Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1167
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: 2521
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Found at i:98 original size:50 final size:50
Alignment explanation
Indices: 19--2469 Score: 1903
Period size: 50 Copynumber: 49.5 Consensus size: 50
9 TTGCAATGTC
* * * *
19 AGGAAAGTAAGATCTGCTGTTGTTGCTTCAATCTGTTCCACTACAACACT
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * ** * * *
69 AGGAAAGTAAGATCCACTGTTGTACCTTCAATCT-TCTTAATTGCAATGTT
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGT-TCCACTGCAACGCT
* *
119 AGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* ** * * *
169 AGGAAAGTAAGAGCCGCTGTTGTAGCTTCAATCT-TCTTAATTGCAATGTT
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGT-TCCACTGCAACGCT
* *
219 AGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* ** * * *
269 AGGAAAGTAAGAGCCGCTGTTGTAGCTTCAATCT-TCTTAATTGCAATGTT
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGT-TCCACTGCAACGCT
* *
319 AGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* ** * * *
369 AGGAAAGTAAGAGCCGCTGTTGTAGCTTCAATCT-TCTTAATTGCAATGTT
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGT-TCCACTGCAACGCT
* *
419 AGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* ** * * *
469 AGGAAAGTAAGAGCCGCTGTTGTAGCTTCAATCT-TCTTAATTGCAATGTT
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGT-TCCACTGCAACGCT
* *
519 AGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* ** * * *
569 AGGAAAGTAAGAGCCGCTGTTGTAGCTTCAATCT-TCTTAATTGCAATGTT
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGT-TCCACTGCAACGCT
* *
619 AGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* ** * *
669 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATG-T
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * *
718 CAGGGAAGTGAGATCCGCTGTTGTAGCTTCAATCTGTTGCACTGCAACGCT
1 -AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
** ** * * *
769 AGGAAAGTAAGATATGCTGTTGTAGCTTCAATCT-TTTAATTGCAATGTCA
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
* *
819 AGG-AAGTAAGATCCGCTATTGTAGCTTCAATCTGTTCCACTGCAATGCT
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * * *
868 AGGAAAGTAAGATCCGCTATTGTAGCTTCAATC--TTCTTATTTGCAATG-T
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTC-CA-CTGCAACGCT
* *
917 CAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
1 -AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * ** * * *
968 AGAAAAGTAAGATCCGCTGTTGTAGCTTTAATCT-TCTTAATTGCAATGTT
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGT-TCCACTGCAACGCT
*
1018 AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
** * *
1068 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT-TCTTAATTGCAATG-T
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGT-TCCACTGCAACGCT
* * * *
1117 CAGGGAAGTAAGACCCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
1 -AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
* ** * * ** * *
1169 -GGAAA-TAAGATTCGCCATTGTGGCCTCAATCT-TTTGATTGCAATG-T
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * *
1215 CAGGGAAGTGAGATTCGCTGTTGTAGCTTCAAT-TGTTCCACTGCAACGCT
1 -AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * * ** * *
1265 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCT-TCTTAATTGCAATG-T
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGT-TCCACTGCAACGCT
* * * *
1314 CAGGGAAGTAAGACCCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
1 -AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
* ** * * ** * *
1366 -GGAAA-TAAGATTCGCCATTGTGGCCTCAATCT-TTTGATTGCAATG-T
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * *
1412 CAGGGAAGTGAGATTCGCTGTTGTAGCTTCAAT-TGTTCCACTGCAACGCT
1 -AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * * ** * *
1462 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCT-TCTTAATTGCAATG-T
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGT-TCCACTGCAACGCT
* * * *
1511 CAGGGAAGTAAGACCCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
1 -AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
* ** * * ** * *
1563 -GGAAA-TAAGATTCGCCATTGTGGCCTCAATCT-TTTGATTGCAATG-T
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * *
1609 CAGGGAAGTGAGATTCGCTGTTGTAGCTTCAAT-TGTTCCACTGCAACGCT
1 -AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * * ** * *
1659 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCT-TCTTAATTGCAATG-T
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGT-TCCACTGCAACGCT
* * * *
1708 CAGGGAAGTAAGACCCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
1 -AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
* ** * * ** * *
1760 -GGAAA-TAAGATTCGCCATTGTGGCCTCAATCT-TTTGATTGCAATG-T
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * *
1806 CAGGGAAGTGAGATTCGCTGTTGTAGCTTCAAT-TGTTCCACTGCAACGCT
1 -AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * * ** * *
1856 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCT-TCTTAATTGCAATG-T
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGT-TCCACTGCAACGCT
* * * *
1905 CAGGGAAGTAAGACCCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
1 -AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
* ** * * ** * *
1957 -GGAAA-TAAGATTCGCCATTGTGGCCTCAATCT-TTTGATTGCAATG-T
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * *
2003 CAGGGAAGTGAGATTCGCTGTTGTAGCTTCAAT-TGTTCCACTGCAACGCT
1 -AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * * ** * *
2053 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCT-TCTTAATTGCAATG-T
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGT-TCCACTGCAACGCT
* * * *
2102 CAGGGAAGTAAGACCCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
1 -AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
* ** * * ** * *
2154 -GGAAA-TAAGATTCGCCATTGTGGCCTCAATCT-TTTGATTGCAATG-T
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * *
2200 CAGGGAAGTGAGATTCGCTGTTGTAGCTTCAAT-TGTTCCACTGCAACGCT
1 -AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * * ** * *
2250 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCT-TCTTAATTGCAATG-T
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGT-TCCACTGCAACGCT
* * * *
2299 CAGGGAAGTAAGACCCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
1 -AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
* ** * * ** * *
2351 -GGAAA-TAAGATTCGCCATTGTGGCCTCAATCT-TTTGATTGCAATG-T
1 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * *
2397 CAGGGAAGTGAGATTCGCTGTTGTAGCTTCAAT-TGTTCCACTGCAACGCT
1 -AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * *
2447 AGGAGAGTAAAATCTGCTGTTGT
1 AGGAAAGTAAGATCCGCTGTTGT
2470 TATCGCAATT
Statistics
Matches: 1839, Mismatches: 461, Indels: 203
0.73 0.18 0.08
Matches are distributed among these distances:
46 7 0.00
48 94 0.05
49 580 0.32
50 1131 0.62
51 17 0.01
52 10 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (50 bp):
AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
Found at i:178 original size:100 final size:100
Alignment explanation
Indices: 5--2469 Score: 3373
Period size: 100 Copynumber: 24.9 Consensus size: 100
1 CTTT
* * * *
5 TTAATTGCAATGTCAGGAAAGTAAGATCTGCTGTTGTTGCTTCAATCTGTTCCACTACAACACTA
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
* *
70 GGAAAGTAAGATCCACTGTTGTACCTTCAATCTTC
66 GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
*
105 TTAATTGCAATGTTAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
*
170 GGAAAGTAAGAGCCGCTGTTGTAGCTTCAATCTTC
66 GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
*
205 TTAATTGCAATGTTAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
*
270 GGAAAGTAAGAGCCGCTGTTGTAGCTTCAATCTTC
66 GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
*
305 TTAATTGCAATGTTAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
*
370 GGAAAGTAAGAGCCGCTGTTGTAGCTTCAATCTTC
66 GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
*
405 TTAATTGCAATGTTAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
*
470 GGAAAGTAAGAGCCGCTGTTGTAGCTTCAATCTTC
66 GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
*
505 TTAATTGCAATGTTAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
*
570 GGAAAGTAAGAGCCGCTGTTGTAGCTTCAATCTTC
66 GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
*
605 TTAATTGCAATGTTAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
*
670 GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTT
66 GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
* * *
705 TTAATTGCAATGTCAGGGAAGTGAGATCCGCTGTTGTAGCTTCAATCTGTTGCACTGCAACGCTA
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
**
770 GGAAAGTAAGATATGCTGTTGTAGCTTCAATCTT-
66 GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
* * * *
804 TTAATTGCAATGTCAAGGAAGTAAGATCCGCTATTGTAGCTTCAATCTGTTCCACTGCAATGCTA
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
*
869 GGAAAGTAAGATCCGCTATTGTAGCTTCAATCTTC
66 GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
*
904 TTATTTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
* *
969 GAAAAGTAAGATCCGCTGTTGTAGCTTTAATCTTC
66 GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
* *
1004 TTAATTGCAATGTTAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
1069 GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
66 GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
* ** *
1104 TTAATTGCAATGTCAGGGAAGTAAGACCCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
* ** * *
1169 -GGAAA-TAAGATTCGCCATTGTGGCCTCAATCTT-
65 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
* *
1202 TTGATTGCAATGTCAGGGAAGTGAGAT-TCGCTGTTGTAGCTTCAAT-TGTTCCACTGCAACGCT
1 TTAATTGCAATGTCAGGGAAGTAAGATCT-GCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * *
1265 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTC
65 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
* ** *
1301 TTAATTGCAATGTCAGGGAAGTAAGACCCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
* ** * *
1366 -GGAAA-TAAGATTCGCCATTGTGGCCTCAATCTT-
65 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
* *
1399 TTGATTGCAATGTCAGGGAAGTGAGAT-TCGCTGTTGTAGCTTCAAT-TGTTCCACTGCAACGCT
1 TTAATTGCAATGTCAGGGAAGTAAGATCT-GCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * *
1462 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTC
65 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
* ** *
1498 TTAATTGCAATGTCAGGGAAGTAAGACCCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
* ** * *
1563 -GGAAA-TAAGATTCGCCATTGTGGCCTCAATCTT-
65 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
* *
1596 TTGATTGCAATGTCAGGGAAGTGAGAT-TCGCTGTTGTAGCTTCAAT-TGTTCCACTGCAACGCT
1 TTAATTGCAATGTCAGGGAAGTAAGATCT-GCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * *
1659 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTC
65 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
* ** *
1695 TTAATTGCAATGTCAGGGAAGTAAGACCCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
* ** * *
1760 -GGAAA-TAAGATTCGCCATTGTGGCCTCAATCTT-
65 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
* *
1793 TTGATTGCAATGTCAGGGAAGTGAGAT-TCGCTGTTGTAGCTTCAAT-TGTTCCACTGCAACGCT
1 TTAATTGCAATGTCAGGGAAGTAAGATCT-GCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * *
1856 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTC
65 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
* ** *
1892 TTAATTGCAATGTCAGGGAAGTAAGACCCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
* ** * *
1957 -GGAAA-TAAGATTCGCCATTGTGGCCTCAATCTT-
65 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
* *
1990 TTGATTGCAATGTCAGGGAAGTGAGAT-TCGCTGTTGTAGCTTCAAT-TGTTCCACTGCAACGCT
1 TTAATTGCAATGTCAGGGAAGTAAGATCT-GCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * *
2053 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTC
65 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
* ** *
2089 TTAATTGCAATGTCAGGGAAGTAAGACCCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
* ** * *
2154 -GGAAA-TAAGATTCGCCATTGTGGCCTCAATCTT-
65 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
* *
2187 TTGATTGCAATGTCAGGGAAGTGAGAT-TCGCTGTTGTAGCTTCAAT-TGTTCCACTGCAACGCT
1 TTAATTGCAATGTCAGGGAAGTAAGATCT-GCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * *
2250 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTC
65 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
* ** *
2286 TTAATTGCAATGTCAGGGAAGTAAGACCCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
1 TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
* ** * *
2351 -GGAAA-TAAGATTCGCCATTGTGGCCTCAATCTT-
65 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
* *
2384 TTGATTGCAATGTCAGGGAAGTGAGAT-TCGCTGTTGTAGCTTCAAT-TGTTCCACTGCAACGCT
1 TTAATTGCAATGTCAGGGAAGTAAGATCT-GCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT
* * *
2447 AGGAGAGTAAAATCTGCTGTTGT
65 AGGAAAGTAAGATCCGCTGTTGT
2470 TATCGCAATT
Statistics
Matches: 2092, Mismatches: 226, Indels: 96
0.87 0.09 0.04
Matches are distributed among these distances:
96 14 0.01
97 126 0.06
98 417 0.20
99 480 0.23
100 1041 0.50
101 14 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (100 bp):
TTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTA
GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTC
Found at i:1309 original size:197 final size:197
Alignment explanation
Indices: 3--2469 Score: 3712
Period size: 197 Copynumber: 12.4 Consensus size: 197
1 CT
* * * * * *
3 TTTTAATTGCAATGTCAGGAAAGTAAGA-TCTGCTGTTGTTGCTTCAATCTGTTCCACTACAACA
1 TTTTGATTGCAATGTCAGGGAAGTGAGATTC-GCTGTTGTAGCTTCAAT-TGTTCCACTGCAACG
* * ** * * *
67 CTAGGAAAGTAAGATCCACTGTTGTACCTTCAATCTTCTTAATTGCAATGTTAGGGAAGTAAGAT
64 CTAGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGAC
** * ** ** * *
132 CTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAAGTAAGAGCCGCTGTTGTAGCT
129 CCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT-GGAAA-TAAGATTCGCCATTGTGGCC
196 TCAATC
192 TCAATC
* * *
202 TTCTTAATTGCAATGTTAGGGAAGTAAGA-TCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAAC
1 TT-TTGATTGCAATGTCAGGGAAGTGAGATTC-GCTGTTGTAGCTTCAAT-TGTTCCACTGCAAC
* * * * *
266 GCTAGGAAAGTAAGAGCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTTAGGGAAGTAAGA
63 GCTAGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGA
* ** * ** ** *
331 TCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAAGTAAGAGCCGCTGTTGTAGC
128 CCCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT-GGAAA-TAAGATTCGCCATTGTGGC
*
395 TTCAATC
191 CTCAATC
* * *
402 TTCTTAATTGCAATGTTAGGGAAGTAAGA-TCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAAC
1 TT-TTGATTGCAATGTCAGGGAAGTGAGATTC-GCTGTTGTAGCTTCAAT-TGTTCCACTGCAAC
* * * * *
466 GCTAGGAAAGTAAGAGCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTTAGGGAAGTAAGA
63 GCTAGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGA
* ** * ** ** *
531 TCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAAGTAAGAGCCGCTGTTGTAGC
128 CCCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT-GGAAA-TAAGATTCGCCATTGTGGC
*
595 TTCAATC
191 CTCAATC
* * *
602 TTCTTAATTGCAATGTTAGGGAAGTAAGA-TCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAAC
1 TT-TTGATTGCAATGTCAGGGAAGTGAGATTC-GCTGTTGTAGCTTCAAT-TGTTCCACTGCAAC
* * * * *
666 GCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTGAGA
63 GCTAGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGA
* * * * ** *
731 TCCGCTGTTGTAGCTTCAATCTGTTGCACTGCAACG-CTAGGAAAGTAAGATAT-GCTGTTGTAG
128 CCCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT-GGAAA-TAAGAT-TCGCCATTGTGG
*
794 CTTCAATC
190 CCTCAATC
* * * * * *
802 TTTTAATTGCAATGTCAAGGAAGTAAGATCCGCTATTGTAGCTTCAATCTGTTCCACTGCAATGC
1 TTTTGATTGCAATGTCAGGGAAGTGAGATTCGCTGTTGTAGCTTCAAT-TGTTCCACTGCAACGC
* * * * * *
867 TAGGAAAGTAAGATCCGCTATTGTAGCTTCAATCTTCTTATTTGCAATGTCAGGGAAGTAAGATC
65 TAGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGACC
** * * * ** * *
932 TGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGAAAAGTAAGATCCGCTGTTGTAGCTT
130 CACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT-GGAAA-TAAGATTCGCCATTGTGGCCT
*
996 TAATC
193 CAATC
* * * *
1001 TTCTTAATTGCAATGTTAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG
1 TT-TTGATTGCAATGTCAGGGAAGTGAGATTCGCTGTTGTAGCTTCAAT-TGTTCCACTGCAACG
* * *
1066 CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGAC
64 CTAGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGAC
1131 CCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCATTGTGGCCTC
129 CCACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCATTGTGGCCTC
1196 AATC
194 AATC
1200 TTTTGATTGCAATGTCAGGGAAGTGAGATTCGCTGTTGTAGCTTCAATTGTTCCACTGCAACGCT
1 TTTTGATTGCAATGTCAGGGAAGTGAGATTCGCTGTTGTAGCTTCAATTGTTCCACTGCAACGCT
1265 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGACCC
66 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGACCC
1330 ACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCATTGTGGCCTCAA
131 ACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCATTGTGGCCTCAA
1395 TC
196 TC
1397 TTTTGATTGCAATGTCAGGGAAGTGAGATTCGCTGTTGTAGCTTCAATTGTTCCACTGCAACGCT
1 TTTTGATTGCAATGTCAGGGAAGTGAGATTCGCTGTTGTAGCTTCAATTGTTCCACTGCAACGCT
1462 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGACCC
66 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGACCC
1527 ACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCATTGTGGCCTCAA
131 ACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCATTGTGGCCTCAA
1592 TC
196 TC
1594 TTTTGATTGCAATGTCAGGGAAGTGAGATTCGCTGTTGTAGCTTCAATTGTTCCACTGCAACGCT
1 TTTTGATTGCAATGTCAGGGAAGTGAGATTCGCTGTTGTAGCTTCAATTGTTCCACTGCAACGCT
1659 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGACCC
66 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGACCC
1724 ACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCATTGTGGCCTCAA
131 ACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCATTGTGGCCTCAA
1789 TC
196 TC
1791 TTTTGATTGCAATGTCAGGGAAGTGAGATTCGCTGTTGTAGCTTCAATTGTTCCACTGCAACGCT
1 TTTTGATTGCAATGTCAGGGAAGTGAGATTCGCTGTTGTAGCTTCAATTGTTCCACTGCAACGCT
1856 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGACCC
66 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGACCC
1921 ACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCATTGTGGCCTCAA
131 ACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCATTGTGGCCTCAA
1986 TC
196 TC
1988 TTTTGATTGCAATGTCAGGGAAGTGAGATTCGCTGTTGTAGCTTCAATTGTTCCACTGCAACGCT
1 TTTTGATTGCAATGTCAGGGAAGTGAGATTCGCTGTTGTAGCTTCAATTGTTCCACTGCAACGCT
2053 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGACCC
66 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGACCC
2118 ACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCATTGTGGCCTCAA
131 ACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCATTGTGGCCTCAA
2183 TC
196 TC
2185 TTTTGATTGCAATGTCAGGGAAGTGAGATTCGCTGTTGTAGCTTCAATTGTTCCACTGCAACGCT
1 TTTTGATTGCAATGTCAGGGAAGTGAGATTCGCTGTTGTAGCTTCAATTGTTCCACTGCAACGCT
2250 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGACCC
66 AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGACCC
2315 ACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCATTGTGGCCTCAA
131 ACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCATTGTGGCCTCAA
2380 TC
196 TC
2382 TTTTGATTGCAATGTCAGGGAAGTGAGATTCGCTGTTGTAGCTTCAATTGTTCCACTGCAACGCT
1 TTTTGATTGCAATGTCAGGGAAGTGAGATTCGCTGTTGTAGCTTCAATTGTTCCACTGCAACGCT
2447 AGGAGAGTAAAATCTGCTGTTGT
66 AGGAGAGTAAAATCTGCTGTTGT
2470 TATCGCAATT
Statistics
Matches: 2208, Mismatches: 54, Indels: 14
0.97 0.02 0.01
Matches are distributed among these distances:
197 1219 0.55
198 42 0.02
199 206 0.09
200 739 0.33
201 2 0.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (197 bp):
TTTTGATTGCAATGTCAGGGAAGTGAGATTCGCTGTTGTAGCTTCAATTGTTCCACTGCAACGCT
AGGAGAGTAAAATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGACCC
ACTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCATTGTGGCCTCAA
TC
Done.