Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1924
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: 48024
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:2256 original size:51 final size:52
Alignment explanation
Indices: 2188--2307 Score: 206
Period size: 51 Copynumber: 2.3 Consensus size: 52
2178 GAAAATTTAT
*
2188 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCT-GGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
2239 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
2291 CTACATGTATCGATACA
1 CTGCATGTATCGATACA
2308 AAGATCAGTG
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
51 38 0.58
52 27 0.42
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:2320 original size:52 final size:51
Alignment explanation
Indices: 2191--2327 Score: 179
Period size: 52 Copynumber: 2.7 Consensus size: 51
2181 AATTTATCTG
* *
2191 CATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGCAAATTTGCCTG
1 CATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGCAAATTTGCCTA
*** *
2242 CATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCTA
1 CATGTATCGATACATAAGATAGTGTATCGATACATCT-GGCAAATTTGCCTA
2294 CATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CATGTATCGATACATAAGAT-AGTGTATCGATACA
2328 ATGTATCGAT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
50 2 0.03
51 34 0.45
52 40 0.53
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (51 bp):
CATGTATCGATACATAAGATAGTGTATCGATACATCTGGCAAATTTGCCTA
Found at i:2334 original size:13 final size:13
Alignment explanation
Indices: 2316--2340 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2306 CAAAGATCAG
2316 TGTATCGATACAA
1 TGTATCGATACAA
2329 TGTATCGATACA
1 TGTATCGATACA
2341 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2424 original size:13 final size:13
Alignment explanation
Indices: 2406--2430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2396 CAAAAAAATA
2406 TGTATCGATACAT
1 TGTATCGATACAT
2419 TGTATCGATACA
1 TGTATCGATACA
2431 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2426 original size:33 final size:33
Alignment explanation
Indices: 2384--2450 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2374 AGTAGCTTAA
2384 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2417 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2450 A
1 A
2451 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:6466 original size:9 final size:8
Alignment explanation
Indices: 6447--6528 Score: 53
Period size: 9 Copynumber: 10.0 Consensus size: 8
6437 CCTTCTCTTC
6447 AGAAAAAA
1 AGAAAAAA
6455 A-AAAGCAAA
1 AGAAA--AAA
6464 A-AAAAAA
1 AGAAAAAA
*
6471 GGAAAAAAA
1 AG-AAAAAA
*
6480 ACAAAAAA
1 AGAAAAAA
*
6488 ACAAAACAA
1 AGAAAA-AA
6497 AGAAAACAA
1 AGAAAA-AA
*
6506 AGAAAAAG
1 AGAAAAAA
*
6514 AG-AGAAA
1 AGAAAAAA
6521 AGAAAAAA
1 AGAAAAAA
6529 CCTACTTAAG
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
7 11 0.18
8 20 0.33
9 29 0.48
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:6467 original size:13 final size:12
Alignment explanation
Indices: 6449--6480 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
6439 TTCTCTTCAG
6449 AAAAAAAAAAGC
1 AAAAAAAAAAGC
*
6461 AAAAAAAAAAGG
1 AAAAAAAAAAGC
6473 AAAAAAAA
1 AAAAAAAA
6481 CAAAAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGC
Found at i:6478 original size:14 final size:13
Alignment explanation
Indices: 6449--6528 Score: 63
Period size: 13 Copynumber: 5.8 Consensus size: 13
6439 TTCTCTTCAG
*
6449 AAAAAAAAAAGCA
1 AAAAAAAAAAGAA
*
6462 AAAAAAAAAGGAA
1 AAAAAAAAAAGAA
6475 AAAAAACAAAA-AA
1 AAAAAA-AAAAGAA
* *
6488 ACAAAACAAAGAA
1 AAAAAAAAAAGAA
6501 AACAAAGAAAAAGAGA
1 AA-AAA-AAAAAGA-A
6517 GAAAAGAAAAAA
1 -AAAA-AAAAAA
6529 CCTACTTAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
12 3 0.06
13 27 0.51
14 6 0.11
15 6 0.11
16 8 0.15
17 3 0.06
ACGTcount: A:0.82, C:0.06, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:6502 original size:22 final size:21
Alignment explanation
Indices: 6451--6512 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
6441 CTCTTCAGAA
**
6451 AAAAAAAAGCAAAAAAAAAAGG
1 AAAAAAAA-CAAAAAAAAAAAC
6473 AAAAAAAACAAAAAAACAAAAC
1 AAAAAAAACAAAAAAA-AAAAC
* *
6495 AAAGAAAACAAAGAAAAA
1 AAAAAAAACAAAAAAAAA
6513 GAGAGAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.29
22 25 0.71
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (21 bp):
AAAAAAAACAAAAAAAAAAAC
Found at i:7572 original size:26 final size:26
Alignment explanation
Indices: 7542--7631 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
7532 AAGTTGGTGG
*
7542 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
7568 CACCTCTTAAAGCCCACAGAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
7597 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
7623 CACCTTTCA
1 CACCTTTCA
7632 AAGCCCACCC
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
25 3 0.06
26 17 0.36
27 8 0.17
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.20
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:7579 original size:55 final size:55
Alignment explanation
Indices: 7495--8227 Score: 1122
Period size: 55 Copynumber: 13.3 Consensus size: 55
7485 TCCGCTTTTT
7495 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
7550 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACAGAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
7605 AGTCCCCAAAGAGCAGGACACCT-TTCAAAGCCCACCCAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
7660 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
7715 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
7770 AGTCCCCAAAAAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
7825 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
7880 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
7935 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
7990 AGTCCTCAAAGAACAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
8045 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
8100 ATTCCCCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
** * * *
8155 AGTCCTCAAAGAGCAGGACGGCT-TTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* *
8210 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
8228 TACAGTTTAT
Statistics
Matches: 630, Mismatches: 37, Indels: 22
0.91 0.05 0.03
Matches are distributed among these distances:
54 13 0.02
55 605 0.96
56 12 0.02
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:7722 original size:29 final size:29
Alignment explanation
Indices: 7690--7777 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
7680 CCTCTTAAAG
7690 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
** * *
7719 CCCA-A-AGAG-CAG-GACACCTCTTAAAG--
1 CCCACACA-AGTTGGTGGCACCT-TT-CAGTC
7745 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
7774 CCCA
1 CCCA
7778 AAAAGCAGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 18
0.62 0.12 0.26
Matches are distributed among these distances:
26 10 0.24
27 9 0.21
28 9 0.21
29 14 0.33
ACGTcount: A:0.26, C:0.35, G:0.19, T:0.19
Consensus pattern (29 bp):
CCCACACAAGTTGGTGGCACCTTTCAGTC
Found at i:8107 original size:29 final size:29
Alignment explanation
Indices: 8075--8155 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 29
8065 CCTCTTAAAG
**
8075 CCCACACAAGTTGGTGGCACCTTTCATTC
1 CCCACACAAGTTGGTGGCACCTTTCAAAC
** * *
8104 CCCA-A-AGAG-CAG-GACACCTTTCAAAG
1 CCCACACA-AGTTGGTGGCACCTTTCAAAC
8130 CCCACACAAGTTGGTGGCACCTTTCA
1 CCCACACAAGTTGGTGGCACCTTTCA
8156 GTCCTCAAAG
Statistics
Matches: 38, Mismatches: 9, Indels: 10
0.67 0.16 0.18
Matches are distributed among these distances:
26 14 0.37
27 5 0.13
28 5 0.13
29 14 0.37
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.21
Consensus pattern (29 bp):
CCCACACAAGTTGGTGGCACCTTTCAAAC
Found at i:8793 original size:21 final size:20
Alignment explanation
Indices: 8766--8842 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 20
8756 TTGAAAAAAA
*
8766 AAATGTATCGATACATTTGT
1 AAATGTATCGATACATTTAT
* *
8786 AGAATGTATCGATACATTCAC
1 A-AATGTATCGATACATTTAT
* *
8807 AAATGTATCGTTACATTCTAC
1 AAATGTATCGATACATT-TAT
8828 AAATGTATCGATACA
1 AAATGTATCGATACA
8843 GGGTCCCAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
20 16 0.33
21 33 0.67
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.34
Consensus pattern (20 bp):
AAATGTATCGATACATTTAT
Found at i:8902 original size:19 final size:19
Alignment explanation
Indices: 8878--8945 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
8868 AATTCAACGA
8878 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
8897 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
8912 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
* *
8929 ATTGTATCAATACATAA
1 TTTGTATCGATACATAA
8946 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 27 0.64
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:8916 original size:32 final size:32
Alignment explanation
Indices: 8880--8942 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
8870 TTCAACGATT
* *
8880 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCAATACAA
8912 TGTATCGATACATAAGTATTGTATCAATACA
1 TGTATCGATACATAAGTATTGTATCAATACA
8943 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCAATACAA
Found at i:8917 original size:13 final size:13
Alignment explanation
Indices: 8899--8923 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8889 ACATAAGTTT
8899 TGTATCGATACAA
1 TGTATCGATACAA
8912 TGTATCGATACA
1 TGTATCGATACA
8924 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:9003 original size:13 final size:13
Alignment explanation
Indices: 8985--9010 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8975 CATTTTTCTG
8985 TGTATCGATACAT
1 TGTATCGATACAT
8998 TGTATCGATACAT
1 TGTATCGATACAT
9011 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:9004 original size:33 final size:33
Alignment explanation
Indices: 8965--9031 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
8955 GCCAAGGAAA
***
8965 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
8998 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
9031 T
1 T
9032 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:11434 original size:51 final size:53
Alignment explanation
Indices: 11370--11711 Score: 201
Period size: 52 Copynumber: 6.5 Consensus size: 53
11360 AGTTTATCAA
* * * *
11370 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
11421 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * *** * * *
11475 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAAT
** ** * * *
11528 CCCGTT-A-TTTCTGAGGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAAT
1 TTC-TTCACAATC---GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAAT
* * *
11582 TT-TTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCCAATT
1 TTCTT-CACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAA-T
* * *
11635 TTCCTT--TAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
11687 TT-TTCACAATCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
11712 CTCGTTATTT
Statistics
Matches: 222, Mismatches: 43, Indels: 51
0.70 0.14 0.16
Matches are distributed among these distances:
50 4 0.02
51 36 0.16
52 84 0.38
53 35 0.16
54 36 0.16
55 24 0.11
57 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:11554 original size:28 final size:27
Alignment explanation
Indices: 11487--11555 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 27
11477 CTTCACAATC
*
11487 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
11514 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
11542 GGGGATACTCCAAC
1 GGGGATACTCCAAC
11556 TCCGGTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:11695 original size:104 final size:103
Alignment explanation
Indices: 11375--11710 Score: 297
Period size: 104 Copynumber: 3.2 Consensus size: 103
11365 ATCAATTCTC
* * * *
11375 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGAT
1 CACAATCGGGGATACTCCAA-TCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
*
11439 ACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
65 ACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTT-TT
* * * ** * * * ** * *
11480 CACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAA--CCCCGTTATTTCTGA
1 CACAATCGGGGATACTCCAATCCGGTTTTATTTTC---AAAACACCAATTTTCCTTTA-ATC---
* * *
11542 GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTT
59 GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAATTTTT
*
11586 CCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGA
1 -CACAATCGGGGATACTCCAATCC-GGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGA
* *
11651 TACTCCAACTCCGATTTTATTTTCAAAAATACCAATTTTT
64 TACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
*
11691 CACAATCGAGGATACTCCAA
1 CACAATCGGGGATACTCCAA
11711 CCTCGTTATT
Statistics
Matches: 177, Mismatches: 38, Indels: 33
0.71 0.15 0.13
Matches are distributed among these distances:
103 6 0.03
104 44 0.25
105 36 0.20
106 18 0.10
107 38 0.21
108 7 0.04
109 28 0.16
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (103 bp):
CACAATCGGGGATACTCCAATCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATA
CTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
Found at i:11740 original size:212 final size:212
Alignment explanation
Indices: 11373--11767 Score: 625
Period size: 212 Copynumber: 1.9 Consensus size: 212
11363 TTATCAATTC
* *
11373 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* *
11438 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* *
11503 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACTCCGGTTTTATC
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACTCCGGTTTTATC
11568 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * *
11585 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGGGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
* *
11649 GATACTCCAACTCCGATTTTATTTTC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
11712 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAAC
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAAC
11768 CCCGTTATTT
Statistics
Matches: 167, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
211 31 0.19
212 102 0.61
213 34 0.20
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (212 bp):
TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACTCCGGTTTTATC
GCTAAAACACTAATTTT
Found at i:11806 original size:28 final size:28
Alignment explanation
Indices: 11700--11799 Score: 123
Period size: 28 Copynumber: 3.6 Consensus size: 28
11690 TCACAATCGA
*
11700 GGATACTCCAACCTCGTTATTTCATCG--G
1 GGATACTCCAACCCCGTTATTT--TCGAAG
* * *
11728 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTATTTTCGAAG
11756 GGATACTCCAACCCCGTTATTTTCGAAG
1 GGATACTCCAACCCCGTTATTTTCGAAG
*
11784 GGATACTCCAATCCCG
1 GGATACTCCAACCCCG
11800 ATTTTTTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
26 2 0.03
28 61 0.97
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTATTTTCGAAG
Found at i:17882 original size:17 final size:17
Alignment explanation
Indices: 17860--17915 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
17850 ATTTCATATT
17860 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTTTTTTTTC
* *
17877 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTTTTTTTTC
** * *
17894 TTCATCTTCTTTCTTTC
1 TTTTTCTTTTTTTTTTC
17911 TTTTT
1 TTTTT
17916 TACCTAACTT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCTTTTTTTTTTC
Found at i:23521 original size:2 final size:2
Alignment explanation
Indices: 23514--23568 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
23504 GTTTTTCTTT
23514 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23556 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
23569 TCCTCTTTCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24638 original size:227 final size:227
Alignment explanation
Indices: 24231--24785 Score: 599
Period size: 227 Copynumber: 2.4 Consensus size: 227
24221 TGATAAGTTT
* * * *
24231 ACTCAAATTAAATGAAGTCTAATAAATTTTTAAATATCTAAATTATGAAAAAATAAAATAAAAAA
1 ACTCAAATTAATTAAAATTTAATAAATTTTTAAATATCTAAATT-T-AAAAAATAAAATAAAAAA
** * * * * *
24296 CAAGAATACCCCAAAACTTTAAGAAGG-AATTAACTAAAAAAAATATTGATGTTGTTGATTAAGT
64 CAAGAATACCCCAAAACTTTAAGAAGGAAAGGAACTAAAAAAAACATTAATATTATTGATTAAAT
* * * * * * *
24360 AATTTAATATTTATTATTTTTTTAAATAAGATCTTAAATTTAAATTTTATAAAT-AAAAGAATCG
129 AATTTAATA-TTATTATATCTTTAAATAAAATATCAAATTTAAACTTTATAAATGAAAA-AATCA
* * * * *
24424 AAGTTAAAAGAG-ATTTTTCCT-TCATAATGAGTTA
192 AAATTAAAAGAGTATTTTTCATCTCACAATAAATTA
* * *
24458 ACTCATATTAATTAAAATTTAATAAATTTTTGAATA-CTTAAATTTAAAAAA-AAACTAAAAAAC
1 ACTCAAATTAATTAAAATTTAATAAATTTTTAAATATC-TAAATTTAAAAAATAAAATAAAAAAC
* *
24521 AAAAATACCCCAAAACTTTAAGAAGGAAAGGAATTGATTAAAAAAACATTAATATTAATTGATTC
65 AAGAATACCCCAAAACTTTAAGAAGGAAAGGAACT-A--AAAAAAACATTAATATT-ATTGATT-
*
24586 AAATAATTTGATA-TA-TATATCTTTAAATAAAATATCAAATTTAAACTTTATAAATGAAAAAAT
125 AAATAATTTAATATTATTATATCTTTAAATAAAATATCAAATTTAAACTTTATAAATGAAAAAAT
* *
24649 CAAAATTAAAAGAGTTTTTTTTATCTCACAATAAATTA
190 CAAAATTAAAAGAGTATTTTTCATCTCACAATAAATTA
* * * *
24687 ACTTAAATTAATTAAAATTTAATACA-CTTTAAATATCTAAATTTTAAAAAATAATAATAAAAAC
1 ACTCAAATTAATTAAAATTTAATAAATTTTTAAATATCTAAA-TTTAAAAAATAA-AATAAAAAA
* *
24751 CAAGAATACCTCAAAACTTTAAGGAGGAAA-GAACT
64 CAAGAATACCCCAAAACTTTAAGAAGGAAAGGAACT
24786 TCACCCTCCA
Statistics
Matches: 272, Mismatches: 42, Indels: 25
0.80 0.12 0.07
Matches are distributed among these distances:
224 36 0.13
225 11 0.04
226 3 0.01
227 85 0.31
228 37 0.14
229 49 0.18
230 17 0.06
231 34 0.12
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (227 bp):
ACTCAAATTAATTAAAATTTAATAAATTTTTAAATATCTAAATTTAAAAAATAAAATAAAAAACA
AGAATACCCCAAAACTTTAAGAAGGAAAGGAACTAAAAAAAACATTAATATTATTGATTAAATAA
TTTAATATTATTATATCTTTAAATAAAATATCAAATTTAAACTTTATAAATGAAAAAATCAAAAT
TAAAAGAGTATTTTTCATCTCACAATAAATTA
Found at i:27976 original size:21 final size:21
Alignment explanation
Indices: 27950--27991 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
27940 GAAAGAATTA
*
27950 AGTAATTAAGTAATTATATGG
1 AGTAATTAAGTAATCATATGG
27971 AGTAATTAAGTAATCATATGG
1 AGTAATTAAGTAATCATATGG
27992 GTAGTTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.36
Consensus pattern (21 bp):
AGTAATTAAGTAATCATATGG
Found at i:36866 original size:236 final size:239
Alignment explanation
Indices: 36443--36912 Score: 738
Period size: 236 Copynumber: 2.0 Consensus size: 239
36433 ATATATGAAC
*
36443 ATATCAATTTATATAAAATAATAATTAATGTGTAAAAATTTTTATAAATTTAAATACTTTTAAAC
1 ATATCAATTTATATAAAAAAATAATTAATGTGTAAAAATTTTTATAAATTTAAATACTTTTAAAC
* *
36508 TCAAAAAAAATAAATAAACATATTATGAAACACAATTTTTTCTGTAAATTGAATCATTATACAAA
66 T----AAAAATAAATAAACATATTATGAAACACAATTTTTTCTATAAATTAAATCATTATACAAA
36573 TTATACAAATATCACAAACTGAAACATTATTCTAACACAACATAGAAACACAAACTTTTCTAAAT
127 TTATACAAATATCACAAACTGAAACATTATTCTAACACAACATAGAAACACAAACTTTTCTAAAT
*
36638 TGAAGTAATGATAAAATATGAATGAATTGATATATGATACAAAAAAAT
192 TGAAATAATGATAAAATATGAATGAATTGATATATGATACAAAAAAAT
*
36686 ATATCAATTTATATAAAACAAATAATTAATGTGT-AAATTTTTTATAAATTTAGAATA-TTTTAA
1 ATATCAATTTATATAAAA-AAATAATTAATGTGTAAAAATTTTTATAAATTTA-AATACTTTTAA
* * *
36749 ACT-AAAA-AAA-AAACATGTTATG-AACATAATTTTTTTTATAAATTAAATCATTATTAC-AAT
64 ACTAAAAATAAATAAACATATTATGAAACACAATTTTTTCTATAAATTAAATCATTA-TACAAAT
*
36809 TATACAAATATCACAAAACTGAGACATTATTCTAACACAACATAGAAACACAAACTTTTCTAAAT
128 TATACAAATATCAC-AAACTGAAACATTATTCTAACACAACATAGAAACACAAACTTTTCTAAAT
36874 TGAAATAATGATAAAATATGAATGAATTGATATATGATA
192 TGAAATAATGATAAAATATGAATGAATTGATATATGATA
36913 TGAAGAGAAC
Statistics
Matches: 214, Mismatches: 9, Indels: 15
0.90 0.04 0.06
Matches are distributed among these distances:
235 44 0.21
236 101 0.47
237 3 0.01
238 4 0.02
243 44 0.21
244 18 0.08
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.34
Consensus pattern (239 bp):
ATATCAATTTATATAAAAAAATAATTAATGTGTAAAAATTTTTATAAATTTAAATACTTTTAAAC
TAAAAATAAATAAACATATTATGAAACACAATTTTTTCTATAAATTAAATCATTATACAAATTAT
ACAAATATCACAAACTGAAACATTATTCTAACACAACATAGAAACACAAACTTTTCTAAATTGAA
ATAATGATAAAATATGAATGAATTGATATATGATACAAAAAAAT
Found at i:36962 original size:16 final size:16
Alignment explanation
Indices: 36940--36996 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
36930 TAATTAAAAG
36940 TAATATAAAAAATA-A
1 TAATATAAAAAATATA
*
36955 TGAATATATATAAATATA
1 T-AATATA-AAAAATATA
36973 TACATAT-AAAAATATA
1 TA-ATATAAAAAATATA
36989 TAA-ATAAA
1 TAATATAAA
36997 TTATTAATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 2 0.06
15 4 0.11
16 16 0.46
17 7 0.20
18 6 0.17
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (16 bp):
TAATATAAAAAATATA
Found at i:36973 original size:8 final size:8
Alignment explanation
Indices: 36960--36994 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
36950 AATAATGAAT
36960 ATATATAA
1 ATATATAA
*
36968 ATATATAC
1 ATATATAA
*
36976 ATATAAAA
1 ATATATAA
36984 ATATATAA
1 ATATATAA
36992 ATA
1 ATA
36995 AATTATTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (8 bp):
ATATATAA
Found at i:37046 original size:17 final size:17
Alignment explanation
Indices: 37017--37049 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
37007 ATAAAAATTT
37017 TAAATATTTTATAATAA
1 TAAATATTTTATAATAA
37034 TAAAT-TTTGTATAATA
1 TAAATATTT-TATAATA
37050 TTTTACCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TAAATATTTTATAATAA
Found at i:40471 original size:42 final size:42
Alignment explanation
Indices: 40413--40497 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
40403 ACGTCATATG
40413 ACTCGAAAATCAAATTAAATCATAAGAAGGT-AAAAAAGTTT
1 ACTCGAAAATCAAATTAAATCATAAGAAGGTAAAAAAAGTTT
40454 ACTCGAAAAATCAAATTAAATCATAAGAAGGTAAAAAAAGTTT
1 ACTCG-AAAATCAAATTAAATCATAAGAAGGTAAAAAAAGTTT
40497 A
1 A
40498 ACCTGGTCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 5 0.12
42 26 0.62
43 11 0.26
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (42 bp):
ACTCGAAAATCAAATTAAATCATAAGAAGGTAAAAAAAGTTT
Found at i:42890 original size:2 final size:2
Alignment explanation
Indices: 42883--42919 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
42873 ATCATTTACA
*
42883 AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42920 AAACTTCGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:43751 original size:25 final size:25
Alignment explanation
Indices: 43721--43768 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
43711 CAAAAAATAT
43721 TTATCAATCAAAAGAAAAATCTATA
1 TTATCAATCAAAAGAAAAATCTATA
43746 TTATCAATCAAAAGAAAAATCTA
1 TTATCAATCAAAAGAAAAATCTA
43769 GAGCTCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.27
Consensus pattern (25 bp):
TTATCAATCAAAAGAAAAATCTATA
Found at i:44907 original size:21 final size:20
Alignment explanation
Indices: 44881--44931 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
44871 TTCAACAAAT
*
44881 TGTATCGATACA-ATAGGGTAA
1 TGTATCGATACATA-AGTG-AA
44902 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
44922 TGTATCGATA
1 TGTATCGATA
44932 TAGGACCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 12 0.43
21 15 0.54
22 1 0.04
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:44925 original size:20 final size:21
Alignment explanation
Indices: 44881--44931 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
44871 TTCAACAAAT
44881 TGTATCGATACAATAGGGTAA
1 TGTATCGATACAATAGGGTAA
*
44902 TGTATCGATAC-ATA-AGTGAA
1 TGTATCGATACAATAGGGT-AA
44922 TGTATCGATA
1 TGTATCGATA
44932 TAGGACCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 15 0.54
21 11 0.39
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (21 bp):
TGTATCGATACAATAGGGTAA
Found at i:45027 original size:12 final size:12
Alignment explanation
Indices: 45010--45041 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
45000 GGTTTTGACC
45010 TAAATGTATCGA
1 TAAATGTATCGA
45022 TAAATGTATCGA
1 TAAATGTATCGA
*
45034 TACATGTA
1 TAAATGTA
45042 GGTAATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (12 bp):
TAAATGTATCGA
Done.