Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3809
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: 66031
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:239 original size:39 final size:39
Alignment explanation
Indices: 125--239 Score: 99
Period size: 41 Copynumber: 2.8 Consensus size: 39
115 CTAGCACAAA
* * *
125 CGCCGCTGAAGACTAAGACCTTTAGCGGCGCTTTAGTGGAAG
1 CGCCGCT-AAGACT-A-ATCTTTAGCGGCGTTTTTGTGGAAG
* * *
167 CGCCGCTAAGACCCTGATCTTTAGCGACATTTTTG-GAGAAG
1 CGCCGCTAAGA--CTAATCTTTAGCGGCGTTTTTGTG-GAAG
208 CGCCGCTAAAGA-TAATCTTTAGCGGCGTTTTT
1 CGCCGCT-AAGACTAATCTTTAGCGGCGTTTTT
240 TTCTCAAACG
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
39 17 0.28
40 1 0.02
41 29 0.48
42 11 0.18
43 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.27
Consensus pattern (39 bp):
CGCCGCTAAGACTAATCTTTAGCGGCGTTTTTGTGGAAG
Found at i:318 original size:85 final size:82
Alignment explanation
Indices: 213--409 Score: 206
Period size: 81 Copynumber: 2.4 Consensus size: 82
203 AGAAGCGCCG
* *** *
213 CTAAAGA--TAATCTTTAGCGGCGTTTTTTTCTCAAACGCCGCAATAGACCCTGATCGTATACCG
1 CTAAAGACCTAATCTTTAGCGGCGCTTTCCCCTC-AACACCGCAATAGACCCTG-TC--ATACCG
* * *
276 GCGCTTTGACCATAAACGCCA
62 GCGCTTCGACCACAAACACCA
* *
297 -TGAAAG-CCTAATCTTTAGCGGCGCTTTCCCCTCAACACTGCAATAGACCCTGTCATAGCGGCG
1 CT-AAAGACCTAATCTTTAGCGGCGCTTTCCCCTCAACACCGCAATAGACCCTGTCATACCGGCG
360 CTTCGACCACAAACACCA
65 CTTCGACCACAAACACCA
*
378 CTAAAGAACCTAATCTTTAGCGGTGC-TTCCCC
1 CTAAAG-ACCTAATCTTTAGCGGCGCTTTCCCC
410 ACAAACGCCG
Statistics
Matches: 96, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
81 27 0.28
82 7 0.07
83 20 0.21
84 21 0.22
85 21 0.22
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (82 bp):
CTAAAGACCTAATCTTTAGCGGCGCTTTCCCCTCAACACCGCAATAGACCCTGTCATACCGGCGC
TTCGACCACAAACACCA
Found at i:424 original size:42 final size:41
Alignment explanation
Indices: 352--485 Score: 126
Period size: 42 Copynumber: 3.2 Consensus size: 41
342 GACCCTGTCA
*
352 TAGCGGCGCTTCGACCACAAACACCACTAAAGAACCTAATCTT
1 TAGCGGCGCTTC-ACCACAAACGCC-CTAAAGAACCTAATCTT
* * *
395 TAGCGGTGCTTCCCCACAAACGCCGCTAAAG-ACCATGATCTT
1 TAGCGGCGCTTCACCACAAACGCC-CTAAAGAACC-TAATCTT
* * ** * *
437 TAGTGGCGTTTTTTCCACAAACGCCCTAAAGACCCTTATCTT
1 TAGCGGCG-CTTCACCACAAACGCCCTAAAGAACCTAATCTT
479 TAGCGGC
1 TAGCGGC
486 ACTTTGACAA
Statistics
Matches: 75, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
41 3 0.04
42 46 0.61
43 26 0.35
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (41 bp):
TAGCGGCGCTTCACCACAAACGCCCTAAAGAACCTAATCTT
Found at i:428 original size:83 final size:84
Alignment explanation
Indices: 220--434 Score: 217
Period size: 83 Copynumber: 2.6 Consensus size: 84
210 CCGCTAAAGA
* *** * *
220 TAATCTTTAGCGGCGTTTTTTTCTCAAACGCCGCAATAGACCCTGATCGTATACCGGCGCTTTGA
1 TAATCTTTAGCGGCGCTTTCCCCACAAACGCCGCAATAGACCCTGATCG-ATACCGGCGCTTCGA
* *
285 CCATAAACGCCATGAAAGCC
65 CCACAAACACCATGAAAGCC
* * * *
305 TAATCTTTAGCGGCGCTTTCCCCTC-AACACTGCAATAGACCCTG-TC-ATAGCGGCGCTTCGAC
1 TAATCTTTAGCGGCGCTTTCCCCACAAACGCCGCAATAGACCCTGATCGATACCGGCGCTTCGAC
367 CACAAACACCACT-AAAGAACC
66 CACAAACACCA-TGAAAG--CC
* *
388 TAATCTTTAGCGGTGC-TTCCCCACAAACGCCGCTAA-AGACCATGATC
1 TAATCTTTAGCGGCGCTTTCCCCACAAACGCCGC-AATAGACCCTGATC
435 TTTAGTGGCG
Statistics
Matches: 109, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
81 27 0.25
82 8 0.07
83 32 0.29
84 21 0.19
85 21 0.19
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (84 bp):
TAATCTTTAGCGGCGCTTTCCCCACAAACGCCGCAATAGACCCTGATCGATACCGGCGCTTCGAC
CACAAACACCATGAAAGCC
Found at i:976 original size:66 final size:65
Alignment explanation
Indices: 852--1015 Score: 215
Period size: 66 Copynumber: 2.5 Consensus size: 65
842 TTGCCGCTCT
* * *
852 GCTT-TCTTGCTGCTGCATCTGCTTTAAGCTGTGCTGGAGTTCTTCATACTTTCGTTGAACCTCA
1 GCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTGCTAGAGTTCTTCATACTTTCGTTGAACCTCA
* *
916 GCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGCTAGAGTTCTTCATATCTTT-TTTGAACCT
1 GCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGT-GCTAGAGTTCTTCATA-CTTTCGTTGAACCT
980 CA
64 CA
* * * *
982 GCTTCTCTCGATGTTGCCTCCGCTTTAAGTTGTG
1 GCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTG
1016 TAATTTGTCA
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 4 0.05
65 26 0.30
66 53 0.61
67 4 0.05
ACGTcount: A:0.13, C:0.26, G:0.20, T:0.41
Consensus pattern (65 bp):
GCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTGCTAGAGTTCTTCATACTTTCGTTGAACCTCA
Found at i:6424 original size:9 final size:9
Alignment explanation
Indices: 6388--6749 Score: 161
Period size: 9 Copynumber: 43.0 Consensus size: 9
6378 AATTGCACGG
6388 GTAAGTTAT
1 GTAAGTTAT
*
6397 GT-A-TTGT
1 GTAAGTTAT
*
6404 GTAAGCTAT
1 GTAAGTTAT
*
6413 GTAAGTTGT
1 GTAAGTTAT
6422 GT-A-TTAT
1 GTAAGTTAT
6429 GTAAGTTAT
1 GTAAGTTAT
6438 -T-A-TTAT
1 GTAAGTTAT
6444 GCTTTAAGTTAT
1 G---TAAGTTAT
*
6456 GTAAGTAAT
1 GTAAGTTAT
6465 GT-A-TTAT
1 GTAAGTTAT
*
6472 GTAAGTTGT
1 GTAAGTTAT
*
6481 GT-A-TAAT
1 GTAAGTTAT
*
6488 GTTAGTTAT
1 GTAAGTTAT
**
6497 CAAAGTTAT
1 GTAAGTTAT
6506 GT-A-TTAT
1 GTAAGTTAT
6513 GTAAGTTAT
1 GTAAGTTAT
*
6522 TTAAGTTAT
1 GTAAGTTAT
*
6531 GTAA--CAT
1 GTAAGTTAT
*
6538 GTAAATTAT
1 GTAAGTTAT
*
6547 GTAAGTTGT
1 GTAAGTTAT
*
6556 GT-A-TAAT
1 GTAAGTTAT
*
6563 GTTAGTTAT
1 GTAAGTTAT
**
6572 CAAAGTTAT
1 GTAAGTTAT
6581 GT-A-TTAT
1 GTAAGTTAT
6588 GTAAGTTAT
1 GTAAGTTAT
*
6597 TTAAGTTAT
1 GTAAGTTAT
*
6606 GTAA--CAT
1 GTAAGTTAT
*
6613 GTAAATTAT
1 GTAAGTTAT
6622 GTAAGTTAT
1 GTAAGTTAT
* *
6631 GTAGGCTAT
1 GTAAGTTAT
* *
6640 GTATGTTAA
1 GTAAGTTAT
*
6649 GTAAGTAAT
1 GTAAGTTAT
6658 GT-A-TTAT
1 GTAAGTTAT
*
6665 GTAAGTTGT
1 GTAAGTTAT
*
6674 GT-A-TAAT
1 GTAAGTTAT
*
6681 GTTAGTTAT
1 GTAAGTTAT
**
6690 CAAAGTTAT
1 GTAAGTTAT
6699 GT-A-TTAT
1 GTAAGTTAT
***
6706 GTGTTTCTAT
1 GTAAGT-TAT
*
6716 TTAAGTTAT
1 GTAAGTTAT
*
6725 GTAAGTTGT
1 GTAAGTTAT
*
6734 GT-A-TTGT
1 GTAAGTTAT
6741 GTAAGTTAT
1 GTAAGTTAT
6750 TAAAAATTGA
Statistics
Matches: 258, Mismatches: 62, Indels: 66
0.67 0.16 0.17
Matches are distributed among these distances:
6 4 0.02
7 69 0.27
8 22 0.09
9 151 0.59
10 6 0.02
11 1 0.00
12 5 0.02
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:6429 original size:16 final size:16
Alignment explanation
Indices: 6410--6689 Score: 99
Period size: 16 Copynumber: 17.8 Consensus size: 16
6400 TTGTGTAAGC
*
6410 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
6426 TATGTAAGTTAT-TAT
1 TATGTAAGTTATGTAT
*
6441 TATGCT---TTAAG--T
1 TATG-TAAGTTATGTAT
*
6453 TATGTAAGTAATGTAT
1 TATGTAAGTTATGTAT
*
6469 TATGTAAGTTGTGTA-
1 TATGTAAGTTATGTAT
*
6484 TA---ATGTTA-G--T
1 TATGTAAGTTATGTAT
**
6494 TATCAAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
6510 TATGTAAGTTATTTAAGT
1 TATGTAAGTTATGT-A-T
*
6528 TATGTAA--CATGTAAAT
1 TATGTAAGTTATGT--AT
*
6544 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* * **
6560 AATGTTAGTTATCAAAGT
1 TATGTAAGTTAT-GTA-T
6578 TATGT-A-TTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
6594 TATTTAAGTTATGTAA
1 TATGTAAGTTATGTAT
* *
6610 CATGTAAATTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
6628 TATGTAGGCTATGTATGT
1 TATGTAAGTTATGTA--T
* *
6646 TAAGTAAGTAATGTAT
1 TATGTAAGTTATGTAT
*
6662 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* *
6678 AATGTTAGTTAT
1 TATGTAAGTTAT
6690 CAAAGTTATG
Statistics
Matches: 193, Mismatches: 44, Indels: 54
0.66 0.15 0.19
Matches are distributed among these distances:
10 2 0.01
11 2 0.01
12 9 0.05
13 8 0.04
14 4 0.02
15 9 0.05
16 105 0.54
17 9 0.05
18 45 0.23
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:6496 original size:25 final size:25
Alignment explanation
Indices: 6448--6676 Score: 189
Period size: 25 Copynumber: 9.1 Consensus size: 25
6438 TATTATGCTT
6448 TAAGTTATGTAAGTAATGT-A-TTATG
1 TAAGTTATGT-A-TAATGTAAGTTATG
* * *
6473 TAAGTTGTGTATAATGTTAGTTATC
1 TAAGTTATGTATAATGTAAGTTATG
* * *
6498 AAAGTTATGTATTATGTAAGTTATT
1 TAAGTTATGTATAATGTAAGTTATG
*
6523 TAAGTTATGTA-ACATGTAAATTATG
1 TAAGTTATGTATA-ATGTAAGTTATG
* * *
6548 TAAGTTGTGTATAATGTTAGTTATC
1 TAAGTTATGTATAATGTAAGTTATG
* * *
6573 AAAGTTATGTATTATGTAAGTTATT
1 TAAGTTATGTATAATGTAAGTTATG
*
6598 TAAGTTATGTA-ACATGTAAATTATG
1 TAAGTTATGTATA-ATGTAAGTTATG
* *
6623 TAAGTTATGTAGGCT-ATGTATGTTAAG
1 TAAGTTATGTA---TAATGTAAGTTATG
* * *
6650 TAAGTAATGTATTATGTAAGTTGTG
1 TAAGTTATGTATAATGTAAGTTATG
6675 TA
1 TA
6677 TAATGTTAGT
Statistics
Matches: 163, Mismatches: 31, Indels: 20
0.76 0.14 0.09
Matches are distributed among these distances:
23 6 0.04
24 3 0.02
25 134 0.82
26 1 0.01
27 19 0.12
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (25 bp):
TAAGTTATGTATAATGTAAGTTATG
Found at i:6527 original size:50 final size:50
Alignment explanation
Indices: 6468--6707 Score: 171
Period size: 50 Copynumber: 4.9 Consensus size: 50
6458 AAGTAATGTA
*
6468 TTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAG
1 TTATGTAAGTTATGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAG
* * * ** * * *
6518 TTATTTAAGTTATGTA-ACATGTAAATTATGTAAGTTGTGTATAATGTTAG
1 TTATGTAAGTTATGTATA-ATGTTAGTTATCAAAGTTATGTATTATGTAAG
** * * ** ** *
6568 TTATCAAAGTTATGTATTATGTAAGTTATTTAAGTTATGTAACATGTAAA
1 TTATGTAAGTTATGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAG
*
6618 TTATGTAAGTTATGTAGGCT-ATG-TA-TGT-T--AAG-TAAGTA--ATGT-A-
1 TTATGTAAGTTATGTA---TAATGTTAGT-TATCAAAGTTATGTATTATGTAAG
*
6661 TTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGT
1 TTATGTAAGTTATGTATAATGTTAGTTATCAAAGTTATGTATTATGT
6708 GTTTCTATTT
Statistics
Matches: 150, Mismatches: 25, Indels: 32
0.72 0.12 0.15
Matches are distributed among these distances:
40 1 0.01
41 3 0.02
42 3 0.02
43 17 0.11
44 1 0.01
45 7 0.05
46 5 0.03
47 5 0.03
48 7 0.05
49 1 0.01
50 94 0.63
51 2 0.01
52 3 0.02
53 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.45
Consensus pattern (50 bp):
TTATGTAAGTTATGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAG
Found at i:6527 original size:75 final size:74
Alignment explanation
Indices: 6446--6633 Score: 306
Period size: 75 Copynumber: 2.5 Consensus size: 74
6436 ATTATTATGC
6446 TTTAAGTTATGTAAGTAATGT-ATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTAT
1 TTTAAGTTATGTAA--AATGTAATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTAT
6510 TATGTAAGTTA
64 TATGTAAGTTA
*
6521 TTTAAGTTATGTAACATGTAAATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATT
1 TTTAAGTTATGTAAAATGT-AATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATT
6586 ATGTAAGTTA
65 ATGTAAGTTA
* *
6596 TTTAAGTTATGTAACATGTAAATTATGTAAGTTATGTA
1 TTTAAGTTATGTAAAATGT-AATTATGTAAGTTGTGTA
6634 GGCTATGTAT
Statistics
Matches: 109, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
73 4 0.04
75 105 0.96
ACGTcount: A:0.35, C:0.02, G:0.18, T:0.46
Consensus pattern (74 bp):
TTTAAGTTATGTAAAATGTAATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTA
TGTAAGTTA
Found at i:6689 original size:25 final size:24
Alignment explanation
Indices: 6654--6707 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
6644 GTTAAGTAAG
** *
6654 TAATG-TATTATGTAAGTTGTGTA
1 TAATGTTATTATCAAAGTTATGTA
6677 TAATGTTAGTTATCAAAGTTATGTA
1 TAATGTTA-TTATCAAAGTTATGTA
*
6702 TTATGT
1 TAATGT
6708 GTTTCTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 5 0.20
24 2 0.08
25 18 0.72
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (24 bp):
TAATGTTATTATCAAAGTTATGTA
Found at i:6838 original size:27 final size:27
Alignment explanation
Indices: 6808--6863 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
6798 TTTATTAAAA
*
6808 ATATAGGTTTTAATATTTTAAAATAAC
1 ATATAGGTTTTAATATTTAAAAATAAC
6835 ATATAGGTTTTAATATTTAAAAATAAC
1 ATATAGGTTTTAATATTTAAAAATAAC
6862 AT
1 AT
6864 TTACAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (27 bp):
ATATAGGTTTTAATATTTAAAAATAAC
Found at i:6972 original size:121 final size:121
Alignment explanation
Indices: 6835--7059 Score: 407
Period size: 121 Copynumber: 1.9 Consensus size: 121
6825 TTAAAATAAC
*
6835 ATATAGGTTTTAATATTTAAAAATAACATTTACAATTATTTTTAAAATTATAAAATTCATT-TCT
1 ATATAGGTTTTAATATTTAAAAATAACATTTACAATTATTTTTAAAATTATAAAATTCATTGAC-
6899 AATAAAATTGAAATATAGGTTATATATCCATACCATATATGGGGTGATATATTAAAA
65 AATAAAATTGAAATATAGGTTATATATCCATACCATATATGGGGTGATATATTAAAA
* *
6956 ATATAGGTTTTAATATTTAAAAATAACATTTACAATTATTTTTAAAATTATCAAATTTATTGACA
1 ATATAGGTTTTAATATTTAAAAATAACATTTACAATTATTTTTAAAATTATAAAATTCATTGACA
7021 ATAAAATTGAAATATAGGTTATATATCCATACCATATAT
66 ATAAAATTGAAATATAGGTTATATATCCATACCATATAT
7060 ATAAATTTTT
Statistics
Matches: 100, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
121 99 0.99
122 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (121 bp):
ATATAGGTTTTAATATTTAAAAATAACATTTACAATTATTTTTAAAATTATAAAATTCATTGACA
ATAAAATTGAAATATAGGTTATATATCCATACCATATATGGGGTGATATATTAAAA
Found at i:7112 original size:18 final size:17
Alignment explanation
Indices: 7089--7159 Score: 61
Period size: 17 Copynumber: 3.8 Consensus size: 17
7079 ATATATAAAG
7089 TTTAAGTAATGTAATATA
1 TTTAAGTAA-GTAATATA
7107 TTTAAGTAATGTAAGTTATAAA
1 TTTAAGTAA-GTAA--TAT--A
**
7129 TTTTTGTAAGTAATATA
1 TTTAAGTAAGTAATATA
*
7146 TTTTAGTAAGTAAT
1 TTTAAGTAAGTAAT
7160 GTAAGTAATG
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
17 14 0.30
18 14 0.30
19 3 0.07
20 3 0.07
21 4 0.09
22 8 0.17
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (17 bp):
TTTAAGTAAGTAATATA
Found at i:7216 original size:13 final size:13
Alignment explanation
Indices: 7200--7290 Score: 73
Period size: 13 Copynumber: 6.9 Consensus size: 13
7190 GTAAGTCGTG
7200 TATTTAAGTAATA
1 TATTTAAGTAATA
7213 TATTTAA-TCCAAT-
1 TATTTAAGT--AATA
* * *
7226 TCTAGTAAGTAATG
1 TAT-TTAAGTAATA
7240 TATTTAAGTAATA
1 TATTTAAGTAATA
7253 TATTTAAGTAAT-
1 TATTTAAGTAATA
*
7265 T-TTAGTAATTAATA
1 TATT--TAAGTAATA
7279 TATTTAAGTAAT
1 TATTTAAGTAAT
7291 GTAAGTTATA
Statistics
Matches: 62, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
11 2 0.03
12 2 0.03
13 46 0.74
14 9 0.15
15 3 0.05
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (13 bp):
TATTTAAGTAATA
Found at i:7305 original size:39 final size:38
Alignment explanation
Indices: 7183--7307 Score: 108
Period size: 40 Copynumber: 3.2 Consensus size: 38
7173 TATATACTTT
** * * *
7183 AATTTTAGTAAGTCGTGTATTTAAGTAATATATTTAATCC
1 AATTTTAGTAAGTAATATATTTAAGTAATATAGTTAA--G
* * *
7223 AATTCTAGTAAGTAATGTATTTAAGTAATATATTTAAG
1 AATTTTAGTAAGTAATATATTTAAGTAATATAGTTAAG
* *
7261 TAATTTTAGTAATTAATATATTTAAGTAATGTAAGTTATA-
1 -AATTTTAGTAAGTAATATATTTAAGTAATAT-AGTTA-AG
7301 AATTTTA
1 AATTTTA
7308 AAAATATATA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
39 34 0.47
40 38 0.52
41 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (38 bp):
AATTTTAGTAAGTAATATATTTAAGTAATATAGTTAAG
Found at i:7356 original size:11 final size:11
Alignment explanation
Indices: 7325--7357 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
7315 ATATATTAAT
7325 AATTCATTGAC
1 AATTCATTGAC
7336 -ATTCATTGAC
1 AATTCATTGAC
*
7346 AATTCACTGAC
1 AATTCATTGAC
7357 A
1 A
7358 GTCAACCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.33
Consensus pattern (11 bp):
AATTCATTGAC
Found at i:10306 original size:9 final size:7
Alignment explanation
Indices: 10265--10307 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
10255 AAATTTTAGT
*
10265 TTTTTTA
1 TTTTATA
*
10272 TTTCAT-
1 TTTTATA
10278 TTTTATA
1 TTTTATA
10285 TTTTATA
1 TTTTATA
10292 TTTTATA
1 TTTTATA
*
10299 TTTTTTA
1 TTTTATA
10306 TT
1 TT
10308 CCAAATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTATA
Found at i:10932 original size:14 final size:14
Alignment explanation
Indices: 10912--10983 Score: 81
Period size: 14 Copynumber: 4.9 Consensus size: 14
10902 CACCCTAAAT
10912 TCCTAACCCCTAAC
1 TCCTAACCCCTAAC
*
10926 TCTTAACCCCTAAATC
1 TCCTAACCCCT-AA-C
* *
10942 TCCTAGCCCCTAAAT
1 TCCTAACCCCT-AAC
10957 TCCTAACCCCTAAC
1 TCCTAACCCCTAAC
*
10971 TCTTAACCCCTAA
1 TCCTAACCCCTAA
10984 ATCCCTAACA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
14 24 0.49
15 12 0.24
16 13 0.27
ACGTcount: A:0.29, C:0.43, G:0.01, T:0.26
Consensus pattern (14 bp):
TCCTAACCCCTAAC
Found at i:10953 original size:45 final size:44
Alignment explanation
Indices: 10904--10990 Score: 165
Period size: 45 Copynumber: 2.0 Consensus size: 44
10894 TTAATTGACA
10904 CCCTAAATTCCTAACCCCTAACTCTTAACCCCTAAATCTCCTAGC
1 CCCTAAATTCCTAACCCCTAACTCTTAACCCCTAAATC-CCTAGC
10949 CCCTAAATTCCTAACCCCTAACTCTTAACCCCTAAATCCCTA
1 CCCTAAATTCCTAACCCCTAACTCTTAACCCCTAAATCCCTA
10991 ACACTAACCC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 4 0.10
45 38 0.90
ACGTcount: A:0.30, C:0.43, G:0.01, T:0.26
Consensus pattern (44 bp):
CCCTAAATTCCTAACCCCTAACTCTTAACCCCTAAATCCCTAGC
Found at i:11005 original size:21 final size:22
Alignment explanation
Indices: 10919--11005 Score: 70
Period size: 21 Copynumber: 4.0 Consensus size: 22
10909 AATTCCTAAC
*
10919 CCCTAACTCTTAACCCCTAAAT
1 CCCTAACACTTAACCCCTAAAT
* * * ** *
10941 CTCCTAGCCCCTAAATTCCT-AAC
1 C-CCTA-ACACTTAACCCCTAAAT
*
10964 CCCTAACTCTTAACCCCTAAAT
1 CCCTAACACTTAACCCCTAAAT
10986 CCCTAACAC-TAACCCCTAAA
1 CCCTAACACTTAACCCCTAAA
11006 CCTTATATCC
Statistics
Matches: 49, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
21 19 0.39
22 15 0.31
23 7 0.14
24 8 0.16
ACGTcount: A:0.32, C:0.43, G:0.01, T:0.24
Consensus pattern (22 bp):
CCCTAACACTTAACCCCTAAAT
Found at i:11007 original size:8 final size:7
Alignment explanation
Indices: 10913--11004 Score: 51
Period size: 7 Copynumber: 12.7 Consensus size: 7
10903 ACCCTAAATT
10913 CCTAACC
1 CCTAACC
*
10920 CCTAACT
1 CCTAACC
*
10927 CTTAACC
1 CCTAACC
*
10934 CCTAAATCT
1 CCT-AA-CC
*
10943 CCTAGCC
1 CCTAACC
**
10950 CCTAAATT
1 CCT-AACC
10958 CCTAACC
1 CCTAACC
*
10965 CCTAACT
1 CCTAACC
*
10972 CTTAACC
1 CCTAACC
*
10979 CCTAAATC
1 CCT-AACC
10987 CCTAA-C
1 CCTAACC
*
10993 ACTAACC
1 CCTAACC
11000 CCTAA
1 CCTAA
11005 ACCTTATATC
Statistics
Matches: 61, Mismatches: 19, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
6 5 0.08
7 39 0.64
8 13 0.21
9 4 0.07
ACGTcount: A:0.32, C:0.43, G:0.01, T:0.24
Consensus pattern (7 bp):
CCTAACC
Found at i:11007 original size:29 final size:29
Alignment explanation
Indices: 10948--11007 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
10938 AATCTCCTAG
* * * *
10948 CCCCTAAATTCCTAACCCCTAACTCTTAA
1 CCCCTAAATCCCTAACCACTAACCCTAAA
10977 CCCCTAAATCCCTAA-CACTAACCCCTAAA
1 CCCCTAAATCCCTAACCACTAA-CCCTAAA
11006 CC
1 CC
11008 TTATATCCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.22
Consensus pattern (29 bp):
CCCCTAAATCCCTAACCACTAACCCTAAA
Found at i:11723 original size:19 final size:19
Alignment explanation
Indices: 11699--11741 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
11689 AAAATTATAT
*
11699 TTTTTATTTTTTTATTTCA
1 TTTTTATTTTTGTATTTCA
*
11718 TTTTTATTTTTGTATTTTA
1 TTTTTATTTTTGTATTTCA
11737 TTTTT
1 TTTTT
11742 TCTTATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTTATTTTTGTATTTCA
Found at i:12154 original size:21 final size:20
Alignment explanation
Indices: 12124--12164 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
12114 CCTAACTCCT
*
12124 AACCCCTAAACCTTAAATCCC
1 AACCCCTAAACCAT-AATCCC
*
12145 AACCCTTAAACCATAATCCC
1 AACCCCTAAACCATAATCCC
12165 TAAATCCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCCCTAAACCATAATCCC
Found at i:13115 original size:41 final size:41
Alignment explanation
Indices: 13055--13334 Score: 375
Period size: 41 Copynumber: 6.8 Consensus size: 41
13045 TTATTATTAC
* * * *
13055 TAGCGGCGCTTTTTTAAAAACGCCGCTAAAGGCCACAGCAA
1 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCAT
* * ** *
13096 TACCGGCGCTTCTTTAAAAACGCCGCTAAAGATCTGAGCAT
1 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCAT
* *
13137 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAAGACAGAGCAT
1 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCAT
* *
13178 TAGCGGCGCATT-TTCAAAAACGCCGCTAAAAGACAGAGCAT
1 TAGCGGCGC-TTCTTCAAAAACGCCGCTAAAGGCCAGAGCAT
*
13219 TAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGCAT
1 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCAT
*
13260 TAGCGGCACTTAC-TCAAAAACGCCGCTAAAGGCCAGAGCAT
1 TAGCGGCGCTT-CTTCAAAAACGCCGCTAAAGGCCAGAGCAT
* *
13301 TAGCGGCGTTTATTCAAAAACGCCGCTAAAGGCC
1 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCC
13335 CCAAAAACTC
Statistics
Matches: 215, Mismatches: 20, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
40 2 0.01
41 211 0.98
42 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.19
Consensus pattern (41 bp):
TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCAT
Found at i:13442 original size:39 final size:40
Alignment explanation
Indices: 13399--13494 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 40
13389 GAAAACGCCG
*
13399 TAATGCT-TATTTTTAGCGGAATTTTTGGATAAGCGCAGC
1 TAATGCTCTATTTTTAGCGGAATTTTTGGAAAAGCGCAGC
** * * ** *
13438 TAATGCTCTACCTTTAGTGGCATTTTTTTAAAAGCGCCGC
1 TAATGCTCTATTTTTAGCGGAATTTTTGGAAAAGCGCAGC
*
13478 TAATGCTCGATTTTTAG
1 TAATGCTCTATTTTTAG
13495 TGGCGTTTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
39 7 0.16
40 38 0.84
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.40
Consensus pattern (40 bp):
TAATGCTCTATTTTTAGCGGAATTTTTGGAAAAGCGCAGC
Found at i:13463 original size:40 final size:40
Alignment explanation
Indices: 13410--13504 Score: 100
Period size: 40 Copynumber: 2.4 Consensus size: 40
13400 AATGCTTATT
* * * *
13410 TTTAGCGGAATTTTTGGATAAGCGCAGCTAATGCTCTACC
1 TTTAGTGGCATTTTTGGAAAAGCGCAGCTAATGCTCGACC
** * **
13450 TTTAGTGGCATTTTTTTAAAAGCGCCGCTAATGCTCGATT
1 TTTAGTGGCATTTTTGGAAAAGCGCAGCTAATGCTCGACC
*
13490 TTTAGTGGCGTTTTT
1 TTTAGTGGCATTTTT
13505 TGTCCAAACG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (40 bp):
TTTAGTGGCATTTTTGGAAAAGCGCAGCTAATGCTCGACC
Found at i:13521 original size:41 final size:40
Alignment explanation
Indices: 13429--13505 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
13419 ATTTTTGGAT
* *
13429 AAGCGCAGCTAATGCTCTACCTTTAGTGGCATTTTTTTAA
1 AAGCGCCGCTAATGCTCGACCTTTAGTGGCATTTTTTTAA
** *
13469 AAGCGCCGCTAATGCTCGATTTTTAGTGGCGTTTTTT
1 AAGCGCCGCTAATGCTCGACCTTTAGTGGCATTTTTT
13506 GTCCAAACGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (40 bp):
AAGCGCCGCTAATGCTCGACCTTTAGTGGCATTTTTTTAA
Found at i:15289 original size:75 final size:75
Alignment explanation
Indices: 15222--15365 Score: 173
Period size: 75 Copynumber: 1.9 Consensus size: 75
15212 GGGCGCAATC
* *
15222 ACCGTTAGTTTATCCAACTAGAGCTAGGCTCACAATTATTATCATCGGCATATCCGACTAGCACT
1 ACCGTTAGTCTATCCAACTAGAGCTAGGCTCACAATTATTATCATCGGCATATCCAACTAGCACT
15287 GGGTAAAAAT
66 GGGTAAAAAT
*** * * ** * *
15297 ATTTTTGGTCTATCCAACTAGAGCTGGGCTCACAATTATTATTGTCGG-TTAATCCAACTAGCGC
1 ACCGTTAGTCTATCCAACTAGAGCTAGGCTCACAATTATTATCATCGGCAT-ATCCAACTAGCAC
15361 TGGGT
65 TGGGT
15366 GCAACCTTTT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
74 1 0.02
75 56 0.98
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (75 bp):
ACCGTTAGTCTATCCAACTAGAGCTAGGCTCACAATTATTATCATCGGCATATCCAACTAGCACT
GGGTAAAAAT
Found at i:15363 original size:40 final size:39
Alignment explanation
Indices: 15233--15364 Score: 107
Period size: 40 Copynumber: 3.4 Consensus size: 39
15223 CCGTTAGTTT
* * *
15233 ATCCAACTAGAGCTAGGCTCACAATTATTATCATCGG-CA
1 ATCCAACTAGAGCTGGGCTCACAATTATTAT-TTCGGTTA
* * *
15272 TATCCGACTAGCA-CTGGG-T-AAAAATATT-TTT-GGTCT-
1 -ATCCAACTAG-AGCTGGGCTCACAATTATTATTTCGGT-TA
15308 ATCCAACTAGAGCTGGGCTCACAATTATTATTGTCGGTTA
1 ATCCAACTAGAGCTGGGCTCACAATTATTATT-TCGGTTA
*
15348 ATCCAACTAGCGCTGGG
1 ATCCAACTAGAGCTGGG
15365 TGCAACCTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
34 1 0.01
35 16 0.22
36 2 0.03
37 8 0.11
38 9 0.12
39 3 0.04
40 32 0.44
41 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (39 bp):
ATCCAACTAGAGCTGGGCTCACAATTATTATTTCGGTTA
Found at i:16919 original size:16 final size:16
Alignment explanation
Indices: 16880--16922 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
16870 AAAAAAAAAA
*
16880 TTGATTGACCAAAATG
1 TTGAGTGACCAAAATG
**
16896 -AAAGTGACCAAAATG
1 TTGAGTGACCAAAATG
16911 TTGAGTGACCAA
1 TTGAGTGACCAA
16923 TTAAAATAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (16 bp):
TTGAGTGACCAAAATG
Found at i:17135 original size:13 final size:13
Alignment explanation
Indices: 17117--17142 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17107 TTATTAATTA
17117 CTTATTTTTTTAT
1 CTTATTTTTTTAT
17130 CTTATTTTTTTAT
1 CTTATTTTTTTAT
17143 TCAATAAATT
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:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
CTTATTTTTTTAT
Found at i:17328 original size:15 final size:16
Alignment explanation
Indices: 17308--17337 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17298 GGGTATAATA
17308 AAATAT-TAAAAGAAT
1 AAATATATAAAAGAAT
17323 AAATATATAAAAGAA
1 AAATATATAAAAGAA
17338 ATGAGACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (16 bp):
AAATATATAAAAGAAT
Found at i:18455 original size:37 final size:36
Alignment explanation
Indices: 18414--18483 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
18404 TTAATCTCAA
*
18414 ATTTAATATATAATTGAA-TTAAATATAGATTTAAAAT
1 ATTTAATAT-TAATTGAAGTAAAATATA-ATTTAAAAT
* *
18451 ATTTAATCTTACTTGAAGTAAAATATAATTTAA
1 ATTTAATATTAATTGAAGTAAAATATAATTTAA
18484 TGAGAATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 13 0.45
37 16 0.55
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (36 bp):
ATTTAATATTAATTGAAGTAAAATATAATTTAAAAT
Found at i:21033 original size:91 final size:90
Alignment explanation
Indices: 20872--21038 Score: 253
Period size: 90 Copynumber: 1.8 Consensus size: 90
20862 GACCACCGCT
*
20872 GGTTTTGCAGTACCGAATTTTGCAGTCTCATGATTGTCTGGCTAGATATGTGAAAACGATGGCTT
1 GGTTTTGCAGTACCGAATTTTGCAATCTCATGATTGTCTGGCTAGATATGTGAAAACGATGGCTT
20937 GTAATTAAACACACCAACATTTGCA
66 GTAATTAAACACACCAACATTTGCA
* * * * * *
20962 GGTTTTGCTGTACTGAATTTTGCAATCTTATGATTGTCATGGTTAGATTTGTGAAAATGATGGCT
1 GGTTTTGCAGTACCGAATTTTGCAATCTCATGATTGTC-TGGCTAGATATGTGAAAACGATGGCT
*
21027 TGTAATTTAACA
65 TGTAATTAAACA
21039 ATTTTTTTCG
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
90 34 0.50
91 34 0.50
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (90 bp):
GGTTTTGCAGTACCGAATTTTGCAATCTCATGATTGTCTGGCTAGATATGTGAAAACGATGGCTT
GTAATTAAACACACCAACATTTGCA
Found at i:23242 original size:390 final size:391
Alignment explanation
Indices: 22517--23302 Score: 1520
Period size: 390 Copynumber: 2.0 Consensus size: 391
22507 ACAACTCAGG
*
22517 TCGAATGGGGATGAACTATTCATTGGCGTCATAGGAGCCACTCTTACTGTTACGAAATATTGGCT
1 TCGAGTGGGGATGAACTATTCATTGGCGTCATAGGAGCCACTCTTACTGTTACGAAATATTGGCT
*
22582 CGAGACTACTGAGCACATTATGACAGATCTTGACTGTACTCCCACTTAGAAATTGAGGGGTGTTG
66 CGAGACTACTGAGCACATTATGACAGATCTTGACTGTACTCCCACTCAGAAATTGAGGGGTGTTG
22647 TGTCTTTACTCTGGGACGAAGCTTATAAGTGGTGGCTGACAGCTAAACAAGGTGCTCAGCCCGAA
131 TGTCTTTACTCTGGGACGAAGCTTATAAGTGGTGGCTGACAGCTAAACAAGGTGCTCAGCCCGAA
*
22712 CAGGTTAACTGGGATTATTTCAAGAACGCCTTTCAGGGTAAGTATGTGGGGGCGAGTTATGTTTA
196 CAGGTTAACTGGGATTATTTCAAGAACGCCTTTCAGGGTAAGTATGTGGGGGCGAGTTATGCTTA
22777 GGCTCATCGACGTGAGTTTATGAGTTTAGTTCAGGGTGACCGATATATGGCTGAATATGAAGCTG
261 GGCTCATCGACGTGAGTTTATGAGTTTAGTTCAGGGTGACCGATATATGGCTGAATATGAAGCTG
22842 AGTTTCTGCGACTGAATAGGTATGCACGGACTTTGGCAGCATTTGACTACGACAGGTGCGTGAGG
326 AGTTTCTGCGACTGAATAGGTATGCACGGACTTTGGCAGCATTTGACTACGACAGGTGCGTGAGG
22907 T
391 T
22908 TCGAGTGGGGATGAACTATTCATTGGCGTCATAGGAGCCACTCTTACTGTTACGAAATATTGGCT
1 TCGAGTGGGGATGAACTATTCATTGGCGTCATAGGAGCCACTCTTACTGTTACGAAATATTGGCT
22973 CGAGACTACTGAGCACATTATGACAGATCTTGACTGTACTCCCACTCAGAAATTGAGGGGTGTTG
66 CGAGACTACTGAGCACATTATGACAGATCTTGACTGTACTCCCACTCAGAAATTGAGGGGTGTTG
*
23038 TGTCTTTACTCT-GGATGAAGCTTATAAGTGGTGGCTGACAGCTAAACAAGGTGCTCAGCCCGAA
131 TGTCTTTACTCTGGGACGAAGCTTATAAGTGGTGGCTGACAGCTAAACAAGGTGCTCAGCCCGAA
23102 CAGGTTAACTGGGATTATTTCAAGAACGCCTTTCAGGGTAAGTATGTGGGGGCGAGTTATGCTTA
196 CAGGTTAACTGGGATTATTTCAAGAACGCCTTTCAGGGTAAGTATGTGGGGGCGAGTTATGCTTA
23167 GGCTCATCGACGTGAGTTTATGAGTTTAGTTCAGGGTGACCGATATATGGCTGAATATGAAGCTG
261 GGCTCATCGACGTGAGTTTATGAGTTTAGTTCAGGGTGACCGATATATGGCTGAATATGAAGCTG
*
23232 AGTTTCTGCGACTGAATAGGTATGCACGGGCTTTGGCAGCATTTGACTACGACAGGTGCGTGAGG
326 AGTTTCTGCGACTGAATAGGTATGCACGGACTTTGGCAGCATTTGACTACGACAGGTGCGTGAGG
23297 T
391 T
23298 TCGAG
1 TCGAG
23303 GAAGGACTGA
Statistics
Matches: 390, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
390 250 0.64
391 140 0.36
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (391 bp):
TCGAGTGGGGATGAACTATTCATTGGCGTCATAGGAGCCACTCTTACTGTTACGAAATATTGGCT
CGAGACTACTGAGCACATTATGACAGATCTTGACTGTACTCCCACTCAGAAATTGAGGGGTGTTG
TGTCTTTACTCTGGGACGAAGCTTATAAGTGGTGGCTGACAGCTAAACAAGGTGCTCAGCCCGAA
CAGGTTAACTGGGATTATTTCAAGAACGCCTTTCAGGGTAAGTATGTGGGGGCGAGTTATGCTTA
GGCTCATCGACGTGAGTTTATGAGTTTAGTTCAGGGTGACCGATATATGGCTGAATATGAAGCTG
AGTTTCTGCGACTGAATAGGTATGCACGGACTTTGGCAGCATTTGACTACGACAGGTGCGTGAGG
T
Found at i:30820 original size:22 final size:22
Alignment explanation
Indices: 30779--30820 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
30769 AATAAAAATA
* *
30779 TGCTATTTTTTTATTGTTTTAC
1 TGCTATTTTCTTATTATTTTAC
*
30801 TGCTATTTTCTTGTTATTTT
1 TGCTATTTTCTTATTATTTT
30821 CTTATATTTT
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:0.10, G:0.10, T:0.69
Consensus pattern (22 bp):
TGCTATTTTCTTATTATTTTAC
Found at i:40407 original size:11 final size:11
Alignment explanation
Indices: 40393--40436 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
40383 AGATAAATAT
40393 TATTTTATTAA
1 TATTTTATTAA
*
40404 TATTTTAATGAGA
1 TATTTT-ATTA-A
*
40417 TATTTTATTAT
1 TATTTTATTAA
40428 TATTTTATT
1 TATTTTATT
40437 TAGTATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 15 0.54
12 6 0.21
13 7 0.25
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:42519 original size:21 final size:21
Alignment explanation
Indices: 42478--42651 Score: 102
Period size: 21 Copynumber: 8.3 Consensus size: 21
42468 TAGCTCTCAC
* * *
42478 GAGTTTCTGTT-AACTCATAT
1 GAGTTTCAGTTCAACCCTTAT
*
42498 GAGTTTCAGTTTAACCCTTAT
1 GAGTTTCAGTTCAACCCTTAT
* * * * *
42519 GGGTTTCCGTTCAGCTCTTTT
1 GAGTTTCAGTTCAACCCTTAT
* * *
42540 GAGCTTCAATTTAACCCTTAT
1 GAGTTTCAGTTCAACCCTTAT
* * * *
42561 GGGTTTCCGTTCAGCTCTTAT
1 GAGTTTCAGTTCAACCCTTAT
*
42582 GAGCTTCCA-TTCAACCCTTAT
1 GAG-TTTCAGTTCAACCCTTAT
* * * *
42603 GGGTTTCCGTTCAGCTCTTAT
1 GAGTTTCAGTTCAACCCTTAT
*
42624 GAGCTTCCA-TTCAACCCTTAT
1 GAG-TTTCAGTTCAACCCTTAT
*
42645 GGGTTTC
1 GAGTTTC
42652 TGTTTAGCAC
Statistics
Matches: 109, Mismatches: 41, Indels: 8
0.69 0.26 0.05
Matches are distributed among these distances:
20 16 0.15
21 87 0.80
22 6 0.06
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.41
Consensus pattern (21 bp):
GAGTTTCAGTTCAACCCTTAT
Found at i:42554 original size:42 final size:42
Alignment explanation
Indices: 42495--42666 Score: 254
Period size: 42 Copynumber: 4.1 Consensus size: 42
42485 TGTTAACTCA
* * *
42495 TATGAGTTTCAGTTTAACCCTTATGGGTTTCCGTTCAGCTCT
1 TATGAGCTTCAATTCAACCCTTATGGGTTTCCGTTCAGCTCT
* *
42537 TTTGAGCTTCAATTTAACCCTTATGGGTTTCCGTTCAGCTCT
1 TATGAGCTTCAATTCAACCCTTATGGGTTTCCGTTCAGCTCT
*
42579 TATGAGCTTCCATTCAACCCTTATGGGTTTCCGTTCAGCTCT
1 TATGAGCTTCAATTCAACCCTTATGGGTTTCCGTTCAGCTCT
* * * *
42621 TATGAGCTTCCATTCAACCCTTATGGGTTTCTGTTTAGCACT
1 TATGAGCTTCAATTCAACCCTTATGGGTTTCCGTTCAGCTCT
42663 TATG
1 TATG
42667 TGCATCTGTG
Statistics
Matches: 121, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 121 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (42 bp):
TATGAGCTTCAATTCAACCCTTATGGGTTTCCGTTCAGCTCT
Found at i:55629 original size:16 final size:16
Alignment explanation
Indices: 55608--55639 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55598 ATTAGAGAAA
55608 ATCCTTCGACAAACCT
1 ATCCTTCGACAAACCT
*
55624 ATCCTTTGACAAACCT
1 ATCCTTCGACAAACCT
55640 TCAGTAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.34, G:0.06, T:0.28
Consensus pattern (16 bp):
ATCCTTCGACAAACCT
Found at i:60197 original size:23 final size:24
Alignment explanation
Indices: 60153--60198 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
60143 TTTCTCACAT
* **
60153 TTTCAATTCAATCATTTTTCCACC
1 TTTCAATTCAATAATTAATCCACC
60177 TTTCAA-TCAATAATTAATCCAC
1 TTTCAATTCAATAATTAATCCAC
60199 AATGCACACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (24 bp):
TTTCAATTCAATAATTAATCCACC
Found at i:60321 original size:17 final size:18
Alignment explanation
Indices: 60296--60365 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 18
60286 AACAAACAAT
60296 TCAAATATT-AATTCATA
1 TCAAATATTCAATTCATA
* * *
60313 TCAATTATTCAATTTAATTCCT
1 TCAAATATTCAA-TTCA-T--A
60335 TCAAATATT-AATTCATA
1 TCAAATATTCAATTCATA
*
60352 TCAATTATTCAATT
1 TCAAATATTCAATT
60366 TAATTCCCAC
Statistics
Matches: 40, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
17 16 0.40
18 6 0.15
19 4 0.10
20 4 0.10
21 2 0.05
22 8 0.20
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (18 bp):
TCAAATATTCAATTCATA
Found at i:60344 original size:39 final size:39
Alignment explanation
Indices: 60295--60372 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
60285 CAACAAACAA
60295 TTCAAATATTAATTCATATCAATTATTCAATTTAATTCC
1 TTCAAATATTAATTCATATCAATTATTCAATTTAATTCC
60334 TTCAAATATTAATTCATATCAATTATTCAATTTAATTCC
1 TTCAAATATTAATTCATATCAATTATTCAATTTAATTCC
60373 CACTCATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (39 bp):
TTCAAATATTAATTCATATCAATTATTCAATTTAATTCC
Found at i:60386 original size:3 final size:3
Alignment explanation
Indices: 60378--60409 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
60368 ATTCCCACTC
60378 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
60410 TTATCTCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:65774 original size:25 final size:25
Alignment explanation
Indices: 65740--65796 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
65730 AGAACTAAAG
*
65740 TCAAGATAGGAAATGGTCATCTTAT
1 TCAAGCTAGGAAATGGTCATCTTAT
65765 TCAAGCTAGGAAATGGTCATCTTAT
1 TCAAGCTAGGAAATGGTCATCTTAT
65790 TCAAGCT
1 TCAAGCT
65797 GAAGGCAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (25 bp):
TCAAGCTAGGAAATGGTCATCTTAT
Done.