Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007272.1 Hibiscus syriacus cultivar Beakdansim tig00019280_pilon, whole genome shotgun sequence
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: 48943
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1634 original size:41 final size:40
Alignment explanation
Indices: 1559--1649 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 40
1549 TAGAAGGATA
* * *
1559 ACATGGCAGTCATATGTGTTGATGTGAATCGATTTTTGTTG
1 ACATGGCA-TCATATGTGCTGATATGAATCGATTTCTGTTG
*
1600 ACATGGCATCCATGTGTGCTGATATGGAAT-GATTTCTGTTG
1 ACATGGCAT-CATATGTGCTGATAT-GAATCGATTTCTGTTG
1641 ACATGGCAT
1 ACATGGCAT
1650 TCACATCATT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
40 1 0.02
41 39 0.89
42 4 0.09
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.37
Consensus pattern (40 bp):
ACATGGCATCATATGTGCTGATATGAATCGATTTCTGTTG
Found at i:3369 original size:26 final size:26
Alignment explanation
Indices: 3332--3394 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
3322 AAATTACAAT
* *
3332 TAATATAATTATGTTATTTAAATTTA
1 TAATATAATTATGATAATTAAATTTA
3358 TAATA-AATTTATGATAATTAAA-TTA
1 TAATATAA-TTATGATAATTAAATTTA
*
3383 TTATGATAATTA
1 TAAT-ATAATTA
3395 AATTAATATG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 8 0.26
26 21 0.68
27 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (26 bp):
TAATATAATTATGATAATTAAATTTA
Found at i:3374 original size:14 final size:15
Alignment explanation
Indices: 3357--3398 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 15
3347 ATTTAAATTT
3357 ATAA-TAAATTTATG
1 ATAATTAAATTTATG
3371 ATAATTAAATTATTATG
1 ATAATTAAA-T-TTATG
3388 ATAATTAAATT
1 ATAATTAAATT
3399 AATATGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.16
15 5 0.20
16 2 0.08
17 14 0.56
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (15 bp):
ATAATTAAATTTATG
Found at i:3386 original size:17 final size:17
Alignment explanation
Indices: 3366--3456 Score: 75
Period size: 17 Copynumber: 5.4 Consensus size: 17
3356 TATAATAAAT
3366 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
3383 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
* *
3400 ATATGATTATTTTTGAAA-T-
1 TTATGA-TA--ATT-AAATTA
*
3419 TT-T-ATCA-TAAATTA
1 TTATGATAATTAAATTA
3433 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
*
3450 ATATGAT
1 TTATGAT
3457 TACTTTTTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
12 3 0.05
13 2 0.03
14 2 0.03
15 1 0.02
16 4 0.07
17 36 0.62
18 3 0.05
19 1 0.02
20 3 0.05
21 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (17 bp):
TTATGATAATTAAATTA
Found at i:3432 original size:50 final size:51
Alignment explanation
Indices: 3376--3472 Score: 178
Period size: 50 Copynumber: 1.9 Consensus size: 51
3366 TTATGATAAT
3376 TAAATTATTATGATAATTAAATTAATATGATTA-TTTTTGAAATTTTATCA
1 TAAATTATTATGATAATTAAATTAATATGATTACTTTTTGAAATTTTATCA
3426 TAAATTATTATGATAATTAAATTAATATGATTACTTTTTTGAAATTT
1 TAAATTATTATGATAATTAAATTAATATGATTAC-TTTTTGAAATTT
3473 AGTTTTATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 33 0.73
52 12 0.27
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (51 bp):
TAAATTATTATGATAATTAAATTAATATGATTACTTTTTGAAATTTTATCA
Found at i:3446 original size:67 final size:67
Alignment explanation
Indices: 3317--3456 Score: 189
Period size: 67 Copynumber: 2.1 Consensus size: 67
3307 ATCCTGACTT
*
3317 ATATGA-AATTACAATTAATATAATTATGTTATTTAAATTTATAATAAATTTATGATAATTAAAT
1 ATATGATAATTACAATTAATATAATTATGTTATTGAAATTTATAATAAATTTATGATAATTAAAT
3381 TA
66 TA
* * *
3383 TTATGATAATTA-AATTAATATGATTAT-TT-TTGAAATTTTATCATAAATTATTATGATAATTA
1 ATATGATAATTACAATTAATATAATTATGTTATTGAAA-TTTATAATAAA-T-TTATGATAATTA
3445 AATTA
63 AATTA
3450 ATATGAT
1 ATATGAT
3457 TACTTTTTTG
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
64 5 0.08
65 12 0.18
66 20 0.31
67 28 0.43
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (67 bp):
ATATGATAATTACAATTAATATAATTATGTTATTGAAATTTATAATAAATTTATGATAATTAAAT
TA
Found at i:4326 original size:20 final size:20
Alignment explanation
Indices: 4293--4353 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
4283 AACCCTTACA
**
4293 AATATCAAGTAGAAGAAAGC
1 AATATCAAACAGAAGAAAGC
*
4313 AATATCAAACAGAAGCAAA-T
1 AATATCAAACAGAAG-AAAGC
* *
4333 AATATAAAACAGAATAAAGC
1 AATATCAAACAGAAGAAAGC
4353 A
1 A
4354 GAATCAATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.09
20 27 0.82
21 3 0.09
ACGTcount: A:0.61, C:0.11, G:0.13, T:0.15
Consensus pattern (20 bp):
AATATCAAACAGAAGAAAGC
Found at i:7053 original size:31 final size:31
Alignment explanation
Indices: 6656--7050 Score: 591
Period size: 31 Copynumber: 12.8 Consensus size: 31
6646 CCTTGATTAG
* *
6656 TTTACATTAACAACAATAAACCA--ATATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
* *
6685 TTTACATCAACAGCAATAAACCAGTATATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
6716 -TTACATCAA-AAGCAATAAACCAGTACATCA
1 TTTACATCAACAA-CAATAAACCAGTACATCA
*
6746 TTTACATCAACAGCAATAAACCAGTACATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
* * *
6777 TTTACATCAACATCAATAAACCAATATATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
*
6808 TTTACATCAACAACAATAAACCAATACATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
*
6839 TTTACATCAACAACAATAAACCAGTACATTA
1 TTTACATCAACAACAATAAACCAGTACATCA
*
6870 TTTACATCAACAACAATAAACCACTACATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
* *
6901 TTTACATCAACAGCAATAAACCAATACATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
*
6932 TTTACATCAACATCAATAAACCAGTACATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
*
6963 TTTACATCAACAACAATAAACCAGTATATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
* * *
6994 TTTACATCAACAACAATAAACCAATATATTA
1 TTTACATCAACAACAATAAACCAGTACATCA
7025 TTTACATCAACAACAATAAACCAGTA
1 TTTACATCAACAACAATAAACCAGTA
7051 TATATATATC
Statistics
Matches: 338, Mismatches: 23, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
29 22 0.07
30 26 0.08
31 289 0.86
32 1 0.00
ACGTcount: A:0.49, C:0.24, G:0.03, T:0.25
Consensus pattern (31 bp):
TTTACATCAACAACAATAAACCAGTACATCA
Found at i:7312 original size:6 final size:6
Alignment explanation
Indices: 7269--7493 Score: 201
Period size: 6 Copynumber: 38.5 Consensus size: 6
7259 GTTTTGAATA
* * * *
7269 GTTTGG GTTCGG GTTTAG GTTCGG GTGTGG GTTT-G GTTTGG GTTT-G
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * * **
7315 GTTTGG GTTTGG ATTTGG GTTTAG GTTTGG GTTCGG G-TTCA GTTTGG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * * *
7362 GTTTGG GTTTAG GTTTAG GTTTGG GTTT-G GTTTGG GTCTGG GTTAGG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * * * * *
7409 GTCTAG GTTTGG GATTGG GTTTGG GTTCGG GTTCGG GTTCGG GTTTGG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * * *
7457 GTTTGG GTCTAG GTTAGG GTTT-- ATTTGG GTTTGG GTT
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTT
7494 AAGGTTAGGG
Statistics
Matches: 173, Mismatches: 40, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
4 3 0.02
5 17 0.10
6 153 0.88
ACGTcount: A:0.05, C:0.04, G:0.45, T:0.45
Consensus pattern (6 bp):
GTTTGG
Found at i:7342 original size:35 final size:35
Alignment explanation
Indices: 7270--7493 Score: 161
Period size: 35 Copynumber: 6.4 Consensus size: 35
7260 TTTTGAATAG
* * ** *
7270 TTTGGGTTCGGGTTTAGGTTCGGGTGTGGGTTTGG
1 TTTGGGTTTGGGTTTGGGTTTAGGTTTGGGTTTGG
7305 TTTGGGTTT-GGTTTGGGTTT-GGATTTGGGTTTAGG
1 TTTGGGTTTGGGTTTGGGTTTAGG-TTTGGGTTT-GG
* ** *
7340 TTTGGGTTCGGG-TTCAGTTTGGGTTTGGGTTTAGG
1 TTTGGGTTTGGGTTTGGGTTTAGGTTTGGGTTT-GG
* * * *
7375 TTTAGGTTTGGGTTT-GGTTTGGGTCTGGGTTAGGG
1 TTTGGGTTTGGGTTTGGGTTTAGGTTTGGGTT-TGG
* * * * * *
7410 TCTAGGTTTGGGATTGGGTTTGGGTTCGGGTTCGGG
1 TTTGGGTTTGGGTTTGGGTTTAGGTTTGGGTT-TGG
* * * *
7446 TTCGGGTTTGGGTTTGGGTCTAGGTTAGGGTTT-A
1 TTTGGGTTTGGGTTTGGGTTTAGGTTTGGGTTTGG
7480 TTTGGGTTTGGGTT
1 TTTGGGTTTGGGTT
7494 AAGGTTAGGG
Statistics
Matches: 155, Mismatches: 27, Indels: 15
0.79 0.14 0.08
Matches are distributed among these distances:
33 2 0.01
34 30 0.19
35 75 0.48
36 48 0.31
ACGTcount: A:0.05, C:0.04, G:0.45, T:0.46
Consensus pattern (35 bp):
TTTGGGTTTGGGTTTGGGTTTAGGTTTGGGTTTGG
Found at i:7493 original size:22 final size:22
Alignment explanation
Indices: 7458--7499 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
7448 CGGGTTTGGG
*
7458 TTTGGGTCTAGGTTAGGGTTTA
1 TTTGGGTCTAGGTTAAGGTTTA
* *
7480 TTTGGGTTTGGGTTAAGGTT
1 TTTGGGTCTAGGTTAAGGTT
7500 AGGGTTTAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.12, C:0.02, G:0.38, T:0.48
Consensus pattern (22 bp):
TTTGGGTCTAGGTTAAGGTTTA
Found at i:7935 original size:114 final size:114
Alignment explanation
Indices: 7803--8013 Score: 361
Period size: 114 Copynumber: 1.9 Consensus size: 114
7793 AATTTGGGTG
7803 TTTGATCGAAAAAAACACG-AAATGATTTGTGTTTAGGTGTTTTTGAAGATCAAATGAGGGTTTT
1 TTTGATCGAAAAAAACACGAAAATGATTTG-GTTTAGGTGTTTTTGAAGATCAAATGAGGGTTTT
7867 GGGGAAGAACTGGGATGAACAAATGAAGAACACGGAAGAATATTTAGGCC
65 GGGGAAGAACTGGGATGAACAAATGAAGAACACGGAAGAATATTTAGGCC
* * *
7917 TTTGATCGAAAAACACACGAAAATGTTTTGGTTTTGGTGTTTTTGAAGATCAAATGAGGGTTTTG
1 TTTGATCGAAAAAAACACGAAAATGATTTGGTTTAGGTGTTTTTGAAGATCAAATGAGGGTTTTG
* *
7982 GGGATGAATTGGGATGAACAAATGAAGAACAC
66 GGGAAGAACTGGGATGAACAAATGAAGAACAC
8014 AATTGATTTT
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
114 82 0.90
115 9 0.10
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.29
Consensus pattern (114 bp):
TTTGATCGAAAAAAACACGAAAATGATTTGGTTTAGGTGTTTTTGAAGATCAAATGAGGGTTTTG
GGGAAGAACTGGGATGAACAAATGAAGAACACGGAAGAATATTTAGGCC
Found at i:8467 original size:18 final size:18
Alignment explanation
Indices: 8444--8688 Score: 219
Period size: 18 Copynumber: 14.1 Consensus size: 18
8434 AACTTTTCAA
8444 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
8462 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
8480 TA-AT-G--AACTATATAA
1 TATATAGTTTA-TATATAC
*
8495 TATATAGTTTACATATAC
1 TATATAGTTTATATATAC
8513 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
8531 TA-AT-G--AACTATATAA
1 TATATAGTTTA-TATATAC
8546 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
** *
8564 TA-AT-GAAATATATATAA
1 TATATAG-TTTATATATAC
*
8581 TGTATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
8599 CATATAGTTTATATATAT
1 TATATAGTTTATATATAC
8617 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
** *
8635 TA-ATAAATTATAT-GA-
1 TATATAGTTTATATATAC
*
8650 TGTATAGTTTTATATATAC
1 TATATAG-TTTATATATAC
*
8669 CATATAGTTTATATATAC
1 TATATAGTTTATATATAC
8687 TA
1 TA
8689 ATGAACTATA
Statistics
Matches: 178, Mismatches: 32, Indels: 34
0.73 0.13 0.14
Matches are distributed among these distances:
14 2 0.01
15 17 0.10
16 11 0.06
17 32 0.18
18 108 0.61
19 8 0.04
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.46
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:8486 original size:51 final size:51
Alignment explanation
Indices: 8413--8710 Score: 365
Period size: 51 Copynumber: 5.8 Consensus size: 51
8403 TAATAAATTA
* *
8413 ATATAGGTTATA-ATACTAATGAACT-TTTCAATATATAGTTTATATATACT
1 ATATAGTTTATATATACTAATGAACTATAT-AATATATAGTTTATATATACT
*
8463 ATATAGTTTATATATACTAATGAACTATATAATATATAGTTTACATATACT
1 ATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACT
8514 ATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACT
1 ATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACT
** * * *
8565 A-AT-G-AAATATATA-TAATGTATAGTTTATATATACCATATAGTTTATATATATT
1 ATATAGTTTATATATACTAATG-A-A--CTATATA-A-TATATAGTTTATATATACT
* * * * *
8618 ATATAGTTTATATATACTAATAAATTATATGATGTATAGTTTTATATATACC
1 ATATAGTTTATATATACTAATGAACTATATAATATATAG-TTTATATATACT
8670 ATATAGTTTATATATACTAATGAACTATATAATATATAGTT
1 ATATAGTTTATATATACTAATGAACTATATAATATATAGTT
8711 CATTTAGTAT
Statistics
Matches: 214, Mismatches: 21, Indels: 25
0.82 0.08 0.10
Matches are distributed among these distances:
47 5 0.02
48 8 0.04
49 2 0.01
50 13 0.06
51 97 0.45
52 49 0.23
53 24 0.11
54 2 0.01
55 2 0.01
56 8 0.04
57 4 0.02
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (51 bp):
ATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACT
Found at i:8544 original size:17 final size:17
Alignment explanation
Indices: 8522--8579 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
8512 CTATATAGTT
*
8522 TATATATACTAATGAAC
1 TATATATACTAATGAAA
**
8539 TATATA-A-TATAT-AGT
1 TATATATACTA-ATGAAA
8554 TTATATATACTAATGAAA
1 T-ATATATACTAATGAAA
8572 TATATATA
1 TATATATA
8580 ATGTATAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 4 0.12
16 8 0.25
17 16 0.50
18 4 0.12
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (17 bp):
TATATATACTAATGAAA
Found at i:8544 original size:33 final size:31
Alignment explanation
Indices: 8507--8668 Score: 153
Period size: 33 Copynumber: 4.7 Consensus size: 31
8497 TATAGTTTAC
8507 ATATACTATATAGTTTATATATACTAATGAACT
1 ATATA-TATATAGTTTATATATACTAATGAA-T
8540 ATATAATATATAGTTTATATATACTAATGAAAT
1 ATAT-ATATATAGTTTATATATACTAATG-AAT
**
8573 ATATATAATGTATAGTTTATATATACCATATAGTTTAT
1 ATATAT-A--TATAGTTTATATATA-C-TA-A-TGAAT
*
8611 ATATATTATATAGTTTATATATACTAATAAATT
1 ATATA-TATATAGTTTATATATACTAATGAA-T
*
8644 ATATGATGTATAGTTTTATATATAC
1 ATAT-ATATATAG-TTTATATATAC
8669 CATATAGTTT
Statistics
Matches: 111, Mismatches: 5, Indels: 25
0.79 0.04 0.18
Matches are distributed among these distances:
32 4 0.04
33 45 0.41
34 17 0.15
35 16 0.14
36 16 0.14
37 2 0.02
38 9 0.08
39 2 0.02
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.46
Consensus pattern (31 bp):
ATATATATATAGTTTATATATACTAATGAAT
Found at i:8754 original size:18 final size:18
Alignment explanation
Indices: 8739--8775 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
8729 AAACTATAGT
*
8739 TTATATATATAGTATATA
1 TTATATAAATAGTATATA
*
8757 TTATATAAATAGTTTATA
1 TTATATAAATAGTATATA
8775 T
1 T
8776 AGTTCACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
TTATATAAATAGTATATA
Found at i:8798 original size:24 final size:24
Alignment explanation
Indices: 8758--8820 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
8748 TAGTATATAT
* *
8758 TATATAAA-TAGTTTATATAGTTCA
1 TATATAAACTA-TATATATAGGTCA
8782 CTA-ATAAACTATATATATAGGTCA
1 -TATATAAACTATATATATAGGTCA
*
8806 TATGTAAACTATATA
1 TATATAAACTATATA
8821 GTTTATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 2 0.06
24 27 0.82
25 4 0.12
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (24 bp):
TATATAAACTATATATATAGGTCA
Found at i:8883 original size:18 final size:18
Alignment explanation
Indices: 8846--8888 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
8836 TCATATGTAA
* * *
8846 ATATCAACTATAGTTTAT
1 ATATAAACTATAATTCAT
*
8864 ATGTAAACTATAATTCAT
1 ATATAAACTATAATTCAT
8882 ATATAAA
1 ATATAAA
8889 TATCAACTAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (18 bp):
ATATAAACTATAATTCAT
Found at i:8938 original size:20 final size:19
Alignment explanation
Indices: 8854--8984 Score: 50
Period size: 20 Copynumber: 7.1 Consensus size: 19
8844 AAATATCAAC
8854 TATAGTTTATATGTAAACTA
1 TATAGTTTATATGTAAA-TA
* *
8874 TA-A-TTCATATATAAATA
1 TATAGTTTATATGTAAATA
* *
8891 TCA-A--CTATA-GTATATA
1 T-ATAGTTTATATGTAAATA
**
8907 TATAGTACATATGTAAACTA
1 TATAGTTTATATGTAAA-TA
*
8927 TATAGTTTATATAGTTTATATA
1 TATAGTTTATAT-G--TAAATA
8949 TATAGTTT-TA--T--ATA
1 TATAGTTTATATGTAAATA
*
8963 TATAGTTCATATGTAAACTA
1 TATAGTTTATATGTAAA-TA
8983 TA
1 TA
8985 GTTCATATAT
Statistics
Matches: 83, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 10 0.12
15 3 0.04
16 8 0.10
17 7 0.08
18 15 0.18
19 6 0.07
20 18 0.22
21 3 0.04
22 10 0.12
23 3 0.04
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (19 bp):
TATAGTTTATATGTAAATA
Found at i:8960 original size:14 final size:14
Alignment explanation
Indices: 8934--8969 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
8924 CTATATAGTT
8934 TATATAG-TTTATA
1 TATATAGTTTTATA
8947 TATATAGTTTTATA
1 TATATAGTTTTATA
8961 TATATAGTT
1 TATATAGTT
8970 CATATGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (14 bp):
TATATAGTTTTATA
Found at i:9002 original size:18 final size:17
Alignment explanation
Indices: 8943--9002 Score: 63
Period size: 18 Copynumber: 3.6 Consensus size: 17
8933 TTATATAGTT
8943 TATATATATAGTT--T-
1 TATATATATAGTTCATA
8957 TATATATATAGTTCATA
1 TATATATATAGTTCATA
* *
8974 TGTAAACTATAGTTCATA
1 TATATA-TATAGTTCATA
8992 TATATAGTATA
1 TATATA-TATA
9003 TAAATATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 13 0.35
16 1 0.03
17 4 0.11
18 19 0.51
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (17 bp):
TATATATATAGTTCATA
Found at i:9003 original size:56 final size:54
Alignment explanation
Indices: 8854--9004 Score: 157
Period size: 56 Copynumber: 2.8 Consensus size: 54
8844 AAATATCAAC
* *
8854 TATAGTTTATATGTAAACTATAATTCATATATA-AATATCA-ACTATAGTATATA
1 TATAGTTCATATGTAAACTATAGTTCATATATATAATAT-ATACTATAGTATATA
* * * **
8907 TATAGTACATATGTAAACTATATAGTTTATATAGT-TTATATATA-TAGTTTTATATA
1 TATAGTTCATATGTAAAC--TATAGTTCATATA-TATAATATATACTA-TAGTATATA
*
8963 TATAGTTCATATGTAAACTATAGTTCATATATATAGTATATA
1 TATAGTTCATATGTAAACTATAGTTCATATATATAATATATA
9005 AATATAAATT
Statistics
Matches: 80, Mismatches: 11, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
53 17 0.21
54 19 0.24
55 14 0.17
56 30 0.38
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (54 bp):
TATAGTTCATATGTAAACTATAGTTCATATATATAATATATACTATAGTATATA
Found at i:9043 original size:7 final size:7
Alignment explanation
Indices: 9033--9064 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
9023 TAGTTTATAT
9033 AACCCTA
1 AACCCTA
9040 AACCCTA
1 AACCCTA
9047 AACCCTA
1 AACCCTA
9054 AACCCTA
1 AACCCTA
9061 AACC
1 AACC
9065 ATATATACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.44, G:0.00, T:0.12
Consensus pattern (7 bp):
AACCCTA
Found at i:9090 original size:22 final size:22
Alignment explanation
Indices: 9059--9113 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
9049 CCCTAAACCC
*
9059 TAAACCATATA-TACTATA-TATA
1 TAAACTATATAGT-CTATATTA-A
*
9081 TAAACTATATAGTTTATATTAA
1 TAAACTATATAGTCTATATTAA
9103 TAAACTATATA
1 TAAACTATATA
9114 ATTTATACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAACTATATAGTCTATATTAA
Found at i:9182 original size:20 final size:20
Alignment explanation
Indices: 9157--9394 Score: 83
Period size: 20 Copynumber: 12.2 Consensus size: 20
9147 TAATATATAA
* *
9157 ATATAAATTGTATAGTTTAT
1 ATATAAACTATATAGTTTAT
* *
9177 ATATAATTAATATATAATTTAT
1 ATATAA--ACTATATAGTTTAT
* *
9199 ATATAAACTATGTAGTTTCT
1 ATATAAACTATATAGTTTAT
** *
9219 ATAT-AGTTCA-ATAGTTCAT
1 ATATAAACT-ATATAGTTTAT
9238 ATATAAACTATATAGTATTAT
1 ATATAAACTATATAGT-TTAT
* * * *
9259 AGTTTATAC-ATGGTA-TATAT
1 A-TATAAACTAT-ATAGTTTAT
* * *
9279 AGTTTATAC-ATA-A-TATAT
1 A-TATAAACTATATAGTTTAT
*
9297 ATATAAAACTATATAATTTAT
1 ATAT-AAACTATATAGTTTAT
*
9318 ATAT-AA-TACATA---TAT
1 ATATAAACTATATAGTTTAT
9333 ATATAAACTATATAGTTTAT
1 ATATAAACTATATAGTTTAT
* * *
9353 ATGTATA-TATATA-TATAT
1 ATATAAACTATATAGTTTAT
* * *
9371 ATATATA-TATATAATATAT
1 ATATAAACTATATAGTTTAT
9390 ATATA
1 ATATA
9395 TATATATATT
Statistics
Matches: 171, Mismatches: 29, Indels: 37
0.72 0.12 0.16
Matches are distributed among these distances:
15 7 0.04
16 2 0.01
17 7 0.04
18 31 0.18
19 34 0.20
20 51 0.30
21 15 0.09
22 24 0.14
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.45
Consensus pattern (20 bp):
ATATAAACTATATAGTTTAT
Found at i:9189 original size:11 final size:11
Alignment explanation
Indices: 9175--9204 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
9165 TGTATAGTTT
9175 ATATATAATTA
1 ATATATAATTA
*
9186 ATATATAATTT
1 ATATATAATTA
9197 ATATATAA
1 ATATATAA
9205 ACTATGTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATATAATTA
Found at i:9279 original size:2 final size:2
Alignment explanation
Indices: 9272--9403 Score: 121
Period size: 2 Copynumber: 66.5 Consensus size: 2
9262 TTATACATGG
* * *
9272 TA TA TA TA GTT TA TA CA TA -A TA TA TA TA TA -A AA CTA TA TA -A
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * *
9313 TT TA TA TA TA -A TA CA TA TA TA TA TA AA CTA TA TA GTT TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
9356 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
9397 TA TA TA T
1 TA TA TA T
9404 TAGTTTTAAT
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
1 5 0.05
2 97 0.92
3 4 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:9286 original size:11 final size:11
Alignment explanation
Indices: 9272--9403 Score: 108
Period size: 11 Copynumber: 11.6 Consensus size: 11
9262 TTATACATGG
* *
9272 TATATATAGTT
1 TATATATAATA
*
9283 TATACATAATA
1 TATATATAATA
9294 TATATATAA-A
1 TATATATAATA
*
9304 -ACTATATAATT
1 TA-TATATAATA
9315 TATATATAATA
1 TATATATAATA
*
9326 CATATATATATA
1 TATATATA-ATA
* *
9338 AACTATATAGTTTA
1 TA-TATATA--ATA
*
9352 TATGTATATATA
1 TATATATA-ATA
9364 TATATATATATA
1 TATATATA-ATA
9376 TATATATAATA
1 TATATATAATA
9387 TATATAT-ATA
1 TATATATAATA
9397 TATATAT
1 TATATAT
9404 TAGTTTTAAT
Statistics
Matches: 102, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
9 1 0.01
10 18 0.18
11 41 0.40
12 27 0.26
13 11 0.11
14 4 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (11 bp):
TATATATAATA
Found at i:9436 original size:40 final size:40
Alignment explanation
Indices: 9383--9464 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 40
9373 ATATATATAT
9383 AATATATATATATATATATATTAGTTTTAATTTTTTTCTCAA
1 AATATATATATATATATATA-T-GTTTTAATTTTTTTCTCAA
*
9425 AATATATATATATATATATATTTTTTAATTTTTTTCTCAA
1 AATATATATATATATATATATGTTTTAATTTTTTTCTCAA
9465 CTTTTGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 18 0.46
41 1 0.03
42 20 0.51
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (40 bp):
AATATATATATATATATATATGTTTTAATTTTTTTCTCAA
Found at i:9898 original size:215 final size:215
Alignment explanation
Indices: 9522--10011 Score: 874
Period size: 215 Copynumber: 2.3 Consensus size: 215
9512 TTGATCCCTT
9522 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
*
9587 TTTTATTTGCATCTAAAATTGACTCATACTTATTACTTATTTCTATTTTTTAATTGGTCCATAAC
66 TTTTATTTGCATCTAAAATTGACTCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAAC
*
9652 TTTTTAAATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTC
131 TTTTTAAATGGGTATAATTCAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTC
9717 AATTTGACCCCTCATCAATG
196 AATTTGACCCCTCATCAATG
9737 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
*
9802 TTTTATTTGCATCTGAAATTGAC-CATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAAC
66 TTTTATTTGCATCTAAAATTGACTCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAAC
* *
9866 TTTTTTAAATGGGTATAATTCATTATTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTT
131 -TTTTTAAATGGGTATAATTCAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTT
* * *
9931 CGATTTGATCCCTCATTAATG
195 CAATTTGACCCCTCATCAATG
* *
9952 TGTGTTGTTTAATTTATTTAAATTTTTATTTATAATTTCATATTTGTTTAATTTAGTCCT
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCT
10012 TAAATTTGTA
Statistics
Matches: 264, Mismatches: 10, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
214 40 0.15
215 224 0.85
ACGTcount: A:0.28, C:0.12, G:0.08, T:0.52
Consensus pattern (215 bp):
TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
TTTTATTTGCATCTAAAATTGACTCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAAC
TTTTTAAATGGGTATAATTCAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTC
AATTTGACCCCTCATCAATG
Found at i:10798 original size:27 final size:29
Alignment explanation
Indices: 10760--10819 Score: 88
Period size: 27 Copynumber: 2.1 Consensus size: 29
10750 TTTAAGCTAT
* *
10760 ATTTATTTTATATTTTT-ATATA-TAATC
1 ATTTAATTTATATTTTTAATATATTAATA
10787 ATTTAATTTATATTTTTAATATATTAATA
1 ATTTAATTTATATTTTTAATATATTAATA
10816 ATTT
1 ATTT
10820 TAGTTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 16 0.55
28 5 0.17
29 8 0.28
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTTAATTTATATTTTTAATATATTAATA
Found at i:10829 original size:29 final size:26
Alignment explanation
Indices: 10760--10830 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 26
10750 TTTAAGCTAT
* *
10760 ATTTATTTTATATTTTTATATATAATC
1 ATTTATTTTAT-TTTTAATATATAATA
10787 ATTTAATTTATATTTTTAATATATTAATA
1 ATTT-ATTT-TATTTTTAATATA-TAATA
10816 ATTTTAGTTTTATTT
1 A-TTTA-TTTTATTT
10831 AATGATTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
27 4 0.11
28 13 0.35
29 14 0.38
30 6 0.16
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (26 bp):
ATTTATTTTATTTTTAATATATAATA
Found at i:11006 original size:21 final size:21
Alignment explanation
Indices: 10982--11041 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
10972 ATTTTTAAAT
**
10982 TTTTTAAAAATATTGGATTTA
1 TTTTTAAAAATATTAAATTTA
* *
11003 TTTTTATACATATTAAATTTA
1 TTTTTAAAAATATTAAATTTA
*
11024 ATTTT-AAAATATTAAATT
1 TTTTTAAAAATATTAAATT
11042 CATTACTATT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (21 bp):
TTTTTAAAAATATTAAATTTA
Found at i:13218 original size:158 final size:158
Alignment explanation
Indices: 12976--13332 Score: 461
Period size: 158 Copynumber: 2.2 Consensus size: 158
12966 GTGGTACATT
* * *
12976 AGCATGTGGTTTAAATTTGGTAAAAAATGA-ACTTAAAATAAATCACAAAATGAATGAATAAGGA
1 AGCATGTGGTTCAAATTTGGTAAAAAA-AATACTTAAAATAAATCACAAAATGAATGAATAAAGA
* * *
13040 GATTATGAAAAATTGAAGGACTAAATTAAAAAATAAAGAAA-ATGTTATAAAAAATAAGAATTGA
65 AATTATGAAAAATTGAAGGACTAAATTAAAAAATAAA-AAATATATTATAAAAAAGAAGAATTGA
*
13104 AAGTAGACATGTATTCTACTATG-GTTAGG
129 AAGTACACATGTATTCTACTATGAGTTAGG
* * * *
13133 AGCATGTGGTTCAAATTTGATAAAAAAACATACTTAAAATAAATGACGAATTGAA-GAAATAAAG
1 AGCATGTGGTTCAAATTTGGTAAAAAAA-ATACTTAAAATAAATCACAAAATGAATG-AATAAAG
* * * * *
13197 AAATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTTATTTTCAAAAAGAGGAATTGA
64 AAATTATGAAAAATTGAAGGACTAAATTAAAAAATAAAAAATATATTATAAAAAAGAAGAATTGA
*
13262 AAGTACACATGTATTCTACTATGATTTAGG
129 AAGTACACATGTATTCTACTATGAGTTAGG
* *
13292 AGCATGTGATACAAATTTGGTAAAAAAAATGGACTTAAAAT
1 AGCATGTGGTTCAAATTTGGTAAAAAAAAT--ACTTAAAAT
13333 GAAGGAGAAA
Statistics
Matches: 173, Mismatches: 20, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
157 30 0.17
158 104 0.60
159 30 0.17
160 9 0.05
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (158 bp):
AGCATGTGGTTCAAATTTGGTAAAAAAAATACTTAAAATAAATCACAAAATGAATGAATAAAGAA
ATTATGAAAAATTGAAGGACTAAATTAAAAAATAAAAAATATATTATAAAAAAGAAGAATTGAAA
GTACACATGTATTCTACTATGAGTTAGG
Found at i:19310 original size:16 final size:16
Alignment explanation
Indices: 19289--19319 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
19279 TTGTTAGGTC
19289 AAAGTTTAAACTTGGA
1 AAAGTTTAAACTTGGA
19305 AAAGTTTAAACTTGG
1 AAAGTTTAAACTTGG
19320 GTTAATAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (16 bp):
AAAGTTTAAACTTGGA
Found at i:19365 original size:21 final size:21
Alignment explanation
Indices: 19341--19384 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
19331 AAAGGATGTA
19341 ATTAAA-ATTAAAATTTTTATT
1 ATTAAATATT-AAATTTTTATT
* *
19362 ATTAAATATTTAATTTTTGTT
1 ATTAAATATTAAATTTTTATT
19383 AT
1 AT
19385 GTAATGTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTAAATATTAAATTTTTATT
Found at i:23758 original size:96 final size:94
Alignment explanation
Indices: 23595--23770 Score: 223
Period size: 96 Copynumber: 1.9 Consensus size: 94
23585 AAAAACTAAT
* * * *
23595 TTTTACATGTAATATAATTTAATAATGTCATAAGTTCTACTTCTTGTTTTATTTAGAAATAAATA
1 TTTTACATGTAATATAATATAATAATATCATAAGTTCTACTTCTTGTTCTATTTAGAAAAAAATA
23660 AAATAATAATATATTAAGAGTAAATAAAATA
66 AAA-AATAATA-ATTAAGAGTAAATAAAATA
* *
23691 TTTTACATGTAATTTACA-ATAATAATATCATAAGTTCTATTTCTTGTTCT-TTTA-AAAAAAAT
1 TTTTACATGTAATATA-ATATAATAATATCATAAGTTCTACTTCTTGTTCTATTTAGAAAAAAA-
*
23753 TTAAAAAATAGTAATTAA
64 -TAAAAAATAATAATTAA
23771 AAGTTATTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
94 11 0.16
95 10 0.14
96 48 0.69
97 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (94 bp):
TTTTACATGTAATATAATATAATAATATCATAAGTTCTACTTCTTGTTCTATTTAGAAAAAAATA
AAAAATAATAATTAAGAGTAAATAAAATA
Found at i:30393 original size:198 final size:198
Alignment explanation
Indices: 30036--30435 Score: 574
Period size: 198 Copynumber: 2.0 Consensus size: 198
30026 AAAAAGGTGC
* *
30036 AAGTAAAAGTATTAAAGCATGTAGTAGATGATGTAGGTATGTAAGAAAATACTAAAGCAAATAGT
1 AAGTAAAAGTATTAAAGCA-GTAGTAGATGATGTAGGTATGTAAGAAAATAATAAAGCAAAAAGT
* *
30101 AGAATTTTTTTTGAAAGTGTTAAAAATAATTGAAAAAAATGAATTTAAAAAATCAAATATTAAAA
65 AGAAATTTGTTTGAAAGTGTTAAAAATAATTGAAAAAAATGAATTT-AAAAATCAAATATTAAAA
* ** * *
30166 AAATTCGTAATCAAAGTAAGAAGTAAAGAAGGCAAC-AGAGGAAGTATG-GAAACTCTAGTTTCA
129 AAAATCACAACCAAAGTAAGAAGTAAAGAAGGCAACGAGAGGAAG-AGGAGAAACTCTAGTTTCA
30229 AAGTGT
193 AAGTGT
* * *
30235 AAGTAAAAGTATTAAAGCA-TAGTAGATGATGTAGGTGTGTAAGAAAGTAATAAATCAAAAAGTA
1 AAGTAAAAGTATTAAAGCAGTAGTAGATGATGTAGGTATGTAAGAAAATAATAAAGCAAAAAGTA
*
30299 GAGAATTTGTTTGGAAGTGTTAAAAATAATTGAGAAAAAATGAATTT-AAAATCAAAATATTAAA
66 GA-AATTTGTTTGAAAGTGTTAAAAATAATTGA-AAAAAATGAATTTAAAAATC-AAATATTAAA
* * *
30363 AAAAATCACAACCAAAGTAAGAAGTAAAGAAGGCAACGGGAGGAAGCGGAGAAACTTTAGTTTCA
128 AAAAATCACAACCAAAGTAAGAAGTAAAGAAGGCAACGAGAGGAAGAGGAGAAACTCTAGTTTCA
30428 AAGTGT
193 AAGTGT
30434 AA
1 AA
30436 ACCTTTCATC
Statistics
Matches: 180, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
197 48 0.27
198 71 0.39
199 61 0.34
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.25
Consensus pattern (198 bp):
AAGTAAAAGTATTAAAGCAGTAGTAGATGATGTAGGTATGTAAGAAAATAATAAAGCAAAAAGTA
GAAATTTGTTTGAAAGTGTTAAAAATAATTGAAAAAAATGAATTTAAAAATCAAATATTAAAAAA
AATCACAACCAAAGTAAGAAGTAAAGAAGGCAACGAGAGGAAGAGGAGAAACTCTAGTTTCAAAG
TGT
Found at i:33216 original size:15 final size:15
Alignment explanation
Indices: 33192--33225 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
33182 CGTCAAGTGT
* *
33192 TGGTGGTGGTGATGA
1 TGGTGATGGTGATCA
33207 TGGTGATGGTGATCA
1 TGGTGATGGTGATCA
33222 TGGT
1 TGGT
33226 AGTGATAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.03, G:0.47, T:0.35
Consensus pattern (15 bp):
TGGTGATGGTGATCA
Found at i:38533 original size:9 final size:10
Alignment explanation
Indices: 38505--38550 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
38495 TTTAAAATAT
38505 ATATATTTGTA
1 ATATATTT-TA
* *
38516 TTATATTTTT
1 ATATATTTTA
38526 AT-TATTTTA
1 ATATATTTTA
38535 ATATATTTT-
1 ATATATTTTA
38544 ATATATT
1 ATATATT
38551 CGTATTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
9 15 0.50
10 8 0.27
11 7 0.23
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (10 bp):
ATATATTTTA
Found at i:38538 original size:28 final size:27
Alignment explanation
Indices: 38505--38566 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
38495 TTTAAAATAT
**
38505 ATATATTTGTATTATATTTTTATTATTTTA
1 ATATA-TTGTA-TATATTCGTATT-TTTTA
*
38535 ATATATTTTATATATTCGTATTTTTTA
1 ATATATTGTATATATTCGTATTTTTTA
38562 ATATA
1 ATATA
38567 ACAAATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 10 0.34
28 10 0.34
29 4 0.14
30 5 0.17
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (27 bp):
ATATATTGTATATATTCGTATTTTTTA
Found at i:38549 original size:11 final size:11
Alignment explanation
Indices: 38502--38549 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
38492 TATTTTAAAA
38502 TATATATATTT
1 TATATATATTT
38513 GTAT-TATATTT
1 -TATATATATTT
38524 T-TAT-TATTT
1 TATATATATTT
38533 TA-ATATATTT
1 TATATATATTT
38543 TATATAT
1 TATATAT
38550 TCGTATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
9 9 0.28
10 9 0.28
11 11 0.34
12 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (11 bp):
TATATATATTT
Found at i:38550 original size:19 final size:20
Alignment explanation
Indices: 38504--38550 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
38494 TTTTAAAATA
*
38504 TATATATTTGTATTATATTT
1 TATATATTTGTAATATATTT
38524 T-TATTATTT-TAATATATTT
1 TATA-TATTTGTAATATATTT
38543 TATATATT
1 TATATATT
38551 CGTATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TATATATTTGTAATATATTT
Found at i:40639 original size:17 final size:16
Alignment explanation
Indices: 40619--40650 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
40609 GGTTATTATA
40619 TAAAATATAAATAAATT
1 TAAAATATAAA-AAATT
40636 TAAAATATAAAAAAT
1 TAAAATATAAAAAAT
40651 AAATCTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAATATAAAAAATT
Found at i:46225 original size:2 final size:2
Alignment explanation
Indices: 46220--46244 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46210 ATACACACGC
46220 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 A
46245 ACAATACAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47089 original size:13 final size:13
Alignment explanation
Indices: 47071--47105 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
47061 TCTCATTCTC
47071 TTTTTTCTTTAAT
1 TTTTTTCTTTAAT
* *
47084 TTTTTTCATTCAT
1 TTTTTTCTTTAAT
47097 TTTTTTCTT
1 TTTTTTCTT
47106 CTGCTCTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTCTTTAAT
Found at i:48609 original size:20 final size:20
Alignment explanation
Indices: 48584--48622 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
48574 AAATAATGTA
48584 ATAATAATATG-ATTTGTATC
1 ATAATAA-ATGCATTTGTATC
48604 ATAATAAATGCATTTGTAT
1 ATAATAAATGCATTTGTAT
48623 GATTCTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (20 bp):
ATAATAAATGCATTTGTATC
Done.