Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold604
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: 40788
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Found at i:159 original size:45 final size:46
Alignment explanation
Indices: 14--246 Score: 308
Period size: 47 Copynumber: 5.0 Consensus size: 46
4 ATAGTATGCG
14 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAA-GCC
*
63 TAATGGCCGAGTGTGATGAATGTGAAAGTGTATATATATGTATAAGGCC
1 TAATGGCCGA-TGTGATGAATGTGAAAGTGTATATATGTG-ATAA-GCC
112 TAATGGCCGATGTGATGAATGTG-AAGTGTATATATGTGATAAGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGCC
* *
157 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATA-AGCC
* * * * * *
204 GAGTGGCCAACGTGATGGATGTGAAAGTGTATAAAT-TGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
247 TCCGAAGGCA
Statistics
Matches: 168, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
45 27 0.16
46 25 0.15
47 47 0.28
48 22 0.13
49 28 0.17
50 19 0.11
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (46 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGCC
Found at i:186 original size:93 final size:94
Alignment explanation
Indices: 14--246 Score: 328
Period size: 93 Copynumber: 2.5 Consensus size: 94
4 ATAGTATGCG
14 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAGTGTGA
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAA-GCCTAATGGCCGAGTGTGA
*
79 TGAATGTGAAAGTGTATATATATGTATAAGGCC
63 TGAATGTGAAAGTGTATATATATG-ACAAGGCC
112 TAATGGCCGATGTGATGAATGTG-AAGTGTATATATGTGATAAGCCTAATGGCCGA-TGTGATGA
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGCCTAATGGCCGAGTGTGATGA
* *
175 ATGTGAAAGTGTATATATGTGACAGGGCC
66 ATGTGAAAGTGTATATATATGACAAGGCC
* * * * * *
204 GAGTGGCCAACGTGATGGATGTGAAAGTGTATAAAT-TGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
247 TCCGAAGGCA
Statistics
Matches: 125, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
92 31 0.25
93 39 0.31
94 13 0.10
95 14 0.11
97 5 0.04
98 23 0.18
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (94 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGCCTAATGGCCGAGTGTGATGA
ATGTGAAAGTGTATATATATGACAAGGCC
Found at i:1845 original size:118 final size:118
Alignment explanation
Indices: 1612--2003 Score: 558
Period size: 118 Copynumber: 3.3 Consensus size: 118
1602 AGAGTGAAAT
* *
1612 TCCGGGCTAA-ATCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
1 TCCGGGCTAAGTTCTCGAAGAGCATTCATGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
1676 TCTGCTAGTGATGTATCCGGGCTAAGTCCGAAGAGCATTCGTGCTAGTGATGTA
66 TCTGCTAGTGATGTATCCGGGCTAAGTCCGAAGAGCATTCGTGCTA-TGATGTA
* *
1730 TCCGGGCTAAGTTC-CGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCAT
1 TCCGGGCTAAGTTCTCGAAGAGCATTCATGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
1794 TCATGCTAGTGATGTATCCGGGCTAAGTCCGAAGAGCATTCGTGCTATGATGTA
66 TC-TGCTAGTGATGTATCCGGGCTAAGTCCGAAGAGCATTCGTGCTATGATGTA
*
1848 TCCGGGCTAAG-TCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
1 TCCGGGCTAAGTTCTCGAAGAGCATTCATGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
* * ** * * * *
1912 TCGTGCTAGTGATATATCCGTGCTAAACCCCGAAGAGCATTTGTGCTGGTGTTATA
66 TC-TGCTAGTGATGTATCCGGGCT-AAGTCCGAAGAGCATTCGTGCT-ATGATGTA
* * * *
1968 TCCGGGCT-AGGTCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTTCTCGAAGAGCATTCATGCTAGTGA
2004 CGTGTATTCG
Statistics
Matches: 248, Mismatches: 20, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
117 2 0.01
118 145 0.58
119 67 0.27
120 34 0.14
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (118 bp):
TCCGGGCTAAGTTCTCGAAGAGCATTCATGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
TCTGCTAGTGATGTATCCGGGCTAAGTCCGAAGAGCATTCGTGCTATGATGTA
Found at i:1891 original size:158 final size:157
Alignment explanation
Indices: 1604--1990 Score: 589
Period size: 158 Copynumber: 2.5 Consensus size: 157
1594 TGAGAATGAG
* * *
1604 AGTGAAAT-TCCGGGCTAAATCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCG
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAG-TCCG
1668 AAGAGCATTCTGCTAGTGATGTATCCGGGCTAAGTCCGAAGAGCATTCGTGCTAGTGATGTATCC
65 AAGAGCATTCTGCTAGTGATGTATCCGGGCTAAGTCCGAAGAGCATTCGTGCTAGTGATGTATCC
*
1733 GGGCTAAGTTCCGAAGAGCATTCATGCT
130 GGACTAAGTTCCGAAGAGCATTCATGCT
* * *
1761 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCGA
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCGA
1826 AGAGCATTCGTGCTA-TGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATC
66 AGAGCATTC-TGCTAGTGATGTATCCGGGCTAAGTC-CGAAGAGCATTCGTGCTAGTGATGTATC
*
1890 CGGACTAAGTTCCGAAGAGCATTCGTGCT
129 CGGACTAAGTTCCGAAGAGCATTCATGCT
* * * * * * *
1919 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTTGTGCTGGTGTTATATCCGGGCTAGGTCCCG
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGT-CCG
1984 AAGAGCA
65 AAGAGCA
1991 ATCATGCTGG
Statistics
Matches: 208, Mismatches: 18, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
157 40 0.19
158 158 0.76
159 10 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (157 bp):
AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCGA
AGAGCATTCTGCTAGTGATGTATCCGGGCTAAGTCCGAAGAGCATTCGTGCTAGTGATGTATCCG
GACTAAGTTCCGAAGAGCATTCATGCT
Found at i:2002 original size:40 final size:40
Alignment explanation
Indices: 1612--1990 Score: 559
Period size: 40 Copynumber: 9.6 Consensus size: 40
1602 AGAGTGAAAT
* *
1612 TCCGGGCTAAATCTCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
* *
1652 TCCGGACTAAGTTCCGAAGAGCATTC-TGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
1691 TCCGGGCTAAGT-CCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
* *
1730 TCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
*
1770 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
1810 TCCGGGCTAAGT-CCGAAGAGCATTCGTGCTA-TGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
*
1848 TCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
* * *
1888 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
* ** * * * *
1928 TCCGTGCTAAACCCCGAAGAGCATTTGTGCTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
*
1968 TCCGGGCTAGGTCCCGAAGAGCA
1 TCCGGGCTAAGTCCCGAAGAGCA
1991 ATCATGCTGG
Statistics
Matches: 310, Mismatches: 25, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
38 32 0.10
39 85 0.27
40 193 0.62
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
Found at i:5701 original size:49 final size:49
Alignment explanation
Indices: 5639--5874 Score: 367
Period size: 47 Copynumber: 4.9 Consensus size: 49
5629 TAGTATGGCG
5639 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
5688 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
5737 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
* *
5784 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGACAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
* * * * *
5831 GAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
5875 TCCCGAAGGG
Statistics
Matches: 176, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
47 95 0.54
48 1 0.01
49 80 0.45
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (49 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
Found at i:7530 original size:120 final size:119
Alignment explanation
Indices: 7250--7682 Score: 638
Period size: 119 Copynumber: 3.6 Consensus size: 119
7240 GAGTGAAATG
* *
7250 TCCGGGCTAAATCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATT
1 TCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
7315 CATGCTAGTGATGTATCC-GGCTAAGTCCGAAGAGCATTCGTGCTAGTGATGTA
66 CATGCTAGTGATGTATCCGGGCTAAGTCCGAAGAGCATTCGTGCTAGTGATGTA
* * *
7368 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
1 TCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
*
7433 CATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
66 CATGCTAGTGATGTATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTAGTGATGTA
*
7488 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAG-TCTCGAAGAGCAT
1 TCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTC-CGAAGAGCAT
* * *
7552 TCGTGCTAGTGATGTAT-CGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
65 TCATGCTAGTGATGTATCCGGGCTAAG-TCCGAAGAGCATTCGTGCTAGTGATGTA
* * * * * * * * *
7607 TCCGTGCTAAACCCCGAAGAGCATTTGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAGCAAT
1 TCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
*
7672 CATGCTGGTGA
66 CATGCTAGTGA
7683 CGTGTATTCG
Statistics
Matches: 286, Mismatches: 24, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
118 78 0.27
119 105 0.37
120 103 0.36
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (119 bp):
TCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
CATGCTAGTGATGTATCCGGGCTAAGTCCGAAGAGCATTCGTGCTAGTGATGTA
Found at i:7681 original size:40 final size:40
Alignment explanation
Indices: 7250--7669 Score: 621
Period size: 40 Copynumber: 10.6 Consensus size: 40
7240 GAGTGAAATG
* *
7250 TCCGGGCTAAATCTCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
* * *
7290 TCCGGACTAAGTTCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
7330 TCC-GGCTAAGT-CCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
* *
7368 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
* *
7408 TCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
*
7448 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
7488 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
*
7528 TCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
* * *
7568 T-CGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
* ** * * * *
7607 TCCGTGCTAAACCCCGAAGAGCATTTGTGCTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
*
7647 TCCGGGCTAGGTCCCGAAGAGCA
1 TCCGGGCTAAGTCCCGAAGAGCA
7670 ATCATGCTGG
Statistics
Matches: 348, Mismatches: 29, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
38 29 0.08
39 49 0.14
40 270 0.78
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
Found at i:7738 original size:159 final size:159
Alignment explanation
Indices: 7264--7682 Score: 502
Period size: 159 Copynumber: 2.6 Consensus size: 159
7254 GGCTAAATCT
* * * *** *
7264 CGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
1 CGAAGAGCATTCATGCTAGTGATATATCCGGGCTAAACCCCGAAGAGCATTCATGCTAGTGATAT
* * * *
7329 ATCC-GGCTAAGT-CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGT-TCCGAAGAGCA
66 ATCCGGGCTAAGTCCCGAAGAGCAATCATGCTAGTGATGTATCCGGGCTAAGTCT-AGAAGAGCA
* * * *
7391 TTCGTGCTAGTGATGTATCCGGGCTAAGTTC
130 TTCGTGCCAGTAATGTAT-CGGACAAAGTTC
* ** *
7422 CGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 CGAAGAGCATTCATGCTAGTGATATATCCGGGCTAAACCCCGAAGAGCATTCATGCTAGTGATAT
* * *
7487 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCTCGAAGAGCAT
66 ATCCGGGCTAAGTCCCGAAGAGCAATCATGCTAGTGATGTATCCGGGCTAAGTCTAGAAGAGCAT
* * *
7552 TCGTGCTAGTGATGTATCGGACTAAGTTC
131 TCGTGCCAGTAATGTATCGGACAAAGTTC
* * ** * *
7581 CGAAGAGCATTCGTGCTAGTGATATATCCGTGCTAAACCCCGAAGAGCATTTGTGCTGGTGTTAT
1 CGAAGAGCATTCATGCTAGTGATATATCCGGGCTAAACCCCGAAGAGCATTCATGCTAGTGATAT
* *
7646 ATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
66 ATCCGGGCTAAGTCCCGAAGAGCAATCATGCTAGTGA
7683 CGTGTATTCG
Statistics
Matches: 239, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
158 66 0.28
159 107 0.45
160 65 0.27
161 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (159 bp):
CGAAGAGCATTCATGCTAGTGATATATCCGGGCTAAACCCCGAAGAGCATTCATGCTAGTGATAT
ATCCGGGCTAAGTCCCGAAGAGCAATCATGCTAGTGATGTATCCGGGCTAAGTCTAGAAGAGCAT
TCGTGCCAGTAATGTATCGGACAAAGTTC
Found at i:11325 original size:49 final size:49
Alignment explanation
Indices: 11263--11933 Score: 1145
Period size: 47 Copynumber: 13.9 Consensus size: 49
11253 TAGTATGGCG
11263 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
*
11312 TAATAGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATATGTGATAAGGCC
*
11363 TAATGGCTGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
11410 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
11459 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
11506 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
11555 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
11604 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
11651 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
11700 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
11747 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
11796 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
* *
11843 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGACAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
* * * * *
11890 GAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
11934 TCCTGAAGGG
Statistics
Matches: 597, Mismatches: 13, Indels: 26
0.94 0.02 0.04
Matches are distributed among these distances:
47 282 0.47
48 1 0.00
49 267 0.45
51 47 0.08
ACGTcount: A:0.32, C:0.08, G:0.29, T:0.30
Consensus pattern (49 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
Found at i:11471 original size:96 final size:97
Alignment explanation
Indices: 11263--11933 Score: 1130
Period size: 96 Copynumber: 7.0 Consensus size: 97
11253 TAGTATGGCG
*
11263 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGAT
11328 GAATGTGAAAGTGTATATATATATGTGATAAGGCC
65 GAATGTGAAAGTG--TATATATATGTGATAAGGCC
*
11363 TAATGGCTGATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 TAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATG
11427 AATGTGAAAGTGTATATATATGTGATAAGGCC
66 AATGTGAAAGTGTATATATATGTGATAAGGCC
11459 TAATGGCCGATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 TAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATG
11523 AATGTGAAAGTGTATATATATGTGATAAGGCC
66 AATGTGAAAGTGTATATATATGTGATAAGGCC
11555 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGAT
11620 GAATGTGAAAGTG--TATATATGTGATAAGGCC
65 GAATGTGAAAGTGTATATATATGTGATAAGGCC
11651 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGAT
11716 GAATGTGAAAGTG--TATATATGTGATAAGGCC
65 GAATGTGAAAGTGTATATATATGTGATAAGGCC
11747 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGAT
11812 GAATGTGAAAGTG--TATATATGTGATAAGGCC
65 GAATGTGAAAGTGTATATATATGTGATAAGGCC
* * * * * *
11843 TAATGGCCGATGTGATGAATGTGAAAGTG-TATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 TAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
11907 GATGTGAAAGTGTATA-A-ATGTGATAAG
66 AATGTGAAAGTGTATATATATGTGATAAG
11934 TCCTGAAGGG
Statistics
Matches: 557, Mismatches: 10, Indels: 14
0.96 0.02 0.02
Matches are distributed among these distances:
94 50 0.09
95 1 0.00
96 385 0.69
98 93 0.17
100 28 0.05
ACGTcount: A:0.32, C:0.08, G:0.29, T:0.30
Consensus pattern (97 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATG
AATGTGAAAGTGTATATATATGTGATAAGGCC
Found at i:16315 original size:22 final size:22
Alignment explanation
Indices: 16290--16336 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
16280 AGGGAGAAGC
* * *
16290 GGCAAACCTTAGTTCCAGAGAG
1 GGCAAACCTTAATCCCAGAAAG
16312 GGCAAACCTTAATCCCAGAAAG
1 GGCAAACCTTAATCCCAGAAAG
16334 GGC
1 GGC
16337 TTACTGTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.26, G:0.26, T:0.15
Consensus pattern (22 bp):
GGCAAACCTTAATCCCAGAAAG
Found at i:17461 original size:33 final size:32
Alignment explanation
Indices: 17379--17462 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
17369 TAGGTGTGGC
* *
17379 CGTGTGAGCCACACGAGCTAGGCCAAATTAGG
1 CGTGTGAGCCACACGGGCAAGGCCAAATTAGG
* * *
17411 CGTATGGGCCACACGGGCAAGGCC-AATCTGGG
1 CGTGTGAGCCACACGGGCAAGGCCAAAT-TAGG
17443 CGTGTGAGCCCACACGGGCA
1 CGTGTGAG-CCACACGGGCA
17463 CGTAGGCCCA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
31 3 0.07
32 29 0.67
33 11 0.26
ACGTcount: A:0.24, C:0.29, G:0.35, T:0.13
Consensus pattern (32 bp):
CGTGTGAGCCACACGGGCAAGGCCAAATTAGG
Found at i:17703 original size:13 final size:13
Alignment explanation
Indices: 17675--17711 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
17665 AAGCATGTTA
*
17675 TATCTGTA-TCTG
1 TATCTGTATTTTG
17687 TATCTGTATTTTG
1 TATCTGTATTTTG
17700 TATCTGT-TTTTG
1 TATCTGTATTTTG
17712 GGGTGGGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.14, C:0.11, G:0.16, T:0.59
Consensus pattern (13 bp):
TATCTGTATTTTG
Found at i:27568 original size:24 final size:24
Alignment explanation
Indices: 27541--27586 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
27531 GAATTTAACA
27541 TTCAAAT-CAGCACACATAGTGCCT
1 TTCAAATAC-GCACACATAGTGCCT
* *
27565 TTCAACTACGCACACGTAGTGC
1 TTCAAATACGCACACATAGTGC
27587 TAGTATCGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.24
Consensus pattern (24 bp):
TTCAAATACGCACACATAGTGCCT
Found at i:30362 original size:40 final size:40
Alignment explanation
Indices: 30268--30412 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
30258 TACTCGAATG
*
30268 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
30309 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
30349 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
30389 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
30413 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:37105 original size:37 final size:38
Alignment explanation
Indices: 37040--37114 Score: 143
Period size: 37 Copynumber: 2.0 Consensus size: 38
37030 TTCATCCTTT
37040 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
37078 TTCATTTCTTTTGG-CGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
37115 GGAGTTCTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 23 0.62
38 14 0.38
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Done.