Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold857
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: 55858
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:184 original size:49 final size:47
Alignment explanation
Indices: 1--319 Score: 507
Period size: 47 Copynumber: 6.7 Consensus size: 47
* *
1 CATTAGGACTTATCACATATATATACACTTTCACATTCATCACATTGGC
1 CATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGC
*
50 CATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGG-
1 CATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
*
96 CAGTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
1 CATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
143 CATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGC
1 CATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGC
*
192 CATTAGGCCTTATCACATATATACACTTTCACATTCATCACATTGGC
1 CATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
239 CATTCA-GCCTTATCACATATATACACTTTCACATTCATCACATCGGC
1 CATT-AGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
* * *
286 CATTAGGCCTTATCACATATGTATACATTCACAT
1 CATTAGGCCTTATCACATATATACACTTTCACAT
320 CACAATTATC
Statistics
Matches: 254, Mismatches: 11, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
46 45 0.18
47 147 0.58
48 1 0.00
49 61 0.24
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.33
Consensus pattern (47 bp):
CATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
Found at i:278 original size:25 final size:25
Alignment explanation
Indices: 203--281 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
193 ATTAGGCCTT
203 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * *
228 ATCACAT-T-GGC-CATTCAGCCTT-
1 ATCACATATATACACTTTCA-CATTC
250 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
275 ATCACAT
1 ATCACAT
282 CGGCCATTAG
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 12 0.29
23 5 0.12
24 5 0.12
25 19 0.46
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:355 original size:143 final size:141
Alignment explanation
Indices: 1--319 Score: 498
Period size: 142 Copynumber: 2.2 Consensus size: 141
* ** * *
1 CATTAGGACTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
1 CATTAGGCCTTATCACATATATATACAC-TTCACATTCATCACATCAGCCATTAGGCCATATCAC
66 ATATATACACTTTCACATTCATCACATCGGCAGTAGGCCTTATCACATATATACACTTTCACATT
65 ATATATACACTTTCACATTCATCACATCGGCAGTAGGCCTTATCACATATATACACTTTCACATT
131 CATCACATCGGC
130 CATCACATCGGC
* *
143 CATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 CATTAGGCCTTATCACATATATATACAC-TTCACATTCATCACATCAGCCATTAGGCCATATCAC
* *
208 ATATATACACTTTCACATTCATCACATTGGCCATTCA-GCCTTATCACATATATACACTTTCACA
65 ATATATACACTTTCACATTCATCACATCGG-CAGT-AGGCCTTATCACATATATACACTTTCACA
272 TTCATCACATCGGC
128 TTCATCACATCGGC
*
286 CATTAGGCCTTATCACATATGTATACA-TTCACAT
1 CATTAGGCCTTATCACATATATATACACTTCACAT
320 CACAATTATC
Statistics
Matches: 169, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
141 7 0.04
142 91 0.54
143 70 0.41
144 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.33
Consensus pattern (141 bp):
CATTAGGCCTTATCACATATATATACACTTCACATTCATCACATCAGCCATTAGGCCATATCACA
TATATACACTTTCACATTCATCACATCGGCAGTAGGCCTTATCACATATATACACTTTCACATTC
ATCACATCGGC
Found at i:6315 original size:13 final size:12
Alignment explanation
Indices: 6271--6394 Score: 54
Period size: 12 Copynumber: 9.8 Consensus size: 12
6261 AAAAACGAAA
*
6271 TGATTAAAAACT
1 TGATGAAAAACT
* * *
6283 TGACGGAAAATT
1 TGATGAAAAACT
*
6295 TTATGAAAAGACT
1 TGATGAAAA-ACT
6308 TGATGAAAAACT
1 TGATGAAAAACT
* *
6320 TTA-AAAATAACT
1 TGATGAAA-AACT
*
6332 TGCT-ACAAAACT
1 TGATGA-AAAACT
*
6344 TGATAAAAAAACT
1 TGAT-GAAAAACT
*
6357 TGGTAATTAAAAACT
1 T-G--ATGAAAAACT
*
6372 TGATAAAATAACT
1 TGATGAAA-AACT
*
6385 AGATGAAAAA
1 TGATGAAAAA
6395 TACTTGAAGA
Statistics
Matches: 84, Mismatches: 18, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
11 3 0.04
12 39 0.46
13 29 0.35
14 3 0.04
15 8 0.10
16 2 0.02
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:6317 original size:25 final size:24
Alignment explanation
Indices: 6276--6322 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
6266 CGAAATGATT
* *
6276 AAAAACTTGACGGAAAATTTTATG
1 AAAAACTTGACGAAAAACTTTATG
*
6300 AAAAGACTTGATGAAAAACTTTA
1 AAAA-ACTTGACGAAAAACTTTA
6323 AAAATAACTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.28
Consensus pattern (24 bp):
AAAAACTTGACGAAAAACTTTATG
Found at i:6353 original size:12 final size:12
Alignment explanation
Indices: 6300--6401 Score: 62
Period size: 12 Copynumber: 7.9 Consensus size: 12
6290 AAATTTTATG
*
6300 AAAAGACTTGAT
1 AAAAAACTTGAT
* *
6312 GAAAAACTTTA-
1 AAAAAACTTGAT
*
6323 AAAATAACTTGCT
1 AAAA-AACTTGAT
*
6336 ACAAAACTTGAT
1 AAAAAACTTGAT
6348 AAAAAAACTTGGTAAT
1 -AAAAAACTT-G--AT
*
6364 TAAAAACTTGAT
1 AAAAAACTTGAT
*
6376 AAAATAACTAGAT
1 AAAA-AACTTGAT
6389 GAAAAATACTTGA
1 -AAAAA-ACTTGA
6402 AGAAAGAAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
11 3 0.04
12 25 0.37
13 19 0.28
14 11 0.16
15 8 0.12
16 2 0.03
ACGTcount: A:0.53, C:0.10, G:0.11, T:0.26
Consensus pattern (12 bp):
AAAAAACTTGAT
Found at i:6370 original size:15 final size:13
Alignment explanation
Indices: 6300--6401 Score: 68
Period size: 13 Copynumber: 7.8 Consensus size: 13
6290 AAATTTTATG
*
6300 AAAAGACTTGAT-
1 AAAAAACTTGATA
*
6312 GAAAAACTT--TA
1 AAAAAACTTGATA
*
6323 AAAATAACTTGCT-
1 AAAA-AACTTGATA
*
6336 ACAAAACTTGATA
1 AAAAAACTTGATA
*
6349 AAAAAACTTGGTA
1 AAAAAACTTGATA
6362 ATTAAAAACTTGATA
1 A--AAAAACTTGATA
* *
6377 AAATAACTAGATGA
1 AAAAAACTTGAT-A
*
6391 AAAATACTTGA
1 AAAAAACTTGA
6402 AGAAAGAAAA
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
10 1 0.01
11 3 0.04
12 19 0.28
13 24 0.35
14 10 0.14
15 12 0.17
ACGTcount: A:0.53, C:0.10, G:0.11, T:0.26
Consensus pattern (13 bp):
AAAAAACTTGATA
Found at i:6393 original size:25 final size:25
Alignment explanation
Indices: 6309--6394 Score: 68
Period size: 28 Copynumber: 3.4 Consensus size: 25
6299 GAAAAGACTT
* *
6309 GATGAAAAACTTTA-AAAATAACTT
1 GATGAAAAACTTGATAAAATAACTA
* * *
6333 GCT-ACAAAACTTGATAAAAAAACTTG
1 GATGA-AAAACTTGATAAAATAAC-TA
*
6359 GTAATTAAAAACTTGATAAAATAACTA
1 G--ATGAAAAACTTGATAAAATAACTA
6386 GATGAAAAA
1 GATGAAAAA
6395 TACTTGAAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
23 1 0.02
24 10 0.21
25 14 0.29
26 2 0.04
27 2 0.04
28 18 0.38
29 1 0.02
ACGTcount: A:0.55, C:0.09, G:0.10, T:0.26
Consensus pattern (25 bp):
GATGAAAAACTTGATAAAATAACTA
Found at i:6418 original size:19 final size:19
Alignment explanation
Indices: 6390--6427 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
6380 TAACTAGATG
*
6390 AAAAATACTTGAA-GAAAGA
1 AAAAACACTT-AATGAAAGA
6409 AAAAACACTTAATGAAAGA
1 AAAAACACTTAATGAAAGA
6428 CTTAATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.63, C:0.08, G:0.13, T:0.16
Consensus pattern (19 bp):
AAAAACACTTAATGAAAGA
Found at i:11340 original size:49 final size:47
Alignment explanation
Indices: 11166--11645 Score: 278
Period size: 47 Copynumber: 10.6 Consensus size: 47
11156 CCCTTCGGGA
* * * * * *
11166 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
11213 CCTGTCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
11260 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
11307 CTTATCACATATATATACACTTTCACATTCATCACATCGG-TA-TA--C
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
** *
11352 ACTT-TCAC--AT-T-CA---TCACATT-GGC-CATTCGGCC-TTA-TC
1 -CTTATCACATATATACACTTTCACATTCATCACA-TCGGCCATTAGGC
* * *
11389 ACATATAT-ACACT-T-T-CACATTCATCA--CATCGGCCATTCGGCC-TTA-TC
1 -C-T-TATCACA-TATATACACTTTCA-CATTCATC--ACA-TCGGCCATTAGGC
* * * * *
11436 ATATATATACACT-T-T-CACATTCATCA--CATCGGCTATTAGGCC--T----
1 CT-TAT-CACA-TATATACACTTTCA-CATTCATC-AC-A-TCGGCCATTAGGC
11479 --TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
11524 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
11573 CTTATCCCATATATACACTTTCACATTCATCACACCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
11620 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
11646 CACAATTATC
Statistics
Matches: 362, Mismatches: 32, Indels: 78
0.77 0.07 0.17
Matches are distributed among these distances:
34 2 0.01
35 5 0.01
36 9 0.02
37 3 0.01
38 2 0.01
39 14 0.04
40 9 0.02
41 15 0.04
42 4 0.01
44 4 0.01
45 12 0.03
46 6 0.02
47 201 0.56
48 1 0.00
49 75 0.21
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:11409 original size:74 final size:75
Alignment explanation
Indices: 11271--11420 Score: 266
Period size: 76 Copynumber: 2.0 Consensus size: 75
11261 TTATCACATA
11271 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATT
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATATACACTTTCACATT
11336 CATCACATCGG
65 CATCACATCGG
* *
11347 TATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC-ATATATACACTTTCACATTC
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACATTC
11411 ATCACATCGG
66 ATCACATCGG
11421 CCATTCGGCC
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
74 30 0.42
76 42 0.58
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (75 bp):
TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACATTC
ATCACATCGG
Found at i:11455 original size:94 final size:94
Alignment explanation
Indices: 11347--11645 Score: 499
Period size: 94 Copynumber: 3.2 Consensus size: 94
11337 ATCACATCGG
*
11347 TATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCA
1 TATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACACTTTCACATTCA
*
11412 TCACATCGGCCATTCGGCCTTATCATATA
66 TCACATCGGCCATTAGGCCTTATCATATA
* *
11441 TATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCA
1 TATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACACTTTCACATTCA
11506 TCACATCGGCCATTAGGCCTTATCACATATA
66 TCACATCGGCCATTAGGCCTTAT--CATATA
*
11537 TATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCCCATATATACACTTTCACATTCA
1 TATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACACTTTCACATTCA
* *
11602 TCACACCGGCCATTAGGCCTTATCACATA
66 TCACATCGGCCATTAGGCCTTATCATATA
* *
11631 TATATACATTCACAT
1 TATACACTTTCACAT
11646 CACAATTATC
Statistics
Matches: 192, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
94 102 0.53
96 90 0.47
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (94 bp):
TATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACACTTTCACATTCA
TCACATCGGCCATTAGGCCTTATCATATA
Found at i:11541 original size:217 final size:217
Alignment explanation
Indices: 11166--11563 Score: 724
Period size: 217 Copynumber: 1.8 Consensus size: 217
11156 CCCTTCGGGA
* * * *
11166 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTCGGCCCTATCACATATATACAC
11231 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
11296 GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGTATACACTTTCACA
131 GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGTATACACTTTCACA
11361 TTCATCACATTGGCCATTCGGC
196 TTCATCACATTGGCCATTCGGC
* * * *
11383 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCATATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTCGGCCCTATCACATATATACAC
11448 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
11513 GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGG
131 GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGG
11564 CCATTCGGCC
Statistics
Matches: 173, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
217 173 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (217 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTCGGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGTATACACTTTCACA
TTCATCACATTGGCCATTCGGC
Found at i:11562 original size:96 final size:96
Alignment explanation
Indices: 11347--11645 Score: 516
Period size: 96 Copynumber: 3.2 Consensus size: 96
11337 ATCACATCGG
*
11347 TATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCA
1 TATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACACTTTCACATTCA
*
11412 TCACATCGGCCATTCGGCCTTAT--CATATA
66 TCACATCGGCCATTAGGCCTTATCACATATA
* *
11441 TATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCA
1 TATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACACTTTCACATTCA
11506 TCACATCGGCCATTAGGCCTTATCACATATA
66 TCACATCGGCCATTAGGCCTTATCACATATA
*
11537 TATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCCCATATATACACTTTCACATTCA
1 TATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACACTTTCACATTCA
*
11602 TCACACCGGCCATTAGGCCTTATCACATATA
66 TCACATCGGCCATTAGGCCTTATCACATATA
11633 TATACA--TTCACAT
1 TATACACTTTCACAT
11646 CACAATTATC
Statistics
Matches: 195, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
94 91 0.47
96 104 0.53
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (96 bp):
TATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACACTTTCACATTCA
TCACATCGGCCATTAGGCCTTATCACATATA
Found at i:11681 original size:143 final size:141
Alignment explanation
Indices: 11347--11645 Score: 463
Period size: 143 Copynumber: 2.1 Consensus size: 141
11337 ATCACATCGG
* ** * *
11347 TATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCA
1 TATACACATTCACATTCATCACATCAGCCATTAGGCCATATCACATATATACACTTTCACATTCA
* * *
11412 TCACATCGGCCATTCGGCCTTATCATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
66 TCACATCGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACACCGGCCATTAGGC
11477 CTTATCACATA
131 CTTATCACATA
* * *
11488 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATT
1 TATACACATTCACATTCATCACATCAGCCATTAGGCCATATCAC--ATATATACACTTTCACATT
*
11553 CATCACATCGGCCATTCGGCCTTATCCCATATATACACTTTCACATTCATCACACCGGCCATTAG
64 CATCACATCGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACACCGGCCATTAG
11618 GCCTTATCACATA
129 GCCTTATCACATA
*
11631 TATATACATTCACAT
1 TATACACATTCACAT
11646 CACAATTATC
Statistics
Matches: 148, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
141 42 0.28
143 106 0.72
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (141 bp):
TATACACATTCACATTCATCACATCAGCCATTAGGCCATATCACATATATACACTTTCACATTCA
TCACATCGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACACCGGCCATTAGGC
CTTATCACATA
Found at i:13651 original size:13 final size:14
Alignment explanation
Indices: 13633--13665 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
13623 ACGTTCTTAG
*
13633 CTCGCA-TATACTA
1 CTCGCAGTATACAA
13646 CTCGCAGTATACAA
1 CTCGCAGTATACAA
13660 CTCGCA
1 CTCGCA
13666 AGCAACACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.24
Consensus pattern (14 bp):
CTCGCAGTATACAA
Found at i:17988 original size:30 final size:30
Alignment explanation
Indices: 17953--18153 Score: 138
Period size: 30 Copynumber: 6.7 Consensus size: 30
17943 TTTCATGGCT
17953 CAATCCCTTTTCATTATTTGATGGTCGTCA
1 CAATCCCTTTTCATTATTTGATGGTCGTCA
* *
17983 TAATCCCTTTTCATT-GTTGATGGTCGTCA
1 CAATCCCTTTTCATTATTTGATGGTCGTCA
* * *** *
18012 CCATCCCTTTTCATAATTTGATAACCG-AA
1 CAATCCCTTTTCATTATTTGATGGTCGTCA
* * * * * ***
18041 GCTATCCCTTTTCATAATTCGATAGCCAAAA
1 -CAATCCCTTTTCATTATTTGATGGTCGTCA
* * * * *
18072 CTATCCCTTTTCATAATTTGATAGCCG-AA
1 CAATCCCTTTTCATTATTTGATGGTCGTCA
* *
18101 GCTATCCCTTTTCATTATTCGATGGTCGTCA
1 -CAATCCCTTTTCATTATTTGATGGTCGTCA
* *
18132 CCATCCCTTTTCATAATTTGAT
1 CAATCCCTTTTCATTATTTGAT
18154 AGCCAAGGCT
Statistics
Matches: 142, Mismatches: 24, Indels: 10
0.81 0.14 0.06
Matches are distributed among these distances:
29 28 0.20
30 111 0.78
31 3 0.02
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (30 bp):
CAATCCCTTTTCATTATTTGATGGTCGTCA
Found at i:18017 original size:29 final size:30
Alignment explanation
Indices: 17953--18025 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 30
17943 TTTCATGGCT
*
17953 CAATCCCTTTTCATTATTTGATGGTCGTCA
1 CAATCCCTTTTCATTAGTTGATGGTCGTCA
*
17983 TAATCCCTTTTCATT-GTTGATGGTCGTCA
1 CAATCCCTTTTCATTAGTTGATGGTCGTCA
*
18012 CCATCCCTTTTCAT
1 CAATCCCTTTTCAT
18026 AATTTGATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 25 0.64
30 14 0.36
ACGTcount: A:0.18, C:0.26, G:0.12, T:0.44
Consensus pattern (30 bp):
CAATCCCTTTTCATTAGTTGATGGTCGTCA
Found at i:18168 original size:30 final size:29
Alignment explanation
Indices: 18014--18180 Score: 185
Period size: 30 Copynumber: 5.6 Consensus size: 29
18004 GGTCGTCACC
*
18014 ATCCCTTTTCATAATTTGATAACCGAAGCT
1 ATCCCTTTTCATAATTTGATAGCC-AAGCT
* *
18044 ATCCCTTTTCATAATTCGATAGCCAAAACT
1 ATCCCTTTTCATAATTTGATAGCC-AAGCT
18074 ATCCCTTTTCATAATTTGATAGCCGAAGCT
1 ATCCCTTTTCATAATTTGATAGCC-AAGCT
* * * *
18104 ATCCCTTTTCATTATTCGATGGTCGTC-A-CC
1 ATCCCTTTTCATAATTTGATAG-C--CAAGCT
18134 ATCCCTTTTCATAATTTGATAGCCAAGGCT
1 ATCCCTTTTCATAATTTGATAGCCAA-GCT
*
18164 ATCCCTTTTCATTATTT
1 ATCCCTTTTCATAATTT
18181 TAATAGCTGA
Statistics
Matches: 115, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
27 1 0.01
28 1 0.01
29 1 0.01
30 109 0.95
31 2 0.02
33 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.39
Consensus pattern (29 bp):
ATCCCTTTTCATAATTTGATAGCCAAGCT
Found at i:18176 original size:60 final size:60
Alignment explanation
Indices: 17985--18179 Score: 286
Period size: 60 Copynumber: 3.3 Consensus size: 60
17975 GGTCGTCATA
* *
17985 ATCCCTTTTCATTGTT-GATGGTCGTCACCATCCCTTTTCATAATTTGATAACCGAAGCT
1 ATCCCTTTTCATTATTCGATGGTCGTCACCATCCCTTTTCATAATTTGATAGCCGAAGCT
* * * *** *
18044 ATCCCTTTTCATAATTCGATAGCCAAAACTATCCCTTTTCATAATTTGATAGCCGAAGCT
1 ATCCCTTTTCATTATTCGATGGTCGTCACCATCCCTTTTCATAATTTGATAGCCGAAGCT
18104 ATCCCTTTTCATTATTCGATGGTCGTCACCATCCCTTTTCATAATTTGATAGCC-AAGGCT
1 ATCCCTTTTCATTATTCGATGGTCGTCACCATCCCTTTTCATAATTTGATAGCCGAA-GCT
18164 ATCCCTTTTCATTATT
1 ATCCCTTTTCATTATT
18180 TTAATAGCTG
Statistics
Matches: 118, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
59 16 0.14
60 102 0.86
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (60 bp):
ATCCCTTTTCATTATTCGATGGTCGTCACCATCCCTTTTCATAATTTGATAGCCGAAGCT
Found at i:22640 original size:40 final size:40
Alignment explanation
Indices: 22590--22690 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 40
22580 AGAGCATTCT
* * *
22590 TTTCAATAGATTCAGTAGGTATGACTTGAGAGCGCATACA
1 TTTCAGTAGATTCAGTAGGTATGACTCGAAAGCGCATACA
* * * **
22630 TTTCAGTAGATTCAGTAAGTATGGCTCGAAAGTGCATATG
1 TTTCAGTAGATTCAGTAGGTATGACTCGAAAGCGCATACA
*
22670 TTTTAGTAGATTCAGTAGGTA
1 TTTCAGTAGATTCAGTAGGTA
22691 CCGCTCGATG
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.34
Consensus pattern (40 bp):
TTTCAGTAGATTCAGTAGGTATGACTCGAAAGCGCATACA
Found at i:26774 original size:27 final size:26
Alignment explanation
Indices: 26712--26774 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 26
26702 TATTAATTTA
* * *
26712 TCTATTTTTTATTTTAATTTTAATAT
1 TCTATTTTTTAATTTAATTGTAACAT
*
26738 TCTTTGTTTTTAATTTAATTGTAACAT
1 TCTAT-TTTTTAATTTAATTGTAACAT
*
26765 TCTAATTTTT
1 TCTATTTTTT
26775 CTTTTGTTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 9 0.30
27 21 0.70
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.65
Consensus pattern (26 bp):
TCTATTTTTTAATTTAATTGTAACAT
Found at i:31021 original size:23 final size:23
Alignment explanation
Indices: 30990--31040 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
30980 ATCTACTTTC
* *
30990 TTACTGTAGTAACTTTT-GGGGTA
1 TTACAGTAGTAA-TTTTCGGGATA
31013 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
31036 TTACA
1 TTACA
31041 TTTCCCTCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:32653 original size:50 final size:50
Alignment explanation
Indices: 32527--32814 Score: 267
Period size: 50 Copynumber: 5.7 Consensus size: 50
32517 TGATAATAAA
* * ** * *
32527 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCCT-GT-
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATATTG
* * * **
32575 ACTGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTTTCATATTG
1 A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATATTG
* ** *
32626 ATGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCA-TG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCAT-ATTG
* * * * * * *
32676 GTGCCAACGCCATGTCCTAAACTTGGTCTTACATGGGACCTTTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATATTG
* *
32726 GTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCAT-A--T---TG
32782 ATGCCAATGCCATGTCCCAGACATGGTCTTACA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACA
32815 CTGGCTCACA
Statistics
Matches: 192, Mismatches: 37, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
48 1 0.01
49 37 0.19
50 118 0.61
51 2 0.01
53 1 0.01
56 33 0.17
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.28
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATATTG
Found at i:35666 original size:19 final size:19
Alignment explanation
Indices: 35635--35684 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
35625 CATTCGGAGG
35635 AAGAAGAAA--AAA-TAAA
1 AAGAAGAAAGGAAATTAAA
**
35651 AAGAAGACAAGGAAATTAGG
1 AAGAAGA-AAGGAAATTAAA
35671 AAGAAGAAAGGAAA
1 AAGAAGAAAGGAAA
35685 ATCGGGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 7 0.25
17 2 0.07
19 10 0.36
20 9 0.32
ACGTcount: A:0.68, C:0.02, G:0.24, T:0.06
Consensus pattern (19 bp):
AAGAAGAAAGGAAATTAAA
Found at i:35686 original size:20 final size:19
Alignment explanation
Indices: 35651--35700 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
35641 AAAAAATAAA
*
35651 AAGAAGACAAGGAAATTAGG
1 AAGAAGA-AAGGAAATCAGG
*
35671 AAGAAGAAAGGAAAATCGGG
1 AAGAAGAAAGG-AAATCAGG
*
35691 AAAAAGAAAG
1 AAGAAGAAAG
35701 AAGAAAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.60, C:0.04, G:0.30, T:0.06
Consensus pattern (19 bp):
AAGAAGAAAGGAAATCAGG
Found at i:38065 original size:5 final size:5
Alignment explanation
Indices: 38055--38080 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
38045 TGAGCATTCG
38055 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
38081 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:38842 original size:30 final size:31
Alignment explanation
Indices: 38803--38862 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
38793 AGATGTGGGA
*
38803 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
38834 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
38863 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:39090 original size:9 final size:9
Alignment explanation
Indices: 39073--39109 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
39063 TATAGTTTGA
39073 TATTCGAAT
1 TATTCGAAT
*
39082 TATTTGAAT
1 TATTCGAAT
*
39091 TATTCAAAT
1 TATTCGAAT
39100 TATTCGAAT
1 TATTCGAAT
39109 T
1 T
39110 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:42331 original size:116 final size:116
Alignment explanation
Indices: 42127--42343 Score: 380
Period size: 116 Copynumber: 1.9 Consensus size: 116
42117 TGATAAATTG
* * *
42127 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAATTTATTAAATTATATACAATTATTAATTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
42192 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTGTGTGAATGTAAAAT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTGTGTGAATGTAAAAT
* * *
42243 TATTAAGTCAAAAAATTGTATTAATGTTTAGTAAAATTATCAAATTATGTAAAATTATTATTTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
42308 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATT
42344 ACGTTAAGGT
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
116 95 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.40
Consensus pattern (116 bp):
TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTGTGTGAATGTAAAAT
Found at i:42369 original size:20 final size:22
Alignment explanation
Indices: 42341--42386 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
42331 CAAATCTAAC
*
42341 ATTACGTTAA-GG-TTAGGGTT
1 ATTAAGTTAAGGGTTTAGGGTT
42361 ATTAAGTTAAGGGTTTAGGGTT
1 ATTAAGTTAAGGGTTTAGGGTT
42383 -TTAA
1 ATTAA
42387 TTGAATTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.39
21 6 0.26
22 8 0.35
ACGTcount: A:0.28, C:0.02, G:0.28, T:0.41
Consensus pattern (22 bp):
ATTAAGTTAAGGGTTTAGGGTT
Found at i:42435 original size:50 final size:51
Alignment explanation
Indices: 42341--42544 Score: 188
Period size: 50 Copynumber: 4.3 Consensus size: 51
42331 CAAATCTAAC
* * * * *
42341 ATTACGTTAAGGTTAGGGTTATTAAGTTAAGGGTTT-AGGGTTTTAATTGA
1 ATTAGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAATTAA
42391 ATTAGGTTAGGGTTAGGGTTTTTAA-TTAAGGGTTTAAGGTTTTTAATTAA
1 ATTAGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAATTAA
* * * *
42441 ATTAGGTTAGGGTT----TTAAATTAAATT-A-GG-TTAGGGTTTTTAA-T-C
1 ATTAGGTTAGGGTTAGGGTT--TTTAAGTTAAGGGTTTAAGGTTTTTAATTAA
*
42485 A--A--TTA-GGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAA
1 ATTAGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAATTAA
42531 ATTAGGTTAGGGTT
1 ATTAGGTTAGGGTT
42545 TTTAATTAAA
Statistics
Matches: 125, Mismatches: 11, Indels: 35
0.73 0.06 0.20
Matches are distributed among these distances:
39 4 0.03
40 3 0.02
41 6 0.05
42 2 0.02
43 4 0.03
44 14 0.11
45 2 0.02
46 15 0.12
47 2 0.02
48 6 0.05
49 12 0.10
50 51 0.41
51 4 0.03
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (51 bp):
ATTAGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAATTAA
Found at i:42461 original size:23 final size:23
Alignment explanation
Indices: 42401--42929 Score: 521
Period size: 23 Copynumber: 22.6 Consensus size: 23
42391 ATTAGGTTAG
*
42401 GGTTAGGGTTTTTAATT-AA--G
1 GGTTAGGGTTTTTAATTAAATTA
*
42421 GGTTTAAGGTTTTTAATTAAATTA
1 GG-TTAGGGTTTTTAATTAAATTA
*
42445 GGTTAGGGTTTTAAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
42468 GGTTAGGGTTTTTAA-TCAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
42490 GGTTAGGGTTTTTAAGTT-AA--G
1 GGTTAGGGTTTTTAA-TTAAATTA
42511 GGTTTAGGGTTTTTAATTAAATTA
1 GG-TTAGGGTTTTTAATTAAATTA
42535 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
42558 GGTTAGGCTATGGTTTTTAATCAAATTA
1 GGTTA-G----GGTTTTTAATTAAATTA
*
42586 --TTAGGGTTTTTAAGTT-AA--G
1 GGTTAGGGTTTTTAA-TTAAATTA
42605 GGTTTAGGGTTTTTAATTAAATTA
1 GG-TTAGGGTTTTTAATTAAATTA
*
42629 GGTTAGGATTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
42652 GGTTAGGCTAGAGTTTTTAATTAAATTA
1 GGTTA-G---G-GTTTTTAATTAAATTA
** *
42680 GGTTAGGGTTTTTGGTACAAATTA
1 GGTTAGGGTTTTTAAT-TAAATTA
*
42704 GGTTAGGATTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
42727 GGTTAGGCTAGGGTTTTCAATTAAATTA
1 GG-T----TAGGGTTTTTAATTAAATTA
*
42755 GGTTAGGGTTTTTAAGTT-AA--G
1 GGTTAGGGTTTTTAA-TTAAATTA
42776 GGTTTAGGGTTTTTAATTAAATTA
1 GG-TTAGGGTTTTTAATTAAATTA
* *
42800 GGTTAGGTTTTTTCATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
42823 GGTTAGGTTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
42846 GGTTAGAGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
* ** *
42869 AGTTAGGGTTTTTGGTACAAATTA
1 GGTTAGGGTTTTTAAT-TAAATTA
42893 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
* *
42916 GGCTAAGGTTTTTA
1 GGTTAGGGTTTTTA
42930 TTACATAAAA
Statistics
Matches: 428, Mismatches: 42, Indels: 75
0.79 0.08 0.14
Matches are distributed among these distances:
20 2 0.00
21 35 0.08
22 69 0.16
23 206 0.48
24 53 0.12
25 1 0.00
26 3 0.01
27 3 0.01
28 56 0.13
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.46
Consensus pattern (23 bp):
GGTTAGGGTTTTTAATTAAATTA
Found at i:43452 original size:18 final size:18
Alignment explanation
Indices: 43429--43463 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43419 CGGAAAAGGA
*
43429 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
43447 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
43464 AAACGCAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:45374 original size:22 final size:22
Alignment explanation
Indices: 45349--45404 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
45339 AAATATAGAT
45349 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
45371 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
45393 TTGAGAGGAATT
1 TTGAGA-GAATT
45405 AAGAGGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 28 0.85
23 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:45377 original size:51 final size:51
Alignment explanation
Indices: 45262--45377 Score: 196
Period size: 51 Copynumber: 2.3 Consensus size: 51
45252 TATTTTAAAA
* * * *
45262 AAGGAAATTTAGAAGAAATTGAAATTAAATATGGATTTGAGAGAATTTTTG
1 AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
45313 AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
1 AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
45364 AAGGAAATTGAGAG
1 AAGGAAATTGAGAG
45378 AATTTTGGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.46, C:0.00, G:0.25, T:0.29
Consensus pattern (51 bp):
AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
Found at i:45818 original size:24 final size:24
Alignment explanation
Indices: 45763--45818 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
45753 TAAAATATTG
* *
45763 ATTTTAAATATTATAATTTTTAAT
1 ATTTTTAATATTATAATTTTCAAT
* *
45787 AGTGTTAATATTATAATTTTCAAT
1 ATTTTTAATATTATAATTTTCAAT
45811 ATTTTTAA
1 ATTTTTAA
45819 ACATACATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (24 bp):
ATTTTTAATATTATAATTTTCAAT
Found at i:46136 original size:19 final size:18
Alignment explanation
Indices: 46103--46140 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
46093 TTCATGTTAT
*
46103 AATTTTAATTTAATAATA
1 AATTTTAAATTAATAATA
46121 AATTTTAAAATTAATAATA
1 AATTTT-AAATTAATAATA
46140 A
1 A
46141 TTTGAGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTTTAAATTAATAATA
Found at i:46142 original size:18 final size:17
Alignment explanation
Indices: 46101--46143 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
46091 ATTTCATGTT
*
46101 ATAATTTTAATTTAATA
1 ATAATTTTAAATTAATA
46118 ATAAATTTTAAAATTAATA
1 AT-AATTTT-AAATTAATA
46137 ATAATTT
1 ATAATTT
46144 GAGAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 2 0.09
18 11 0.48
19 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAATTTTAAATTAATA
Found at i:46150 original size:18 final size:19
Alignment explanation
Indices: 46112--46150 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
46102 TAATTTTAAT
*
46112 TTAATAATAAATTTTAAAA
1 TTAATAATAAATTTGAAAA
*
46131 TTAATAAT-AATTTGAGAA
1 TTAATAATAAATTTGAAAA
46149 TT
1 TT
46151 TAAATAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (19 bp):
TTAATAATAAATTTGAAAA
Found at i:46153 original size:19 final size:18
Alignment explanation
Indices: 46109--46159 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
46099 TTATAATTTT
*
46109 AATTTAATAATAAATTTTA
1 AATTTAATAAT-AATTTGA
*
46128 AAATTAATAATAATTTGA
1 AATTTAATAATAATTTGA
46146 GAATTTAAATAATA
1 -AATTT-AATAATA
46160 TTCCTAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.22
19 14 0.52
20 7 0.26
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (18 bp):
AATTTAATAATAATTTGA
Found at i:46269 original size:23 final size:23
Alignment explanation
Indices: 46239--46283 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
46229 TTAATAATAA
46239 ATATTTT-ACAATATAAAATATGG
1 ATATTTTAACAATAT-AAATATGG
*
46262 ATATTTTAATAATATAAATATG
1 ATATTTTAACAATATAAATATG
46284 AGTATCTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (23 bp):
ATATTTTAACAATATAAATATGG
Found at i:46275 original size:38 final size:33
Alignment explanation
Indices: 46191--46253 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
46181 CATTTACATT
*
46191 AATATTTTAATAATAAATATATTACAATCTATG
1 AATATTTTAATAATAAATATATTACAATATATG
*
46224 AATA-TTTAATAATAAATATTTTACAATATA
1 AATATTTTAATAATAAATATATTACAATATA
46254 AAATATGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (33 bp):
AATATTTTAATAATAAATATATTACAATATATG
Found at i:48078 original size:50 final size:50
Alignment explanation
Indices: 48003--48239 Score: 271
Period size: 50 Copynumber: 4.7 Consensus size: 50
47993 GTGATGTTGC
**
48003 TAGGTCATGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAAATG-A
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCG-AATGAA
* *
48053 TAGGTCGCATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATG-A
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GAATGAA
* * * * * **
48103 TAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAAT-GAA
* * * *
48154 TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATGAA
* *
48204 AATGGTCAAATGTGTAGTACTATGTGCAGGCTACTA
1 TA-GGTCACATGTGTAGTACTATGTGCAGGCTACTA
48240 TGTGAACCGG
Statistics
Matches: 161, Mismatches: 22, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
49 3 0.02
50 87 0.54
51 71 0.44
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (50 bp):
TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATGAA
Found at i:48249 original size:102 final size:101
Alignment explanation
Indices: 48062--48249 Score: 288
Period size: 102 Copynumber: 1.9 Consensus size: 101
48052 ATAGGTCGCA
* **
48062 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTACTATGT
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGAAAGGTCAAATGTGTAGTACTATGT
*
48127 GCAGGCTACTATGCGTACCGGATAGCTTCGATCACG
66 GCAGGCTACTATGCGAACCGGATAGCTTCGATCACG
* *
48163 TGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GGATGAAAATGGTCAAATGTGTAGTACTAT
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATG-AAA-GGTCAAATGTGTAGTACTAT
*
48227 GTGCAGGCTACTATGTGAACCGG
64 GTGCAGGCTACTATGCGAACCGG
48250 GTATCATTTA
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
100 4 0.05
101 35 0.45
102 39 0.50
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (101 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGAAAGGTCAAATGTGTAGTACTATGT
GCAGGCTACTATGCGAACCGGATAGCTTCGATCACG
Found at i:51385 original size:78 final size:78
Alignment explanation
Indices: 51247--51469 Score: 206
Period size: 78 Copynumber: 2.8 Consensus size: 78
51237 TTGAATGCTG
* * * * * * *
51247 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAAACCGGGCTAAG-TCCCGAAGGCAT
51310 TTGTGCGAG-A-TACAA
63 TTGTGCGAGCATTA-AA
* * *
51325 GTTCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATA-TAAATCCGGGTTAAGTCCCGAAGGCAT
1 --TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCAT
*
51388 TCGTGCGAGTCATTAAA
63 TTGTGCGAG-CATTAAA
* * *
51405 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
51470 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 13, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
77 1 0.01
78 52 0.43
79 43 0.35
80 23 0.19
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGCATTAAA
Found at i:51416 original size:40 final size:38
Alignment explanation
Indices: 51247--51467 Score: 182
Period size: 39 Copynumber: 5.6 Consensus size: 38
51237 TTGAATGCTG
* * * * *
51247 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGT-ATTAAA
**
51287 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAG-A-TACAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTATTA-AA
*
51325 GTTCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAG-ATATAAA
1 --TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTAT-TAAA
51365 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGT-ATTAAA
* *
51405 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAG-TATTAAA
* * *
51444 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
51468 TGAACGAGGA
Statistics
Matches: 154, Mismatches: 13, Indels: 29
0.79 0.07 0.15
Matches are distributed among these distances:
37 2 0.01
38 16 0.10
39 64 0.42
40 61 0.40
41 11 0.07
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (38 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTATTAAA
Found at i:51487 original size:79 final size:79
Alignment explanation
Indices: 51327--51502 Score: 189
Period size: 79 Copynumber: 2.3 Consensus size: 79
51317 AGATACAAGT
* * *
51327 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATATAAATCCGGGTTAAGTCCCGAAGGCATTCG
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATATAAAACCGGGCTAAGTCCCGAAGGCATTCG
** *
51391 TGCGAGTCATTAAA
66 AACGAGTCACTAAA
* * * *
51405 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATA-TAAAACCGGGCTAAGTCCCGAAGGCATTC
* *
51469 GAACGAG-GAGCTATA
65 GAACGAGTCA-CTAAA
*
51484 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
51503 TACGTGATTT
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
78 38 0.46
79 44 0.54
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATATAAAACCGGGCTAAGTCCCGAAGGCATTCG
AACGAGTCACTAAA
Done.