Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003819.1 Hibiscus syriacus cultivar Beakdansim tig00008192_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 184856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9561 original size:45 final size:45
Alignment explanation
Indices: 9423--9533 Score: 213
Period size: 45 Copynumber: 2.5 Consensus size: 45
9413 CAGAACGACT
9423 CTAAACCTAATGCGGAGAATGATACCGAAGCCGATGGCAAGGAGC
1 CTAAACCTAATGCGGAGAATGATACCGAAGCCGATGGCAAGGAGC
9468 CTAAACCTAATGCGGAGAATGATACCGAAGCCGATGGCAAGGAGC
1 CTAAACCTAATGCGGAGAATGATACCGAAGCCGATGGCAAGGAGC
*
9513 CTAAACCTAATGCAGAGAATG
1 CTAAACCTAATGCGGAGAATG
9534 TCGTCGAAGA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.37, C:0.22, G:0.27, T:0.14
Consensus pattern (45 bp):
CTAAACCTAATGCGGAGAATGATACCGAAGCCGATGGCAAGGAGC
Found at i:9567 original size:45 final size:45
Alignment explanation
Indices: 9423--9568 Score: 170
Period size: 45 Copynumber: 3.2 Consensus size: 45
9413 CAGAACGACT
* * * *
9423 CTAAACCTAATGCGGAGAATGATACCGAAGCCGATGGCAAGGAGC
1 CTAAACCTAATGCAGAGAATGATACCGAAGACAAAGGCAAGGAGC
* * * *
9468 CTAAACCTAATGCGGAGAATGATACCGAAGCCGATGGCAAGGAGC
1 CTAAACCTAATGCAGAGAATGATACCGAAGACAAAGGCAAGGAGC
*
9513 CTAAACCTAATGCAGAGAATG-T-CGTCGAAGACAAAGGCAAAGAGC
1 CTAAACCTAATGCAGAGAATGATAC--CGAAGACAAAGGCAAGGAGC
*
9558 CTAACCCTAAT
1 CTAAACCTAAT
9569 ACAAAGAAGT
Statistics
Matches: 93, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
43 1 0.01
44 1 0.01
45 91 0.98
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.14
Consensus pattern (45 bp):
CTAAACCTAATGCAGAGAATGATACCGAAGACAAAGGCAAGGAGC
Found at i:14454 original size:20 final size:19
Alignment explanation
Indices: 14429--14543 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 19
14419 AATTGGGAAA
14429 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACT-ACT
14449 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATAC-TACT
* *
14469 ATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATACTAC--T
* *
14490 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACT-ACT
* * *
14510 TTCGCAACGCGATAATACAT
1 ATCGCAATGCGATACTAC-T
14530 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
14544 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.06
20 46 0.59
21 25 0.32
22 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (19 bp):
ATCGCAATGCGATACTACT
Found at i:14491 original size:61 final size:62
Alignment explanation
Indices: 14426--14543 Score: 168
Period size: 61 Copynumber: 1.9 Consensus size: 62
14416 GTGAATTGGG
* * * *
14426 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTAC-T-ATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA-ATACATAATCGCAATGCGATAATAC
*
14487 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATAATACATAATCGCAATGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATACATAATCGCAATGCGAT
14544 TTTCAAAGCG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 3 0.06
61 34 0.68
62 13 0.26
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (62 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATACATAATCGCAATGCGATAATAC
Found at i:14494 original size:41 final size:41
Alignment explanation
Indices: 14449--14543 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
14439 GATACTGACT
* *
14449 ATCGCAATGCGATACTTACTATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATACTGACTATCGCAACGCGATAATACAAA
* * * *
14490 ATCGCAACGAGATACTGACTTTCGCAACGCGATAATACATA
1 ATCGCAATGCGATACTGACTATCGCAACGCGATAATACAAA
14531 ATCGCAATGCGAT
1 ATCGCAATGCGAT
14544 TTTCAAAGCG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (41 bp):
ATCGCAATGCGATACTGACTATCGCAACGCGATAATACAAA
Found at i:14738 original size:22 final size:22
Alignment explanation
Indices: 14710--14753 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
14700 CACTCTCTCA
*
14710 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
*
14732 CCCATCTCCGGCAAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
14754 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCCGTC
Found at i:15059 original size:20 final size:20
Alignment explanation
Indices: 15005--15063 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
14995 TTTATTCTCT
**
15005 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
15025 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
15045 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
15064 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:15254 original size:25 final size:24
Alignment explanation
Indices: 15200--15254 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
15190 TGTTTATTAT
* *
15200 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
15224 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
15250 TGTTT
1 TGTTT
15255 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:16401 original size:18 final size:18
Alignment explanation
Indices: 16380--16424 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
16370 TCCACTTTGG
*
16380 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
16398 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
16416 GAGCCATCA
1 GAGCCATCA
16425 TCTGATCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:17411 original size:19 final size:19
Alignment explanation
Indices: 17389--17519 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
17379 GGAAATTACT
17389 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
17408 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
17422 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
17441 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
* *
17455 TTCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
**
17474 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
17488 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
17507 ATCGCAACGCGAA
1 ATCGCAATGCGAA
17520 TTTAATTTCG
Statistics
Matches: 83, Mismatches: 14, Indels: 30
0.65 0.11 0.24
Matches are distributed among these distances:
14 26 0.31
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.47
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:17431 original size:33 final size:33
Alignment explanation
Indices: 17389--17515 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
17379 GGAAATTACT
17389 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
17422 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
17454 TTTCGCAATGCGAAATAAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
17488 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
17516 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:17496 original size:66 final size:66
Alignment explanation
Indices: 17390--17522 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
17380 GAAATTACTA
* *
17390 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
17455 T
66 T
*
17456 TCGCAATGCGAAATAAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
17521 T
66 T
17522 T
1 T
17523 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:17547 original size:14 final size:14
Alignment explanation
Indices: 17530--17586 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
17520 TTTAATTTCG
17530 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
17544 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
17563 CGTTGCGATCCTCT
1 CGTTGCGATTCTCT
17577 CGTTGCGATT
1 CGTTGCGATT
17587 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:17566 original size:33 final size:33
Alignment explanation
Indices: 17515--17596 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
17505 AAATCGCAAC
* * *
17515 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATCCTCTCGTT
17548 GCGATTTTCATTTCGCGTTGCGATCCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATCCTCTCGTT
17581 GCGATTTTCATTTCGC
1 GCGATTTTCATTTCGC
17597 ATTACGATAG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATCCTCTCGTT
Found at i:17730 original size:14 final size:14
Alignment explanation
Indices: 17711--17747 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
17701 CATCAATTAA
*
17711 ACAAATCAACTTTT
1 ACAAATCAACATTT
*
17725 ACAAATCACCATTT
1 ACAAATCAACATTT
17739 ACAAATCAA
1 ACAAATCAA
17748 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:19145 original size:21 final size:21
Alignment explanation
Indices: 19115--19279 Score: 68
Period size: 21 Copynumber: 7.9 Consensus size: 21
19105 TGAATGGTGG
*
19115 GAGGGACCTCTTCAACGATGA
1 GAGGGGCCTCTTCAACGATGA
* * * * *
19136 TAGTGGCCTCTTGAACGGTGG
1 GAGGGGCCTCTTCAACGATGA
* * *
19157 GAGGGGACTC-TCGAGGAATGA
1 GAGGGGCCTCTTCAACG-ATGA
*
19178 TAGGGGCCTCTTCAACGAT-A
1 GAGGGGCCTCTTCAACGATGA
* * * **
19198 GGAGTGGACTCTTGAGGGATGA
1 -GAGGGGCCTCTTCAACGATGA
* * * *
19220 CAGTGGCCTCTTGAACG-TGG
1 GAGGGGCCTCTTCAACGATGA
* * *
19240 GAGGGGACTC-TCGAGGAATGA
1 GAGGGGCCTCTTCAACG-ATGA
*
19261 TAGGGGCCTCTTCAACGAT
1 GAGGGGCCTCTTCAACGAT
19280 AGGAGTGGAC
Statistics
Matches: 97, Mismatches: 40, Indels: 14
0.64 0.26 0.09
Matches are distributed among these distances:
19 3 0.03
20 13 0.13
21 72 0.74
22 9 0.09
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (21 bp):
GAGGGGCCTCTTCAACGATGA
Found at i:19160 original size:42 final size:41
Alignment explanation
Indices: 19101--19302 Score: 167
Period size: 42 Copynumber: 4.8 Consensus size: 41
19091 GTGAATCGGG
* *
19101 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGATAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGATAGTGGC
* *
19143 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGATAGTGGC
* * * * * *
19185 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGATAGTGGC
* *
19227 CTCTTGAAC-GTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGATAGTGGC
* * * * *
19268 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGA
19303 CAGGCGAGTC
Statistics
Matches: 125, Mismatches: 26, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
40 3 0.02
41 33 0.26
42 79 0.63
43 10 0.08
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGATAGTGGC
Found at i:19266 original size:83 final size:84
Alignment explanation
Indices: 19131--19305 Score: 334
Period size: 83 Copynumber: 2.1 Consensus size: 84
19121 CCTCTTCAAC
*
19131 GATGATAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
19196 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
19215 GATGACAGTGGCCTCTTGAAC-GTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
19279 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
19298 GATGACAG
1 GATGACAG
19306 GCGAGTCGGG
Statistics
Matches: 90, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
83 70 0.78
84 20 0.22
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:19698 original size:91 final size:90
Alignment explanation
Indices: 19523--19707 Score: 300
Period size: 91 Copynumber: 2.0 Consensus size: 90
19513 ATTTCAAACT
*
19523 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
19588 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
19616 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
19680 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
19707 T
1 T
19708 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 42 0.48
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:21463 original size:14 final size:14
Alignment explanation
Indices: 21444--21499 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
21434 GAAAATGACT
21444 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
21458 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
21475 TTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
21491 ATCGCAACG
1 ATCGCAACG
21500 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.12
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:21480 original size:33 final size:33
Alignment explanation
Indices: 21420--21516 Score: 158
Period size: 33 Copynumber: 2.9 Consensus size: 33
21410 ACGAGATAAT
*
21420 GAGAATCGCAACGCGAAAATGACTATCGCAACGA
1 GAGAATCGCAACGCG-AAATGAATATCGCAACGA
*
21454 GAGAATCGCAACGCGAAATGATTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAATATCGCAACGA
*
21487 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAATATCGCAA
21517 TGCGAAATGA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 45 0.75
34 15 0.25
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAATATCGCAACGA
Found at i:21523 original size:52 final size:52
Alignment explanation
Indices: 21396--21573 Score: 189
Period size: 52 Copynumber: 3.4 Consensus size: 52
21386 CTTTTGGTTG
* * * * * *
21396 AAATGAAAATCGCAACGAGATAATGAGAATCGCAACGCGAAAAT-GACTATCGCA
1 AAATGAAAATCGCAATGCGA-AATGAAAATCGCAACGAGAGAATCG-C-AACGCA
* * * ** *
21450 ACGA-GAGAATCGCAACGCGAAATGATTATCGCAACGAGAGAATCGCAACGCG
1 A-AATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCA
*
21502 AAATGAAAATCGCAATGCGAAATGAAAATCGCAATGAGAGAATCGCAACGCA
1 AAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCA
21554 AAATGAAAATCGCAATGCGA
1 AAATGAAAATCGCAATGCGA
21574 TTTTGGTTTC
Statistics
Matches: 105, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
51 1 0.01
52 67 0.64
53 20 0.19
54 16 0.15
55 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (52 bp):
AAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCA
Found at i:21528 original size:19 final size:19
Alignment explanation
Indices: 21395--21573 Score: 118
Period size: 19 Copynumber: 10.1 Consensus size: 19
21385 TCTTTTGGTT
*
21395 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
21414 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
21434 GAAAATGACTATCGCAA--C
1 G-AAATGAAAATCGCAACGC
*
21452 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
21468 GAAATGATTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
21485 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
21501 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
*
21520 GAAATGAAAATCGCAA--T
1 GAAATGAAAATCGCAACGC
*
21537 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
21553 AAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
21572 GA
1 GA
21574 TTTTGGTTTC
Statistics
Matches: 124, Mismatches: 19, Indels: 34
0.70 0.11 0.19
Matches are distributed among these distances:
14 28 0.23
15 3 0.02
16 4 0.03
17 3 0.02
18 5 0.04
19 52 0.42
20 28 0.23
21 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:21602 original size:19 final size:19
Alignment explanation
Indices: 21569--21635 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
21559 AAAATCGCAA
**
21569 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
21588 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
21607 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
21627 TGCGATTTT
1 TGCGATTTT
21636 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:22198 original size:20 final size:20
Alignment explanation
Indices: 22157--22268 Score: 118
Period size: 20 Copynumber: 5.5 Consensus size: 20
22147 GCTATGTAAA
* *
22157 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
22177 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* * *
22197 TCGCATTGTGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
* *
22218 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTAT
**
22238 TCGTGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
22258 TCGCATTGCGA
1 TCGCATTGCGA
22269 ATTATGAAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
19 3 0.04
20 55 0.73
21 17 0.23
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:22223 original size:41 final size:40
Alignment explanation
Indices: 22175--22268 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 40
22165 CGATAGTAAG
* * *
22175 ATTCGCATTGCGATTTACGTATTCGCATTGTGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* ** *
22215 AATTCGCATTGCGATTTACTTAATCGTGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
22256 ATTCGCATTGCGA
1 ATTCGCATTGCGA
22269 ATTATGAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 13 0.28
41 33 0.72
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.41
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:22289 original size:21 final size:21
Alignment explanation
Indices: 22265--22320 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
22255 TATTCGCATT
*
22265 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
22286 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
22306 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
22321 TGCTTTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:22411 original size:21 final size:20
Alignment explanation
Indices: 22382--22433 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
22372 TTTACTTATC
22382 CGCATTGCGAATTGGGAAAAT
1 CGCATTGCGAATT-GGAAAAT
*
22403 CGCAATGCGAAATTGGAAAAT
1 CGCATTGCG-AATTGGAAAAT
22424 CGCATTGCGA
1 CGCATTGCGA
22434 TAGTCATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.82
22 4 0.14
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (20 bp):
CGCATTGCGAATTGGAAAAT
Found at i:25121 original size:128 final size:128
Alignment explanation
Indices: 24743--25155 Score: 756
Period size: 128 Copynumber: 3.2 Consensus size: 128
24733 GAGTTTTAAA
* *
24743 CCCCTGGGAACACGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGA
1 CCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGA
*
24808 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCGCA
66 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCGCG
*
24871 CCCCCGGGAACGCGCCTTAATG-GAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGA
1 CCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGA
24935 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCGCG
66 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCGCG
* *
24998 TCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCTGA
1 CCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGA
25063 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCGCG
66 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCGCG
*
25126 CCCCCGGGAACGCGCCTTTATGTGAATAGT
1 CCCCCGGGAACGCGCCTTCATGTGAATAGT
25156 ACTCCGATTA
Statistics
Matches: 275, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
127 124 0.45
128 151 0.55
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (128 bp):
CCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGA
GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCGCG
Found at i:36486 original size:55 final size:55
Alignment explanation
Indices: 36150--36485 Score: 477
Period size: 55 Copynumber: 6.2 Consensus size: 55
36140 TCCACTATCA
** * * * *
36150 ATACGGAAATTCATAAACTTATTATGAATTTCTT-AGTTTTGCACACAAAGTGCTC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAG-TTTACACATAAAGTGCCC
* * *
36205 ATACGGGAATTCATCCACTTAGTATGAA--T-TT-A-TTTACACATAAAGTACTC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
*
36255 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACATATAAAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
* *
36310 ATACAGAAATTCATCCACTTAGTATGAATTTCTTTAGTTTACACATAAAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
*
36365 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCTC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
* *
36420 ATACGGAAATTTATCCACATAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
*
36475 ATACGAAAATT
1 ATACGGAAATT
36486 TTCTTAAGTT
Statistics
Matches: 255, Mismatches: 21, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
50 42 0.16
52 4 0.02
53 3 0.01
54 1 0.00
55 205 0.80
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (55 bp):
ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
Found at i:36495 original size:37 final size:37
Alignment explanation
Indices: 36448--36522 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
36438 ATAGTATGAA
36448 TTTCTTAAGTTTACACATAAAGTGCCCATACGAAAAT
1 TTTCTTAAGTTTACACATAAAGTGCCCATACGAAAAT
*
36485 TTTCTTAAGTTTACACATAAAGTGCCCATACGGAAAT
1 TTTCTTAAGTTTACACATAAAGTGCCCATACGAAAAT
36522 T
1 T
36523 CATAAACAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (37 bp):
TTTCTTAAGTTTACACATAAAGTGCCCATACGAAAAT
Found at i:37052 original size:21 final size:21
Alignment explanation
Indices: 37027--37079 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
37017 CCCCTCTTGG
*
37027 TATCGACACTACTTGAATCGA
1 TATCGATACTACTTGAATCGA
*
37048 TATCGATACCACTTGAATCGA
1 TATCGATACTACTTGAATCGA
37069 TATCGATACTA
1 TATCGATACTA
37080 TTTATAATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (21 bp):
TATCGATACTACTTGAATCGA
Found at i:40997 original size:2 final size:2
Alignment explanation
Indices: 40990--41028 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
40980 TTTCCAGATT
40990 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41029 TTAAACATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41707 original size:46 final size:46
Alignment explanation
Indices: 41607--41699 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
41597 AATATACCGC
*
41607 TATGCATTTTCATTTGTGGCATCCTTTCATGCCAATTATGCATTGT
1 TATGCATTTTCATTTATGGCATCCTTTCATGCCAATTATGCATTGT
*
41653 TATGCATTTTCATTTATGTCATCCTTTCATGCCAATTATGCATTGT
1 TATGCATTTTCATTTATGGCATCCTTTCATGCCAATTATGCATTGT
41699 T
1 T
41700 CTTCATTTCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.20, C:0.19, G:0.13, T:0.47
Consensus pattern (46 bp):
TATGCATTTTCATTTATGGCATCCTTTCATGCCAATTATGCATTGT
Found at i:42032 original size:55 final size:55
Alignment explanation
Indices: 41992--42447 Score: 666
Period size: 55 Copynumber: 8.3 Consensus size: 55
41982 AAACTTATTG
* * *
41992 TGAATTTCTT-AGTTTTGCACACAAAGTGCTCATACAGAAATTCATCCACTTAGTA
1 TGAATTTCTTAAG-TTTACACATAAAGTGCCCATACAGAAATTCATCCACTTAGTA
*
42047 TGAATTTCTTAAGTTTACACATAAAGTGCCCATACGGAAATTCATCCACTTAGTA
1 TGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCACTTAGTA
*
42102 TGAATTTCTTAAGTTTACACATAAAGTGCCCATA-TGAAAATTCATCCACTTAGTA
1 TGAATTTCTTAAGTTTACACATAAAGTGCCCATACAG-AAATTCATCCACTTAGTA
*
42157 TGAATTTCTTAAGTTTACACATAAAGTGCCCATA-TGAAAATTCATCCACTTAGTA
1 TGAATTTCTTAAGTTTACACATAAAGTGCCCATACAG-AAATTCATCCACTTAGTA
* ** ** *
42212 TGAATTTCTTAAGTTTACACATAAAGTGCCCATATAGAAATTCATAAACAAATTA
1 TGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCACTTAGTA
* *
42267 TGAATTTCTTAAGTTTACACATAAAGTGCCCATACAAAAATTCATCCGCTTAGTA
1 TGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCACTTAGTA
**
42322 TGAATTTCTTAAGTTTACACATAAAGTGCCCATATGGAAATTCATCCACTTAGTA
1 TGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCACTTAGTA
* ** ** *
42377 TGAATTTCTTAAGTTTACACATAAAGTGCCCATACGGAAATTCATAAACAAATTA
1 TGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCACTTAGTA
42432 TGAATTTCTTAAGTTT
1 TGAATTTCTTAAGTTT
42448 TTACACACTC
Statistics
Matches: 369, Mismatches: 29, Indels: 6
0.91 0.07 0.01
Matches are distributed among these distances:
54 1 0.00
55 365 0.99
56 3 0.01
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (55 bp):
TGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCACTTAGTA
Found at i:42271 original size:165 final size:165
Alignment explanation
Indices: 41992--42447 Score: 745
Period size: 165 Copynumber: 2.8 Consensus size: 165
41982 AAACTTATTG
* * * *
41992 TGAATTTCTT-AGTTTTGCACACAAAGTGCTCATA-CAGAAATTCATCCACTTAGTATGAATTTC
1 TGAATTTCTTAAG-TTTACACATAAAGTGCCCATATGA-AAATTCATCCACTTAGTATGAATTTC
** ** *
42055 TTAAGTTTACACATAAAGTGCCCATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTAC
64 TTAAGTTTACACATAAAGTGCCCATACGGAAATTCATAAACAAATTATGAATTTCTTAAGTTTAC
**
42120 ACATAAAGTGCCCATATGAAAATTCATCCACTTAGTA
129 ACATAAAGTGCCCATACAAAAATTCATCCACTTAGTA
42157 TGAATTTCTTAAGTTTACACATAAAGTGCCCATATGAAAATTCATCCACTTAGTATGAATTTCTT
1 TGAATTTCTTAAGTTTACACATAAAGTGCCCATATGAAAATTCATCCACTTAGTATGAATTTCTT
**
42222 AAGTTTACACATAAAGTGCCCATATAGAAATTCATAAACAAATTATGAATTTCTTAAGTTTACAC
66 AAGTTTACACATAAAGTGCCCATACGGAAATTCATAAACAAATTATGAATTTCTTAAGTTTACAC
*
42287 ATAAAGTGCCCATACAAAAATTCATCCGCTTAGTA
131 ATAAAGTGCCCATACAAAAATTCATCCACTTAGTA
*
42322 TGAATTTCTTAAGTTTACACATAAAGTGCCCATATGGAAATTCATCCACTTAGTATGAATTTCTT
1 TGAATTTCTTAAGTTTACACATAAAGTGCCCATATGAAAATTCATCCACTTAGTATGAATTTCTT
42387 AAGTTTACACATAAAGTGCCCATACGGAAATTCATAAACAAATTATGAATTTCTTAAGTTT
66 AAGTTTACACATAAAGTGCCCATACGGAAATTCATAAACAAATTATGAATTTCTTAAGTTT
42448 TTACACACTC
Statistics
Matches: 272, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
165 269 0.99
166 3 0.01
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (165 bp):
TGAATTTCTTAAGTTTACACATAAAGTGCCCATATGAAAATTCATCCACTTAGTATGAATTTCTT
AAGTTTACACATAAAGTGCCCATACGGAAATTCATAAACAAATTATGAATTTCTTAAGTTTACAC
ATAAAGTGCCCATACAAAAATTCATCCACTTAGTA
Found at i:42769 original size:22 final size:20
Alignment explanation
Indices: 42723--42796 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
42713 TTCTGGCTCA
**
42723 ATGGTATCGATACCCCTATT
1 ATGGTATCGATACTACTATT
42743 ATGGTATCGATACTACTATGTT
1 ATGGTATCGATACTACTA--TT
42765 ATGGTA-CTGATACTA-TATT
1 ATGGTATC-GATACTACTATT
* *
42784 ACGGTACCGATAC
1 ATGGTATCGATAC
42797 CATTTTTGCA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
19 12 0.26
20 17 0.36
21 3 0.06
22 15 0.32
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (20 bp):
ATGGTATCGATACTACTATT
Found at i:42780 original size:19 final size:19
Alignment explanation
Indices: 42756--42796 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
42746 GTATCGATAC
* * *
42756 TACTATGTTATGGTACTGA
1 TACTATATTACGGTACCGA
42775 TACTATATTACGGTACCGA
1 TACTATATTACGGTACCGA
42794 TAC
1 TAC
42797 CATTTTTGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (19 bp):
TACTATATTACGGTACCGA
Found at i:43837 original size:15 final size:15
Alignment explanation
Indices: 43817--43854 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
43807 AATTTTGAAA
43817 TTGCTTTTCCTAGAT
1 TTGCTTTTCCTAGAT
*
43832 TTGCTTTTCCTATAT
1 TTGCTTTTCCTAGAT
43847 TTGCTTTT
1 TTGCTTTT
43855 GCAATTCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.11, T:0.61
Consensus pattern (15 bp):
TTGCTTTTCCTAGAT
Found at i:46384 original size:3 final size:3
Alignment explanation
Indices: 46376--46483 Score: 146
Period size: 3 Copynumber: 36.0 Consensus size: 3
46366 TTATTTATTA
*
46376 AAT AAT AAT AAT -AT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * *
46421 AAT AAT TAT TAT AAT AAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
46469 TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
46484 TTTAAATGAA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.02
3 88 0.95
4 3 0.03
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:47202 original size:76 final size:76
Alignment explanation
Indices: 46615--47175 Score: 1088
Period size: 76 Copynumber: 7.4 Consensus size: 76
46605 GAAACGTTGA
*
46615 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
46680 AGGCTTTTTGG
66 AGGCTTTTTGG
*
46691 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
46755 AGGCTTTTTGG
66 AGGCTTTTTGG
46766 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
46831 AGGCTTTTTGG
66 AGGCTTTTTGG
46842 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
46907 AGGCTTTTTGG
66 AGGCTTTTTGG
46918 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
46983 AGGCTTTTTGG
66 AGGCTTTTTGG
46994 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
47059 AGGCTTTTTGG
66 AGGCTTTTTGG
47070 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
47135 AGGCTTTTTGG
66 AGGCTTTTTGG
*
47146 AAACATCATGCACTGAAGGGCTTACAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
47176 TGGGAAATAG
Statistics
Matches: 481, Mismatches: 3, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 0.15
76 407 0.85
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:50525 original size:83 final size:83
Alignment explanation
Indices: 50419--50636 Score: 375
Period size: 83 Copynumber: 2.6 Consensus size: 83
50409 ATACCAAACT
*
50419 AGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT-
1 AGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTTATCTTCTAAACTCAATGATTG
50483 GTTCTGTCCAAACCAGATC
66 GTTCTGTCC-AACCAGATC
* * *
50502 AGATAACTCAAAGAACACTTCCAGAAGATGATATTGGCAAATTTATCTTCTGAATTCAATGATTG
1 AGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTTATCTTCTAAACTCAATGATTG
*
50567 GTTCTGTTCAACCAGATC
66 GTTCTGTCCAACCAGATC
50585 AGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTTATCTTCTA
1 AGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTTATCTTCTA
50637 GTTAATGTTT
Statistics
Matches: 127, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
83 119 0.94
84 8 0.06
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.29
Consensus pattern (83 bp):
AGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTTATCTTCTAAACTCAATGATTG
GTTCTGTCCAACCAGATC
Found at i:52779 original size:7 final size:7
Alignment explanation
Indices: 52763--52817 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 7
52753 CTTGATTCAA
*
52763 TTTTCCT
1 TTTTCTT
52770 TTTTCTT
1 TTTTCTT
52777 TTTT-TT
1 TTTTCTT
52783 TTCTT-TT
1 TT-TTCTT
*
52790 TTTT-TC
1 TTTTCTT
52796 TTTTCTT
1 TTTTCTT
52803 TTTTCTT
1 TTTTCTT
*
52810 TCTTCTT
1 TTTTCTT
52817 T
1 T
52818 CTTTGCTGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 11 0.26
7 31 0.74
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTCTT
Found at i:52785 original size:11 final size:11
Alignment explanation
Indices: 52769--52821 Score: 72
Period size: 11 Copynumber: 4.8 Consensus size: 11
52759 TCAATTTTCC
52769 TTTTTCTTTTT
1 TTTTTCTTTTT
52780 TTTTTC-TTTT
1 TTTTTCTTTTT
52790 TTTTTCTTTTCT
1 TTTTTCTTTT-T
*
52802 TTTTTCTTTCT
1 TTTTTCTTTTT
*
52813 TCTTTCTTT
1 TTTTTCTTT
52822 GCTGGATGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
10 10 0.26
11 18 0.47
12 10 0.26
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:59741 original size:3 final size:3
Alignment explanation
Indices: 59733--59842 Score: 141
Period size: 3 Copynumber: 36.0 Consensus size: 3
59723 TTATTTATTA
59733 AAT AAT AAT AAT ATAT AAT -AT AAT AAT AAAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
* * *
59779 ATAT AAT AAT AAT ACT AAT ACT AAT AAT AAT ACT AAT AAT AAT AAT
1 A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
59825 AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
59843 TTTAAATGAA
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
2 2 0.02
3 82 0.88
4 9 0.10
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:60816 original size:198 final size:203
Alignment explanation
Indices: 60422--60832 Score: 645
Period size: 198 Copynumber: 2.0 Consensus size: 203
60412 GATGAAAGGT
* * * * *
60422 TTACACTTTGAAACTAAAGTTTCTTTGCTTCCTCCCATTGTCTTTTTTACTTCTTACTTTGGTTG
1 TTACACTTTGAAACTAAAGTTTCTATGCTTCCTCCCATTGCCATCTTTACTTCTTACTTTGATTG
* *
60487 TGGATTTTTTTTTAAATATTTTGATTTTTAAATTCATTTTTTTCAATTATTTTTAACACTTCCAA
66 TGGATATTTTTTTAAATATTTTAATTTTTAAATTCA-TTTTTTCAATTATTTTTAACACTTCCAA
*
60552 ACAAATTCTCTACTATTTGCTTTAGTACTTTCTTACACACCTACATCATCTACTACATGCTTTAC
130 ACAAATTCTCTACTATTTGATTTAGTACTTTCTTACACACCTACATCATCTACTACATGCTTTAC
60617 TACTTTTAC
195 TACTTTTAC
* *
60626 TTACACTTTGAAACTAGAGTTTCTATGCTTCCT-CCAGTTGCCATCTTTGCTTCTTACTTTGATT
1 TTACACTTTGAAACTAAAGTTTCTATGCTTCCTCCCA-TTGCCATCTTTACTTCTTACTTTGATT
60690 GT-GA-ATTTTTTT-AATATTTTAATTTTTAAATTCA-TTTTTCAATTATTTTTAACACTTCCAA
65 GTGGATATTTTTTTAAATATTTTAATTTTTAAATTCATTTTTTCAATTATTTTTAACACTTCCAA
* * *
60751 A-AAATTCTCTACTATTTGATTTGGTACTTTCTTACACACTTACATCATCTACTACATGTTTTAC
130 ACAAATTCTCTACTATTTGATTTAGTACTTTCTTACACACCTACATCATCTACTACATGCTTTAC
60815 TACTTTTAC
195 TACTTTTAC
60824 TTACACTTT
1 TTACACTTT
60833 TTTTTTCAAA
Statistics
Matches: 193, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
198 77 0.40
199 28 0.15
201 21 0.11
202 7 0.04
203 5 0.03
204 55 0.28
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.49
Consensus pattern (203 bp):
TTACACTTTGAAACTAAAGTTTCTATGCTTCCTCCCATTGCCATCTTTACTTCTTACTTTGATTG
TGGATATTTTTTTAAATATTTTAATTTTTAAATTCATTTTTTCAATTATTTTTAACACTTCCAAA
CAAATTCTCTACTATTTGATTTAGTACTTTCTTACACACCTACATCATCTACTACATGCTTTACT
ACTTTTAC
Found at i:60898 original size:16 final size:17
Alignment explanation
Indices: 60865--60905 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
60855 AGAATATTTT
60865 TTTTTA-TTTACATGTA
1 TTTTTATTTTACATGTA
*
60881 TTTTTATTTTATAT-TA
1 TTTTTATTTTACATGTA
60897 TTTTGTATT
1 TTTT-TATT
60906 ATGAATAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (17 bp):
TTTTTATTTTACATGTA
Found at i:65516 original size:16 final size:16
Alignment explanation
Indices: 65495--65526 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
65485 TTTTGTACAC
*
65495 TGCAAGTAAACAATAA
1 TGCAAGCAAACAATAA
65511 TGCAAGCAAACAATAA
1 TGCAAGCAAACAATAA
65527 AACAACTGCA
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:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (16 bp):
TGCAAGCAAACAATAA
Found at i:74285 original size:14 final size:15
Alignment explanation
Indices: 74254--74290 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
74244 TCTATCTCAT
74254 TTTTGATTTCCTTTA
1 TTTTGATTTCCTTTA
*
74269 TTTTGTTTTCC-TTA
1 TTTTGATTTCCTTTA
74283 TTTT-ATTT
1 TTTTGATTT
74291 GTTTTTAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 3 0.15
14 7 0.35
15 10 0.50
ACGTcount: A:0.11, C:0.11, G:0.05, T:0.73
Consensus pattern (15 bp):
TTTTGATTTCCTTTA
Found at i:86449 original size:20 final size:20
Alignment explanation
Indices: 86398--86450 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
86388 AATGTTTTAA
*
86398 AGTATCGATAC-TTATATAG
1 AGTATCGATACTTTACATAG
* *
86417 AGTATTGAAACTTTAGCAT-G
1 AGTATCGATACTTTA-CATAG
86437 AGTATCGATACTTT
1 AGTATCGATACTTT
86451 CAATCTATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 9 0.33
20 16 0.59
21 2 0.07
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (20 bp):
AGTATCGATACTTTACATAG
Found at i:87004 original size:17 final size:17
Alignment explanation
Indices: 86984--87018 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
86974 AGTAGAATAG
86984 AACAGATAATAGAACAA
1 AACAGATAATAGAACAA
* *
87001 AACAGTTAGTAGAACAA
1 AACAGATAATAGAACAA
87018 A
1 A
87019 TAGCAGTAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.11, G:0.14, T:0.14
Consensus pattern (17 bp):
AACAGATAATAGAACAA
Found at i:89381 original size:18 final size:19
Alignment explanation
Indices: 89350--89387 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
89340 GAAATGAAAG
*
89350 TTTTCAAAGTTTTGGGTTT
1 TTTTCAAAGATTTGGGTTT
*
89369 TTTTCAAA-ATTTGTGTTT
1 TTTTCAAAGATTTGGGTTT
89387 T
1 T
89388 CTTTTTACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.18, C:0.05, G:0.16, T:0.61
Consensus pattern (19 bp):
TTTTCAAAGATTTGGGTTT
Found at i:92985 original size:2 final size:2
Alignment explanation
Indices: 92980--93008 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
92970 TTAATCATTA
92980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
93009 ATGATATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:97709 original size:88 final size:88
Alignment explanation
Indices: 97617--97792 Score: 205
Period size: 88 Copynumber: 2.0 Consensus size: 88
97607 AATAAATCAA
97617 TATTT-TTCTCATTTTAAAAAACAGAAAAATAAAT-CAAACGATTT-ATTTCCTTTCACAAAACA
1 TATTTATT-TCATTTTAAAAAACAGAAAAATAAATCCAAA-GATTTAATTT-CTTTCACAAAACA
*
97679 GGAAAATAAATCAAACAATTTGTTTC
63 GGAAAATAAATCAAACAATTTATTTC
* * * * * * * *
97705 TATTTATTTCCTTTTACAAAATAGGAAAATAATTCCAAATATTTAATTTCTTTTACAAAATAGGA
1 TATTTATTTCATTTTAAAAAACAGAAAAATAAATCCAAAGATTTAATTTCTTTCACAAAACAGGA
* *
97770 AAATAAATCCAACGATTTATTTC
66 AAATAAATCAAACAATTTATTTC
97793 GTTTTACATA
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
88 64 0.86
89 10 0.14
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.37
Consensus pattern (88 bp):
TATTTATTTCATTTTAAAAAACAGAAAAATAAATCCAAAGATTTAATTTCTTTCACAAAACAGGA
AAATAAATCAAACAATTTATTTC
Found at i:97749 original size:39 final size:39
Alignment explanation
Indices: 97705--97800 Score: 140
Period size: 39 Copynumber: 2.5 Consensus size: 39
97695 AATTTGTTTC
*
97705 TATTTATTTCCTTTTACAAAATAGGAAAATAATTCCAAA
1 TATTTATTTCCTTTTACAAAATAGGAAAATAAATCCAAA
*
97744 TATTTAATTT-CTTTTACAAAATAGGAAAATAAATCCAAC
1 TATTT-ATTTCCTTTTACAAAATAGGAAAATAAATCCAAA
* *
97783 GATTTATTTCGTTTTACA
1 TATTTATTTCCTTTTACA
97801 TATCAAATTC
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
38 4 0.08
39 43 0.84
40 4 0.08
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (39 bp):
TATTTATTTCCTTTTACAAAATAGGAAAATAAATCCAAA
Found at i:97867 original size:38 final size:38
Alignment explanation
Indices: 97824--97938 Score: 144
Period size: 39 Copynumber: 3.0 Consensus size: 38
97814 CAAAATTCTC
* *
97824 AGGAAAATAAATTTACCGATTTATTTCCTTTTCAAAAT
1 AGGAAAATAAATTAAACGATTTATTTCCTTTTCAAAAT
* *
97862 AGGAAAATAAATTCAAA-AATTTATTTCCTTTTACAAAAC
1 AGGAAAATAAATT-AAACGATTTATTTCCTTTT-CAAAAT
* *
97901 AAGAAAATAAATCAAACGATTTATTTCCTTTT-AAAAT
1 AGGAAAATAAATTAAACGATTTATTTCCTTTTCAAAAT
97938 A
1 A
97939 TAATCATATA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
37 5 0.08
38 30 0.45
39 31 0.47
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.36
Consensus pattern (38 bp):
AGGAAAATAAATTAAACGATTTATTTCCTTTTCAAAAT
Found at i:97910 original size:39 final size:40
Alignment explanation
Indices: 97842--98028 Score: 141
Period size: 39 Copynumber: 4.5 Consensus size: 40
97832 AAATTTACCG
* *
97842 ATTTATTTCCTTTT-CAAAA-TAGGAAAATAAATTCAAAA
1 ATTTATTTCCTTTTACAAAACAAAGAAAATAAATTCAAAA
*
97880 ATTTATTTCCTTTTACAAAAC-AAGAAAATAAA-TCAAACG
1 ATTTATTTCCTTTTACAAAACAAAGAAAATAAATTCAAA-A
* *
97919 ATTTATTTCCTTTTAAAATATAATCATATAAGAAAATAAATTCAATA
1 ATTTATTTCCTTTT-ACA-A-AA-C--A-AAGAAAATAAATTCAAAA
* * * *
97966 ATTTATTT-CTTTATTCAAGATTCCAAAGAAAATAAATTTAACA
1 ATTTATTTCCTTT-TACAA-A--ACAAAGAAAATAAATTCAAAA
*
98009 ATTTATTTCCTTTAACAAAA
1 ATTTATTTCCTTTTACAAAA
98029 TAGAATCATT
Statistics
Matches: 119, Mismatches: 14, Indels: 30
0.73 0.09 0.18
Matches are distributed among these distances:
38 19 0.16
39 29 0.24
40 2 0.02
41 1 0.01
42 3 0.03
43 28 0.24
44 5 0.04
45 2 0.02
46 6 0.05
47 20 0.17
48 4 0.03
ACGTcount: A:0.47, C:0.12, G:0.04, T:0.38
Consensus pattern (40 bp):
ATTTATTTCCTTTTACAAAACAAAGAAAATAAATTCAAAA
Found at i:98279 original size:58 final size:56
Alignment explanation
Indices: 97982--98335 Score: 267
Period size: 58 Copynumber: 6.2 Consensus size: 56
97972 TTCTTTATTC
* * *
97982 AAGATTC-CAAAGAAAATAAATTTAACAATTTATTTCCTTTAACAAA-ATAGAATCATTT
1 AAGATTCTC-AAGAAAATAAATTCAACAATTT-TTTTC-TT-ACAAAGTTAGAATCATTT
* * *
98040 AAGATTCTCATGAAAATAAATTTAACAATTTATTAACTT-TTACAAA-ATAGAATCATTT
1 AAGATTCTCAAGAAAATAAATTCAACAATTT-TT---TTCTTACAAAGTTAGAATCATTT
* * * * **
98098 AAGATTCTCATGAAAATAAATTTAACAATTTATTTT-TTA-AAGGATAGAATCATCC
1 AAGATTCTCAAGAAAATAAATTCAACAATTT-TTTTCTTACAAAGTTAGAATCATTT
* * * * * *
98153 ACA-ATTCTCAAGAAAAAAAATTCGACAACTTTTTTCTTGCAAAGTTAAAAT-ATTC
1 A-AGATTCTCAAGAAAATAAATTCAACAATTTTTTTCTTACAAAGTTAGAATCATTT
* * * *
98208 AAGATT-TCTAAGGAAATAAATTCAAGAGTTTGTTTTCCTTATAAAGTTAGAATCATTT
1 AAGATTCTC-AAGAAAATAAATTCAACAATTT-TTTT-CTTACAAAGTTAGAATCATTT
* * * *
98266 AAGATTCTCAAGGAAATAAATTCAACAATCTATTTTCCTTACAAAGTTAAAATCAATGT
1 AAGATTCTCAAGAAAATAAATTCAACAAT-T-TTTTTCTTACAAAGTTAGAATC-ATTT
98325 AAGATTCTCAA
1 AAGATTCTCAA
98336 TGATTTATTT
Statistics
Matches: 248, Mismatches: 31, Indels: 33
0.79 0.10 0.11
Matches are distributed among these distances:
54 9 0.04
55 64 0.26
56 13 0.05
57 13 0.05
58 124 0.50
59 23 0.09
60 1 0.00
61 1 0.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.35
Consensus pattern (56 bp):
AAGATTCTCAAGAAAATAAATTCAACAATTTTTTTCTTACAAAGTTAGAATCATTT
Found at i:98502 original size:45 final size:45
Alignment explanation
Indices: 98452--98590 Score: 174
Period size: 45 Copynumber: 3.1 Consensus size: 45
98442 GAATCAATCC
* * *
98452 TTTAATTTTACCAACCCAATAATCAAAATGAACTAGTCCTTTGAT
1 TTTAATTTTACAAACCCAATAATCAAAAGGAACTAATCCTTTGAT
* * *
98497 TTTAATTTT-CTAAATCCAATAATCGAAAGGAATTAATCCTTTGAT
1 TTTAATTTTAC-AAACCCAATAATCAAAAGGAACTAATCCTTTGAT
* *
98542 TTTACTTTTGA-AAACACAATAATCAAAAGGAACTAATCCTTTGAT
1 TTTAATTTT-ACAAACCCAATAATCAAAAGGAACTAATCCTTTGAT
98587 TTTA
1 TTTA
98591 CTGTTGATAA
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
44 1 0.01
45 79 0.99
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (45 bp):
TTTAATTTTACAAACCCAATAATCAAAAGGAACTAATCCTTTGAT
Found at i:98591 original size:45 final size:44
Alignment explanation
Indices: 98467--98614 Score: 179
Period size: 45 Copynumber: 3.3 Consensus size: 44
98457 TTTTACCAAC
* * * * *
98467 CCAATAATCAAAATGAACTAGTCCTTTGATTTTAATTTTCTAAAT
1 CCAATAATCAAAAGGAACTAATCCTTTGATTTTACTTTT-GAAAA
* *
98512 CCAATAATCGAAAGGAATTAATCCTTTGATTTTACTTTTGAAAA
1 CCAATAATCAAAAGGAACTAATCCTTTGATTTTACTTTTGAAAA
* *
98556 CACAATAATCAAAAGGAACTAATCCTTTGATTTTACTGTTGATAAC
1 C-CAATAATCAAAAGGAACTAATCCTTTGATTTTACTTTTGA-AAA
*
98602 CCAATAATAAAAA
1 CCAATAATCAAAA
98615 ACCTTGGATT
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
44 4 0.04
45 82 0.92
46 3 0.03
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (44 bp):
CCAATAATCAAAAGGAACTAATCCTTTGATTTTACTTTTGAAAA
Found at i:98833 original size:14 final size:15
Alignment explanation
Indices: 98814--98846 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
98804 GTTATATGGT
98814 AATAATACCAT-AAC
1 AATAATACCATGAAC
*
98828 AATAATATCATGAAC
1 AATAATACCATGAAC
98843 AATA
1 AATA
98847 TCATGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (15 bp):
AATAATACCATGAAC
Found at i:99059 original size:14 final size:14
Alignment explanation
Indices: 99040--99089 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 14
99030 AAAAGGCAAC
99040 TCACCATGTGCTAG
1 TCACCATGTGCTAG
*
99054 TCACCATGCGCTAG
1 TCACCATGTGCTAG
* *
99068 TCACCATGTGTTAA
1 TCACCATGTGCTAG
99082 TCACCATG
1 TCACCATG
99090 CATTTGTGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (14 bp):
TCACCATGTGCTAG
Found at i:100204 original size:35 final size:35
Alignment explanation
Indices: 100140--100206 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
100130 GAACTTGCCG
* *
100140 TAAGGAATTACCAGTTCGATCGGTCTGAACCTATA
1 TAAGGAACTACCAGTTCGATCGATCTGAACCTATA
*
100175 TAAGGAACTACCAGTTTGATCGAAT-TGAACCT
1 TAAGGAACTACCAGTTCGATCG-ATCTGAACCT
100207 GCAGAGACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 27 0.96
36 1 0.04
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (35 bp):
TAAGGAACTACCAGTTCGATCGATCTGAACCTATA
Found at i:102635 original size:103 final size:103
Alignment explanation
Indices: 102451--102675 Score: 396
Period size: 103 Copynumber: 2.2 Consensus size: 103
102441 GTCGAGGGTC
*
102451 TATGTGGTCCTTAGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTAGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
102516 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
102554 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTAGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
102619 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
102657 TATGTGGTCCTTATGGACA
1 TATGTGGTCCTTAGGGACA
102676 GTATTATATG
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTAGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:102734 original size:23 final size:23
Alignment explanation
Indices: 102684--102752 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
102674 CAGTATTATA
* * *
102684 TGGCACTACGGTACAATTCTACG
1 TGGCACTACGGTGCAATTATATG
* *
102707 CGGCACTCCGGTGCAATTATATG
1 TGGCACTACGGTGCAATTATATG
***
102730 TGGCACTTTAGTGCAATTATATG
1 TGGCACTACGGTGCAATTATATG
102753 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATATG
Found at i:108265 original size:22 final size:21
Alignment explanation
Indices: 108240--108284 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
108230 TTGTCAAAGC
108240 CAAAGTCAACGGTCAGACCGGT
1 CAAAGTCAACGGTCA-ACCGGT
* *
108262 CAAAGTCAATGGTCAACGGGT
1 CAAAGTCAACGGTCAACCGGT
108283 CA
1 CA
108285 GGTCAAAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.33, C:0.24, G:0.27, T:0.16
Consensus pattern (21 bp):
CAAAGTCAACGGTCAACCGGT
Found at i:108347 original size:20 final size:20
Alignment explanation
Indices: 108301--108350 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
108291 AGTCAACAGG
* *
108301 TTGGGTCGGGTTGACTCAGT
1 TTGGGTCAGGCTGACTCAGT
** *
108321 TCAGGTCAGGCTGACTCGGT
1 TTGGGTCAGGCTGACTCAGT
108341 TTGGGTCAGG
1 TTGGGTCAGG
108351 TTGGGTCGGT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.12, C:0.18, G:0.40, T:0.30
Consensus pattern (20 bp):
TTGGGTCAGGCTGACTCAGT
Found at i:110651 original size:36 final size:36
Alignment explanation
Indices: 110548--110654 Score: 92
Period size: 36 Copynumber: 3.0 Consensus size: 36
110538 CACCTAAGAT
* * *
110548 CCGTAAGGAATTACTAGCTCGATTGGTCTGAACCTA
1 CCGTAAGGAATTACCAGTTCGATAGGTCTGAACCTA
** * * ** * *
110584 -TATAAAGAATTACCAATTTAACCAAGT-TGAACCTA
1 CCGTAAGGAATTACCAGTTCGA-TAGGTCTGAACCTA
110619 CCGTAAGGAATTACCAGTTCGATAGGTCTGAACCTA
1 CCGTAAGGAATTACCAGTTCGATAGGTCTGAACCTA
110655 TATAAGGATT
Statistics
Matches: 49, Mismatches: 19, Indels: 6
0.66 0.26 0.08
Matches are distributed among these distances:
35 24 0.49
36 25 0.51
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (36 bp):
CCGTAAGGAATTACCAGTTCGATAGGTCTGAACCTA
Found at i:112394 original size:20 final size:19
Alignment explanation
Indices: 112363--112410 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
112353 CAACAAGTCA
*
112363 GGTCGGGTTGACTTGGTTCG
1 GGTCGGG-TGACTCGGTTCG
112383 GGTCAGGGTGACTCGGTTCG
1 GGTC-GGGTGACTCGGTTCG
112403 GGTCGGGT
1 GGTCGGGT
112411 TGGGCTGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 19 0.73
21 3 0.12
ACGTcount: A:0.06, C:0.17, G:0.48, T:0.29
Consensus pattern (19 bp):
GGTCGGGTGACTCGGTTCG
Found at i:115065 original size:18 final size:18
Alignment explanation
Indices: 115006--115069 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
114996 ACTTTTAAAT
*
115006 TTTTTAATAGTGTTTT-TA
1 TTTTTAATA-TTTTTTATA
* *
115024 TTTTTAATAACTTTCTA-A
1 TTTTTAAT-ATTTTTTATA
*
115042 TATTTAATATTTTTTATA
1 TTTTTAATATTTTTTATA
115060 TTTTT-ATATT
1 TTTTTAATATT
115070 GAAATTTAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
17 11 0.31
18 24 0.67
19 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTTAATATTTTTTATA
Found at i:115658 original size:2 final size:2
Alignment explanation
Indices: 115651--115698 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
115641 ATATTATGTC
115651 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
115693 AT AT AT
1 AT AT AT
115699 TAAAACTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118526 original size:63 final size:62
Alignment explanation
Indices: 118427--118570 Score: 261
Period size: 63 Copynumber: 2.3 Consensus size: 62
118417 ATTAATTGTG
118427 TTACATGTTCTCTACATTTGTTTACTGAAATTGGTTCTAGGTTAATTATGTACTAAAATTTTC
1 TTACATGTTCTCTACATTTGTTTACTGAAATTGGTTCTAGGTTAATTATGTACT-AAATTTTC
* *
118490 TTACATGTTCTCTACATTTGTTTACTGAAATTGGTTCTAGGTTAATTGTGTACTGAATTTTC
1 TTACATGTTCTCTACATTTGTTTACTGAAATTGGTTCTAGGTTAATTATGTACTAAATTTTC
118552 TTACATGTTCTCTACATTT
1 TTACATGTTCTCTACATTT
118571 CAATTTCAGG
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
62 26 0.33
63 53 0.67
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.49
Consensus pattern (62 bp):
TTACATGTTCTCTACATTTGTTTACTGAAATTGGTTCTAGGTTAATTATGTACTAAATTTTC
Found at i:131855 original size:100 final size:100
Alignment explanation
Indices: 131677--131942 Score: 496
Period size: 100 Copynumber: 2.6 Consensus size: 100
131667 CAAGTAAAGG
*
131677 AAGATGATGCTTCAACCATAATAAAACGCCATAGGCCATTTCAAGAAGTGAAATACAGGTCCAAG
1 AAGA-GATGCTTCAACCATAATAAAACACCATAGGCCATTTCAAGAAGTGAAATACAGGTCCAAG
*
131742 ACATCACGCTTTGAAACAGTACAGCACGATGTTTAT
65 ACATCACGCTTTGAAACAGTACAGCACGATGTTGAT
*
131778 AAGAGATGCTTCAACCATAATAACACACCATAGGCCATTTCAAGAAGTGAAATACAGGTCCAAGA
1 AAGAGATGCTTCAACCATAATAAAACACCATAGGCCATTTCAAGAAGTGAAATACAGGTCCAAGA
131843 CATCACGCTTTGAAACAGTACAGCACGATGTTGAT
66 CATCACGCTTTGAAACAGTACAGCACGATGTTGAT
131878 AAGAGATGCTTCAACCATAATAAAACACCATAGGCCATTTCAAGAAGTGAAATACAGGTCCAAGA
1 AAGAGATGCTTCAACCATAATAAAACACCATAGGCCATTTCAAGAAGTGAAATACAGGTCCAAGA
131943 GGGATAGTGA
Statistics
Matches: 161, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
100 157 0.98
101 4 0.02
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (100 bp):
AAGAGATGCTTCAACCATAATAAAACACCATAGGCCATTTCAAGAAGTGAAATACAGGTCCAAGA
CATCACGCTTTGAAACAGTACAGCACGATGTTGAT
Found at i:135621 original size:22 final size:22
Alignment explanation
Indices: 135596--135637 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
135586 CAAGGGAAAG
135596 CATTGAACT-TCATAGAAAATTC
1 CATTGAA-TATCATAGAAAATTC
135618 CATTGAATATCATAGAAAAT
1 CATTGAATATCATAGAAAAT
135638 ACCACAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (22 bp):
CATTGAATATCATAGAAAATTC
Found at i:135685 original size:29 final size:28
Alignment explanation
Indices: 135653--135738 Score: 100
Period size: 31 Copynumber: 2.9 Consensus size: 28
135643 AAAATTTTGG
* *
135653 TTAGTGACCAAAATATAATTATTGAAATT
1 TTAGTGACCAAAGTATAATT-TTGAAAGT
*
135682 TTAGTGGCCAAAGTATAAATTTTAGAAAAGT
1 TTAGTGACCAAAGTAT-AATTTT-G-AAAGT
*
135713 TTAGGGACCAAAGTATAATTTTGAAA
1 TTAGTGACCAAAGTATAATTTTGAAA
135739 AGTTATGTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
28 3 0.06
29 17 0.35
30 11 0.22
31 18 0.37
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (28 bp):
TTAGTGACCAAAGTATAATTTTGAAAGT
Found at i:135724 original size:31 final size:29
Alignment explanation
Indices: 135653--135742 Score: 103
Period size: 29 Copynumber: 3.0 Consensus size: 29
135643 AAAATTTTGG
* * *
135653 TTAGTGACCAAAATATAATTATTG-AAATT
1 TTAGTGGCCAAAGTATAATT-TTGAAAAGT
135682 TTAGTGGCCAAAGTATAAATTTTAGAAAAGT
1 TTAGTGGCCAAAGTAT-AATTTT-GAAAAGT
135713 TTAG-GGACCAAAGTATAATTTTGAAAAGT
1 TTAGTGG-CCAAAGTATAATTTTGAAAAGT
135742 T
1 T
135743 ATGTATTTTG
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
29 24 0.44
30 13 0.24
31 17 0.31
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.34
Consensus pattern (29 bp):
TTAGTGGCCAAAGTATAATTTTGAAAAGT
Found at i:136554 original size:17 final size:17
Alignment explanation
Indices: 136534--136577 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
136524 AAGTTAGGGT
136534 TTTGGTATGATGTTGAA
1 TTTGGTATGATGTTGAA
* *
136551 TTTGGGTATGATTTTGAT
1 TTT-GGTATGATGTTGAA
*
136569 TTTGATATG
1 TTTGGTATG
136578 GTTAAGATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.52
Consensus pattern (17 bp):
TTTGGTATGATGTTGAA
Found at i:136558 original size:18 final size:18
Alignment explanation
Indices: 136537--136572 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
136527 TTAGGGTTTT
136537 GGTATGATGTTGAATTTG
1 GGTATGATGTTGAATTTG
* *
136555 GGTATGATTTTGATTTTG
1 GGTATGATGTTGAATTTG
136573 ATATGGTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (18 bp):
GGTATGATGTTGAATTTG
Found at i:138815 original size:27 final size:26
Alignment explanation
Indices: 138753--138816 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 26
138743 CAATACCTGT
*
138753 ATATTCTATATGGCACTATATGTACAA
1 ATATT-TATATGGCACTAAATGTACAA
*
138780 AT-TGGTTATATGGCACTAAATGTGCAA
1 ATAT--TTATATGGCACTAAATGTACAA
138807 CATATTTATA
1 -ATATTTATA
138817 CTCATCATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
26 1 0.03
27 26 0.84
28 3 0.10
29 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (26 bp):
ATATTTATATGGCACTAAATGTACAA
Found at i:139979 original size:14 final size:14
Alignment explanation
Indices: 139957--139987 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
139947 GGGGTTTTAG
139957 TTTAGGGTTTGGGA
1 TTTAGGGTTTGGGA
*
139971 TTTATGGTTTGGGA
1 TTTAGGGTTTGGGA
139985 TTT
1 TTT
139988 GAGATTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.35, T:0.52
Consensus pattern (14 bp):
TTTAGGGTTTGGGA
Found at i:139988 original size:21 final size:21
Alignment explanation
Indices: 139943--139995 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
139933 AGAATTTAGA
*
139943 ATTTGGGGTTTTAGTTTAGGG
1 ATTTGGGATTTTAGTTTAGGG
*
139964 -TTTGGGATTTATGGTTT-GGG
1 ATTTGGGATTT-TAGTTTAGGG
*
139984 ATTTGAGATTTT
1 ATTTGGGATTTT
139996 GGGGGTGGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.15, C:0.00, G:0.34, T:0.51
Consensus pattern (21 bp):
ATTTGGGATTTTAGTTTAGGG
Found at i:145103 original size:17 final size:17
Alignment explanation
Indices: 145081--145113 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
145071 TATTTTATGA
*
145081 AAGAAAAAGAATAAAAT
1 AAGAAAAAGAACAAAAT
145098 AAGAAAAAGAACAAAA
1 AAGAAAAAGAACAAAA
145114 AAATATGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.03, G:0.12, T:0.06
Consensus pattern (17 bp):
AAGAAAAAGAACAAAAT
Found at i:147940 original size:29 final size:30
Alignment explanation
Indices: 147904--148009 Score: 76
Period size: 29 Copynumber: 3.5 Consensus size: 30
147894 TAGTGGTAAG
* * *
147904 AAAT-TTATTTTTATGTTAGTAT-TT-TTT
1 AAATATTATTTTTATATTAATATATTATGT
147931 AAATAGTTATTATTTTATATTAATATATTATGT
1 AAATA-TTA-T-TTTTATATTAATATATTATGT
* * *
147964 AAATATTATTTTT-TATTAAAATAATATTT
1 AAATATTATTTTTATATTAATATATTATGT
*
147993 ATATAATTATTATTTAT
1 AAAT-ATTATT-TTTAT
148010 TTAGAATTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
27 4 0.06
29 19 0.30
30 11 0.17
31 16 0.25
32 6 0.10
33 7 0.11
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (30 bp):
AAATATTATTTTTATATTAATATATTATGT
Found at i:149723 original size:21 final size:21
Alignment explanation
Indices: 149699--149746 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
149689 ACAGGGGTAC
* *
149699 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
149720 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
149741 ATGCCA
1 ATGCCA
149747 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:149864 original size:21 final size:21
Alignment explanation
Indices: 149756--149858 Score: 154
Period size: 21 Copynumber: 4.9 Consensus size: 21
149746 ATCTCCGCAG
* *
149756 GGTTACATTCCGAGCCCG-CA
1 GGTTACATGCCTAGCCCGCCA
* *
149776 GGGTTACTTTCCTAGCCCGCCA
1 -GGTTACATGCCTAGCCCGCCA
149798 GGTTACATGCCTAGCCCGCCA
1 GGTTACATGCCTAGCCCGCCA
149819 GGTTACATGCCTAGCCCGCCA
1 GGTTACATGCCTAGCCCGCCA
149840 GGTTACATGCCTAGCCCGC
1 GGTTACATGCCTAGCCCGC
149859 AGGGTTTTAT
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
21 75 0.97
22 2 0.03
ACGTcount: A:0.17, C:0.37, G:0.24, T:0.21
Consensus pattern (21 bp):
GGTTACATGCCTAGCCCGCCA
Found at i:150443 original size:33 final size:34
Alignment explanation
Indices: 150384--150480 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
150374 AAATGTTTTT
*
150384 AAAATACAAATTATATTATTCAAAATTTAAAATA
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
150418 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* *
150451 AAAATATAAATTATAGTATTCAAAATTTAA
1 AAAATAAAAATTATATTATTCAAAATTTAA
150481 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCAAAATTTAAAATA
Found at i:150487 original size:34 final size:33
Alignment explanation
Indices: 150382--150487 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
150372 ATAAATGTTT
*
150382 TTAAAATACAAATTATATTATTCAAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCAAAATTT-AAA
* *
150416 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCAAAATTTAAA
* *
150448 TTTAAAATATAAATTATAGTATTCAAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCAAAATTTAA-A
150483 TTAAA
1 TTAAA
150488 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCAAAATTTAAA
Found at i:151100 original size:128 final size:128
Alignment explanation
Indices: 150872--151727 Score: 1631
Period size: 128 Copynumber: 6.7 Consensus size: 128
150862 AGTTATTCAA
*
150872 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
150937 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGT
*
151000 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
151065 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGT
*
151128 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
151193 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGT
*
151256 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGGCATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
*
151321 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGT
151384 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
* *
151449 GACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCATTCATATGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGT
*
151512 ACTAATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
*
151577 GACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGT
151640 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
151705 GACGAAATAATGGAAGGCGCGCC
66 GACGAAATAATGGAAGGCGCGCC
151728 TTCATATGAA
Statistics
Matches: 717, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 717 1.00
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (128 bp):
ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGT
Found at i:151825 original size:8 final size:8
Alignment explanation
Indices: 151812--151850 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
151802 TCACAATCTT
151812 TCAAATTC
1 TCAAATTC
151820 TCAAATTC
1 TCAAATTC
* *
151828 CCAAACTC
1 TCAAATTC
151836 T-AAATTC
1 TCAAATTC
151843 TCAAATTC
1 TCAAATTC
151851 CCTGAAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.33
Consensus pattern (8 bp):
TCAAATTC
Found at i:156034 original size:31 final size:33
Alignment explanation
Indices: 155986--156064 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 33
155976 TTTAAATAGT
* *
155986 TATTATATTTTATATT-AAT-ATATTTATGTAAA
1 TATTAT-TTTTTTATTAAATAATATTTATATAAA
*
156018 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATT-AAATAATATTTATATAAA
*
156052 TATTATTTATTTA
1 TATTATTTTTTTA
156065 GAATTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 8 0.20
32 6 0.15
33 3 0.08
34 23 0.57
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (33 bp):
TATTATTTTTTTATTAAATAATATTTATATAAA
Found at i:156056 original size:34 final size:31
Alignment explanation
Indices: 155976--156064 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
155966 TTAGTATTTT
* * *
155976 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTTTTATTAATATA
* *
156008 TTTATGTAAATATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTTATT--AAT-ATA
*
156042 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTTTTTTA
156065 GAATTATTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 8 0.17
32 12 0.26
33 3 0.07
34 23 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTTTATTAATATA
Found at i:159639 original size:11 final size:10
Alignment explanation
Indices: 159625--159670 Score: 65
Period size: 11 Copynumber: 4.4 Consensus size: 10
159615 TCATTTTTTA
*
159625 AAAAATAAAT
1 AAAAATGAAT
159635 AAAAATGCAAT
1 AAAAATG-AAT
159646 AAAAATGAATT
1 AAAAATGAA-T
159657 AAAAATGAAT
1 AAAAATGAAT
159667 AAAA
1 AAAA
159671 TTCAATACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
10 13 0.39
11 20 0.61
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.20
Consensus pattern (10 bp):
AAAAATGAAT
Found at i:159650 original size:21 final size:21
Alignment explanation
Indices: 159625--159670 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
159615 TCATTTTTTA
159625 AAAAAT-AAATAAAAATGCAAT
1 AAAAATGAAATAAAAATG-AAT
*
159646 AAAAATGAATTAAAAATGAAT
1 AAAAATGAAATAAAAATGAAT
159667 AAAA
1 AAAA
159671 TTCAATACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.20
Consensus pattern (21 bp):
AAAAATGAAATAAAAATGAAT
Found at i:160937 original size:10 final size:10
Alignment explanation
Indices: 160882--160940 Score: 73
Period size: 10 Copynumber: 5.7 Consensus size: 10
160872 TTTACATTAT
*
160882 ATTTTTATTG
1 ATTTTTATTC
*
160892 AATTTTATTC
1 ATTTTTATTC
160902 ATTTTTAATTC
1 ATTTTT-ATTC
160913 ATTTTTATTGC
1 ATTTTTATT-C
*
160924 ATTTTTATTT
1 ATTTTTATTC
160934 ATTTTTA
1 ATTTTTA
160941 AAAAAGTGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
10 23 0.53
11 20 0.47
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (10 bp):
ATTTTTATTC
Found at i:160937 original size:21 final size:20
Alignment explanation
Indices: 160882--160940 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
160872 TTTACATTAT
* *
160882 ATTTTTATTGAATTTTATTC
1 ATTTTTATTCATTTTTATTC
160902 ATTTTTAATTCATTTTTATTGC
1 ATTTTT-ATTCATTTTTATT-C
*
160924 ATTTTTATTTATTTTTA
1 ATTTTTATTCATTTTTA
160941 AAAAAGTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.18
21 21 0.62
22 7 0.21
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (20 bp):
ATTTTTATTCATTTTTATTC
Found at i:162173 original size:11 final size:11
Alignment explanation
Indices: 162125--162182 Score: 73
Period size: 11 Copynumber: 5.4 Consensus size: 11
162115 AGTAACCAAC
162125 ATAACAAACTA
1 ATAACAAACTA
* *
162136 ATAACCAGCTA
1 ATAACAAACTA
**
162147 ATAAC-AACCC
1 ATAACAAACTA
162157 ATAACAAACTA
1 ATAACAAACTA
162168 ATAACAAACTA
1 ATAACAAACTA
162179 ATAA
1 ATAA
162183 TACTCTAACA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
10 7 0.18
11 32 0.82
ACGTcount: A:0.59, C:0.22, G:0.02, T:0.17
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:163973 original size:11 final size:11
Alignment explanation
Indices: 163925--163982 Score: 73
Period size: 11 Copynumber: 5.4 Consensus size: 11
163915 AGTAACCAAC
163925 ATAACAAACTA
1 ATAACAAACTA
* *
163936 ATAACCAGCTA
1 ATAACAAACTA
**
163947 ATAAC-AACCC
1 ATAACAAACTA
163957 ATAACAAACTA
1 ATAACAAACTA
163968 ATAACAAACTA
1 ATAACAAACTA
163979 ATAA
1 ATAA
163983 TACTCTAACA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
10 7 0.18
11 32 0.82
ACGTcount: A:0.59, C:0.22, G:0.02, T:0.17
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:169227 original size:14 final size:14
Alignment explanation
Indices: 169204--169251 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
169194 TTCGATTATA
*
169204 TGTTCGTTTATGTT
1 TGTTCATTTATGTT
169218 TGTTCATTTA----
1 TGTTCATTTATGTT
169228 TGTTCATTTATGTT
1 TGTTCATTTATGTT
*
169242 CGTTCATTTA
1 TGTTCATTTA
169252 CGTTCGTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 10 0.36
14 18 0.64
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.60
Consensus pattern (14 bp):
TGTTCATTTATGTT
Found at i:169237 original size:24 final size:24
Alignment explanation
Indices: 169192--169327 Score: 152
Period size: 24 Copynumber: 5.7 Consensus size: 24
169182 CGTTCGTGAA
169192 CGTTCGATTATATGTTCGTTTATGTT
1 CGTTC-ATT-TATGTTCGTTTATGTT
* *
169218 TGTTCATTTATGTTCATTTATGTT
1 CGTTCATTTATGTTCGTTTATGTT
* ** *
169242 CGTTCATTTACGTTCGTGAACGTT
1 CGTTCATTTATGTTCGTTTATGTT
*
169266 AG---ATTATATGTTCGTTTATGTT
1 CGTTCATT-TATGTTCGTTTATGTT
*
169288 CGTTCATTTATGTTCATTTATGTT
1 CGTTCATTTATGTTCGTTTATGTT
169312 CGTTCATTTATGTTCG
1 CGTTCATTTATGTTCG
169328 AACAGAGGGC
Statistics
Matches: 90, Mismatches: 16, Indels: 10
0.78 0.14 0.09
Matches are distributed among these distances:
21 3 0.03
22 13 0.14
24 64 0.71
25 6 0.07
26 4 0.04
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.54
Consensus pattern (24 bp):
CGTTCATTTATGTTCGTTTATGTT
Found at i:169248 original size:70 final size:70
Alignment explanation
Indices: 169169--169327 Score: 291
Period size: 70 Copynumber: 2.3 Consensus size: 70
169159 CAAATGGCTC
* *
169169 GTTCGTTCATTTACGTTCGTGAACGTTCGATTATATGTTCGTTTATGTTTGTTCATTTATGTTCA
1 GTTCGTTCATTTACGTTCGTGAACGTTAGATTATATGTTCGTTTATGTTCGTTCATTTATGTTCA
169234 TTTAT
66 TTTAT
169239 GTTCGTTCATTTACGTTCGTGAACGTTAGATTATATGTTCGTTTATGTTCGTTCATTTATGTTCA
1 GTTCGTTCATTTACGTTCGTGAACGTTAGATTATATGTTCGTTTATGTTCGTTCATTTATGTTCA
169304 TTTAT
66 TTTAT
*
169309 GTTCGTTCATTTATGTTCG
1 GTTCGTTCATTTACGTTCG
169328 AACAGAGGGC
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 86 1.00
ACGTcount: A:0.17, C:0.13, G:0.18, T:0.52
Consensus pattern (70 bp):
GTTCGTTCATTTACGTTCGTGAACGTTAGATTATATGTTCGTTTATGTTCGTTCATTTATGTTCA
TTTAT
Found at i:169256 original size:14 final size:14
Alignment explanation
Indices: 169229--169258 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
169219 GTTCATTTAT
*
169229 GTTCATTTATGTTC
1 GTTCATTTACGTTC
169243 GTTCATTTACGTTC
1 GTTCATTTACGTTC
169257 GT
1 GT
169259 GAACGTTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.17, G:0.17, T:0.53
Consensus pattern (14 bp):
GTTCATTTACGTTC
Found at i:169297 original size:14 final size:14
Alignment explanation
Indices: 169275--169327 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
169265 TAGATTATAT
*
169275 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
169289 GTTCATTTA---T-
1 GTTCATTTATGTTC
169299 GTTCATTTATGTTC
1 GTTCATTTATGTTC
169313 GTTCATTTATGTTC
1 GTTCATTTATGTTC
169327 G
1 G
169328 AACAGAGGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 23 0.68
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:169607 original size:23 final size:23
Alignment explanation
Indices: 169581--169646 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
169571 TTTTTTGTGT
*
169581 GTTTG-TGTTGTTCGTTTATGTTC
1 GTTTGTTG-TGTTCGTTTATATTC
*
169604 GTTTATTGTGTTCGTTTATATTC
1 GTTTGTTGTGTTCGTTTATATTC
*
169627 GTTCGTTCGTGTTCGTTTAT
1 GTTTGTT-GTGTTCGTTTAT
169647 TGTTTAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
23 23 0.62
24 14 0.38
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.59
Consensus pattern (23 bp):
GTTTGTTGTGTTCGTTTATATTC
Done.