Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2339
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: 68245
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:1290 original size:18 final size:18
Alignment explanation
Indices: 1269--1339 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
1259 CCTGTCATCC
*
1269 CTCCTCTCTCTATTATCT
1 CTCCTATCTCTATTATCT
* *
1287 CTCCTGTCTCTCCTACTATCATCC
1 CTCC--TATCT-CTA-T-T-ATCT
*
1311 CTCCTATCTCTACTATCT
1 CTCCTATCTCTATTATCT
1329 CTCCTATCTCT
1 CTCCTATCTCT
1340 CCTCCTATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
18 18 0.42
19 1 0.02
20 5 0.12
21 6 0.14
22 5 0.12
23 1 0.02
24 7 0.16
ACGTcount: A:0.13, C:0.42, G:0.01, T:0.44
Consensus pattern (18 bp):
CTCCTATCTCTATTATCT
Found at i:1309 original size:42 final size:42
Alignment explanation
Indices: 1254--1372 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
1244 TTCTTCTCTC
* * *
1254 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCT
* *
1296 CTCCTACTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCT
* *
1338 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1373 TTGAGGGCTA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCT
Found at i:1314 original size:24 final size:23
Alignment explanation
Indices: 1254--1363 Score: 78
Period size: 21 Copynumber: 5.1 Consensus size: 23
1244 TTCTTCTCTC
* *
1254 CTCCTCCTGTCATCCCTCC-TCT
1 CTCCTACTATCATCCCTCCTTCT
*
1276 CT-CTA-T-T-ATCTCTCCTGTCT
1 CTCCTACTATCATCCCTCCT-TCT
*
1296 CTCCTACTATCATCCCTCC-TAT
1 CTCCTACTATCATCCCTCCTTCT
1318 CT-CTACTATC-T--CTCCTATCT
1 CTCCTACTATCATCCCTCCT-TCT
*
1338 CTCCTCCTATCATCCCTCCTCTCT
1 CTCCTACTATCATCCCTCCT-TCT
1362 CT
1 CT
1364 TCTTTCTCTT
Statistics
Matches: 69, Mismatches: 7, Indels: 22
0.70 0.07 0.22
Matches are distributed among these distances:
18 11 0.16
19 1 0.01
20 11 0.16
21 20 0.29
22 8 0.12
23 1 0.01
24 17 0.25
ACGTcount: A:0.11, C:0.46, G:0.02, T:0.41
Consensus pattern (23 bp):
CTCCTACTATCATCCCTCCTTCT
Found at i:1340 original size:9 final size:9
Alignment explanation
Indices: 1282--1342 Score: 65
Period size: 9 Copynumber: 7.1 Consensus size: 9
1272 CTCTCTCTAT
1282 TATCTCTCC
1 TATCTCTCC
*
1291 TGTCTCTCC
1 TATCTCTCC
*
1300 TA-CTAT-C
1 TATCTCTCC
*
1307 -ATCCCTCC
1 TATCTCTCC
*
1315 TATCTCTAC
1 TATCTCTCC
1324 TATCTCTCC
1 TATCTCTCC
1333 TATCTCTCC
1 TATCTCTCC
1342 T
1 T
1343 CCTATCATCC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
6 1 0.02
7 3 0.07
8 4 0.10
9 33 0.80
ACGTcount: A:0.13, C:0.43, G:0.02, T:0.43
Consensus pattern (9 bp):
TATCTCTCC
Found at i:6100 original size:165 final size:166
Alignment explanation
Indices: 5822--6278 Score: 643
Period size: 165 Copynumber: 2.8 Consensus size: 166
5812 GCCAAACACC
5822 AGGGATTAAATAGCAAATTTTAGTTTTTAAAGGTAAAATCATCATTTTAGTCATTTTTAAAGATT
1 AGGGATTAAATAGCAAATTTTAGTTTTTAAAGGTAAAATCATCATTTTAGTCATTTTTAAAGATT
* * *
5887 TCTATTATTCCTATGGCCTTCCGTAGGGGTACAA-AAATTTTCAAAACTTTTCATATCCTCTCAG
66 TCTATTATTCCTATGGCCTTCCGTAAGGGTA-AAGAAATTTTCAAAACTTTTCGTATCCTCTCAA
** * *
5951 TTTTCTGTTAAGTACA-AAATGAAATTTTTAAAAGTTT
130 TTTTCCATCAAGTA-AGAAATGAAATTTTCAAAAGTTT
* * * * *
5988 AGGGATTAAATACCAAATTTTAG-TTTTAAAGATAAAATCAACATTTTAGTCATTTATAATGATT
1 AGGGATTAAATAGCAAATTTTAGTTTTTAAAGGTAAAATCATCATTTTAGTCATTTTTAAAGATT
* * * *
6052 TCTATTATTCCTATGGCCTTTCGTAAGGATAAAGAAATTTTTAAAACTTTTCGTATCTTCTCAAT
66 TCTATTATTCCTATGGCCTTCCGTAAGGGTAAAGAAATTTTCAAAACTTTTCGTATCCTCTCAAT
**
6117 TTTCCATCGGGTAAGAAATGAAATTTTCAAAAGTTT
131 TTTCCATCAAGTAAGAAATGAAATTTTCAAAAGTTT
* *
6153 AAGGATTAAATAGCAAATTTTAGTTTTTAGAGGTAAAATCATCATTTTAGTCATTTTTAAAGATT
1 AGGGATTAAATAGCAAATTTTAGTTTTTAAAGGTAAAATCATCATTTTAGTCATTTTTAAAGATT
* * * *
6218 TCTATTATT-CTCATGGCCTTCCATAAGGGTATAGAAATTTTCAAGACTCTTCGTATCCTCT
66 TCTATTATTCCT-ATGGCCTTCCGTAAGGGTAAAGAAATTTTCAAAACTTTTCGTATCCTCT
6279 TGGTTTTTCA
Statistics
Matches: 254, Mismatches: 33, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
164 3 0.01
165 143 0.56
166 108 0.43
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (166 bp):
AGGGATTAAATAGCAAATTTTAGTTTTTAAAGGTAAAATCATCATTTTAGTCATTTTTAAAGATT
TCTATTATTCCTATGGCCTTCCGTAAGGGTAAAGAAATTTTCAAAACTTTTCGTATCCTCTCAAT
TTTCCATCAAGTAAGAAATGAAATTTTCAAAAGTTT
Found at i:9478 original size:12 final size:11
Alignment explanation
Indices: 9456--9531 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
9446 AGAGAAAGAA
*
9456 GAGAGAGGAGG
1 GAGATAGGAGG
9467 GATGATAGGAGG
1 GA-GATAGGAGG
*
9479 AGAGACAGGA--
1 -GAGATAGGAGG
*
9489 GAGATAGTA--
1 GAGATAGGAGG
9498 GAGATAGGAGG
1 GAGATAGGAGG
9509 GATGATAGGAGG
1 GA-GATAGGAGG
*
9521 AGAGACAGGAG
1 -GAGATAGGAG
9532 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:9488 original size:24 final size:24
Alignment explanation
Indices: 9455--9540 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
9445 AAGAGAAAGA
*
9455 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
9479 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
9497 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
9521 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
9541 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:9507 original size:42 final size:42
Alignment explanation
Indices: 9446--9564 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
9436 TAGCCCTCAA
* *
9446 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
9488 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
9530 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
9565 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:28123 original size:42 final size:42
Alignment explanation
Indices: 28068--28186 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
28058 TTCTTCTCTC
* *
28068 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
28110 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
28152 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
28187 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:28127 original size:12 final size:11
Alignment explanation
Indices: 28101--28176 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
28091 TCTATTATCT
*
28101 CTCCTGTCTCTC
1 CTCCTATCTC-C
28113 CTCCTATCATCC
1 CTCCTATC-TCC
28125 CTCCTATCT--
1 CTCCTATCTCC
*
28134 CTACTATCT--
1 CTCCTATCTCC
*
28143 CTCCTGTCTCTC
1 CTCCTATCTC-C
28155 CTCCTATCATCC
1 CTCCTATC-TCC
*
28167 CTCCTCTCTC
1 CTCCTATCTC
28177 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:28128 original size:24 final size:24
Alignment explanation
Indices: 28092--28177 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
28082 CCTCCTCTCT
* *
28092 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
28116 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
28137 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
28158 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
28178 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:28152 original size:18 final size:18
Alignment explanation
Indices: 28083--28153 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
28073 CCTGTCATCC
* *
28083 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
28101 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
28123 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
28143 CTCCTGTCTCT
1 CTCCTGTCTCT
28154 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:33231 original size:29 final size:28
Alignment explanation
Indices: 33174--33263 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 28
33164 TGCCATGGAT
*
33174 TTGTGGGCTTGAA-AAGGGTGCCATTAAC
1 TTGTGGGCTT-AAGAAGGGTGCCACTAAC
*
33202 TTGTGGGCTTAAGAGAGGATGCCACTAAC
1 TTGTGGGCTTAAGA-AGGGTGCCACTAAC
* ** *
33231 TTGTGGACTTTTGAAAGGGTGTCACTAAC
1 TTGTGGGCTTAAG-AAGGGTGCCACTAAC
33260 TTGT
1 TTGT
33264 AGACTTTTGA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 2 0.04
28 11 0.21
29 38 0.73
30 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.31
Consensus pattern (28 bp):
TTGTGGGCTTAAGAAGGGTGCCACTAAC
Found at i:33268 original size:29 final size:29
Alignment explanation
Indices: 33224--33280 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
33214 GAGAGGATGC
*
33224 CACTAACTTGTGGACTTTTGAAAGGGTGT
1 CACTAACTTGTAGACTTTTGAAAGGGTGT
33253 CACTAACTTGTAGACTTTTGAAAGGGTG
1 CACTAACTTGTAGACTTTTGAAAGGGTG
33281 CCAGTGACGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (29 bp):
CACTAACTTGTAGACTTTTGAAAGGGTGT
Found at i:33420 original size:28 final size:29
Alignment explanation
Indices: 33384--33514 Score: 133
Period size: 29 Copynumber: 4.5 Consensus size: 29
33374 CTAGCTAGTG
*
33384 TGGGCTTT-AAAGAGG-TGCCACTGACTCA
1 TGGGCTTTGAAA-AGGATGCCACTGACTTA
*
33412 TGGGCTTT-AAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTA
* * * *
33440 TGGGTTTTGAAAAGGGTGCAACGGACTTA
1 TGGGCTTTGAAAAGGATGCCACTGACTTA
** *
33469 TGGGCTTTGAAAAGGATGCCACCAACTAA
1 TGGGCTTTGAAAAGGATGCCACTGACTTA
33498 TGTGGACTTTGAAAAGG
1 TG-GG-CTTTGAAAAGG
33515 TTTGGTTGCC
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
27 3 0.03
28 29 0.34
29 41 0.48
30 2 0.02
31 11 0.13
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (29 bp):
TGGGCTTTGAAAAGGATGCCACTGACTTA
Found at i:33511 original size:31 final size:30
Alignment explanation
Indices: 33473--33742 Score: 155
Period size: 31 Copynumber: 8.3 Consensus size: 30
33463 GACTTATGGG
**
33473 CTTTGAAAAGGATGCCACCAACTAATGTGGA
1 CTTTGAAAAGG-TGCCACCAACTTGTGTGGA
* **
33504 CTTTGAAAAGGTTTGGTTGCCACTAACTTGTGTAAA
1 CTTTGAAAA-----GG-TGCCACCAACTTGTGTGGA
**
33540 CTTTGAATGGGGTGCCACCAACTTGTGTGGA
1 CTTTGAA-AAGGTGCCACCAACTTGTGTGGA
* * **
33571 -TTTTAACTATGGTGCCACCAACTCCTGTGGA
1 CTTTGAA--AAGGTGCCACCAACTTGTGTGGA
**
33602 CTTTGAAAAGGTTGCCACCAACTCATGTGGA
1 CTTTGAAAAGG-TGCCACCAACTTGTGTGGA
** *
33633 CTTTGACTGAGGTTCCACCAACTTGTGTGGA
1 CTTTGA-AAAGGTGCCACCAACTTGTGTGGA
**
33664 CTTTGAAAAGGATTGTGCCACTGACTTGTGTGGA
1 CTTTGAAAA-G---GTGCCACCAACTTGTGTGGA
*
33698 CTTTGAAAAAGGTTAAGTGCCACCGACTTGTGTGGA
1 CTTTG-AAAA-G----GTGCCACCAACTTGTGTGGA
*
33734 CTTTAAAAA
1 CTTTGAAAA
33743 TGATTTGGTT
Statistics
Matches: 189, Mismatches: 34, Indels: 28
0.75 0.14 0.11
Matches are distributed among these distances:
30 9 0.05
31 92 0.49
32 10 0.05
34 22 0.12
35 10 0.05
36 46 0.24
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (30 bp):
CTTTGAAAAGGTGCCACCAACTTGTGTGGA
Found at i:33618 original size:62 final size:64
Alignment explanation
Indices: 33551--33701 Score: 182
Period size: 62 Copynumber: 2.4 Consensus size: 64
33541 TTTGAATGGG
*
33551 GTGCCACCAACTTGTGTGGATTTTAACT-ATGGTGCCACCAACTCCTGTGGACTTTGAAAAGG-T
1 GTGCCACCAACTTGTGTGGACTTTAACTGA-GGTGCCACCAACTCCTGTGGACTTTGAAAAGGAT
** * * **
33614 -TGCCACCAACTCATGTGGACTTTGACTGAGGTTCCACCAACTTGTGTGGACTTTGAAAAGGATT
1 GTGCCACCAACTTGTGTGGACTTTAACTGAGGTGCCACCAACTCCTGTGGACTTTGAAAAGGA-T
**
33678 GTGCCACTGACTTGTGTGGACTTT
1 GTGCCACCAACTTGTGTGGACTTT
33702 GAAAAAGGTT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
62 52 0.71
63 1 0.01
64 1 0.01
65 19 0.26
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.31
Consensus pattern (64 bp):
GTGCCACCAACTTGTGTGGACTTTAACTGAGGTGCCACCAACTCCTGTGGACTTTGAAAAGGAT
Found at i:33660 original size:93 final size:94
Alignment explanation
Indices: 33485--33663 Score: 225
Period size: 93 Copynumber: 1.9 Consensus size: 94
33475 TTGAAAAGGA
* ** *
33485 TGCCACCAACTAATGTGGACTTTGAAAAGGTTTGGTTGCCACTAACTTGTGTAAACTTTGAATGG
1 TGCCACCAACTAATGTGGACTTTGAAAA----TGGTTGCCACCAACTCATGTAAACTTTGAATGA
33550 GGTGCCACCAACTTGTGTGGATTTTAACTATGG
62 GGTGCCACCAACTTGTGTGGATTTTAACTATGG
** ** * *
33583 TGCCACCAACTCCTGTGGACTTTGAAAA-GGTTGCCACCAACTCATGTGGACTTTGACTGAGGTT
1 TGCCACCAACTAATGTGGACTTTGAAAATGGTTGCCACCAACTCATGTAAACTTTGAATGAGGTG
33647 CCACCAACTTGTGTGGA
66 CCACCAACTTGTGTGGA
33664 CTTTGAAAAG
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
93 45 0.63
98 26 0.37
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (94 bp):
TGCCACCAACTAATGTGGACTTTGAAAATGGTTGCCACCAACTCATGTAAACTTTGAATGAGGTG
CCACCAACTTGTGTGGATTTTAACTATGG
Found at i:33696 original size:34 final size:35
Alignment explanation
Indices: 33647--33774 Score: 134
Period size: 36 Copynumber: 3.6 Consensus size: 35
33637 GACTGAGGTT
*
33647 CCACCAACTTGTGTGGACTTTGAAAAGGATT-GTG
1 CCACCGACTTGTGTGGACTTTGAAAAGGATTAGTG
*
33681 CCACTGACTTGTGTGGACTTTGAAAAAGG-TTAAGTG
1 CCACCGACTTGTGTGGACTTTG-AAAAGGATT-AGTG
* * *
33717 CCACCGACTTGTGTGGACTTTAAAAATGATTTGGTTG
1 CCACCGACTTGTGTGGACTTTGAAAAGGA-TTAG-TG
* * *
33754 GCATCAACTTGTGTGGACTTT
1 CCACCGACTTGTGTGGACTTT
33775 AAGTGCCACC
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
34 22 0.28
35 11 0.14
36 24 0.30
37 22 0.28
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (35 bp):
CCACCGACTTGTGTGGACTTTGAAAAGGATTAGTG
Found at i:42866 original size:12 final size:11
Alignment explanation
Indices: 42849--42919 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 11
42839 AAGAACAGAG
42849 AGGAGGGATGAT
1 AGGAGGGA-GAT
*
42861 AGGAGGAGAGAC
1 AGGAGG-GAGAT
42873 AGGA--GAGAT
1 AGGAGGGAGAT
*
42882 AGTA--GAGAT
1 AGGAGGGAGAT
42891 AGGAGGGATGAT
1 AGGAGGGA-GAT
*
42903 AGGAGGAGAGAC
1 AGGAGG-GAGAT
42915 AGGAG
1 AGGAG
42920 AGATAATAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
9 15 0.31
11 2 0.04
12 28 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.48, T:0.10
Consensus pattern (11 bp):
AGGAGGGAGAT
Found at i:42895 original size:42 final size:42
Alignment explanation
Indices: 42845--42952 Score: 189
Period size: 42 Copynumber: 2.6 Consensus size: 42
42835 GAGAAAGAAC
*
42845 AGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGTAG
1 AGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAG
*
42887 AGATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAG
1 AGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAG
*
42929 AGAGAGGAGGGATGACAGGAGGAG
1 AGAGAGGAGGGATGATAGGAGGAG
42953 GAGAGAAGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.41, C:0.03, G:0.47, T:0.09
Consensus pattern (42 bp):
AGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAG
Found at i:57554 original size:42 final size:42
Alignment explanation
Indices: 57499--57617 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
57489 TTCTTCTCTC
* *
57499 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
57541 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
57583 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
57618 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:57558 original size:12 final size:11
Alignment explanation
Indices: 57532--57607 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
57522 TCTATTATCT
*
57532 CTCCTGTCTCTC
1 CTCCTATCTC-C
57544 CTCCTATCATCC
1 CTCCTATC-TCC
57556 CTCCTATCT--
1 CTCCTATCTCC
*
57565 CTACTATCT--
1 CTCCTATCTCC
*
57574 CTCCTGTCTCTC
1 CTCCTATCTC-C
57586 CTCCTATCATCC
1 CTCCTATC-TCC
*
57598 CTCCTCTCTC
1 CTCCTATCTC
57608 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:57559 original size:24 final size:24
Alignment explanation
Indices: 57523--57608 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
57513 CCTCCTCTCT
* *
57523 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
57547 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
57568 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
57589 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
57609 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:57583 original size:18 final size:18
Alignment explanation
Indices: 57514--57584 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
57504 CCTGTCATCC
* *
57514 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
57532 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
57554 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
57574 CTCCTGTCTCT
1 CTCCTGTCTCT
57585 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:65646 original size:42 final size:42
Alignment explanation
Indices: 65599--65709 Score: 168
Period size: 42 Copynumber: 2.6 Consensus size: 42
65589 CTTCTTCTCT
* * * * *
65599 TCTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCTTATC
1 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCCCCTATC
*
65641 TCTCCTCCTATCTTCCCTCCTATCTCTACTATCTCCCCTATC
1 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCCCCTATC
65683 TCTCCTCCTATCATCCCTCCTATCTCT
1 TCTCCTCCTATCATCCCTCCTATCTCT
65710 TCTTTCTCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.11, C:0.46, G:0.01, T:0.42
Consensus pattern (42 bp):
TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCCCCTATC
Found at i:65659 original size:12 final size:11
Alignment explanation
Indices: 65637--65708 Score: 71
Period size: 12 Copynumber: 6.5 Consensus size: 11
65627 TTATCTCTCT
65637 TATCTCTCCTCC
1 TATCTC-CCTCC
65649 TATCTTCCCTCC
1 TATC-TCCCTCC
*
65661 TATCT--CTAC
1 TATCTCCCTCC
65670 TATCT-CC-CC
1 TATCTCCCTCC
65679 TATCTCTCCTCC
1 TATCTC-CCTCC
65691 TATCATCCCTCC
1 TATC-TCCCTCC
65703 TATCTC
1 TATCTC
65709 TTCTTTCTCT
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
9 14 0.27
10 1 0.02
11 5 0.10
12 28 0.54
13 4 0.08
ACGTcount: A:0.12, C:0.47, G:0.00, T:0.40
Consensus pattern (11 bp):
TATCTCCCTCC
Found at i:67374 original size:30 final size:30
Alignment explanation
Indices: 67338--67417 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 30
67328 GAGGAGGGAT
**
67338 GATAGGAGGAGAGACAGGAGAGATAGTAGA
1 GATAGGAGGAGAGACAGGAGAGATAACAGA
67368 GATAGGAGGAGAGACAGGAGAGATAACAGA
1 GATAGGAGGAGAGACAGGAGAGATAACAGA
*
67398 GAAAGGAGG-GATGACAGGAG
1 GATAGGAGGAGA-GACAGGAG
67418 GAGGAGAGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 2 0.04
30 44 0.96
ACGTcount: A:0.44, C:0.05, G:0.44, T:0.07
Consensus pattern (30 bp):
GATAGGAGGAGAGACAGGAGAGATAACAGA
Found at i:67377 original size:21 final size:21
Alignment explanation
Indices: 67353--67392 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
67343 GAGGAGAGAC
* *
67353 AGGAGAGATAGTAGAGATAGG
1 AGGAGAGACAGGAGAGATAGG
67374 AGGAGAGACAGGAGAGATA
1 AGGAGAGACAGGAGAGATA
67393 ACAGAGAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.42, T:0.10
Consensus pattern (21 bp):
AGGAGAGACAGGAGAGATAGG
Done.