Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_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: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 43
Found at i:3538038 original size:4 final size:4
Alignment explanation
Indices: 3537996--3538051 Score: 51
Period size: 4 Copynumber: 13.2 Consensus size: 4
3537986 CCTCTTTTTA
* *
3537996 TATT TATT ACTATT AATT TA-T TATT ATATT ATTTT TATT TATT TATT
1 TATT TATT --TATT TATT TATT TATT -TATT -TATT TATT TATT TATT
3538043 TATT TATT T
1 TATT TATT T
3538052 TAATATATCT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
3 3 0.07
4 29 0.66
5 8 0.18
6 4 0.09
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (4 bp):
TATT
Found at i:3538053 original size:21 final size:21
Alignment explanation
Indices: 3538011--3538052 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3538001 ATTACTATTA
3538011 ATTTATTATTATATTATTTTT
1 ATTTATTATTATATTATTTTT
3538032 ATTTATTTATT-TATTTATTTT
1 ATTTA-TTATTATA-TTATTTT
3538053 AATATATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
ATTTATTATTATATTATTTTT
Found at i:3542810 original size:21 final size:21
Alignment explanation
Indices: 3542786--3542829 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3542776 TCCAACACTG
**
3542786 CCTTCACTGTTTCCACCACCT
1 CCTTCACCATTTCCACCACCT
3542807 CCTTCACCATTTCCACCACCT
1 CCTTCACCATTTCCACCACCT
3542828 CC
1 CC
3542830 ATACGTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.52, G:0.02, T:0.30
Consensus pattern (21 bp):
CCTTCACCATTTCCACCACCT
Found at i:3542940 original size:99 final size:100
Alignment explanation
Indices: 3542797--3543057 Score: 308
Period size: 100 Copynumber: 2.6 Consensus size: 100
3542787 CTTCACTGTT
* ** * *
3542797 TCCACCACCTCCTTCACCATTTCCACCACCTCCATACGTTTACAAATCTCCACCATCTCCACCAA
1 TCCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAATCTCCACCACCTCCACCAA
* * * * * *
3542862 AACACAAGGAGCAGA-GCTCGTACTACTATAAGTC
66 AACACAAGGAACAAACCCCCATAATACTATAAGTC
* * * **
3542896 TCCACCACCACCTTCACCATCCCCACCTCCTCCATACGTCTACAAATATCCACTACCTCCACTGA
1 TCCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAATCTCCACCACCTCCACCAA
*
3542961 AACACGAGGAACAAACCCCCATAATACTATAAGTC
66 AACACAAGGAACAAACCCCCATAATACTATAAGTC
* * * * * *
3542996 TCCTCCACTACCTTCACCATCCTCACCACCTCCACACGTCTATAAATCTCCACCACCACCAC
1 TCCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAATCTCCACCACCTCCAC
3543058 TTAATTTTTT
Statistics
Matches: 135, Mismatches: 26, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
99 67 0.50
100 68 0.50
ACGTcount: A:0.30, C:0.43, G:0.06, T:0.21
Consensus pattern (100 bp):
TCCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAATCTCCACCACCTCCACCAA
AACACAAGGAACAAACCCCCATAATACTATAAGTC
Found at i:3550873 original size:59 final size:59
Alignment explanation
Indices: 3550781--3550895 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 59
3550771 AATAGATGGA
* * * * *
3550781 TAAGTGTCCTATCAAACCCTCCTAGTCGTAATGAAAAGGTAAACTCGATAATATGGACC
1 TAAGTGTCCTATCAAACCCTCCTAGTAGCAATGAAAAGGAAAAATCAATAATATGGACC
* *
3550840 TAAGTGTCCTATCGAACCCTCCTATTAGCAATGAAAAGGAAAAATCAATAATATGG
1 TAAGTGTCCTATCAAACCCTCCTAGTAGCAATGAAAAGGAAAAATCAATAATATGG
3550896 CTCTAACCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (59 bp):
TAAGTGTCCTATCAAACCCTCCTAGTAGCAATGAAAAGGAAAAATCAATAATATGGACC
Found at i:3551180 original size:43 final size:47
Alignment explanation
Indices: 3551128--3551234 Score: 125
Period size: 50 Copynumber: 2.3 Consensus size: 47
3551118 ATAACTAATG
*
3551128 AATAAAATAATAACAAACT-AAA-CATGTATTAAC-T-C-TAATTCCT
1 AATAAAATAATAA-AAACTAAAATAATGTATTAACTTACTTAATTCCT
*
3551171 AATAAAATAATAATAACTAAAAATAATGTATTAACTTAACCTTAATTCCT
1 AATAAAATAATAAAAACT-AAAATAATGTATTAACTT-A-CTTAATTCCT
3551221 AATAAAATAATAAA
1 AATAAAATAATAAA
3551235 TCTAATCCCA
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
42 4 0.08
43 13 0.25
44 3 0.06
45 10 0.19
46 1 0.02
49 1 0.02
50 21 0.40
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (47 bp):
AATAAAATAATAAAAACTAAAATAATGTATTAACTTACTTAATTCCT
Found at i:3552858 original size:2 final size:2
Alignment explanation
Indices: 3552851--3552886 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3552841 AACATGTATG
3552851 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
3552887 ATACACAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3552960 original size:10 final size:10
Alignment explanation
Indices: 3552945--3552970 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3552935 AGTTTTATAA
3552945 TAATTAATAT
1 TAATTAATAT
3552955 TAATTAATAT
1 TAATTAATAT
3552965 TAATTA
1 TAATTA
3552971 TATAGTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TAATTAATAT
Found at i:3566878 original size:42 final size:42
Alignment explanation
Indices: 3566814--3566903 Score: 153
Period size: 42 Copynumber: 2.1 Consensus size: 42
3566804 ATATGCACCT
* *
3566814 CATGCAACATTAACTCTCCTTACTAATTGTACTTAAGCACTA
1 CATGGAACATTAACTCTCCTTACTAATTGTACTGAAGCACTA
*
3566856 CATGGAACATTAATTCTCCTTACTAATTGTACTGAAGCACTA
1 CATGGAACATTAACTCTCCTTACTAATTGTACTGAAGCACTA
3566898 CATGGA
1 CATGGA
3566904 GACACTCAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.32
Consensus pattern (42 bp):
CATGGAACATTAACTCTCCTTACTAATTGTACTGAAGCACTA
Found at i:3572242 original size:21 final size:21
Alignment explanation
Indices: 3572218--3572270 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
3572208 TGGGCTAGAA
*
3572218 GTATCAATACTCATATA-TAAG
1 GTATCGATACTCATA-AGTAAG
*
3572239 GTATTGATACT-ATAAGTAAG
1 GTATCGATACTCATAAGTAAG
3572259 GTATCGATACTC
1 GTATCGATACTC
3572271 GTACGAGGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 17 0.63
21 9 0.33
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (21 bp):
GTATCGATACTCATAAGTAAG
Found at i:3581544 original size:21 final size:20
Alignment explanation
Indices: 3581510--3581549 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3581500 TAGTTTTAAG
*
3581510 TATTTTAATTAGGATTTATT
1 TATTTTAATTAGGAATTATT
*
3581530 TATTTATATTTAGGAATTAT
1 TATTT-TAATTAGGAATTAT
3581550 CTTTACCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (20 bp):
TATTTTAATTAGGAATTATT
Found at i:3585319 original size:6 final size:6
Alignment explanation
Indices: 3585308--3585365 Score: 55
Period size: 6 Copynumber: 9.7 Consensus size: 6
3585298 CGTTTGTGCA
* * * * *
3585308 ATTTTT ATTTTT ATTTTC AATTTT ATTTTT CTGATTT A-TTTT GTTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT AT-TTTT ATTTTT ATTTTT
3585356 ATTTTT ATTT
1 ATTTTT ATTT
3585366 GATATTTCAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
5 3 0.08
6 34 0.85
7 3 0.08
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.76
Consensus pattern (6 bp):
ATTTTT
Found at i:3585590 original size:27 final size:28
Alignment explanation
Indices: 3585559--3585638 Score: 126
Period size: 28 Copynumber: 2.9 Consensus size: 28
3585549 AACAGTGCTG
3585559 AAAAACTGATTTGGTTCGAACAATGTAA
1 AAAAACTGATTTGGTTCGAACAATGTAA
*
3585587 AAAAACTGATTTGGTTTGAACAATGT-A
1 AAAAACTGATTTGGTTCGAACAATGTAA
**
3585614 AAAAACTGATTTCATTCGAACAATG
1 AAAAACTGATTTGGTTCGAACAATG
3585639 CAGAAAATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
27 23 0.48
28 25 0.52
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (28 bp):
AAAAACTGATTTGGTTCGAACAATGTAA
Found at i:3585645 original size:28 final size:28
Alignment explanation
Indices: 3585548--3585645 Score: 117
Period size: 28 Copynumber: 3.5 Consensus size: 28
3585538 TACACTGTTT
* *
3585548 GAACAGTGCTGAAAAACTGATTTGGTTC
1 GAACAATGCAGAAAAACTGATTTGGTTC
* * *
3585576 GAACAATGTAAAAAAACTGATTTGGTTT
1 GAACAATGCAGAAAAACTGATTTGGTTC
* **
3585604 GAACAATGTA-AAAAACTGATTTCATTC
1 GAACAATGCAGAAAAACTGATTTGGTTC
3585631 GAACAATGCAGAAAA
1 GAACAATGCAGAAAA
3585646 TACATAGGAG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
27 23 0.38
28 37 0.62
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (28 bp):
GAACAATGCAGAAAAACTGATTTGGTTC
Found at i:3585800 original size:35 final size:34
Alignment explanation
Indices: 3585761--3585835 Score: 105
Period size: 35 Copynumber: 2.2 Consensus size: 34
3585751 AGTGCAGTGT
*
3585761 AAAAAAAACAGTGCAATTTTGGTTCGAACAGTTAA
1 AAAAAAAACAGTACAATTTTGGTTCGAACAG-TAA
* **
3585796 AAAAATAGTAGTACAATTTTGGTTCGAACAGTAA
1 AAAAAAAACAGTACAATTTTGGTTCGAACAGTAA
3585830 AAAAAA
1 AAAAAA
3585836 GAGAAAATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
34 8 0.23
35 27 0.77
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.25
Consensus pattern (34 bp):
AAAAAAAACAGTACAATTTTGGTTCGAACAGTAA
Found at i:3586122 original size:19 final size:19
Alignment explanation
Indices: 3586098--3586142 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
3586088 GGGGTAGAAT
3586098 TTGCTTTCA-AATTTTTCGC
1 TTGCTTTCACAA-TTTTCGC
3586117 TTGCTTTCACAATTTTCGC
1 TTGCTTTCACAATTTTCGC
3586136 TTGCTTT
1 TTGCTTT
3586143 TTTTATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 23 0.92
20 2 0.08
ACGTcount: A:0.13, C:0.22, G:0.11, T:0.53
Consensus pattern (19 bp):
TTGCTTTCACAATTTTCGC
Found at i:3588644 original size:12 final size:12
Alignment explanation
Indices: 3588629--3588653 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3588619 CTTTATCTTA
3588629 TATTTAATTATT
1 TATTTAATTATT
3588641 TATTTAATTATT
1 TATTTAATTATT
3588653 T
1 T
3588654 TATTCTTATT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTAATTATT
Found at i:3602878 original size:16 final size:16
Alignment explanation
Indices: 3602857--3602889 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3602847 CCCATTTATC
3602857 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
3602873 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
3602889 A
1 A
3602890 AAACACACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTTAAAACACACTT
Found at i:3604681 original size:2 final size:2
Alignment explanation
Indices: 3604674--3604704 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3604664 TTGAGAAATA
3604674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3604705 GTTTTCATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3605204 original size:23 final size:21
Alignment explanation
Indices: 3605152--3605231 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
3605142 ACAGAACCCC
* **
3605152 AGGGGGTATCGATTCCCCTGT
1 AGGGGGAATCGATTCCCCTCA
*
3605173 GGGGGGAATCGATTCCCCTTCAA
1 AGGGGGAATCGATTCCCC-TC-A
*
3605196 AGGGGGAATCGGTT-CCCTCA
1 AGGGGGAATCGATTCCCCTCA
*
3605216 TGGGGG-ATCGATTCCC
1 AGGGGGAATCGATTCCC
3605232 TCTGCACAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
19 6 0.12
20 8 0.17
21 18 0.38
22 4 0.08
23 12 0.25
ACGTcount: A:0.17, C:0.25, G:0.34, T:0.24
Consensus pattern (21 bp):
AGGGGGAATCGATTCCCCTCA
Found at i:3616453 original size:44 final size:45
Alignment explanation
Indices: 3616405--3616712 Score: 350
Period size: 44 Copynumber: 7.1 Consensus size: 45
3616395 GCAAAAACGA
* * * * *
3616405 TAAGGTCTTATCCTTGCATATAGCAAAAGAG-TCT-GGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAACAAAAGAGACCTGGGGGAAACTG
*
3616449 TAAGGCTTACCCTTGCACACAACAAAGGA-ACCT--GGGAAACTG
1 TAAGGCTTACCCTTGCACACAACAAAAGAGACCTGGGGGAAACTG
* *
3616491 TAAGGCTTACCCTTACACACAAC-AAAGGGACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAACAAAAGAGACCTGGGGGAAACTG
* * * *
3616535 TAAGACTTACCCTTGCACACAGC-AAAGGGACCTGGGGGAAAGTG
1 TAAGGCTTACCCTTGCACACAACAAAAGAGACCTGGGGGAAACTG
* *
3616579 TAAGGCTTACCCTTGCACACAGCAAAGGA-ACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAACAAAAGAGACCTGGGGGAAACTG
* * *
3616623 TAAGGCTTACCCTTGCATACAACAAATG-GACCTGGGGAAAACTG
1 TAAGGCTTACCCTTGCACACAACAAAAGAGACCTGGGGGAAACTG
* * *
3616667 TAAGGCTTACCCTTACACACATC-AAAGGGACCTGGGGG-AACTG
1 TAAGGCTTACCCTTGCACACAACAAAAGAGACCTGGGGGAAACTG
3616710 TAA
1 TAA
3616713 CGGTAATTAA
Statistics
Matches: 231, Mismatches: 26, Indels: 15
0.85 0.10 0.06
Matches are distributed among these distances:
41 3 0.01
42 35 0.15
43 32 0.14
44 158 0.68
45 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (45 bp):
TAAGGCTTACCCTTGCACACAACAAAAGAGACCTGGGGGAAACTG
Found at i:3616616 original size:88 final size:88
Alignment explanation
Indices: 3616439--3616712 Score: 428
Period size: 88 Copynumber: 3.1 Consensus size: 88
3616429 AAAAGAGTCT
*
3616439 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCT--GGGAAACTGTAAGGCTTACC
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGGAAACTGTAAGGCTTACC
3616502 CTTACACACAACAAAGGGACCTG
66 CTTACACACAACAAAGGGACCTG
* * *
3616525 GGGGAAACTGTAAGACTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAAGTGTAAGGCTTACC
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGGAAACTGTAAGGCTTACC
* * *
3616590 CTTGCACACAGCAAAGGAACCTG
66 CTTACACACAACAAAGGGACCTG
* * *
3616613 GGGGAAACTGTAAGGCTTACCCTTGCATACAACAAATGGACCTGGGGAAAACTGTAAGGCTTACC
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGGAAACTGTAAGGCTTACC
*
3616678 CTTACACACATCAAAGGGACCTG
66 CTTACACACAACAAAGGGACCTG
3616701 GGGG-AACTGTAA
1 GGGGAAACTGTAA
3616713 CGGTAATTAA
Statistics
Matches: 170, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
86 40 0.24
87 8 0.05
88 122 0.72
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.17
Consensus pattern (88 bp):
GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGGAAACTGTAAGGCTTACC
CTTACACACAACAAAGGGACCTG
Found at i:3616665 original size:132 final size:130
Alignment explanation
Indices: 3616439--3616712 Score: 442
Period size: 132 Copynumber: 2.1 Consensus size: 130
3616429 AAAAGAGTCT
3616439 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACCCT
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACCCT
* *
3616504 TACACACAACAAAGGGACCTGGGGGAAACTGTAAGACTTACCCTTGCACACAGCAAAGGGACCTG
66 TACACACAACAAAGGGACCTGGGGAAAACTGTAAGACTTACCCTTACACACAGCAAAGGGACCTG
* *
3616569 GGGGAAAGTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTGTAAGGCTTACC
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCT--GGGAAACTGTAAGGCTTACC
* * * * *
3616634 CTTGCATACAACAAATGGACCTGGGGAAAACTGTAAGGCTTACCCTTACACACATCAAAGGGACC
64 CTTACACACAACAAAGGGACCTGGGGAAAACTGTAAGACTTACCCTTACACACAGCAAAGGGACC
3616699 TG
129 TG
3616701 GGGG-AACTGTAA
1 GGGGAAACTGTAA
3616713 CGGTAATTAA
Statistics
Matches: 132, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
130 41 0.31
131 7 0.05
132 84 0.64
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.17
Consensus pattern (130 bp):
GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACCCT
TACACACAACAAAGGGACCTGGGGAAAACTGTAAGACTTACCCTTACACACAGCAAAGGGACCTG
Found at i:3622364 original size:65 final size:65
Alignment explanation
Indices: 3622260--3622390 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
3622250 GAGATAATGT
*
3622260 GAGATAATAATTATGAATAAAGAATACATAAATTTATATGGAAATTTTAAAATAGAAAAGATACG
1 GAGATAATAATCATGAATAAAGAATACATAAATTTATATGGAAATTTTAAAATAGAAAAGATACG
*
3622325 GAGATAATAATCATGAATAAAGAATACATAAATTTATATGTAAATTTTAAAATAGAAAAGATACG
1 GAGATAATAATCATGAATAAAGAATACATAAATTTATATGGAAATTTTAAAATAGAAAAGATACG
3622390 G
1 G
3622391 TAGAAAAGTT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (65 bp):
GAGATAATAATCATGAATAAAGAATACATAAATTTATATGGAAATTTTAAAATAGAAAAGATACG
Found at i:3634331 original size:20 final size:20
Alignment explanation
Indices: 3634293--3634342 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3634283 TTTTCTGGGC
3634293 AGTACCGATACTTTATGAAT
1 AGTACCGATACTTTATGAAT
* *
3634313 AGTACTGATACTATT-TGAAC
1 AGTACCGATACT-TTATGAAT
*
3634333 AATACCGATA
1 AGTACCGATA
3634343 TTGTTCACGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (20 bp):
AGTACCGATACTTTATGAAT
Found at i:3645020 original size:21 final size:21
Alignment explanation
Indices: 3644996--3645046 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
3644986 GCTTTACCAG
3644996 TATCGATACTATGCTTCATGA
1 TATCGATACTATGCTTCATGA
* *
3645017 TATCGATACTATGCTTTATGG
1 TATCGATACTATGCTTCATGA
3645038 TATCGATAC
1 TATCGATAC
3645047 CACTGTGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (21 bp):
TATCGATACTATGCTTCATGA
Found at i:3655632 original size:45 final size:45
Alignment explanation
Indices: 3655607--3655823 Score: 281
Period size: 45 Copynumber: 4.8 Consensus size: 45
3655597 TATAACATCA
* * **
3655607 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAATATACT
1 TTTCTGTTGATAATGTACCCATATGCATTTCAACTCTAGCATACT
* * * ** * * *
3655652 TGTATGTTGATAATGTACCAATATATATCTCAACCCTAGTATACT
1 TTTCTGTTGATAATGTACCCATATGCATTTCAACTCTAGCATACT
* *
3655697 TTTATGTTGATAATGTACCTATATGCATTTCAACTCTAGCATACT
1 TTTCTGTTGATAATGTACCCATATGCATTTCAACTCTAGCATACT
*
3655742 TTTCTGTTGATAATGTATCCATATGCATTTCAACTCTAGCATACT
1 TTTCTGTTGATAATGTACCCATATGCATTTCAACTCTAGCATACT
* *
3655787 TTTCTGTTGATAATGCACCCATAAGCATTTCAACTCT
1 TTTCTGTTGATAATGTACCCATATGCATTTCAACTCT
3655824 GGTATCCTTT
Statistics
Matches: 149, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 149 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (45 bp):
TTTCTGTTGATAATGTACCCATATGCATTTCAACTCTAGCATACT
Found at i:3655855 original size:90 final size:90
Alignment explanation
Indices: 3655611--3655860 Score: 193
Period size: 90 Copynumber: 2.8 Consensus size: 90
3655601 ACATCATTTC
* * ** * **** *
3655611 TGTTGATAATGCACCCATATGCATTTCAACTATAATATA-CTTGTATGTTGATAATGTA-CCAAT
1 TGTTGATAATGCACCCATAAGCATTTCAACTCTAGCATACCTT-TCTACCAATAATGCATCC-AT
* * *
3655674 ATATATCTCAACCCTAGTATACTTTTA
64 ATACATTTCAACCCTAGCATACTTTTA
* * * * **** *
3655701 TGTTGATAATGTACCTATATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGTATCCATAT
1 TGTTGATAATGCACCCATAAGCATTTCAACTCTAGCATACCTTTCTACCAATAATGCATCCATAT
* * *
3655766 GCATTTCAACTCTAGCATACTTTTC
66 ACATTTCAACCCTAGCATACTTTTA
* *
3655791 TGTTGATAATGCACCCATAAGCATTTCAACTCTGGTAT-CCTTTCATACCAATAATGCA-CACAT
1 TGTTGATAATGCACCCATAAGCATTTCAACTCTAGCATACCTTTC-TACCAATAATGCATC-CAT
3655854 ATACATT
64 ATACATT
3655861 ATTCTTTTAT
Statistics
Matches: 131, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
89 6 0.05
90 121 0.92
91 4 0.03
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.38
Consensus pattern (90 bp):
TGTTGATAATGCACCCATAAGCATTTCAACTCTAGCATACCTTTCTACCAATAATGCATCCATAT
ACATTTCAACCCTAGCATACTTTTA
Found at i:3656381 original size:22 final size:20
Alignment explanation
Indices: 3656343--3656420 Score: 88
Period size: 22 Copynumber: 3.8 Consensus size: 20
3656333 TGGCCGTTCA
3656343 GTATCGATACCCCTACTAGG
1 GTATCGATACCCCTACTAGG
*
3656363 GTATCGATACTACCCTACTATG
1 GTATCGATAC--CCCTACTAGG
*
3656385 GTATCGATACCCCTTACCA--
1 GTATCGATACCCC-TACTAGG
3656404 GTATCGATACCCTCTAC
1 GTATCGATACCC-CTAC
3656421 CATTATCAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
19 15 0.29
20 14 0.27
21 4 0.08
22 19 0.37
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (20 bp):
GTATCGATACCCCTACTAGG
Found at i:3656407 original size:19 final size:18
Alignment explanation
Indices: 3656341--3656433 Score: 78
Period size: 19 Copynumber: 4.7 Consensus size: 18
3656331 TCTGGCCGTT
3656341 CAGTATCGATACCCCTAC
1 CAGTATCGATACCCCTAC
*
3656359 TAGGGTATCGATACTACCCTAC
1 CA--GTATCGATAC--CCCTAC
*
3656381 TATGGTATCGATACCCCTTAC
1 CA--GTATCGATACCCC-TAC
3656402 CAGTATCGATACCCTCTAC
1 CAGTATCGATACCC-CTAC
* *
3656421 CATTATCAATACC
1 CAGTATCGATACC
3656434 AAAATTAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
18 1 0.02
19 26 0.41
20 14 0.22
21 4 0.06
22 19 0.30
ACGTcount: A:0.28, C:0.32, G:0.12, T:0.28
Consensus pattern (18 bp):
CAGTATCGATACCCCTAC
Found at i:3656496 original size:22 final size:21
Alignment explanation
Indices: 3656461--3656515 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
3656451 GGCCCAGAAT
*
3656461 CGATACCCT-TACTATGGTAT
1 CGATACCCTATACTATGGTAC
*
3656481 CTATACCACTATACTATGGTAC
1 CGATACC-CTATACTATGGTAC
3656503 CGATACCCCTATA
1 CGATA-CCCTATA
3656516 TGGTATTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 6 0.21
21 2 0.07
22 19 0.66
23 2 0.07
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.31
Consensus pattern (21 bp):
CGATACCCTATACTATGGTAC
Found at i:3656544 original size:29 final size:29
Alignment explanation
Indices: 3656511--3656569 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3656501 ACCGATACCC
3656511 CTATATGGTATTGATACCAAAACTAGGTT
1 CTATATGGTATTGATACCAAAACTAGGTT
3656540 CTATATGGTATTGATACCAAAACTAGGTT
1 CTATATGGTATTGATACCAAAACTAGGTT
3656569 C
1 C
3656570 GATGTTACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (29 bp):
CTATATGGTATTGATACCAAAACTAGGTT
Found at i:3661977 original size:3 final size:3
Alignment explanation
Indices: 3661969--3662035 Score: 68
Period size: 3 Copynumber: 23.0 Consensus size: 3
3661959 TCATTTCGTT
** * *
3661969 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TAA ATA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3662016 TTA -TA TATA TTA -TA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA
3662036 ATAAATAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 6 0.12
3 43 0.83
4 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:3661991 original size:15 final size:16
Alignment explanation
Indices: 3661971--3662015 Score: 76
Period size: 15 Copynumber: 2.9 Consensus size: 16
3661961 ATTTCGTTTT
3661971 ATTATTATTATTA-AA
1 ATTATTATTATTATAA
3661986 ATTATTATTATTATAA
1 ATTATTATTATTATAA
3662002 A-TATTATTATTATA
1 ATTATTATTATTATA
3662016 TTATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 26 0.90
16 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTATTATTATTATAA
Found at i:3663444 original size:351 final size:351
Alignment explanation
Indices: 3662793--3663494 Score: 1244
Period size: 351 Copynumber: 2.0 Consensus size: 351
3662783 ACCCTCATCA
* *
3662793 AAACGACACCGTTTTGATGAAATGTATATGCGTAATTTAGGGGATGGTCTAATTACGTCCGCAGT
1 AAACGACACCGTTTTGATGAAAGGTATATGCGTAATTTAGGGGATGGTCCAATTACGTCCGCAGT
*
3662858 GTTTAAAGTTTGTAATCTTTACGATTTAGTCACTGTAATTAATTTCAATATATTTTAATTTGAAT
66 GTTTAAAGTTTGTAATCTTTACGATTTAGTCACTATAATTAATTTCAATATATTTTAATTTGAAT
* *
3662923 TCTTAATTTGATTTACTTTATACTTTAGTCCCTTACCATATTTATATAACATTTAGGATAAATAA
131 TCTTAATTTCATTTACTATATACTTTAGTCCCTTACCATATTTATATAACATTTAGGATAAATAA
3662988 CCTATTTAGCCCCTATTAATTTTAATAAATTTTATTTAATCCCAAATAATTAATATAGGATAAAT
196 CCTATTTAGCCCCTATTAATTTTAATAAATTTTATTTAATCCCAAATAATTAATATAGGATAAAT
* *
3663053 CACACTGCTAATACTTAGTTTTTATAATATTCATAATTAGAGCCTTTAATTTTAATATGTTATTT
261 CACACTGCTAATACTTAGTTTTTATAATATCCAGAATTAGAGCCTTTAATTTTAATATGTTATTT
3663118 TAATAACTTTCATTTTACAATAAGTT
326 TAATAACTTTCATTTTACAATAAGTT
** * *
3663144 AAACGACGTCGTTTTGAT-AAAGGCTATATGCGTAATTTAGGGGATGGTCCAATTACGTCTGTAG
1 AAACGACACCGTTTTGATGAAAGG-TATATGCGTAATTTAGGGGATGGTCCAATTACGTCCGCAG
* *
3663208 TGTTTAAAGTTTGTAATCTTTACGATTTAGTCACTATAATTAATTTCAATATGTTTTAATTTGAT
65 TGTTTAAAGTTTGTAATCTTTACGATTTAGTCACTATAATTAATTTCAATATATTTTAATTTGAA
* * *
3663273 TTCTTAATTTCATTTACTATATACTTTAGTCCCTTGCCATGTTTATATAATATTTAGGATAAATA
130 TTCTTAATTTCATTTACTATATACTTTAGTCCCTTACCATATTTATATAACATTTAGGATAAATA
3663338 ACCTATTTAGCCCCTATTAATTTTAATAAATTTTATTTAATCCCAAATAATTAATATAGGATAAA
195 ACCTATTTAGCCCCTATTAATTTTAATAAATTTTATTTAATCCCAAATAATTAATATAGGATAAA
3663403 TCACACTGCTAATACTTAGTTTTTATAATATCCAGAATTAGAGCCTTTAATTTTAATATGTTATT
260 TCACACTGCTAATACTTAGTTTTTATAATATCCAGAATTAGAGCCTTTAATTTTAATATGTTATT
3663468 TTAATAACTTTCATTTTACAATAAGTT
325 TTAATAACTTTCATTTTACAATAAGTT
3663495 TTGTTATTTT
Statistics
Matches: 334, Mismatches: 16, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
350 4 0.01
351 330 0.99
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (351 bp):
AAACGACACCGTTTTGATGAAAGGTATATGCGTAATTTAGGGGATGGTCCAATTACGTCCGCAGT
GTTTAAAGTTTGTAATCTTTACGATTTAGTCACTATAATTAATTTCAATATATTTTAATTTGAAT
TCTTAATTTCATTTACTATATACTTTAGTCCCTTACCATATTTATATAACATTTAGGATAAATAA
CCTATTTAGCCCCTATTAATTTTAATAAATTTTATTTAATCCCAAATAATTAATATAGGATAAAT
CACACTGCTAATACTTAGTTTTTATAATATCCAGAATTAGAGCCTTTAATTTTAATATGTTATTT
TAATAACTTTCATTTTACAATAAGTT
Found at i:3663647 original size:2 final size:2
Alignment explanation
Indices: 3663635--3663665 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3663625 TATATTAGTC
3663635 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3663666 TTGTTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3664663 original size:45 final size:45
Alignment explanation
Indices: 3664613--3664890 Score: 315
Period size: 45 Copynumber: 6.2 Consensus size: 45
3664603 AATACATCAT
* * * *
3664613 TATGCACTTTAAACTATAACATA-TTTTCTGTTAATAATGCACCCA
1 TATGCA-TTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
* * * * * *
3664658 TATGCATTTTAACTATAGTATACTTCTATGTTGATAATGTACCCA
1 TATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
* * * * * * *
3664703 TATACATCTCAACCCTAGTATAATTTTATGTTGATAATGTACCCA
1 TATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
*
3664748 TATACATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
1 TATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
*
3664793 TATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACTCA
1 TATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
* * * ***
3664838 TATGCATTTCAACTCTGGCATCCTTTCCTGCCAATAATGCACCCA
1 TATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
3664883 TATGCATT
1 TATGCATT
3664891 ATTCTTTTAT
Statistics
Matches: 203, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
44 13 0.06
45 190 0.94
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (45 bp):
TATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
Found at i:3665415 original size:22 final size:20
Alignment explanation
Indices: 3665371--3665425 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
3665361 TGGCCCTTCA
3665371 GTATCGATACCCCTACAAGG
1 GTATCGATACCCCTACAAGG
* *
3665391 GTATCGATACTACCCTACTATG
1 GTATCGATAC--CCCTACAAGG
*
3665413 GTATTGATACCCC
1 GTATCGATACCCC
3665426 CAACCAGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.43
22 17 0.57
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.27
Consensus pattern (20 bp):
GTATCGATACCCCTACAAGG
Found at i:3665515 original size:22 final size:21
Alignment explanation
Indices: 3665470--3665524 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
3665460 GGCCCAGTAT
*
3665470 CGATACCCT-TACCATGGTAT
1 CGATACCCTATACCATGGTAC
*
3665490 CGATACCACTATACTATGGTAC
1 CGATACC-CTATACCATGGTAC
3665512 CGATACCCCTATA
1 CGATA-CCCTATA
3665525 TGGTATCGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 7 0.23
21 2 0.07
22 19 0.63
23 2 0.07
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (21 bp):
CGATACCCTATACCATGGTAC
Found at i:3665537 original size:95 final size:96
Alignment explanation
Indices: 3665369--3665595 Score: 269
Period size: 95 Copynumber: 2.4 Consensus size: 96
3665359 TCTGGCCCTT
* * * * ** **
3665369 CAGTATCGATACCCCTACAAGGGTATCGATACTACCCTACTATGGTATTGATACCCCCAACCAGT
1 CAGTATCGATACCCTTACCATGGTATCGATACCACTATACTATGGTACCGATACCCCCAACCAGT
**
3665434 ATCAATACCAAAATTAGATTCAATG-TGGCC
66 ATCAATACCAAAATTAGATTCAATGTTACCC
* **
3665464 CAGTATCGATACCCTTACCATGGTATCGATACCACTATACTATGGTACCGATACCCCTATA-TGG
1 CAGTATCGATACCCTTACCATGGTATCGATACCACTATACTATGGTACCGATACCCCCA-ACCAG
* * *
3665528 TATCGATACCAAAATTAGGTTCGATGTTACCC
65 TATCAATACCAAAATTAGATTCAATGTTACCC
* *
3665560 CGGTATCGATACCCTCACCATGGTATCGATACCACT
1 CAGTATCGATACCCTTACCATGGTATCGATACCACT
3665596 TCGTTAGGTG
Statistics
Matches: 112, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
95 74 0.66
96 38 0.34
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (96 bp):
CAGTATCGATACCCTTACCATGGTATCGATACCACTATACTATGGTACCGATACCCCCAACCAGT
ATCAATACCAAAATTAGATTCAATGTTACCC
Found at i:3666457 original size:10 final size:10
Alignment explanation
Indices: 3666444--3666469 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3666434 TGCATTCATT
3666444 TTGCATTCCA
1 TTGCATTCCA
3666454 TTGCATTCCA
1 TTGCATTCCA
3666464 TTGCAT
1 TTGCAT
3666470 GGCATATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.27, G:0.12, T:0.42
Consensus pattern (10 bp):
TTGCATTCCA
Found at i:3667092 original size:3 final size:3
Alignment explanation
Indices: 3667084--3667121 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3667074 TCCTCGTAGC
3667084 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3667122 GTATTAAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3672034 original size:13 final size:13
Alignment explanation
Indices: 3671971--3672034 Score: 51
Period size: 13 Copynumber: 5.0 Consensus size: 13
3671961 TTAATATTAC
*
3671971 TTTTGAAAAGTGA
1 TTTTGAAAAGTGT
3671984 TTTTGAAAAGTG-
1 TTTTGAAAAGTGT
* * * **
3671996 TTGTAAACAAATAC
1 TTTTGAA-AAGTGT
3672010 TTTTG-AAAGTGT
1 TTTTGAAAAGTGT
3672022 TTTTGAAAAGTGT
1 TTTTGAAAAGTGT
3672035 AGTTTAAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
12 13 0.33
13 23 0.59
14 3 0.08
ACGTcount: A:0.36, C:0.03, G:0.20, T:0.41
Consensus pattern (13 bp):
TTTTGAAAAGTGT
Found at i:3673814 original size:31 final size:31
Alignment explanation
Indices: 3673779--3673889 Score: 98
Period size: 31 Copynumber: 3.4 Consensus size: 31
3673769 ATAGGTCCAT
*
3673779 AAGGAATTACCAGTCGATGTTGAACCTATAA
1 AAGGAATTACCAGTCGATGCTGAACCTATAA
* * * *
3673810 AAGGAATTACCA-ACAACGACTGAACCTGCAAGAGA
1 AAGGAATTACCAGTCGATG-CTGAACCT---ATA-A
* *
3673845 TAAGGAATTACCAGTCGGTGCTGAACCTATAC
1 -AAGGAATTACCAGTCGATGCTGAACCTATAA
3673877 AAGGAATTACCAG
1 AAGGAATTACCAG
3673890 CAGCGACTGA
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
30 3 0.05
31 32 0.52
33 2 0.03
34 2 0.03
35 1 0.02
36 20 0.32
37 2 0.03
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.20
Consensus pattern (31 bp):
AAGGAATTACCAGTCGATGCTGAACCTATAA
Found at i:3673885 original size:67 final size:67
Alignment explanation
Indices: 3673777--3673903 Score: 209
Period size: 67 Copynumber: 1.9 Consensus size: 67
3673767 CCATAGGTCC
*
3673777 ATAAGGAATTACCAGTCGATGTTGAACCTATAAAAGGAATTACCAACAACGACTGAACCTGCAAG
1 ATAAGGAATTACCAGTCGATGCTGAACCTATAAAAGGAATTACCAACAACGACTGAACCTGCAAG
3673842 AG
66 AG
* * * *
3673844 ATAAGGAATTACCAGTCGGTGCTGAACCTATACAAGGAATTACCAGCAGCGACTGAACCT
1 ATAAGGAATTACCAGTCGATGCTGAACCTATAAAAGGAATTACCAACAACGACTGAACCT
3673904 ACCAGTCTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 55 1.00
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (67 bp):
ATAAGGAATTACCAGTCGATGCTGAACCTATAAAAGGAATTACCAACAACGACTGAACCTGCAAG
AG
Found at i:3673900 original size:31 final size:31
Alignment explanation
Indices: 3673799--3673904 Score: 97
Period size: 31 Copynumber: 3.3 Consensus size: 31
3673789 CAGTCGATGT
* *
3673799 TGAACCTATAAAAGGAATTACCAACAACGAC
1 TGAACCTATAAAAGGAATTACCAGCAGCGAC
* * *
3673830 TGAACCTGCAAGAGATAAGGAATTACCAGTCGGTG-C
1 TGAACCT---ATA-A-AAGGAATTACCAG-CAGCGAC
*
3673866 TGAACCTATACAAGGAATTACCAGCAGCGAC
1 TGAACCTATAAAAGGAATTACCAGCAGCGAC
3673897 TGAACCTA
1 TGAACCTA
3673905 CCAGTCTTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
30 3 0.05
31 29 0.49
33 2 0.03
34 2 0.03
35 1 0.02
36 20 0.34
37 2 0.03
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.18
Consensus pattern (31 bp):
TGAACCTATAAAAGGAATTACCAGCAGCGAC
Found at i:3678200 original size:21 final size:23
Alignment explanation
Indices: 3678157--3678211 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
3678147 TATCTATATT
3678157 ATTATTATTATAATTATAATAATA
1 ATTATTATTATAATTAT-ATAATA
*
3678181 ATTATTATT-TTATTAT-TAATA
1 ATTATTATTATAATTATATAATA
*
3678202 AATATTATTA
1 ATTATTATTA
3678212 CAGGCCCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 13 0.46
23 6 0.21
24 9 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTATTATTATAATTATATAATA
Found at i:3678211 original size:3 final size:3
Alignment explanation
Indices: 3678144--3678198 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
3678134 TTCATTTTAA
* * * *
3678144 TAT TAT CTA- TAT TAT TAT TAT TAT AAT TAT AAT AAT AAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3678189 T-T TAT TAT TA
1 TAT TAT TAT TA
3678199 ATAAATATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 4 0.09
3 39 0.87
4 2 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:3679945 original size:23 final size:25
Alignment explanation
Indices: 3679910--3679958 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
3679900 CCTTTTCTAA
*
3679910 TATTTTTAAATAAA-TAA-ATATTT
1 TATTTATAAATAAATTAATATATTT
*
3679933 TATTTATATATAAATTAATATATTT
1 TATTTATAAATAAATTAATATATTT
3679958 T
1 T
3679959 TCATAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.55
24 3 0.14
25 7 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TATTTATAAATAAATTAATATATTT
Found at i:3680278 original size:12 final size:12
Alignment explanation
Indices: 3680240--3680278 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3680230 TGGCGACTCC
3680240 CAAATTATTTTT
1 CAAATTATTTTT
* *
3680252 AAAACTATTTATT
1 CAAATTATTT-TT
3680265 CAAATTATTTTT
1 CAAATTATTTTT
3680277 CA
1 CA
3680279 CGCCAAGTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (12 bp):
CAAATTATTTTT
Found at i:3680456 original size:28 final size:26
Alignment explanation
Indices: 3680425--3680491 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 26
3680415 TAATTCTTTC
3680425 TTTTCAAAATTTTTATATATACTTATT
1 TTTTCAAAATTTTTATATATA-TTATT
* *
3680452 ATTTTCATAA-TATTA-ATATATTATT
1 -TTTTCAAAATTTTTATATATATTATT
*
3680477 TTTT-AATATTTTTAT
1 TTTTCAAAATTTTTAT
3680492 TTTATTTTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
23 2 0.06
24 8 0.25
25 5 0.16
26 5 0.16
27 4 0.12
28 8 0.25
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTCAAAATTTTTATATATATTATT
Found at i:3683806 original size:15 final size:15
Alignment explanation
Indices: 3683786--3683817 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3683776 GATCAATACC
3683786 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
3683801 TTTTGCATACATTCA
1 TTTTGCATACATGCA
3683816 TT
1 TT
3683818 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:3685701 original size:33 final size:33
Alignment explanation
Indices: 3685659--3685725 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
3685649 TCATCAAGAG
3685659 AAAGGGCATGAAATTCAACTATGTCCTGAATTT
1 AAAGGGCATGAAATTCAACTATGTCCTGAATTT
3685692 AAAGGGCATGAAATTCAACTATGTCCTGAATTT
1 AAAGGGCATGAAATTCAACTATGTCCTGAATTT
3685725 A
1 A
3685726 GGGATTTGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (33 bp):
AAAGGGCATGAAATTCAACTATGTCCTGAATTT
Found at i:3687642 original size:9 final size:9
Alignment explanation
Indices: 3687628--3687659 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
3687618 AAATGGCAAT
3687628 CATTCTTTA
1 CATTCTTTA
3687637 CATTCTTTA
1 CATTCTTTA
3687646 CATTCTTTA
1 CATTCTTTA
3687655 CATTC
1 CATTC
3687660 ATTATTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.22, C:0.25, G:0.00, T:0.53
Consensus pattern (9 bp):
CATTCTTTA
Found at i:3692890 original size:114 final size:113
Alignment explanation
Indices: 3692693--3693237 Score: 839
Period size: 114 Copynumber: 4.8 Consensus size: 113
3692683 TAGCAAAGAT
* **
3692693 TCAAATCCATCAC--AATGGATCAGCTTTTCCAGTTAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
3692756 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
3692804 TCAAATCCATCACTTAATGGATCAGCTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGC-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
3692869 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
3692918 TCAAATCCATCACTTGATGGATCAGCTTTTTCCAGAGAAAGTTCATAATGATAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGC-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
*
3692983 AAGAAGGAAAAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
3693032 TCAAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * *
3693097 AGAAGAAAGAAGAAATT-ATAATGAGAAGAACTTATTCAACTTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * ** * ** *
3693144 TTAAATTCATCACTCGGTGGATCAGCAATGCCAGTTAGAGTTCATAATGAGAAG-ACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
3693208 AGAAGAAAGAAGAAATT-ATAATGAGAAGAA
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAA
3693238 CGAAGAAATT
Statistics
Matches: 408, Mismatches: 23, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
111 53 0.13
112 70 0.17
113 64 0.16
114 221 0.54
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:3693244 original size:134 final size:136
Alignment explanation
Indices: 3693097--3693374 Score: 488
Period size: 134 Copynumber: 2.1 Consensus size: 136
3693087 ACTCATCTGA
*
3693097 AGAAGAAAGAAGAAATTATAATGAGAAGAACTTATTCAACTTTTTGCTTAAATTCATCACTCGGT
1 AGAAGAACGAAGAAATTATAATGAGAAGAACTTATTCAACTTTTTGCTTAAATTCATCACTCGGT
* * *
3693162 GGATCAGCAATGCCAGTTAGAGTTCATAATGAGAAG-ACTCATCTGAAGAAGAAAGAAGAAATT-
66 GGATCAGCAATGCCAGTTAGAGTTAATAATAAGAAGAACTCATCTGAAGAAGAAAAAAGAAATTC
3693225 ATAATG
131 ATAATG
3693231 AGAAGAACGAAGAAATTATAATGAGAAGAACTTATTCAACTTTTTGCTTAAATTCATCACTCGGT
1 AGAAGAACGAAGAAATTATAATGAGAAGAACTTATTCAACTTTTTGCTTAAATTCATCACTCGGT
* *
3693296 GGATCAGCAATGCCAGTTAGAGTTAATAATAAGAAGAACTCATCTGAAGAATAAAAAAGAAGTTC
66 GGATCAGCAATGCCAGTTAGAGTTAATAATAAGAAGAACTCATCTGAAGAAGAAAAAAGAAATTC
3693361 ATAATG
131 ATAATG
3693367 AGAAGAAC
1 AGAAGAAC
3693375 TTATTCAACT
Statistics
Matches: 136, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
134 98 0.72
135 24 0.18
136 14 0.10
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.26
Consensus pattern (136 bp):
AGAAGAACGAAGAAATTATAATGAGAAGAACTTATTCAACTTTTTGCTTAAATTCATCACTCGGT
GGATCAGCAATGCCAGTTAGAGTTAATAATAAGAAGAACTCATCTGAAGAAGAAAAAAGAAATTC
ATAATG
Found at i:3693261 original size:23 final size:23
Alignment explanation
Indices: 3693208--3693261 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
3693198 ACTCATCTGA
*
3693208 AGAAGAAAGAAGAAATTATAATG
1 AGAAGAACGAAGAAATTATAATG
3693231 AGAAGAACGAAGAAATTATAATG
1 AGAAGAACGAAGAAATTATAATG
3693254 AGAAGAAC
1 AGAAGAAC
3693262 TTATTCAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.59, C:0.04, G:0.22, T:0.15
Consensus pattern (23 bp):
AGAAGAACGAAGAAATTATAATG
Found at i:3693373 original size:113 final size:112
Alignment explanation
Indices: 3693231--3693595 Score: 523
Period size: 113 Copynumber: 3.2 Consensus size: 112
3693221 AATTATAATG
*
3693231 AGAAGAACGAAGAAATTATAATGAGAAGAACTTATTCAACTTTTTGCTTAAATTCATCACTCGGT
1 AGAAGAAAGAAGAAATTATAATGAGAAGAACTTATTCAACTTTTTGCTTAAATTCATCACTCGGT
* *
3693296 GGATCAGCAATGCCAGTTAGAGTTAATAATAAGAAGAACTCATCTGA
66 GGATCAGCAATGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
* * *
3693343 AGAATAAAAAAGAAGTTCATAATGAGAAGAACTTATTCAACTTTTTGCTTAAATTCATCACTCGG
1 AGAAGAAAGAAGAAATT-ATAATGAGAAGAACTTATTCAACTTTTTGCTTAAATTCATCACTCGG
3693408 TGGATCAGCAATGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
65 TGGATCAGCAATGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
* * * * *
3693456 AGAGGAAAGAAGAAATTATAATGAGAAGAACTTATTCAACTTTTTTCTTAAATTCATTACTTGAT
1 AGAAGAAAGAAGAAATTATAATGAGAAGAACTTATTCAACTTTTTGCTTAAATTCATCACTCGGT
* ** * ** * *
3693521 GGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGA
66 GGATCAGCAATGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
* *
3693568 AGAAGGAAGAAGAAGTTCATAATGAGAA
1 AGAAGAAAGAAGAAATT-ATAATGAGAA
3693596 AAGCTTGTTC
Statistics
Matches: 226, Mismatches: 25, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
112 110 0.49
113 116 0.51
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (112 bp):
AGAAGAAAGAAGAAATTATAATGAGAAGAACTTATTCAACTTTTTGCTTAAATTCATCACTCGGT
GGATCAGCAATGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
Found at i:3694012 original size:24 final size:24
Alignment explanation
Indices: 3693966--3694023 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
3693956 CTATATTATT
3693966 ATTATTATTATTATAATTATAATA
1 ATTATTATTATTATAATTATAATA
*
3693990 ATTATTATTATT-TTATTATTAATA
1 ATTATTATTATTATAATTA-TAATA
*
3694014 AATATTATTA
1 ATTATTATTA
3694024 CATGCCCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 5 0.16
24 26 0.84
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTATTATTATTATAATTATAATA
Found at i:3694023 original size:3 final size:3
Alignment explanation
Indices: 3693950--3694010 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
3693940 TTCATTTTAA
* * *
3693950 TAT TAT CTA- TAT TAT TAT TAT TAT TAT TAT AAT TAT AAT AAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3693995 TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TA
3694011 ATAAATATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
2 4 0.08
3 45 0.88
4 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3695705 original size:112 final size:110
Alignment explanation
Indices: 3695560--3695769 Score: 253
Period size: 111 Copynumber: 1.9 Consensus size: 110
3695550 CCTGTTTTAA
* * * *
3695560 TATTTTTTTTTCAATATTAAGAAAGGGCAGTCTTAAAACAACTGGATGTCTATTTTCTGATATTT
1 TATTTTTTTTTCAATATGAAGAAAGAGCAGTCTTAAAACAACTAGAAGTC-ATTTTCTGATATTT
* *
3695625 TTAAATAAATAAATATCCTATTT-TATATTAATTGTTTTAATTATT
65 CTAAATAAATAAATATCCTATTTATATATAAATTGTTTTAATTATT
* ** * *
3695670 TATTTATTTTTT-AATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCTGATAT
1 TATTT-TTTTTTCAATAT-GAAG-AAAGAGCAGTCTTAAAACAACTAGAAGTCATTTTCTGATAT
**
3695734 TTCTAAATAAATAAATATTTTATTTATATATAAATT
63 TTCTAAATAAATAAATATCCTATTTATATATAAATT
3695770 AATATATTTT
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
110 10 0.12
111 42 0.51
112 31 0.37
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.46
Consensus pattern (110 bp):
TATTTTTTTTTCAATATGAAGAAAGAGCAGTCTTAAAACAACTAGAAGTCATTTTCTGATATTTC
TAAATAAATAAATATCCTATTTATATATAAATTGTTTTAATTATT
Found at i:3695766 original size:23 final size:25
Alignment explanation
Indices: 3695731--3695779 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
3695721 CCTTTTCTGA
*
3695731 TATTTCTAAATAAA-TAA-ATATTT
1 TATTTATAAATAAATTAATATATTT
*
3695754 TATTTATATATAAATTAATATATTT
1 TATTTATAAATAAATTAATATATTT
3695779 T
1 T
3695780 TCATAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.55
24 3 0.14
25 7 0.32
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
TATTTATAAATAAATTAATATATTT
Found at i:3696446 original size:20 final size:20
Alignment explanation
Indices: 3696424--3696621 Score: 191
Period size: 20 Copynumber: 9.8 Consensus size: 20
3696414 TTCACGTTGC
*
3696424 ATTTCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATTTTCA
* *
3696444 ATTTCGCGTTGCGATAGTTGA
1 ATTTCGCGTTGCGAT-TTTCA
** * *
3696465 AAATCGCGTTGCGATAGTTGA
1 ATTTCGCGTTGCGAT-TTTCA
** * *
3696486 AAATCGCGTTGCAATTTTCC
1 ATTTCGCGTTGCGATTTTCA
* *
3696506 ATTTCGCGTTGCGATAGTTGA
1 ATTTCGCGTTGCGAT-TTTCA
** * *
3696527 AAATCGTGTTGC-ACTTTTCC
1 ATTTCGCGTTGCGA-TTTTCA
3696547 ATTTCGCGTTGCGATTTTCA
1 ATTTCGCGTTGCGATTTTCA
3696567 ATTTCGCGTTGCGATTTTCA
1 ATTTCGCGTTGCGATTTTCA
*
3696587 ATTTCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATTTTCA
3696607 ATTTCGCGTTGCGAT
1 ATTTCGCGTTGCGAT
3696622 AGTCTACAGT
Statistics
Matches: 148, Mismatches: 26, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
20 100 0.68
21 48 0.32
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (20 bp):
ATTTCGCGTTGCGATTTTCA
Found at i:3696473 original size:21 final size:21
Alignment explanation
Indices: 3696447--3696538 Score: 114
Period size: 21 Copynumber: 4.4 Consensus size: 21
3696437 ATTTTCCATT
3696447 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
3696468 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
3696489 TCGCGTTGCAAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
3696509 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
3696530 TCGTGTTGC
1 TCGCGTTGC
3696539 ACTTTTCCAT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 14 0.25
21 43 0.75
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:3696503 original size:62 final size:61
Alignment explanation
Indices: 3696427--3696581 Score: 213
Period size: 62 Copynumber: 2.5 Consensus size: 61
3696417 ACGTTGCATT
*
3696427 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGA-TAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGC-ACT-GTTCAAAA
* * * * **
3696489 TCGCGTTGCAATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGTGTTGCACTTTTCCATT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCACTGTTCAAAA
*
3696550 TCGCGTTGCGATTTTCAATTTCGCGTTGCGAT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
3696582 TTTCAATTTC
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
61 34 0.41
62 49 0.59
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (61 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCACTGTTCAAAA
Found at i:3696513 original size:41 final size:41
Alignment explanation
Indices: 3696468--3696601 Score: 189
Period size: 41 Copynumber: 3.3 Consensus size: 41
3696458 TAGTTGAAAA
3696468 TCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATT
* *
3696509 TCGCGTTGCGATAGTTGAAAATCGTGTTGCACTTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATT
* * ** * *
3696550 TCGCGTTGCGAT-TTTCAATTTCGCGTTGCGATTTTCAATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATT
3696590 TCGCGTTGCGAT
1 TCGCGTTGCGAT
3696602 TTTCCATTTC
Statistics
Matches: 83, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 32 0.39
41 51 0.61
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (41 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATT
Found at i:3696658 original size:19 final size:19
Alignment explanation
Indices: 3696634--3696701 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
3696624 TCTACAGTTG
3696634 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
** *
3696653 TCGTTGCGATAGT-CATAGTT
1 TCGTTGCGATTTTCCA-A-AT
3696673 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
3696693 TCGTTGCGA
1 TCGTTGCGA
3696702 AAATTCGTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 2 0.05
19 21 0.54
20 2 0.05
21 12 0.31
22 2 0.05
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:3696683 original size:40 final size:41
Alignment explanation
Indices: 3696593--3696701 Score: 168
Period size: 40 Copynumber: 2.7 Consensus size: 41
3696583 TTCAATTTCG
*
3696593 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
*
3696635 CGTTGCGATTTTCCAAATTCGTTGCGATAGTC-ATAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
3696675 CGTTGCGATTTTCCAAATTCGTTGCGA
1 CGTTGCGATTTTCCAAATTCGTTGCGA
3696702 AAATTCGTTG
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
40 34 0.53
41 13 0.20
42 14 0.22
43 3 0.05
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:3696698 original size:101 final size:99
Alignment explanation
Indices: 3696438--3696701 Score: 232
Period size: 101 Copynumber: 2.6 Consensus size: 99
3696428 CGCGTTGCGA
* * ** * * * *
3696438 TTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTT
1 TTTTCCAATTC-CGTTGCGATAG-TCAAGTTCGCGTTGCGAT-TTTCAAATTC-CGTTGCGATTT
3696503 TCCATTTCGCGTTGCGATAGTTGAAAATCGTGTTGCAC
62 TCCATTTCGCGTTGCGATAGTTGAAAATCGTGTTGCAC
* ** * *
3696541 TTTTCCATTTCGCGTTGCGATTTTCAATTTCGCGTTGCGATTTTCAATTTCGCGTTGCGATTTTC
1 TTTTCCAATTC-CGTTGCGATAGTCAAGTTCGCGTTGCGATTTTCAAATTC-CGTTGCGATTTTC
* * *
3696606 CATTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGA-
64 CATTTCGCGTTGCGATAGT-TGAAAATCGT-GTTGC-AC
3696643 TTTTCCAAATT-CGTTGCGATAGTCATAGTT-GTCGTTGCGATTTTCCAAATT-CGTTGCGA
1 TTTTCC-AATTCCGTTGCGATAGTCA-AGTTCG-CGTTGCGATTTT-CAAATTCCGTTGCGA
3696702 AAATTCGTTG
Statistics
Matches: 136, Mismatches: 18, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
101 64 0.47
102 42 0.31
103 30 0.22
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.40
Consensus pattern (99 bp):
TTTTCCAATTCCGTTGCGATAGTCAAGTTCGCGTTGCGATTTTCAAATTCCGTTGCGATTTTCCA
TTTCGCGTTGCGATAGTTGAAAATCGTGTTGCAC
Found at i:3696838 original size:21 final size:22
Alignment explanation
Indices: 3696798--3696849 Score: 97
Period size: 21 Copynumber: 2.4 Consensus size: 22
3696788 TTCCATTTCG
3696798 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
3696820 CGTTGCGATAGTC-ACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
3696841 CGTTGCGAT
1 CGTTGCGAT
3696850 TTTCCAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.35
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:3696969 original size:6 final size:6
Alignment explanation
Indices: 3696958--3696998 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
3696948 GAAGACACGT
3696958 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC -CGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
3696999 CGAGACGGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.32, C:0.51, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:3697540 original size:15 final size:15
Alignment explanation
Indices: 3697522--3697554 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3697512 GTCGGGTCGG
3697522 GTCGTGGTAATACGT
1 GTCGTGGTAATACGT
3697537 GTCGTGGTAATACGT
1 GTCGTGGTAATACGT
3697552 GTC
1 GTC
3697555 TTCGACACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.15, G:0.33, T:0.33
Consensus pattern (15 bp):
GTCGTGGTAATACGT
Found at i:3697542 original size:5 final size:5
Alignment explanation
Indices: 3697488--3697525 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
3697478 CCGTCTCGTC
3697488 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG
3697526 TGGTAATACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.00, C:0.21, G:0.58, T:0.21
Consensus pattern (5 bp):
TCGGG
Found at i:3702462 original size:24 final size:24
Alignment explanation
Indices: 3702417--3702475 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 24
3702407 TTAATATTTA
3702417 AAAAACTAAATATAAAAAATTATT
1 AAAAACTAAATATAAAAAATTATT
*
3702441 AAAAAC-AAATAT--TAAATTATT
1 AAAAACTAAATATAAAAAATTATT
* *
3702462 AAAAATTATATATA
1 AAAAACTAAATATA
3702476 TATATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 13 0.43
22 5 0.17
23 6 0.20
24 6 0.20
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (24 bp):
AAAAACTAAATATAAAAAATTATT
Found at i:3702475 original size:2 final size:2
Alignment explanation
Indices: 3702468--3702498 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3702458 TATTAAAAAT
3702468 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
3702499 TCAAAATACA
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:3705415 original size:15 final size:15
Alignment explanation
Indices: 3705395--3705431 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
3705385 ATATTTAGCT
*
3705395 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
3705410 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
3705425 GGGCGGG
1 GGGCGGG
3705432 TACCACTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.70, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:3705578 original size:16 final size:17
Alignment explanation
Indices: 3705549--3705590 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 17
3705539 CATCCCTATG
3705549 TATGTATGATGCATGTA
1 TATGTATGATGCATGTA
3705566 TATGTAT-ATGCATG--
1 TATGTATGATGCATGTA
3705580 TATGTATGATG
1 TATGTATGATG
3705591 TGTGTGTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.29
15 3 0.12
16 7 0.29
17 7 0.29
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.43
Consensus pattern (17 bp):
TATGTATGATGCATGTA
Found at i:3706174 original size:2 final size:2
Alignment explanation
Indices: 3706169--3706199 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3706159 TATGTGTGTG
3706169 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
3706200 CATAATTCAA
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:3706234 original size:15 final size:15
Alignment explanation
Indices: 3706214--3706242 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3706204 ATTCAATTTT
3706214 TAAAAATAATAAAAG
1 TAAAAATAATAAAAG
3706229 TAAAAATAATAAAA
1 TAAAAATAATAAAA
3706243 ATTATAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
TAAAAATAATAAAAG
Found at i:3706519 original size:31 final size:31
Alignment explanation
Indices: 3706453--3706527 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
3706443 TATTATAACT
**
3706453 TTAGTGACCAATTTGTTATAAATTAATAATG
1 TTAGTGACCAATTTGTTATAAATTAATAAAA
* * *
3706484 TTAGTTACCGATTTGTTAT-AATTCGATAAAA
1 TTAGTGACCAATTTGTTATAAATT-AATAAAA
3706515 TTAGTGA-CAATTT
1 TTAGTGACCAATTT
3706528 CATTACTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
30 9 0.25
31 27 0.75
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (31 bp):
TTAGTGACCAATTTGTTATAAATTAATAAAA
Found at i:3706678 original size:17 final size:17
Alignment explanation
Indices: 3706656--3706697 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
3706646 AAGGAGGATG
3706656 AAATAAATCATTTAATA
1 AAATAAATCATTTAATA
3706673 AAATAAATCATTTAATA
1 AAATAAATCATTTAATA
3706690 AAATAAAT
1 AAATAAAT
3706698 TCAATGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAAATCATTTAATA
Found at i:3706712 original size:25 final size:25
Alignment explanation
Indices: 3706682--3706730 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
3706672 AAAATAAATC
3706682 ATTTAATAAAATAAATTCAATGATA
1 ATTTAATAAAATAAATTCAATGATA
3706707 ATTTAATAAAATAAATTCAATGAT
1 ATTTAATAAAATAAATTCAATGAT
3706731 TTTAACTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (25 bp):
ATTTAATAAAATAAATTCAATGATA
Found at i:3706782 original size:73 final size:73
Alignment explanation
Indices: 3706705--3706861 Score: 314
Period size: 73 Copynumber: 2.2 Consensus size: 73
3706695 AATTCAATGA
3706705 TAATTTAATAAAATAAATTCAATGATTTTAACTATTTTTTATAATATCATAATTAATATAAAATC
1 TAATTTAATAAAATAAATTCAATGATTTTAACTATTTTTTATAATATCATAATTAATATAAAATC
3706770 AAGTTTAC
66 AAGTTTAC
3706778 TAATTTAATAAAATAAATTCAATGATTTTAACTATTTTTTATAATATCATAATTAATATAAAATC
1 TAATTTAATAAAATAAATTCAATGATTTTAACTATTTTTTATAATATCATAATTAATATAAAATC
3706843 AAGTTTAC
66 AAGTTTAC
3706851 TAATTTAATAA
1 TAATTTAATAA
3706862 TTTAATAAAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 84 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (73 bp):
TAATTTAATAAAATAAATTCAATGATTTTAACTATTTTTTATAATATCATAATTAATATAAAATC
AAGTTTAC
Found at i:3706883 original size:17 final size:17
Alignment explanation
Indices: 3706861--3706910 Score: 100
Period size: 17 Copynumber: 2.9 Consensus size: 17
3706851 TAATTTAATA
3706861 ATTTAATAAAATAAATC
1 ATTTAATAAAATAAATC
3706878 ATTTAATAAAATAAATC
1 ATTTAATAAAATAAATC
3706895 ATTTAATAAAATAAAT
1 ATTTAATAAAATAAAT
3706911 TCAATGATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTTAATAAAATAAATC
Found at i:3706925 original size:25 final size:25
Alignment explanation
Indices: 3706895--3706943 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
3706885 AAAATAAATC
3706895 ATTTAATAAAATAAATTCAATGATA
1 ATTTAATAAAATAAATTCAATGATA
3706920 ATTTAATAAAATAAATTCAATGAT
1 ATTTAATAAAATAAATTCAATGAT
3706944 TTTAACTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (25 bp):
ATTTAATAAAATAAATTCAATGATA
Found at i:3707038 original size:17 final size:17
Alignment explanation
Indices: 3707011--3707057 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
3707001 AAATTAATAA
3707011 TTAAT-AAATAAATCAT
1 TTAATAAAATAAATCAT
3707027 TTAATAAAATAAATCAT
1 TTAATAAAATAAATCAT
3707044 TTAATAAAATAAAT
1 TTAATAAAATAAAT
3707058 TCAATGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 5 0.17
17 25 0.83
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAATAAAATAAATCAT
Found at i:3707050 original size:147 final size:139
Alignment explanation
Indices: 3706778--3707065 Score: 404
Period size: 147 Copynumber: 2.0 Consensus size: 139
3706768 TCAAGTTTAC
3706778 TAATTTAATAAAATAAATTCAATGATTTTAACTATTTTTTATAATATCATAATTAATATAAAATC
1 TAATTTAATAAAATAAATTCAATGATTTTAACTATTTTTTATAATATCATAATT-ATATAAAATC
*
3706843 AAGTTTACTAATTTAATAATTTAATAAAATAAATCATTTAATAAAATAAATCATTTAATAAAATA
65 AAGTTTACTAAATTAATAATTTAATAAAATAAATCATTTAATAAAATAAATCATTTAATAAAATA
3706908 AATTCAATGA
130 AATTCAATGA
*
3706918 TAATTTAATAAAATAAATTCAATGATTTTAACTATTTTTTAACATAATTAAT-ATAATT-TCATT
1 TAATTTAATAAAATAAATTCAATGATTTTAACTATTTTTT---ATAA-T-ATCATAATTAT-ATA
*
3706981 AAATCTAAGTTTTAATTAAAAAATTAATAA-TTAAT-AAATAAATCATTTAATAAAATAAATCAT
60 AAATC-AAG-TTT-ACT---AAATTAATAATTTAATAAAATAAATCATTTAATAAAATAAATCAT
3707044 TTAATAAAATAAATTCAATGA
119 TTAATAAAATAAATTCAATGA
3707065 T
1 T
3707066 TTTAACTATT
Statistics
Matches: 133, Mismatches: 3, Indels: 17
0.87 0.02 0.11
Matches are distributed among these distances:
140 40 0.30
142 1 0.01
143 11 0.08
144 10 0.08
145 5 0.04
146 2 0.02
147 50 0.38
148 5 0.04
149 9 0.07
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (139 bp):
TAATTTAATAAAATAAATTCAATGATTTTAACTATTTTTTATAATATCATAATTATATAAAATCA
AGTTTACTAAATTAATAATTTAATAAAATAAATCATTTAATAAAATAAATCATTTAATAAAATAA
ATTCAATGA
Found at i:3725956 original size:46 final size:46
Alignment explanation
Indices: 3725888--3726033 Score: 134
Period size: 46 Copynumber: 3.2 Consensus size: 46
3725878 AAAATAATCG
* * *
3725888 AATAACATGTTGGTACATCCTTATCGGATGATAAAGTTCAATACCA
1 AATAACAAGATGGTGCATCCTTATCGGATGATAAAGTTCAATACCA
* * * * *
3725934 AATAATAGGATGGTGCATCCTTATCGGATAATAGCA-TTCAATATCA
1 AATAACAAGATGGTGCATCCTTATCGGATGATA-AAGTTCAATACCA
* ** * * *
3725980 AATAACAAGTTGGTGCAT-CTGTATCAAATGGTAAAGTTTAATACTA
1 AATAACAAGATGGTGCATCCT-TATCGGATGATAAAGTTCAATACCA
3726026 AATAACAA
1 AATAACAA
3726034 TAATAAAATA
Statistics
Matches: 79, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
45 3 0.04
46 75 0.95
47 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (46 bp):
AATAACAAGATGGTGCATCCTTATCGGATGATAAAGTTCAATACCA
Found at i:3727843 original size:29 final size:31
Alignment explanation
Indices: 3727804--3727874 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 31
3727794 TCAACTTATT
*
3727804 AAATATATTTTAGTCTTATTTTAA-CT-TAA
1 AAATATATTTTAGTCTTATCTTAATCTATAA
* * *
3727833 AAGTATATTTTATTCTTATCTTAATTTATAA
1 AAATATATTTTAGTCTTATCTTAATCTATAA
3727864 AAATATATTTT
1 AAATATATTTT
3727875 TAATTAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 21 0.60
30 1 0.03
31 13 0.37
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.54
Consensus pattern (31 bp):
AAATATATTTTAGTCTTATCTTAATCTATAA
Found at i:3727900 original size:127 final size:122
Alignment explanation
Indices: 3727749--3727978 Score: 282
Period size: 122 Copynumber: 1.8 Consensus size: 122
3727739 CCACATACTA
* * * * * *
3727749 AATTAAATTCACATCTTCACATTAAAAATATATTTAATTTTTATCTCAACTTATTAAATATATTT
1 AATTAAATTCACATATTAAAATT-AAAA-ATA--T-ATTTTTATCTCAAATAATTAAATATAATT
3727814 TAGTCTTATTTTAACTTAAAAGTATAT-TTTATTCTTATCTTAATTTATAAAAATATATTTTT
61 TAGTCTTATTTTAACTTAAAA-TATATATTTATTCTTATCTTAATTTATAAAAATATATTTTT
* * * *
3727876 AATTAAATTCATATATTAAAATTAAAAATATATTTTTATCTTAAATAATTTAATATAATTTATTC
1 AATTAAATTCACATATTAAAATTAAAAATATATTTTTATCTCAAATAATTAAATATAATTTAGTC
* * *
3727941 TTATTTTAATTTAAAATATATATTTATTTTTATTTTAA
66 TTATTTTAACTTAAAATATATATTTATTCTTATCTTAA
3727979 CTTGAAAATA
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
121 5 0.06
122 57 0.64
123 1 0.01
125 3 0.03
126 4 0.04
127 19 0.21
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.52
Consensus pattern (122 bp):
AATTAAATTCACATATTAAAATTAAAAATATATTTTTATCTCAAATAATTAAATATAATTTAGTC
TTATTTTAACTTAAAATATATATTTATTCTTATCTTAATTTATAAAAATATATTTTT
Found at i:3728009 original size:56 final size:57
Alignment explanation
Indices: 3727927--3728050 Score: 153
Period size: 57 Copynumber: 2.2 Consensus size: 57
3727917 TAAATAATTT
* * *
3727927 AATATAATTTATTCTTATTTTAATTTA-AAATATATATTTATTTTTATTTTAACTTGA
1 AATATATTTTATTCTTATCTTAATTTAGAAATATAT-TTTAATTTTATTTTAACTTGA
* * * *
3727984 AA-ATATTTTATTGTTATCTTAATTTATGAAATCTATTTTAATTTTATTTTAATTTTA
1 AATATATTTTATTCTTATCTTAATTTA-GAAATATATTTTAATTTTATTTTAACTTGA
3728041 AATATATTTT
1 AATATATTTT
3728051 TAAAAGTATA
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
56 21 0.37
57 22 0.39
58 14 0.25
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.59
Consensus pattern (57 bp):
AATATATTTTATTCTTATCTTAATTTAGAAATATATTTTAATTTTATTTTAACTTGA
Found at i:3728023 original size:30 final size:28
Alignment explanation
Indices: 3727909--3728050 Score: 103
Period size: 29 Copynumber: 4.9 Consensus size: 28
3727899 AAAAATATAT
*
3727909 TTTTATCTTAAATAATTT-AATATAATTT-A
1 TTTTATCTT-AAT--TTTAAATATATTTTAA
* * *
3727938 TTCTTATTTTAATTTAAAATATATATTTAT
1 TT-TTATCTTAATTTTAAATATAT-TTTAA
* * *
3727968 TTTTATTTTAACTTGAAA-ATATTTT-A
1 TTTTATCTTAATTTTAAATATATTTTAA
*
3727994 TTGTTATCTTAATTTATGAAATCTATTTTAA
1 TT-TTATCTTAATTT-T-AAATATATTTTAA
*
3728025 TTTTATTTTAATTTTAAATATATTTT
1 TTTTATCTTAATTTTAAATATATTTT
3728051 TAAAAGTATA
Statistics
Matches: 91, Mismatches: 13, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
26 2 0.02
27 15 0.16
28 20 0.22
29 26 0.29
30 25 0.27
31 3 0.03
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (28 bp):
TTTTATCTTAATTTTAAATATATTTTAA
Found at i:3728074 original size:29 final size:30
Alignment explanation
Indices: 3728040--3728120 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 30
3728030 TTTTAATTTT
*
3728040 AAATATATTTTTAAAAGT-ATATAAGAATA
1 AAATATATTTTTAAAAGTAAAATAAGAATA
* ** *
3728069 AGATATATTTTT-AATTTAAAATAAGATTA
1 AAATATATTTTTAAAAGTAAAATAAGAATA
*
3728098 AAATATATTTTTAAAATTAAAAT
1 AAATATATTTTTAAAAGTAAAAT
3728121 TAAAATATAT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 3 0.07
29 31 0.72
30 9 0.21
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (30 bp):
AAATATATTTTTAAAAGTAAAATAAGAATA
Found at i:3728126 original size:25 final size:24
Alignment explanation
Indices: 3728083--3728132 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
3728073 ATATTTTTAA
*
3728083 TTTAAAATAAGATTAAAATATATT
1 TTTAAAATAAAATTAAAATATATT
3728107 TTTAAAATTAAAATTAAAATATATT
1 TTTAAAA-TAAAATTAAAATATATT
3728132 T
1 T
3728133 AATAAGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TTTAAAATAAAATTAAAATATATT
Found at i:3728514 original size:35 final size:35
Alignment explanation
Indices: 3728475--3728550 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
3728465 AACACATTCA
*
3728475 TCAATTATATTCTAAACC-CTAAAATCCAAAATACT
1 TCAATTACATTCTAAACCTC-AAAATCCAAAATACT
*
3728510 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCTCAAAATCCAAAATACT
3728545 TCAATT
1 TCAATT
3728551 CCATGACCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 37 0.97
36 1 0.03
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (35 bp):
TCAATTACATTCTAAACCTCAAAATCCAAAATACT
Found at i:3728568 original size:35 final size:35
Alignment explanation
Indices: 3728475--3728570 Score: 104
Period size: 35 Copynumber: 2.7 Consensus size: 35
3728465 AACACATTCA
* * * *
3728475 TCAATTATATTCTAAACCCTAAAATCCAAAATACT
1 TCAATTACATACTAAACCCCAAATTCCAAAATACT
* *
3728510 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATACTAAACCCCAAATTCCAAAATACT
* *
3728545 TCAATTCCATGAC-CAACCCCAAATTC
1 TCAATTACAT-ACTAAACCCCAAATTC
3728571 ATAATCCATT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 51 0.98
36 1 0.02
ACGTcount: A:0.42, C:0.28, G:0.01, T:0.29
Consensus pattern (35 bp):
TCAATTACATACTAAACCCCAAATTCCAAAATACT
Found at i:3728996 original size:143 final size:142
Alignment explanation
Indices: 3728731--3729018 Score: 443
Period size: 148 Copynumber: 2.0 Consensus size: 142
3728721 AAATACTCAA
3728731 TTCAGTTTATAAAATAGTTGACTTGAAATTTTTTCACTTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAGTTTATAAAATAGTTGACTTGAAATTTTTTCACTTTGAGTTTATAAAATTTAAATCAAGTC
3728796 GAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATACTTATCATATTATAATATTATTT
66 GAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATACTTATCATA-TATAATATTATTT
3728861 AATTCTAATTCAT
130 AATTCTAATTCAT
* *
3728874 TTCAGTTTATAAAATAGTTGACTATGAATTTTTTTGA-TTTGAGTTTATAAAATTTAAATCAAGT
1 TTCAGTTTATAAAATAGTTGACT-TGAAATTTTTTCACTTTGAGTTTATAAAATTTAAATCAAGT
* * *
3728938 CGAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATAATATAATA
65 C-----GAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATACTTATCAT-ATATAATA
*
3729003 TTATTTGATTCTAATT
124 TTATTTAATTCTAATT
3729019 TAAATAGTTT
Statistics
Matches: 132, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
143 51 0.39
144 11 0.08
148 69 0.52
149 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (142 bp):
TTCAGTTTATAAAATAGTTGACTTGAAATTTTTTCACTTTGAGTTTATAAAATTTAAATCAAGTC
GAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATACTTATCATATATAATATTATTTA
ATTCTAATTCAT
Found at i:3729578 original size:35 final size:36
Alignment explanation
Indices: 3729517--3729593 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 36
3729507 GGGGTTGGGC
3729517 ATGTAATTAAAGTATTTTTGGAATTTGAGGTTTAGA
1 ATGTAATTAAAGTATTTTTGGAATTTGAGGTTTAGA
3729553 ATGTAATTAAAGTA-TTTTGGAATTTGAGGTTTAGA
1 ATGTAATTAAAGTATTTTTGGAATTTGAGGTTTAGA
3729588 ATGTAA
1 ATGTAA
3729594 ATGCAAGCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 27 0.66
36 14 0.34
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (36 bp):
ATGTAATTAAAGTATTTTTGGAATTTGAGGTTTAGA
Found at i:3730954 original size:6 final size:6
Alignment explanation
Indices: 3730943--3731005 Score: 81
Period size: 6 Copynumber: 10.5 Consensus size: 6
3730933 GAACTTTTAA
* * *
3730943 GTCAGG GTCAGG GTCAGG GTCAGG GTCAGG GTTAGG GTTAAG GTCAGG
1 GTCAGG GTCAGG GTCAGG GTCAGG GTCAGG GTCAGG GTCAGG GTCAGG
* *
3730991 GTTAGG GTTAGG GTC
1 GTCAGG GTCAGG GTC
3731006 TTATGGTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.17, C:0.11, G:0.48, T:0.24
Consensus pattern (6 bp):
GTCAGG
Found at i:3730966 original size:18 final size:18
Alignment explanation
Indices: 3730943--3731005 Score: 90
Period size: 18 Copynumber: 3.5 Consensus size: 18
3730933 GAACTTTTAA
*
3730943 GTCAGGGTCAGGGTCAGG
1 GTCAGGGTCAGGGTTAGG
3730961 GTCAGGGTCAGGGTTAGG
1 GTCAGGGTCAGGGTTAGG
* *
3730979 GTTAAGGTCAGGGTTAGG
1 GTCAGGGTCAGGGTTAGG
*
3730997 GTTAGGGTC
1 GTCAGGGTC
3731006 TTATGGTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.17, C:0.11, G:0.48, T:0.24
Consensus pattern (18 bp):
GTCAGGGTCAGGGTTAGG
Found at i:3732023 original size:4 final size:4
Alignment explanation
Indices: 3732014--3732040 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3732004 ATTAGTAATA
3732014 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
3732041 ATTAGTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:3739584 original size:41 final size:41
Alignment explanation
Indices: 3739534--3739635 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
3739524 AGGTTTTATG
* * *
3739534 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTTACA
* * * **
3739575 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATT
1 GATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGACTTACA
3739617 GATGGCCCGAAGGACTTAT
1 GATGGCCCGAAGGACTTAT
3739636 AAATCGTGAA
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 16 0.33
42 33 0.67
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTTACA
Found at i:3739805 original size:214 final size:212
Alignment explanation
Indices: 3739296--3739835 Score: 805
Period size: 212 Copynumber: 2.5 Consensus size: 212
3739286 ATATTGGTGC
* * * * * * * ** *
3739296 AAAACATCCTGCCCAAAGGTCTTATGGATGACCCGAAGGATTTATCATCTCGCTCGAGAGAATCA
1 AAAACATCCTACCCGAAGGTTTTATGGATGACCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
* * *
3739361 CAAATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTATAA
*
3739426 ATCATGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTAAAACATCATTTTTTT
131 ATCATGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTAAAACATCATTTTTCT
3739491 CATTTCAAATTCATGTG
196 CATTTCAAATTCATGTG
* * *
3739508 AAAACATCATACCTGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTTTTATGGATGACCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
3739573 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTATAA
* * * *
3739638 ATCGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAATATCA-TTT
131 ATCATGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAA-TTC--CATCTTAAAACATCATTTT
**
3739702 TCTCATTTTC-CTTTCATGTG
193 TCTCA-TTTCAAATTCATGTG
*
3739722 AAAACATCCTACCCGAAGGTTTTATGGATTACCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTTTTATGGATGACCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
*
3739787 TAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGG
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGG
3739836 AGTTGCTTCA
Statistics
Matches: 296, Mismatches: 28, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
212 152 0.51
213 3 0.01
214 124 0.42
215 17 0.06
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (212 bp):
AAAACATCCTACCCGAAGGTTTTATGGATGACCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTATAA
ATCATGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTAAAACATCATTTTTCT
CATTTCAAATTCATGTG
Found at i:3739829 original size:42 final size:41
Alignment explanation
Indices: 3739743--3739834 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 41
3739733 CCCGAAGGTT
* * * * * *
3739743 TTATGGATTACCCGAAGGACTTATCATCTTGCTCTAAAGGC
1 TTATAGATGACCCGAAGGACTTAGCATCATGCTCGAAAGAC
*
3739784 TTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGAC
1 TTATAGATGACCCGAAGGACTT-AGCATCATGCTCGAAAGAC
*
3739826 TTATTGATG
1 TTATAGATG
3739835 GAGTTGCTTC
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 19 0.45
42 23 0.55
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (41 bp):
TTATAGATGACCCGAAGGACTTAGCATCATGCTCGAAAGAC
Found at i:3739881 original size:37 final size:35
Alignment explanation
Indices: 3739837--3739907 Score: 83
Period size: 37 Copynumber: 2.0 Consensus size: 35
3739827 TATTGATGGA
3739837 GTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATG
1 GTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATG
*
3739872 GAATTGCTTCACT-CAT-TTCCGGTGAAGGCTTAAGAT
1 G--TTGCTTCACTAC-TCTT-TGGTGAAGGCTTAAGAT
3739908 TACCCTGAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
35 1 0.03
36 3 0.10
37 27 0.87
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (35 bp):
GTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATG
Found at i:3740017 original size:116 final size:116
Alignment explanation
Indices: 3739779--3740244 Score: 453
Period size: 116 Copynumber: 4.1 Consensus size: 116
3739769 TCTTGCTCTA
* *
3739779 AAGGCTTATAGATGACCC-GAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGAGTTGCT
1 AAGGCTTA-AGATGACCCTG-AGGACTTAATCATCATGCTCGAAAGACTTATTGATGGAGTTGCT
* * *
3739843 TCACTACTCTTTGGTGAAGGCTTAAGATGGAATTGCTTCACTCATT-TCCGGTG
64 TCACTACTCTTCGGTGAAGGCTTAAGATTGAGTTGCTTCACT-ATTCTCCGGTG
* * ** *
3739896 AAGGCTTAAGATTACCCTGAGGACTTAATCATCATGCTC-AGAAGGCTTGCTGATGGATTTGCTT
1 AAGGCTTAAGATGACCCTGAGGACTTAATCATCATGCTCGA-AAGACTTATTGATGGAGTTGCTT
*
3739960 CACTACTCTTCGGTGAAGGCTTAAGATTGAGTTACTTCACTATTCTCCGGTG
65 CACTACTCTTCGGTGAAGGCTTAAGATTGAGTTGCTTCACTATTCTCCGGTG
* * *** ** * * * *
3740012 GAGGCTTAGGATGGTGCT--TCAC-TACTCCTC-TG-T-G-AAGGCTTA-AGAT-G-GTT-CTTC
1 AAGGCTTAAGATGACCCTGAGGACTTAATCATCATGCTCGAAAGACTTATTGATGGAGTTGCTTC
* * * *
3740066 ACTACTCTTCTGTGAAGGCTTAAGATTTAGTTGCTTCAGTATTATCCGGTG
66 ACTACTCTTCGGTGAAGGCTTAAGATTGAGTTGCTTCACTATTCTCCGGTG
* *
3740117 AAGGCTTAAGAGTG-CCTTGAGGACTTAATCATCATGCTCGAAAGACTTATTGATGGAGTTGTTT
1 AAGGCTTAAGA-TGACCCTGAGGACTTAATCATCATGCTCGAAAGACTTATTGATGGAGTTGCTT
* * * * *
3740181 CACTACTCTTTGGTGAAGGCTTCAGA-TG-GTTTTCTTCACTACTCTCTGGTG
65 CACTACTCTTCGGTGAAGGCTTAAGATTGAG-TTGCTTCACTATTCTCCGGTG
*
3740232 AAGGCTTCAGATG
1 AAGGCTTAAGATG
3740245 GTTTACTTCA
Statistics
Matches: 281, Mismatches: 51, Indels: 37
0.76 0.14 0.10
Matches are distributed among these distances:
105 60 0.21
106 4 0.01
107 3 0.01
108 9 0.03
109 9 0.03
110 1 0.00
111 2 0.01
112 9 0.03
113 9 0.03
114 6 0.02
115 34 0.12
116 126 0.45
117 9 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (116 bp):
AAGGCTTAAGATGACCCTGAGGACTTAATCATCATGCTCGAAAGACTTATTGATGGAGTTGCTTC
ACTACTCTTCGGTGAAGGCTTAAGATTGAGTTGCTTCACTATTCTCCGGTG
Found at i:3740051 original size:34 final size:34
Alignment explanation
Indices: 3739955--3740453 Score: 303
Period size: 34 Copynumber: 13.9 Consensus size: 34
3739945 CTGATGGATT
* *
3739955 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGAG
1 TGCTTCACTACTCCTCTGTGAAGGCTTAAGA-TG-G
* * * * *
3739991 TTACTTCACTA-TTCTCCGGTGGAGGCTTAGGATGG
1 -TGCTTCACTACTCCT-CTGTGAAGGCTTAAGATGG
3740026 TGCTTCACTACTCCTCTGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCCTCTGTGAAGGCTTAAGATGG
* * *
3740060 TTCTTCACTACTCTTCTGTGAAGGCTTAAGATTTAGT
1 TGCTTCACTACTCCTCTGTGAAGGCTTAAGA--T-GG
* ** *
3740097 TGCTTCAGTA-TTATCCGGTGAAGGCTTAAGA--G
1 TGCTTCACTACTCCT-CTGTGAAGGCTTAAGATGG
* * * * *
3740129 TGCCTTGAGGACTTAATCATCATGCTCGAAAGACTTATTGATGGAG
1 TG-CTT---CAC-TACTCCTC-TG-T-G-AAGGCTTA-AGAT-G-G
* * *
3740175 TTGTTTCACTACT-CTTTGGTGAAGGCTTCAGATGG
1 -TGCTTCACTACTCCTCT-GTGAAGGCTTAAGATGG
* *
3740210 TTTTCTTCACTACT-CTCTGGTGAAGGCTTCAGATGG
1 --TGCTTCACTACTCCTCT-GTGAAGGCTTAAGATGG
* * * *
3740246 TTTACTTCACTA-TTCTCAAGTGAAGGCTTAGGATGG
1 --TGCTTCACTACTCCTC-TGTGAAGGCTTAAGATGG
*
3740282 TTCTTCACTACTCCTCTGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCCTCTGTGAAGGCTTAAGATGG
* *
3740316 TGCTTCACTACTCTTCTATGAAGGCTTAAGATTGAG
1 TGCTTCACTACTCCTCTGTGAAGGCTTAAGA-TG-G
* * * *
3740352 TTTCTTCACTATTCTTCGGTGAAGGCTTAAGATGG
1 -TGCTTCACTACTCCTCTGTGAAGGCTTAAGATGG
* *
3740387 TTTGCTTCACTA-TTCTCCGTGAAGGCTTAAGATGG
1 --TGCTTCACTACTCCTCTGTGAAGGCTTAAGATGG
*
3740422 TGCTTCACTACTCTTCTGTGAAGGCTTAAGAT
1 TGCTTCACTACTCCTCTGTGAAGGCTTAAGAT
3740454 TGACTTGCCC
Statistics
Matches: 372, Mismatches: 58, Indels: 67
0.75 0.12 0.13
Matches are distributed among these distances:
32 2 0.01
33 13 0.03
34 125 0.34
35 33 0.09
36 83 0.22
37 80 0.22
38 10 0.03
39 2 0.01
40 3 0.01
41 9 0.02
42 5 0.01
43 2 0.01
46 3 0.01
47 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (34 bp):
TGCTTCACTACTCCTCTGTGAAGGCTTAAGATGG
Found at i:3740219 original size:36 final size:34
Alignment explanation
Indices: 3740174--3740453 Score: 269
Period size: 36 Copynumber: 8.0 Consensus size: 34
3740164 TATTGATGGA
* *
3740174 GTTGTTTCACTACTCTTTGGTGAAGGCTTCAGATG
1 GTTGCTTCACTACTCTTT-GTGAAGGCTTAAGATG
* * *
3740209 GTTTTCTTCACTACTCTCTGGTGAAGGCTTCAGATG
1 G-TTGCTTCACTACTCT-TTGTGAAGGCTTAAGATG
* * ** *
3740245 GTTTACTTCACTATTCTCAAGTGAAGGCTTAGGATG
1 G-TTGCTTCACTACTCT-TTGTGAAGGCTTAAGATG
*
3740281 GTT-CTTCACTACTCCTCTGTGAAGGCTTAAGATG
1 GTTGCTTCACTACT-CTTTGTGAAGGCTTAAGATG
*
3740315 G-TGCTTCACTACTCTTCTATGAAGGCTTAAGATTG
1 GTTGCTTCACTACTCTT-TGTGAAGGCTTAAGA-TG
* * *
3740350 AGTTTCTTCACTATTCTTCGGTGAAGGCTTAAGATG
1 -GTTGCTTCACTACTCTT-TGTGAAGGCTTAAGATG
* **
3740386 GTTTGCTTCACTATTCTCCGTGAAGGCTTAAGATG
1 G-TTGCTTCACTACTCTTTGTGAAGGCTTAAGATG
3740421 G-TGCTTCACTACTCTTCTGTGAAGGCTTAAGAT
1 GTTGCTTCACTACTCTT-TGTGAAGGCTTAAGAT
3740454 TGACTTGCCC
Statistics
Matches: 210, Mismatches: 25, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
33 16 0.08
34 64 0.30
35 25 0.12
36 77 0.37
37 28 0.13
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (34 bp):
GTTGCTTCACTACTCTTTGTGAAGGCTTAAGATG
Found at i:3740434 original size:106 final size:106
Alignment explanation
Indices: 3740179--3740456 Score: 361
Period size: 106 Copynumber: 2.6 Consensus size: 106
3740169 ATGGAGTTGT
* ** * * *
3740179 TTCACTACTCTTTGGTGAAGGCTTCAGATGGTTTTCTTCACTACTC-TCTGGTGAAGGCTTCAGA
1 TTCACTACTCCTCCGTGAAGGCTTAAGATGG--TGCTTCACTACTCTTCT-GTGAAGGCTTAAGA
*
3740243 -TG-GTTTACTTCACTATTCTCAAGTGAAGGCTTAGGATGGTTC
63 TTGAGTTTACTTCACTATTCTCAAGTGAAGGCTTAAGATGGTTC
* *
3740285 TTCACTACTCCTCTGTGAAGGCTTAAGATGGTGCTTCACTACTCTTCTATGAAGGCTTAAGATTG
1 TTCACTACTCCTCCGTGAAGGCTTAAGATGGTGCTTCACTACTCTTCTGTGAAGGCTTAAGATTG
*
3740350 AGTTT-CTTCACTATTCTTC-GGTGAAGGCTTAAGATGGTTTGC
66 AGTTTACTTCACTATTC-TCAAGTGAAGGCTTAAGATGG-TT-C
*
3740392 TTCACTA-TTCTCCGTGAAGGCTTAAGATGGTGCTTCACTACTCTTCTGTGAAGGCTTAAGATTG
1 TTCACTACTCCTCCGTGAAGGCTTAAGATGGTGCTTCACTACTCTTCTGTGAAGGCTTAAGATTG
3740456 A
66 A
3740457 CTTGCCCCAA
Statistics
Matches: 154, Mismatches: 12, Indels: 12
0.87 0.07 0.07
Matches are distributed among these distances:
104 24 0.16
105 32 0.21
106 90 0.58
107 8 0.05
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (106 bp):
TTCACTACTCCTCCGTGAAGGCTTAAGATGGTGCTTCACTACTCTTCTGTGAAGGCTTAAGATTG
AGTTTACTTCACTATTCTCAAGTGAAGGCTTAAGATGGTTC
Found at i:3744452 original size:9 final size:9
Alignment explanation
Indices: 3744438--3744558 Score: 143
Period size: 9 Copynumber: 12.7 Consensus size: 9
3744428 TTCCTTATTA
3744438 TTTTTTTTC
1 TTTTTTTTC
3744447 TTTTTTTCTC
1 TTTTTTT-TC
*
3744457 TTTTTCTTCTT
1 TTTTT-TT-TC
3744468 TTTTTTCTTC
1 TTTTTT-TTC
3744478 TTTTTTTTC
1 TTTTTTTTC
3744487 TTTTTTTTC
1 TTTTTTTTC
*
3744496 TTTTGTTTC
1 TTTTTTTTC
*
3744505 TTTTGTTTC
1 TTTTTTTTC
3744514 TTTTTGTTTC
1 TTTTT-TTTC
3744524 TTTTTTTTC
1 TTTTTTTTC
3744533 TTTTTTTATTC
1 -TTTTTT-TTC
*
3744544 TTTTTTTCC
1 TTTTTTTTC
3744553 TTTTTT
1 TTTTTT
3744559 CTTTCATTTT
Statistics
Matches: 101, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
9 52 0.51
10 36 0.36
11 13 0.13
ACGTcount: A:0.01, C:0.13, G:0.02, T:0.83
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:3744460 original size:19 final size:19
Alignment explanation
Indices: 3744438--3744558 Score: 142
Period size: 19 Copynumber: 6.3 Consensus size: 19
3744428 TTCCTTATTA
3744438 TTTTTTTTCTTTTTTTCTC
1 TTTTTTTTCTTTTTTTCTC
*
3744457 TTTTTCTTCTTTTTTTTCTTC
1 TTTTTTTTC-TTTTTTTC-TC
3744478 TTTTTTTTCTTTTTTT-TC
1 TTTTTTTTCTTTTTTTCTC
*
3744496 TTTTGTTTCTTTTGTTTCT-
1 TTTTTTTTCTTTT-TTTCTC
*
3744515 TTTTGTTTCTTTTTTT-TC
1 TTTTTTTTCTTTTTTTCTC
3744533 TTTTTTTATTCTTTTTTTC-C
1 -TTTTTT-TTCTTTTTTTCTC
3744553 TTTTTT
1 TTTTTT
3744559 CTTTCATTTT
Statistics
Matches: 90, Mismatches: 4, Indels: 16
0.82 0.04 0.15
Matches are distributed among these distances:
17 1 0.01
18 17 0.19
19 35 0.39
20 27 0.30
21 10 0.11
ACGTcount: A:0.01, C:0.13, G:0.02, T:0.83
Consensus pattern (19 bp):
TTTTTTTTCTTTTTTTCTC
Found at i:3744482 original size:39 final size:37
Alignment explanation
Indices: 3744438--3744569 Score: 149
Period size: 39 Copynumber: 3.4 Consensus size: 37
3744428 TTCCTTATTA
3744438 TTTTTTTTCTTTTTTTCTCTTTTTCTTCTTTTTTTTCTT
1 TTTTTTTTCTTTTTTTCTCTTTTT-TTCTTTTTTTTC-T
*
3744477 CTTTTTTTTCTTTTTTT-TCTTTTGTTTCTTTTGTTTCT
1 -TTTTTTTTCTTTTTTTCTCTTTT-TTTCTTTTTTTTCT
* * *
3744515 TTTTGTTTCTTTTTTTTCTTTTTTTATTCTTTTTTTCCT
1 TTTTTTTTC-TTTTTTTCTCTTTTT-TTCTTTTTTTTCT
*
3744554 TTTTTCTTTCATTTTT
1 TTTTT-TTTCTTTTTT
3744570 CGAGTGTAGT
Statistics
Matches: 80, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
37 8 0.10
38 9 0.11
39 42 0.52
40 21 0.26
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.83
Consensus pattern (37 bp):
TTTTTTTTCTTTTTTTCTCTTTTTTTCTTTTTTTTCT
Found at i:3744569 original size:1 final size:1
Alignment explanation
Indices: 3744438--3744550 Score: 64
Period size: 1 Copynumber: 113.0 Consensus size: 1
3744428 TTCCTTATTA
* * * * * * * * * *
3744438 TTTTTTTTCTTTTTTTCTCTTTTTCTTCTTTTTTTTCTTCTTTTTTTTCTTTTTTTTCTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * *
3744503 TCTTTTGTTTCTTTTTGTTTCTTTTTTTTCTTTTTTTATTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3744551 CCTTTTTTCT
Statistics
Matches: 76, Mismatches: 36, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.01, C:0.12, G:0.03, T:0.84
Consensus pattern (1 bp):
T
Found at i:3757363 original size:41 final size:41
Alignment explanation
Indices: 3757317--3757401 Score: 125
Period size: 41 Copynumber: 2.1 Consensus size: 41
3757307 AGATTGTGGT
* **
3757317 GTGGCTTTGTTGGTGTGGTCCTGCAGAGAAGATTTAGAAGA
1 GTGGCTTTGTTGGTGTGATCCCACAGAGAAGATTTAGAAGA
* *
3757358 GTGGCTTTGTTGGTGTGATCCCATAGAGAAGATTTGGAAGA
1 GTGGCTTTGTTGGTGTGATCCCACAGAGAAGATTTAGAAGA
3757399 GTG
1 GTG
3757402 CAGGGATAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.22, C:0.09, G:0.36, T:0.32
Consensus pattern (41 bp):
GTGGCTTTGTTGGTGTGATCCCACAGAGAAGATTTAGAAGA
Found at i:3757749 original size:113 final size:113
Alignment explanation
Indices: 3757632--3757847 Score: 328
Period size: 113 Copynumber: 1.9 Consensus size: 113
3757622 ATTTTCAACG
* * * *
3757632 GAATGACTATTCCATCACAAATTAAATT-GTTATATTTTAATTAAAGTTTAA-TAAAATTTCCGA
1 GAATGACTATTCAATCACAAATTAAATTAG-TATATTTTAATTAAAGTTGAACAAAAATTT-CAA
* * *
3757695 CGGAATTATTGTCACTTCATAAATTAAATTGATATTTTTTATTTCTGACA
64 CAGAATCATTATCACTTCATAAATTAAATTGATATTTTTTATTTCTGACA
3757745 GAATGACTATTCAATCACAAATTAAATTAGTATATTTTAATTAAAGTTGAACAAAAATTTCAACA
1 GAATGACTATTCAATCACAAATTAAATTAGTATATTTTAATTAAAGTTGAACAAAAATTTCAACA
*
3757810 GAATCATTATCCCTTCATAAATTAAATTGATATTTTTT
66 GAATCATTATCACTTCATAAATTAAATTGATATTTTTT
3757848 TATTGAAATA
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
113 85 0.91
114 8 0.09
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.41
Consensus pattern (113 bp):
GAATGACTATTCAATCACAAATTAAATTAGTATATTTTAATTAAAGTTGAACAAAAATTTCAACA
GAATCATTATCACTTCATAAATTAAATTGATATTTTTTATTTCTGACA
Found at i:3760083 original size:12 final size:12
Alignment explanation
Indices: 3760068--3760100 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3760058 AAATGTAATA
*
3760068 TTTTT-TATGCT
1 TTTTTATATACT
3760079 TTTTTATATACT
1 TTTTTATATACT
3760091 TTTTTATATA
1 TTTTTATATA
3760101 TTCGAGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.70
Consensus pattern (12 bp):
TTTTTATATACT
Found at i:3763444 original size:45 final size:45
Alignment explanation
Indices: 3763385--3763476 Score: 132
Period size: 45 Copynumber: 2.0 Consensus size: 45
3763375 ATTCCAGCAG
* *
3763385 CTCCACGTTACAAATTCTA-TCAGCTTCTAGCACTGCCAGCAGCCC
1 CTCCACGTTACAAATTCCAGT-AGCTTCCAGCACTGCCAGCAGCCC
* *
3763430 CTCCACGTTGCAAATTCCAGTAGCTTCCAGCACTGCCAGCAGTCC
1 CTCCACGTTACAAATTCCAGTAGCTTCCAGCACTGCCAGCAGCCC
3763475 CT
1 CT
3763477 TCACATCCCC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 41 0.98
46 1 0.02
ACGTcount: A:0.23, C:0.38, G:0.15, T:0.24
Consensus pattern (45 bp):
CTCCACGTTACAAATTCCAGTAGCTTCCAGCACTGCCAGCAGCCC
Found at i:3764879 original size:93 final size:94
Alignment explanation
Indices: 3764771--3764944 Score: 305
Period size: 93 Copynumber: 1.9 Consensus size: 94
3764761 AGATGTCATT
*
3764771 TTCTGATACTTTTAAATGAATACATATTTTATTTATAATTTATAAAAATCATTTTATATATG-TT
1 TTCTGATACTTTTAAATGAATAAATATTTTATTTATAATTTATAAAAATCATTTTATATATGTTT
3764835 TTTTCTTTAAAATTCTACGACTGAATCTG
66 TTTTCTTTAAAATTCTACGACTGAATCTG
* * *
3764864 TTCTGGTATTTTTAAATGAATAAATATTTTATTTATAATTTATAAAAATTATTTTATATATGTTT
1 TTCTGATACTTTTAAATGAATAAATATTTTATTTATAATTTATAAAAATCATTTTATATATGTTT
3764929 TTTTCTTTAAAATTCT
66 TTTTCTTTAAAATTCT
3764945 GCTATTGAAT
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
93 58 0.76
94 18 0.24
ACGTcount: A:0.34, C:0.07, G:0.06, T:0.53
Consensus pattern (94 bp):
TTCTGATACTTTTAAATGAATAAATATTTTATTTATAATTTATAAAAATCATTTTATATATGTTT
TTTTCTTTAAAATTCTACGACTGAATCTG
Found at i:3764981 original size:93 final size:91
Alignment explanation
Indices: 3764794--3764981 Score: 218
Period size: 93 Copynumber: 2.0 Consensus size: 91
3764784 AAATGAATAC
3764794 ATATTTTATTTATAATTTATAAAAATCATTTTATATATGTTTTTTCTTTAAAATTCTACGACTGA
1 ATATTTTATTTATAATTTATAAAAATCATTTTATATATGTTTTTTCTTTAAAATTCTACGACTGA
* ** * **
3764859 ATCTGTTCTGGTATTTTTAAATGAATAA
66 ATCTGATAAGGGATTCATAAAT--ATAA
* * * *
3764887 ATATTTTATTTATAATTTATAAAAATTATTTTATATATGTTTTTTTCTTTAAAATTCTGCTATTG
1 ATATTTTATTTATAATTTATAAAAATCATTTTATATATG-TTTTTTCTTTAAAATTCTACGACTG
3764952 AATCTGGAATAAGAGGA-TCATAAAT-TAA
65 AATCT-G-ATAAG-GGATTCATAAATATAA
3764980 AT
1 AT
3764982 TTATATTCGA
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
93 43 0.53
94 27 0.33
95 1 0.01
96 8 0.10
97 2 0.02
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.49
Consensus pattern (91 bp):
ATATTTTATTTATAATTTATAAAAATCATTTTATATATGTTTTTTCTTTAAAATTCTACGACTGA
ATCTGATAAGGGATTCATAAATATAA
Found at i:3768665 original size:11 final size:11
Alignment explanation
Indices: 3768649--3768673 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3768639 TCAGAAAAGA
3768649 AAAAAGAGAAG
1 AAAAAGAGAAG
3768660 AAAAAGAGAAG
1 AAAAAGAGAAG
3768671 AAA
1 AAA
3768674 GAAAAATAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAAGAGAAG
Done.