Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008308.1 Hibiscus syriacus cultivar Beakdansim tig00110998_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: 1044366
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:951181 original size:19 final size:19
Alignment explanation
Indices: 951087--951221 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
951077 TAGTTTACTT
* *
951087 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
951107 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
951126 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
951145 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
951159 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
951178 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
951192 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
951211 TCGCAATGCGA
1 TCGCAACGCGA
951222 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:951239 original size:19 final size:19
Alignment explanation
Indices: 951217--951345 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
951207 AAAATCGCAA
951217 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
951236 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
951250 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
951269 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
951283 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
951302 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
951321 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
951341 TGCGA
1 TGCGA
951346 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:951259 original size:33 final size:33
Alignment explanation
Indices: 951217--951308 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
951207 AAAATCGCAA
951217 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
951250 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
951283 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
951309 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:951548 original size:93 final size:93
Alignment explanation
Indices: 951389--951862 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
951379 TTGAATGGAT
951389 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
951454 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
951482 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
951547 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
951575 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
951640 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
951668 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
951733 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
951761 AAATTTACTTTTAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
951826 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
951854 AAATTTACT
1 AAATTTACT
951863 AAGCAATCTA
Statistics
Matches: 377, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 377 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:953587 original size:14 final size:14
Alignment explanation
Indices: 953568--953657 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
953558 TTGAAATGAA
953568 AATCGCAACGAGAG
1 AATCGCAACGAGAG
953582 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
953599 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
953615 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
953634 AATCGCAACGAGAG
1 AATCGCAACGAGAG
953648 AATCGCAACG
1 AATCGCAACG
953658 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:953605 original size:33 final size:33
Alignment explanation
Indices: 953560--953674 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
953550 TCTTTTGGTT
953560 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
953593 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
953626 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
953659 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
953675 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:953606 original size:19 final size:18
Alignment explanation
Indices: 953567--953679 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
953557 GTTGAAATGA
953567 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
953582 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
953599 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
953615 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
953632 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
953648 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
953665 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
953680 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:953710 original size:14 final size:14
Alignment explanation
Indices: 953691--953744 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
953681 TTTGGTTTCG
953691 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
953705 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
953724 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
953738 CGTTGCG
1 CGTTGCG
953745 CTTTTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.07, C:0.26, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:953723 original size:33 final size:33
Alignment explanation
Indices: 953675--953755 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
953665 AAAATCGCAA
**
953675 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
953708 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
953741 TGCGCTTTTCATTTC
1 TGCGATTTTCATTTC
953756 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.07, C:0.23, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:953791 original size:41 final size:41
Alignment explanation
Indices: 953731--953808 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
953721 TCGCGTTGCG
* *
953731 ATTCTCTCGTTGCGCTTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
953772 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
953809 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:953807 original size:21 final size:21
Alignment explanation
Indices: 953732--953807 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
953722 CGCGTTGCGA
*
953732 TTCTCTCGTTGCGCTTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
953753 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
953773 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
953794 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
953808 CTCTTCTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 17 0.37
21 29 0.63
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:953934 original size:33 final size:33
Alignment explanation
Indices: 953887--953957 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
953877 AATACTAACT
* *
953887 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
953920 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
953953 TGAAA
1 TGAAA
953958 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:954189 original size:22 final size:22
Alignment explanation
Indices: 954137--954191 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
954127 TGGTTGTGAG
**
954137 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
954159 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
954181 GGATTTCTTCG
1 GGATTTCTTCG
954192 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:954362 original size:20 final size:20
Alignment explanation
Indices: 954337--954530 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
954327 CTTTAAATAT
954337 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
954357 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
954379 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
954398 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
954418 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
954438 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
954458 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
954478 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
954498 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
954518 CGCGTTGCGATTT
1 CGCGTTGCGATTT
954531 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:954524 original size:60 final size:60
Alignment explanation
Indices: 954337--954530 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
954327 CTTTAAATAT
**
954337 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
954398 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
954458 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
954518 CGCGTTGCGATTT
1 CGCGTTGCGATTT
954531 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:954547 original size:21 final size:21
Alignment explanation
Indices: 954517--954599 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
954507 ATTTTCATAT
*
954517 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
954538 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
954559 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
* *
954580 TCGCGTTGTGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
954600 CTGATTTGCG
Statistics
Matches: 46, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
20 1 0.02
21 43 0.93
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:955157 original size:31 final size:30
Alignment explanation
Indices: 955116--955197 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
955106 TTATAAAAAA
*
955116 TAAT-AAATATAATTTATAATAATTTTATT-T
1 TAATAAAATATAA-TAATAATAATTTT-TTAT
*
955146 TAATAAAATATAATAATCATAATTTTTTAT
1 TAATAAAATATAATAATAATAATTTTTTAT
*
955176 TTATAAAATTATAGAT-ATAATA
1 TAATAAAA-TATA-ATAATAATA
955198 TTTACATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
29 2 0.05
30 23 0.52
31 17 0.39
32 2 0.05
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
TAATAAAATATAATAATAATAATTTTTTAT
Found at i:955168 original size:30 final size:31
Alignment explanation
Indices: 955116--955184 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
955106 TTATAAAAAA
*
955116 TAAT-AAATATAATTTATAATAATTTTATT-T
1 TAATAAAATATAATTAATAATAATTTT-TTAT
*
955146 TAATAAAATATAA-TAATCATAATTTTTTAT
1 TAATAAAATATAATTAATAATAATTTTTTAT
*
955176 TTATAAAAT
1 TAATAAAAT
955185 TATAGATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.06
30 24 0.71
31 8 0.24
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (31 bp):
TAATAAAATATAATTAATAATAATTTTTTAT
Found at i:955669 original size:23 final size:23
Alignment explanation
Indices: 955619--955663 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
955609 AGCTTATTTT
*
955619 ATTATATAAGCGCTAACTATTAC
1 ATTATATAAGCGCTAACTAATAC
* *
955642 ATTATATAAGCGGTACCTAATA
1 ATTATATAAGCGCTAACTAATA
955664 TGTTATTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTAACTAATAC
Found at i:955719 original size:87 final size:86
Alignment explanation
Indices: 955516--955747 Score: 347
Period size: 87 Copynumber: 2.7 Consensus size: 86
955506 TAATAAATTA
* *
955516 AATAATTAACCTATTTTATTATATAAGCGCTATCTATTACGTTATATAAGTGCTACCTAATATGT
1 AATAATTAACCTATTTTATTATATAAGCGCTAACTATTACATTATATAAGTGCTACCTAATATGT
** *
955581 TTTGTGCTTGATAATGTTTTC
66 TTTGTGCTTGATAATACTTCC
* * * * *
955602 AGTAATTAGCTTATTTTATTATATAAGCGCTAACTATTACATTATATAAGCGGTACCTAATATGT
1 AATAATTAACCTATTTTATTATATAAGCGCTAACTATTACATTATATAAGTGCTACCTAATATGT
*
955667 TATTGTGTTTGATAATACTTCC
66 T-TTGTGCTTGATAATACTTCC
*
955689 AATAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGTGCTACCTA
1 AATAATTAACCTATTTTATTATATAAGCGCTAACTATTACATTATATAAGTGCTACCTA
955748 TTACATTATA
Statistics
Matches: 128, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
86 59 0.46
87 69 0.54
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.43
Consensus pattern (86 bp):
AATAATTAACCTATTTTATTATATAAGCGCTAACTATTACATTATATAAGTGCTACCTAATATGT
TTTGTGCTTGATAATACTTCC
Found at i:955799 original size:156 final size:156
Alignment explanation
Indices: 955619--955914 Score: 511
Period size: 156 Copynumber: 1.9 Consensus size: 156
955609 AGCTTATTTT
* *
955619 ATTATATAAGCGCTAACTATTACATTATATAAGCGGTACCTAATATGTTATTGTGTTTGATAATA
1 ATTATATAAGCGCCAACTATTACATTATATAAGCGGTACCTAATATGTTATTGTGCTTGATAATA
*
955684 CTTCCAATAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGTGCTACCTAT
66 CTTCCAATAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAT
*
955749 TACATTATATAAGTGCTACCTATTAC
131 TACATCATATAAGTGCTACCTATTAC
* * *
955775 ATTATATAAGCGCCACCTATTACATTATATAAGTGGTACCTAATATGTTATTGTGCTTGATAATG
1 ATTATATAAGCGCCAACTATTACATTATATAAGCGGTACCTAATATGTTATTGTGCTTGATAATA
* *
955840 TTTCCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAT
66 CTTCCAATAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAT
955905 TACATCATAT
131 TACATCATAT
955915 TTTTACTTGT
Statistics
Matches: 131, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
156 131 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.40
Consensus pattern (156 bp):
ATTATATAAGCGCCAACTATTACATTATATAAGCGGTACCTAATATGTTATTGTGCTTGATAATA
CTTCCAATAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAT
TACATCATATAAGTGCTACCTATTAC
Found at i:955825 original size:23 final size:23
Alignment explanation
Indices: 955697--955816 Score: 186
Period size: 23 Copynumber: 5.2 Consensus size: 23
955687 CCAATAATTA
** *
955697 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGTGCT
955720 ACCTATTACATTATATAAGTGCT
1 ACCTATTACATTATATAAGTGCT
955743 ACCTATTACATTATATAAGTGCT
1 ACCTATTACATTATATAAGTGCT
* *
955766 ACCTATTACATTATATAAGCGCC
1 ACCTATTACATTATATAAGTGCT
*
955789 ACCTATTACATTATATAAGTGGT
1 ACCTATTACATTATATAAGTGCT
955812 ACCTA
1 ACCTA
955817 ATATGTTATT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 89 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (23 bp):
ACCTATTACATTATATAAGTGCT
Found at i:955888 original size:23 final size:23
Alignment explanation
Indices: 955853--955914 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
955843 CCAGTAATTA
**
955853 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
955876 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
955899 ACCTATTACATCATAT
1 ACCTATTACATTATAT
955915 TTTTACTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:957369 original size:22 final size:23
Alignment explanation
Indices: 957323--957369 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
957313 ATGTTCATTT
*
957323 TACATAACTTAGAAAGAAAAAAA
1 TACATAACTTACAAAGAAAAAAA
* *
957346 TACATAAC-TACAAATATAAAAA
1 TACATAACTTACAAAGAAAAAAA
957368 TA
1 TA
957370 ATATATCTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21
Consensus pattern (23 bp):
TACATAACTTACAAAGAAAAAAA
Found at i:962008 original size:19 final size:19
Alignment explanation
Indices: 961984--962034 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
961974 AGACTTAGTG
961984 CATCGGTACACTAGGGGTA
1 CATCGGTACACTAGGGGTA
*
962003 CATCGGTACATTAGGGGTA
1 CATCGGTACACTAGGGGTA
962022 CATCGGTACACTA
1 CATCGGTACACTA
962035 ATTACATTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (19 bp):
CATCGGTACACTAGGGGTA
Found at i:964905 original size:22 final size:22
Alignment explanation
Indices: 964875--964953 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
964865 TGCATAGTGT
*
964875 ATCGATGCAATTCAAGGAATGC
1 ATCGATGCAATTCAAGGAATTC
* * *
964897 ATCGGTGCACTTCATA-G--TTT
1 ATCGATGCAATTCA-AGGAATTC
964917 ATCGATGCATATTCAAGGAATTC
1 ATCGATGCA-ATTCAAGGAATTC
* *
964940 ATCGGTGCACTTCA
1 ATCGATGCAATTCA
964954 TAATGTATCG
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
20 10 0.23
21 5 0.12
22 17 0.40
23 11 0.26
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.30
Consensus pattern (22 bp):
ATCGATGCAATTCAAGGAATTC
Found at i:964945 original size:43 final size:43
Alignment explanation
Indices: 964855--964969 Score: 178
Period size: 43 Copynumber: 2.7 Consensus size: 43
964845 CGACGAGTGT
* *
964855 ATCGATGCACTGCATAGTGTATCGATGCA-ATTCAAGGAATGC
1 ATCGGTGCACTTCATAGTGTATCGATGCATATTCAAGGAATGC
* *
964897 ATCGGTGCACTTCATAGTTTATCGATGCATATTCAAGGAATTC
1 ATCGGTGCACTTCATAGTGTATCGATGCATATTCAAGGAATGC
*
964940 ATCGGTGCACTTCATAATGTATCGATGCAT
1 ATCGGTGCACTTCATAGTGTATCGATGCAT
964970 GTTGCACAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
42 26 0.39
43 40 0.61
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (43 bp):
ATCGGTGCACTTCATAGTGTATCGATGCATATTCAAGGAATGC
Found at i:964968 original size:20 final size:20
Alignment explanation
Indices: 964852--964968 Score: 74
Period size: 20 Copynumber: 5.6 Consensus size: 20
964842 ACCCGACGAG
* *
964852 TGTATCGATGCACTGCATAG
1 TGTATCGATGCACTTCATAA
* *
964872 TGTATCGATGCAATTCAAGGAA
1 TGTATCGATGCACTTC-A-TAA
* * *
964894 TGCATCGGTGCACTTCATAG
1 TGTATCGATGCACTTCATAA
* * *
964914 TTTATCGATGCATATTCAAGGAA
1 TGTATCGATGCA-CTTC-A-TAA
*
964937 T-TCATCGGTGCACTTCATAA
1 TGT-ATCGATGCACTTCATAA
964957 TGTATCGATGCA
1 TGTATCGATGCA
964969 TGTTGCACAA
Statistics
Matches: 71, Mismatches: 19, Indels: 14
0.68 0.18 0.13
Matches are distributed among these distances:
20 35 0.49
21 7 0.10
22 19 0.27
23 10 0.14
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (20 bp):
TGTATCGATGCACTTCATAA
Found at i:970750 original size:19 final size:19
Alignment explanation
Indices: 970726--970776 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
970716 AGACTTATTG
*
970726 CATCGGTAAACTAGGGGTA
1 CATCGGTACACTAGGGGTA
970745 CATCGGTACACTAGGGGTA
1 CATCGGTACACTAGGGGTA
970764 CATCGGTACACTA
1 CATCGGTACACTA
970777 ATTACATTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (19 bp):
CATCGGTACACTAGGGGTA
Found at i:973090 original size:16 final size:16
Alignment explanation
Indices: 973063--973108 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
973053 GATATGAGAA
973063 AAATTCAATTTAAATTT
1 AAATT-AATTTAAATTT
*
973080 AAATTAATTTAATTTT
1 AAATTAATTTAAATTT
*
973096 AAAATAATGTTAA
1 AAATTAAT-TTAA
973109 TAAATAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (16 bp):
AAATTAATTTAAATTT
Found at i:973592 original size:3 final size:3
Alignment explanation
Indices: 973586--973643 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
973576 TTTTTTTGTA
**
973586 TAT TAT TAT CGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
973634 TAT TAT TAT T
1 TAT TAT TAT T
973644 TAATTTACAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:976332 original size:22 final size:23
Alignment explanation
Indices: 976284--976344 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
976274 AATACTCAAT
*
976284 TTTTCAAAATAAAATTCATAATCG
1 TTTTAAAAATAAAATT-ATAATCG
* *
976308 TTTTAAAAATAATATT-TAATTG
1 TTTTAAAAATAAAATTATAATCG
976330 TTTTACAAAA-AAAAT
1 TTTTA-AAAATAAAAT
976345 GGTTATGACA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 14 0.44
23 4 0.12
24 14 0.44
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (23 bp):
TTTTAAAAATAAAATTATAATCG
Found at i:979606 original size:26 final size:25
Alignment explanation
Indices: 979575--979654 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 25
979565 CCAATTTTTG
979575 ACATTCTATCTCTTTGAGACCTTG-A
1 ACATTCT-TCTCTTTGAGACCTTGAA
* *
979600 A-A-TATTCT-TTT-CGACCTTGAA
1 ACATTCTTCTCTTTGAGACCTTGAA
*
979621 ACATTCCCTCTCTTTGAGACCTTGAA
1 ACATT-CTTCTCTTTGAGACCTTGAA
979647 ACATTCTT
1 ACATTCTT
979655 TCCACCTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
20 7 0.16
21 5 0.12
22 4 0.09
23 3 0.07
24 4 0.09
25 6 0.14
26 14 0.33
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (25 bp):
ACATTCTTCTCTTTGAGACCTTGAA
Found at i:980291 original size:11 final size:11
Alignment explanation
Indices: 980261--980299 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
980251 AAACAAAGAG
980261 CAAAG-AAAAT
1 CAAAGAAAAAT
*
980271 CAAAGCAAAAT
1 CAAAGAAAAAT
*
980282 CAAAGAAAAAG
1 CAAAGAAAAAT
980293 CAAAGAA
1 CAAAGAA
980300 CAAAAGAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 5 0.19
11 21 0.81
ACGTcount: A:0.69, C:0.13, G:0.13, T:0.05
Consensus pattern (11 bp):
CAAAGAAAAAT
Found at i:981479 original size:12 final size:12
Alignment explanation
Indices: 981462--981536 Score: 51
Period size: 12 Copynumber: 5.6 Consensus size: 12
981452 GATTGAGAAA
981462 CATACATCAACT
1 CATACATCAACT
*
981474 CATACATACATATAT
1 CATACAT-CA-A-CT
981489 ACATACATCAACT
1 -CATACATCAACT
*
981502 CATACATACATATAT
1 CATACAT-CA-A-CT
*
981517 ACATACATCAACA
1 -CATACATCAACT
981530 CATACAT
1 CATACAT
981537 GCATGTTACA
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
12 21 0.42
13 5 0.10
14 4 0.08
15 6 0.12
16 14 0.28
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (12 bp):
CATACATCAACT
Found at i:981480 original size:16 final size:16
Alignment explanation
Indices: 981461--981536 Score: 87
Period size: 16 Copynumber: 5.2 Consensus size: 16
981451 AGATTGAGAA
981461 ACATACATCAACTCAT
1 ACATACATCAACTCAT
981477 ACATACAT--A-T-AT
1 ACATACATCAACTCAT
981489 ACATACATCAACTCAT
1 ACATACATCAACTCAT
981505 ACATACAT--A-T-AT
1 ACATACATCAACTCAT
*
981517 ACATACATCAACACAT
1 ACATACATCAACTCAT
981533 ACAT
1 ACAT
981537 GCATGTTACA
Statistics
Matches: 51, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
12 20 0.39
13 2 0.04
14 4 0.08
15 1 0.02
16 24 0.47
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (16 bp):
ACATACATCAACTCAT
Found at i:981492 original size:28 final size:28
Alignment explanation
Indices: 981461--981536 Score: 143
Period size: 28 Copynumber: 2.7 Consensus size: 28
981451 AGATTGAGAA
981461 ACATACATCAACTCATACATACATATAT
1 ACATACATCAACTCATACATACATATAT
981489 ACATACATCAACTCATACATACATATAT
1 ACATACATCAACTCATACATACATATAT
*
981517 ACATACATCAACACATACAT
1 ACATACATCAACTCATACAT
981537 GCATGTTACA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (28 bp):
ACATACATCAACTCATACATACATATAT
Found at i:981536 original size:4 final size:4
Alignment explanation
Indices: 981474--981524 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
981464 TACATCAACT
* *
981474 CATA CATA CATA TATA CATA CAT- CA-A C-T- CATA CATA CATA TATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
981518 CATA CAT
1 CATA CAT
981525 CAACACATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 1 0.03
3 4 0.10
4 34 0.87
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (4 bp):
CATA
Found at i:982179 original size:103 final size:101
Alignment explanation
Indices: 982007--982230 Score: 276
Period size: 103 Copynumber: 2.2 Consensus size: 101
981997 AACAAATTGC
* * *
982007 GTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACTTAAACAAAATTA
1 GTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACTTAAACAAAAGTA
* *
982072 ATCTCACCTT-AGATTGTTGTTTCTTTC-AAAAC-AATTTT
66 ATCTCA-CTTGAGATCG-T-TTTC--TCAAAAACAAACTTT
* * *
982110 GTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACATTAAAC-AAAGT
1 GTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCAC-TTAAACAAAAGT
*
982174 GATCTCACTTGAGATCGTTTTCTCAAAAACAAACTTT
65 AATCTCACTTGAGATCGTTTTCTCAAAAACAAACTTT
*
982211 GTCTCGCTTGAGACAATTTC
1 GTCTCGCTTGAGACATTTTC
982231 TATAAAAACA
Statistics
Matches: 106, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
99 2 0.02
100 5 0.05
101 27 0.25
102 4 0.04
103 62 0.58
104 6 0.06
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (101 bp):
GTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACTTAAACAAAAGTA
ATCTCACTTGAGATCGTTTTCTCAAAAACAAACTTT
Found at i:982238 original size:36 final size:35
Alignment explanation
Indices: 982198--982295 Score: 101
Period size: 36 Copynumber: 2.8 Consensus size: 35
982188 TCGTTTTCTC
*
982198 AAAAACAAACTTT-GTCTCGCTTGAGACAATTTCTAT
1 AAAAACAAA-TTTCGTCTCGCTTGAGACAATATCT-T
* ** *
982234 AAAAACAAATTTGGTCTCATTTGAGACTATATCTT
1 AAAAACAAATTTCGTCTCGCTTGAGACAATATCTT
* *
982269 -AAAGCAAATTTCATCTCGCTTGAGACA
1 AAAAACAAATTTCGTCTCGCTTGAGACA
982296 TCATTTTCTC
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
34 21 0.41
35 4 0.08
36 26 0.51
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (35 bp):
AAAAACAAATTTCGTCTCGCTTGAGACAATATCTT
Found at i:982619 original size:28 final size:29
Alignment explanation
Indices: 982536--982862 Score: 201
Period size: 29 Copynumber: 11.0 Consensus size: 29
982526 GTTTCTCTTG
982536 AAAAATCTTTGAGTTT-TTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTT-CTTTTGAAT
* *
982565 AAAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTTCTTTTGAAT
*
982594 AAATATCTTTGAG-TTGTTTCTTTTG-A-
1 AAAAATCTTTGAGTTTGTTTCTTTTGAAT
* * *
982620 AAAAATCTTTGAGTCTATTTATTTT-AA-
1 AAAAATCTTTGAGTTTGTTTCTTTTGAAT
*** *
982647 AACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAA-
1 AA-AAA--------TCT-TTGAGTTTGTTTCTTTTGAAT
*
982685 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTTCTTTTGAAT
* *
982714 AAAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTTCTTTTGAAT
* *
982743 AAATATCTTTGAG-TCGTTTCTTTTG---
1 AAAAATCTTTGAGTTTGTTTCTTTTGAAT
*
982768 AAAAATCTTTGAGTTTGTTTCTTTGGAA-
1 AAAAATCTTTGAGTTTGTTTCTTTTGAAT
* * * *
982796 ACAAAATTTTTTCTCTCTTAAGATAGTTTCTTTTGAAAC
1 A-AAAA-------TCT-TTGAGTTTGTTTCTTTTG-AAT
982835 AAAAATCTTTGAGTTTGTTTCTTTTGAA
1 AAAAATCTTTGAGTTTGTTTCTTTTGAA
982863 ACAAAATTTT
Statistics
Matches: 235, Mismatches: 34, Indels: 58
0.72 0.10 0.18
Matches are distributed among these distances:
25 12 0.05
26 22 0.09
27 12 0.05
28 40 0.17
29 83 0.35
30 17 0.07
31 3 0.01
36 6 0.03
37 29 0.12
38 10 0.04
39 1 0.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (29 bp):
AAAAATCTTTGAGTTTGTTTCTTTTGAAT
Found at i:982712 original size:149 final size:148
Alignment explanation
Indices: 982514--982862 Score: 540
Period size: 149 Copynumber: 2.4 Consensus size: 148
982504 ACGATTTTTG
*
982514 TCTCTTGAGACAGTTTCTCTTG--AAAAATCTTTGAGTTTTTTCCTTTTGAATAAAAATCTTGGA
1 TCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGA
*
982577 GTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAAATCTTTGAGTCTATTTAT
66 GTTTGTTCCTTTTGAATAAATATCTTTGAGTCGTTTCTTTTG-AAAAATCTTTGAGTCTATTTAT
* *
982642 TTTAAAACAAAGTTTTGTC
130 TTGAAAACAAAATTTTGTC
982661 TCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGA
1 TCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGA
* * *
982726 GTTTGTTCCTTTTGAATAAATATCTTTGAGTCGTTTCTTTTGAAAAATCTTTGAGTTTGTTTCTT
66 GTTTGTTCCTTTTGAATAAATATCTTTGAGTCGTTTCTTTTGAAAAATCTTTGAGTCTATTTATT
* *
982791 TGGAAACAAAATTTTTTC
131 TGAAAACAAAATTTTGTC
* * * *
982809 TCTCTTAAGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTTGAA
1 TCTCTTGAGACAGTTTCTCTTG-AA-AAAAATCTTTGAGTTTGTTCCTTTTGAA
982863 ACAAAATTTT
Statistics
Matches: 185, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
147 22 0.12
148 53 0.29
149 83 0.45
150 27 0.15
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (148 bp):
TCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGA
GTTTGTTCCTTTTGAATAAATATCTTTGAGTCGTTTCTTTTGAAAAATCTTTGAGTCTATTTATT
TGAAAACAAAATTTTGTC
Found at i:982826 original size:37 final size:36
Alignment explanation
Indices: 982784--982905 Score: 123
Period size: 37 Copynumber: 3.5 Consensus size: 36
982774 CTTTGAGTTT
*
982784 GTTTCTTTGGAAACAAAATTTTTTCTCTCTTAAGATA
1 GTTTCTTTTGAAACAAAA-TTTTTCTCTCTTAAGATA
* * * *
982821 GTTTCTTTTGAAACAAAA-----ATCT-TTGAGTTT
1 GTTTCTTTTGAAACAAAATTTTTCTCTCTTAAGATA
982851 GTTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTTGAAACAAAATTTT-TCTCTCTTAAGATA
*
982888 ATTTCTTTTGAAA-AAAAT
1 GTTTCTTTTGAAACAAAAT
982906 CTTTAAATCT
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
30 23 0.34
31 3 0.04
36 8 0.12
37 34 0.50
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (36 bp):
GTTTCTTTTGAAACAAAATTTTTCTCTCTTAAGATA
Found at i:982864 original size:67 final size:65
Alignment explanation
Indices: 982759--982909 Score: 243
Period size: 67 Copynumber: 2.3 Consensus size: 65
982749 CTTTGAGTCG
* *
982759 TTTCTTTTG--AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTTTCTCTCTTAAGATAG
1 TTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
*
982822 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTG-AA-AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
982887 AA
64 AA
982889 TTTCTTTTGAAAAAAATCTTT
1 TTTCTTTTGAAAAAAATCTTT
982910 AAATCTGTTT
Statistics
Matches: 81, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
63 9 0.11
65 10 0.12
66 2 0.02
67 60 0.74
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (65 bp):
TTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
Found at i:982957 original size:64 final size:65
Alignment explanation
Indices: 982758--982983 Score: 210
Period size: 67 Copynumber: 3.5 Consensus size: 65
982748 TCTTTGAGTC
* * * * *
982758 GTTTCTTTTG--AAAAATCTTTGAGTTTGTTTCT-TTGGAAACAAAATTTTTTCTCTCTTAAGAT
1 GTTTCTTTTGAAAAAAATCTTTGAATATGTTTCTCTT-GAAACAAAATTTTGTATCTCTTAAGAC
982820 A
65 A
* * * *
982821 GTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGA
1 GTTTCTTTTG-AA-AAAAATCTTTGAATATGTTTCTCTTGAAACAAAATTTTGTATCTCTTAAGA
*
982886 TA
64 CA
* * * * *
982888 ATTTCTTTTGAAAAAAATCTTTAAATCTGTTTCTCTT-AAA-ATGAATTTTGTATCTCTTGAGAC
1 GTTTCTTTTGAAAAAAATCTTTGAATATGTTTCTCTTGAAACA-AAATTTTGTATCTCTTAAGAC
*
982951 C
65 A
**
982952 GTTTCTTTTTGAAGTAAATCTTTGAATATGTT
1 GTTTC-TTTTGAAAAAAATCTTTGAATATGTT
982984 CATTTTGAAA
Statistics
Matches: 140, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
63 11 0.08
64 24 0.17
65 43 0.31
66 2 0.01
67 58 0.41
68 2 0.01
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (65 bp):
GTTTCTTTTGAAAAAAATCTTTGAATATGTTTCTCTTGAAACAAAATTTTGTATCTCTTAAGACA
Found at i:983292 original size:62 final size:63
Alignment explanation
Indices: 983148--983299 Score: 186
Period size: 63 Copynumber: 2.4 Consensus size: 63
983138 AGATCCATCA
*
983148 TTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAATC
1 TTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTGTGAAAAAATC
* * * **
983211 TTTGAGTCTATTTAC-TTTGAAACAAAGTTTTGTCTCTCTTGAGACAA-TT-TTGTGAAAAAATC
1 TTTGAGTCTGTTT-CTTTTGAAACAAAATTTTATCTCT-TAAAGACAATTTCTTGTGAAAAAATC
*
983273 TTTGAGAT-TGTTTCTTTTGAAAAAAAA
1 TTTGAG-TCTGTTTCTTTTGAAACAAAA
983300 AATCTTTGAG
Statistics
Matches: 76, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
61 1 0.01
62 32 0.42
63 35 0.46
64 8 0.11
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.43
Consensus pattern (63 bp):
TTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTGTGAAAAAATC
Found at i:983303 original size:31 final size:31
Alignment explanation
Indices: 983265--983330 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
983255 CAATTTTGTG
* *
983265 AAAAAATCTTTGAGATTGTTTCTTTTGAAAA
1 AAAAAATCTTTGAGATTGTTCCCTTTGAAAA
* *
983296 AAAAAATCTTTGAGTTTGTTCCCTTTGAAAC
1 AAAAAATCTTTGAGATTGTTCCCTTTGAAAA
983327 AAAA
1 AAAA
983331 TTTTGTCTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (31 bp):
AAAAAATCTTTGAGATTGTTCCCTTTGAAAA
Found at i:983398 original size:40 final size:40
Alignment explanation
Indices: 983343--983422 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
983333 TTGTCTCTCG
*
983343 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
*
983383 AGACAACTTCTTTTGAAAATACCCACATTTGATATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
983423 CTATTAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
Found at i:983764 original size:63 final size:62
Alignment explanation
Indices: 983666--983783 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 62
983656 GAAACAAAAC
*
983666 AAACATCTTTGAGATCATTTCCCTTTAAACGAATTTTGTCTCATTT-GAGACAGTTTTCCTTT
1 AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTC-TTTGGAGACAGTTTTCCTTT
*
983728 AAACAATCTTTGAG-TCGTTT-CCTTTGAAACAAAATTTTGTCTCTTTGGAGACAGTT
1 AAAC-ATCTTTGAGATCATTTCCCTTT-AAAC-AAATTTTGTCTCTTTGGAGACAGTT
983784 GCTTTTGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
61 5 0.10
62 16 0.32
63 29 0.58
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.42
Consensus pattern (62 bp):
AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTCTTTGGAGACAGTTTTCCTTT
Found at i:983831 original size:28 final size:28
Alignment explanation
Indices: 983800--983881 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
983790 GAAACACATC
*
983800 ATCTTTGAGTTTGTTTTTCTTGAAACGA
1 ATCTTTGAGTTTGTTTTTCTTGAAACAA
*
983828 ATCTTTGGGTTTGTTTCTT-TTGAAACAA
1 ATCTTTGAGTTTGTTT-TTCTTGAAACAA
* *
983856 ATCTTT-AATTTGGTTTCTCTTGAAAC
1 ATCTTTGAGTTT-GTTTTTCTTGAAAC
983882 CATAATTCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
27 4 0.09
28 40 0.87
29 2 0.04
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (28 bp):
ATCTTTGAGTTTGTTTTTCTTGAAACAA
Found at i:983969 original size:40 final size:40
Alignment explanation
Indices: 983910--984364 Score: 235
Period size: 40 Copynumber: 10.8 Consensus size: 40
983900 CCAACCGTCC
* * *
983910 TCATCACGTAGGAATCGTGTCATCCCCAGACCAGATCTCT
1 TCATCACGTAGGAACCGTGTCATCCCTAGACCAGACCTCT
* * *
983950 TCATCACGTATGAGCCGTGTCA-CCCTAGATAACCAG-CCGTCC
1 TCATCACGTAGGAACCGTGTCATCCCTAG---ACCAGACC-TCT
* *
983992 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCA-ACCGTCC
1 TCATCACGTAGGAACCGTGTCATC-CC--TAGA---CCAGACC-TCT
* * *
984038 TCATCACGTAGGAATCGTGTCATCCCCAGACCAGATCTCT
1 TCATCACGTAGGAACCGTGTCATCCCTAGACCAGACCTCT
* * *
984078 TCATCACGTATGAGCCGTGTCA-CCCTAGATAACCAG-CCGTCC
1 TCATCACGTAGGAACCGTGTCATCCCTAG---ACCAGACC-TCT
* *
984120 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAACCGTGTCATC-CC--TAGA---CCAGACCTCT
* * *
984166 TCATCACGTATGAGCCGTGTCATTCCCT-GACCAGATCTCT
1 TCATCACGTAGGAACCGTGTCA-TCCCTAGACCAGACCTCT
* * *
984206 TCATCACGTATGAGCCGTGTCA-CCCTAGATAACCAG-CCGTCC
1 TCATCACGTAGGAACCGTGTCATCCCTAG---ACCAGACC-TCT
* * *
984248 TCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAACCGTGTCATC-CC--TAGA---CCAGACCTCT
* * * * * * ** *
984294 TCATCACGTATGAGCAGTGTCAACCCTCGACTAGATTTCC
1 TCATCACGTAGGAACCGTGTCATCCCTAGACCAGACCTCT
*
984334 TCATCACGTAGGAACCATGTCA-CCCTTAGAC
1 TCATCACGTAGGAACCGTGTCATCCC-TAGAC
984365 GACCCGAACT
Statistics
Matches: 322, Mismatches: 53, Indels: 80
0.71 0.12 0.18
Matches are distributed among these distances:
38 4 0.01
39 14 0.04
40 102 0.32
41 5 0.02
42 77 0.24
43 14 0.04
44 7 0.02
45 4 0.01
46 91 0.28
47 4 0.01
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (40 bp):
TCATCACGTAGGAACCGTGTCATCCCTAGACCAGACCTCT
Found at i:984122 original size:128 final size:128
Alignment explanation
Indices: 983889--984303 Score: 699
Period size: 128 Copynumber: 3.2 Consensus size: 128
983879 AACCATAATT
* *
983889 CCTTAAGATGGCCA-ACCGTCCTCATCACGTAGGAATCGTGTCATCCCCAGACCAGATCTCTTCA
1 CCTTTAGATGGCCAGAAC-TCCTCATCACGTAGGAATCGTGTCATCCCCAGACCAGATCTCTTCA
983953 TCACGTATGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
65 TCACGTATGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
*
984017 CCTTTAGATGGCCA-ACCGTCCTCATCACGTAGGAATCGTGTCATCCCCAGACCAGATCTCTTCA
1 CCTTTAGATGGCCAGAAC-TCCTCATCACGTAGGAATCGTGTCATCCCCAGACCAGATCTCTTCA
984081 TCACGTATGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
65 TCACGTATGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
* * ** * *
984145 CCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCTGACCAGATCTCTTCAT
1 CCTTTAGATGGCCAGAACTCCTCATCACGTAGGAATCGTGTCATCCCCAGACCAGATCTCTTCAT
*
984210 CACGTATGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCA
66 CACGTATGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
*
984273 CCTTTAGATGGCCAGAACTCTTCATCACGTA
1 CCTTTAGATGGCCAGAACTCCTCATCACGTA
984304 TGAGCAGTGT
Statistics
Matches: 277, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
128 275 0.99
129 2 0.01
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (128 bp):
CCTTTAGATGGCCAGAACTCCTCATCACGTAGGAATCGTGTCATCCCCAGACCAGATCTCTTCAT
CACGTATGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
Found at i:984186 original size:88 final size:82
Alignment explanation
Indices: 984032--984187 Score: 222
Period size: 88 Copynumber: 1.8 Consensus size: 82
984022 AGATGGCCAA
* *
984032 CCGTCCTCATCACGTAGGAATCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTG
1 CCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGCCGTG
984097 TCACCCTAGATAACCAG
66 TCACCCTAGATAACCAG
* *
984114 CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGA
1 CCGTCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGAACTCTTCATCACGTATGA
984179 GCCGTGTCA
60 GCCGTGTCA
984188 TTCCCTGACC
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
82 28 0.44
83 2 0.03
85 3 0.05
88 31 0.48
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (82 bp):
CCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGCCGTG
TCACCCTAGATAACCAG
Found at i:984304 original size:128 final size:128
Alignment explanation
Indices: 983910--984359 Score: 697
Period size: 128 Copynumber: 3.5 Consensus size: 128
983900 CCAACCGTCC
*
983910 TCATCACGTAGGAATCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC
1 TCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC
* *
983975 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCA-ACCGTCC
66 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC-TCT
*
984038 TCATCACGTAGGAATCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC
1 TCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC
984103 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
* * * *
984166 TCATCACGTATGAGCCGTGTCATTCCCTGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC
1 TCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC
*
984231 TAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCT
66 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
* * * * * * * * * *
984294 TCATCACGTATGAGCAGTGTCAACCCTC-GACTAGATTTCCTCATCACGTAGGAACCATGTCACC
1 TCATCACGTAGGAACCGTGTCATCCC-CAGACCAGATCTCTTCATCACGTATGAGCCGTGTCACC
984358 CT
65 CT
984360 TAGACGACCC
Statistics
Matches: 303, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
128 300 0.99
129 3 0.01
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (128 bp):
TCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC
TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:984563 original size:3 final size:3
Alignment explanation
Indices: 984557--984622 Score: 107
Period size: 3 Copynumber: 22.3 Consensus size: 3
984547 TTTTTTTGTA
**
984557 TAT TAT TAT CGT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
984604 TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
984623 TAATTTACAT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:987322 original size:22 final size:23
Alignment explanation
Indices: 987274--987333 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 23
987264 AATACTCAAT
*
987274 TTTTCAAAATAAAATTCATAATCG
1 TTTTAAAAATAAAATT-ATAATCG
* *
987298 TTTTAAAAATAATATT-TAATTG
1 TTTTAAAAATAAAATTATAATCG
*
987320 TTTTACAAA-AAAAT
1 TTTTAAAAATAAAAT
987334 GGTTATGACA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 4 0.13
22 13 0.42
24 14 0.45
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (23 bp):
TTTTAAAAATAAAATTATAATCG
Found at i:990315 original size:31 final size:31
Alignment explanation
Indices: 990239--990302 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
990229 AGTTACGTCG
990239 GGGACCATATTGCAAACGGACTAAATGTTGA
1 GGGACCATATTGCAAACGGACTAAATGTTGA
*
990270 GGGACCACATTGCAAACGGACTAAATGTT-A
1 GGGACCATATTGCAAACGGACTAAATGTTGA
990300 GGG
1 GGG
990303 GATTATATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.20
Consensus pattern (31 bp):
GGGACCATATTGCAAACGGACTAAATGTTGA
Found at i:992367 original size:31 final size:31
Alignment explanation
Indices: 992323--992387 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
992313 AACATATTAA
* * *
992323 TCCCCCAATATTTAGTTCATTTGCAATATGG
1 TCCCACAACATTTAGTCCATTTGCAATATGG
* *
992354 TCCCACAACATTTAGTCCGTTTGTAATATGG
1 TCCCACAACATTTAGTCCATTTGCAATATGG
992385 TCC
1 TCC
992388 TTGACGTAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (31 bp):
TCCCACAACATTTAGTCCATTTGCAATATGG
Found at i:1016701 original size:117 final size:117
Alignment explanation
Indices: 1016561--1016788 Score: 386
Period size: 117 Copynumber: 1.9 Consensus size: 117
1016551 CTTATAAATA
*
1016561 GGTTCATCAATTAAAAAACATGAAGAAGAATTCAAATTCAGTTTCTATAGTAATTCTAAAAAGAA
1 GGTTCATCAATTAAAAAACATGAAAAAGAATTCAAATTCAGTTTCTATAGTAATTCTAAAAAGAA
* *
1016626 TAGCACTAGTTATATAGCATTGCTAAAAGTGAATAAA-GACAATATTTAAACG
66 TAACACAAGTTATATAGCATTGCTAAAAGTGAATAAAGGA-AATATTTAAACG
* *
1016678 GGTTCATCAATTAAAAAATATGAAAAATAATTCAAATTCAGTTTCTATAGTAATTCTAAAAAGAA
1 GGTTCATCAATTAAAAAACATGAAAAAGAATTCAAATTCAGTTTCTATAGTAATTCTAAAAAGAA
*
1016743 TAACACAAGTTATATAGCATTGCTAGAAGTGAATAAAGGAAATATT
66 TAACACAAGTTATATAGCATTGCTAAAAGTGAATAAAGGAAATATT
1016789 GAATGATAAG
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
117 102 0.98
118 2 0.02
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (117 bp):
GGTTCATCAATTAAAAAACATGAAAAAGAATTCAAATTCAGTTTCTATAGTAATTCTAAAAAGAA
TAACACAAGTTATATAGCATTGCTAAAAGTGAATAAAGGAAATATTTAAACG
Found at i:1018304 original size:7 final size:7
Alignment explanation
Indices: 1018267--1018302 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
1018257 GAAGGGGAAA
1018267 GCTTGAG
1 GCTTGAG
1018274 GCTTGAG
1 GCTTGAG
1018281 GCTTGAG
1 GCTTGAG
1018288 GCTTGAG
1 GCTTGAG
*
1018295 GGTTGAG
1 GCTTGAG
1018302 G
1 G
1018303 GTAAAACTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.11, G:0.47, T:0.28
Consensus pattern (7 bp):
GCTTGAG
Found at i:1018975 original size:31 final size:29
Alignment explanation
Indices: 1018939--1019005 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
1018929 TTACTCATTA
* *
1018939 AACTTTACTCTTTTTCCTATTTCACTCACTG
1 AACTTTAAT-TTTTTCC-AATTCACTCACTG
* *
1018970 TACTTTTAATTTTTTTCAATTCACTCACTG
1 AAC-TTTAATTTTTTCCAATTCACTCACTG
1019000 AACTTT
1 AACTTT
1019006 GACATTGTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
29 3 0.10
30 14 0.47
31 8 0.27
32 5 0.17
ACGTcount: A:0.22, C:0.24, G:0.03, T:0.51
Consensus pattern (29 bp):
AACTTTAATTTTTTCCAATTCACTCACTG
Found at i:1025954 original size:20 final size:20
Alignment explanation
Indices: 1025929--1025968 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1025919 TTTTGGTGCA
*
1025929 GAGGGAATCGATCCCCCCTT
1 GAGGGAAACGATCCCCCCTT
*
1025949 GAGGGAAACGATTCCCCCTT
1 GAGGGAAACGATCCCCCCTT
1025969 TGAAGGGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.20
Consensus pattern (20 bp):
GAGGGAAACGATCCCCCCTT
Found at i:1025983 original size:23 final size:21
Alignment explanation
Indices: 1025929--1025989 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 21
1025919 TTTTGGTGCA
*
1025929 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAAACGATTCCCCCCTT
*
1025949 GAGGGAAACGATTCCCCCTTT
1 GAGGGAAACGATTCCCCCCTT
*
1025970 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAAACGATTCCCCC
1025990 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.29
21 9 0.26
22 1 0.03
23 15 0.43
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAAACGATTCCCCCCTT
Found at i:1026015 original size:19 final size:20
Alignment explanation
Indices: 1025972--1026009 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1025962 CCCCCTTTGA
*
1025972 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
1025992 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
1026010 CTGGGGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:1027921 original size:9 final size:8
Alignment explanation
Indices: 1027899--1027949 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
1027889 TGTTTCAACA
1027899 TTTTGGAT
1 TTTTGGAT
1027907 ATTTTGGAT
1 -TTTTGGAT
1027916 TGTTT-GAT
1 T-TTTGGAT
1027924 TTTGTGGAT
1 TTT-TGGAT
*
1027933 TGTTGGA-
1 TTTTGGAT
1027940 TTTTGGAT
1 TTTTGGAT
1027948 TT
1 TT
1027950 ATGAATGGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:1027933 original size:17 final size:17
Alignment explanation
Indices: 1027901--1027944 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1027891 TTTCAACATT
1027901 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
1027918 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
1027935 TTGGATTTTG
1 TTGGATTTTG
1027945 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:1028704 original size:75 final size:74
Alignment explanation
Indices: 1028522--1028724 Score: 241
Period size: 74 Copynumber: 2.8 Consensus size: 74
1028512 CAAAGCCAAA
* * * * **
1028522 AATTACAGATTGCTCAGAGGGAACC-ATTCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATT-CCCCCTAAACAGTT
1028586 TGGCTCCGAG
65 TGGCTCCGAG
* * *
1028596 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACTGATTCCCCCTAAACATTTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
* *
1028661 TGTTCCGAG
66 GGCTCCGAG
* * *
1028670 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGG-GGTACCGATTCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCT
1028725 GTTCAACGGT
Statistics
Matches: 111, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
73 14 0.13
74 68 0.61
75 29 0.26
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (74 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
GGCTCCGAG
Found at i:1035115 original size:2 final size:2
Alignment explanation
Indices: 1035108--1035179 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
1035098 TTTTCGTGAT
1035108 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1035150 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1035180 CTCTTGATTA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1039510 original size:43 final size:43
Alignment explanation
Indices: 1039462--1039615 Score: 145
Period size: 43 Copynumber: 3.5 Consensus size: 43
1039452 AAGCATAGTA
*
1039462 TTCACGGAAGAGTAGTGGAATCAAATCAACCTTGAATCTGATC
1 TTCACGGAAGAGTAGTGGAAACAAATCAACCTTGAATCTGATC
* * **
1039505 TTCACGGAAGAGTAGT-GAAACAGATTCTTTTTAA--TTCAATCCAATC
1 TTCACGGAAGAGTAGTGGAAACA-AATC-----AACCTTGAATCTGATC
* * *
1039551 TCCACGGAAGAGTAGTGGAAGCAAATCAACCTCGAATCTGATC
1 TTCACGGAAGAGTAGTGGAAACAAATCAACCTTGAATCTGATC
*
1039594 TTCACGAAAGAGTAGT-GAAACA
1 TTCACGGAAGAGTAGTGGAAACA
1039616 GATTCTTCTC
Statistics
Matches: 87, Mismatches: 15, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
41 2 0.02
42 10 0.11
43 41 0.47
46 27 0.31
47 5 0.06
48 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (43 bp):
TTCACGGAAGAGTAGTGGAAACAAATCAACCTTGAATCTGATC
Found at i:1039928 original size:13 final size:14
Alignment explanation
Indices: 1039905--1039938 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
1039895 GTTTTGTTTC
1039905 ATTATAATTATATT
1 ATTATAATTATATT
1039919 ATTA-AATTATATT
1 ATTATAATTATATT
1039932 ATTATAA
1 ATTATAA
1039939 CTTGTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTATAATTATATT
Found at i:1041330 original size:21 final size:22
Alignment explanation
Indices: 1041306--1041346 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1041296 ATTAATCTAT
1041306 TTTAATATTATAATA-ATATTA
1 TTTAATATTATAATAGATATTA
* *
1041327 TTTATTTTTATAATAGATAT
1 TTTAATATTATAATAGATAT
1041347 ATTAAGTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAATATTATAATAGATATTA
Found at i:1043220 original size:14 final size:15
Alignment explanation
Indices: 1043166--1043223 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 15
1043156 GACTAATATG
1043166 AAATAAATAATATAAA
1 AAATAAATAATAT-AA
1043182 AGTAATACAATTAATATTAA
1 A--AATA-AA-TAATA-TAA
1043202 AAATAAATAATAT-A
1 AAATAAATAATATAA
1043216 AAATAAAT
1 AAATAAAT
1043224 TTAAAAGCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 9 0.24
15 1 0.03
16 6 0.16
17 2 0.05
18 8 0.22
19 2 0.05
20 8 0.22
21 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (15 bp):
AAATAAATAATATAA
Done.