Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2531
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: 87780
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:415 original size:15 final size:15
Alignment explanation
Indices: 395--430 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
385 AAGAAGCAGG
395 GAAGAAGA-GAAGCGA
1 GAAGAAGAGGAAG-GA
410 GAAGAAGAGGAAGGA
1 GAAGAAGAGGAAGGA
425 GAAGAA
1 GAAGAA
431 AAAGAGGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.56, C:0.03, G:0.42, T:0.00
Consensus pattern (15 bp):
GAAGAAGAGGAAGGA
Found at i:534 original size:2 final size:2
Alignment explanation
Indices: 527--560 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
517 GAAAAATGTG
* *
527 TA TA TA TA TA TA TA TA TA TC TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
561 AGTATAGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1824 original size:27 final size:27
Alignment explanation
Indices: 1773--1840 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 27
1763 AGTTAGGGTG
1773 AAAAATATTTATTTTTAAACTTGTTATA
1 AAAAATATTTATTTTTAAAC-TGTTATA
* *
1801 AAAATATATTTATTTTTTAA-TGTTTTA
1 AAAA-ATATTTATTTTTAAACTGTTATA
1828 AAAAATATTTATT
1 AAAAATATTTATT
1841 CATAACGTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 9 0.24
27 10 0.27
28 4 0.11
29 14 0.38
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (27 bp):
AAAAATATTTATTTTTAAACTGTTATA
Found at i:2387 original size:25 final size:27
Alignment explanation
Indices: 2343--2397 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
2333 TTATCTTTAA
* * *
2343 ATTTTTAAAATAAGAGTAAT-TAATTT
1 ATTTTTAAAATAAAAATAATATAATAT
2369 ATTTTT-AAATAAAAATAATATAATAT
1 ATTTTTAAAATAAAAATAATATAATAT
2395 ATT
1 ATT
2398 AATATCAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (27 bp):
ATTTTTAAAATAAAAATAATATAATAT
Found at i:2668 original size:16 final size:17
Alignment explanation
Indices: 2647--2690 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
2637 TTTATATTTA
*
2647 AAAATATTAAAA-AAAT
1 AAAATAATAAAATAAAT
2663 AAAATAATAAAATAAAT
1 AAAATAATAAAATAAAT
*
2680 -AATTAATAAAA
1 AAAATAATAAAA
2691 AAGCATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAATAATAAAATAAAT
Found at i:5858 original size:240 final size:240
Alignment explanation
Indices: 5435--5917 Score: 966
Period size: 240 Copynumber: 2.0 Consensus size: 240
5425 TTATCAAGTA
5435 ACGAACCAAGAGGGGGGGTGAATTGGTTCTTTTCGAATTTTCGATTTTGAAACAACACAATTCGA
1 ACGAACCAAGAGGGGGGGTGAATTGGTTCTTTTCGAATTTTCGATTTTGAAACAACACAATTCGA
5500 AATGAAAAGAGATTAGGGGAAGGAAAACTTGACACAAGATATTTATAGAGGTTCGGTCCAAACAT
66 AATGAAAAGAGATTAGGGGAAGGAAAACTTGACACAAGATATTTATAGAGGTTCGGTCCAAACAT
5565 GGCACCAACATCCTCTCTCCTCGACACTTCCTTGTCGAGTGATTACCCAATTCACTAACCGAATT
131 GGCACCAACATCCTCTCTCCTCGACACTTCCTTGTCGAGTGATTACCCAATTCACTAACCGAATT
5630 GATTACCTTTAAGGCAAAGGTATAACCTTACAACTCATATCTTTT
196 GATTACCTTTAAGGCAAAGGTATAACCTTACAACTCATATCTTTT
5675 ACGAACCAAGAGGGGGGGTGAATTGGTTCTTTTCGAATTTTCGATTTTGAAACAACACAATTCGA
1 ACGAACCAAGAGGGGGGGTGAATTGGTTCTTTTCGAATTTTCGATTTTGAAACAACACAATTCGA
5740 AATGAAAAGAGATTAGGGGAAGGAAAACTTGACACAAGATATTTATAGAGGTTCGGTCCAAACAT
66 AATGAAAAGAGATTAGGGGAAGGAAAACTTGACACAAGATATTTATAGAGGTTCGGTCCAAACAT
5805 GGCACCAACATCCTCTCTCCTCGACACTTCCTTGTCGAGTGATTACCCAATTCACTAACCGAATT
131 GGCACCAACATCCTCTCTCCTCGACACTTCCTTGTCGAGTGATTACCCAATTCACTAACCGAATT
5870 GATTACCTTTAAGGCAAAGGTATAACCTTACAACTCATATCTTTT
196 GATTACCTTTAAGGCAAAGGTATAACCTTACAACTCATATCTTTT
5915 ACG
1 ACG
5918 GGCTAAGATA
Statistics
Matches: 243, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
240 243 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (240 bp):
ACGAACCAAGAGGGGGGGTGAATTGGTTCTTTTCGAATTTTCGATTTTGAAACAACACAATTCGA
AATGAAAAGAGATTAGGGGAAGGAAAACTTGACACAAGATATTTATAGAGGTTCGGTCCAAACAT
GGCACCAACATCCTCTCTCCTCGACACTTCCTTGTCGAGTGATTACCCAATTCACTAACCGAATT
GATTACCTTTAAGGCAAAGGTATAACCTTACAACTCATATCTTTT
Found at i:6119 original size:32 final size:30
Alignment explanation
Indices: 6083--6141 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
6073 GAAATCAAAT
6083 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
6115 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
6142 CTTTGATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:6409 original size:10 final size:10
Alignment explanation
Indices: 6375--6402 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
6365 TTTGAAAATA
6375 TAGCCGTTTC
1 TAGCCGTTTC
6385 TAGCCGTTTC
1 TAGCCGTTTC
6395 TAGCCGTT
1 TAGCCGTT
6403 ACAAGCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.29, G:0.21, T:0.39
Consensus pattern (10 bp):
TAGCCGTTTC
Found at i:6451 original size:13 final size:13
Alignment explanation
Indices: 6433--6490 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
6423 AATGTTTTTG
6433 TGTATCGATACAT
1 TGTATCGATACAT
6446 TGTATCGATACATACTTT
1 TGTATCGATAC--A---T
6464 GTGTATCGATACAT
1 -TGTATCGATACAT
6478 TGTATCGATACAT
1 TGTATCGATACAT
6491 ACTTTGTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 24 0.62
14 1 0.03
15 1 0.03
17 1 0.03
18 1 0.03
19 11 0.28
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6470 original size:19 final size:19
Alignment explanation
Indices: 6446--6508 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
6436 ATCGATACAT
6446 TGTATCGATACATACTTTG
1 TGTATCGATACATACTTTG
6465 TGTATCGATAC--A---T-
1 TGTATCGATACATACTTTG
6478 TGTATCGATACATACTTTG
1 TGTATCGATACATACTTTG
6497 TGTATCGATACA
1 TGTATCGATACA
6509 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
17 1 0.03
18 1 0.03
19 23 0.61
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATACTTTG
Found at i:6470 original size:32 final size:32
Alignment explanation
Indices: 6429--6508 Score: 160
Period size: 32 Copynumber: 2.5 Consensus size: 32
6419 ATACAATGTT
6429 TTTGTGTATCGATACATTGTATCGATACATAC
1 TTTGTGTATCGATACATTGTATCGATACATAC
6461 TTTGTGTATCGATACATTGTATCGATACATAC
1 TTTGTGTATCGATACATTGTATCGATACATAC
6493 TTTGTGTATCGATACA
1 TTTGTGTATCGATACA
6509 AGTTTGGCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (32 bp):
TTTGTGTATCGATACATTGTATCGATACATAC
Found at i:6585 original size:20 final size:20
Alignment explanation
Indices: 6539--6612 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
6529 ATCCCAATGA
***
6539 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGAAT
6560 CATGTATCGATACATTGCAA-
1 CATGTATCGATACATTG-AAT
6580 CATGTATCGATACATTGAAT
1 CATGTATCGATACATTGAAT
*
6600 TATGTATCGATAC
1 CATGTATCGATAC
6613 TTTTAAGGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 2 0.04
20 30 0.64
21 15 0.32
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:8560 original size:21 final size:20
Alignment explanation
Indices: 8531--8573 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
8521 GACTAGTGTG
* *
8531 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
8552 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
8572 GG
1 GG
8574 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:9023 original size:13 final size:13
Alignment explanation
Indices: 9005--9041 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
8995 TAATCCCCCC
9005 GTATCGATACATT
1 GTATCGATACATT
9018 GTATCGATACATT
1 GTATCGATACATT
9031 GTATCGATACA
1 GTATCGATACA
9042 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:21494 original size:20 final size:20
Alignment explanation
Indices: 21465--21517 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
21455 TTTAATTAGT
*
21465 TGTATCGATACATTGAAAAA
1 TGTATTGATACATTGAAAAA
21485 TGTATTGATACATTGAAAAA
1 TGTATTGATACATTGAAAAA
*
21505 TGTATTAATACAT
1 TGTATTGATACAT
21518 CTAGGTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (20 bp):
TGTATTGATACATTGAAAAA
Found at i:21559 original size:20 final size:20
Alignment explanation
Indices: 21534--21578 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
21524 AAAAAGACAA
*
21534 AATGTATCGATATATTAAAG
1 AATGTATCGATACATTAAAG
*
21554 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTAAAG
21574 AATGT
1 AATGT
21579 GTCAAGACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTAAAG
Found at i:28000 original size:962 final size:961
Alignment explanation
Indices: 25867--29695 Score: 6445
Period size: 962 Copynumber: 4.0 Consensus size: 961
25857 GAGACATCGA
* * *
25867 GTGGTACATATGCTTCGTTTAACACCTTTAGCAATGCATTTCGATGAACC-TCTGAATTAAAAAG
1 GTGGTACATATGCTTCGTTTAACACCTTCAGCAATGCATTTCGGTGAACCTTC-GAATTAAGAAG
* * * * *
25931 C-AA-AGAGCATAGAAATCTTTGTAGGTTCTTTGCTTAGTTGATCCACAATACTATATTCGCTGT
65 CAAAGAGAGCACAGAAATCTTTGCAGGTTGTTTGCATAGTTGATCCACAATACTATATTCACTGT
* * *
25994 GCTTGATGAACTTGAGAAACTCTGTAGCCTCATCTTCATTCACTGTTTCTCTGACTTTTTCTAGC
130 GCTTGATGAACTTGAGAAACTCTGTAGCTTCATCTTCATTCACCGTTTCTTTGACTTTTTCTAGC
* *
26059 TCTAGGTTCTTCGCTTGTTTTTGAAAGGTACTGGTGCTTGGAGATGCATCAACCTTCTATTTTTT
195 TCTAGGTTCTTCGCTTGTTTTTGAAAGGTACTGGTGCTTGGAAATGCATCAACCTTCTATTTTTC
* * *
26124 TTGAATTGGGGG-GCATAACACCTACAACTACAGGTTAGGTGACTAACCTTTGACAGTTCCATCA
260 TTGAATTGGGGGAGCATAACACCTACCACTACGGGTTAGGTGACTAACCCTTGACAGTTCCATCA
* * * * *
26188 AAGCAGACGAGGGAGCTTGTTCTCCAATTATCACTACCTGATTCTCGTACCTCCAAGGGACTACT
325 CAGCAGCCGAGGGAGTTTGTTCTCCAATTATCACTACCTGATTCTCGTACCTCCAAAGGACTGCT
** * * *
26253 TTGTTGCTCTTATATGAGAACTATTTAGGTACCACCATGACTAATATTGGTGTAGGTGTCGAAAA
390 TTGTTGCTCTTATATGAGAACGGTTTAGGTACCTCCACGACTAATATTGGTGTAGGTGTCGAAGA
* * * *
26318 ACTAGCCTCAAAACTTGACTTGCCAAAAAGAATTAAGGCTCGATTCCTCTTGTAAGGTGGCTGCG
455 ACTAGCCTCAAAACTTGACTTGCCAAAAAGAATTAAGGGTCGATTCCTCCTGTAAGGTGGCTACA
*
26383 TTGCTTTCTCGCCTATCATGTTGATGGATTCGACAGCAGGTGTGGCTTCATGATAAAATTTTATC
520 TTGCTTTCTCGCCTATCATGTTGATGGATTCGACAGCAGGTGTGGCTTCATGATAAAATTCTATC
26448 TGACCTTCATCCATCATTCTCTAAACCATGGCCCTAAACTTCTTGCATGTTTGTAAGGTATGACC
585 TGACCTTCATCCATCATTCTCTAAACCATGGCCCTAAACTTCTTGCATGTTTGTAAGGTATGACC
*
26513 TACAACAGTGTGGAAGTCATAGAAGTTGTCGAGCTTATCTTTCAACTTTTTCACTGTC-TTAAGC
650 TACAACAGTGTGGAAGTCATAGAAGTTGTCGAGCTTATCTTTCAACTTTTTCACT-ACATTAAGC
26577 AAACCGACTTGACTCAATGCTTCCCAAACTAAGAACATTGGCATCCTTACTTCCTCTATGCTTAT
714 AAACCGACTTGACTCAATGCTTCCCAAACTAAGAACATTGGCATCCTTACTTCCTCTATGCTTAT
*
26642 CTTAACTTTATATTTATTCTCGATGCCAATCATGTTTGCATCTGGTTCTGTATGGTTTGATAAAG
779 CTTAACTTTATATTTATTCTCGATGCCAATCATGTTTGCATCTGGTTCTGTATGGTTTGGTAAAG
* * *
26707 GATTCGCGGGAACATTAAGTCCTTGATTTGTCTCGAACTGCAGCACCTTCGAGTCGATGAGACTT
844 GATTCGCGGCAACATTAGGTCCTTGATTTGTCCCGAACTGCAGCACCTTCGAGTCGATGAGACTT
26772 TGCACTTTTCTTTTAAGGGCAATGCAACTTTTGATGTCATACAGAGATGTTGG
909 TGCACTTTTCTTTTAAGGGCAATGCAACTTTTGATGTCATACAGAGATGTTGG
26825 GTGGTACATATGCTTCGTTTAACACCTTCAGCAATGCATTTCGGTGAACCTTCGAATTAAGAAGC
1 GTGGTACATATGCTTCGTTTAACACCTTCAGCAATGCATTTCGGTGAACCTTCGAATTAAGAAGC
* *
26890 AAAGAGAGCACAGCAATCTTTGCAGGTTGTTTGCATAGTTGATCCACAATACTATATTCACTATG
66 AAAGAGAGCACAGAAATCTTTGCAGGTTGTTTGCATAGTTGATCCACAATACTATATTCACTGTG
26955 CTTGATGAACTTGAGAAACTCTGTAGCTTCATCTTCATTCACCGTTTCTTTGACTTTTTCTAAGC
131 CTTGATGAACTTGAGAAACTCTGTAGCTTCATCTTCATTCACCGTTTCTTTGACTTTTTCT-AGC
*
27020 TCTAGGTTCTTCGCTTGTTTTTGAAAGGTATTGGTGCTTGGAAATGCATCAACCTTCTATTTTTC
195 TCTAGGTTCTTCGCTTGTTTTTGAAAGGTACTGGTGCTTGGAAATGCATCAACCTTCTATTTTTC
*
27085 TTGAATTGGGGGAGCATAACACCTACCACTACGGGTTAGGTGACTAACCCTTGACAGTTCCATCG
260 TTGAATTGGGGGAGCATAACACCTACCACTACGGGTTAGGTGACTAACCCTTGACAGTTCCATCA
* *
27150 CAGCAGCCGAGGGAGTTTGTTCTCCAATTATCACTACGTGATTCTCGTACCTCTAAAGGACTGCT
325 CAGCAGCCGAGGGAGTTTGTTCTCCAATTATCACTACCTGATTCTCGTACCTCCAAAGGACTGCT
27215 TTGTTGCTCTTATATGAGAACGGTTTAGGTACCTCCACGACTAATATTGGTGTAGGTGTCGAAGA
390 TTGTTGCTCTTATATGAGAACGGTTTAGGTACCTCCACGACTAATATTGGTGTAGGTGTCGAAGA
*
27280 ACTAGCCTCAAAACTTGACTTGCCAAAAAGAATTAAGGGTCGATTCCTCCTGTAAGGTGGCTACG
455 ACTAGCCTCAAAACTTGACTTGCCAAAAAGAATTAAGGGTCGATTCCTCCTGTAAGGTGGCTACA
27345 TTGCTTTCTCGCCTATCATGTTGATGGATTCGACAGCAGGTGTGGCTTCATGATAAAATTCTATC
520 TTGCTTTCTCGCCTATCATGTTGATGGATTCGACAGCAGGTGTGGCTTCATGATAAAATTCTATC
27410 TGACCTTCATCCATCATTCTCTAAACCATGGCCCTAAACTTCTTGCATGTTTGTAAGGTATGACC
585 TGACCTTCATCCATCATTCTCTAAACCATGGCCCTAAACTTCTTGCATGTTTGTAAGGTATGACC
*
27475 TACAACAGTGTGGAAGTCATAGAAGTTGTCGAGCTTATCTTTCAACTTTTTCACTGTC-TTAAGC
650 TACAACAGTGTGGAAGTCATAGAAGTTGTCGAGCTTATCTTTCAACTTTTTCACT-ACATTAAGC
27539 AAACCGACTTGACTCAATGCTTCCCAAACTAAGAACATTGGCATCCTTACTTCCTCTATGCTTAT
714 AAACCGACTTGACTCAATGCTTCCCAAACTAAGAACATTGGCATCCTTACTTCCTCTATGCTTAT
27604 CTTAACTTTATATTTATTCTCGATGCCAATCATGTTTGCATCTGGTTCTGTATGGTTTGGTAAAG
779 CTTAACTTTATATTTATTCTCGATGCCAATCATGTTTGCATCTGGTTCTGTATGGTTTGGTAAAG
*
27669 GATTCGCGGCAACATTAGGTCCTTGATTTGTCTCGAACTGCAGCACCTTCGAGTCGATGAGACTT
844 GATTCGCGGCAACATTAGGTCCTTGATTTGTCCCGAACTGCAGCACCTTCGAGTCGATGAGACTT
27734 TGCACTTTTCTTTTAAGGGCAATGCAACTTTTGATGTCATACAGAGATGTTGG
909 TGCACTTTTCTTTTAAGGGCAATGCAACTTTTGATGTCATACAGAGATGTTGG
27787 GTGGTACATATGCTTCGTTTAACACCTTCAGCAATGCATTTCGGTGAACCTTCGAATTAAGAAGC
1 GTGGTACATATGCTTCGTTTAACACCTTCAGCAATGCATTTCGGTGAACCTTCGAATTAAGAAGC
*
27852 AAAGAGAGCACAGAAATCTTTGCAGGTTTTTTGCATAGTTGATCCACAATACTATATTCACTGTG
66 AAAGAGAGCACAGAAATCTTTGCAGGTTGTTTGCATAGTTGATCCACAATACTATATTCACTGTG
*
27917 CTTGATGAACTTGAGAAACTCTGTAGCTTCATCTTCATTCACCATTTCTTTGACTTTTTCTAAGC
131 CTTGATGAACTTGAGAAACTCTGTAGCTTCATCTTCATTCACCGTTTCTTTGACTTTTTCT-AGC
* *
27982 TCTGGGTTCTTCGCTTGTTTTTGAAAGGTATTGGTGCTTGGAAATGCATCAACCTTCTATTTTTC
195 TCTAGGTTCTTCGCTTGTTTTTGAAAGGTACTGGTGCTTGGAAATGCATCAACCTTCTATTTTTC
* *
28047 TTGAATTTGGGGAGCATAACACCTACCACTACGGGTTAGGTGACTAACCCTTGACAGTTCCATCG
260 TTGAATTGGGGGAGCATAACACCTACCACTACGGGTTAGGTGACTAACCCTTGACAGTTCCATCA
* *
28112 CAGCAGCCGAGGGAGTTTGTTCTCCAATTATCACTACGTGATTCTCGTACCTCTAAAGGACTGCT
325 CAGCAGCCGAGGGAGTTTGTTCTCCAATTATCACTACCTGATTCTCGTACCTCCAAAGGACTGCT
28177 TTGTTGCTCTTATATGAGAACGGTTTAGGTACCTCCACGACTAATATTGGTGTAGGTGTCGAAGA
390 TTGTTGCTCTTATATGAGAACGGTTTAGGTACCTCCACGACTAATATTGGTGTAGGTGTCGAAGA
* *
28242 ACTAGCCTCAAAACTTGACTTGCCAAAAAGAATTAA-AGTCGATTCCTCCCGTAAGGTGGCTACA
455 ACTAGCCTCAAAACTTGACTTGCCAAAAAGAATTAAGGGTCGATTCCTCCTGTAAGGTGGCTACA
* ** *
28306 TTGCTTTGTCTTCTATCATGTTGATGGATTCGACAGCAGGTGTGGCTTCATGATAGAATTCTATC
520 TTGCTTTCTCGCCTATCATGTTGATGGATTCGACAGCAGGTGTGGCTTCATGATAAAATTCTATC
* * * * * *
28371 TGGCCTTCATCCATCATTCTTTGAACTATGGCCCTAAACTCCTTGCATGTTTGTAAGGTATGACT
585 TGACCTTCATCCATCATTCTCTAAACCATGGCCCTAAACTTCTTGCATGTTTGTAAGGTATGACC
*
28436 TACAACAGTGTGGAAGTCATAGAAGTTGTCGAGCTTATCTTTCAACTTTTTCGCTACATTAAGCA
650 TACAACAGTGTGGAAGTCATAGAAGTTGTCGAGCTTATCTTTCAACTTTTTCACTACATTAAGCA
* * *
28501 ATCCGACTTGACTCAATGCTTCCCAAACTAAGAACATTGGCATCCTTACTTCTTCTATGGTTATC
715 AACCGACTTGACTCAATGCTTCCCAAACTAAGAACATTGGCATCCTTACTTCCTCTATGCTTATC
28566 TTAACTTTATATTTATTCTCGATGCCAATCATGTTTGCATCTGGTTCTGTATGGTTTGGTAAAGG
780 TTAACTTTATATTTATTCTCGATGCCAATCATGTTTGCATCTGGTTCTGTATGGTTTGGTAAAGG
*
28631 ATTCACGGCAACATTAGGTCCTT-AGTTTGTCCCGAACTGCAGCACCTTCGAGTCGATGAGACTT
845 ATTCGCGGCAACATTAGGTCCTTGA-TTTGTCCCGAACTGCAGCACCTTCGAGTCGATGAGACTT
* * * ***
28695 TGCACTTTTCTTTTAAGGGCAATGCAACTTTCGATGTCATACAAAGACGTCCA
909 TGCACTTTTCTTTTAAGGGCAATGCAACTTTTGATGTCATACAGAGATGTTGG
* ** *
28748 ATGGTACATATGCTTCGTTTAACACCTTCAGCAATGCATTTAAGTGAACCTCCGAATTAAGAAGC
1 GTGGTACATATGCTTCGTTTAACACCTTCAGCAATGCATTTCGGTGAACCTTCGAATTAAGAAGC
* * *
28813 AAAGAGAGCACAAAAATCTTTGCAGGTTGTTTGCTTAGTTGATCCACAATACTATATTCGCTGTG
66 AAAGAGAGCACAGAAATCTTTGCAGGTTGTTTGCATAGTTGATCCACAATACTATATTCACTGTG
* * *
28878 CTTGATGAACTTAAGAAACTTTGTAGCTTCATCTTTATTCACCGTTTCTTTGACTTTTTCTAGCT
131 CTTGATGAACTTGAGAAACTCTGTAGCTTCATCTTCATTCACCGTTTCTTTGACTTTTTCTAGCT
* * * *
28943 TTGGGTTCTTCGCTTGTTTTTGAAAGGTACTAGTGCTTGGAAATGCATCAACCTTCTATTTTTCA
196 CTAGGTTCTTCGCTTGTTTTTGAAAGGTACTGGTGCTTGGAAATGCATCAACCTTCTATTTTTCT
* *
29008 TGAATTGGGGGAGCATAACACCTACCACTACGGGTTAGGTGACTAACCCCTAACAGTTCCATCAC
261 TGAATTGGGGGAGCATAACACCTACCACTACGGGTTAGGTGACTAACCCTTGACAGTTCCATCAC
* * *
29073 AGCAGTCAAGGGAGTTTGTTCTCCAATTATCACTACCTGATTCTCGTACCTCCAAGGGACTGCTT
326 AGCAGCCGAGGGAGTTTGTTCTCCAATTATCACTACCTGATTCTCGTACCTCCAAAGGACTGCTT
29138 TGTTGCTCTTATATGAGAACGGTTTAGGTACCTCCACGACTAATATTGGTGTAGGTGTCGAAGAA
391 TGTTGCTCTTATATGAGAACGGTTTAGGTACCTCCACGACTAATATTGGTGTAGGTGTCGAAGAA
* * *
29203 CTAGCCTCAAAACTTGACTTGCCAAAAAGAATTAAGGGTCAATTCCT-CTCGTAAGATGGCTGCA
456 CTAGCCTCAAAACTTGACTTGCCAAAAAGAATTAAGGGTCGATTCCTCCT-GTAAGGTGGCTACA
* * * *
29267 TTGCTTTGTCTCCTATCATTTTGATGGATTCGACAGCAGGTGTGGCTTCATGATAGAATTCTATC
520 TTGCTTTCTCGCCTATCATGTTGATGGATTCGACAGCAGGTGTGGCTTCATGATAAAATTCTATC
* *
29332 TGGCCTTCATCCATCATTCTCTGAACCATGGCCCTAAAC-TCTTTGCATGTTTGTAAGGTATGAC
585 TGACCTTCATCCATCATTCTCTAAACCATGGCCCTAAACTTC-TTGCATGTTTGTAAGGTATGAC
* **
29396 CTACAACAGTGTGGAAGTCATAGAAGTTATCGAGCTTATCTTTCAACTTTTTTGCTACATTAAGC
649 CTACAACAGTGTGGAAGTCATAGAAGTTGTCGAGCTTATCTTTCAACTTTTTCACTACATTAAGC
* * * * *
29461 AATCCGACTTGACTTAATGCTTCCCAAACTAAGAACATCGGCATCCTTACCTCTTCTATGCTTAT
714 AAACCGACTTGACTCAATGCTTCCCAAACTAAGAACATTGGCATCCTTACTTCCTCTATGCTTAT
*
29526 CTTAACTTTATATTTATTCTCGATGCCAATCATGTTTGCATTTGGTTCTGTATGGTTTGGTAAAG
779 CTTAACTTTATATTTATTCTCGATGCCAATCATGTTTGCATCTGGTTCTGTATGGTTTGGTAAAG
* *
29591 GATTCGCGGCAACATTAGGTCCTTGATTTGTCCCGAACTACAGCACCTTCGATTCGATGAGACTT
844 GATTCGCGGCAACATTAGGTCCTTGATTTGTCCCGAACTGCAGCACCTTCGAGTCGATGAGACTT
* * * *
29656 TACACTTTTCTTTTAAGGGCATTACAATTTTTGATGTCAT
909 TGCACTTTTCTTTTAAGGGCAATGCAACTTTTGATGTCAT
29696 GCCCCGCTAC
Statistics
Matches: 2738, Mismatches: 122, Indels: 19
0.95 0.04 0.01
Matches are distributed among these distances:
958 59 0.02
959 4 0.00
960 402 0.15
961 1121 0.41
962 1152 0.42
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (961 bp):
GTGGTACATATGCTTCGTTTAACACCTTCAGCAATGCATTTCGGTGAACCTTCGAATTAAGAAGC
AAAGAGAGCACAGAAATCTTTGCAGGTTGTTTGCATAGTTGATCCACAATACTATATTCACTGTG
CTTGATGAACTTGAGAAACTCTGTAGCTTCATCTTCATTCACCGTTTCTTTGACTTTTTCTAGCT
CTAGGTTCTTCGCTTGTTTTTGAAAGGTACTGGTGCTTGGAAATGCATCAACCTTCTATTTTTCT
TGAATTGGGGGAGCATAACACCTACCACTACGGGTTAGGTGACTAACCCTTGACAGTTCCATCAC
AGCAGCCGAGGGAGTTTGTTCTCCAATTATCACTACCTGATTCTCGTACCTCCAAAGGACTGCTT
TGTTGCTCTTATATGAGAACGGTTTAGGTACCTCCACGACTAATATTGGTGTAGGTGTCGAAGAA
CTAGCCTCAAAACTTGACTTGCCAAAAAGAATTAAGGGTCGATTCCTCCTGTAAGGTGGCTACAT
TGCTTTCTCGCCTATCATGTTGATGGATTCGACAGCAGGTGTGGCTTCATGATAAAATTCTATCT
GACCTTCATCCATCATTCTCTAAACCATGGCCCTAAACTTCTTGCATGTTTGTAAGGTATGACCT
ACAACAGTGTGGAAGTCATAGAAGTTGTCGAGCTTATCTTTCAACTTTTTCACTACATTAAGCAA
ACCGACTTGACTCAATGCTTCCCAAACTAAGAACATTGGCATCCTTACTTCCTCTATGCTTATCT
TAACTTTATATTTATTCTCGATGCCAATCATGTTTGCATCTGGTTCTGTATGGTTTGGTAAAGGA
TTCGCGGCAACATTAGGTCCTTGATTTGTCCCGAACTGCAGCACCTTCGAGTCGATGAGACTTTG
CACTTTTCTTTTAAGGGCAATGCAACTTTTGATGTCATACAGAGATGTTGG
Found at i:38000 original size:20 final size:20
Alignment explanation
Indices: 37975--38031 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
37965 GTAAAAAGAC
37975 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
37995 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
* * *
38015 AAAATATATCAATACAT
1 AGAATGTATCGATACAT
38032 CTAGGTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.30
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:40383 original size:17 final size:17
Alignment explanation
Indices: 40345--40383 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
40335 TTTATCAAAA
*
40345 AATTTCCAAAACTATTT
1 AATTTCCAAAACTATCT
* *
40362 CATTTCCAAAATTATCT
1 AATTTCCAAAACTATCT
40379 AATTT
1 AATTT
40384 TCCTTTCACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTTCCAAAACTATCT
Found at i:44727 original size:16 final size:16
Alignment explanation
Indices: 44708--44773 Score: 105
Period size: 16 Copynumber: 4.1 Consensus size: 16
44698 TTTTTTTTAA
*
44708 AAATTATTTTAATTTT
1 AAATTATTTTAAATTT
44724 AAATTATTTTAAATTT
1 AAATTATTTTAAATTT
*
44740 AAATTATTTTAATTTT
1 AAATTATTTTAAATTT
*
44756 AAATTTTTTTAAATTT
1 AAATTATTTTAAATTT
44772 AA
1 AA
44774 GTTTATATCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AAATTATTTTAAATTT
Found at i:44744 original size:32 final size:32
Alignment explanation
Indices: 44708--44834 Score: 123
Period size: 32 Copynumber: 3.8 Consensus size: 32
44698 TTTTTTTTAA
44708 AAATTATTTTAATTTTAAATTATTTTAAATTT
1 AAATTATTTTAATTTTAAATTATTTTAAATTT
*
44740 AAATTATTTTAATTTTAAATTTTTTTAAATTT
1 AAATTATTTTAATTTTAAATTATTTTAAATTT
* *
44772 AAGTTTATATCATTTTGATTTTAAATTA-TTTAATACTT
1 AA----AT-T-ATTTTAATTTTAAATTATTTTAA-ATTT
** *
44810 CGATTAATTTAA-TTTAAATTATTTT
1 AAATTATTTTAATTTTAAATTATTTT
44835 GAGTTAAAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 16
0.77 0.08 0.16
Matches are distributed among these distances:
31 9 0.11
32 41 0.52
33 1 0.01
34 2 0.03
36 2 0.03
37 6 0.08
38 18 0.23
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (32 bp):
AAATTATTTTAATTTTAAATTATTTTAAATTT
Found at i:44926 original size:17 final size:17
Alignment explanation
Indices: 44890--44924 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
44880 TCATTTTAAG
44890 TTAATATTCGAATTATT
1 TTAATATTCGAATTATT
44907 TTAAT-TTCGAATTATT
1 TTAATATTCGAATTATT
44923 TT
1 TT
44925 TAGTTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (17 bp):
TTAATATTCGAATTATT
Found at i:46414 original size:3 final size:3
Alignment explanation
Indices: 46406--46444 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
46396 TTCAGTTTTC
* *
46406 AAT AAT AAT AAT AAT AAT AAT AAT AA- CAT AAT TAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
46445 TAAAAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.03
3 30 0.97
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:47315 original size:21 final size:20
Alignment explanation
Indices: 47269--47315 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
47259 AATTTAGTTT
47269 ATAAACTTATAAAAAAATTA
1 ATAAACTTATAAAAAAATTA
*
47289 ATTAAATTTATAATATAAAA-TA
1 A-TAAACTTATAA-A-AAAATTA
47311 ATAAA
1 ATAAA
47316 ATAAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 14 0.61
22 4 0.17
23 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
ATAAACTTATAAAAAAATTA
Found at i:47362 original size:22 final size:21
Alignment explanation
Indices: 47334--47383 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
47324 ATTAATCTCT
*
47334 TTTAAAATTTTTATATAATTTC
1 TTTAAAATATTTA-ATAATTTC
* *
47356 TTTAAAAAATTTAATCATTTC
1 TTTAAAATATTTAATAATTTC
47377 -TTAAAAT
1 TTTAAAAT
47384 CTATCTATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.25
21 7 0.29
22 11 0.46
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTAAAATATTTAATAATTTC
Found at i:47464 original size:16 final size:15
Alignment explanation
Indices: 47414--47464 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
47404 CAACAACCAC
47414 TTTTTTAAATATTAT
1 TTTTTTAAATATTAT
*
47429 TTTTTTAAA-ATAAAT
1 TTTTTTAAATAT-TAT
47444 TTTTTTAAATCATTAT
1 TTTTTTAAAT-ATTAT
47460 CTTTT
1 -TTTT
47465 ATTTAAATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 2 0.07
15 20 0.67
16 2 0.07
17 6 0.20
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTTAAATATTAT
Found at i:48822 original size:21 final size:20
Alignment explanation
Indices: 48798--48844 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
48788 TATTAGTTAG
48798 AAATTAATTA-AAAAAATTAAA
1 AAATTAATTATAAAAAA-T-AA
48819 AAATT-ATTATAAAAAATAA
1 AAATTAATTATAAAAAATAA
48838 AAATTAA
1 AAATTAA
48845 AGATATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 7 0.29
20 6 0.25
21 11 0.46
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATTAATTATAAAAAATAA
Found at i:48832 original size:20 final size:21
Alignment explanation
Indices: 48798--48844 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
48788 TATTAGTTAG
*
48798 AAATTAATTAAAAAAATTAAA
1 AAATTAATTAAAAAAAATAAA
*
48819 AAATT-ATTATAAAAAAT-AA
1 AAATTAATTAAAAAAAATAAA
48838 AAATTAA
1 AAATTAA
48845 AGATATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 7 0.30
20 11 0.48
21 5 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATTAATTAAAAAAAATAAA
Found at i:49952 original size:13 final size:13
Alignment explanation
Indices: 49934--49959 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49924 TACAGCAAGT
49934 ATGTATCGATACA
1 ATGTATCGATACA
49947 ATGTATCGATACA
1 ATGTATCGATACA
49960 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:52200 original size:21 final size:21
Alignment explanation
Indices: 52167--52211 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
52157 TTGCAAGTTG
*
52167 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
52189 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
52209 AAA
1 AAA
52212 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:54049 original size:16 final size:16
Alignment explanation
Indices: 54013--54049 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
54003 GATAAAAATG
54013 TCCAAAATGAGAAAGC
1 TCCAAAATGAGAAAGC
54029 T-CAAAATGA-AGAAGC
1 TCCAAAATGAGA-AAGC
54044 TCCAAA
1 TCCAAA
54050 CGAAATTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.05
15 13 0.68
16 5 0.26
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (16 bp):
TCCAAAATGAGAAAGC
Found at i:56138 original size:20 final size:20
Alignment explanation
Indices: 56059--56138 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
56049 AATGTCCAAA
*
56059 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
56079 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
56104 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
56124 TTGTATCGATACATT
1 ATGTATCGATACATT
56139 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:56142 original size:13 final size:13
Alignment explanation
Indices: 56124--56162 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
56114 ACATTTTTCT
56124 TTGTATCGATACA
1 TTGTATCGATACA
56137 TTGTATCGATACA
1 TTGTATCGATACA
*
56150 CTGTATCGATACA
1 TTGTATCGATACA
56163 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:56307 original size:21 final size:21
Alignment explanation
Indices: 56283--56329 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
56273 AAATCTTTTG
56283 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
56304 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
56324 CAAAAT
1 CAAAAT
56330 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:56326 original size:20 final size:19
Alignment explanation
Indices: 56285--56327 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
56275 ATCTTTTGCA
56285 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
56305 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
56325 AAA
1 AAA
56328 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:58754 original size:17 final size:18
Alignment explanation
Indices: 58732--58765 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
58722 TGTAATTTTT
58732 TCTTTTATTA-TTATTTA
1 TCTTTTATTATTTATTTA
58749 TCTTTTATTATTTATTT
1 TCTTTTATTATTTATTT
58766 TTAATGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (18 bp):
TCTTTTATTATTTATTTA
Found at i:58758 original size:14 final size:13
Alignment explanation
Indices: 58739--58768 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
58729 TTTTCTTTTA
58739 TTATTATTTATCTT
1 TTATTATTTAT-TT
58753 TTATTATTTATTT
1 TTATTATTTATTT
58766 TTA
1 TTA
58769 ATGTTTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (13 bp):
TTATTATTTATTT
Found at i:59460 original size:11 final size:11
Alignment explanation
Indices: 59444--59468 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59434 TTTATTTTGT
59444 TTATCACAAGG
1 TTATCACAAGG
59455 TTATCACAAGG
1 TTATCACAAGG
59466 TTA
1 TTA
59469 CCCTATTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (11 bp):
TTATCACAAGG
Found at i:66134 original size:21 final size:21
Alignment explanation
Indices: 66101--66140 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
66091 GAATATTTTA
** *
66101 AAAAATATTTATATAAATAAT
1 AAAAATAAATATAAAAATAAT
66122 AAAAATAAATATAAAAATA
1 AAAAATAAATATAAAAATA
66141 TTATTTAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAATAAATATAAAAATAAT
Found at i:67106 original size:2 final size:2
Alignment explanation
Indices: 67099--67123 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
67089 ATTTATATTT
67099 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
67124 TAATGTAATG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:68702 original size:134 final size:134
Alignment explanation
Indices: 68543--68800 Score: 471
Period size: 134 Copynumber: 1.9 Consensus size: 134
68533 TCTAATAAAT
* * *
68543 CTAAAATTAATTAATTTAAATGTTAAACCCGATTGACTTGACTTAAAATGATCTAAGTCCCAAAT
1 CTAAAACTAATTAATTTAAATGTTAAACCCGATTGACTTAACTTAAAATGATCTAAGTCCAAAAT
*
68608 AACCTGGATCTGATTAGCTCAAGCGTTAAATCTAATTGATTTGAGTCCGAAATAATTGATTAGCT
66 AACCTGAATCTGATTAGCTCAAGCGTTAAATCTAATTGATTTGAGTCCGAAATAATTGATTAGCT
68673 CAAC
131 CAAC
*
68677 CTAAAACTAATTAATTTAAATGTTAAACTCGATTGACTTAACTTAAAATGATCTAAGTCCAAAAT
1 CTAAAACTAATTAATTTAAATGTTAAACCCGATTGACTTAACTTAAAATGATCTAAGTCCAAAAT
68742 AACCTGAATCTGATTAGCTCAAGCGTTAAATCTAATTGATTTGAGTCCGAAATAATTGA
66 AACCTGAATCTGATTAGCTCAAGCGTTAAATCTAATTGATTTGAGTCCGAAATAATTGA
68801 AAATAACTTA
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
134 119 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (134 bp):
CTAAAACTAATTAATTTAAATGTTAAACCCGATTGACTTAACTTAAAATGATCTAAGTCCAAAAT
AACCTGAATCTGATTAGCTCAAGCGTTAAATCTAATTGATTTGAGTCCGAAATAATTGATTAGCT
CAAC
Found at i:68821 original size:16 final size:15
Alignment explanation
Indices: 68800--68861 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 15
68790 GAAATAATTG
68800 AAAATAACTTAAAACT
1 AAAATAA-TTAAAACT
68816 AAAATAATCT-AAACT
1 AAAATAAT-TAAAACT
*
68831 CAAAATAATTCAAAACA
1 -AAAATAATT-AAAACT
*
68848 AAAAAAATTTAAAA
1 AAAATAA-TTAAAA
68862 ATTTAAAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 7 0.18
16 26 0.67
17 6 0.15
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATAATTAAAACT
Found at i:68846 original size:32 final size:32
Alignment explanation
Indices: 68800--68860 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
68790 GAAATAATTG
* *
68800 AAAATAACTTAAAACTAAAATAATCTAAACTC
1 AAAATAACTTAAAACAAAAAAAATCTAAACTC
*
68832 AAAATAA-TTCAAAACAAAAAAAATTTAAA
1 AAAATAACTT-AAAACAAAAAAAATCTAAA
68861 AATTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 2 0.08
32 23 0.92
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (32 bp):
AAAATAACTTAAAACAAAAAAAATCTAAACTC
Found at i:69004 original size:15 final size:15
Alignment explanation
Indices: 68984--69015 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
68974 ATACTAAAAA
68984 TTTAATACTTAATTT
1 TTTAATACTTAATTT
*
68999 TTTAATATTTAATTT
1 TTTAATACTTAATTT
69014 TT
1 TT
69016 AATTTATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTAATACTTAATTT
Found at i:74034 original size:249 final size:249
Alignment explanation
Indices: 73596--74094 Score: 998
Period size: 249 Copynumber: 2.0 Consensus size: 249
73586 CAAGGTGGAG
73596 AAGGAATGTGGCTCGAAGACTTTCGTCGGCCAAATTCTATGTGATCAAGAAATAGAGCTAAGTGC
1 AAGGAATGTGGCTCGAAGACTTTCGTCGGCCAAATTCTATGTGATCAAGAAATAGAGCTAAGTGC
73661 ATGAGAATATCTTTAAGAAAAGTCCTATTGGTTAAGATGTTCATATATCAAGTAAAATTGCAAGA
66 ATGAGAATATCTTTAAGAAAAGTCCTATTGGTTAAGATGTTCATATATCAAGTAAAATTGCAAGA
73726 CAGTTGTTCTTGGAGTACAAGTAAAATAGGTCTTGGAGTGTATAGAGATAAATCCTAATTGAACA
131 CAGTTGTTCTTGGAGTACAAGTAAAATAGGTCTTGGAGTGTATAGAGATAAATCCTAATTGAACA
73791 ATAAATTAAAAATAGTTTATTAAAGGATTCACTTTATTGTTTTGACAAGACCAA
196 ATAAATTAAAAATAGTTTATTAAAGGATTCACTTTATTGTTTTGACAAGACCAA
73845 AAGGAATGTGGCTCGAAGACTTTCGTCGGCCAAATTCTATGTGATCAAGAAATAGAGCTAAGTGC
1 AAGGAATGTGGCTCGAAGACTTTCGTCGGCCAAATTCTATGTGATCAAGAAATAGAGCTAAGTGC
73910 ATGAGAATATCTTTAAGAAAAGTCCTATTGGTTAAGATGTTCATATATCAAGTAAAATTGCAAGA
66 ATGAGAATATCTTTAAGAAAAGTCCTATTGGTTAAGATGTTCATATATCAAGTAAAATTGCAAGA
73975 CAGTTGTTCTTGGAGTACAAGTAAAATAGGTCTTGGAGTGTATAGAGATAAATCCTAATTGAACA
131 CAGTTGTTCTTGGAGTACAAGTAAAATAGGTCTTGGAGTGTATAGAGATAAATCCTAATTGAACA
74040 ATAAATTAAAAATAGTTTATTAAAGGATTCACTTTATTGTTTTGACAAGACCAA
196 ATAAATTAAAAATAGTTTATTAAAGGATTCACTTTATTGTTTTGACAAGACCAA
74094 A
1 A
74095 CAAAAATTGG
Statistics
Matches: 250, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
249 250 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (249 bp):
AAGGAATGTGGCTCGAAGACTTTCGTCGGCCAAATTCTATGTGATCAAGAAATAGAGCTAAGTGC
ATGAGAATATCTTTAAGAAAAGTCCTATTGGTTAAGATGTTCATATATCAAGTAAAATTGCAAGA
CAGTTGTTCTTGGAGTACAAGTAAAATAGGTCTTGGAGTGTATAGAGATAAATCCTAATTGAACA
ATAAATTAAAAATAGTTTATTAAAGGATTCACTTTATTGTTTTGACAAGACCAA
Found at i:75380 original size:24 final size:26
Alignment explanation
Indices: 75353--75401 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
75343 TTTTTTTATG
75353 TGATGTGA-TA-TAATTTTTTATAAA
1 TGATGTGATTATTAATTTTTTATAAA
75377 TGATGTGATTTATTAATTTTTTATA
1 TGATGTGA-TTATTAATTTTTTATA
75402 TGAGATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.36
26 2 0.09
27 12 0.55
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (26 bp):
TGATGTGATTATTAATTTTTTATAAA
Found at i:81438 original size:29 final size:29
Alignment explanation
Indices: 81383--81440 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
81373 CAAATTCTTA
**
81383 TTTTATTTTTTAAAATATTATCTATATAT
1 TTTTATTTTTTAAAATATTATAAATATAT
*
81412 TTTTATATTTTTAATATA-TATAAATATAT
1 TTTTAT-TTTTTAAAATATTATAAATATAT
81441 ATATTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTATTTTTTAAAATATTATAAATATAT
Found at i:87070 original size:23 final size:21
Alignment explanation
Indices: 87022--87072 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
87012 AAATTAAGTC
* *
87022 AAAATTAGATTAATAATATTT
1 AAAATTAGAGTAAAAATATTT
*
87043 TAAATTATGAGTAAAAATTATTT
1 AAAATTA-GAGTAAAAA-TATTT
87066 AAAATTA
1 AAAATTA
87073 AATTAATGCG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 6 0.25
22 7 0.29
23 11 0.46
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (21 bp):
AAAATTAGAGTAAAAATATTT
Found at i:87666 original size:30 final size:28
Alignment explanation
Indices: 87630--87699 Score: 115
Period size: 30 Copynumber: 2.5 Consensus size: 28
87620 GAGCATGAAA
87630 ATGCACTAAAAGATTGATTTATTCACTGAC
1 ATGCACTAAAAGATTGA-TTATTCA-TGAC
87660 ATGCACTAAAAGATTGATTATTCATGAC
1 ATGCACTAAAAGATTGATTATTCATGAC
87688 A-GCACTAAAAGA
1 ATGCACTAAAAGA
87700 GTGACCACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 11 0.28
28 5 0.12
29 7 0.17
30 17 0.43
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (28 bp):
ATGCACTAAAAGATTGATTATTCATGAC
Done.