCTCATTTGAGGCACGAACTAAACTCTATAGAAAATAGTGAGAAGAAAAGTCT
* * ** *
4342 TTCCTACGAAACCAAAGTCACTAATACCATATATGTTAAAGAGAAGAATATGTTTATGGTACCTA
195 TTCCTACCAAACCAAAGACACTAATACCATATAACTTAAAGAGAAAAATATGTTTATGGTACCTA
* * * **
4407 ATCTTGAACAAAATTGGGATTATTATGAGAATTCAAGTTCATCTCATTTAAGGGATAAACTTTGA
260 ATCTTGAACAAAAATGGGATTATTATAAGAATCCAAGTTCATCTCATTTAAAAGATAAACTTTGA
* * *
4472 TTCTATGAAAATGGTGATAAAAAAACTTTTCTTGCAAAGCCAAACTATTAATGTCATGTATCTCA
325 TTCTATGAAAATGGTGATAAAAAAACTTTTCCTGCAAAGCCAAACCATTAATGTCATGCATCTCA
* *
4537 ACGAGGATTTTTTGTGCCCAATAATGAAAAGAATGGAGACAATTACAAGAATCCATGTTCAACTC
390 ACGAGGATTTTTGGTGCCCAATAACGAAAAGAATGGAGACAATTACAAGAATCCATGTTCAACTC
4602 ATTTAAGAGATG
455 ATTTAAGAGATG
* * * * * *
4614 AACTTTGATTCTATGAAAAATAGGGGTAAGAAAAACTTTTCTTGC-ACATCAAAGCATTATTGTC
1 AACTTTGATTCTATGAAAAATAGGGGAAAGAAAAACTTTTCTTACGACATCAAAG-ATCACTATA
*
4678 ATGTAT-CCAATGAAGGGAACATATTTTTCATTCTCAATCTCGAAAAGAAAAAAGACTATTACAA
65 ATGTATCCCAATGAAGGGAACATATTTTTCATTCTCAATCTCGAAAAGAAAAAA-ACTAATACAA
* * *
4742 GAATCAATGTTCGTCTCATTTGAGGCACGAACTTAGACTCTATAGAAAATGGTG-GAAAGAAAAG
129 GAATCAATATTCGTCTCATTTGAGGCACGAAC-TAAACTCTATAGAAAATAGTGAG-AAGAAAAG
* * * * * *
4806 -CTTTTCTTGCCAAACCAAA-ACA-TCAATATCATGTAACTTAATGAGAAAAATGTGTTTATGGT
192 TC-TTTCCTACCAAACCAAAGACACT-AATACCATATAACTTAAAGAGAAAAATATGTTTATGGT
* * ** *
4868 GCCTAATCTT-AA-AAAGAATGGAGATTATTATAAGAATCCATGTTTGTCTCATTTAAAAGATGA
255 ACCTAATCTTGAACAAA-AATGG-GATTATTATAAGAATCCAAGTTCATCTCATTTAAAAGATAA
* *
4931 ACTTTGATTCTATGAAAAATGGTGGTAAAAAAAGCTTTTCCTGTAAAGCCAAACCATTAATGTCA
318 ACTTTGATTCTATG-AAAATGGTGATAAAAAAA-CTTTTCCTGCAAAGCCAAACCATTAATGTCA
* * *
4996 TGCATC-CTAATGAGGATTTTTGGTGCCCAATCACGAAAAGAA-GGAGACAATTACAATAATCCA
381 TGCATCTC-AACGAGGATTTTTGGTGCCCAATAACGAAAAGAATGGAGACAATTACAAGAATCCA
* *
5059 TGTTCATCTCATTTAAGAGCT-
445 TGTTCAACTCATTTAAGAGATG
*
5080 AACTTTGATTCTACGAAAAATAGGGG
1 AACTTTGATTCTATGAAAAATAGGGG
5106 GGAAAAAGTT
Statistics
Matches: 419, Mismatches: 61, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
464 3 0.01
465 55 0.13
466 200 0.48
467 98 0.23
468 63 0.15
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (466 bp):
AACTTTGATTCTATGAAAAATAGGGGAAAGAAAAACTTTTCTTACGACATCAAAGATCACTATAA
TGTATCCCAATGAAGGGAACATATTTTTCATTCTCAATCTCGAAAAGAAAAAAACTAATACAAGA
ATCAATATTCGTCTCATTTGAGGCACGAACTAAACTCTATAGAAAATAGTGAGAAGAAAAGTCTT
TCCTACCAAACCAAAGACACTAATACCATATAACTTAAAGAGAAAAATATGTTTATGGTACCTAA
TCTTGAACAAAAATGGGATTATTATAAGAATCCAAGTTCATCTCATTTAAAAGATAAACTTTGAT
TCTATGAAAATGGTGATAAAAAAACTTTTCCTGCAAAGCCAAACCATTAATGTCATGCATCTCAA
CGAGGATTTTTGGTGCCCAATAACGAAAAGAATGGAGACAATTACAAGAATCCATGTTCAACTCA
TTTAAGAGATG
Found at i:5147 original size:149 final size:152
Alignment explanation
Indices: 4448--5239 Score: 515
Period size: 159 Copynumber: 5.2 Consensus size: 152
4438 TTCAAGTTCA
* * * * *
4448 TCTCATTTAAGGGATAAACTTTGATTCTATG-AAAATGGTGATAAAAAAA-CTTTTCTTGCAAAG
1 TCTCATTTAAGAGATAAACTTTGATTCTACGAAAAATGGTGGTAAAAAAAGCTTTTCCTGTAAAG
* * * ** * * *
4511 CCAAACTATTAATGTCATGTAT-CTCAACGAGGATTTTTTGTGCCCAATAATGAAAAGAATGGAG
66 CCAAACCATTAATATCATGCATAC-CAATAAGGATTTTTGGTGCCCAATCACGAAAAGAATGGAG
* * **
4575 ACAATTACAAGAATCCATGTTCA
130 ACTATTATAAGAATCCATGTTTG
* * * * * *
4598 ACTCATTTAAGAGATGAACTTTGATTCTATGAAAAATAGG-GGTAAGAAAAA-CTTTTCTTGCAC
1 TCTCATTTAAGAGATAAACTTTGATTCTACGAAAAAT-GGTGGTAA-AAAAAGCTTTTCCTGTAA
* * * * * ** * * *
4661 A-TCAAAGCATTATTGTCATGTAT-CCAATGAAGGGAACATATTTTTCATTCTCAATCTCGAAAA
64 AGCCAAACCATTAATATCATGCATACCAAT-AA-GG-----ATTTTTGGTGCCCAATCACGAAAA
*** * * *
4724 GAAAAAAGACTATTACAAGAATCAATGTTCG
122 GAATGGAGACTATTATAAGAATCCATGTTTG
* ** * * * * *
4755 TCTCATTTGAG-GCACGAACTTAGACTCTA-TAGAAAATGGTGG-AAAGAAAAGCTTTTCTTGCC
1 TCTCATTTAAGAG-ATAAACTTTGATTCTACGA-AAAATGGTGGTAAA-AAAAGCTTTTCCTG-T
* * * * ** * ***
4817 AAA-CCAAAACATCAATATCATGTA-ACTTAATGAGAAAAATGTGTTTATGGTGCCTAATCTTAA
62 AAAGCCAAACCATTAATATCATGCATAC-CAAT---AAGGA--T-TTT-TGGTGCCCAATCACGA
*
4880 AAAGAATGGAGATTATTATAAGAATCCATGTTTG
119 AAAGAATGGAGACTATTATAAGAATCCATGTTTG
* * *
4914 TCTCATTTAAAAGATGAACTTTGATTCTATGAAAAATGGTGGTAAAAAAAGCTTTTCCTGTAAAG
1 TCTCATTTAAGAGATAAACTTTGATTCTACGAAAAATGGTGGTAAAAAAAGCTTTTCCTGTAAAG
* *
4979 CCAAACCATTAATGTCATGCAT-CCTAATGAGGATTTTTGGTGCCCAATCACGAAAAGAA-GGAG
66 CCAAACCATTAATATCATGCATACC-AATAAGGATTTTTGGTGCCCAATCACGAAAAGAATGGAG
* * * **
5042 ACAATTACAATAATCCATGTTCA
130 ACTATTATAAGAATCCATGTTTG
* **
5065 TCTCATTTAAGAGCT-AACTTTGATTCTACGAAAAATAGG-GG-GGAAAAAG-TTTTCCTTGTAA
1 TCTCATTTAAGAGATAAACTTTGATTCTACGAAAAAT-GGTGGTAAAAAAAGCTTTTCC-TGTAA
* * * * *
5126 AGCCAAACCATTAGTATCATGCATACCAATAAGGATTTTTTGTGCTCAGTCATGAAAA-AATGGA
64 AGCCAAACCATTAATATCATGCATACCAATAAGGATTTTTGGTGCCCAATCACGAAAAGAATGGA
*
5190 AACTATTATAAGAATCCATGTTTG
129 GACTATTATAAGAATCCATGTTTG
* *
5214 TCTCATTTGAGGGATAAACTTTGATT
1 TCTCATTTAAGAGATAAACTTTGATT
5240 TTAAGGAAAA
Statistics
Matches: 507, Mismatches: 100, Indels: 70
0.75 0.15 0.10
Matches are distributed among these distances:
148 8 0.02
149 92 0.18
150 65 0.13
151 65 0.13
152 39 0.08
153 3 0.01
154 1 0.00
155 2 0.00
156 12 0.02
157 81 0.16
158 26 0.05
159 105 0.21
160 5 0.01
161 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (152 bp):
TCTCATTTAAGAGATAAACTTTGATTCTACGAAAAATGGTGGTAAAAAAAGCTTTTCCTGTAAAG
CCAAACCATTAATATCATGCATACCAATAAGGATTTTTGGTGCCCAATCACGAAAAGAATGGAGA
CTATTATAAGAATCCATGTTTG
Found at i:5963 original size:398 final size:400
Alignment explanation
Indices: 5207--6005 Score: 950
Period size: 398 Copynumber: 2.0 Consensus size: 400
5197 ATAAGAATCC
* * * * *
5207 ATGTTTGTCTCATTTGAGGGATAAACTTTGATTTTAAGGAAAATGAGTTAAAGAAAAGCTTTCCT
1 ATGTTTATCTCATTTGAGGCATAAACTTTGATTTTAAGGAAAATAAGTGAAAGAAAAGCTTTCCC
* * *
5272 TGCAAAAGCAAATCATTAATAACATGTATCCTAATGAGGAGAACATGTTTATGGTGCCTAATCAT
66 AGCAAAAGCAAATCATCAATAACATGTATCCTAATAAGGAGAACATGTTTATGGTGCCTAATCAT
* * *
5337 GAAAAGAATAAAGATCATTACTAGAATCAATGTTTGTCTCATTTGAGGAACAAACTTAGACATCA
131 GAAAAGAATAAAGATCACTACTAGAATCAATATTTGTCTCATTTGAGGAACAAACTTAAACATCA
* * **
5402 CAAAAAATGGTGGGAAGAAAAGCCTTTTCTACGAATCCAAAGCATCAATATCGTGTATCCTAATG
196 CAAAAAATGGTGGGAAGAAAAGCCTTTTCTACAAAGCCAAAGCATCAATATAATGTATCCTAATG
* *** * * * *
5467 AAAAGGATGTAATTATGGTGCCAAATCTTGAAAGAAATAAGGATTATTATGAGAATCCTTGTTTG
261 AAAAGAATGTAATTACAATGCCAAATCTTAAAAGAAATAAGGATTATGATGAGAATCCATATTTG
**
5532 TCTCATTTAAGAGATGAACTCTAATTCTATG-AAAATGATGGTGAGAAAAGCTTTTCTTGCGCAG
326 TCTCATTTAAGAGATGAACTCTAATTCTATGAAAAATGATGGT-AGAAAAGCTTTTCTTGCAAAG
*
5596 CCTAACCATCA
390 CCAAACCATCA
* ***
5607 ATGTTTATCTCATTTGTGGCATAAACTTTTGATTTTAAGGAAAATAAG-GAAAGATTTGCTTTCC
1 ATGTTTATCTCATTTGAGGCATAAAC-TTTGATTTTAAGGAAAATAAGTGAAAGAAAAGCTTTCC
** * * * **
5671 CAGGGAAAGCAAATCATCAATATCGTGTATGCTAATAAGGAGAATGTGTTTATGGTGCCTAATCA
65 CAGCAAAAGCAAATCATCAATAACATGTATCCTAATAAGGAGAACATGTTTATGGTGCCTAATCA
* * * ** *
5736 TGAAAA-AATAGAGATCGCTACTAGAATCCATATTTGTC-CTATTTGAGGTGCGAACTTAAAC-T
130 TGAAAAGAATAAAGATCACTACTAGAATCAATATTTGTCTC-ATTTGAGGAACAAACTTAAACAT
* * * *
5798 CTATAGAAAATGGT-GGAAGAAAAGCC-TTTCTTGCAAAGCCAAAGCATCAATTTAATGTATCCT
194 C-ACAAAAAATGGTGGGAAGAAAAGCCTTTTC-TACAAAGCCAAAGCATCAATATAATGTATCCT
* * ** * **
5861 AATGACAAGAATGT-GTTGACAATGCTTATTCTTAAAA-AGAATGGGGATTATGATGAGAATCCA
257 AATGAAAAGAATGTAATT-ACAATGCCAAATCTTAAAAGA-AATAAGGATTATGATGAGAATCCA
* * * *
5924 TATTTGTCTCATTTAAGAGATGAACTTTGATTTTATGAAAAATGGTGGTAGAAAAGCTTTTCTTG
320 TATTTGTCTCATTTAAGAGATGAACTCTAATTCTATGAAAAATGATGGTAGAAAAGCTTTTCTTG
5989 CAAAGCCAAACCATCA
385 CAAAGCCAAACCATCA
6005 A
1 A
6006 AGTCATGTCT
Statistics
Matches: 334, Mismatches: 58, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
397 7 0.02
398 148 0.44
399 64 0.19
400 95 0.28
401 20 0.06
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.31
Consensus pattern (400 bp):
ATGTTTATCTCATTTGAGGCATAAACTTTGATTTTAAGGAAAATAAGTGAAAGAAAAGCTTTCCC
AGCAAAAGCAAATCATCAATAACATGTATCCTAATAAGGAGAACATGTTTATGGTGCCTAATCAT
GAAAAGAATAAAGATCACTACTAGAATCAATATTTGTCTCATTTGAGGAACAAACTTAAACATCA
CAAAAAATGGTGGGAAGAAAAGCCTTTTCTACAAAGCCAAAGCATCAATATAATGTATCCTAATG
AAAAGAATGTAATTACAATGCCAAATCTTAAAAGAAATAAGGATTATGATGAGAATCCATATTTG
TCTCATTTAAGAGATGAACTCTAATTCTATGAAAAATGATGGTAGAAAAGCTTTTCTTGCAAAGC
CAAACCATCA
Found at i:6152 original size:151 final size:151
Alignment explanation
Indices: 5915--6295 Score: 417
Period size: 151 Copynumber: 2.5 Consensus size: 151
5905 GGATTATGAT
* * * * * ***
5915 GAGAATCCATATTTGTCTCATTTAAGAGATGAACTTTGATTTTATGAAAAATGGTGGTAGAAAAG
1 GAGAATCTATGTTTGTCTCATTTAAGAGATAAACTTTGATTTTAAGGAAAATGGTCAAAGAAAAG
* * * ** * * *
5980 CTTTTCTTGCAAAGCCAAACCATCAAAGTCATGTCTCTCAAAGGGGCTTTTTGGTTCCCAATCTC
66 CTTTTCTTGCAAAGCCAAACCATCAAAGTCATGTATCCCAAAGAGAATTTTTAGTGCCCAATCAC
*
6045 AAAAAGAAT-GA-AACTATTAC
131 AAAAAGAATGGAGAACAATT-C
*
6065 GAGAATCTATGTTTGTCTCATTTAAGAGATAAACTTTTATTTTAAGGAAAATAGGTCAAAGAAAA
1 GAGAATCTATGTTTGTCTCATTTAAGAGATAAACTTTGATTTTAAGGAAAAT-GGTCAAAGAAAA
* ** *
6130 GCTTTTCTTACAAAGCCAAACCATCAATTTCATGTATCCCAATGAGAATTTTTAGTGCCCAATCA
65 GCTTTTCTTGCAAAGCCAAACCATCAAAGTCATGTATCCCAAAGAGAATTTTTAGTGCCCAATCA
* * *
6195 CGAAAGGAATGGAGACCAATTC
130 CAAAAAGAATGGAGAACAATTC
* * * * *
6217 TAGAATCCT-TGTTTATCTCATTTGAGAAATAAACTTTGATTTTAAGGAAAATGGGACAAAGAAA
1 GAGAAT-CTATGTTTGTCTCATTTAAGAGATAAACTTTGATTTTAAGGAAAAT-GGTCAAAGAAA
* *
6281 AACTTTCCTTGCAAA
64 AGCTTTTCTTGCAAA
6296 AGCAAATCAT
Statistics
Matches: 192, Mismatches: 35, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
150 46 0.24
151 70 0.36
152 69 0.36
153 7 0.04
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (151 bp):
GAGAATCTATGTTTGTCTCATTTAAGAGATAAACTTTGATTTTAAGGAAAATGGTCAAAGAAAAG
CTTTTCTTGCAAAGCCAAACCATCAAAGTCATGTATCCCAAAGAGAATTTTTAGTGCCCAATCAC
AAAAAGAATGGAGAACAATTC
Found at i:7632 original size:23 final size:23
Alignment explanation
Indices: 7572--7635 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
7562 TTTGTGATTC
7572 TTTCTTTTAATTTTTTTGCCAACT
1 TTTC-TTTAATTTTTTTGCCAACT
* *
7596 TTTTTTTAATTTTTTTGTCAACT
1 TTTCTTTAATTTTTTTGCCAACT
*
7619 TCTTCTTTGATTTTTTT
1 T-TTCTTTAATTTTTTT
7636 TTGGAATGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (23 bp):
TTTCTTTAATTTTTTTGCCAACT
Found at i:9616 original size:33 final size:32
Alignment explanation
Indices: 9555--9616 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
9545 AAAGGATGGA
* *
9555 CTTTGAATTTAAGAAAAATGAGATAAAAAAAG
1 CTTTGAATTTAAGAAAAAAGAGAAAAAAAAAG
*
9587 CTTTGAATTTAAGGAAAAAAG-GCAAAAAAA
1 CTTTGAATTTAA-GAAAAAAGAGAAAAAAAA
9617 TCTTTTCTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 19 0.73
33 7 0.27
ACGTcount: A:0.56, C:0.05, G:0.16, T:0.23
Consensus pattern (32 bp):
CTTTGAATTTAAGAAAAAAGAGAAAAAAAAAG
Done.