Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold321
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: 1029294
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.30
Warning! 84004 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:8095 original size:29 final size:29
Alignment explanation
Indices: 8058--8119 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
8048 TCCCCGTGAA
8058 AAGTAGTATCAGAGCTGTAGGTTTGAACC
1 AAGTAGTATCAGAGCTGTAGGTTTGAACC
* * *
8087 AAGTGGTATCTGAGCTGTTGGTTTGAACC
1 AAGTAGTATCAGAGCTGTAGGTTTGAACC
8116 AAGT
1 AAGT
8120 TGATATTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (29 bp):
AAGTAGTATCAGAGCTGTAGGTTTGAACC
Found at i:18391 original size:29 final size:29
Alignment explanation
Indices: 18354--18415 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
18344 TCCCCGTGAA
18354 AAGTAGTATCAGAGCTGTAGGTTTGAACC
1 AAGTAGTATCAGAGCTGTAGGTTTGAACC
* * *
18383 AAGTGGTATCTGAGCTGTTGGTTTGAACC
1 AAGTAGTATCAGAGCTGTAGGTTTGAACC
18412 AAGT
1 AAGT
18416 TGATATTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (29 bp):
AAGTAGTATCAGAGCTGTAGGTTTGAACC
Found at i:23725 original size:54 final size:55
Alignment explanation
Indices: 23639--23800 Score: 157
Period size: 56 Copynumber: 2.9 Consensus size: 55
23629 ACATTCTATT
* * * * *
23639 TTTTTTTAATTTGGTACAAAGGTGCCAACCATCAGTGTCCCAGCACCCGAAA-T-
1 TTTTTTAAATTTGGTACAAGGGTGTCGACCATCAGTGTCCCAGCACCCAAAACTA
** * * ** * **
23692 TTATTTTAAATTTGGTACTGGGGTGTCGGCCATCAATGTATCAACACAAAAAAGCTA
1 TT-TTTTAAATTTGGTACAAGGGTGTCGACCATCAGTGTCCCAGCACCCAAAA-CTA
*
23749 TTTTTTAAATTTGGTACAAGGGTGTCGATCATCAGTGTCCCAGCACCCAAAA
1 TTTTTTAAATTTGGTACAAGGGTGTCGACCATCAGTGTCCCAGCACCCAAAA
23801 AAATATTTTT
Statistics
Matches: 81, Mismatches: 24, Indels: 5
0.74 0.22 0.05
Matches are distributed among these distances:
53 2 0.02
54 36 0.44
56 41 0.51
57 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (55 bp):
TTTTTTAAATTTGGTACAAGGGTGTCGACCATCAGTGTCCCAGCACCCAAAACTA
Found at i:36461 original size:19 final size:19
Alignment explanation
Indices: 36434--36477 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
36424 GGTAGAGGTA
* *
36434 TTTTCTTTTATTTGGTTTT
1 TTTTGTTTTATTTGCTTTT
*
36453 TTTTGTTTTTTTTGCTTTT
1 TTTTGTTTTATTTGCTTTT
36472 TATTTG
1 T-TTTG
36478 CTCGTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.05, C:0.05, G:0.11, T:0.80
Consensus pattern (19 bp):
TTTTGTTTTATTTGCTTTT
Found at i:36472 original size:11 final size:11
Alignment explanation
Indices: 36449--36498 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
36439 TTTTATTTGG
36449 TTTTTTTTG--
1 TTTTTTTTGCT
36458 TTTTTTTTGCT
1 TTTTTTTTGCT
*
36469 TTTTATTTGCT
1 TTTTTTTTGCT
* *
36480 CGTTTTTTTACT
1 -TTTTTTTTGCT
36492 TTTTTTT
1 TTTTTTT
36499 ACTTTTTTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 9 0.27
11 16 0.48
12 8 0.24
ACGTcount: A:0.04, C:0.08, G:0.08, T:0.80
Consensus pattern (11 bp):
TTTTTTTTGCT
Found at i:36497 original size:10 final size:10
Alignment explanation
Indices: 36449--36506 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
36439 TTTTATTTGG
*
36449 TTTTTTTT-G
1 TTTTTTTTAC
*
36458 TTTTTTTTGC
1 TTTTTTTTAC
*
36468 TTTTTATTTGC
1 TTTTT-TTTAC
36479 TCGTTTTTTTAC
1 T--TTTTTTTAC
36491 TTTTTTTTAC
1 TTTTTTTTAC
36501 TTTTTT
1 TTTTTT
36507 GCCCCCACTG
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
9 8 0.19
10 20 0.47
11 6 0.14
12 5 0.12
13 4 0.09
ACGTcount: A:0.05, C:0.09, G:0.07, T:0.79
Consensus pattern (10 bp):
TTTTTTTTAC
Found at i:41781 original size:9 final size:8
Alignment explanation
Indices: 41734--41781 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
41724 AAGAAAGGAA
41734 AAAAAAAG
1 AAAAAAAG
* *
41742 AATAAAAC
1 AAAAAAAG
* *
41750 AAACAAAT
1 AAAAAAAG
41758 AAATAAAAG
1 AAA-AAAAG
41767 AAAAAAAG
1 AAAAAAAG
41775 AAAAAAA
1 AAAAAAA
41782 TGAAGAGTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
8 26 0.81
9 6 0.19
ACGTcount: A:0.83, C:0.04, G:0.06, T:0.06
Consensus pattern (8 bp):
AAAAAAAG
Found at i:49438 original size:21 final size:21
Alignment explanation
Indices: 49414--49465 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
49404 ATTGTTTTCT
*
49414 ATCTCACCGCTACAGTACCAA
1 ATCTCACCGCTACAGTAACAA
*
49435 ATCTCACCGCTACAGTAACTA
1 ATCTCACCGCTACAGTAACAA
49456 ATCTCACCGC
1 ATCTCACCGC
49466 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.38, G:0.10, T:0.21
Consensus pattern (21 bp):
ATCTCACCGCTACAGTAACAA
Found at i:51839 original size:13 final size:13
Alignment explanation
Indices: 51821--51846 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51811 ACAGCCGATG
51821 AGTACTGGAATGC
1 AGTACTGGAATGC
51834 AGTACTGGAATGC
1 AGTACTGGAATGC
51847 TTGAGAGCAT
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:0.31, T:0.23
Consensus pattern (13 bp):
AGTACTGGAATGC
Found at i:53013 original size:12 final size:12
Alignment explanation
Indices: 52996--53020 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52986 GGTGTTTATT
52996 CGGTTAACCGAC
1 CGGTTAACCGAC
53008 CGGTTAACCGAC
1 CGGTTAACCGAC
53020 C
1 C
53021 CGAAATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:53116 original size:18 final size:18
Alignment explanation
Indices: 53093--53133 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
53083 TTTTTTTCAA
*
53093 AAATTAACCGAATTAACT
1 AAATTAACCGAATTAACC
*
53111 AAATTACCCGAATTAACC
1 AAATTAACCGAATTAACC
53129 AAATT
1 AAATT
53134 GAATCACTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.20, G:0.05, T:0.27
Consensus pattern (18 bp):
AAATTAACCGAATTAACC
Found at i:53280 original size:18 final size:18
Alignment explanation
Indices: 53240--53283 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
53230 TAATTTTATG
**
53240 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
53258 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
53276 CTTGGGTT
1 ATTGGGTT
53284 TAGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:57889 original size:33 final size:33
Alignment explanation
Indices: 57847--57916 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
57837 TTTTTCCGCA
*
57847 TTTCACCTGAAAGCGCTTCCAGCTGGAAGTGTT
1 TTTCACCTGAAAGCGCTTCCAGCAGGAAGTGTT
*
57880 TTTCACCTGAAAGCGCTTCTAGCAGGAAGTGTT
1 TTTCACCTGAAAGCGCTTCCAGCAGGAAGTGTT
57913 TTTC
1 TTTC
57917 TATATTTCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (33 bp):
TTTCACCTGAAAGCGCTTCCAGCAGGAAGTGTT
Found at i:57937 original size:41 final size:41
Alignment explanation
Indices: 57880--57972 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
57870 TGGAAGTGTT
* *
57880 TTTCACCTGAAAGCGCTTCTAGCAGGAAGTGTTTTTCTATA
1 TTTCACCTGAAAGCGCTTCAAGCAGGAAGTGTTTTTCTACA
* **
57921 TTTCACTTGAAAGCGCTTCAAGTTGGAAGTGTTTTTCTACA
1 TTTCACCTGAAAGCGCTTCAAGCAGGAAGTGTTTTTCTACA
57962 TTTCACCTGAA
1 TTTCACCTGAA
57973 CTAGAAGTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (41 bp):
TTTCACCTGAAAGCGCTTCAAGCAGGAAGTGTTTTTCTACA
Found at i:60120 original size:73 final size:73
Alignment explanation
Indices: 60001--60139 Score: 260
Period size: 73 Copynumber: 1.9 Consensus size: 73
59991 CCCTTTCATA
*
60001 AAAATTTAAGCTTTTTAAATCTCAATAACTATTGTTGCAATTATTTTATTATATCTCAATTGTGT
1 AAAATTTAAGCTTTTTAAATCTCAATAACTATTGTTGCAATTATTTTATCATATCTCAATTGTGT
60066 AAAAAAGT
66 AAAAAAGT
*
60074 AAAATTTAAGCTTTTTAAATCTTAATAACTATTGTTGCAATTATTTTATCATATCTCAATTGTGT
1 AAAATTTAAGCTTTTTAAATCTCAATAACTATTGTTGCAATTATTTTATCATATCTCAATTGTGT
60139 A
66 A
60140 TCAAATAGAT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (73 bp):
AAAATTTAAGCTTTTTAAATCTCAATAACTATTGTTGCAATTATTTTATCATATCTCAATTGTGT
AAAAAAGT
Found at i:62576 original size:82 final size:82
Alignment explanation
Indices: 62415--62576 Score: 218
Period size: 82 Copynumber: 2.0 Consensus size: 82
62405 TTACCCACCT
* *
62415 CAAATAAAATACAAATTATTAAATTTAATATTTTCAATAATATTTAATGTTAATAAAAAATAATT
1 CAAATAAAATACAAATTATTAAATTTAATATTTTCAATAATACTTAATATTAATAAAAAATAATT
* *
62480 TATTATTTATAAAATAC
66 TATTATTAACAAAATAC
* ** * *
62497 CAAATAAAATACAGATTATTAGGTTTAATATTTTCAATTATACTTAATATT-ATAAAAAAATACT
1 CAAATAAAATACAAATTATTAAATTTAATATTTTCAATAATACTTAATATTAAT-AAAAAATAAT
*
62561 TTTTTATTAACAAAAT
65 TTATTATTAACAAAAT
62577 GTGTCACTTA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
81 2 0.03
82 67 0.97
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.41
Consensus pattern (82 bp):
CAAATAAAATACAAATTATTAAATTTAATATTTTCAATAATACTTAATATTAATAAAAAATAATT
TATTATTAACAAAATAC
Found at i:70318 original size:12 final size:12
Alignment explanation
Indices: 70297--70328 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
70287 ATAGGGTTAA
*
70297 AGAAGGCATTCC
1 AGAAGACATTCC
70309 AGAAGACATTCC
1 AGAAGACATTCC
70321 AGAAGACA
1 AGAAGACA
70329 ATATTGTAGT
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:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (12 bp):
AGAAGACATTCC
Found at i:71848 original size:31 final size:29
Alignment explanation
Indices: 71781--71853 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
71771 GGCTCAAGTT
* *
71781 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
**
71810 ACATTTTAGTCACTTATGTTATCATGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
71841 ACATTTTAGTCAC
1 ACATTTTAGTCAC
71854 CGAGCCGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 20 0.53
30 2 0.05
31 16 0.42
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:88402 original size:17 final size:17
Alignment explanation
Indices: 88367--88402 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
88357 ATGACATTGA
**
88367 TTATTACAAAATATTTT
1 TTATTACAAAATAAATT
88384 TTATTACAAAATAAATT
1 TTATTACAAAATAAATT
88401 TT
1 TT
88403 GATTGTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATTACAAAATAAATT
Found at i:89540 original size:30 final size:30
Alignment explanation
Indices: 89506--89568 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
89496 ACTTATTTTA
89506 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
89536 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
89566 TTG
1 TTG
89569 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:92853 original size:22 final size:22
Alignment explanation
Indices: 92825--92870 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
92815 TTTTTCTATT
92825 TACATGTGTGGGGTAAAAGTAC
1 TACATGTGTGGGGTAAAAGTAC
92847 TACATGTGTGGGGTAAAAGTAC
1 TACATGTGTGGGGTAAAAGTAC
92869 TA
1 TA
92871 AGGAGGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (22 bp):
TACATGTGTGGGGTAAAAGTAC
Found at i:94256 original size:20 final size:20
Alignment explanation
Indices: 94224--94263 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
94214 AAATCAAAGT
94224 AATTTTCAAATTTTGAAAATA
1 AATTTTCAAATTTT-AAAATA
94245 AATTTT-AAATTTTAAAATA
1 AATTTTCAAATTTTAAAATA
94264 TTTATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 7 0.37
21 6 0.32
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
AATTTTCAAATTTTAAAATA
Found at i:94308 original size:16 final size:17
Alignment explanation
Indices: 94283--94315 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
94273 ATTCTAATAT
94283 TTAT-ATTTTTTAAAAA
1 TTATAATTTTTTAAAAA
94299 TTATAATTTTTTAAAAA
1 TTATAATTTTTTAAAAA
94316 AACTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATAATTTTTTAAAAA
Found at i:94597 original size:22 final size:21
Alignment explanation
Indices: 94572--94613 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
94562 CCGAAAATCC
94572 AAATAAAAAAGACAAAACTATT
1 AAATAAAAAAGA-AAAACTATT
* *
94594 AAATTAAAAGGAAAAACTAT
1 AAATAAAAAAGAAAAACTAT
94614 GTTATTTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.19
Consensus pattern (21 bp):
AAATAAAAAAGAAAAACTATT
Found at i:99773 original size:15 final size:16
Alignment explanation
Indices: 99753--99782 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
99743 GGTTAACAAA
99753 TTTTCCA-TCTTCATT
1 TTTTCCATTCTTCATT
99768 TTTTCCATTCTTCAT
1 TTTTCCATTCTTCAT
99783 ACCAAGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.13, C:0.27, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTCCATTCTTCATT
Found at i:100039 original size:35 final size:36
Alignment explanation
Indices: 99997--100066 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 36
99987 TTAAGTTAAA
**
99997 CAAACATGTTTGTGAACAT-TAAACGAACATGTTCT
1 CAAACATGTTCATGAACATATAAACGAACATGTTCT
**
100032 CAAACATGTTCATGAACATATAATTGAACATGTTC
1 CAAACATGTTCATGAACATATAAACGAACATGTTC
100067 ACGAACAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 17 0.57
36 13 0.43
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (36 bp):
CAAACATGTTCATGAACATATAAACGAACATGTTCT
Found at i:100294 original size:301 final size:302
Alignment explanation
Indices: 99898--100501 Score: 1095
Period size: 301 Copynumber: 2.0 Consensus size: 302
99888 GAGCTTGAAT
* *
99898 GAACGGACCTCTTTTCATGTTCGTTTGTTTATTTTTAAGTTTGTTTGTGTTCGTTAAGAATTTTA
1 GAACGGACCTCTTTTCATGTTCGTTTGTTTATTTTTAAGTTTGTTCGTGTTCGTTAAGAATTTCA
99963 AAATTTTTGTTTGTGTTCATTCGCTTAAGTTAAACAAACATGTTTGTGAACATTAAACGAACATG
66 AAATTTTTGTTTGTGTTCATTCGCTTAAGTTAAACAAACATGTTTGTGAACATTAAACGAACATG
100028 TTCTCAAACATGTTCATGAACATATAATTGAACATGTTCACGAACAATGTAATAATAAACAAACC
131 TTCTCAAACATGTTCATGAACATATAATTGAACATGTTCACGAACAATGTAATAATAAACAAACC
*
100093 AACAATAAATAAAC-ATATATATATATTATTTTTTAGATATAAACTAGTCAAATATAAATATTAA
196 AACAATAAATAAACAATATATATATATTATTTTTTAGATATAAAATAGTCAAATATAAATATTAA
100157 TAATTATATTATAAATAAAAAAGCATACAAACCATAATATAC
261 TAATTATATTATAAATAAAAAAGCATACAAACCATAATATAC
100199 GAACGGACCTCTTTTCATGTTCGTTTGTTTATTTTTAAGTTTGTTCGTGTTCGTTAAGAATTTCA
1 GAACGGACCTCTTTTCATGTTCGTTTGTTTATTTTTAAGTTTGTTCGTGTTCGTTAAGAATTTCA
*
100264 AAATTTTT-TTTCGTGTTCGTTCGCTTAAGTTAAACAAACATGTTTGTGAACATTAAACGAACAT
66 AAATTTTTGTTT-GTGTTCATTCGCTTAAGTTAAACAAACATGTTTGTGAACATTAAACGAACAT
*
100328 GTTCTCAAACATGTTCATGAACATATAATTGAGCATGTTCACGAACAATGTAATAATAAACAAAC
130 GTTCTCAAACATGTTCATGAACATATAATTGAACATGTTCACGAACAATGTAATAATAAACAAAC
100393 CAACAATAAATAAACATATATATATATATATTATTTTTTAGATATAAAATAGTCAAATATAAATA
195 CAACAATAAATAAAC--A-ATATATATATATTATTTTTTAGATATAAAATAGTCAAATATAAATA
* *
100458 TTAATAATTATTTTATAAATAAAAAAGCATACAAACCGTAATAT
257 TTAATAATTATATTATAAATAAAAAAGCATACAAACCATAATAT
100502 TTTTATTAAT
Statistics
Matches: 291, Mismatches: 7, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
300 3 0.01
301 201 0.69
305 87 0.30
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.38
Consensus pattern (302 bp):
GAACGGACCTCTTTTCATGTTCGTTTGTTTATTTTTAAGTTTGTTCGTGTTCGTTAAGAATTTCA
AAATTTTTGTTTGTGTTCATTCGCTTAAGTTAAACAAACATGTTTGTGAACATTAAACGAACATG
TTCTCAAACATGTTCATGAACATATAATTGAACATGTTCACGAACAATGTAATAATAAACAAACC
AACAATAAATAAACAATATATATATATTATTTTTTAGATATAAAATAGTCAAATATAAATATTAA
TAATTATATTATAAATAAAAAAGCATACAAACCATAATATAC
Found at i:110972 original size:41 final size:40
Alignment explanation
Indices: 110878--111026 Score: 201
Period size: 41 Copynumber: 3.7 Consensus size: 40
110868 TTTAACATAT
110878 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTAGA
*
110918 TCACCGGCACTTAGCCTGCTAGGTTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT-AGA
* * * **
110959 TCACCGGCACTTAGCCTGCTAGACTTAAAGTCTGAATTATT
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG-ATTAGA
*
111000 TCACCGGC-CTTAAGCCTGCTAGACTTA
1 TCACCGGCACTT-AGCCTGCTAGGCTTA
111027 AAGTCCGAAT
Statistics
Matches: 99, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
40 39 0.39
41 57 0.58
42 3 0.03
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (40 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTAGA
Found at i:119521 original size:9 final size:10
Alignment explanation
Indices: 119501--119525 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
119491 AATATTTTTG
119501 AAATTTTAAA
1 AAATTTTAAA
119511 AAATTTTAAA
1 AAATTTTAAA
119521 AAATT
1 AAATT
119526 AATTAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AAATTTTAAA
Found at i:129457 original size:27 final size:30
Alignment explanation
Indices: 129399--129460 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
129389 ATAAATTATT
* * *
129399 ATAAATTTATTAATATTTTGTAAACATAAA
1 ATAAAATTATTAATATTTTGAAAAAATAAA
129429 ATAAAATT-TTAATATTTT-AAAAAAT-AA
1 ATAAAATTATTAATATTTTGAAAAAATAAA
129456 ATAAA
1 ATAAA
129461 TTAATTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 7 0.24
28 5 0.17
29 10 0.34
30 7 0.24
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (30 bp):
ATAAAATTATTAATATTTTGAAAAAATAAA
Found at i:142219 original size:22 final size:21
Alignment explanation
Indices: 142184--142260 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 21
142174 AAAGGGTATC
* *
142184 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
142205 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
142228 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
142247 TATATATCATATCT
1 TACAAATCATATCT
142261 AAGATTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 17 0.37
21 4 0.09
22 15 0.33
23 10 0.22
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:142227 original size:23 final size:22
Alignment explanation
Indices: 142184--142241 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
142174 AAAGGGTATC
* *
142184 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
142205 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
142228 TGCATATCATATCT
1 TACAAATCATATCT
142242 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:142244 original size:19 final size:19
Alignment explanation
Indices: 142220--142272 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
142210 AATCATATCT
142220 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
142239 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
142258 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
142273 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:142556 original size:19 final size:20
Alignment explanation
Indices: 142524--142561 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
142514 AGGCTTACAT
142524 ATTCTATCAATTTGATCCTA
1 ATTCTATCAATTTGATCCTA
142544 ATTCTAT-AATTTGATCCT
1 ATTCTATCAATTTGATCCT
142562 CAAATTTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.47
Consensus pattern (20 bp):
ATTCTATCAATTTGATCCTA
Found at i:149351 original size:24 final size:23
Alignment explanation
Indices: 149289--149358 Score: 59
Period size: 24 Copynumber: 3.0 Consensus size: 23
149279 ACGTTTTCAG
*
149289 ATGCAATTCAAATACAGATTCAA
1 ATGCAATTCAAATACAGAATCAA
** * * *
149312 ATATAATCTTAGATACAGAATCAT
1 ATGCAAT-TCAAATACAGAATCAA
*
149336 ATGCAATATCAAATACAAAATCA
1 ATGCAAT-TCAAATACAGAATCA
149359 GATCCTATCC
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
23 5 0.15
24 29 0.85
ACGTcount: A:0.50, C:0.16, G:0.07, T:0.27
Consensus pattern (23 bp):
ATGCAATTCAAATACAGAATCAA
Found at i:152949 original size:40 final size:40
Alignment explanation
Indices: 152894--153055 Score: 324
Period size: 40 Copynumber: 4.0 Consensus size: 40
152884 CTTAGTAAGC
152894 TCGTATAACTTAAACTTAAACTTATCGAATAAGTATTTAT
1 TCGTATAACTTAAACTTAAACTTATCGAATAAGTATTTAT
152934 TCGTATAACTTAAACTTAAACTTATCGAATAAGTATTTAT
1 TCGTATAACTTAAACTTAAACTTATCGAATAAGTATTTAT
152974 TCGTATAACTTAAACTTAAACTTATCGAATAAGTATTTAT
1 TCGTATAACTTAAACTTAAACTTATCGAATAAGTATTTAT
153014 TCGTATAACTTAAACTTAAACTTATCGAATAAGTATTTAT
1 TCGTATAACTTAAACTTAAACTTATCGAATAAGTATTTAT
153054 TC
1 TC
153056 AAACCATTCA
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 122 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (40 bp):
TCGTATAACTTAAACTTAAACTTATCGAATAAGTATTTAT
Found at i:169676 original size:37 final size:37
Alignment explanation
Indices: 169619--169746 Score: 177
Period size: 37 Copynumber: 3.5 Consensus size: 37
169609 TGGTGTGTTT
* *
169619 TCGGTTGGACTAGCTTTTATGAGCATCTGGCGAGTTA
1 TCGGGTGGACTAGCTCTTATGAGCATCTGGCGAGTTA
* *
169656 TCGGGTGGACTAGCTCTTATGAGCATCAGGCGTGTTA
1 TCGGGTGGACTAGCTCTTATGAGCATCTGGCGAGTTA
* *
169693 TCAGGTGGATTAGCTCTTATGAGCATCTGGC-ATGTTA
1 TCGGGTGGACTAGCTCTTATGAGCATCTGGCGA-GTTA
*
169730 TCGGGTGGATTAGCTCT
1 TCGGGTGGACTAGCTCT
169747 CACGAGCGTG
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
37 81 1.00
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.34
Consensus pattern (37 bp):
TCGGGTGGACTAGCTCTTATGAGCATCTGGCGAGTTA
Found at i:173455 original size:17 final size:17
Alignment explanation
Indices: 173433--173466 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
173423 GAAAATAGGG
173433 GAAAGAAAGAAGA-AAAA
1 GAAAGAAA-AAGAGAAAA
173450 GAAAGAAAAAGAGAAAA
1 GAAAGAAAAAGAGAAAA
173467 TAGGGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
GAAAGAAAAAGAGAAAA
Found at i:173530 original size:32 final size:32
Alignment explanation
Indices: 173489--173556 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
173479 AGCTTGGAGT
173489 TTAATTTGGTAAGTCAATTAAGCCCTTTTCTC
1 TTAATTTGGTAAGTCAATTAAGCCCTTTTCTC
173521 TTAATTTGGTAAGTCAATTAAGCCCTTTTCTC
1 TTAATTTGGTAAGTCAATTAAGCCCTTTTCTC
173553 TTAA
1 TTAA
173557 GTTCATAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (32 bp):
TTAATTTGGTAAGTCAATTAAGCCCTTTTCTC
Found at i:176167 original size:42 final size:42
Alignment explanation
Indices: 176109--176221 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
176099 ATACGGGAAG
*** *
176109 AGGACAT-GAGCATGTGTCCAGGTTGTGTGAGTCACACGGGCA
1 AGGACATGGAG-ATGTGTCCAGGCCATGTGAGCCACACGGGCA
* * **
176151 AGGACATGGGGGTGTGTTGAGGCCATGTGAGCCACACGGGCA
1 AGGACATGGAGATGTGTCCAGGCCATGTGAGCCACACGGGCA
* *
176193 AGGACATGGAGATGTGTCCAAGCCGTGTG
1 AGGACATGGAGATGTGTCCAGGCCATGTG
176222 GCATATAAAT
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
42 54 0.96
43 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (42 bp):
AGGACATGGAGATGTGTCCAGGCCATGTGAGCCACACGGGCA
Found at i:178313 original size:23 final size:23
Alignment explanation
Indices: 178253--178316 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
178243 TATAAATTTT
* * *
178253 TAAAACATTATTAAAATTTATAAA
1 TAAAA-ATTATTAAAAATAAAAAA
*
178277 T-AAAATTAAATAAAAATAAAAAA
1 TAAAAATT-ATTAAAAATAAAAAA
178300 TAAAAATTATTAAAAAT
1 TAAAAATTATTAAAAAT
178317 CATTTAAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
22 3 0.09
23 23 0.70
24 7 0.21
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAAAATTATTAAAAATAAAAAA
Found at i:178627 original size:19 final size:19
Alignment explanation
Indices: 178589--178627 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
178579 TTTTTTAATG
*
178589 AAAATTTTCAAATTTATTT
1 AAAATTTTAAAATTTATTT
178608 AAAATTTTAATAATTT-TTT
1 AAAATTTTAA-AATTTATTT
178627 A
1 A
178628 CGAATTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
AAAATTTTAAAATTTATTT
Found at i:191684 original size:27 final size:28
Alignment explanation
Indices: 191643--191705 Score: 110
Period size: 27 Copynumber: 2.3 Consensus size: 28
191633 GATGAAATTG
191643 TAAAATCTAACAAAATAGGGGAAAACTA
1 TAAAATCTAACAAAATAGGGGAAAACTA
*
191671 TAAAATCTAA-AAAATAGGGGGAAACTA
1 TAAAATCTAACAAAATAGGGGAAAACTA
191698 TAAAATCT
1 TAAAATCT
191706 GGAAAACAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 24 0.71
28 10 0.29
ACGTcount: A:0.56, C:0.10, G:0.14, T:0.21
Consensus pattern (28 bp):
TAAAATCTAACAAAATAGGGGAAAACTA
Found at i:192886 original size:23 final size:22
Alignment explanation
Indices: 192839--192889 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
192829 ATAAAAATAA
192839 AAATTATAAAAAATCATTAAATT
1 AAATTATAAAAAAT-ATTAAATT
*
192862 AAATTCTAAAAAAT-TTAAAATT
1 AAATTATAAAAAATATT-AAATT
*
192884 TAATTA
1 AAATTA
192890 AAATTGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 9 0.38
23 13 0.54
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATTATAAAAAATATTAAATT
Found at i:192894 original size:18 final size:18
Alignment explanation
Indices: 192871--192914 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
192861 TAAATTCTAA
192871 AAAATTTAAAA-TTTAATT
1 AAAATTTAAAACTTTAA-T
* *
192889 AAAATTGAAAACTTTTAT
1 AAAATTTAAAACTTTAAT
192907 AAAATTTA
1 AAAATTTA
192915 TAAAAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (18 bp):
AAAATTTAAAACTTTAAT
Found at i:196722 original size:34 final size:35
Alignment explanation
Indices: 196656--196730 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 35
196646 TCTTTTAGTT
**
196656 TTTAGGGTTTATGTGTTCACGCAAGATTGAAAGCAG
1 TTTAGGGTTTATGTCATCACG-AAGATTGAAAGCAG
*
196692 TTTAGGGTTTATGTCATCACG-AGATTGAAAGTAG
1 TTTAGGGTTTATGTCATCACGAAGATTGAAAGCAG
196726 TTTAG
1 TTTAG
196731 TATGGAGAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 17 0.47
36 19 0.53
ACGTcount: A:0.28, C:0.09, G:0.27, T:0.36
Consensus pattern (35 bp):
TTTAGGGTTTATGTCATCACGAAGATTGAAAGCAG
Found at i:199418 original size:21 final size:24
Alignment explanation
Indices: 199380--199426 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
199370 GAAGATACAC
199380 ATAATTACTAAATATTT-AAATAAA
1 ATAATTAC-AAATATTTAAAATAAA
199404 ATAATTA-AAAT-TTTAAAATAAA
1 ATAATTACAAATATTTAAAATAAA
199426 A
1 A
199427 AATAATAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 3 0.14
22 12 0.55
24 7 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
ATAATTACAAATATTTAAAATAAA
Found at i:199523 original size:134 final size:135
Alignment explanation
Indices: 199365--199640 Score: 536
Period size: 134 Copynumber: 2.0 Consensus size: 135
199355 GTCATAATAG
199365 TAATAGAAGATACACATAATTACTAAATATTTAAATAAAATAATTAAAATTTTAAAATAAAAAAT
1 TAATAGAAGATACACATAATTACTAAATATTTAAATAAAATAATTAAAATTTTAAAATAAAAAAT
199430 AATAAACAAAATTGAATTATGAATTTAAAACAATGTAAGCTTGATTGGAAGAATCAATCACCTCT
66 AATAAACAAAATTGAATTATGAATTTAAAACAATGTAAGCTTGATTGGAAGAATCAATCACCTCT
199495 ATTTC
131 ATTTC
199500 TAATAGAAGATA-ACATAATTACTAAATATTTAAATAAAATAATTAAAATTTTAAAATAAAAAAT
1 TAATAGAAGATACACATAATTACTAAATATTTAAATAAAATAATTAAAATTTTAAAATAAAAAAT
199564 AATAAACAAAATTGAATTATGAATTTAAAACAATGTAAGCTTGATTGGAAGAATCAATCACCTCT
66 AATAAACAAAATTGAATTATGAATTTAAAACAATGTAAGCTTGATTGGAAGAATCAATCACCTCT
199629 ATTTC
131 ATTTC
199634 TATATAG
1 TA-ATAG
199641 TGTACAGCTG
Statistics
Matches: 140, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
134 124 0.89
135 16 0.11
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (135 bp):
TAATAGAAGATACACATAATTACTAAATATTTAAATAAAATAATTAAAATTTTAAAATAAAAAAT
AATAAACAAAATTGAATTATGAATTTAAAACAATGTAAGCTTGATTGGAAGAATCAATCACCTCT
ATTTC
Found at i:199552 original size:21 final size:24
Alignment explanation
Indices: 199509--199560 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
199499 CTAATAGAAG
*
199509 ATAACATAATTACTAAATATTT-AA
1 ATAAAATAATTAC-AAATATTTAAA
199533 ATAAAATAATTA-AAAT-TTTAAA
1 ATAAAATAATTACAAATATTTAAA
199555 ATAAAA
1 ATAAAA
199561 AATAATAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 3 0.12
22 12 0.46
24 11 0.42
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAAAATAATTACAAATATTTAAA
Found at i:201719 original size:3 final size:3
Alignment explanation
Indices: 201700--201739 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
201690 CCAAAACCAT
*
201700 TCC TCC TTC T-C TCCC TCC TCC TCC TCC TCC TCC TCC TCC T
1 TCC TCC TCC TCC T-CC TCC TCC TCC TCC TCC TCC TCC TCC T
201740 TATCCGTCGC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (3 bp):
TCC
Found at i:212772 original size:9 final size:9
Alignment explanation
Indices: 212760--212790 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
212750 CATAACCTCT
212760 GCAGCAGCG
1 GCAGCAGCG
212769 GCAGCAGCG
1 GCAGCAGCG
212778 GCAGCAGCAG
1 GCAGCAGC-G
212788 GCA
1 GCA
212791 ATACACAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 17 0.81
10 4 0.19
ACGTcount: A:0.26, C:0.32, G:0.42, T:0.00
Consensus pattern (9 bp):
GCAGCAGCG
Found at i:215334 original size:96 final size:96
Alignment explanation
Indices: 215220--215400 Score: 303
Period size: 96 Copynumber: 1.9 Consensus size: 96
215210 AGGGTTTAGG
215220 TTAATTATAAATTTT-AAAAAATTAGATTAGGGTTTAACGTTTAT-GGTTTTTAAGGAAAAAATC
1 TTAATTATAAATTTTAAAAAAATTAGATTAGGGTTTAACGTTT-TGGGTTTTTAAGG-AAAAATC
215283 AAATAAATTAGGGTTTGGGGTTACTTAAGTAAA
64 AAATAAATTAGGGTTTGGGGTTACTTAAGTAAA
**
215316 TTAATTATAAATTTTAAAAAAATTAGATTAGGGTTTAGTGTTTTGGGTTTTTAAGGAAAAATCAA
1 TTAATTATAAATTTTAAAAAAATTAGATTAGGGTTTAACGTTTTGGGTTTTTAAGGAAAAATCAA
*
215381 ATAAATTAGTGTTTGGGGTT
66 ATAAATTAGGGTTTGGGGTT
215401 TAGGGTTACT
Statistics
Matches: 80, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
96 44 0.55
97 36 0.45
ACGTcount: A:0.39, C:0.02, G:0.19, T:0.40
Consensus pattern (96 bp):
TTAATTATAAATTTTAAAAAAATTAGATTAGGGTTTAACGTTTTGGGTTTTTAAGGAAAAATCAA
ATAAATTAGGGTTTGGGGTTACTTAAGTAAA
Found at i:215663 original size:126 final size:126
Alignment explanation
Indices: 215432--215727 Score: 470
Period size: 126 Copynumber: 2.4 Consensus size: 126
215422 TTTGTTAATT
*
215432 TAAAA-AAGCTCCTACGTGGACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAG
1 TAAAAGAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAG
* * * *
215496 ACGTTTCTGAGCAAATAGTGTCAAAAACGTTTTAAGTAGGATGCATTGTTAGCAAAAGTAC
66 ACGTTTCTGAGCAAATAGTGTCAAAAACGTTTCAAGCAGGATGCAATGTCAGCAAAAGTAC
* * *
215557 TAAAAGAAGCTCCCACATGGACGCTCTTTTGCTACAGTTGTTTCTGAAAAAATAATTTTGAGAAG
1 TAAAAGAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAG
215622 ACGTTTCTGAGCAAATAGTGTCAAAAAC-TCTTCAAGCAGGATGCAATGTCAGCAAAAGTAC
66 ACGTTTCTGAGCAAATAGTGTCAAAAACGT-TTCAAGCAGGATGCAATGTCAGCAAAAGTAC
* * *
215683 TGAAAGAAGCTCCCACGTGTACGCTTTTTTGCTACAGTAGTTCCT
1 TAAAAGAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCCT
215728 ATTTGGACTG
Statistics
Matches: 155, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
125 6 0.04
126 149 0.96
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (126 bp):
TAAAAGAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAG
ACGTTTCTGAGCAAATAGTGTCAAAAACGTTTCAAGCAGGATGCAATGTCAGCAAAAGTAC
Found at i:219467 original size:604 final size:604
Alignment explanation
Indices: 218319--219526 Score: 2416
Period size: 604 Copynumber: 2.0 Consensus size: 604
218309 TATATAATCA
218319 AGCAAATGCAACATAACTTGGCATTATTTGCATTACAAATGACAAATTAAACCATTATAATTAAA
1 AGCAAATGCAACATAACTTGGCATTATTTGCATTACAAATGACAAATTAAACCATTATAATTAAA
218384 CATGATAAATATTTAAAATAATTCAAATTTTATTAAGTAAATATACCATAATTTTTGCAGCTTCA
66 CATGATAAATATTTAAAATAATTCAAATTTTATTAAGTAAATATACCATAATTTTTGCAGCTTCA
218449 GTAGTCATAGGAGATCCATATTTCTTTCTATGTGTAATGTCAAAAAGCTGAAGGCATCTAACTTT
131 GTAGTCATAGGAGATCCATATTTCTTTCTATGTGTAATGTCAAAAAGCTGAAGGCATCTAACTTT
218514 TTGACCAGACGACAATTCGTACAATATAGTAGGAAAGATGTTATTTAGTAGAAGGTAATTAATAT
196 TTGACCAGACGACAATTCGTACAATATAGTAGGAAAGATGTTATTTAGTAGAAGGTAATTAATAT
218579 TTGACACAATTAATAAATTCAAAATACCTCATCATCAACTACACAAGCAAAATTTTTCGACCCAG
261 TTGACACAATTAATAAATTCAAAATACCTCATCATCAACTACACAAGCAAAATTTTTCGACCCAG
218644 TAATGTGCGTGAATTTTTATTTTTGCCTACTTGTAGTTCCAACTCGCTCACGGTCCTACATTATT
326 TAATGTGCGTGAATTTTTATTTTTGCCTACTTGTAGTTCCAACTCGCTCACGGTCCTACATTATT
218709 ATTATGTATATAATAAATACTATAAACCGGAATAATTATAAGAGTTTGGAAGTACGTAATACCTC
391 ATTATGTATATAATAAATACTATAAACCGGAATAATTATAAGAGTTTGGAAGTACGTAATACCTC
218774 TCCTTTTTTTGAATTCTAAAATCTAATTGCATCTTCCCATTGGTACCTTAGCATTCCTGGCGGGA
456 TCCTTTTTTTGAATTCTAAAATCTAATTGCATCTTCCCATTGGTACCTTAGCATTCCTGGCGGGA
218839 CATTTCGCAATTTCTCTTCGAAGCTTATATTTTTCTTAAAATATTCTTTTTTTAAAGTACTTTTA
521 CATTTCGCAATTTCTCTTCGAAGCTTATATTTTTCTTAAAATATTCTTTTTTTAAAGTACTTTTA
218904 TGGTCTCTTCAAATATTTG
586 TGGTCTCTTCAAATATTTG
218923 AGCAAATGCAACATAACTTGGCATTATTTGCATTACAAATGACAAATTAAACCATTATAATTAAA
1 AGCAAATGCAACATAACTTGGCATTATTTGCATTACAAATGACAAATTAAACCATTATAATTAAA
218988 CATGATAAATATTTAAAATAATTCAAATTTTATTAAGTAAATATACCATAATTTTTGCAGCTTCA
66 CATGATAAATATTTAAAATAATTCAAATTTTATTAAGTAAATATACCATAATTTTTGCAGCTTCA
219053 GTAGTCATAGGAGATCCATATTTCTTTCTATGTGTAATGTCAAAAAGCTGAAGGCATCTAACTTT
131 GTAGTCATAGGAGATCCATATTTCTTTCTATGTGTAATGTCAAAAAGCTGAAGGCATCTAACTTT
219118 TTGACCAGACGACAATTCGTACAATATAGTAGGAAAGATGTTATTTAGTAGAAGGTAATTAATAT
196 TTGACCAGACGACAATTCGTACAATATAGTAGGAAAGATGTTATTTAGTAGAAGGTAATTAATAT
219183 TTGACACAATTAATAAATTCAAAATACCTCATCATCAACTACACAAGCAAAATTTTTCGACCCAG
261 TTGACACAATTAATAAATTCAAAATACCTCATCATCAACTACACAAGCAAAATTTTTCGACCCAG
219248 TAATGTGCGTGAATTTTTATTTTTGCCTACTTGTAGTTCCAACTCGCTCACGGTCCTACATTATT
326 TAATGTGCGTGAATTTTTATTTTTGCCTACTTGTAGTTCCAACTCGCTCACGGTCCTACATTATT
219313 ATTATGTATATAATAAATACTATAAACCGGAATAATTATAAGAGTTTGGAAGTACGTAATACCTC
391 ATTATGTATATAATAAATACTATAAACCGGAATAATTATAAGAGTTTGGAAGTACGTAATACCTC
219378 TCCTTTTTTTGAATTCTAAAATCTAATTGCATCTTCCCATTGGTACCTTAGCATTCCTGGCGGGA
456 TCCTTTTTTTGAATTCTAAAATCTAATTGCATCTTCCCATTGGTACCTTAGCATTCCTGGCGGGA
219443 CATTTCGCAATTTCTCTTCGAAGCTTATATTTTTCTTAAAATATTCTTTTTTTAAAGTACTTTTA
521 CATTTCGCAATTTCTCTTCGAAGCTTATATTTTTCTTAAAATATTCTTTTTTTAAAGTACTTTTA
219508 TGGTCTCTTCAAATATTTG
586 TGGTCTCTTCAAATATTTG
219527 CTAATGCTTT
Statistics
Matches: 604, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
604 604 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.37
Consensus pattern (604 bp):
AGCAAATGCAACATAACTTGGCATTATTTGCATTACAAATGACAAATTAAACCATTATAATTAAA
CATGATAAATATTTAAAATAATTCAAATTTTATTAAGTAAATATACCATAATTTTTGCAGCTTCA
GTAGTCATAGGAGATCCATATTTCTTTCTATGTGTAATGTCAAAAAGCTGAAGGCATCTAACTTT
TTGACCAGACGACAATTCGTACAATATAGTAGGAAAGATGTTATTTAGTAGAAGGTAATTAATAT
TTGACACAATTAATAAATTCAAAATACCTCATCATCAACTACACAAGCAAAATTTTTCGACCCAG
TAATGTGCGTGAATTTTTATTTTTGCCTACTTGTAGTTCCAACTCGCTCACGGTCCTACATTATT
ATTATGTATATAATAAATACTATAAACCGGAATAATTATAAGAGTTTGGAAGTACGTAATACCTC
TCCTTTTTTTGAATTCTAAAATCTAATTGCATCTTCCCATTGGTACCTTAGCATTCCTGGCGGGA
CATTTCGCAATTTCTCTTCGAAGCTTATATTTTTCTTAAAATATTCTTTTTTTAAAGTACTTTTA
TGGTCTCTTCAAATATTTG
Found at i:235593 original size:21 final size:21
Alignment explanation
Indices: 235563--235602 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
235553 TAACGCGCAC
*
235563 TTCATTAAAAATTCAAAAATG
1 TTCATAAAAAATTCAAAAATG
* *
235584 TTCATAAAAATTTTAAAAA
1 TTCATAAAAAATTCAAAAA
235603 CTATCTATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (21 bp):
TTCATAAAAAATTCAAAAATG
Found at i:238648 original size:129 final size:130
Alignment explanation
Indices: 238499--238763 Score: 516
Period size: 129 Copynumber: 2.1 Consensus size: 130
238489 ATATAAATAT
238499 ATAT-TTTTTACTTTTTTTTAAATAATATGGGCAAGTCTAAAATGAATTTAAGTTAGCCATTTAC
1 ATATGTTTTTACTTTTTTTTAAATAATATGGGCAAGTCTAAAATGAATTTAAGTTAGCCATTTAC
238563 AAATATAAATGAACTTGGGCAAAATTTTAAACTCATATTTCTGGTCGGGTTTGGGCAAGCATAAA
66 AAATATAAATGAACTTGGGCAAAATTTTAAACTCATATTTCTGGTCGGGTTTGGGCAAGCATAAA
238628 ATATGTTTTTAC-TTTTTTTAAATAATATGGGCAAGTCTAAAATGAATTTAAGTTAGCCATTTAC
1 ATATGTTTTTACTTTTTTTTAAATAATATGGGCAAGTCTAAAATGAATTTAAGTTAGCCATTTAC
238692 AAATATAAATGAACTTGGGCAAAATTTTAAACTCATATTTCTGGTCGGGTTTGGGCAAGCATAAA
66 AAATATAAATGAACTTGGGCAAAATTTTAAACTCATATTTCTGGTCGGGTTTGGGCAAGCATAAA
238757 ATATGTT
1 ATATGTT
238764 AATATATAGG
Statistics
Matches: 135, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
129 128 0.95
130 7 0.05
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (130 bp):
ATATGTTTTTACTTTTTTTTAAATAATATGGGCAAGTCTAAAATGAATTTAAGTTAGCCATTTAC
AAATATAAATGAACTTGGGCAAAATTTTAAACTCATATTTCTGGTCGGGTTTGGGCAAGCATAAA
Found at i:240172 original size:83 final size:83
Alignment explanation
Indices: 240010--240169 Score: 209
Period size: 83 Copynumber: 2.0 Consensus size: 83
240000 CTTTAACCAA
* ** **
240010 GATTCAATTGTTAAATAAATCTTTTATAAATATATTTTGGCATAAATATTGTCAAAAAGTCCTTG
1 GATTCAATTGTTAAATAAATATTTTATAAATATATTTTAACATAAATATCCTCAAAAAGTCCTTG
*
240075 TTAAATAATTAAAAATAG
66 TAAAATAATTAAAAATAG
* * * *
240093 GATTCAATTTTTAAATAAATATTTTATAAATTTATTTTAACAT-AA-ATCCT-AAAAATTTCTTG
1 GATTCAATTGTTAAATAAATATTTTATAAATATATTTTAACATAAATATCCTCAAAAAGTCCTTG
240155 TAAAATAATTAAAAA
66 TAAAATAATTAAAAA
240170 AAAATTAATT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
80 24 0.36
81 3 0.04
82 2 0.03
83 38 0.57
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (83 bp):
GATTCAATTGTTAAATAAATATTTTATAAATATATTTTAACATAAATATCCTCAAAAAGTCCTTG
TAAAATAATTAAAAATAG
Found at i:257510 original size:15 final size:15
Alignment explanation
Indices: 257490--257541 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
257480 GGTGGTGCAG
*
257490 CTCCTCCGCCACCAC
1 CTCCTCCACCACCAC
* *
257505 CTCCTCCTCCTCCAC
1 CTCCTCCACCACCAC
257520 CTCCTCCACCACCAC
1 CTCCTCCACCACCAC
*
257535 CCCCTCC
1 CTCCTCC
257542 TCCTGCCATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.12, C:0.69, G:0.02, T:0.17
Consensus pattern (15 bp):
CTCCTCCACCACCAC
Found at i:268280 original size:44 final size:44
Alignment explanation
Indices: 268187--268286 Score: 119
Period size: 44 Copynumber: 2.3 Consensus size: 44
268177 GTAGAGCAAG
*
268187 ATGAAGCTACAAATCCTATATCCCTGAAGCAGCAATGGATCAGA
1 ATGAAGCTACAAATCCTATACCCCTGAAGCAGCAATGGATCAGA
* * ** * * **
268231 TTGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTTGGA
1 ATGAAGCTACAAATCCTATACCCCTGAAGCAGCAATGGATCAGA
268275 ATGAAGCTACAA
1 ATGAAGCTACAA
268287 CTACAAATCT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (44 bp):
ATGAAGCTACAAATCCTATACCCCTGAAGCAGCAATGGATCAGA
Found at i:268416 original size:187 final size:185
Alignment explanation
Indices: 268144--268612 Score: 577
Period size: 187 Copynumber: 2.5 Consensus size: 185
268134 GGATTGAAGT
* *
268144 TACCATAACGAATCTTATCTCCTTGAAGTTGTAGTAGAGCAAGATGAAGCTACAAATCCTATATC
1 TACCATAGCGAATCTTATCTCCTTGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCCTATATC
** * * *
268209 CCTGAAGCAGCAATGGATCAGATTGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTTGG
66 CCTGAAGTTGCAGTGGATCAGATTGAAGCTACAATTCCTATACCCCTGAAGTTGCAATAGGTTGG
* * * *
268274 AATGAAGCTACAACTACAAATCTTATACCCCTAAAGTTGCAGTAGGCCGAGTCGAATC
131 AATAAAGCTACAACTACAAATCATATACCCCTAAAGTTGC-G--GGCCGAATCGAAAC
* * *
268332 TACCATAGC-ATATC-TATCTCCCTGAAGTTGTAGTGGAGCAAGATAAAGCTACAAATCCTACAT
1 TACCATAGCGA-ATCTTATCTCCTTGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCCTATAT
* * **
268395 CCCTGAAGTTGTAGTGGATCAGATTGAAGCTACAATTTCTATACCTTTGAAGTTGCAATAGGTTG
65 CCCTGAAGTTGCAGTGGATCAGATTGAAGCTACAATTCCTATACCCCTGAAGTTGCAATAGGTTG
* * * * ** *
268460 GAATAAAGTTGCAACTACAAATCATATACCCTTGAAGTTGCGGGTTGAATTGAAAC
130 GAATAAAGCTACAACTACAAATCATATACCCCTAAAGTTGCGGGCCGAATCGAAAC
* * * *
268516 TACCATAGCGAATCTTATCTCCTTGAAGTTGCAGTGGAACATA-TTGAAGCTACAAATCCTATAC
1 TACCATAGCGAATCTTATCTCCTTGAAGTTGTAGTGGAGCA-AGATGAAGCTACAAATCCTATAT
* *
268580 CCCTGAAGTTGCAGTAGG-TCGGATTGAATCTAC
65 CCCTGAAGTTGCAGT-GGATCAGATTGAAGCTAC
268613 CATAGCAAAT
Statistics
Matches: 241, Mismatches: 35, Indels: 13
0.83 0.12 0.04
Matches are distributed among these distances:
184 21 0.09
185 68 0.28
186 4 0.02
187 137 0.57
188 11 0.05
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (185 bp):
TACCATAGCGAATCTTATCTCCTTGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCCTATATC
CCTGAAGTTGCAGTGGATCAGATTGAAGCTACAATTCCTATACCCCTGAAGTTGCAATAGGTTGG
AATAAAGCTACAACTACAAATCATATACCCCTAAAGTTGCGGGCCGAATCGAAAC
Found at i:268606 original size:44 final size:43
Alignment explanation
Indices: 268539--268740 Score: 147
Period size: 44 Copynumber: 4.4 Consensus size: 43
268529 CTTATCTCCT
* *
268539 TGAAGTTGCAGTGGAACATATTGAAGCTACAAATCCTATACCCC
1 TGAAGTTGCAGTGG-TCAGATTGAAGCTACAAATCCTATACCCC
* * * **
268583 TGAAGTTGCAGTAGGTCGGATTGAATCTACCATAGCAAATCTTAT-CTTTC
1 TGAAGTTGCAGT-GGTCAGATTG-A---AGC-TA-CAAATCCTATAC-CCC
* * *
268633 TAAAGTTGCAGTGGAGCAAGA-TGAAGCTACAAATCCTATATCCC
1 TGAAGTTGCAGTGG-TC-AGATTGAAGCTACAAATCCTATACCCC
* ** *
268677 TGAAGTTGCAGTTGATTGGATTGAAGCTACAATTCCTATACCCC
1 TGAAGTTGCAG-TGGTCAGATTGAAGCTACAAATCCTATACCCC
268721 TGAAGTTGCAGTGGGTCAGA
1 TGAAGTTGCAGT-GGTCAGA
268741 ATACAAACTA
Statistics
Matches: 119, Mismatches: 25, Indels: 28
0.69 0.15 0.16
Matches are distributed among these distances:
43 3 0.03
44 73 0.61
45 7 0.06
46 2 0.02
48 2 0.02
49 6 0.05
50 24 0.20
51 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (43 bp):
TGAAGTTGCAGTGGTCAGATTGAAGCTACAAATCCTATACCCC
Found at i:268628 original size:94 final size:92
Alignment explanation
Indices: 268100--268706 Score: 334
Period size: 94 Copynumber: 6.5 Consensus size: 92
268090 AATAAAACAG
* ** * * * * *
268100 TACAAATTCTATACCTTTAAAGTTGTAGTGGGTCGGATTGAAGTTACCATAACGAATCTTATCTC
1 TACAAATCCTATACCCCTGAAGTTGCAGT-GGTCGGATTGAAGCTACCATAGCAAATC-TATCTC
* * *
268165 CTTGAAGTTGTAGTAGAGCAAGATGAAGC
64 CTTGAAGTTGCAGTGGAACAAGATGAAGC
* ** * * * *
268194 TACAAATCCTATATCCCTGAAGCAGCAATGGATCAGATTGAAGCTACAAT-TC----CTATAC-C
1 TACAAATCCTATACCCCTGAAGTTGCAGTGG-TCGGATTGAAGCTACCATAGCAAATCTAT-CTC
* * * *
268253 CCTGAAGTTGCAGTGGGTTGGAATGAAGCT-ACAAC
64 CTTGAAGTTGCA----G-TGGAA-CAAGATGA-AGC
* * * * * *
268288 TACAAATCTTATACCCCTAAAGTTGCAGTAGG-CCGAGTCGAATCTACCATAGCATATCTATCTC
1 TACAAATCCTATACCCCTGAAGTTGCAGT-GGTCGGA-TTGAAGCTACCATAGCAAATCTATCTC
* * * *
268352 CCTGAAGTTGTAGTGGAGCAAGATAAAGC
64 CTTGAAGTTGCAGTGGAACAAGATGAAGC
* * * * **
268381 TACAAATCCTACATCCCTGAAGTTGTAGTGGATCAGATTGAAGCTA-C--A--ATTTCTATAC-C
1 TACAAATCCTATACCCCTGAAGTTGCAGTGG-TCGGATTGAAGCTACCATAGCAAATCTAT-CTC
* * *
268440 TTTGAAGTTGCAATAGGTTGGAATAAAGTTGCAA-C
64 CTTGAAGTTGC---A-G-TGGAA-CAAGATG-AAGC
* * * * * *
268475 TACAAATCATATACCCTTGAAGTTGC-G-GGTTGAATTGAAACTACCATAGCGAATCTTATCTCC
1 TACAAATCCTATACCCCTGAAGTTGCAGTGGTCGGATTGAAGCTACCATAGCAAATC-TATCTCC
*
268538 TTGAAGTTGCAGTGGAACATA-TTGAAGC
65 TTGAAGTTGCAGTGGAACA-AGATGAAGC
*
268566 TACAAATCCTATACCCCTGAAGTTGCAGTAGGTCGGATTGAATCTACCATAGCAAATCTTATCT-
1 TACAAATCCTATACCCCTGAAGTTGCAGT-GGTCGGATTGAAGCTACCATAGCAAATC-TATCTC
* * *
268630 TTCTAAAGTTGCAGTGGAGCAAGATGAAGC
64 CT-TGAAGTTGCAGTGGAACAAGATGAAGC
* * *
268660 TACAAATCCTATATCCCTGAAGTTGCAGTTGATTGGATTGAAGCTAC
1 TACAAATCCTATACCCCTGAAGTTGCAG-TGGTCGGATTGAAGCTAC
268707 AATTCCTATA
Statistics
Matches: 390, Mismatches: 80, Indels: 86
0.70 0.14 0.15
Matches are distributed among these distances:
88 30 0.08
89 3 0.01
90 3 0.01
91 40 0.10
92 15 0.04
93 55 0.14
94 203 0.52
95 7 0.02
96 3 0.01
97 14 0.04
98 1 0.00
99 16 0.04
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (92 bp):
TACAAATCCTATACCCCTGAAGTTGCAGTGGTCGGATTGAAGCTACCATAGCAAATCTATCTCCT
TGAAGTTGCAGTGGAACAAGATGAAGC
Found at i:268817 original size:139 final size:138
Alignment explanation
Indices: 268234--268845 Score: 381
Period size: 139 Copynumber: 4.4 Consensus size: 138
268224 GATCAGATTG
* * ** * *
268234 AAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTTGGAATGAAGCTACAACTACAAATCTTA
1 AAGCTACAAATCCTATACCCCTGAAGTTGCAGTGTGTCAGATTGAAG------CTACAAATCCTA
* * * * * * ** *
268299 TACCCCTAAAGTTGCAGTAGGCCGAGT-CGAATCTACCATAGCATATC-TATCTCCCTGAAGTTG
60 TACCCCTGAAGTTGCAGTAGGTCGAATAC-AAACTACAATAGCAAATCTTATCTATCTAAAGTTG
* *
268362 TAGTGGAGCAAGATA
124 CAATGGAGCAAGATA
* * * * * *
268377 AAGCTACAAATCCTACATCCCTGAAGTTGTAGTG-GATCAGATTGAAGCTACAATTTCTATACCT
1 AAGCTACAAATCCTATACCCCTGAAGTTGCAGTGTG-TCAGATTGAAGCTACAAATCCTATACCC
* * * ** * * ** *
268441 TTGAAGTTGCAATAGGTTGGAATA-AAGTTGCAACTA-CAAATCATATACCCT-TGAAGTTGC--
65 CTGAAGTTGCAGTAGG-TCGAATACAAACTACAA-TAGCAAATCTTAT-CTATCTAAAGTTGCAA
* *
268501 GGGTTG-AATTGA-A
127 TGG-AGCAA--GATA
* * * * * *
268514 ACTACCATAGCGAATCTTAT-CTCCTTGAAGTTGCAGTG-GAACATATTGAAGCTACAAATCCTA
1 A--AGC-TA-CAAATCCTATAC-CCCTGAAGTTGCAGTGTG-TCAGATTGAAGCTACAAATCCTA
* ** * * *
268577 TACCCCTGAAGTTGCAGTAGGTCGGATTGAATCTACCATAGCAAATCTTATCTTTCTAAAGTTGC
60 TACCCCTGAAGTTGCAGTAGGTCGAATACAAACTACAATAGCAAATCTTATCTATCTAAAGTTGC
* *
268642 AGTGGAGCAAGATG
125 AATGGAGCAAGATA
* ** *
268656 AAGCTACAAATCCTATATCCCTGAAGTTGCAGT-TGATTGGATTGAAGCTACAATTCCTATACCC
1 AAGCTACAAATCCTATACCCCTGAAGTTGCAGTGTG-TCAGATTGAAGCTACAAATCCTATACCC
* * * *
268720 CTGAAGTTGCAGTGGGTCAGAATACAAACTACAAT-GACGAATCTTATCTCAT-TGAGGTTGCAA
65 CTGAAGTTGCAGTAGGTC-GAATACAAACTACAATAG-CAAATCTTATCT-ATCTAAAGTTGCAA
268783 TGGAGCAAGATA
127 TGGAGCAAGATA
*
268795 AAGCTACAAATCCTATGCCCCTGAAGTTGCAGTGTGTCAGATTGAAGCTAC
1 AAGCTACAAATCCTATACCCCTGAAGTTGCAGTGTGTCAGATTGAAGCTAC
268846 CATAGCGAAT
Statistics
Matches: 361, Mismatches: 81, Indels: 58
0.72 0.16 0.12
Matches are distributed among these distances:
136 4 0.01
137 39 0.11
138 83 0.23
139 91 0.25
140 15 0.04
141 84 0.23
142 3 0.01
143 42 0.12
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (138 bp):
AAGCTACAAATCCTATACCCCTGAAGTTGCAGTGTGTCAGATTGAAGCTACAAATCCTATACCCC
TGAAGTTGCAGTAGGTCGAATACAAACTACAATAGCAAATCTTATCTATCTAAAGTTGCAATGGA
GCAAGATA
Found at i:268984 original size:94 final size:93
Alignment explanation
Indices: 268698--268984 Score: 313
Period size: 94 Copynumber: 3.0 Consensus size: 93
268688 TTGATTGGAT
* * *
268698 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCAGAATACAAACTACAATGACGAATC
1 TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCAGAAT-GAAACTACAAAG-CGAATC
* *
268763 TTATCTCATTGAGGTTGCAATGGAGCAAGA
64 TTATCTCCTTGAAGTTGCAATGGAGCAAGA
* * * * * *
268793 TAAAGCTACAAATCCTATGCCCCTGAAGTTGCAGTGTGTCAGATTGAAGCTACCATAGCGAATCT
1 TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTA-CAAAGCGAATCT
* * * * * *
268858 TACCTCCCTAAAGTTGCAGTGGAGTAAAA
65 TATCTCCTTGAAGTTGCAATGGAGCAAGA
* * * * ** *
268887 TGAAGATACAAATCCTATATCCTTGAAGTTACAGTGGGTTGGAATGAAACTACAACAGCAAATCT
1 TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTACAA-AGCGAATCT
*
268952 TATCTCCTTGAAGTTGCAATAGAGCAAGA
65 TATCTCCTTGAAGTTGCAATGGAGCAAGA
268981 TGAA
1 TGAA
268985 ACTGTGCCAC
Statistics
Matches: 153, Mismatches: 37, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
93 2 0.01
94 108 0.71
95 43 0.28
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (93 bp):
TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTACAAAGCGAATCTT
ATCTCCTTGAAGTTGCAATGGAGCAAGA
Found at i:270550 original size:20 final size:21
Alignment explanation
Indices: 270515--270555 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
270505 TACTTTTATC
270515 TTTGATTTATTATCATTATTA
1 TTTGATTTATTATCATTATTA
*
270536 TTTGATTT-TTTTCATTATTA
1 TTTGATTTATTATCATTATTA
270556 AATATGGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (21 bp):
TTTGATTTATTATCATTATTA
Found at i:280940 original size:21 final size:21
Alignment explanation
Indices: 280916--281059 Score: 85
Period size: 21 Copynumber: 6.9 Consensus size: 21
280906 TCTCACGAGC
*
280916 TTCTGTTTAACTCATATGAGT
1 TTCTGTTTAACTCTTATGAGT
* * * *
280937 TTCTGTTAAACCCTAATGGGT
1 TTCTGTTTAACTCTTATGAGT
* * * *
280958 TTCCGTTCAGCTC-TATTGAGC
1 TTCTGTTTAACTCTTA-TGAGT
* * *
280979 TTCTGTTTAACCCTTACGGGT
1 TTCTGTTTAACTCTTATGAGT
* * *
281000 TTCTGTTCAGCTCTTATGAGC
1 TTCTGTTTAACTCTTATGAGT
* *
281021 TTCCGTTTAACCCTTAT-AGGT
1 TTCTGTTTAACTCTTATGA-GT
* *
281042 TTCTGTTTAGCACTTATG
1 TTCTGTTTAACTCTTATG
281060 TGATTTTGTT
Statistics
Matches: 86, Mismatches: 33, Indels: 7
0.68 0.26 0.06
Matches are distributed among these distances:
20 2 0.02
21 82 0.95
22 2 0.02
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.43
Consensus pattern (21 bp):
TTCTGTTTAACTCTTATGAGT
Found at i:281000 original size:42 final size:42
Alignment explanation
Indices: 280930--281059 Score: 145
Period size: 42 Copynumber: 3.1 Consensus size: 42
280920 GTTTAACTCA
* * * *
280930 TATGAGTTTCTGTTAAACCCTAATGGGTTTCCGTTCAGCTC-
1 TATGAGCTTCTGTTTAACCCTTACGGGTTTCCGTTCAGCTCT
*
280971 TATTGAGCTTCTGTTTAACCCTTACGGGTTTCTGTTCAGCTCT
1 TA-TGAGCTTCTGTTTAACCCTTACGGGTTTCCGTTCAGCTCT
* ** * * *
281014 TATGAGCTTCCGTTTAACCCTTATAGGTTTCTGTTTAGCACT
1 TATGAGCTTCTGTTTAACCCTTACGGGTTTCCGTTCAGCTCT
281056 TATG
1 TATG
281060 TGATTTTGTT
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
41 2 0.03
42 73 0.95
43 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (42 bp):
TATGAGCTTCTGTTTAACCCTTACGGGTTTCCGTTCAGCTCT
Found at i:281025 original size:63 final size:63
Alignment explanation
Indices: 280894--281027 Score: 144
Period size: 63 Copynumber: 2.1 Consensus size: 63
280884 TCGTGTTTAC
* * * *
280894 CTTCCGTTTAGCTCTCACGAGCTTCTGTTTAACTCATATGAGTTTCTGTTAAACCCTAATGGG
1 CTTCCGTTCAGCTCTCACGAGCTTCTGTTTAACCCATACGAGTTTCTGTTAAACCCTAATGAG
* * * * * * * *
280957 TTTCCGTTCAGCTCT-ATTGAGCTTCTGTTTAACCCTTACGGGTTTCTGTTCAGCTCTTATGAG
1 CTTCCGTTCAGCTCTCA-CGAGCTTCTGTTTAACCCATACGAGTTTCTGTTAAACCCTAATGAG
281020 CTTCCGTT
1 CTTCCGTT
281028 TAACCCTTAT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
62 1 0.02
63 56 0.98
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (63 bp):
CTTCCGTTCAGCTCTCACGAGCTTCTGTTTAACCCATACGAGTTTCTGTTAAACCCTAATGAG
Found at i:286154 original size:18 final size:18
Alignment explanation
Indices: 286131--286166 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
286121 ACAATTAGAT
286131 AGTTACTATTCACACTCA
1 AGTTACTATTCACACTCA
*
286149 AGTTACTATTTACACTCA
1 AGTTACTATTCACACTCA
286167 CACTCACACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (18 bp):
AGTTACTATTCACACTCA
Found at i:295626 original size:31 final size:31
Alignment explanation
Indices: 295588--295650 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
295578 AATACACTTA
*
295588 AATAATGTTTATTAAATAACATCCAAATGCT
1 AATAATGTCTATTAAATAACATCCAAATGCT
295619 AATAATGTCTATTAAATAACATCCAAATGCT
1 AATAATGTCTATTAAATAACATCCAAATGCT
295650 A
1 A
295651 GTTACTTGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.33
Consensus pattern (31 bp):
AATAATGTCTATTAAATAACATCCAAATGCT
Found at i:299490 original size:31 final size:31
Alignment explanation
Indices: 299417--299490 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
299407 TTTCAAAGTA
* * *
299417 TTTCTCAACTTGTTTTGATTTGATTAGAAGG
1 TTTCTAAACTTTTTTTGATTTGATTAAAAGG
299448 TTTCTAAACTTTTTTTGATTTGATTAAAAGG
1 TTTCTAAACTTTTTTTGATTTGATTAAAAGG
299479 TTTCTAAACTTT
1 TTTCTAAACTTT
299491 CCTTAAAGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (31 bp):
TTTCTAAACTTTTTTTGATTTGATTAAAAGG
Found at i:310348 original size:2 final size:2
Alignment explanation
Indices: 310341--310369 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
310331 AGCATCCTTT
310341 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
310370 TCATAAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:312406 original size:17 final size:17
Alignment explanation
Indices: 312384--312421 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
312374 TATGTACACC
*
312384 AAATATTCGAATTAAAA
1 AAATATTCAAATTAAAA
*
312401 AAATATTCAAATTATAA
1 AAATATTCAAATTAAAA
312418 AAAT
1 AAAT
312422 CAACTTAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (17 bp):
AAATATTCAAATTAAAA
Found at i:312986 original size:21 final size:21
Alignment explanation
Indices: 312962--313002 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
312952 TCAAAACAAC
312962 ATAGTTTT-ACCTTTTAACTTG
1 ATAGTTTTGA-CTTTTAACTTG
312983 ATAGTTTTGACTTTTAACTT
1 ATAGTTTTGACTTTTAACTT
313003 TAGAAAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.54
Consensus pattern (21 bp):
ATAGTTTTGACTTTTAACTTG
Found at i:313357 original size:19 final size:19
Alignment explanation
Indices: 313336--313378 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
313326 TTTTTAAAAA
313336 TTTATAATTTTAAAAATTAT
1 TTTA-AATTTTAAAAATTAT
*
313356 TTTCAAATTTTGAAAATTAT
1 TTT-AAATTTTAAAAATTAT
313376 TTT
1 TTT
313379 GATTTTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTAAATTTTAAAAATTAT
Found at i:313386 original size:20 final size:20
Alignment explanation
Indices: 313341--313378 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
313331 AAAAATTTAT
313341 AATTTTAAAAATTATTTTCA
1 AATTTTAAAAATTATTTTCA
*
313361 AATTTTGAAAATTATTTT
1 AATTTTAAAAATTATTTT
313379 GATTTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
AATTTTAAAAATTATTTTCA
Found at i:317535 original size:101 final size:102
Alignment explanation
Indices: 317404--317615 Score: 354
Period size: 103 Copynumber: 2.1 Consensus size: 102
317394 AAACATTTAA
* * *
317404 TTAATTAAATAAAATTTTGTTTCGATGATTTATCTATTTTTTAACTTACATA-ATTTTTATTTAA
1 TTAATTAAATAAAATTTTATTTAGATGATTTATCTATTTTTTAACTTAAATACATTTTTATTTAA
*
317468 ATATTTTCTATATTACTATTTATTTTAAATTTTGGTT
66 ATATTATCTATATTACTATTTATTTTAAATTTTGGTT
*
317505 TTAATTAAATAAAATTTTATTTAGATGATTTATCTATTTTTTAACTTAAATACTTTTTTTATTTA
1 TTAATTAAATAAAATTTTATTTAGATGATTTATCTATTTTTTAACTTAAATAC-ATTTTTATTTA
*
317570 TATATTATCTATATTACTATTTATTTTAAATTTTGGTT
65 AATATTATCTATATTACTATTTATTTTAAATTTTGGTT
317608 TTAATTAA
1 TTAATTAA
317616 TATTGAATTT
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
101 49 0.48
103 54 0.52
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (102 bp):
TTAATTAAATAAAATTTTATTTAGATGATTTATCTATTTTTTAACTTAAATACATTTTTATTTAA
ATATTATCTATATTACTATTTATTTTAAATTTTGGTT
Found at i:318098 original size:24 final size:24
Alignment explanation
Indices: 318070--318121 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
318060 TTTCTAGAAG
* *
318070 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTAGTAGTATAATAT
*
318094 ATTTAGCATTTAGTAGTATAATTT
1 ATTTAGCATTTAGTAGTATAATAT
318118 ATTT
1 ATTT
318122 GACCTACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTAGTAGTATAATAT
Found at i:320543 original size:12 final size:12
Alignment explanation
Indices: 320522--320574 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
320512 ATTTTTAACA
*
320522 TTAAAACATACT
1 TTAAATCATACT
*
320534 TTAAATCATATT
1 TTAAATCATACT
* *
320546 TTATTTATTATACT
1 TTA--AATCATACT
320560 TTAAATCATACT
1 TTAAATCATACT
320572 TTA
1 TTA
320575 GATTTGATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
12 23 0.72
14 9 0.28
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (12 bp):
TTAAATCATACT
Found at i:320899 original size:113 final size:113
Alignment explanation
Indices: 320763--320983 Score: 433
Period size: 113 Copynumber: 2.0 Consensus size: 113
320753 AAATTTTTAA
320763 AAAAAATTAATTTATCTAGTAACTAAAAAATAATCAGTAACTCTTATATAATATTTTCAAGAATA
1 AAAAAATTAATTTATCTAGTAACTAAAAAATAATCAGTAACTCTTATATAATATTTTCAAGAATA
320828 AATTTTTGCAATGGAAATATAAAGTTGTTTTGACTATTTTTATTTTTT
66 AATTTTTGCAATGGAAATATAAAGTTGTTTTGACTATTTTTATTTTTT
*
320876 AAAAAATTAATTTATCTATTAACTAAAAAATAATCAGTAACTCTTATATAATATTTTCAAGAATA
1 AAAAAATTAATTTATCTAGTAACTAAAAAATAATCAGTAACTCTTATATAATATTTTCAAGAATA
320941 AATTTTTGCAATGGAAATATAAAGTTGTTTTGACTATTTTTAT
66 AATTTTTGCAATGGAAATATAAAGTTGTTTTGACTATTTTTAT
320984 AACGACCCCA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 107 1.00
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (113 bp):
AAAAAATTAATTTATCTAGTAACTAAAAAATAATCAGTAACTCTTATATAATATTTTCAAGAATA
AATTTTTGCAATGGAAATATAAAGTTGTTTTGACTATTTTTATTTTTT
Found at i:325071 original size:68 final size:68
Alignment explanation
Indices: 324754--325072 Score: 298
Period size: 68 Copynumber: 4.7 Consensus size: 68
324744 TGTCCTAGTG
* *
324754 GACTTCATATGTTGTCATAGCCCAGCTATGGTCTTACACGATATAG-AGCCATGTTTACTATCCT
1 GACTTCATATGTTGCCATAGCCCAGCTATGGTCTTACACGATATGGTA-CCATGTTTACTATCCT
324818 GGCA
65 GGCA
* * * * * * * ** * * *
324822 AAATTCATATATTTCTATAGCCCAACTATGGTCTTACACAATATGGTGTCATGTTAACTATCTTA
1 GACTTCATATGTTGCCATAGCCCAGCTATGGTCTTACACGATATGGTACCATGTTTACTATCCTG
* *
324887 ACG
66 GCA
* * * * * * * *
324890 GGCTTCATATGTTGCCATATCCCAGCTATAGTCTTACAGGATATAGTATCATGTTTACTGTCTTG
1 GACTTCATATGTTGCCATAGCCCAGCTATGGTCTTACACGATATGGTACCATGTTTACTATCCTG
**
324955 GTG
66 GCA
* * * * * * *
324958 GACTTCATATGTTGCAATAACCCAGCTATGGTTTTACATGATATGGTACCATGTTTATTGTCCTC
1 GACTTCATATGTTGCCATAGCCCAGCTATGGTCTTACACGATATGGTACCATGTTTACTATCCTG
325023 GCA
66 GCA
* * *
325026 GACTTTATATGTTGCCATAGCCCAGCTATGGTTTTACACGGTATGGT
1 GACTTCATATGTTGCCATAGCCCAGCTATGGTCTTACACGATATGGT
325073 GTTGTGCACC
Statistics
Matches: 198, Mismatches: 52, Indels: 2
0.79 0.21 0.01
Matches are distributed among these distances:
68 198 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (68 bp):
GACTTCATATGTTGCCATAGCCCAGCTATGGTCTTACACGATATGGTACCATGTTTACTATCCTG
GCA
Found at i:328306 original size:22 final size:21
Alignment explanation
Indices: 328281--328353 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 21
328271 TGCTGAGCGA
*
328281 TAGGCATCGAAGTGCGAATTAG
1 TAGGCA-CGTAGTGCGAATTAG
* *
328303 TAGGCACTGTAGAGCAAATTAG
1 TAGGCAC-GTAGTGCGAATTAG
* *
328325 TAGGCACCGTACTGCGAATCAG
1 TAGGCA-CGTAGTGCGAATTAG
328347 TAGGCAC
1 TAGGCAC
328354 CATAGTGAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.05
22 39 0.93
23 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.21
Consensus pattern (21 bp):
TAGGCACGTAGTGCGAATTAG
Found at i:328354 original size:22 final size:22
Alignment explanation
Indices: 328293--328354 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
328283 GGCATCGAAG
* *
328293 TGCGAATTAGTAGGCACTGTAG
1 TGCGAATTAGTAGGCACCGTAC
* *
328315 AGCAAATTAGTAGGCACCGTAC
1 TGCGAATTAGTAGGCACCGTAC
*
328337 TGCGAATCAGTAGGCACC
1 TGCGAATTAGTAGGCACC
328355 ATAGTGAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (22 bp):
TGCGAATTAGTAGGCACCGTAC
Found at i:330313 original size:25 final size:25
Alignment explanation
Indices: 330267--330325 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
330257 TCTCATCATT
330267 AATGTGCCATATCACAAGCCAAAACA
1 AATG-GCCATATCACAAGCCAAAACA
*
330293 AATGGCCATTTCAACAA-CCAAAACA
1 AATGGCCATATC-ACAAGCCAAAACA
*
330318 CATGGCCA
1 AATGGCCA
330326 ACAATAGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 22 0.73
26 8 0.27
ACGTcount: A:0.44, C:0.29, G:0.12, T:0.15
Consensus pattern (25 bp):
AATGGCCATATCACAAGCCAAAACA
Found at i:330919 original size:25 final size:25
Alignment explanation
Indices: 330885--330949 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
330875 TCCTGCACAT
*
330885 GTATGCTCTCACGAGCTGTAAATCG
1 GTATGCTCTCACAAGCTGTAAATCG
330910 GTATGCTCTCACAAGCTGTAAATCG
1 GTATGCTCTCACAAGCTGTAAATCG
* *
330935 GTATACTCTTACAAG
1 GTATGCTCTCACAAG
330950 TTGTGGGTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (25 bp):
GTATGCTCTCACAAGCTGTAAATCG
Found at i:331166 original size:2 final size:2
Alignment explanation
Indices: 331159--331193 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
331149 AATCGGTATC
331159 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
331194 GACATTTCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:334349 original size:19 final size:17
Alignment explanation
Indices: 334326--334383 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 17
334316 TATTTTTTAT
334326 ATATTGTATATGATATGA
1 ATATT-TATATGATATGA
334344 ATTATTCTATATGATATTGA
1 A-TATT-TATATGATA-TGA
*
334364 ATATTTATAT-ATATGT
1 ATATTTATATGATATGA
334380 ATAT
1 ATAT
334384 GAATTGATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
16 6 0.17
17 3 0.08
18 6 0.17
19 17 0.47
20 4 0.11
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (17 bp):
ATATTTATATGATATGA
Found at i:334374 original size:20 final size:19
Alignment explanation
Indices: 334327--334421 Score: 64
Period size: 22 Copynumber: 4.6 Consensus size: 19
334317 ATTTTTTATA
*
334327 TATTGTATATGATATGAAT
1 TATTATATATGATATGAAT
*
334346 TATTCTATATGATATTGAAT
1 TATTATATATGATA-TGAAT
*
334366 ATTTATATATATGTATATGAAT
1 -TAT-TATATATG-ATATGAAT
* * *
334388 TGATGATAAAATGAAATGAGAT
1 T-ATTAT-ATATGATATGA-AT
*
334410 TATGATATATGA
1 TATTATATATGA
334422 ATGGTTGATG
Statistics
Matches: 61, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
19 13 0.21
20 10 0.16
21 15 0.25
22 20 0.33
23 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.15, T:0.43
Consensus pattern (19 bp):
TATTATATATGATATGAAT
Found at i:337026 original size:42 final size:41
Alignment explanation
Indices: 336957--337069 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 41
336947 ACATCATTAT
* *
336957 CAGAAACCC-GAAGGG-TGAACAAAAGCTCATAAAAGCTAAA
1 CAGAAACCCATAAGGGTTGAAC-AGAGCTCATAAAAGCTAAA
* * *
336997 CAGAAACCCATAAGGGTTGAACGAGAGCTCTTAAGAGCTGAA
1 CAGAAACCCATAAGGGTTGAAC-AGAGCTCATAAAAGCTAAA
** *
337039 TGGAAACCCATAAGGGTTAAACAGAAGCTCA
1 CAGAAACCCATAAGGGTTGAACAG-AGCTCA
337070 ATAGAGCTGA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
40 9 0.15
41 7 0.12
42 44 0.73
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.14
Consensus pattern (41 bp):
CAGAAACCCATAAGGGTTGAACAGAGCTCATAAAAGCTAAA
Found at i:337076 original size:42 final size:42
Alignment explanation
Indices: 336974--337119 Score: 134
Period size: 42 Copynumber: 3.5 Consensus size: 42
336964 CCGAAGGGTG
* * * * *
336974 AACAAAAGCTCATAAAAGCTAAACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTA
* *
337016 AAC-GAGAGCTCTTAAGAGCTGAATGGAAACCCATAAGGGTTA
1 AACAGA-AGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTA
* ** * *
337058 AACAGAAGCTCA-ATAGAGCTGAACGAAAACTTATATGAGTTA
1 AACAGAAGCTCATA-AGAGCTGAACGGAAACCCATAAGGGTTA
* *
337100 AACAGAAGCTCGTGAGAGCT
1 AACAGAAGCTCATAAGAGCT
337120 AAACAAAAAG
Statistics
Matches: 84, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
41 2 0.02
42 80 0.95
43 2 0.02
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.18
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTA
Found at i:341272 original size:2 final size:2
Alignment explanation
Indices: 341265--341299 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
341255 NNGAAAGCTG
341265 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
341300 GACATTTCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:344455 original size:19 final size:17
Alignment explanation
Indices: 344432--344489 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 17
344422 TATTTTTTAT
344432 ATATTGTATATGATATGA
1 ATATT-TATATGATATGA
344450 ATTATTCTATATGATATTGA
1 A-TATT-TATATGATA-TGA
*
344470 ATATTTATAT-ATATGT
1 ATATTTATATGATATGA
344486 ATAT
1 ATAT
344490 GAATTGATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
16 6 0.17
17 3 0.08
18 6 0.17
19 17 0.47
20 4 0.11
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (17 bp):
ATATTTATATGATATGA
Found at i:344480 original size:20 final size:19
Alignment explanation
Indices: 344433--344527 Score: 64
Period size: 22 Copynumber: 4.6 Consensus size: 19
344423 ATTTTTTATA
*
344433 TATTGTATATGATATGAAT
1 TATTATATATGATATGAAT
*
344452 TATTCTATATGATATTGAAT
1 TATTATATATGATA-TGAAT
*
344472 ATTTATATATATGTATATGAAT
1 -TAT-TATATATG-ATATGAAT
* * *
344494 TGATGATAAAATGAAATGAGAT
1 T-ATTAT-ATATGATATGA-AT
*
344516 TATGATATATGA
1 TATTATATATGA
344528 ATGGTTGATG
Statistics
Matches: 61, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
19 13 0.21
20 10 0.16
21 15 0.25
22 20 0.33
23 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.15, T:0.43
Consensus pattern (19 bp):
TATTATATATGATATGAAT
Found at i:347132 original size:42 final size:41
Alignment explanation
Indices: 347063--347175 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 41
347053 ACATCATTAT
* *
347063 CAGAAACCC-GAAGGG-TGAACAAAAGCTCATAAAAGCTAAA
1 CAGAAACCCATAAGGGTTGAAC-AGAGCTCATAAAAGCTAAA
* * *
347103 CAGAAACCCATAAGGGTTGAACGAGAGCTCTTAAGAGCTGAA
1 CAGAAACCCATAAGGGTTGAAC-AGAGCTCATAAAAGCTAAA
** *
347145 TGGAAACCCATAAGGGTTAAACAGAAGCTCA
1 CAGAAACCCATAAGGGTTGAACAG-AGCTCA
347176 ATAGAGCTGA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
40 9 0.15
41 7 0.12
42 44 0.73
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.14
Consensus pattern (41 bp):
CAGAAACCCATAAGGGTTGAACAGAGCTCATAAAAGCTAAA
Found at i:347182 original size:42 final size:42
Alignment explanation
Indices: 347080--347225 Score: 134
Period size: 42 Copynumber: 3.5 Consensus size: 42
347070 CCGAAGGGTG
* * * * *
347080 AACAAAAGCTCATAAAAGCTAAACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTA
* *
347122 AAC-GAGAGCTCTTAAGAGCTGAATGGAAACCCATAAGGGTTA
1 AACAGA-AGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTA
* ** * *
347164 AACAGAAGCTCA-ATAGAGCTGAACGAAAACTTATATGAGTTA
1 AACAGAAGCTCATA-AGAGCTGAACGGAAACCCATAAGGGTTA
* *
347206 AACAGAAGCTCGTGAGAGCT
1 AACAGAAGCTCATAAGAGCT
347226 AAACAAAAAG
Statistics
Matches: 84, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
41 2 0.02
42 80 0.95
43 2 0.02
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.18
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTA
Found at i:349978 original size:17 final size:16
Alignment explanation
Indices: 349947--349990 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
349937 AAATTTAAAC
*
349947 ATTTTATTGAAATAAT
1 ATTTTATTAAAATAAT
349963 ATTTTAATTAAAATAAT
1 ATTTT-ATTAAAATAAT
349980 -TTTTATTAAAA
1 ATTTTATTAAAA
349991 AATTATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 7 0.27
16 9 0.35
17 10 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
ATTTTATTAAAATAAT
Found at i:351006 original size:68 final size:68
Alignment explanation
Indices: 350897--351027 Score: 226
Period size: 68 Copynumber: 1.9 Consensus size: 68
350887 CGCCAGTTCA
* *
350897 CAAAATCGTAAATAAAGACAATTCTCACCAACGAAAAGAGGAAGACATTCAGTTATCAGATTTAC
1 CAAAATCGTAAATAAAGACAATTCCCACCAACGAAAAGAGGAAGACATTCAGTTAGCAGATTTAC
350962 CCT
66 CCT
* *
350965 CAAAATCGTAAATAAAGATAATTCCCACCTACGAAAAGAGGAAGACATTCAGTTAGCAGATTT
1 CAAAATCGTAAATAAAGACAATTCCCACCAACGAAAAGAGGAAGACATTCAGTTAGCAGATTT
351028 TACCTTGATA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (68 bp):
CAAAATCGTAAATAAAGACAATTCCCACCAACGAAAAGAGGAAGACATTCAGTTAGCAGATTTAC
CCT
Found at i:357721 original size:27 final size:29
Alignment explanation
Indices: 357690--357745 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
357680 ACTTAATAAA
*
357690 ATTT-GTGA-TTTTAATTTCTATACTTTT
1 ATTTGGTGATTTTTAATCTCTATACTTTT
* *
357717 ATTTGGTTATTTTTAGTCTCTATACTTTT
1 ATTTGGTGATTTTTAATCTCTATACTTTT
357746 CAAATTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 4 0.17
28 3 0.12
29 17 0.71
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (29 bp):
ATTTGGTGATTTTTAATCTCTATACTTTT
Found at i:358867 original size:22 final size:21
Alignment explanation
Indices: 358823--358867 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
358813 CTGCCTTTGG
* * *
358823 TGTTGTGACACAGCCTGATGA
1 TGTTGCGACACACCCTGAAGA
358844 TGTTGCGACACACCCCTGAAGA
1 TGTTGCGACACA-CCCTGAAGA
358866 TG
1 TG
358868 AGCATACTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (21 bp):
TGTTGCGACACACCCTGAAGA
Found at i:364115 original size:27 final size:28
Alignment explanation
Indices: 364085--364153 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 28
364075 CCATGGTACT
*
364085 CTCCCATGAGTACCCTTCC-ACGATATC
1 CTCCCATGAGTACCCTTCCAACGATACC
*
364112 CTCCCATGAGTATCC-TCCAACGATACC
1 CTCCCATGAGTACCCTTCCAACGATACC
*
364139 CTTCCAT-AGTACCCT
1 CTCCCATGAGTACCCT
364154 CCCATTGGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 9 0.25
27 27 0.75
ACGTcount: A:0.23, C:0.41, G:0.10, T:0.26
Consensus pattern (28 bp):
CTCCCATGAGTACCCTTCCAACGATACC
Found at i:364127 original size:14 final size:14
Alignment explanation
Indices: 364085--364129 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
364075 CCATGGTACT
*
364085 CTCCCATGAGTACC
1 CTCCCATGAGTATC
* *
364099 CTTCCACGA-TATC
1 CTCCCATGAGTATC
364112 CTCCCATGAGTATC
1 CTCCCATGAGTATC
364126 CTCC
1 CTCC
364130 AACGATACCC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.20, C:0.42, G:0.11, T:0.27
Consensus pattern (14 bp):
CTCCCATGAGTATC
Found at i:366624 original size:12 final size:13
Alignment explanation
Indices: 366606--366637 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
366596 GGTGTTATAA
366606 AAACTAAATAATT
1 AAACTAAATAATT
366619 -AACTAAATAATT
1 AAACTAAATAATT
366631 AAACTAA
1 AAACTAA
366638 GAAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (13 bp):
AAACTAAATAATT
Found at i:369479 original size:16 final size:16
Alignment explanation
Indices: 369455--369488 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
369445 AATTCATCAT
369455 TTGGAGAACTCTAAGG
1 TTGGAGAACTCTAAGG
* *
369471 TTGGTGAACTCTAGGG
1 TTGGAGAACTCTAAGG
369487 TT
1 TT
369489 TGACAGACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.32, T:0.32
Consensus pattern (16 bp):
TTGGAGAACTCTAAGG
Found at i:373240 original size:43 final size:43
Alignment explanation
Indices: 373185--373303 Score: 145
Period size: 42 Copynumber: 2.8 Consensus size: 43
373175 TTTAGCGGGG
* * *
373185 CTTGTCAGAAACGCCGCTGCAAAACATAACTTTTAGCGACGCTT
1 CTTGTCAAAAACGCCGCT-AAAAACATAACATTTAGCGACGCTT
* *
373229 -TTGTCACAAACGCCGCTATAAAACA-AACCTTTAGCGACGCTT
1 CTTGTCAAAAACGCCGCTA-AAAACATAACATTTAGCGACGCTT
*
373271 CTCG-CAAAAACGCCGCTAAAAACATAACATTTA
1 CTTGTCAAAAACGCCGCTAAAAACATAACATTTA
373304 AAAAAACATT
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
41 6 0.09
42 36 0.55
43 24 0.36
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (43 bp):
CTTGTCAAAAACGCCGCTAAAAACATAACATTTAGCGACGCTT
Found at i:373717 original size:43 final size:43
Alignment explanation
Indices: 373651--373741 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
373641 CACATTGCAA
* ** *
373651 GGTAATAAAAAATACAATGCATTTTTTTAATCAAGTAAATCTT
1 GGTAATAAAAAATACAATACATTTACTTAATCAAGGAAATCTT
* * *
373694 GGTAATAAAAGATATAATACATTTACTTAATTAAGGAAATCTT
1 GGTAATAAAAAATACAATACATTTACTTAATCAAGGAAATCTT
373737 -GTAAT
1 GGTAAT
373742 GAACTCAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 5 0.12
43 36 0.88
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (43 bp):
GGTAATAAAAAATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:385158 original size:7 final size:7
Alignment explanation
Indices: 385143--385277 Score: 67
Period size: 7 Copynumber: 19.0 Consensus size: 7
385133 ATCTAAACAT
385143 TAAACCCC
1 TAAA-CCC
385151 TAAACCC
1 TAAACCC
*
385158 T-ATCCC
1 TAAACCC
385164 TTAAACCC
1 -TAAACCC
* *
385172 TAAATCA
1 TAAACCC
* * *
385179 AAAAACA
1 TAAACCC
385186 TAAACCC
1 TAAACCC
385193 TAAACCC
1 TAAACCC
* *
385200 TTAGCCC
1 TAAACCC
*
385207 TTAACCCC
1 -TAAACCC
*
385215 TAAACCT
1 TAAACCC
*
385222 TGAACCC
1 TAAACCC
*
385229 -CAACCC
1 TAAACCC
*
385235 TTAAACCA
1 -TAAACCC
*
385243 TAAACCA
1 TAAACCC
*
385250 TAAACCA
1 TAAACCC
*
385257 TAAACCA
1 TAAACCC
*
385264 TAATCCC
1 TAAACCC
385271 TAAACCC
1 TAAACCC
385278 ATTATTAGTT
Statistics
Matches: 99, Mismatches: 23, Indels: 11
0.74 0.17 0.08
Matches are distributed among these distances:
6 9 0.09
7 73 0.74
8 17 0.17
ACGTcount: A:0.42, C:0.38, G:0.01, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:385981 original size:13 final size:14
Alignment explanation
Indices: 385963--385992 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
385953 TCTTAAATCT
385963 TAAACCCTAAAC-A
1 TAAACCCTAAACTA
385976 TAAACCCTAAACTA
1 TAAACCCTAAACTA
385990 TAA
1 TAA
385993 TGATAATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:386184 original size:38 final size:37
Alignment explanation
Indices: 386142--386246 Score: 111
Period size: 40 Copynumber: 2.7 Consensus size: 37
386132 GAAAAATGCC
386142 GCTAATGCTCATTTTTAGCGGTGTTTCCAAAAAGCGCT
1 GCTAATGCTCATTTTTAGCGG-GTTTCCAAAAAGCGCT
* ***
386180 GCTAATGCTCGATCTTTAGCAGCGGTTTTTGAAAAGCGCT
1 GCTAATGCTC-ATTTTTAGC-G-GGTTTCCAAAAAGCGCT
*
386220 GCTAATGCTTGATTTTTAGCGGCGTTT
1 GCTAATGC-TCATTTTTAGCGG-GTTT
386247 TTTTATCCAA
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
38 11 0.20
39 13 0.23
40 30 0.54
41 2 0.04
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (37 bp):
GCTAATGCTCATTTTTAGCGGGTTTCCAAAAAGCGCT
Found at i:386220 original size:40 final size:40
Alignment explanation
Indices: 386171--386249 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
386161 GGTGTTTCCA
386171 AAAAGCGCTGCTAATGCTCGATCTTTAGCAGCGGTTTTTG
1 AAAAGCGCTGCTAATGCTCGATCTTTAGCAGCGGTTTTTG
* * * *
386211 AAAAGCGCTGCTAATGCTTGATTTTTAGCGGCGTTTTTT
1 AAAAGCGCTGCTAATGCTCGATCTTTAGCAGCGGTTTTT
386250 TATCCAAACG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.37
Consensus pattern (40 bp):
AAAAGCGCTGCTAATGCTCGATCTTTAGCAGCGGTTTTTG
Found at i:393031 original size:14 final size:14
Alignment explanation
Indices: 393012--393039 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
393002 NTCTAATACT
393012 AATAGAATAGAAAA
1 AATAGAATAGAAAA
393026 AATAGAATAGAAAA
1 AATAGAATAGAAAA
393040 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:400669 original size:1 final size:1
Alignment explanation
Indices: 400636--400661 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
400626 CTTCAAATTC
400636 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
400662 GCATTTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:400973 original size:5 final size:5
Alignment explanation
Indices: 400965--401010 Score: 76
Period size: 5 Copynumber: 9.4 Consensus size: 5
400955 GCTTAGAGAG
*
400965 GCCAG GCCAT GCCAT GCCAT GCCAT GCCAT GCCAT GCCAT G-CAT GC
1 GCCAT GCCAT GCCAT GCCAT GCCAT GCCAT GCCAT GCCAT GCCAT GC
401011 GCCTAGCCCT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
4 4 0.10
5 35 0.90
ACGTcount: A:0.20, C:0.39, G:0.24, T:0.17
Consensus pattern (5 bp):
GCCAT
Found at i:406705 original size:42 final size:42
Alignment explanation
Indices: 406629--406842 Score: 216
Period size: 42 Copynumber: 5.0 Consensus size: 42
406619 TTGTTACTAA
* *
406629 ATTTGTTGTTTTAAATCGATTTTTTTCTTCTTTGAATCGATT
1 ATTTGTTGTTTTAAATCGATTCTTTACTTCTTTGAATCGATT
* * * *
406671 ATTTGTTATTTAAAATTGATTCTTTACTTATTTGAATCGATT
1 ATTTGTTGTTTTAAATCGATTCTTTACTTCTTTGAATCGATT
* * * *
406713 CATTATTGTTGTTTTAAATCGGTTATTTGCTTCTTT-AATTGATT
1 -A-T-TTGTTGTTTTAAATCGATTCTTTACTTCTTTGAATCGATT
* *
406757 CATAATTGTTGTCTTAAATTGATTCTTTACTTCTTTGAATCGATT
1 -AT--TTGTTGTTTTAAATCGATTCTTTACTTCTTTGAATCGATT
* * * *
406802 GTTTGTTGTTTTAAATCGATTCATTAC-TGTTTGAATTGATT
1 ATTTGTTGTTTTAAATCGATTCTTTACTTCTTTGAATCGATT
406843 CTTTATTATT
Statistics
Matches: 141, Mismatches: 26, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
41 12 0.09
42 58 0.41
43 2 0.01
44 38 0.27
45 31 0.22
ACGTcount: A:0.23, C:0.09, G:0.13, T:0.55
Consensus pattern (42 bp):
ATTTGTTGTTTTAAATCGATTCTTTACTTCTTTGAATCGATT
Found at i:406733 original size:24 final size:23
Alignment explanation
Indices: 406630--406826 Score: 71
Period size: 21 Copynumber: 9.0 Consensus size: 23
406620 TGTTACTAAA
*
406630 TTTGTTGTTTTAAATCGATT-TT
1 TTTGTTGTTTTAAATCGATTCAT
* * *
406652 TTTCTT-CTTTGAATCGATT-A-
1 TTTGTTGTTTTAAATCGATTCAT
* * *
406672 TTTGTTATTTAAAATTGATTC-T
1 TTTGTTGTTTTAAATCGATTCAT
** * *
406694 TTACTT-ATTTGAATCGATTCAT
1 TTTGTTGTTTTAAATCGATTCAT
*
406716 TATTGTTGTTTTAAATCGGTT-A-
1 T-TTGTTGTTTTAAATCGATTCAT
* *
406738 TTTGCTT-CTTT-AATTGATTCAT
1 TTTG-TTGTTTTAAATCGATTCAT
* * *
406760 AATTGTTGTCTTAAATTGATTC-T
1 -TTTGTTGTTTTAAATCGATTCAT
** * * *
406783 TTACTT-CTTTGAATCGATT--G
1 TTTGTTGTTTTAAATCGATTCAT
406803 TTTGTTGTTTTAAATCGATTCAT
1 TTTGTTGTTTTAAATCGATTCAT
406826 T
1 T
406827 ACTGTTTGAA
Statistics
Matches: 121, Mismatches: 39, Indels: 29
0.64 0.21 0.15
Matches are distributed among these distances:
20 15 0.12
21 57 0.47
22 19 0.16
23 11 0.09
24 19 0.16
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.56
Consensus pattern (23 bp):
TTTGTTGTTTTAAATCGATTCAT
Found at i:406794 original size:89 final size:84
Alignment explanation
Indices: 406630--406822 Score: 246
Period size: 89 Copynumber: 2.2 Consensus size: 84
406620 TGTTACTAAA
* *
406630 TTTGTTGTTTTAAATCGATTTTTTTCTTCTTTGAATCGATTATTTGTTATTTAAAATTGATTCTT
1 TTTGTTGTTTTAAATCGATTATTTGCTTCTTTGAATCGATTATTTGTTATTTAAAATTGATTCTT
*
406695 TACTTATTTGAATCGATTCAT
66 TACTTATTTGAATCGATT--G
* * *
406716 TATTGTTGTTTTAAATCGGTTATTTGCTTCTTT-AATTGATTCATAATTGTTGTCTT-AAATTGA
1 T-TTGTTGTTTTAAATCGATTATTTGCTTCTTTGAATCGATT-AT--TTGTTAT-TTAAAATTGA
*
406779 TTCTTTACTTCTTTGAATCGATTG
61 TTCTTTACTTATTTGAATCGATTG
406803 TTTGTTGTTTTAAATCGATT
1 TTTGTTGTTTTAAATCGATT
406823 CATTACTGTT
Statistics
Matches: 94, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
86 26 0.28
87 31 0.33
89 35 0.37
90 2 0.02
ACGTcount: A:0.22, C:0.09, G:0.12, T:0.56
Consensus pattern (84 bp):
TTTGTTGTTTTAAATCGATTATTTGCTTCTTTGAATCGATTATTTGTTATTTAAAATTGATTCTT
TACTTATTTGAATCGATTG
Found at i:408891 original size:24 final size:24
Alignment explanation
Indices: 408844--408891 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
408834 TCGTTTTGTG
**
408844 GCAAAGAATGAATTGACGGTAAAT
1 GCAAAGAATGAATTGACGACAAAT
*
408868 GCAAAGGATGAATTGACGACAAAT
1 GCAAAGAATGAATTGACGACAAAT
408892 TACCTAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.25, T:0.19
Consensus pattern (24 bp):
GCAAAGAATGAATTGACGACAAAT
Found at i:409804 original size:41 final size:41
Alignment explanation
Indices: 409741--409849 Score: 164
Period size: 41 Copynumber: 2.6 Consensus size: 41
409731 CTTAATTTAA
* * *
409741 CAGATTCACCGACACTTGGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
409783 CAGATCACCGGCACTTAGCCTGATAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
409824 CAGATCACCGGCACTTAGCCTGCTAG
1 CAGATCACCGGCACTTAGCCTGCTAG
409850 ACGTATAGTC
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 57 0.93
42 4 0.07
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
Found at i:412171 original size:42 final size:42
Alignment explanation
Indices: 412119--412230 Score: 179
Period size: 42 Copynumber: 2.7 Consensus size: 42
412109 GAGTTTCAGG
* *
412119 TAACGCTTATGGGTTTTCGTTCAGCTCTTTTGAGCTTCAGTT
1 TAACCCTTATGGGTTTTCGTTCAGCTCTTTTGAGCTTCAATT
* *
412161 TAACCCTTATGGGTTTTCGTTCAGCTCTTTTGGGCTTTAATT
1 TAACCCTTATGGGTTTTCGTTCAGCTCTTTTGAGCTTCAATT
*
412203 TAACCCTTATGGGTTTTCGTTTAGCTCT
1 TAACCCTTATGGGTTTTCGTTCAGCTCT
412231 CATAACCTTC
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (42 bp):
TAACCCTTATGGGTTTTCGTTCAGCTCTTTTGAGCTTCAATT
Found at i:412225 original size:21 final size:21
Alignment explanation
Indices: 412158--412225 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
412148 TTGAGCTTCA
412158 GTTTAACCCTTATGGGTTTTC
1 GTTTAACCCTTATGGGTTTTC
* * * * * *
412179 GTTCAGCTCTTTTGGGCTTTA
1 GTTTAACCCTTATGGGTTTTC
*
412200 ATTTAACCCTTATGGGTTTTC
1 GTTTAACCCTTATGGGTTTTC
412221 GTTTA
1 GTTTA
412226 GCTCTCATAA
Statistics
Matches: 33, Mismatches: 14, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.15, C:0.18, G:0.19, T:0.49
Consensus pattern (21 bp):
GTTTAACCCTTATGGGTTTTC
Found at i:415876 original size:44 final size:44
Alignment explanation
Indices: 415827--415967 Score: 237
Period size: 44 Copynumber: 3.2 Consensus size: 44
415817 CACTGCGGGT
415827 TAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTCAGGGAGA
1 TAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTCAGGGAGA
* * *
415871 TAGGACTTGCAATCTTCAACCTATTCCATTACTGGTCTGGGAGA
1 TAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTCAGGGAGA
*
415915 TAGGACTTGCAATCTTCAACCTATTTCACTGCTGGTCAGGGAGA
1 TAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTCAGGGAGA
*
415959 TGGGACTTG
1 TAGGACTTG
415968 TGGCTTAAAT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 89 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (44 bp):
TAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTCAGGGAGA
Done.