Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_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: 4740655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 24
Found at i:1741087 original size:18 final size:19
Alignment explanation
Indices: 1741064--1741120 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 19
1741054 TATAATATTA
1741064 TTATAAATATATAA-AATT
1 TTATAAATATATAACAATT
**
1741082 TTATAAAT-TAATAATTATT
1 TTATAAATAT-ATAACAATT
*
1741101 TTATAATAAATATAACAATT
1 TTATAA-ATATATAACAATT
1741121 AATAAATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
17 1 0.03
18 12 0.39
19 9 0.29
20 8 0.26
21 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TTATAAATATATAACAATT
Found at i:1741099 original size:43 final size:40
Alignment explanation
Indices: 1741031--1741114 Score: 98
Period size: 43 Copynumber: 2.0 Consensus size: 40
1741021 AACAATATTC
* *
1741031 ATAAAATTATTATAAATAACCATTATAATATTATTATAAATAT
1 ATAAAATTATTATAAATAACAATTAT--T-TTATAATAAATAT
*
1741074 ATAAAATT-TTATAAATTAATAATTATTTTATAATAAATAT
1 ATAAAATTATTATAAA-TAACAATTATTTTATAATAAATAT
1741114 A
1 A
1741115 ACAATTAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
40 13 0.35
41 1 0.03
42 7 0.19
43 16 0.43
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (40 bp):
ATAAAATTATTATAAATAACAATTATTTTATAATAAATAT
Found at i:1741141 original size:39 final size:40
Alignment explanation
Indices: 1741061--1741142 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 40
1741051 CATTATAATA
* *
1741061 TTATTATAAATATATAAAATTTTATAAATTAATAATTATT
1 TTATAATAAATATATAAAATTTAATAAATTAATAATTATT
* *
1741101 TTATAATAAATATA-ACAA-TTAATAAATTTAATGATTATT
1 TTATAATAAATATATAAAATTTAATAAA-TTAATAATTATT
1741140 TTA
1 TTA
1741143 AGTAAATGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 7 0.19
39 17 0.46
40 13 0.35
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (40 bp):
TTATAATAAATATATAAAATTTAATAAATTAATAATTATT
Found at i:1743747 original size:35 final size:35
Alignment explanation
Indices: 1743688--1743799 Score: 147
Period size: 35 Copynumber: 3.2 Consensus size: 35
1743678 AAAACATTCC
* *
1743688 TCAATTTCATTATAAATCCC-AAATTTCAAAGTAAT
1 TCAATTTCATTCTAAA-CCCTAAATTTCAAAATAAT
*
1743723 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
* *
1743758 TCAATTACATTCTAAACCCTAAA-TTCTAAAATACT
1 TCAATTTCATTCTAAACCCTAAATTTC-AAAATAAT
1743793 TCAATTT
1 TCAATTT
1743800 AAGGAGAAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 5 0.07
35 63 0.93
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
Found at i:1744864 original size:35 final size:34
Alignment explanation
Indices: 1744815--1744927 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 34
1744805 TAAAAAGACA
* *
1744815 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGGG-TTTAGAAT
*
1744850 GTAATTGAATTATTTTGGAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTT-GGGTTTAGAAT
*
1744885 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTG-GGTTTAGAAT
1744920 GAAATTGA
1 GAAATTGA
1744928 GAATTGTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 67 0.94
36 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTGGAATTTGGGTTTAGAAT
Found at i:1746554 original size:21 final size:21
Alignment explanation
Indices: 1746530--1746575 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1746520 ATGATGGTCT
* *
1746530 GGTTTTGGCGCTGCCCTTTCA
1 GGTTTCGGCGCTGCACTTTCA
* *
1746551 GGTTTCGGTGCTGCACTTTCT
1 GGTTTCGGCGCTGCACTTTCA
1746572 GGTT
1 GGTT
1746576 GACTGTAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.04, C:0.24, G:0.30, T:0.41
Consensus pattern (21 bp):
GGTTTCGGCGCTGCACTTTCA
Found at i:1751451 original size:40 final size:40
Alignment explanation
Indices: 1751406--1751487 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
1751396 CGAAGTAAAC
1751406 CTGTTTATTTCCATTGCTAGAGTACTAGATAAATCAGTGT
1 CTGTTTATTTCCATTGCTAGAGTACTAGATAAATCAGTGT
1751446 CTGTTTATTTCCATTGCTAGAGTACTAGATAAATCAGTGT
1 CTGTTTATTTCCATTGCTAGAGTACTAGATAAATCAGTGT
1751486 CT
1 CT
1751488 TGACAAATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (40 bp):
CTGTTTATTTCCATTGCTAGAGTACTAGATAAATCAGTGT
Found at i:1752946 original size:3 final size:3
Alignment explanation
Indices: 1752938--1753018 Score: 162
Period size: 3 Copynumber: 27.0 Consensus size: 3
1752928 AAATTCACTT
1752938 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1752986 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1753019 AATGAAATTA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:1754427 original size:22 final size:22
Alignment explanation
Indices: 1754399--1754440 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1754389 ACCCTGACAC
1754399 ACTTTATTTACCTGTTAGACGA
1 ACTTTATTTACCTGTTAGACGA
*
1754421 ACTTTATTTACCTTTTAGAC
1 ACTTTATTTACCTGTTAGAC
1754441 ACCCTTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (22 bp):
ACTTTATTTACCTGTTAGACGA
Found at i:1754447 original size:22 final size:22
Alignment explanation
Indices: 1754394--1754447 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1754384 AAATCACCCT
1754394 GACACACTTTATTTACCTGTTA
1 GACACACTTTATTTACCTGTTA
*
1754416 GACGA-ACTTTATTTACCTTTTA
1 GAC-ACACTTTATTTACCTGTTA
*
1754438 GACACCCTTT
1 GACACACTTT
1754448 CATCTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 26 0.93
23 1 0.04
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (22 bp):
GACACACTTTATTTACCTGTTA
Found at i:1755077 original size:36 final size:37
Alignment explanation
Indices: 1755037--1755122 Score: 103
Period size: 36 Copynumber: 2.4 Consensus size: 37
1755027 GGTAATAATA
*
1755037 TAAAATTATATTATTT-GAATTATTTACGTTTATGTG
1 TAAAATTATATTATTTAAAATTATTTACGTTTATGTG
1755073 TAAAA--A-ATTATGTGTAAAATTATTTACGTTTATGTG
1 TAAAATTATATTAT-T-TAAAATTATTTACGTTTATGTG
1755109 TAAAATT-T-TTATTT
1 TAAAATTATATTATTT
1755123 TGTTATATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
33 5 0.12
34 2 0.05
35 2 0.05
36 30 0.70
37 4 0.09
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.51
Consensus pattern (37 bp):
TAAAATTATATTATTTAAAATTATTTACGTTTATGTG
Found at i:1759617 original size:19 final size:19
Alignment explanation
Indices: 1759593--1759645 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
1759583 GAATGCATTT
1759593 TATGCATCGATGCACATAC
1 TATGCATCGATGCACATAC
1759612 TATGCATCGATGCACATAC
1 TATGCATCGATGCACATAC
1759631 TATGCATCGATGCAC
1 TATGCATCGATGCAC
1759646 TTAGTACATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (19 bp):
TATGCATCGATGCACATAC
Found at i:1759690 original size:20 final size:20
Alignment explanation
Indices: 1759665--1759711 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1759655 TTGATGAATT
1759665 GATGCACAAGACCATGTATC
1 GATGCACAAGACCATGTATC
* *
1759685 GATGCAGAGGACCATGTATC
1 GATGCACAAGACCATGTATC
1759705 GATGCAC
1 GATGCAC
1759712 TGAGAGTCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (20 bp):
GATGCACAAGACCATGTATC
Found at i:1767153 original size:3 final size:3
Alignment explanation
Indices: 1767145--1767169 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1767135 TCCTCTCGTG
1767145 CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC C
1767170 GGCTTCGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:1768218 original size:45 final size:46
Alignment explanation
Indices: 1768169--1768256 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
1768159 GAACATCGAA
* * *
1768169 TGCATTTTATGCATCGATGCAC-ATACTATGCATCGATGCACTTAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
1768214 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
1768257 CAGGCTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.54
46 18 0.46
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
Found at i:1770483 original size:29 final size:29
Alignment explanation
Indices: 1770449--1770520 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
1770439 AAAAAAATTA
* *
1770449 ATTAAATAAAATATTA-AAAATTTTAAAT
1 ATTAAATAAAATATAACAAAATATTAAAT
1770477 AGTTAAATAAAATACTAACAAAATATTAAAT
1 A-TTAAATAAAATA-TAACAAAATATTAAAT
1770508 A-T-AATAAAATATA
1 ATTAAATAAAATATA
1770521 TCTTAAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 2 0.05
28 10 0.26
29 13 0.33
30 2 0.05
31 12 0.31
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.33
Consensus pattern (29 bp):
ATTAAATAAAATATAACAAAATATTAAAT
Found at i:1770518 original size:17 final size:18
Alignment explanation
Indices: 1770486--1770519 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1770476 TAGTTAAATA
1770486 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
1770504 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
1770520 ATCTTAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:1772947 original size:37 final size:39
Alignment explanation
Indices: 1772891--1772965 Score: 95
Period size: 37 Copynumber: 2.0 Consensus size: 39
1772881 GAGACATTAT
1772891 TTAAAAAAATTTAAGTTG-AATT-TATGAT-ATTTTAATA
1 TTAAAAAAATTTAAGTTGAAATTCTAT-ATAATTTTAATA
*
1772928 TTAAAAAATATTT-ATTTGAAATTCTATATAATTTTAAT
1 TTAAAAAA-ATTTAAGTTGAAATTCTATATAATTTTAAT
1772966 TTATAATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
37 12 0.36
38 10 0.30
39 11 0.33
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.48
Consensus pattern (39 bp):
TTAAAAAAATTTAAGTTGAAATTCTATATAATTTTAATA
Found at i:1780050 original size:22 final size:22
Alignment explanation
Indices: 1780008--1780062 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
1779998 GTAATATAAT
1780008 TTTATATAGG-AT-GATTCATTA
1 TTTAT-TAGGAATAGATTCATTA
*
1780029 TCTT-TTAGGAATAGATTTATTA
1 T-TTATTAGGAATAGATTCATTA
1780051 TTTATTAGGAAT
1 TTTATTAGGAAT
1780063 TAAGATTGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 4 0.14
21 6 0.21
22 19 0.66
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.49
Consensus pattern (22 bp):
TTTATTAGGAATAGATTCATTA
Found at i:1793263 original size:23 final size:23
Alignment explanation
Indices: 1793206--1793302 Score: 113
Period size: 23 Copynumber: 4.2 Consensus size: 23
1793196 CAGCTCATAT
* * *
1793206 AAATGCACCGAAGTACCACATAG
1 AAATGCACCGAAGTGCCGCGTAG
** * * *
1793229 ATTTTCACCGAAGTGTCGCGTAA
1 AAATGCACCGAAGTGCCGCGTAG
*
1793252 AAATGCATCGAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCGCGTAG
1793275 AAATGCACCGAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCGCGTAG
1793298 AAATG
1 AAATG
1793303 TCTCTAAGGA
Statistics
Matches: 59, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.19
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCGCGTAG
Found at i:1802422 original size:18 final size:19
Alignment explanation
Indices: 1802399--1802452 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
1802389 TTAGGGTTTT
1802399 TATTTATAAATATAAA-AA
1 TATTTATAAATATAAATAA
*
1802417 TATTTATAAAAATAAATAA
1 TATTTATAAATATAAATAA
*
1802436 -ATTTAAAAATACTAAAT
1 TATTTATAAATA-TAAAT
1802453 TGTGACACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 24 0.77
19 7 0.23
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
TATTTATAAATATAAATAA
Found at i:1803163 original size:21 final size:20
Alignment explanation
Indices: 1803134--1803192 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
1803124 GAAACAAGTT
1803134 AATA-TATTTTTTATTTAT-A
1 AATATTATTTTTTATTT-TGA
* *
1803153 AATATTTATTTATAATTTTGA
1 AATA-TTATTTTTTATTTTGA
1803174 AATATTATTTTATTATTTT
1 AATATTATTTT-TTATTTT
1803193 TACAATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 4 0.12
20 7 0.22
21 21 0.66
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
AATATTATTTTTTATTTTGA
Found at i:1806573 original size:35 final size:35
Alignment explanation
Indices: 1806527--1806705 Score: 132
Period size: 35 Copynumber: 5.1 Consensus size: 35
1806517 TAAATATTAC
*
1806527 CTTCTTCTTCCATCAAACTTGGCCTTCTCGAGAAA
1 CTTCTTCTTCCATCAAACCTGGCCTTCTCGAGAAA
* * ** ** *
1806562 CTTCTTGTTCCATCAAACCTGACCCCCTAAAAAAA
1 CTTCTTCTTCCATCAAACCTGGCCTTCTCGAGAAA
* * * * *
1806597 CTTCTTATTCAATCAAACATGGCTTTCT-GGGAAA
1 CTTCTTCTTCCATCAAACCTGGCCTTCTCGAGAAA
* * *
1806631 CTTC-TCGTTCTATCAAA-CTCGCCTTTCTC-ATAAAA
1 CTTCTTC-TTCCATCAAACCTGGCC-TTCTCGA-GAAA
* **
1806666 CTTCTTCTTTCATCAAACCTGGTTTTCTCGAGAAA
1 CTTCTTCTTCCATCAAACCTGGCCTTCTCGAGAAA
1806701 CTTCT
1 CTTCT
1806706 CGTTTCTAAA
Statistics
Matches: 106, Mismatches: 31, Indels: 14
0.70 0.21 0.09
Matches are distributed among these distances:
33 4 0.04
34 20 0.19
35 76 0.72
36 6 0.06
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.35
Consensus pattern (35 bp):
CTTCTTCTTCCATCAAACCTGGCCTTCTCGAGAAA
Found at i:1808008 original size:4 final size:4
Alignment explanation
Indices: 1807999--1808086 Score: 77
Period size: 4 Copynumber: 21.0 Consensus size: 4
1807989 ATTTTTAATA
* * * *
1807999 ATTT ATTT ATTT ATTT AATA ATTTT GTTT AATTT ATTT ATCT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT A-TTT ATTT -ATTT ATTT ATTT ATTT ATTT
* * *
1808049 CAAATT ATTT ATTC ATTT ATTT ATTT ATTT AGTT ATTT
1 --ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1808087 CGAATTTGTT
Statistics
Matches: 66, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
4 59 0.89
5 4 0.06
6 3 0.05
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.66
Consensus pattern (4 bp):
ATTT
Found at i:1808016 original size:30 final size:30
Alignment explanation
Indices: 1807954--1808086 Score: 106
Period size: 30 Copynumber: 4.2 Consensus size: 30
1807944 TAGAGATAAT
* * *
1807954 TTATATTTATTAATTTGTTTTAAATTTTTTTAA
1 TTATTTTTATTAATTT-ATTT--ATTTATTTAA
*
1807987 TTATTTTTAATAATTTATTTATTTATTTAA
1 TTATTTTTATTAATTTATTTATTTATTTAA
* * *
1808017 TAATTTTGT-TTAATTTATTTATCTATTTAT
1 TTATTTT-TATTAATTTATTTATTTATTTAA
* *
1808047 TTCAAATTATTTATTCATTTATTTATTTATTTAG
1 TT---ATT-TTTATTAATTTATTTATTTATTTAA
1808081 TTATTT
1 TTATTT
1808087 CGAATTTGTT
Statistics
Matches: 82, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
30 35 0.43
31 4 0.05
32 3 0.04
33 18 0.22
34 22 0.27
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (30 bp):
TTATTTTTATTAATTTATTTATTTATTTAA
Found at i:1808037 original size:22 final size:21
Alignment explanation
Indices: 1807963--1808037 Score: 82
Period size: 20 Copynumber: 3.6 Consensus size: 21
1807953 TTTATATTTA
* *
1807963 TTAATTTGTTTTA-AATTTTT
1 TTAATTTATTTAATAATTTTT
* *
1807983 TTAATTATTTTTAATAATTTAT
1 TTAATT-TATTTAATAATTTTT
1808005 TT-ATTTATTTAATAATTTTGT
1 TTAATTTATTTAATAATTTT-T
1808026 TTAATTTATTTA
1 TTAATTTATTTA
1808038 TCTATTTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
20 18 0.39
21 11 0.24
22 17 0.37
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (21 bp):
TTAATTTATTTAATAATTTTT
Found at i:1808044 original size:34 final size:34
Alignment explanation
Indices: 1807985--1808079 Score: 108
Period size: 34 Copynumber: 2.9 Consensus size: 34
1807975 AAATTTTTTT
*
1807985 AATTATTT-TTAA-TAATTTATTTATTTATTTAA
1 AATTATTTATTAATTTATTTATTTATTTATTTAA
* *
1808017 TAATT-TTGT-TTAATTTATTTATCTATTTATTTCA
1 -AATTATT-TATTAATTTATTTATTTATTTATTTAA
*
1808051 AATTATTTATTCATTTATTTATTTATTTA
1 AATTATTTATTAATTTATTTATTTATTTA
1808080 GTTATTTCGA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
32 2 0.04
33 14 0.26
34 37 0.70
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (34 bp):
AATTATTTATTAATTTATTTATTTATTTATTTAA
Found at i:1809703 original size:32 final size:32
Alignment explanation
Indices: 1809642--1809704 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
1809632 ATTTGTAATT
* * * *
1809642 TTTTTAGTTATTTGAACTGTATTTTCTTTTTC
1 TTTTTAGTTAATCGAACTATATTTACTTTTTC
*
1809674 TTTTTAGTTAATCGAACTATGTTTACTTTTT
1 TTTTTAGTTAATCGAACTATATTTACTTTTT
1809705 TGTTTAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.19, C:0.10, G:0.10, T:0.62
Consensus pattern (32 bp):
TTTTTAGTTAATCGAACTATATTTACTTTTTC
Found at i:1809799 original size:17 final size:17
Alignment explanation
Indices: 1809749--1809799 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
1809739 TAGTTTTTTA
1809749 AATTTGTTTAAATTATT
1 AATTTGTTTAAATTATT
***
1809766 AATCAACTTTAAATTATT
1 AAT-TTGTTTAAATTATT
*
1809784 AATTTGTTTAAGTTAT
1 AATTTGTTTAAATTAT
1809800 CATTGAACAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (17 bp):
AATTTGTTTAAATTATT
Found at i:1813047 original size:3 final size:3
Alignment explanation
Indices: 1813041--1813109 Score: 99
Period size: 3 Copynumber: 24.0 Consensus size: 3
1813031 TCCATTTTTT
* *
1813041 TTA TTA TTA TTA TT- TTA TTA TTA -TA TTA TTA TTA TTA ATA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1813087 TTA TTA TT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
1813110 AATAATAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 6 0.10
3 53 0.90
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1813056 original size:14 final size:14
Alignment explanation
Indices: 1813039--1813108 Score: 92
Period size: 14 Copynumber: 5.1 Consensus size: 14
1813029 TATCCATTTT
1813039 TTTTATTATTATTA
1 TTTTATTATTATTA
1813053 TTTTATTATTA-TA
1 TTTTATTATTATTA
1813066 --TTATTATTATTAA
1 TTTTATTATTATT-A
* *
1813079 TATTAATATTATTA
1 TTTTATTATTATTA
1813093 TTTTATTATTATTA
1 TTTTATTATTATTA
1813107 TT
1 TT
1813109 AAATAATAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
11 9 0.18
12 1 0.02
13 3 0.06
14 26 0.53
15 10 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTATTATTATTA
Found at i:1813058 original size:11 final size:12
Alignment explanation
Indices: 1813041--1813109 Score: 99
Period size: 11 Copynumber: 6.0 Consensus size: 12
1813031 TCCATTTTTT
1813041 TTATTATTATTA
1 TTATTATTATTA
1813053 TT-TTATTATTA
1 TTATTATTATTA
1813064 -TATTATTATTA
1 TTATTATTATTA
* *
1813075 TTAATATTAATA
1 TTATTATTATTA
1813087 TTATTATT-TTA
1 TTATTATTATTA
1813098 TTATTATTATTA
1 TTATTATTATTA
1813110 AATAATAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
10 1 0.02
11 28 0.56
12 21 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTATTATTATTA
Found at i:1821576 original size:22 final size:22
Alignment explanation
Indices: 1821551--1821594 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1821541 TCTTCGTTAC
1821551 ATCAGAAATTGAAGTTCGTTGT
1 ATCAGAAATTGAAGTTCGTTGT
1821573 ATCAGAAATTGAAGTTCGTTGT
1 ATCAGAAATTGAAGTTCGTTGT
1821595 TGACGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (22 bp):
ATCAGAAATTGAAGTTCGTTGT
Found at i:1827898 original size:122 final size:122
Alignment explanation
Indices: 1827679--1827979 Score: 548
Period size: 122 Copynumber: 2.5 Consensus size: 122
1827669 CACTCGATGG
* *
1827679 ATCAACATTTCCAGAGGATTTCATAATGAGAAGAACTCATCTGAATAGGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
*
1827744 TGAGAAGAACTTGTTCAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCAGC
66 TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
1827801 ATCAACATTTCCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
*
1827866 TGAGAAGAACTTGTTCAACCTTTTTCTCGACTCTATCACAGAAGGAGATAGATCAGC
66 TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
* *
1827923 ATCAATATTTCCAGAGGAGTTCATAATGAGAAGAACACATCTGAAGAGGAAGAAGAA
1 ATCAACATTTCCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAA
1827980 CTTGTTAAAC
Statistics
Matches: 173, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
122 173 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (122 bp):
ATCAACATTTCCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
Found at i:1828050 original size:105 final size:105
Alignment explanation
Indices: 1827868--1828084 Score: 380
Period size: 105 Copynumber: 2.1 Consensus size: 105
1827858 GTTCATAATG
* * * *
1827868 AGAAGAACTTGTTCAACCTTTTTCTCGACTCTATCACAGAAGGAGATAGATCAGCATCAATATTT
1 AGAAGAACTTGTTAAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAACATCAACATTT
1827933 CCAGAGGAGTTCATAATGAGAAGAACACATCTGAAGAGGA
66 CCAGAGGAGTTCATAATGAGAAGAACACATCTGAAGAGGA
*
1827973 AGAAGAACTTGTTAAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCAACATCAACATTT
1 AGAAGAACTTGTTAAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAACATCAACATTT
*
1828038 CCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGA
66 CCAGAGGAGTTCATAATGAGAAGAACACATCTGAAGAGGA
1828078 AGAAGAA
1 AGAAGAA
1828085 GTTCATAATG
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 106 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (105 bp):
AGAAGAACTTGTTAAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAACATCAACATTT
CCAGAGGAGTTCATAATGAGAAGAACACATCTGAAGAGGA
Found at i:1828099 original size:122 final size:120
Alignment explanation
Indices: 1827973--1828345 Score: 500
Period size: 122 Copynumber: 3.2 Consensus size: 120
1827963 CTGAAGAGGA
* ** *
1827973 AGAAGAACTTGTTAAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCAACATCAACATTT
1 AGAAGAACTTGTTCAACCTTTTGCTCAATTCTATCACAGAA--AGATAGATCAACATCAACATTT
1828038 CCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
64 CCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
* * * *
1828095 AGAAGAACTTGTTCAACCTTTTACTCAATTCTATCACAGAAATAGATATATCAGCATCAATATTT
1 AGAAGAACTTGTTCAACCTTTTGCTCAATTCTATCACAG-AA-AGATAGATCAACATCAACATTT
*
1828160 CCAGAGGAGTTCATATTGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
64 CCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
1828217 AGAAGAACTTGTTCAACCTTTTGCTCAATTCTAT--C---------GATCAACATCAACATTTCC
1 AGAAGAACTTGTTCAACCTTTTGCTCAATTCTATCACAGAAAGATAGATCAACATCAACATTTCC
* *
1828271 AGAAGG-GTTAATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATG
66 AG-AGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
* *
1828326 AGAAAAACTTGTTCGACCTT
1 AGAAGAACTTGTTCAACCTT
1828346 AGCTTGATTC
Statistics
Matches: 230, Mismatches: 19, Indels: 17
0.86 0.07 0.06
Matches are distributed among these distances:
109 82 0.36
110 3 0.01
120 1 0.00
122 142 0.62
123 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (120 bp):
AGAAGAACTTGTTCAACCTTTTGCTCAATTCTATCACAGAAAGATAGATCAACATCAACATTTCC
AGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
Found at i:1828150 original size:227 final size:227
Alignment explanation
Indices: 1827746--1828345 Score: 837
Period size: 227 Copynumber: 2.6 Consensus size: 227
1827736 GTTCATAATG
* *
1827746 AGAAGAACTTGTTCAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCAGCATCAACATTT
1 AGAAGAACTTGTTAAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCAACATCAACATTT
1827811 CCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAAC
66 CCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAAC
* * *
1827876 TTGTTCAACCTTTTTCTCGACTCTATCACAGAAGGAGATAGATCAGCATCAATATTTCCAGAGGA
131 TTGTTCAACCTTTTACTCAACTCTATCACAGAAAGAGATAGATCAGCATCAATATTTCCAGAGGA
1827941 GTTCATAATGAGAAGAACACATCTGAAGAGGA
196 GTTCATAATGAGAAGAACACATCTGAAGAGGA
1827973 AGAAGAACTTGTTAAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCAACATCAACATTT
1 AGAAGAACTTGTTAAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCAACATCAACATTT
1828038 CCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAAC
66 CCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAAC
* * *
1828103 TTGTTCAACCTTTTACTCAATTCTATCACAGAAATAGATATATCAGCATCAATATTTCCAGAGGA
131 TTGTTCAACCTTTTACTCAACTCTATCACAGAAAGAGATAGATCAGCATCAATATTTCCAGAGGA
* *
1828168 GTTCATATTGAGAAGAACTCATCTGAAGAGGA
196 GTTCATAATGAGAAGAACACATCTGAAGAGGA
* * **** * * ** ** **** *
1828200 AGAAGAAGTTCATAATGAGAAGAACTTG-TTCAAC-CTTTTGCTCAATTCTATCGATCAACATCA
1 AGAAGAACTT-GT--T-A-AACCTTTTGCTT-GACTCTATCACAGAAGGAGATAGATCAACATCA
* *
1828263 ACATTTCCAGAAGG-GTTAATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGA
60 ACATTTCCAG-AGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGA
* *
1828327 GAAAAACTTGTTCGACCTT
124 GAAGAACTTGTTCAACCTT
1828346 AGCTTGATTC
Statistics
Matches: 335, Mismatches: 31, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
227 226 0.67
228 1 0.00
230 1 0.00
231 97 0.29
232 10 0.03
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (227 bp):
AGAAGAACTTGTTAAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCAACATCAACATTT
CCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAAC
TTGTTCAACCTTTTACTCAACTCTATCACAGAAAGAGATAGATCAGCATCAATATTTCCAGAGGA
GTTCATAATGAGAAGAACACATCTGAAGAGGA
Found at i:1828263 original size:109 final size:109
Alignment explanation
Indices: 1828144--1828345 Score: 325
Period size: 109 Copynumber: 1.9 Consensus size: 109
1828134 AAATAGATAT
* * * *
1828144 ATCAGCATCAATATTTCCAG-AGGAGTTCATATTGAGAAGAACTCATCTGAAGAGGAAGAAGAAG
1 ATCAACATCAACATTTCCAGAAGG-GTTAATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAG
*
1828208 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAATTCTATCG
65 TTCATAATGAGAAAAACTTGTTCAACCTTTTGCTCAATTCTATCG
*
1828253 ATCAACATCAACATTTCCAGAAGGGTTAATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGT
1 ATCAACATCAACATTTCCAGAAGGGTTAATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGT
*
1828318 TCATAATGAGAAAAACTTGTTCGACCTT
66 TCATAATGAGAAAAACTTGTTCAACCTT
1828346 AGCTTGATTC
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
109 82 0.96
110 3 0.04
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (109 bp):
ATCAACATCAACATTTCCAGAAGGGTTAATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGT
TCATAATGAGAAAAACTTGTTCAACCTTTTGCTCAATTCTATCG
Found at i:1828448 original size:139 final size:137
Alignment explanation
Indices: 1828259--1828621 Score: 439
Period size: 139 Copynumber: 2.6 Consensus size: 137
1828249 ATCGATCAAC
* * * * * *
1828259 ATCAACATTTCCAGAAG-GGTTAATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAATATTTCCAGAAGAAGTTCATAATGAGAATAACTCATCTGAAGAGGAAGAAGAAATTCATA
* * * *
1828323 ATGAGAAAAACTTGTTCGACCTTAG-CTTGATTCATCA-TCTATGGAGTTGAATGAAAGAAGAAC
66 ATGAGAAGAACTTGTTC-ACCTTAGCCTTAATTCATCACT-TATGAAGTTGAATCAAAGAAG--C
1828386 CTCAGTTGAGG
127 CTCAGTTGAGG
* *
1828397 ATCAATATTTCCAGAAGAAGTTCATAATGAGAATAACTCGTCTGAAAAGGAAGAAGAAATTCATA
1 ATCAATATTTCCAGAAGAAGTTCATAATGAGAATAACTCATCTGAAGAGGAAGAAGAAATTCATA
* * * * *
1828462 ATGAGAAGAACTTGTTCAACTTTGCCTTAATTCATCACTTATGAAGTTGAATCAATGATGCCTCT
66 ATGAGAAGAACTTGTTCACCTTAGCCTTAATTCATCACTTATGAAGTTGAATCAAAGAAGCCTCA
*
1828527 TTTGAGG
131 GTTGAGG
* * *
1828534 A-CCATCATTCCCAGAAGGAA-TTCATAATAAGAATAACTCATCTGAAGAGGAAGAAGAAATTCA
1 ATCAAT-ATTTCCAGAA-GAAGTTCATAATGAGAATAACTCATCTGAAGAGGAAGAAGAAATTCA
1828597 TAATGAGAAGAACTTGTTCAACCTT
64 TAATGAGAAGAACTTGTTC-ACCTT
1828622 TTGCTAGATT
Statistics
Matches: 195, Mismatches: 24, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
136 3 0.02
137 79 0.41
138 28 0.14
139 84 0.43
140 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (137 bp):
ATCAATATTTCCAGAAGAAGTTCATAATGAGAATAACTCATCTGAAGAGGAAGAAGAAATTCATA
ATGAGAAGAACTTGTTCACCTTAGCCTTAATTCATCACTTATGAAGTTGAATCAAAGAAGCCTCA
GTTGAGG
Found at i:1828591 original size:137 final size:138
Alignment explanation
Indices: 1828259--1828618 Score: 446
Period size: 137 Copynumber: 2.6 Consensus size: 138
1828249 ATCGATCAAC
* * * * *
1828259 ATCAA-CATTTCCAGAAGG-GTTAATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT
1 ATCAATCATTTCCAGAAGGAATTCATAATGAGAATAACTCATCTGAAGAGGAAGAAGAAATTCAT
* * * * *
1828322 AATGAGAAAAACTTGTTCGACCTTAGCTTGATTCATCATCTATGGAGTTGAATGAAAGAAGAACC
66 AATGAGAAGAACTTGTTC-AACTTAGCTTAATTCATCATCTATGAAGTTGAATCAAAGAAG-ACC
1828387 TCAGTTGAGG
129 TCAGTTGAGG
* *
1828397 ATCAAT-ATTTCCAGAA-GAAGTTCATAATGAGAATAACTCGTCTGAAAAGGAAGAAGAAATTCA
1 ATCAATCATTTCCAGAAGGAA-TTCATAATGAGAATAACTCATCTGAAGAGGAAGAAGAAATTCA
* * *
1828460 TAATGAGAAGAACTTGTTCAACTTTGCCTTAATTCATCA-CTTATGAAGTTGAATCAATGATG-C
65 TAATGAGAAGAACTTGTTCAACTTAG-CTTAATTCATCATC-TATGAAGTTGAATCAAAGAAGAC
**
1828523 CTCTTTTGAGG
128 CTCAGTTGAGG
* * *
1828534 A-CCATCATTCCCAGAAGGAATTCATAATAAGAATAACTCATCTGAAGAGGAAGAAGAAATTCAT
1 ATCAATCATTTCCAGAAGGAATTCATAATGAGAATAACTCATCTGAAGAGGAAGAAGAAATTCAT
1828598 AATGAGAAGAACTTGTTCAAC
66 AATGAGAAGAACTTGTTCAAC
1828619 CTTTTGCTAG
Statistics
Matches: 193, Mismatches: 22, Indels: 15
0.84 0.10 0.07
Matches are distributed among these distances:
136 3 0.02
137 83 0.43
138 24 0.12
139 83 0.43
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (138 bp):
ATCAATCATTTCCAGAAGGAATTCATAATGAGAATAACTCATCTGAAGAGGAAGAAGAAATTCAT
AATGAGAAGAACTTGTTCAACTTAGCTTAATTCATCATCTATGAAGTTGAATCAAAGAAGACCTC
AGTTGAGG
Found at i:1828867 original size:3 final size:3
Alignment explanation
Indices: 1828854--1828931 Score: 117
Period size: 3 Copynumber: 27.0 Consensus size: 3
1828844 TTGGTTTTTT
*
1828854 TTA TTA GTA TTA TTA TTA TT- TTA TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1828900 ATA TTA TTA TTA TTA TTA TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1828932 AATAATAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
2 6 0.09
3 62 0.91
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1829737 original size:15 final size:16
Alignment explanation
Indices: 1829717--1829748 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1829707 CTCGTCTAGA
1829717 GAGAGAATG-AGAAAT
1 GAGAGAATGAAGAAAT
1829732 GAGAGAATGAAGAAAT
1 GAGAGAATGAAGAAAT
1829748 G
1 G
1829749 GCCTTAAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.53, C:0.00, G:0.34, T:0.12
Consensus pattern (16 bp):
GAGAGAATGAAGAAAT
Found at i:1830494 original size:2 final size:2
Alignment explanation
Indices: 1830487--1830513 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1830477 AACCTAAATA
1830487 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 A
1830514 AAAATATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1836064 original size:31 final size:31
Alignment explanation
Indices: 1835994--1836121 Score: 125
Period size: 31 Copynumber: 4.1 Consensus size: 31
1835984 GTCGAGGGTT
*
1835994 TACCTATGTTCTATGGAACATATGGACAGAA
1 TACCTATGTTCTATGGAACATATGGACAGTA
* * *
1836025 TTACCTATG-TCTTTCGAGACATATGGATAGTA
1 -TACCTATGTTCTATGGA-ACATATGGACAGTA
* * *
1836057 TACCTATGTTCTAAGGAGCATATGGACAGTT
1 TACCTATGTTCTATGGAACATATGGACAGTA
* * * *
1836088 TACCTAGGTTCTTTGGAACCTATGGATAGT-
1 TACCTATGTTCTATGGAACATATGGACAGTA
1836118 TACC
1 TACC
1836122 GAGGTTCTTT
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
30 4 0.05
31 49 0.63
32 25 0.32
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (31 bp):
TACCTATGTTCTATGGAACATATGGACAGTA
Found at i:1836101 original size:63 final size:61
Alignment explanation
Indices: 1835993--1836121 Score: 170
Period size: 63 Copynumber: 2.1 Consensus size: 61
1835983 AGTCGAGGGT
* *
1835993 TTACCTATGTTCTATGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGATAG
1 TTACCTATGTTCTAAGGAACATATGGACAGAATTACCTAGGTCTTTCGA-ACATATGGATAG
* * * *
1836055 TATACCTATGTTCTAAGGAGCATATGGACAG-TTTACCTAGGTTCTTTGGAACCTATGGATAG
1 T-TACCTATGTTCTAAGGAACATATGGACAGAATTACCTAGG-TCTTTCGAACATATGGATAG
1836117 TTACC
1 TTACC
1836122 GAGGTTCTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
61 4 0.07
62 21 0.36
63 34 0.58
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (61 bp):
TTACCTATGTTCTAAGGAACATATGGACAGAATTACCTAGGTCTTTCGAACATATGGATAG
Found at i:1840486 original size:63 final size:62
Alignment explanation
Indices: 1840407--1840527 Score: 172
Period size: 63 Copynumber: 1.9 Consensus size: 62
1840397 GAGGGTTTAC
*
1840407 CTATGTTCTACGGAACATATGGACAGAATTACCTA-TGTCTTTCGAGACATATGGACAGTATAA
1 CTATGTTCTAAGGAACATATGGACAG-ATTACCTAGTGTCTTTCGA-ACATATGGACAGTATAA
* * * *
1840470 CTATGTTCTAAGGAACATATGGACAGTTTACCTAGTTTCTTTGGAACCTATGGACAGT
1 CTATGTTCTAAGGAACATATGGACAGATTACCTAGTGTCTTTCGAACATATGGACAGT
1840528 TATCGAGGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
62 19 0.37
63 33 0.63
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (62 bp):
CTATGTTCTAAGGAACATATGGACAGATTACCTAGTGTCTTTCGAACATATGGACAGTATAA
Found at i:1840528 original size:31 final size:31
Alignment explanation
Indices: 1840401--1840528 Score: 134
Period size: 31 Copynumber: 4.1 Consensus size: 31
1840391 AGAGTCGAGG
*
1840401 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTATGGAACATATGGACA
* * *
1840432 GAATTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTATGGA-ACATATGGACA
* * *
1840464 GTATAACTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTATGGAACATATGGACA
* *
1840495 GTTTACCTA-GTTTCTTTGGAACCTATGGACA
1 GTTTACCTATG-TTCTATGGAACATATGGACA
1840526 GTT
1 GTT
1840529 ATCGAGGTTC
Statistics
Matches: 78, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
30 1 0.01
31 51 0.65
32 26 0.33
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTATGGAACATATGGACA
Found at i:1843794 original size:63 final size:63
Alignment explanation
Indices: 1843656--1843814 Score: 174
Period size: 63 Copynumber: 2.5 Consensus size: 63
1843646 AATTGTTCAA
* * * * *
1843656 GGTGTATCGATGCACATGAAGTGCATCGATGCACTCCTTTAAAATAAAACATCGAATGCCATC
1 GGTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAACATCGAAGGCCATC
* * * ** *
1843719 AGCGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATGAAACATCGAAGGTGATT
1 GGTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAACATCGAAGGCCATC
* *** *
1843782 GGTGTATTGATGCATGGGTAGTGTATCGATGCA
1 GGTGTATCGATGCACAAGTAGTGCATCGATGCA
1843815 TGAGTAGTGC
Statistics
Matches: 78, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
63 78 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (63 bp):
GGTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAACATCGAAGGCCATC
Found at i:1843807 original size:19 final size:19
Alignment explanation
Indices: 1843783--1843831 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1843773 AAGGTGATTG
* *
1843783 GTGTATTGATGCATGGGTA
1 GTGTATCGATGCATGAGTA
1843802 GTGTATCGATGCATGAGTA
1 GTGTATCGATGCATGAGTA
*
1843821 GTGCATCGATG
1 GTGTATCGATG
1843832 AACATGTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.22, C:0.10, G:0.35, T:0.33
Consensus pattern (19 bp):
GTGTATCGATGCATGAGTA
Found at i:1844932 original size:31 final size:31
Alignment explanation
Indices: 1844831--1844958 Score: 105
Period size: 31 Copynumber: 4.1 Consensus size: 31
1844821 AGAGTCGATG
*
1844831 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
* *** * *
1844862 GAATTACCTATG-TCTTTCGAGACATATAGAAA
1 G-TTTACCTATGTTCTAAGGA-ACATATGGACA
* *
1844894 GTATACCTATGTTCTAAGGAATATATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
* ** * *
1844925 GTTTACCTAGGTTCTTTGGAACTTATGGATA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
1844956 GTT
1 GTT
1844959 ACCGAGGTTC
Statistics
Matches: 73, Mismatches: 21, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
31 49 0.67
32 24 0.33
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTAAGGAACATATGGACA
Found at i:1846263 original size:39 final size:40
Alignment explanation
Indices: 1846220--1846326 Score: 119
Period size: 39 Copynumber: 2.7 Consensus size: 40
1846210 GCCAAATATG
* * *
1846220 AAGACTCCATGATTGCATGGTGTCTTCAGGCAAAT-GAAA
1 AAGACTCCACGACTGCATGGCGTCTTCAGGCAAATAGAAA
* * * * *
1846259 AAGACCCCACAACTGCATGGCATCTTCAGGTAAATAGAGA
1 AAGACTCCACGACTGCATGGCGTCTTCAGGCAAATAGAAA
*
1846299 AA-ACTCCACGACTGCACGGCGTCTTCAG
1 AAGACTCCACGACTGCATGGCGTCTTCAG
1846327 ACCAATTAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
39 50 0.91
40 5 0.09
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (40 bp):
AAGACTCCACGACTGCATGGCGTCTTCAGGCAAATAGAAA
Found at i:1848133 original size:60 final size:60
Alignment explanation
Indices: 1848062--1848183 Score: 145
Period size: 60 Copynumber: 2.0 Consensus size: 60
1848052 TTATAATTAC
* * * * * *
1848062 AAGGACCAAAATAGTACAAATAGGAATTTAAAGGACTAAAATAGCAAAAATAGAATCTTA
1 AAGGACCAAAATAGAAAAAATAGAAACTTAAAGGACTAAAATAGCAAAAACAGAAACTTA
* * * * *
1848122 AAGGACTAAAATAGAAAAAATAGAAACTTGAATGACTAAAATAGTAAATACAGAAACTTA
1 AAGGACCAAAATAGAAAAAATAGAAACTTAAAGGACTAAAATAGCAAAAACAGAAACTTA
1848182 AA
1 AA
1848184 TGATTAAACA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.57, C:0.09, G:0.14, T:0.20
Consensus pattern (60 bp):
AAGGACCAAAATAGAAAAAATAGAAACTTAAAGGACTAAAATAGCAAAAACAGAAACTTA
Found at i:1848177 original size:30 final size:30
Alignment explanation
Indices: 1848069--1848191 Score: 129
Period size: 30 Copynumber: 4.1 Consensus size: 30
1848059 TACAAGGACC
* * * * *
1848069 AAAATAGTACAAATAGGAATTTAAAGGACT
1 AAAATAGAAAAAATAGAAACTTAAATGACT
* * *
1848099 AAAATAGCAAAAATAGAATCTTAAAGGACT
1 AAAATAGAAAAAATAGAAACTTAAATGACT
*
1848129 AAAATAGAAAAAATAGAAACTTGAATGACT
1 AAAATAGAAAAAATAGAAACTTAAATGACT
* * * *
1848159 AAAATAGTAAATACAGAAACTTAAATGATT
1 AAAATAGAAAAAATAGAAACTTAAATGACT
1848189 AAA
1 AAA
1848192 CATTAATTAC
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.58, C:0.07, G:0.13, T:0.22
Consensus pattern (30 bp):
AAAATAGAAAAAATAGAAACTTAAATGACT
Found at i:1849038 original size:16 final size:17
Alignment explanation
Indices: 1849005--1849038 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1848995 TTCGAAGCTT
1849005 CTCTCTATTTTCTCTCC
1 CTCTCTATTTTCTCTCC
*
1849022 CTCTGTATTTT-TCTCC
1 CTCTCTATTTTCTCTCC
1849038 C
1 C
1849039 CCACCGAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.06, C:0.38, G:0.03, T:0.53
Consensus pattern (17 bp):
CTCTCTATTTTCTCTCC
Found at i:1851095 original size:10 final size:10
Alignment explanation
Indices: 1851040--1851098 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
1851030 CTTTACATTA
1851040 TATTTTTATT
1 TATTTTTATT
* *
1851050 GAATTTTATT
1 TATTTTTATT
* *
1851060 CATTTTCAATT
1 TATTTT-TATT
*
1851071 CATTTTTATT
1 TATTTTTATT
1851081 GTATTTTTATT
1 -TATTTTTATT
1851092 TATTTTT
1 TATTTTT
1851099 TAAAAAAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 22 0.55
11 18 0.45
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.69
Consensus pattern (10 bp):
TATTTTTATT
Found at i:1851096 original size:21 final size:20
Alignment explanation
Indices: 1851040--1851098 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
1851030 CTTTACATTA
* *
1851040 TATTTTTATTGAATTTTATT
1 TATTTTTATTCATTTTTATT
* *
1851060 CATTTTCAATTCATTTTTATT
1 TATTTT-TATTCATTTTTATT
*
1851081 GTATTTTTATTTATTTTT
1 -TATTTTTATTCATTTTT
1851099 TAAAAAAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 5 0.17
21 20 0.67
22 5 0.17
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.69
Consensus pattern (20 bp):
TATTTTTATTCATTTTTATT
Found at i:1852626 original size:21 final size:21
Alignment explanation
Indices: 1852597--1852638 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1852587 GGAATTATTA
*
1852597 TAATATTTTAAAATTAATAAT
1 TAATATTTTAAAATAAATAAT
* *
1852618 TAATTTTTTATAATAAATAAT
1 TAATATTTTAAAATAAATAAT
1852639 ATTAATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATATTTTAAAATAAATAAT
Found at i:1852666 original size:22 final size:22
Alignment explanation
Indices: 1852611--1852663 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
1852601 ATTTTAAAAT
*
1852611 TAATAATTAATTTTTTATAATAAA
1 TAAT-ATTAA-TTATTATAATAAA
*
1852635 TAATATTAATTATTATATTAAA
1 TAATATTAATTATTATAATAAA
1852657 TGAATAT
1 T-AATAT
1852664 AATAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 12 0.46
23 10 0.38
24 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TAATATTAATTATTATAATAAA
Found at i:1856452 original size:20 final size:20
Alignment explanation
Indices: 1856427--1856464 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1856417 ATAACTGCAG
1856427 ACAAAAAA-AATATAATTAGT
1 ACAAAAAATAAT-TAATTAGT
1856447 ACAAAAAATAATTAATTA
1 ACAAAAAATAATTAATTA
1856465 ATAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
ACAAAAAATAATTAATTAGT
Found at i:1856478 original size:21 final size:21
Alignment explanation
Indices: 1856452--1856491 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1856442 TTAGTACAAA
*
1856452 AAATAATTAATTAA-TAAATTT
1 AAATAAATAA-TAATTAAATTT
1856473 AAATAAATAATAATTAAAT
1 AAATAAATAATAATTAAAT
1856492 AAATATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATAAATAATAATTAAATTT
Found at i:1856489 original size:15 final size:15
Alignment explanation
Indices: 1856453--1856515 Score: 60
Period size: 15 Copynumber: 4.4 Consensus size: 15
1856443 TAGTACAAAA
*
1856453 AATAATT-AATTAAT
1 AATAATTAAATAAAT
*
1856467 AA-ATTTAAATAAAT
1 AATAATTAAATAAAT
1856481 AATAATTAAATAAAT
1 AATAATTAAATAAAT
* * *
1856496 ATTATTTTAATAAA-
1 AATAATTAAATAAAT
1856510 AATAAT
1 AATAAT
1856516 ATTTATATAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
13 3 0.08
14 14 0.36
15 22 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAATTAAATAAAT
Found at i:1858693 original size:27 final size:27
Alignment explanation
Indices: 1858663--1858721 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
1858653 TATGTGTTGC
* *
1858663 TTTTCGAATTAAGTTTAATAATTTTAA
1 TTTTAGAATTAAATTTAATAATTTTAA
** * *
1858690 TTTTAGTGTTAAATTTAATCATTTTAT
1 TTTTAGAATTAAATTTAATAATTTTAA
1858717 TTTTA
1 TTTTA
1858722 TTACATAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.58
Consensus pattern (27 bp):
TTTTAGAATTAAATTTAATAATTTTAA
Found at i:1860962 original size:17 final size:17
Alignment explanation
Indices: 1860936--1860989 Score: 90
Period size: 17 Copynumber: 3.2 Consensus size: 17
1860926 TGGCCTACTA
*
1860936 GACTTAGACCCTTGCTG
1 GACTTGGACCCTTGCTG
*
1860953 GACTTGGACCCTTGTTG
1 GACTTGGACCCTTGCTG
1860970 GACTTGGACCCTTGCTG
1 GACTTGGACCCTTGCTG
1860987 GAC
1 GAC
1860990 CTGAAAAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.30
Consensus pattern (17 bp):
GACTTGGACCCTTGCTG
Found at i:1861034 original size:22 final size:21
Alignment explanation
Indices: 1860993--1861055 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
1860983 GCTGGACCTG
* *
1860993 AAAAGAAAAAAAAAACAAAAGA
1 AAAATAAAAATAAAA-AAAAGA
1861015 AAGAACT-AAAATAAAAAAAAGA
1 AA-AA-TAAAAATAAAAAAAAGA
1861037 AAAATAAATAATAAAAAAA
1 AAAATAAA-AATAAAAAAA
1861056 TTAAACAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
20 1 0.03
21 4 0.11
22 20 0.57
23 10 0.29
ACGTcount: A:0.83, C:0.03, G:0.06, T:0.08
Consensus pattern (21 bp):
AAAATAAAAATAAAAAAAAGA
Found at i:1861299 original size:38 final size:38
Alignment explanation
Indices: 1861112--1861472 Score: 344
Period size: 40 Copynumber: 9.9 Consensus size: 38
1861102 TTCAAAAACA
* * *
1861112 TTTTCAAAACTGTATATTATATATA---TTTAAAAATG
1 TTTTAAAAACTATATATTATATATATGTTTTCAAAATG
*
1861147 TTTTCAAAAAAACTATATATTATATATATATTTTTCAAAATG
1 TTTT---AAAAACTATATATTATATATAT-GTTTTCAAAATG
*
1861189 TTTTCAAAACTATATATTATATATATATGTTTTCAAAATG
1 TTTTAAAAACTATATA-T-TATATATATGTTTTCAAAATG
1861229 TTTTAAAAACTATATAATATATATATATGTTTTCAAAATG
1 TTTTAAAAACTATAT-AT-TATATATATGTTTTCAAAATG
1861269 TTTTAAAAACTATATATTATATATATGTTTTC------
1 TTTTAAAAACTATATATTATATATATGTTTTCAAAATG
1861301 ----AAAAACTATATATTATATA-A-GTTTTCAAAATG
1 TTTTAAAAACTATATATTATATATATGTTTTCAAAATG
* *
1861333 TCTTAAAAATTATATATTATATATATGTTTTC------
1 TTTTAAAAACTATATATTATATATATGTTTTCAAAATG
1861365 ----AAAAACTATATATTATATA-A-GTTTTCAAAATG
1 TTTTAAAAACTATATATTATATATATGTTTTCAAAATG
* *
1861397 TCTTAAAAACTATATATTATATATATTTTTTTTCAAAATG
1 TTTTAAAAACTATATATTATATATA--TGTTTTCAAAATG
* *
1861437 TTTTAAAAACTATATAATATATATATTTTTTCAAAA
1 TTTTAAAAACTATATATTATATATATGTTTTCAAAA
1861473 ACCGATTTTA
Statistics
Matches: 279, Mismatches: 11, Indels: 69
0.78 0.03 0.19
Matches are distributed among these distances:
26 12 0.04
27 2 0.01
28 37 0.13
35 4 0.01
36 37 0.13
37 2 0.01
38 51 0.18
39 13 0.05
40 98 0.35
41 10 0.04
42 13 0.05
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (38 bp):
TTTTAAAAACTATATATTATATATATGTTTTCAAAATG
Found at i:1861317 original size:26 final size:28
Alignment explanation
Indices: 1861266--1861394 Score: 124
Period size: 28 Copynumber: 4.4 Consensus size: 28
1861256 TGTTTTCAAA
1861266 ATGTTTT-AAAAACTATATATTATATAT
1 ATGTTTTCAAAAACTATATATTATATAT
1861293 ATGTTTTCAAAAACTATATATTATATA-
1 ATGTTTTCAAAAACTATATATTATATAT
*
1861320 A-GTTTTCAAAATGTCTTAAAAATTATATATTATATAT
1 ATGTTTTCAAAA--AC-T----A-T--ATATTATATAT
1861357 ATGTTTTCAAAAACTATATATTATATA-
1 ATGTTTTCAAAAACTATATATTATATAT
1861384 A-GTTTTCAAAA
1 ATGTTTTCAAAA
1861395 TGTCTTAAAA
Statistics
Matches: 87, Mismatches: 2, Indels: 27
0.75 0.02 0.23
Matches are distributed among these distances:
26 20 0.23
27 9 0.10
28 30 0.34
29 1 0.01
30 1 0.01
31 1 0.01
33 1 0.01
34 1 0.01
35 1 0.01
36 11 0.13
37 1 0.01
38 10 0.11
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (28 bp):
ATGTTTTCAAAAACTATATATTATATAT
Found at i:1861333 original size:64 final size:64
Alignment explanation
Indices: 1861226--1861427 Score: 334
Period size: 64 Copynumber: 3.1 Consensus size: 64
1861216 TGTTTTCAAA
*
1861226 ATGTTTT-AAAAACTATATAATATATATATATGTTTTCAAAATGTTTTAAAAACTATATATTATA
1 ATGTTTTCAAAAACTATAT-AT-TATATA-A-GTTTTCAAAATGTCTTAAAAACTATATATTATA
1861290 TAT
62 TAT
*
1861293 ATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAATGTCTTAAAAATTATATATTATATAT
1 ATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAATGTCTTAAAAACTATATATTATATAT
1861357 ATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAATGTCTTAAAAACTATATATTATATAT
1 ATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAATGTCTTAAAAACTATATATTATATAT
*
1861421 ATTTTTT
1 ATGTTTT
1861428 TTCAAAATGT
Statistics
Matches: 130, Mismatches: 4, Indels: 5
0.94 0.03 0.04
Matches are distributed among these distances:
64 103 0.79
65 1 0.01
66 6 0.05
67 9 0.07
68 11 0.08
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (64 bp):
ATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAATGTCTTAAAAACTATATATTATATAT
Found at i:1867927 original size:20 final size:21
Alignment explanation
Indices: 1867880--1867930 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1867870 GATAAGAAAT
*
1867880 AATAAGTAAAAAAATCAAAGGA
1 AATAAG-AAAAAAATCAAAGAA
*
1867902 AA-AAGAAAAAAAT-AAATAA
1 AATAAGAAAAAAATCAAAGAA
1867921 AATAAGAAAA
1 AATAAGAAAA
1867931 TGAAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 6 0.23
20 15 0.58
21 3 0.12
22 2 0.08
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (21 bp):
AATAAGAAAAAAATCAAAGAA
Found at i:1868025 original size:31 final size:30
Alignment explanation
Indices: 1867911--1868033 Score: 113
Period size: 31 Copynumber: 3.9 Consensus size: 30
1867901 AAAAAGAAAA
* * *
1867911 AAATAAATAAAATAAGAAAATGAAAAATATT
1 AAATAAATAAAAGAA-AAAAAGCAAAATATT
* * *
1867942 AAATAAATCAAAAGGGAAAAAAG-TAAATCAATA
1 AAATAAAT-AAAA-GAAAAAAAGCAAAAT--ATT
1867975 AAATAAATAAAAGAAAAAAATGCAAAATATT
1 AAATAAATAAAAGAAAAAAA-GCAAAATATT
* *
1868006 AAATAAATCAAAGAAAAAAAACAAAATA
1 AAATAAATAAAAGAAAAAAAGCAAAATA
1868034 AAATGAAAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
30 7 0.09
31 40 0.53
32 14 0.18
33 15 0.20
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (30 bp):
AAATAAATAAAAGAAAAAAAGCAAAATATT
Found at i:1868110 original size:3 final size:3
Alignment explanation
Indices: 1868067--1868091 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1868057 GAAGTAAATA
1868067 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1868092 GGTAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1869316 original size:13 final size:13
Alignment explanation
Indices: 1869298--1869327 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1869288 GAAAAAAAGC
1869298 AAAATAAAGAAAT
1 AAAATAAAGAAAT
*
1869311 AAAATAAATAAAT
1 AAAATAAAGAAAT
1869324 AAAA
1 AAAA
1869328 ACAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (13 bp):
AAAATAAAGAAAT
Found at i:1869348 original size:20 final size:20
Alignment explanation
Indices: 1869311--1869347 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1869301 ATAAAGAAAT
1869311 AAAATAAATAAATAAAAACA
1 AAAATAAATAAATAAAAACA
1869331 AAAATAAAT-AATAAAAA
1 AAAATAAATAAATAAAAA
1869348 AATTAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAATAAATAAATAAAAACA
Found at i:1869354 original size:16 final size:15
Alignment explanation
Indices: 1869298--1869350 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
1869288 GAAAAAAAGC
*
1869298 AAAATAAAGAAATAAA
1 AAAATAAA-TAATAAA
*
1869314 ATAAATAAATAAAAACA
1 A-AAATAAATAATAA-A
1869331 AAAATAAATAATAAA
1 AAAATAAATAATAAA
1869346 AAAAT
1 AAAAT
1869351 TAAAACAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 6 0.19
16 17 0.53
17 9 0.28
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (15 bp):
AAAATAAATAATAAA
Found at i:1869435 original size:34 final size:36
Alignment explanation
Indices: 1869391--1869457 Score: 102
Period size: 34 Copynumber: 1.9 Consensus size: 36
1869381 TCAAAATTTT
*
1869391 AAAATATTTTCAAAACA-TATAT-TATATATATGTA
1 AAAATATTTTCAAAAAACTATATATATATATATGTA
*
1869425 AAAATGTTTTCAAAAAACTATATATATATATAT
1 AAAATATTTTCAAAAAACTATATATATATATAT
1869458 ATATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 15 0.52
35 5 0.17
36 9 0.31
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (36 bp):
AAAATATTTTCAAAAAACTATATATATATATATGTA
Found at i:1869448 original size:2 final size:2
Alignment explanation
Indices: 1869443--1869473 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1869433 TTCAAAAAAC
1869443 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 T
1869474 CAAAATGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1869481 original size:50 final size:46
Alignment explanation
Indices: 1869407--1869506 Score: 146
Period size: 50 Copynumber: 2.1 Consensus size: 46
1869397 TTTTCAAAAC
*
1869407 ATATATTATATATATGTAAAAATGTTTTCAAAAAACTATATATATATAT
1 ATATATTATATATATATAAAAATGTTTTC--AAAACTATATAT-TATAT
*
1869456 ATATATATATATATATATCAAAATGTTTTCAAAACTATATATTATAT
1 ATATAT-TATATATATATAAAAATGTTTTCAAAACTATATATTATAT
1869503 ATAT
1 ATAT
1869507 GTTTTCAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
47 9 0.19
48 12 0.25
49 6 0.12
50 21 0.44
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (46 bp):
ATATATTATATATATATAAAAATGTTTTCAAAACTATATATTATAT
Found at i:1869494 original size:26 final size:27
Alignment explanation
Indices: 1869461--1869516 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1869451 TATATATATA
1869461 TATATATATATATCAAAATGTTTTCAAAAC
1 TATATAT-TATAT--AAATGTTTTCAAAAC
*
1869491 TATATATTATATATATGTTTTCAAAA
1 TATATATTATATAAATGTTTTCAAAA
1869517 TGTTTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 13 0.52
29 5 0.20
30 7 0.28
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (27 bp):
TATATATTATATAAATGTTTTCAAAAC
Found at i:1869495 original size:38 final size:38
Alignment explanation
Indices: 1869453--1869684 Score: 163
Period size: 38 Copynumber: 6.4 Consensus size: 38
1869443 TATATATATA
*
1869453 TATATATATATATATAT-ATATCAAAATGTTTTCAAAAC
1 TATATAT-TATATATATGATATCAAAATGTTTTAAAAAC
* *
1869491 TATATATTATATATATGTTTTCAAAATGTTTTAAAAAC
1 TATATATTATATATATGATATCAAAATGTTTTAAAAAC
*
1869529 TATATATTATATATATG---------T-TTTCAAAAAC
1 TATATATTATATATATGATATCAAAATGTTTTAAAAAC
* * *
1869557 AATATATTATATATAT--TTTCAAAATATATTTTTAAAAAC
1 TATATATTATATATATGATATC-AAA-AT-GTTTTAAAAAC
* * * * * *
1869596 TATATATTATATA-A-GTTTTCATAATATCTTAAGAAC
1 TATATATTATATATATGATATCAAAATGTTTTAAAAAC
*
1869632 TATACATTATATATAT-ATATTCAAAATGTTTTAAAAAAC
1 TATATATTATATATATGATA-TCAAAATGTTTT-AAAAAC
*
1869671 TATATAATATATAT
1 TATATATTATATAT
1869685 TTTCAAAAAC
Statistics
Matches: 155, Mismatches: 20, Indels: 37
0.73 0.09 0.17
Matches are distributed among these distances:
28 24 0.15
29 1 0.01
36 20 0.13
37 14 0.09
38 54 0.35
39 42 0.27
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (38 bp):
TATATATTATATATATGATATCAAAATGTTTTAAAAAC
Found at i:1869568 original size:26 final size:28
Alignment explanation
Indices: 1869516--1869580 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
1869506 TGTTTTCAAA
*
1869516 ATGTTTT-AAAAACTATATATTATATAT
1 ATGTTTTCAAAAACAATATATTATATAT
1869543 ATGTTTTCAAAAACAATATATTATATAT
1 ATGTTTTCAAAAACAATATATTATATAT
1869571 A--TTTTCAAAA
1 ATGTTTTCAAAA
1869581 TATATTTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 9 0.25
27 7 0.19
28 20 0.56
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (28 bp):
ATGTTTTCAAAAACAATATATTATATAT
Found at i:1869568 original size:103 final size:104
Alignment explanation
Indices: 1869454--1869657 Score: 263
Period size: 103 Copynumber: 2.0 Consensus size: 104
1869444 ATATATATAT
*
1869454 ATATATATATATATATATATC-AAA-AT-GTTTTCAAAACTATATATTATATATATGTTTTCAAA
1 ATATATATATATATAT-TATCAAAATATAGTTTTAAAAACTATATATTATATA-A-GTTTTCAAA
* * * * *
1869516 ATGTTTTAAAAACTATATATTATATATATGTTTTCAAAAACA
63 ATATCTTAAAAACTATACATTATATATATATATTCAAAAACA
* * *
1869558 ATATAT-TATATATATTTTCAAAATATATTTTTAAAAACTATATATTATATAAGTTTTCATAATA
1 ATATATATATATATATTATCAAAATATAGTTTTAAAAACTATATATTATATAAGTTTTCAAAATA
*
1869622 TCTTAAGAACTATACATTATATATATATATTCAAAA
66 TCTTAAAAACTATACATTATATATATATATTCAAAA
1869658 TGTTTTAAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
102 3 0.03
103 53 0.61
104 9 0.10
105 22 0.25
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (104 bp):
ATATATATATATATATTATCAAAATATAGTTTTAAAAACTATATATTATATAAGTTTTCAAAATA
TCTTAAAAACTATACATTATATATATATATTCAAAAACA
Found at i:1869585 original size:15 final size:15
Alignment explanation
Indices: 1869565--1869603 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1869555 ACAATATATT
*
1869565 ATATATATTTTCAAA
1 ATATATATTTTAAAA
1869580 ATATAT-TTTTAAAA
1 ATATATATTTTAAAA
1869594 ACTATATATT
1 A-TATATATT
1869604 ATATAAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 8 0.38
15 11 0.52
16 2 0.10
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATATTTTAAAA
Found at i:1869594 original size:39 final size:37
Alignment explanation
Indices: 1869541--1869692 Score: 132
Period size: 39 Copynumber: 4.0 Consensus size: 37
1869531 TATATTATAT
1869541 ATATGTTTTCAAAAACAATATATTATATATATTTTCAAAA
1 ATAT-TTTT-AAAAACAATATATTATATATATTTTC-AAA
* *
1869581 TATATTTTTAAAAACTATATATTATATA-AGTTTTCATA
1 -ATATTTTTAAAAACAATATATTATATATA-TTTTCAAA
* * * *
1869619 ATA-TCTTAAGAACTATACATTATATATATATATTCAAA
1 ATATTTTTAAAAACAATATATTATATATAT-T-TTCAAA
* * *
1869657 AT-GTTTTAAAAA-ACTATATAATATATATTTTCAAA
1 ATATTTTTAAAAACAATATATTATATATATTTTCAAA
1869692 A
1 A
1869693 ACAGATTTTT
Statistics
Matches: 94, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
35 7 0.07
36 22 0.23
37 17 0.18
38 17 0.18
39 23 0.24
40 4 0.04
41 4 0.04
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (37 bp):
ATATTTTTAAAAACAATATATTATATATATTTTCAAA
Found at i:1875109 original size:21 final size:21
Alignment explanation
Indices: 1875068--1875109 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1875058 TTTAAAAATA
*
1875068 TAAATTATAAAATATATTTTT
1 TAAATTATAAAATATACTTTT
1875089 TAAATCTATAAAA-ATACTTTT
1 TAAAT-TATAAAATATACTTTT
1875110 ATTTTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAATTATAAAATATACTTTT
Found at i:1878841 original size:28 final size:28
Alignment explanation
Indices: 1878805--1878858 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1878795 AAATTTGTAA
*
1878805 TTTTTTAGTTAATCGAACTCCATTTTCT
1 TTTTTTAGTTAATCGAACCCCATTTTCT
1878833 TTTTTTAGTTAATCGAACCCCATTTT
1 TTTTTTAGTTAATCGAACCCCATTTT
1878859 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (28 bp):
TTTTTTAGTTAATCGAACCCCATTTTCT
Found at i:1881238 original size:20 final size:20
Alignment explanation
Indices: 1881215--1881255 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1881205 CAACGCGAAC
*
1881215 TCCAATTTTGCAACACAGTT
1 TCCAAATTTGCAACACAGTT
*
1881235 TCCAAATTTGCAACTCAGTT
1 TCCAAATTTGCAACACAGTT
1881255 T
1 T
1881256 ATGCAATCGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (20 bp):
TCCAAATTTGCAACACAGTT
Found at i:1881285 original size:20 final size:19
Alignment explanation
Indices: 1881262--1881335 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 19
1881252 GTTTATGCAA
1881262 TCGCAACGCAAATTTCTTTC
1 TCGCAACGC-AATTTCTTTC
* *
1881282 TCGCAACTCAATTTC-TGC
1 TCGCAACGCAATTTCTTTC
*
1881300 AATCGCAACGCGAATTTTTTTC
1 --TCGCAACGC-AATTTCTTTC
*
1881322 TCGCAACACAATTT
1 TCGCAACGCAATTT
1881336 TCCAAATTCG
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
18 2 0.05
19 11 0.25
20 24 0.55
21 5 0.11
22 2 0.05
ACGTcount: A:0.27, C:0.28, G:0.11, T:0.34
Consensus pattern (19 bp):
TCGCAACGCAATTTCTTTC
Found at i:1881288 original size:40 final size:40
Alignment explanation
Indices: 1881244--1881335 Score: 139
Period size: 40 Copynumber: 2.3 Consensus size: 40
1881234 TTCCAAATTT
*
1881244 GCAACTCAGTTTATGCAATCGCAACGCAAATTTCTTTCTC
1 GCAACTCAATTTATGCAATCGCAACGCAAATTTCTTTCTC
* * *
1881284 GCAACTCAATTTCTGCAATCGCAACGCGAATTTTTTTCTC
1 GCAACTCAATTTATGCAATCGCAACGCAAATTTCTTTCTC
*
1881324 GCAACACAATTT
1 GCAACTCAATTT
1881336 TCCAAATTCG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (40 bp):
GCAACTCAATTTATGCAATCGCAACGCAAATTTCTTTCTC
Found at i:1881357 original size:40 final size:40
Alignment explanation
Indices: 1881259--1881357 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 40
1881249 TCAGTTTATG
* * * * *
1881259 CAATCGCAACGCAAATTTCTTTCTCGCAACTCAATTTCTG
1 CAATCGCAACCCGAATTTTTTTCTCGCAACACAATTTCTC
*
1881299 CAATCGCAACGCGAATTTTTTTCTCGCAACACAATTT-TC
1 CAATCGCAACCCGAATTTTTTTCTCGCAACACAATTTCTC
1881338 CAAATTCGCAACCCG-ATTTT
1 C-AA-TCGCAACCCGAATTTT
1881358 CAAATTTGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
39 2 0.04
40 41 0.79
41 9 0.17
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.32
Consensus pattern (40 bp):
CAATCGCAACCCGAATTTTTTTCTCGCAACACAATTTCTC
Found at i:1881363 original size:20 final size:20
Alignment explanation
Indices: 1881322--1881410 Score: 79
Period size: 21 Copynumber: 4.3 Consensus size: 20
1881312 AATTTTTTTC
* *
1881322 TCGCAACACAATTTTCCAAAT
1 TCGCAACCCGATTTT-CAAAT
1881343 TCGCAACCCGATTTTCAAAT
1 TCGCAACCCGATTTTCAAAT
* * *
1881363 TTGCAACACGGAATTTCAAAT
1 TCGCAAC-CCGATTTTCAAAT
* * **
1881384 TCACAACTCGATTTTTGAAT
1 TCGCAACCCGATTTTCAAAT
1881404 TCGCAAC
1 TCGCAAC
1881411 GCGAATTTCT
Statistics
Matches: 54, Mismatches: 13, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 25 0.46
21 29 0.54
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.30
Consensus pattern (20 bp):
TCGCAACCCGATTTTCAAAT
Found at i:1881410 original size:41 final size:40
Alignment explanation
Indices: 1881322--1881419 Score: 108
Period size: 41 Copynumber: 2.4 Consensus size: 40
1881312 AATTTTTTTC
*
1881322 TCGCAACAC-AATTTTCCAAATTCGCAACCCGATTTTCAAAT
1 TCGCAACACGAA-TTT-CAAATTCACAACCCGATTTTCAAAT
* * **
1881363 TTGCAACACGGAATTTCAAATTCACAACTCGATTTTTGAAT
1 TCGCAACAC-GAATTTCAAATTCACAACCCGATTTTCAAAT
*
1881404 TCGCAACGCGAATTTC
1 TCGCAACACGAATTTC
1881420 TTTTTCGTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
40 7 0.15
41 36 0.75
42 3 0.06
43 2 0.04
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.31
Consensus pattern (40 bp):
TCGCAACACGAATTTCAAATTCACAACCCGATTTTCAAAT
Found at i:1881526 original size:20 final size:18
Alignment explanation
Indices: 1881503--1881549 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
1881493 GATTTTCGAA
1881503 TTCGCAACATGAATTTTAAT
1 TTCGCAACA-G-ATTTTAAT
* *
1881523 TTCGCAACAGCTTTTATT
1 TTCGCAACAGATTTTAAT
1881541 TTCGCAACA
1 TTCGCAACA
1881550 CAAATGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 15 0.60
19 1 0.04
20 9 0.36
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (18 bp):
TTCGCAACAGATTTTAAT
Found at i:1881707 original size:14 final size:15
Alignment explanation
Indices: 1881688--1881725 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1881678 TCCCCATCTC
1881688 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1881702 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1881718 TAATTTTT
1 TAATTTTT
1881726 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1882346 original size:12 final size:12
Alignment explanation
Indices: 1882325--1882358 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1882315 ACCACATTTC
*
1882325 CAATACCAAACA
1 CAATATCAAACA
1882337 CAATATCAAACA
1 CAATATCAAACA
1882349 CAATATCAAA
1 CAATATCAAA
1882359 ACCCACAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.59, C:0.26, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1882535 original size:24 final size:24
Alignment explanation
Indices: 1882484--1882537 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1882474 TTATTCGAAA
*
1882484 TTTGATCTTGGTAAATACCCGGAC
1 TTTGATCTTGGTAAATACCCAGAC
* * *
1882508 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTAAATACCCAGAC
1882532 TTTGAT
1 TTTGAT
1882538 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTAAATACCCAGAC
Found at i:1882725 original size:12 final size:12
Alignment explanation
Indices: 1882708--1882732 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1882698 ATATAACCCT
1882708 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1882720 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1882732 G
1 G
1882733 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1883628 original size:14 final size:14
Alignment explanation
Indices: 1883609--1883640 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1883599 CAGTAGCCAT
1883609 GGATGCTAACAATG
1 GGATGCTAACAATG
1883623 GGATGCTAACAATG
1 GGATGCTAACAATG
1883637 GGAT
1 GGAT
1883641 ACTGCCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.31, T:0.22
Consensus pattern (14 bp):
GGATGCTAACAATG
Found at i:1884839 original size:18 final size:18
Alignment explanation
Indices: 1884816--1884851 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1884806 AAGCAAAAGG
*
1884816 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1884834 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1884852 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1886584 original size:21 final size:21
Alignment explanation
Indices: 1886560--1886657 Score: 135
Period size: 21 Copynumber: 4.7 Consensus size: 21
1886550 GTGAATCGGG
* *
1886560 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
1886581 CTCTTGAATGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
1886602 CTCTTGAACAATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
1886623 CTCTTGAACGAT-AGGAGGGGC
1 CTCTTGAACGATGA-GAGGGGC
*
1886644 CTCTTAAACGATGA
1 CTCTTGAACGATGA
1886658 CAGGTGAATC
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
20 1 0.01
21 66 0.97
22 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:1886737 original size:4 final size:4
Alignment explanation
Indices: 1886721--1886766 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
1886711 AGGCCGCTAA
* * *
1886721 AAAT AAAT TAAT AAAT AAAT CAGT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1886767 TGCCGAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:1887008 original size:63 final size:63
Alignment explanation
Indices: 1886914--1887035 Score: 149
Period size: 63 Copynumber: 1.9 Consensus size: 63
1886904 ACCACGTAAA
* * * *
1886914 GCACCATTGTCATCGCGTAAAATATCTACCTCA-CAACGTAAAG-ACCGTACCTCATCACGCCAT
1 GCACCATTGTCATCACGTAAAATACCGACCTCATC-ACGCAAAGCACCG-ACCTCATCACGCCAT
* * *
1886977 GCACCATTGTCGTCACGTAAAGTACCGACCTCATCACGCAAAGCACTGACCTCATCACG
1 GCACCATTGTCATCACGTAAAATACCGACCTCATCACGCAAAGCACCGACCTCATCACG
1887036 TAACTCCCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
63 46 0.92
64 4 0.08
ACGTcount: A:0.30, C:0.34, G:0.15, T:0.20
Consensus pattern (63 bp):
GCACCATTGTCATCACGTAAAATACCGACCTCATCACGCAAAGCACCGACCTCATCACGCCAT
Found at i:1887013 original size:21 final size:21
Alignment explanation
Indices: 1886989--1887038 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1886979 ACCATTGTCG
*
1886989 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
* *
1887010 TCACGCAAAGCACTGACCTCA
1 TCACGTAAAGCACCGACCTCA
1887031 TCACGTAA
1 TCACGTAA
1887039 CTCCCCTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.18
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:1888689 original size:20 final size:20
Alignment explanation
Indices: 1888666--1888711 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1888656 AAACTTAAAT
1888666 TCACAACAAGAAAATGAAAA
1 TCACAACAAGAAAATGAAAA
**
1888686 TCACAACGCGAAAATGAAAA
1 TCACAACAAGAAAATGAAAA
1888706 TCACAA
1 TCACAA
1888712 AGCGAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.59, C:0.20, G:0.11, T:0.11
Consensus pattern (20 bp):
TCACAACAAGAAAATGAAAA
Found at i:1888716 original size:20 final size:20
Alignment explanation
Indices: 1888675--1888718 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1888665 TTCACAACAA
*
1888675 GAAAATGAAAATCACAACGC
1 GAAAATGAAAATCACAAAGC
1888695 GAAAATGAAAATCACAAAGC
1 GAAAATGAAAATCACAAAGC
1888715 GAAA
1 GAAA
1888719 CTAAAATCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.59, C:0.16, G:0.16, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCACAAAGC
Found at i:1888773 original size:20 final size:20
Alignment explanation
Indices: 1888735--1888773 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1888725 TCGTGTTGCG
**
1888735 ATTTTCGTGTTGCTTATTTC
1 ATTTTCGTGTTGCGAATTTC
1888755 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
1888774 AAGTTTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.18, T:0.56
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:1888780 original size:20 final size:20
Alignment explanation
Indices: 1888737--1888780 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1888727 GTGTTGCGAT
** * *
1888737 TTTCGTGTTGCTTATTTCAT
1 TTTCGTGTTGCGAATTTAAG
1888757 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTGCGAATTTAAG
1888777 TTTC
1 TTTC
1888781 AAAAATTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:1890763 original size:11 final size:11
Alignment explanation
Indices: 1890747--1890772 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1890737 TGCTTATTAG
1890747 ATTTTGTATAT
1 ATTTTGTATAT
1890758 ATTTTGTATAT
1 ATTTTGTATAT
1890769 ATTT
1 ATTT
1890773 AGTAGTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (11 bp):
ATTTTGTATAT
Found at i:1896134 original size:5 final size:5
Alignment explanation
Indices: 1896124--1898095 Score: 3623
Period size: 5 Copynumber: 399.4 Consensus size: 5
1896114 AACTTCATTT
1896124 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1896174 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1896224 TGTTA TGTTA TGTTA TGTTA TGTTTA TGTTA TGTTA TGTT- TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TG-TTA TGTTA TGTTA TGTTA TGTTA TGTTA
1896274 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1896324 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1896374 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1896424 TG-TA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1896473 TGTTA TGTTA TGTTA TGTTA TG-T- TGTTA TGTTA TGTTA TGTTA -GTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1896520 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1896570 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1896620 TGTTA TGTTA TG-TA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1896669 TGTT- TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1896718 TGTTA TG-TA TGTTA -GTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TG-TTA
1896767 TG-TA TGTTA TGTTA TGTTA TGTTA TGTTA TG-TA TGTTA TGTTA -GTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
*
1896814 -GTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGATA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1896863 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1896913 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1896963 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTT- TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897012 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897062 TGTTA TGTTA TG-TA TGTTA TGTTA TGTTA TGTTA TG-TA TGTTA TG-TA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897109 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897159 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TG-TA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897208 TGTTA TG-T- TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897256 TGTTA TGTTA TGTT- TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897305 TGTTA TGTTA TG-TA TGTTA TGTTGTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TG-T-TA TGTTA TGTTA TGTTA TGTTA TGTTA
1897356 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897406 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897456 TGTTA TGTTA TGTTA TGTTTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TG--TTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897508 TG-TA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897557 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TG-TA TGTTA TGTTA TG-TA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897605 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897655 TG-T- TGTTA TGTTA TGTTA TGTTA TG-T- TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897701 TGTTA TGTTTA TGTTA TGTTA TGTTA TGGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TG-TTA TGTTA TGTTA TGTTA T-GTTA TGTTA TGTTA TGTTA TGTTA
1897753 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
*
1897803 TGTTT TGTTA TGTTA T-TTA TGTTA TGTTA TGTTA TG-T- TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897850 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897900 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897950 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TG-TA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1897999 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1898049 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TG
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TG
1898096 AATTATGTTG
Statistics
Matches: 1923, Mismatches: 4, Indels: 80
0.96 0.00 0.04
Matches are distributed among these distances:
3 10 0.01
4 102 0.05
5 1780 0.93
6 22 0.01
7 9 0.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
TGTTA
Found at i:1899197 original size:20 final size:20
Alignment explanation
Indices: 1899172--1899220 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1899162 GGTTGTTTCT
1899172 AGCCGTTGGGGATGTTTTGG
1 AGCCGTTGGGGATGTTTTGG
1899192 AGCCGTTGGGGATGTTTTGG
1 AGCCGTTGGGGATGTTTTGG
*
1899212 AGCTGTTGG
1 AGCCGTTGG
1899221 TGATTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.10, C:0.10, G:0.45, T:0.35
Consensus pattern (20 bp):
AGCCGTTGGGGATGTTTTGG
Found at i:1899983 original size:237 final size:236
Alignment explanation
Indices: 1899534--1900005 Score: 788
Period size: 237 Copynumber: 2.0 Consensus size: 236
1899524 ATATCGATAT
1899534 TGTTCATGTAGTAATGATACTGTAAGAACAGTATCGGTACTACGTACCCAGAAAACTGTTTTGTG
1 TGTTCATGTAGTAATGATACTGTAAGAACAGTATCGGTACTACGTACCCAGAAAACTGTTTTGTG
1899599 CTCAAATTCTAGTTTAATGGACTTTGAATTTATTTTTGAAAATTTTGAACAAATTCAATCAAGTC
66 CTCAAATTCTAGTTTAATGGACTTTGAATTTATTTTTGAAAATTTTGAACAAATTCAATCAAGTC
1899664 CAAAAAAATTTCGCCTTAATTTGTTATATCAAAATATTATAAAACATGGTTCAAGAATCTACCCT
131 CAAAAAAATTTCGCCTTAATTTGTTATATCAAAATATTATAAAACATGGTTCAAGAATCTACCCT
**
1899729 TTTTTGATATAACAAAATATTTGAAAAATTGTTTTGGCAAAC
196 TTTTTGATATAACAAAATATTTG-AAAATCATTTTGGCAAAC
*
1899771 TGTTCATGTA-TTATCGATACTGTAAGAACAGTATCGGTACTACGTACCCAGAAAAACTGTTTTG
1 TGTTCATGTAGTAAT-GATACTGTAAGAACAGTATCGGTACTACGTACCCAG-AAAACTGTTTTG
1899835 TGCTCAAATTCTAGTTTAATGGACTTTGAA-TTATTTTTGAAAATTTTGAACAAATTCAATCAAG
64 TGCTCAAATTCTAGTTTAATGGACTTTGAATTTATTTTTGAAAATTTTGAACAAATTCAATCAAG
* * * * * * *
1899899 TCCAAAAACATTTTGTCTTAATTTGTTATATCAAAATATTATAAAATATTGTTCAATAATCTCCC
129 TCCAAAAAAATTTCGCCTTAATTTGTTATATCAAAATATTATAAAACATGGTTCAAGAATCTACC
*
1899964 CATTTTTT-ATATGACAAAATATTTGAAAATCATTTTGGCAAA
194 C-TTTTTTGATATAACAAAATATTTGAAAATCATTTTGGCAAA
1900006 ACTCCTTAAT
Statistics
Matches: 221, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
236 18 0.08
237 155 0.70
238 48 0.22
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (236 bp):
TGTTCATGTAGTAATGATACTGTAAGAACAGTATCGGTACTACGTACCCAGAAAACTGTTTTGTG
CTCAAATTCTAGTTTAATGGACTTTGAATTTATTTTTGAAAATTTTGAACAAATTCAATCAAGTC
CAAAAAAATTTCGCCTTAATTTGTTATATCAAAATATTATAAAACATGGTTCAAGAATCTACCCT
TTTTTGATATAACAAAATATTTGAAAATCATTTTGGCAAAC
Found at i:1905020 original size:20 final size:20
Alignment explanation
Indices: 1904977--1905020 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1904967 TTTTGCAGAA
* * *
1904977 AAATTATCCCCAACGTCTCC
1 AAATCATCCCCAACGACTAC
*
1904997 AAATCATCCCCAACGACTAG
1 AAATCATCCCCAACGACTAC
1905017 AAAT
1 AAAT
1905021 GGACACAAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.34, G:0.07, T:0.20
Consensus pattern (20 bp):
AAATCATCCCCAACGACTAC
Found at i:1906824 original size:150 final size:149
Alignment explanation
Indices: 1906602--1906877 Score: 328
Period size: 150 Copynumber: 1.8 Consensus size: 149
1906592 CGATATTAAT
* * * * *
1906602 CATGTCTATCAAGCCATTTTAGTTTGTTCTTCATGCACAAAACCAATCTTTGGATCCATTTTGAA
1 CATGTCTATAAAGCCATTTTAGTTTCTTATTCATGCACAAAACCAAGCTTTGGATCCATTTTCAA
* ** * * *
1906667 CTCGATTTTTACCTTTCTTACAATGA-CTCGTATGTGTATATATTAACCTCAATTGAAAGATTAG
66 CTCGATTTTTAACTCGCTTACAAT-ATATCGTATGTGTAGATATTAACCTCAACTGAAAGATTAG
1906731 TACCAATATTACACTTATAA
130 TACCAATATTACACTTATAA
* *
1906751 CATGTCTATAAAGCCATTTTCTA-TCTTCTTATTCTTGCATAAAA-CAAGCTTTGGAAT-CATTT
1 CATGTCTATAAAGCCA-TTT-TAGT-TTCTTATTCATGCACAAAACCAAGCTTTGG-ATCCATTT
* *
1906813 TCAA-TGCGATTTTTAACTCGCTTACAATATATCGTATGTGTCGATATTGACCTCAACTGAAAGA
62 TCAACT-CGATTTTTAACTCGCTTACAATATATCGTATGTGTAGATATTAACCTCAACTGAAAGA
1906877 T
126 T
1906878 AAATTCTAAT
Statistics
Matches: 106, Mismatches: 15, Indels: 11
0.80 0.11 0.08
Matches are distributed among these distances:
149 17 0.16
150 70 0.66
151 19 0.18
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (149 bp):
CATGTCTATAAAGCCATTTTAGTTTCTTATTCATGCACAAAACCAAGCTTTGGATCCATTTTCAA
CTCGATTTTTAACTCGCTTACAATATATCGTATGTGTAGATATTAACCTCAACTGAAAGATTAGT
ACCAATATTACACTTATAA
Found at i:1912234 original size:39 final size:39
Alignment explanation
Indices: 1912180--1912258 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
1912170 AAGCGTCTTC
*
1912180 TTCAATTTTAACACATATTTCTCTTTTCTGACTTTCACA
1 TTCAATTTTAACACATATTTCTCTTTTCCGACTTTCACA
*
1912219 TTCAATTTTAACACATATTTGTCTTTTCCGACTTTCACA
1 TTCAATTTTAACACATATTTCTCTTTTCCGACTTTCACA
1912258 T
1 T
1912259 ACTTGGGTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.25, C:0.23, G:0.04, T:0.48
Consensus pattern (39 bp):
TTCAATTTTAACACATATTTCTCTTTTCCGACTTTCACA
Found at i:1921240 original size:32 final size:32
Alignment explanation
Indices: 1921165--1921281 Score: 110
Period size: 32 Copynumber: 3.5 Consensus size: 32
1921155 GGATGATTAT
*
1921165 CGGATCGGTTGATTTTTGGATCGGGTCAGGTCAATAC
1 CGGATCGGTTGATTTTT-G---GGTTC-GGTCAATAC
* *
1921202 CAGATCGGTTGATTTTTGGGTTCGGTTAATAC
1 CGGATCGGTTGATTTTTGGGTTCGGTCAATAC
* * * *
1921234 CGGATCGATTAGA-TTTCGGGTTGGGTCAATAT
1 CGGATCGGTT-GATTTTTGGGTTCGGTCAATAC
1921266 CGGATCGGTTGATTTT
1 CGGATCGGTTGATTTT
1921282 CGGTTTAGGT
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
31 2 0.03
32 43 0.63
33 6 0.09
36 1 0.01
37 16 0.24
ACGTcount: A:0.19, C:0.14, G:0.31, T:0.37
Consensus pattern (32 bp):
CGGATCGGTTGATTTTTGGGTTCGGTCAATAC
Found at i:1921283 original size:32 final size:32
Alignment explanation
Indices: 1921185--1921294 Score: 123
Period size: 32 Copynumber: 3.4 Consensus size: 32
1921175 GATTTTTGGA
* *
1921185 TCGGGTCAGGTCAATACCAGATCGGTTGATTT
1 TCGGGTTAGGTCAATACCGGATCGGTTGATTT
* * * *
1921217 TTGGGTTCGGTTAATACCGGATCGATTAGA-TT
1 TCGGGTTAGGTCAATACCGGATCGGTT-GATTT
* *
1921249 TCGGGTTGGGTCAATATCGGATCGGTTGATTT
1 TCGGGTTAGGTCAATACCGGATCGGTTGATTT
*
1921281 TCGGTTTAGGTCAA
1 TCGGGTTAGGTCAA
1921295 CCTTTAGATC
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
31 2 0.03
32 59 0.94
33 2 0.03
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.35
Consensus pattern (32 bp):
TCGGGTTAGGTCAATACCGGATCGGTTGATTT
Found at i:1921548 original size:30 final size:30
Alignment explanation
Indices: 1921514--1921573 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1921504 CTTATAATAC
* *
1921514 GTGTTAGAATTTGTTATCAAAATTTTATAT
1 GTGTTAAAATTTGTTACCAAAATTTTATAT
*
1921544 GTGTTAAAATTTGTTACCAAATTTTTATAT
1 GTGTTAAAATTTGTTACCAAAATTTTATAT
1921574 TAATATCGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (30 bp):
GTGTTAAAATTTGTTACCAAAATTTTATAT
Found at i:1922087 original size:14 final size:16
Alignment explanation
Indices: 1922056--1922095 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1922046 TAGGTTAAAG
1922056 TATAATTTTATTTATA
1 TATAATTTTATTTATA
1922072 TATAATTTCT-TTTATA
1 TATAATTT-TATTTATA
*
1922088 TATTATTT
1 TATAATTT
1922096 AAAAATGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TATAATTTTATTTATA
Found at i:1925484 original size:17 final size:17
Alignment explanation
Indices: 1925462--1925518 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
1925452 TGCTTTCGGA
1925462 TTGGGTTAATATTTAGT
1 TTGGGTTAATATTTAGT
**
1925479 TTGGGTTTCT-TTTAGT
1 TTGGGTTAATATTTAGT
* *
1925495 TTGGGTTAAAATTCAGT
1 TTGGGTTAATATTTAGT
1925512 TTGGGTT
1 TTGGGTT
1925519 TCTTTCGGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 13 0.39
17 20 0.61
ACGTcount: A:0.18, C:0.04, G:0.26, T:0.53
Consensus pattern (17 bp):
TTGGGTTAATATTTAGT
Found at i:1930812 original size:17 final size:17
Alignment explanation
Indices: 1930790--1930823 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1930780 GGTTCCGTTC
1930790 CTAATCACTGCCCATCA
1 CTAATCACTGCCCATCA
1930807 CTAATCACTGCCCATCA
1 CTAATCACTGCCCATCA
1930824 TATTCGTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.41, G:0.06, T:0.24
Consensus pattern (17 bp):
CTAATCACTGCCCATCA
Found at i:1931938 original size:20 final size:20
Alignment explanation
Indices: 1931913--1931958 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1931903 CTGTTGGTAG
1931913 CGATACTGACCCTTCAGTAT
1 CGATACTGACCCTTCAGTAT
* *
1931933 CGATACTGATCCTTGAGTAT
1 CGATACTGACCCTTCAGTAT
*
1931953 CAATAC
1 CGATAC
1931959 CTACCTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (20 bp):
CGATACTGACCCTTCAGTAT
Found at i:1940812 original size:13 final size:13
Alignment explanation
Indices: 1940794--1940819 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1940784 GTCATAAATC
1940794 TATGACGCGCATT
1 TATGACGCGCATT
1940807 TATGACGCGCATT
1 TATGACGCGCATT
1940820 GCGCGTCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
TATGACGCGCATT
Done.