Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 27 of 126
Found at i:5826556 original size:14 final size:13
Alignment explanation
Indices: 5826529--5826569 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
5826519 CTAATGTCAG
5826529 AAGAAATCGAAAAA
1 AAGAAAT-GAAAAA
5826543 AAGCAAATGAAAAA
1 AAG-AAATGAAAAA
5826557 AAGAAA-GAAAAA
1 AAGAAATGAAAAA
5826569 A
1 A
5826570 GCCAAGGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.27
13 3 0.12
14 12 0.46
15 4 0.15
ACGTcount: A:0.76, C:0.05, G:0.15, T:0.05
Consensus pattern (13 bp):
AAGAAATGAAAAA
Found at i:5829273 original size:32 final size:31
Alignment explanation
Indices: 5829211--5829275 Score: 85
Period size: 32 Copynumber: 2.1 Consensus size: 31
5829201 CTTAGCAAGC
* * *
5829211 AAATTAAGGTGTAATTATTAATATATAATAT
1 AAATTAAGGTGTAATTATGAACATAAAATAT
*
5829242 AAATGTAAGGTGTAATTATGGACATAAAATAT
1 AAAT-TAAGGTGTAATTATGAACATAAAATAT
5829274 AA
1 AA
5829276 TTTTAGTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 4 0.14
32 25 0.86
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.35
Consensus pattern (31 bp):
AAATTAAGGTGTAATTATGAACATAAAATAT
Found at i:5830280 original size:14 final size:14
Alignment explanation
Indices: 5830253--5830300 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
5830243 TAAAAAAGTA
5830253 ATAAAAAATGATAAAC
1 ATAAAAAA--ATAAAC
*
5830269 ATAAAAAAATAAAT
1 ATAAAAAAATAAAC
*
5830283 ATAAAAGCAATAAAC
1 ATAAAA-AAATAAAC
5830298 ATA
1 ATA
5830301 TATAATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 11 0.39
15 9 0.32
16 8 0.29
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.19
Consensus pattern (14 bp):
ATAAAAAAATAAAC
Found at i:5839122 original size:16 final size:16
Alignment explanation
Indices: 5839103--5839138 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5839093 TTTTCAAACC
5839103 TTTTCTTCTTCATTTAT
1 TTTTCTT-TTCATTTAT
*
5839120 TTTTCTTTTCTTTTAT
1 TTTTCTTTTCATTTAT
5839136 TTT
1 TTT
5839139 GTGAATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTCTTTTCATTTAT
Found at i:5839489 original size:15 final size:15
Alignment explanation
Indices: 5839469--5839498 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5839459 TATTTTCCAA
5839469 CTTTTTTTTGTCTTT
1 CTTTTTTTTGTCTTT
*
5839484 CTTTTTTTTTTCTTT
1 CTTTTTTTTGTCTTT
5839499 AAATTTAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (15 bp):
CTTTTTTTTGTCTTT
Found at i:5839633 original size:22 final size:22
Alignment explanation
Indices: 5839607--5839675 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
5839597 GTTTTAGTAT
5839607 TATTTTTTTAAAAAAATATTAA
1 TATTTTTTTAAAAAAATATTAA
5839629 TATTTTTTTAAAAAAATATTAA
1 TATTTTTTTAAAAAAATATTAA
5839651 TA-TTTTTT---AAAATATTAA
1 TATTTTTTTAAAAAAATATTAA
5839669 TATTTTT
1 TATTTTT
5839676 ACTTATTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
18 12 0.26
19 4 0.09
21 6 0.13
22 24 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTTTTTAAAAAAATATTAA
Found at i:5839664 original size:18 final size:19
Alignment explanation
Indices: 5839618--5839675 Score: 82
Period size: 18 Copynumber: 2.9 Consensus size: 19
5839608 ATTTTTTTAA
5839618 AAAAATATTAATATTTTTTT
1 AAAAATATTAATA-TTTTTT
5839638 AAAAAAATATTAATATTTTTT
1 --AAAAATATTAATATTTTTT
5839659 -AAAATATTAATATTTTT
1 AAAAATATTAATATTTTT
5839676 ACTTATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.47
21 6 0.17
22 13 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AAAAATATTAATATTTTTT
Found at i:5840155 original size:18 final size:17
Alignment explanation
Indices: 5840126--5840159 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
5840116 GTTGGCCCTA
5840126 TTCTCTTTCCTTCTCTT
1 TTCTCTTTCCTTCTCTT
5840143 TTCTCTATTCCTTCTCT
1 TTCTCT-TTCCTTCTCT
5840160 CTCATTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.62
Consensus pattern (17 bp):
TTCTCTTTCCTTCTCTT
Found at i:5840969 original size:16 final size:16
Alignment explanation
Indices: 5840948--5840981 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5840938 TATTTTTTTA
*
5840948 TATTTTTCTATTAATT
1 TATTTTGCTATTAATT
*
5840964 TATTTTGCTATTATTT
1 TATTTTGCTATTAATT
5840980 TA
1 TA
5840982 ATTTATTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.68
Consensus pattern (16 bp):
TATTTTGCTATTAATT
Found at i:5842803 original size:21 final size:21
Alignment explanation
Indices: 5842778--5842826 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
5842768 GAGGTATATG
*
5842778 TTAGGGTTTAAGATTTTAAAA
1 TTAGGGTTTAAGAGTTTAAAA
* * *
5842799 TTA-GGTTTTAGGGTTTAAAG
1 TTAGGGTTTAAGAGTTTAAAA
5842819 TTAGGGTT
1 TTAGGGTT
5842827 GTGGTTTCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.45
Consensus pattern (21 bp):
TTAGGGTTTAAGAGTTTAAAA
Found at i:5842866 original size:33 final size:32
Alignment explanation
Indices: 5842805--5842866 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
5842795 AAAATTAGGT
*
5842805 TTTAGGGTTTAAAGTTAGGGTTGTGGTTTCGA
1 TTTAGGGTTTAAAGTTAGGGTAGTGGTTTCGA
*
5842837 TTTAGGGTTTTAAATTTAGGGCTAG-GGTTT
1 TTTAGGG-TTTAAAGTTAGGG-TAGTGGTTT
5842867 AGGGTTTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 7 0.27
33 17 0.65
34 2 0.08
ACGTcount: A:0.19, C:0.03, G:0.32, T:0.45
Consensus pattern (32 bp):
TTTAGGGTTTAAAGTTAGGGTAGTGGTTTCGA
Found at i:5843951 original size:12 final size:12
Alignment explanation
Indices: 5843934--5843958 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5843924 TGGCTAAACC
5843934 TCCAACTTGGTT
1 TCCAACTTGGTT
5843946 TCCAACTTGGTT
1 TCCAACTTGGTT
5843958 T
1 T
5843959 TCTCAATAGT
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:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (12 bp):
TCCAACTTGGTT
Found at i:5846029 original size:33 final size:35
Alignment explanation
Indices: 5845982--5846061 Score: 101
Period size: 33 Copynumber: 2.3 Consensus size: 35
5845972 CCTAAAAGGA
*
5845982 CTTGGATATCACCATCGAGAAA-TTTTG-TAAAAG
1 CTTGGATATCACCATCGAGAAAGTTTTGAGAAAAG
* *
5846015 CTTGGGTATTACCATCGAGAAAGTTTTGAGAAAAG
1 CTTGGATATCACCATCGAGAAAGTTTTGAGAAAAG
**
5846050 CTCAGATATCAC
1 CTTGGATATCAC
5846062 TACTAAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 20 0.53
34 5 0.13
35 13 0.34
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (35 bp):
CTTGGATATCACCATCGAGAAAGTTTTGAGAAAAG
Found at i:5846695 original size:18 final size:19
Alignment explanation
Indices: 5846663--5846708 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
5846653 AATTTTCTCA
*
5846663 ATTTTTCTTCTTTTTCCTTT
1 ATTTTT-TTCTTTTTCCTCT
*
5846683 CTTTTTTTC-TTTTCCTCT
1 ATTTTTTTCTTTTTCCTCT
5846701 ATTTTTTT
1 ATTTTTTT
5846709 TGTTTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 15 0.65
19 3 0.13
20 5 0.22
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (19 bp):
ATTTTTTTCTTTTTCCTCT
Found at i:5846706 original size:19 final size:18
Alignment explanation
Indices: 5846663--5846714 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
5846653 AATTTTCTCA
*
5846663 ATTTTTCTTCTTTTTCCTT
1 ATTTTTTTTC-TTTTCCTT
5846682 -TCTTTTTTTCTTTTCCTCT
1 AT-TTTTTTTCTTTTCCT-T
*
5846701 ATTTTTTTTGTTTT
1 ATTTTTTTTCTTTT
5846715 TTTATTCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 8 0.29
19 19 0.68
20 1 0.04
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (18 bp):
ATTTTTTTTCTTTTCCTT
Found at i:5848959 original size:15 final size:15
Alignment explanation
Indices: 5848941--5848977 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
5848931 TTTTTTTTTA
5848941 TTTTTTTGCCTCTAT
1 TTTTTTTGCCTCTAT
5848956 TTTTTTTGCCTCTAT
1 TTTTTTTGCCTCTAT
5848971 TTTTTTT
1 TTTTTTT
5848978 TGGCATGCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.73
Consensus pattern (15 bp):
TTTTTTTGCCTCTAT
Found at i:5856773 original size:5 final size:5
Alignment explanation
Indices: 5856765--5856834 Score: 51
Period size: 5 Copynumber: 14.8 Consensus size: 5
5856755 ATAAAACCAG
* ** *
5856765 AAAAT AAAAT AAAAA AAAAT AAGCT -AAA- AATAT AAAAT -AAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
*
5856812 -CAA- AAAAT AAAAAT AAAAT AAAA
1 AAAAT AAAAT -AAAAT AAAAT AAAA
5856835 AAAGAAAACC
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
4 11 0.22
5 33 0.67
6 5 0.10
ACGTcount: A:0.79, C:0.03, G:0.01, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:5856781 original size:13 final size:13
Alignment explanation
Indices: 5856751--5856842 Score: 71
Period size: 13 Copynumber: 6.8 Consensus size: 13
5856741 GAAATTTCTC
**
5856751 AAAAATAAAACCA
1 AAAAATAAAATAA
*
5856764 GAAAATAAAATAA
1 AAAAATAAAATAA
5856777 AAAAA-AATAAGCTAA
1 AAAAATAA-AA--TAA
*
5856792 AAATATAAAATAA
1 AAAAATAAAATAA
5856805 ATAAAATCAAAA-AA
1 A-AAAAT-AAAATAA
5856819 TAAAAATAAAATAA
1 -AAAAATAAAATAA
*
5856833 AAAAAGAAAA
1 AAAAATAAAA
5856843 CCTGGCGATT
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
12 2 0.03
13 33 0.52
14 13 0.20
15 14 0.22
16 2 0.03
ACGTcount: A:0.78, C:0.04, G:0.03, T:0.14
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:5856783 original size:28 final size:27
Alignment explanation
Indices: 5856751--5856837 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 27
5856741 GAAATTTCTC
*
5856751 AAAAATAAAACCAGAAAATAAAATAAAA
1 AAAAATAAAACTA-AAAATAAAATAAAA
*
5856779 AAAAAT-AAGCTAAAAATATAAAATAAATA
1 AAAAATAAAACT-AAAA-ATAAAATAAA-A
5856808 AAATCAA-AAAA-TAAAAATAAAATAAAA
1 AAA--AATAAAACTAAAAATAAAATAAAA
5856835 AAA
1 AAA
5856838 GAAAACCTGG
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
27 10 0.20
28 27 0.54
29 8 0.16
30 1 0.02
31 4 0.08
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.15
Consensus pattern (27 bp):
AAAAATAAAACTAAAAATAAAATAAAA
Found at i:5856827 original size:19 final size:19
Alignment explanation
Indices: 5856765--5856842 Score: 66
Period size: 19 Copynumber: 3.9 Consensus size: 19
5856755 ATAAAACCAG
*
5856765 AAAATAAAATAAAAAAAAAT
1 AAAATAAAA-AAAGAAAAAT
** *
5856785 AAGCTAAAAATATAAAATAAAT
1 AAAATAAAAA-A-AGAA-AAAT
* *
5856807 AAAATCAAAAAATAAAAAT
1 AAAATAAAAAAAGAAAAAT
5856826 AAAATAAAAAAAGAAAA
1 AAAATAAAAAAAGAAAA
5856843 CCTGGCGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
19 20 0.43
20 11 0.23
21 5 0.11
22 11 0.23
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (19 bp):
AAAATAAAAAAAGAAAAAT
Found at i:5857221 original size:20 final size:20
Alignment explanation
Indices: 5857193--5857234 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
5857183 TTTCATGTTC
5857193 TTCTAAAAAAT-CCAAATTT
1 TTCTAAAAAATCCCAAATTT
5857212 TTCTAGAAAAATCCCAAATTT
1 TTCTA-AAAAATCCCAAATTT
5857233 TT
1 TT
5857235 GCAAATTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.24
20 6 0.29
21 10 0.48
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.38
Consensus pattern (20 bp):
TTCTAAAAAATCCCAAATTT
Found at i:5857690 original size:3 final size:3
Alignment explanation
Indices: 5857665--5857791 Score: 93
Period size: 3 Copynumber: 43.3 Consensus size: 3
5857655 AAGGAAAAAA
* * * **
5857665 AAT AAA AAT AAA AAT AA- AAT AAT AAT GAT AAT TCT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
5857712 AAT AAT AAT AAT ACT AAT AA- ACT -AT GAAC AAT -AT CAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
* * *
5857755 AAT AGT AAA AAT AAT AAT ATAT AAT -AT AAC AAT AAT A
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT A
5857792 CTATAATATG
Statistics
Matches: 94, Mismatches: 23, Indels: 14
0.72 0.18 0.11
Matches are distributed among these distances:
2 8 0.09
3 82 0.87
4 4 0.04
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5858453 original size:120 final size:119
Alignment explanation
Indices: 5857995--5859415 Score: 1021
Period size: 118 Copynumber: 12.0 Consensus size: 119
5857985 AATAACTATA
* * * ** **
5857995 ATGAAACCATGAGTCAAGAATGAAGCGACCAAGATCGCGTCGAAGTTGAAAATAAATGA-TCGGG
1 ATGAAACCACGAGTCAA-AATGAAGCGACCAAGATCGAGTCGAGGTCAAAAATAAATGACT-AAG
** * * * *
5858059 ATGGAACCATGAGTCATGAGAAATGATATGGACTGAGCCAAGATCATGTGA-TCGAG
64 ACAGAACCATGAGTCATAAGAAATGATCTGGACTGAGCCAAGATCAGGTGACT-GGG
* * * * * * * * ** * ** *
5858115 ACGAAACCATGAGTC-AAATGAGGCAACCAGGACCAAGTTGAGGTTGAAAATAAATAACCGAGAT
1 ATGAAACCACGAGTCAAAATGAAGCGACCAAGATCGAGTCGAGGTCAAAAATAAATGACTAAGAC
* * * * * *
5858179 GGAACCACGAGTCATAAGAAATGATCTAGATTGAGCCAAGATCAGGTTATTGGG
66 AGAACCATGAGTCATAAGAAATGATCTGGACTGAGCCAAGATCAGGTGACTGGG
* * * *
5858233 ATGAAATCACGAGTC-AAATGAGGTGACCAAGATCGAGTCGAGGTCAAAAAATAAATGACCAAGA
1 ATGAAACCACGAGTCAAAATGAAGCGACCAAGATCGAGTCGAGGTC-AAAAATAAATGACTAAGA
* * *
5858297 C-GAAACCATGAGTCATAAGAAATGGTCTAGACTGAGCCAAGATTAGGTGACTGGG
65 CAG-AACCATGAGTCATAAGAAATGATCTGGACTGAGCCAAGATCAGGTGACTGGG
* * * *
5858352 ATGAAACCACGAGTCAAAAATGAAGCAACTAGGATCGAGTCGAGGTAAAAAATAAATGACTAAGA
1 ATGAAACCACGAGTC-AAAATGAAGCGACCAAGATCGAGTCGAGGTCAAAAATAAATGACTAAGA
* * * * * * *
5858417 CAGAATCACGAGTCATAAGAAATAATCTGGATTGAGCTACGATCAAGTGACTGGG
65 CAGAACCATGAGTCATAAGAAATGATCTGGACTGAGCCAAGATCAGGTGACTGGG
* * * * ** ** **
5858472 ATGAAACCACTAGTC-AAATG-AGATGACCAAGACCAAGTTAAGGTTGAAAATAAATGACCGAGA
1 ATGAAACCACGAGTCAAAATGAAG-CGACCAAGATCGAGTCGAGGTCAAAAATAAATGACTAAGA
** * * *
5858535 TGGAACCATGAGTCAT----AATGATTTGGACTGAGCCAAGATCAGATGA-TCAGG
65 CAGAACCATGAGTCATAAGAAATGATCTGGACTGAGCCAAGATCAGGTGACT-GGG
* * * * * * * * * *
5858586 ATGAAATCACGAGT-TAAATGAGGTGACCAAGATTGAGTCAACGTCAAAAATAAATGAATGAGAT
1 ATGAAACCACGAGTCAAAATGAAGCGACCAAGATCGAGTCGAGGTCAAAAATAAATGACTAAGAC
* * * *
5858650 GGAACCATGAGTCATAAGAAATGGTTTGGACTGAGCCAAGATCAGGTGATTGGG
66 AGAACCATGAGTCATAAGAAATGATCTGGACTGAGCCAAGATCAGGTGACTGGG
* * * *
5858704 ATAAAATCACGAGTCAAAAATGAAGCGACCAAGA-CTGAATCGAGGTCAAAAATAAATGATTGAA
1 ATGAAACCACGAGTC-AAAATGAAGCGACCAAGATC-GAGTCGAGGTCAAAAATAAATGACT-AA
* * * * * *
5858768 -ACAAAACCATAAGTCCATAAGAAATGATCTGGACTAAGCCAAGATCAAGTAACCGGG
63 GACAGAACCATGAGT-CATAAGAAATGATCTGGACTGAGCCAAGATCAGGTGACTGGG
* * *
5858825 ATGAAACCACGAGTCAAAAATGAAGCGACCAAGATCGAGTCAAGATCAAAAATAAATGA-TCAGG
1 ATGAAACCACGAGTC-AAAATGAAGCGACCAAGATCGAGTCGAGGTCAAAAATAAATGACT-AAG
* * * * * * * *
5858889 A-TGAAACCATAAGTTATAAGAAATAATTTGGATTGAGCCAAGATTAGGTGACCT-GA
64 ACAG-AACCATGAGTCATAAGAAATGATCTGGACTGAGCCAAGATCAGGTGA-CTGGG
* ** * * * * * *
5858945 ATGAAACCACGAGTCAAAAATGAAGTGATTAGGATCGAGTTGAGGTTAAAAATAAATAAATGAGA
1 ATGAAACCACGAGTC-AAAATGAAGCGACCAAGATCGAGTCGAGGTCAAAAATAAATGACTAAGA
* ** * * * *
5859010 -TGAAACCACAAGTCATAA-AAATTGATCTGGACTAAGCCAAGATTAGATGATTGGG
65 CAG-AACCATGAGTCATAAGAAA-TGATCTGGACTGAGCCAAGATCAGGTGACTGGG
* * * *
5859065 ATGAAACCACGAGTC-AAATAAAGTGACC-AGAACCGAGTCGAGGTCAAAAATAAAT-AATCAAG
1 ATGAAACCACGAGTCAAAATGAAGCGACCAAG-ATCGAGTCGAGGTCAAAAATAAATGACT-AAG
* * * * * * * **
5859127 ATAAAACCATGAGTCATAAGAAATGATCTGAACTAAGCTAAGATAAGGTG-GTCGAA
64 ACAGAACCATGAGTCATAAGAAATGATCTGGACTGAGCCAAGATCAGGTGACT-GGG
* * * * * **
5859183 ATAAAACCACGAGT-TAAATG-AGACGACCAGGATCGAGTTGAGCTCAAAAATAAATGA-TCGGA
1 ATGAAACCACGAGTCAAAATGAAG-CGACCAAGATCGAGTCGAGGTCAAAAATAAATGACTAAG-
* * * * **
5859245 ACAGAACCACGAGTCATAAGAAATGGTTTGGACTGAGCCAAGATCAAGTGA-TCAAG
64 ACAGAACCATGAGTCATAAGAAATGATCTGGACTGAGCCAAGATCAGGTGACT-GGG
* ** *
5859301 ATGAAACCACGAGTCAAAAATGAAGCGACCATGA-CTGAGTTAAGGTCAAAAATAAATGACTGAG
1 ATGAAACCACGAGTC-AAAATGAAGCGACCAAGATC-GAGTCGAGGTCAAAAATAAATGACTAAG
* * * *
5859365 A-TGAAACCATGAGTCATAATAAATGATTTGGACTGAGCCAAAATCAGGTGA
64 ACAG-AACCATGAGTCATAAGAAATGATCTGGACTGAGCCAAGATCAGGTGA
5859416 GTGATAATAG
Statistics
Matches: 1045, Mismatches: 211, Indels: 90
0.78 0.16 0.07
Matches are distributed among these distances:
113 1 0.00
114 89 0.09
115 1 0.00
117 10 0.01
118 374 0.36
119 89 0.09
120 350 0.33
121 130 0.12
122 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.19
Consensus pattern (119 bp):
ATGAAACCACGAGTCAAAATGAAGCGACCAAGATCGAGTCGAGGTCAAAAATAAATGACTAAGAC
AGAACCATGAGTCATAAGAAATGATCTGGACTGAGCCAAGATCAGGTGACTGGG
Found at i:5858980 original size:593 final size:591
Alignment explanation
Indices: 5858020--5859410 Score: 1516
Period size: 593 Copynumber: 2.3 Consensus size: 591
5858010 AAGAATGAAG
* ** *
5858020 CGACCAAGATCGCGTCGAAG-TTGAAAATAAATGATCGGGATGGAACCATGAGTCATGAGAAATG
1 CGACCAAGATCGAGTC-AAGCTCAAAAATAAATGATC-GGATGGAACCATGAGTCATAAGAAATG
* * * * * * * *
5858084 ATATGGACTGAGCCAAGATCATGTGATCGAGACGAAACCATGAGTC--AAATGAGGCAACCAGGA
64 GTTTGGACTGAGCCAAGATCAAGTGATCGAGATGAAACCACGAGTCAAAAATGAAGCGACCAAGA
* ** * * * * * *
5858147 C-CAAGTTGAGGTTGAAAATAAATAACCGAGATGGAACCACGAGTCATAAGAAATGATCTAGATT
129 CTGAA-TTGAGGTCAAAAATAAATGACTGAGATGAAACCATGAGTCATAAGAAATGATCTGGACT
* * ** * * * * *
5858211 GAGCCAAGATCAGGTTATTGGGATGAAATCACGAGTCAAATGAGGTGACCAAGATCGAGTCGAGG
193 GAGCCAAGATCAAGTAACCGGGATGAAACCACGAGTCAAATGAAGCGACCAAGATCGAGTCAAGA
* **
5858276 TCAAAAAATAAATGACCAAGACGAAACCATGAGTCATAAGAAATGGTCTAGACTGAGCCAAGATT
258 TCAAAAAATAAATGACCAAGACGAAACCATAAGTCATAAGAAATAATCTAGACTGAGCCAAGATT
*
5858341 AGGTGACTGGGATGAAACCACGAGTCAAAAATGAAGCAACTAGGATCGAGTCGAGGTAAAAAATA
323 AGGTGACTGGAATGAAACCACGAGTCAAAAATGAAGCAACTAGGATCGAGTCGAGGTAAAAAATA
* * * * * * * *
5858406 AATGACTAAGACAG-AATCACGAGTCATAAGAAA-TAATCTGGATTGAGCTACGATCAAG-TGAC
388 AATAAATAAGA-AGAAACCACAAGTCATAA-AAATTAATCTGGACTAAGCCAAGAT-AAGATGAC
* * * ** *
5858468 TGGGATGAAACCACTAGTCAAAT-GAGATGACCA-AGACCAAGTTAAGGTTGAAAATAAATGACC
450 TGGGATGAAACCACGAGTCAAATAAAG-TGACCAGA-ACCAAGTCAAGGTCAAAAATAAATAACC
* ** * * * * * * *
5858531 GAGATGGAACCATGAGTCAT-AATGATTTGGACTGAGCCAAGATCAGATGATC-AGGATGAAATC
513 AAGATAAAACCATGAGTCATAAATGATCTGAACTAAGCCAAGATAAGATGATCGA-AATAAAACC
*
5858594 ACGAGTTAAATGAGG
577 ACGAGTTAAATGAGA
* *
5858609 TGACCAAGATTGAGTCAA-CGTCAAAAATAAATGAAT-GAGATGGAACCATGAGTCATAAGAAAT
1 CGACCAAGATCGAGTCAAGC-TCAAAAATAAATG-ATCG-GATGGAACCATGAGTCATAAGAAAT
* * * * *
5858672 GGTTTGGACTGAGCCAAGATCAGGTGATTGGGATAAAATCACGAGTCAAAAATGAAGCGACCAAG
63 GGTTTGGACTGAGCCAAGATCAAGTGATCGAGATGAAACCACGAGTCAAAAATGAAGCGACCAAG
* * * ** *
5858737 ACTGAATCGAGGTCAAAAATAAATGATTGAAACAAAACCATAAGTCCATAAGAAATGATCTGGAC
128 ACTGAATTGAGGTCAAAAATAAATGACTGAGATGAAACCATGAGT-CATAAGAAATGATCTGGAC
*
5858802 TAAGCCAAGATCAAGTAACCGGGATGAAACCACGAGTCAAAAATGAAGCGACCAAGATCGAGTCA
192 TGAGCCAAGATCAAGTAACCGGGATGAAACCACGAGTC--AAATGAAGCGACCAAGATCGAGTCA
* * * * * * *
5858867 AGATC-AAAAATAAATGATCAGGATGAAACCATAAGTTATAAGAAATAATTTGGATTGAGCCAAG
255 AGATCAAAAAATAAATGACCAAGACGAAACCATAAGTCATAAGAAATAATCTAGACTGAGCCAAG
** * * *
5858931 ATTAGGTGACCT-GAATGAAACCACGAGTCAAAAATGAAGTGATTAGGATCGAGTTGAGGTTAAA
320 ATTAGGTGA-CTGGAATGAAACCACGAGTCAAAAATGAAGCAACTAGGATCGAGTCGAGGTAAAA
* * * *
5858995 AATAAATAAATGAGATGAAACCACAAGTCATAAAAATTGATCTGGACTAAGCCAAGATTAGATGA
384 AATAAATAAATAAGAAGAAACCACAAGTCATAAAAATTAATCTGGACTAAGCCAAGATAAGATGA
* * * *
5859060 TTGGGATGAAACCACGAGTCAAATAAAGTGACCAGAACCGAGTCGAGGTCAAAAATAAATAATCA
449 CTGGGATGAAACCACGAGTCAAATAAAGTGACCAGAACCAAGTCAAGGTCAAAAATAAATAACCA
* * *
5859125 AGATAAAACCATGAGTCATAAGAAATGATCTGAACTAAGCTAAGATAAGGTGGTCGAAATAAAAC
514 AGATAAAACCATGAGTCAT---AAATGATCTGAACTAAGCCAAGATAAGATGATCGAAATAAAAC
5859190 CACGAGTTAAATGAGA
576 CACGAGTTAAATGAGA
* ** ** *
5859206 CGACCAGGATCGAGTTGAGCTCAAAAATAAATGATCGGAACAGAACCACGAGTCATAAGAAATGG
1 CGACCAAGATCGAGTCAAGCTCAAAAATAAATGATCGG-ATGGAACCATGAGTCATAAGAAATGG
* *
5859271 TTTGGACTGAGCCAAGATCAAGTGATCAAGATGAAACCACGAGTCAAAAATGAAGCGACCATGAC
65 TTTGGACTGAGCCAAGATCAAGTGATCGAGATGAAACCACGAGTCAAAAATGAAGCGACCAAGAC
* * * *
5859336 TGAGTTAAGGTCAAAAATAAATGACTGAGATGAAACCATGAGTCATAATAAATGATTTGGACTGA
130 TGAATTGAGGTCAAAAATAAATGACTGAGATGAAACCATGAGTCATAAGAAATGATCTGGACTGA
*
5859401 GCCAAAATCA
195 GCCAAGATCA
5859411 GGTGAGTGAT
Statistics
Matches: 656, Mismatches: 122, Indels: 41
0.80 0.15 0.05
Matches are distributed among these distances:
588 3 0.00
589 86 0.13
590 2 0.00
591 42 0.06
592 57 0.09
593 214 0.33
594 31 0.05
596 31 0.05
597 188 0.29
598 2 0.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.19
Consensus pattern (591 bp):
CGACCAAGATCGAGTCAAGCTCAAAAATAAATGATCGGATGGAACCATGAGTCATAAGAAATGGT
TTGGACTGAGCCAAGATCAAGTGATCGAGATGAAACCACGAGTCAAAAATGAAGCGACCAAGACT
GAATTGAGGTCAAAAATAAATGACTGAGATGAAACCATGAGTCATAAGAAATGATCTGGACTGAG
CCAAGATCAAGTAACCGGGATGAAACCACGAGTCAAATGAAGCGACCAAGATCGAGTCAAGATCA
AAAAATAAATGACCAAGACGAAACCATAAGTCATAAGAAATAATCTAGACTGAGCCAAGATTAGG
TGACTGGAATGAAACCACGAGTCAAAAATGAAGCAACTAGGATCGAGTCGAGGTAAAAAATAAAT
AAATAAGAAGAAACCACAAGTCATAAAAATTAATCTGGACTAAGCCAAGATAAGATGACTGGGAT
GAAACCACGAGTCAAATAAAGTGACCAGAACCAAGTCAAGGTCAAAAATAAATAACCAAGATAAA
ACCATGAGTCATAAATGATCTGAACTAAGCCAAGATAAGATGATCGAAATAAAACCACGAGTTAA
ATGAGA
Found at i:5860543 original size:41 final size:41
Alignment explanation
Indices: 5860497--5860580 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 41
5860487 TTTTTTTTGC
* * * *
5860497 TTTTTTCTGGGTTGAGCATATTAGCATTTTGCCTCATCAAT
1 TTTTTTCTGGGTGGAGCACATTAGCATTTTACATCATCAAT
* * * *
5860538 TTTTTTTTTGGTGGAGCACATTGGTATTTTACATCATCAAT
1 TTTTTTCTGGGTGGAGCACATTAGCATTTTACATCATCAAT
5860579 TT
1 TT
5860581 CTCTTCTTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (41 bp):
TTTTTTCTGGGTGGAGCACATTAGCATTTTACATCATCAAT
Found at i:5864341 original size:7 final size:7
Alignment explanation
Indices: 5864317--5864384 Score: 50
Period size: 7 Copynumber: 9.4 Consensus size: 7
5864307 GAAATTTCTC
5864317 AAAAAT-
1 AAAAATA
*
5864323 AAAAACA
1 AAAAATA
5864330 AAAAATA
1 AAAAATA
*
5864337 TAAAATA
1 AAAAATA
5864344 AAAGAAGCTA
1 AAA-AA--TA
5864354 AAAAATA
1 AAAAATA
*
5864361 TAAAATCA
1 AAAAAT-A
5864369 AAAAAT-
1 AAAAATA
*
5864375 CAAAATA
1 AAAAATA
5864382 AAA
1 AAA
5864385 TGAAAAAAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
6 10 0.21
7 23 0.48
8 8 0.17
9 2 0.04
10 5 0.10
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:5865221 original size:3 final size:3
Alignment explanation
Indices: 5865213--5865328 Score: 123
Period size: 3 Copynumber: 39.3 Consensus size: 3
5865203 AAATAAAAAG
* * *
5865213 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAC AAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
5865261 AAT AA- ACT -AT ATAC AAT -AT CAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5865304 AAT AAT ATAT AAT -AT AAT AAT AAT A
1 AAT AAT A-AT AAT AAT AAT AAT AAT A
5865329 CTATATTATA
Statistics
Matches: 94, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
2 6 0.06
3 83 0.88
4 5 0.05
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:5867042 original size:10 final size:10
Alignment explanation
Indices: 5867029--5867074 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
5867019 AGAAATTAAA
5867029 AAAAAAAGAG
1 AAAAAAAGAG
**
5867039 AAAAAAATTG
1 AAAAAAAGAG
*
5867049 AAAAAAATA-
1 AAAAAAAGAG
5867058 AAAAAAAGAG
1 AAAAAAAGAG
5867068 AAAAAAA
1 AAAAAAA
5867075 AGTAGTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
9 8 0.26
10 23 0.74
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.07
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:5867106 original size:21 final size:21
Alignment explanation
Indices: 5867048--5867111 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
5867038 GAAAAAAATT
*
5867048 GAAAAAAATAAAAAA-AAGAG
1 GAAAAAAATAAAAAACAAAAG
* *
5867068 AAAAAAAAGTAGTGAAAACAAAAG
1 GAAAAAAA-TA--AAAAACAAAAG
5867092 GAAAAAAATAAAAAACAAAA
1 GAAAAAAATAAAAAACAAAA
5867112 ACAATAAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
20 7 0.20
21 11 0.31
23 6 0.17
24 11 0.31
ACGTcount: A:0.78, C:0.03, G:0.12, T:0.06
Consensus pattern (21 bp):
GAAAAAAATAAAAAACAAAAG
Found at i:5870250 original size:25 final size:25
Alignment explanation
Indices: 5870222--5870276 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
5870212 AAAGAACAAC
*
5870222 AATATATAACAAATGACATAATTAA
1 AATATACAACAAATGACATAATTAA
* ** *
5870247 AATATGCATGAAATTACATAATTAA
1 AATATACAACAAATGACATAATTAA
5870272 AATAT
1 AATAT
5870277 GCATGAAATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.31
Consensus pattern (25 bp):
AATATACAACAAATGACATAATTAA
Found at i:5870277 original size:25 final size:25
Alignment explanation
Indices: 5870232--5870290 Score: 100
Period size: 25 Copynumber: 2.3 Consensus size: 25
5870222 AATATATAAC
*
5870232 AAATGACATAATTAAAATATGCATG
1 AAATTACATAATTAAAATATGCATG
5870257 AAATTACATAATTAAAATATGCATG
1 AAATTACATAATTAAAATATGCATG
5870282 AAATGTACA
1 AAAT-TACA
5870291 CACATAAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 28 0.88
26 4 0.12
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (25 bp):
AAATTACATAATTAAAATATGCATG
Found at i:5870332 original size:16 final size:18
Alignment explanation
Indices: 5870313--5870353 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
5870303 AACTTTTCTT
5870313 TTTTTGT-ATTTTT-ATA
1 TTTTTGTCATTTTTCATA
* *
5870329 TTTTTTTCATTTTTCATT
1 TTTTTGTCATTTTTCATA
5870347 TTTTTGT
1 TTTTTGT
5870354 GGGAAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 6 0.30
17 6 0.30
18 8 0.40
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.78
Consensus pattern (18 bp):
TTTTTGTCATTTTTCATA
Found at i:5870334 original size:17 final size:18
Alignment explanation
Indices: 5870306--5870353 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
5870296 AAACACAAAC
5870306 TTTTC-TTTTTTTGT-AT
1 TTTTCATTTTTTTGTCAT
5870322 TTTT-ATATTTTTT-TCAT
1 TTTTCAT-TTTTTTGTCAT
5870339 TTTTCATTTTTTTGT
1 TTTTCATTTTTTTGT
5870354 GGGAAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 6 0.22
17 18 0.67
18 3 0.11
ACGTcount: A:0.10, C:0.06, G:0.04, T:0.79
Consensus pattern (18 bp):
TTTTCATTTTTTTGTCAT
Found at i:5870403 original size:10 final size:9
Alignment explanation
Indices: 5870383--5870416 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
5870373 AATCAAAACA
5870383 TTTTTTCAT
1 TTTTTTCAT
*
5870392 TTTTTTCAA
1 TTTTTTCAT
*
5870401 TTTTTTGAT
1 TTTTTTCAT
5870410 TTTTTTC
1 TTTTTTC
5870417 CAAAATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:5870405 original size:18 final size:18
Alignment explanation
Indices: 5870382--5870416 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5870372 AAATCAAAAC
5870382 ATTTTTTCATTTTTTTCA
1 ATTTTTTCATTTTTTTCA
*
5870400 ATTTTTTGATTTTTTTC
1 ATTTTTTCATTTTTTTC
5870417 CAAAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.74
Consensus pattern (18 bp):
ATTTTTTCATTTTTTTCA
Found at i:5871335 original size:17 final size:17
Alignment explanation
Indices: 5871278--5871337 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
5871268 ATACAATATG
*
5871278 AATGCATGATAATATAA
1 AATGCATGATAATAAAA
* * * **
5871295 TATGAATGATAGAGAATG
1 AATGCATGATA-ATAAAA
5871313 AATGCATGATAATAAAA
1 AATGCATGATAATAAAA
5871330 AATGCATG
1 AATGCATG
5871338 TGATGATAAG
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
17 20 0.65
18 11 0.35
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (17 bp):
AATGCATGATAATAAAA
Found at i:5871443 original size:27 final size:26
Alignment explanation
Indices: 5871378--5871437 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
5871368 GCATGAATGA
* *
5871378 TTTTAGAGTTTAGGGTCTAGGTTAGGG
1 TTTTAGAGTTTAGGGTTTAGGTTA-GC
* *
5871405 TTTAAGATTTTAGGGTTTAGTGTTAGC
1 TTTTAGAGTTTAGGGTTTAG-GTTAGC
5871432 TTTTAG
1 TTTTAG
5871438 GATTTAAGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.20, C:0.03, G:0.30, T:0.47
Consensus pattern (26 bp):
TTTTAGAGTTTAGGGTTTAGGTTAGC
Found at i:5873237 original size:27 final size:29
Alignment explanation
Indices: 5873207--5873286 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
5873197 ATTTATTATT
* *
5873207 TTAGTTGTGT-TCTT-GTATATATTCATG
1 TTAGTTGTGTCTATTCGTATATATCCATG
* *
5873234 TTAGCTGTGTCTATTCGTGTATATCCATG
1 TTAGTTGTGTCTATTCGTATATATCCATG
** *
5873263 TTAGTCATGTCTATTCGTGTATAT
1 TTAGTTGTGTCTATTCGTATATAT
5873287 TCATATTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 9 0.20
28 3 0.07
29 32 0.73
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (29 bp):
TTAGTTGTGTCTATTCGTATATATCCATG
Found at i:5873262 original size:29 final size:29
Alignment explanation
Indices: 5873224--5873311 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
5873214 TGTTCTTGTA
* *
5873224 TATATTCATGTTAG-CTGTGTCTATTCGTG
1 TATATCCATGTTAGTC-ATGTCTATTCGTG
5873253 TATATCCATGTTAGTCATGTCTATTCGTG
1 TATATCCATGTTAGTCATGTCTATTCGTG
* * * * *
5873282 TATATTCATATTATTCTTGTTTATTCGTG
1 TATATCCATGTTAGTCATGTCTATTCGTG
5873311 T
1 T
5873312 TGTGTTTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 50 0.98
30 1 0.02
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (29 bp):
TATATCCATGTTAGTCATGTCTATTCGTG
Found at i:5877199 original size:61 final size:61
Alignment explanation
Indices: 5877045--5877222 Score: 198
Period size: 61 Copynumber: 2.9 Consensus size: 61
5877035 AAAATTAAAA
* * * *
5877045 TGAGATTATTTAAGGCATTTCTAGCCAAAAATGCCTTGAATAATCCCATTCAAATTTTTTTT
1 TGAGATTATTCAAGGCATTTTTAACCAAAAATGCCTTGAATAATCCC-TTCAAATTTTTTTG
* * * **
5877107 TTAGATTATTCATA-GCATTTTTTTACCAAAAATGCCTTTAATAATCCCTTCCTA-TTTTTTG
1 TGAGATTATTCA-AGGCA-TTTTTAACCAAAAATGCCTTGAATAATCCCTTCAAATTTTTTTG
* *
5877168 TGGGATTATTCAAGGCATTTTTAACCAAAAAATACCTTGAATAATCCCTTACAAA
1 TGAGATTATTCAAGGCATTTTTAACC-AAAAATGCCTTGAATAATCCCTT-CAAA
5877223 AAATTAAATA
Statistics
Matches: 95, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
60 9 0.09
61 40 0.42
62 19 0.20
63 27 0.28
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (61 bp):
TGAGATTATTCAAGGCATTTTTAACCAAAAATGCCTTGAATAATCCCTTCAAATTTTTTTG
Found at i:5878277 original size:27 final size:27
Alignment explanation
Indices: 5878223--5878278 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
5878213 ATGTTATTTG
* *
5878223 TTCTTTCTTTGTTATGATATTCTATGC
1 TTCTGTCTTTGTTATGATATTATATGC
*
5878250 TTCTGTCTTTGTTATGATATTATGTGC
1 TTCTGTCTTTGTTATGATATTATATGC
5878277 TT
1 TT
5878279 ATTATTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.59
Consensus pattern (27 bp):
TTCTGTCTTTGTTATGATATTATATGC
Found at i:5893004 original size:24 final size:23
Alignment explanation
Indices: 5892977--5893027 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
5892967 TTTTCTTGCT
5892977 TTTGGTTAGTCCTTGCTTGACAAA
1 TTTGGTTAGTCCTTGCTTGAC-AA
*
5893001 TTTGGTTAGTCCTTGCTTGTCAA
1 TTTGGTTAGTCCTTGCTTGACAA
5893024 TTTG
1 TTTG
5893028 TCAAGGGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.47
Consensus pattern (23 bp):
TTTGGTTAGTCCTTGCTTGACAA
Found at i:5901878 original size:6 final size:6
Alignment explanation
Indices: 5901863--5901893 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5901853 GTAGTAGTTA
*
5901863 CCGTTT CCGTTG CCGTTG CCGTTG CCGTTG C
1 CCGTTG CCGTTG CCGTTG CCGTTG CCGTTG C
5901894 TTCCCATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.35, G:0.29, T:0.35
Consensus pattern (6 bp):
CCGTTG
Found at i:5908137 original size:61 final size:61
Alignment explanation
Indices: 5908042--5908166 Score: 241
Period size: 61 Copynumber: 2.0 Consensus size: 61
5908032 AAAATATCCT
5908042 TAGGGGTATTTTAGTAATTTAATCTTTTCAAGGTTAATTTTTTGTAAAACACTCCAGATCA
1 TAGGGGTATTTTAGTAATTTAATCTTTTCAAGGTTAATTTTTTGTAAAACACTCCAGATCA
*
5908103 TAGGGGTATTTTAGTAATTTAATCTTTTCAAGGTTAATTTTTTGTAAAACACTCCATATCA
1 TAGGGGTATTTTAGTAATTTAATCTTTTCAAGGTTAATTTTTTGTAAAACACTCCAGATCA
5908164 TAG
1 TAG
5908167 TTTTATATTA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (61 bp):
TAGGGGTATTTTAGTAATTTAATCTTTTCAAGGTTAATTTTTTGTAAAACACTCCAGATCA
Found at i:5908375 original size:143 final size:144
Alignment explanation
Indices: 5908109--5908415 Score: 350
Period size: 143 Copynumber: 2.1 Consensus size: 144
5908099 ATCATAGGGG
* * *
5908109 TATTTT-AGTAATTTAATCTTTTCAAGGTTAATTTTTTGTAAAACACTCCATATCATAGTTTTAT
1 TATTTTCA-TAATTTGACCTTTTCAAGGTTAATTTTTTGTAAAACACTCCAGATCATAGTTTTAT
* * * * *
5908173 ATTATTTCATTAATTTTGATGCATTAAAAACCTTGATCGCACTATTGAAGGTGTGAAATTACCAA
65 ATCATTTCATGAATTTTGATGCATTAAAAACCTTGATAGCACTATTGAAGGAGTAAAATTACCAA
*
5908238 AATACCCTTAA-AGA
130 AATACCCCTAATAGA
* * * * * *
5908252 TATTTTCATAATTTGACCTTTTCGAGGTTGATTTTTTGTGAAACGCTTCAGATCATATTTTTATA
1 TATTTTCATAATTTGACCTTTTCAAGGTTAATTTTTTGTAAAACACTCCAGATCATAGTTTTATA
* * * * ** *
5908317 TCATTTGATGATTTTTGATGCATTAAAAACTTTGATAGCAC-ATTGGATGGAGTAAAATTATTAT
66 TCATTTCATGAATTTTGATGCATTAAAAACCTTGATAGCACTATT-GAAGGAGTAAAATTACCAA
* *
5908381 AATGCCCCTAATAGG
130 AATACCCCTAATAGA
*
5908396 TAATTTCATAATTTGACCTT
1 TATTTTCATAATTTGACCTT
5908416 CCCATTGTTG
Statistics
Matches: 136, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
142 3 0.02
143 111 0.82
144 22 0.16
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (144 bp):
TATTTTCATAATTTGACCTTTTCAAGGTTAATTTTTTGTAAAACACTCCAGATCATAGTTTTATA
TCATTTCATGAATTTTGATGCATTAAAAACCTTGATAGCACTATTGAAGGAGTAAAATTACCAAA
ATACCCCTAATAGA
Found at i:5910046 original size:13 final size:13
Alignment explanation
Indices: 5909923--5910116 Score: 109
Period size: 13 Copynumber: 14.8 Consensus size: 13
5909913 TCCAAATCCC
* *
5909923 AAACCGAAACCTT
1 AAACCTAAACCCT
*
5909936 AAATCTTAAACCCT
1 AAA-CCTAAACCCT
*
5909950 AAACCTCAAACCGT
1 AAACCT-AAACCCT
5909964 AAACCTAAATCCC-
1 AAACCTAAA-CCCT
*
5909977 AAATCCTAAA-TCT
1 AAA-CCTAAACCCT
* *
5909990 AAACTTTAAA-CAT
1 AAAC-CTAAACCCT
5910003 AAACCTTAAACCCT
1 AAACC-TAAACCCT
* *
5910017 AAACCCCAAACCTT
1 AAA-CCTAAACCCT
*
5910031 AAATCTAAACCCT
1 AAACCTAAACCCT
5910044 AAACCTAAA-CC-
1 AAACCTAAACCCT
5910055 AAACCCT-AACCCT
1 AAA-CCTAAACCCT
*
5910068 AAATCCT-AACCTT
1 AAA-CCTAAACCCT
*
5910081 AAACCTAAATCCT
1 AAACCTAAACCCT
*
5910094 -AACTTTAAACCC-
1 AAAC-CTAAACCCT
5910106 AAACCCTAAAC
1 AAA-CCTAAAC
5910117 TTTCCCCAAA
Statistics
Matches: 140, Mismatches: 25, Indels: 32
0.71 0.13 0.16
Matches are distributed among these distances:
11 5 0.04
12 15 0.11
13 73 0.52
14 45 0.32
15 2 0.01
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.21
Consensus pattern (13 bp):
AAACCTAAACCCT
Found at i:5910087 original size:19 final size:19
Alignment explanation
Indices: 5910002--5910096 Score: 95
Period size: 19 Copynumber: 4.9 Consensus size: 19
5909992 ACTTTAAACA
*
5910002 TAAACCTTAAACCCTAAACCC
1 TAAACC-TAAATCCT-AACCC
*
5910023 CAAACCTTAAAT-CTAAACCC
1 TAAACC-TAAATCCT-AACCC
*
5910043 TAAACCTAAA-CCAAACCC
1 TAAACCTAAATCCTAACCC
* *
5910061 TAACCCTAAATCCTAACCT
1 TAAACCTAAATCCTAACCC
5910080 TAAACCTAAATCCTAAC
1 TAAACCTAAATCCTAAC
5910097 TTTAAACCCA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
18 14 0.22
19 27 0.42
20 13 0.20
21 10 0.16
ACGTcount: A:0.44, C:0.36, G:0.00, T:0.20
Consensus pattern (19 bp):
TAAACCTAAATCCTAACCC
Found at i:5910101 original size:19 final size:19
Alignment explanation
Indices: 5910024--5910114 Score: 87
Period size: 19 Copynumber: 4.8 Consensus size: 19
5910014 CCTAAACCCC
*
5910024 AAACCTTAAAT-CTAAACCCT
1 AAACC-TAAATCCT-AACCTT
* *
5910044 AAACCTAAA-CCAAACCCT
1 AAACCTAAATCCTAACCTT
*
5910062 AACCCTAAATCCTAACCTT
1 AAACCTAAATCCTAACCTT
*
5910081 AAACCTAAATCCTAACTTT
1 AAACCTAAATCCTAACCTT
* *
5910100 AAACCCAAACCCTAA
1 AAACCTAAATCCTAA
5910115 ACTTTCCCCA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
18 14 0.23
19 42 0.69
20 5 0.08
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (19 bp):
AAACCTAAATCCTAACCTT
Found at i:5910111 original size:6 final size:7
Alignment explanation
Indices: 5909942--5910116 Score: 99
Period size: 7 Copynumber: 26.7 Consensus size: 7
5909932 CCTTAAATCT
5909942 TAAACCC
1 TAAACCC
5909949 TAAA-CC
1 TAAACCC
*
5909955 TCAAACCG
1 T-AAACCC
5909963 TAAA-CC
1 TAAACCC
5909969 TAAATCCC
1 TAAA-CCC
*
5909977 -AAATCC
1 TAAACCC
*
5909983 TAAA-TC
1 TAAACCC
**
5909989 TAAACTT
1 TAAACCC
*
5909996 TAAA-CA
1 TAAACCC
*
5910002 TAAACCT
1 TAAACCC
5910009 TAAACCC
1 TAAACCC
5910016 TAAACCC
1 TAAACCC
* *
5910023 CAAACCT
1 TAAACCC
*
5910030 TAAA-TC
1 TAAACCC
5910036 TAAACCC
1 TAAACCC
5910043 TAAA-CC
1 TAAACCC
5910049 TAAA-CC
1 TAAACCC
5910055 -AAACCC
1 TAAACCC
5910061 T-AACCC
1 TAAACCC
*
5910067 TAAATCC
1 TAAACCC
*
5910074 T-AACCT
1 TAAACCC
5910080 TAAA-CC
1 TAAACCC
*
5910086 TAAATCC
1 TAAACCC
**
5910093 T-AACTT
1 TAAACCC
5910099 TAAACCC
1 TAAACCC
5910106 -AAACCC
1 TAAACCC
5910112 TAAAC
1 TAAAC
5910117 TTTCCCCAAA
Statistics
Matches: 129, Mismatches: 24, Indels: 30
0.70 0.13 0.16
Matches are distributed among these distances:
5 3 0.02
6 57 0.44
7 65 0.50
8 4 0.03
ACGTcount: A:0.45, C:0.34, G:0.01, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:5911316 original size:153 final size:158
Alignment explanation
Indices: 5911113--5911426 Score: 372
Period size: 166 Copynumber: 2.0 Consensus size: 158
5911103 AAAAAATTTT
* * **
5911113 AATTCAAAAAAATTGTTTTTATTTTAATTTCCTTGTTTCAAAATAACAT-AA-AATTA-AAAAAA
1 AATTCAAAAAAATTGTTTTTATTTTAATTTCCTTATTTCAAAAGAACATAAACAAAAAGAAAAAA
* *
5911175 C-T-A-TGTTTTACATTTAATGCATATTTTAATTATGTCAGTT-ATTTAAATTGTTGTTATTTAT
66 CATAAGTGTTTTACATTTAATGCATATTTTAATTATGTCACTTAATTTAAATTATTGTTATTTAT
* * * *
5911236 TCTGTTTCTAATAGTTGTGGGGCATAAG
131 TATATTTCTAATAATTGTGGAGCATAAG
* *
5911264 AATTCAAAAAATAATTGTTTTTATTTTAATTTCCTTATTTCAAAGGAGCATAAAACAAAAAGAAA
1 AATTC-AAAAA-AATTGTTTTTATTTTAATTTCCTTATTTCAAAAGAACAT-AAACAAAAAGAAA
* *
5911329 AAACTATGAATGTGTGTTTTACATTTCATGCATATTTTAATTATTTCACTTAATTTAAATTATTG
63 AAAC-AT-AA---GTGTTTTACATTTAATGCATATTTTAATTATGTCACTTAATTTAAATTATTG
*
5911394 TTATTTATTATATTTTTAATAATTGTGGAGCAT
123 TTATTTATTATATTTCTAATAATTGTGGAGCAT
5911427 TTAGGATAGG
Statistics
Matches: 133, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
151 5 0.04
152 5 0.04
153 35 0.26
155 2 0.02
156 3 0.02
157 7 0.05
159 1 0.01
161 1 0.01
165 34 0.26
166 40 0.30
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.46
Consensus pattern (158 bp):
AATTCAAAAAAATTGTTTTTATTTTAATTTCCTTATTTCAAAAGAACATAAACAAAAAGAAAAAA
CATAAGTGTTTTACATTTAATGCATATTTTAATTATGTCACTTAATTTAAATTATTGTTATTTAT
TATATTTCTAATAATTGTGGAGCATAAG
Found at i:5912349 original size:30 final size:30
Alignment explanation
Indices: 5912313--5912370 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5912303 TAATAGATAG
* *
5912313 TACATGCATTTCATTTTACACACATTTTAA
1 TACATGCATTCCATTTCACACACATTTTAA
*
5912343 TACATGCATTCCATTTCATACACATTTT
1 TACATGCATTCCATTTCACACACATTTT
5912371 TAAAGTAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.43
Consensus pattern (30 bp):
TACATGCATTCCATTTCACACACATTTTAA
Found at i:5913552 original size:10 final size:10
Alignment explanation
Indices: 5913539--5913572 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
5913529 AAATGCAAAG
5913539 AAAAAAGAAA
1 AAAAAAGAAA
5913549 AAAAAAGAAA
1 AAAAAAGAAA
*
5913559 AAGAAAGAAA
1 AAAAAAGAAA
5913569 AAAA
1 AAAA
5913573 TGAAATCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:5913555 original size:17 final size:17
Alignment explanation
Indices: 5913535--5913571 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5913525 GGAGAAATGC
5913535 AAAGAAAAAAGAAA-AAA
1 AAAG-AAAAAGAAAGAAA
5913552 AAAGAAAAAGAAAGAAA
1 AAAGAAAAAGAAAGAAA
5913569 AAA
1 AAA
5913572 ATGAAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGAAAGAAA
Found at i:5915162 original size:19 final size:19
Alignment explanation
Indices: 5915138--5915175 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5915128 AATAACATAT
5915138 ATCATGCAATAAAAATAAA
1 ATCATGCAATAAAAATAAA
*
5915157 ATCATGCAATAATAATAAA
1 ATCATGCAATAAAAATAAA
5915176 TAAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.24
Consensus pattern (19 bp):
ATCATGCAATAAAAATAAA
Found at i:5915313 original size:22 final size:23
Alignment explanation
Indices: 5915288--5915332 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5915278 CATGCAATTT
*
5915288 AATATAT-AATCATAAAAATAAA
1 AATATATAAACCATAAAAATAAA
*
5915310 AATATATAAACCATACAAATAAA
1 AATATATAAACCATAAAAATAAA
5915333 CATGCAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (23 bp):
AATATATAAACCATAAAAATAAA
Found at i:5915317 original size:55 final size:54
Alignment explanation
Indices: 5915256--5915410 Score: 177
Period size: 55 Copynumber: 2.9 Consensus size: 54
5915246 ATCATGAATT
*
5915256 AAATATAT-AAACATGTAATAAACATGCAATTTAATATATAATCATAAAAATAA
1 AAATATATAAAACATGTAATAAACATGCAATTAAATATATAATCATAAAAATAA
* ** * * ** *
5915309 AAATATATAAACCATACAAATAAACATGCAATTAAATATACAACCATGTAAGTAA
1 AAATATATAAAACAT-GTAATAAACATGCAATTAAATATATAATCATAAAAATAA
* * *
5915364 TAATATATAAATCATGTAAATAAACATGTAATTAAATATATAATCAT
1 AAATATATAAAACATGT-AATAAACATGCAATTAAATATATAATCAT
5915411 GCAAATTCAT
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
53 8 0.10
54 5 0.06
55 70 0.84
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.30
Consensus pattern (54 bp):
AAATATATAAAACATGTAATAAACATGCAATTAAATATATAATCATAAAAATAA
Found at i:5915392 original size:35 final size:32
Alignment explanation
Indices: 5915353--5915416 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
5915343 AATATACAAC
*
5915353 CATGTAAGTAATAATATATAAATCATGTAAATAAA
1 CATGTAA-TAA-AATATAT-AATCATGCAAATAAA
*
5915388 CATGTAATTAAATATATAATCATGCAAAT
1 CATGTAATAAAATATATAATCATGCAAAT
5915417 TCATGCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 11 0.41
33 7 0.26
34 2 0.07
35 7 0.26
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.33
Consensus pattern (32 bp):
CATGTAATAAAATATATAATCATGCAAATAAA
Found at i:5916069 original size:12 final size:12
Alignment explanation
Indices: 5916052--5916081 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5916042 ACTAACAAAA
5916052 CAAAAATTAAAC
1 CAAAAATTAAAC
5916064 CAAAAATTAAAC
1 CAAAAATTAAAC
*
5916076 TAAAAA
1 CAAAAA
5916082 AAATTAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (12 bp):
CAAAAATTAAAC
Found at i:5916486 original size:41 final size:42
Alignment explanation
Indices: 5916384--5916535 Score: 144
Period size: 41 Copynumber: 3.6 Consensus size: 42
5916374 ATAACTGAGA
* * * * * * * *
5916384 CTTTAAAACTTTTGAAAAATAAAGTGCTTCCTCATAACTGAGG
1 CTTTGAAAC-TTTGGAAAATAAAATGCTCCCCCACAATTGAAG
* ***
5916427 CTTTGGAACTTTGGAAAATAAAATGCTCCCCTTTAATT-AAG
1 CTTTGAAACTTTGGAAAATAAAATGCTCCCCCACAATTGAAG
* * *
5916468 GTTTGAAACTTTGAAAAATAAAATACTCCCCCACAATTGAAG
1 CTTTGAAACTTTGGAAAATAAAATGCTCCCCCACAATTGAAG
5916510 CTTTGAAACGTTTGGAAAATAAAATG
1 CTTTGAAAC-TTTGGAAAATAAAATG
5916536 AGATCATTTT
Statistics
Matches: 87, Mismatches: 20, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
41 33 0.38
42 33 0.38
43 21 0.24
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (42 bp):
CTTTGAAACTTTGGAAAATAAAATGCTCCCCCACAATTGAAG
Found at i:5916726 original size:13 final size:13
Alignment explanation
Indices: 5916708--5916732 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5916698 TTCCAAACAT
5916708 ATGCAATGAATGC
1 ATGCAATGAATGC
5916721 ATGCAATGAATG
1 ATGCAATGAATG
5916733 AAAAGATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (13 bp):
ATGCAATGAATGC
Found at i:5918284 original size:23 final size:24
Alignment explanation
Indices: 5918245--5918297 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
5918235 TTAGCATGGT
5918245 TAAACAAAGCCTATTTAA-AGCCAA
1 TAAA-AAAGCCTATTTAAGAGCCAA
*
5918269 TAAAAAAGCCCT-TTTAAGAGCCCA
1 TAAAAAAG-CCTATTTAAGAGCCAA
5918293 TAAAA
1 TAAAA
5918298 TGCATCAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.49, C:0.21, G:0.09, T:0.21
Consensus pattern (24 bp):
TAAAAAAGCCTATTTAAGAGCCAA
Found at i:5918789 original size:144 final size:144
Alignment explanation
Indices: 5918624--5918970 Score: 446
Period size: 144 Copynumber: 2.4 Consensus size: 144
5918614 TGGCCCTCTT
* * * *
5918624 AAGCTCAAATTTTCATGAAACTTTCTAGATCTTAATTTCATAATATTTCATGATTTTTTATATAT
1 AAGCTCAAATTTTCATGAAACTTT-TAGATCTAAATTTTATAATATTTCATGATTTTTGATACAT
* *
5918689 TTA-AATCATAGCAGTACCCTAAAAAGTGTGAAATTACTAAAATACCTTTATAAGAGTATTTTTG
65 TTAGAATCACAGCAGTACCCTAAAAAGTGTGAAATTACTAAAATACCTATATAAGAGTATTTTTG
5918753 TAATTT-ACCATTCCC
130 TAATTTAACC-TTCCC
* * * * *
5918768 GAGCTCAAATTTTCATGAAACTTTTAGATCTAAATTTTATAATATTTCATAAATTTTGGTGCATT
1 AAGCTCAAATTTTCATGAAACTTTTAGATCTAAATTTTATAATATTTCATGATTTTTGATACATT
* * * * *
5918833 TAGAATCACAGCAGTACCTTGATAAGTTTGAAATTACTAAAATACCTATATATGAGTATTTTTGT
66 TAGAATCACAGCAGTACCCTAAAAAGTGTGAAATTACTAAAATACCTATATAAGAGTATTTTTGT
* **
5918898 AATTTAATCTTCTT
131 AATTTAACCTTCCC
* * * *
5918912 AAGATCAGATTTTCATGAAACTTTTCATATCTGAATTTTATAATATTTCATGATTTTTG
1 AAGCTCAAATTTTCATGAAACTTTT-AGATCTAAATTTTATAATATTTCATGATTTTTG
5918971 GGGTTTTAAA
Statistics
Matches: 174, Mismatches: 26, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
143 35 0.20
144 108 0.62
145 31 0.18
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.43
Consensus pattern (144 bp):
AAGCTCAAATTTTCATGAAACTTTTAGATCTAAATTTTATAATATTTCATGATTTTTGATACATT
TAGAATCACAGCAGTACCCTAAAAAGTGTGAAATTACTAAAATACCTATATAAGAGTATTTTTGT
AATTTAACCTTCCC
Found at i:5923536 original size:30 final size:30
Alignment explanation
Indices: 5923502--5923562 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5923492 ATACATGCAT
* *
5923502 TGCATCCCATCTACATCAATAGATAGTACA
1 TGCATCCCATCCACAACAATAGATAGTACA
* * *
5923532 TGCATTCCATCCATAACAATGGATAGTACA
1 TGCATCCCATCCACAACAATAGATAGTACA
5923562 T
1 T
5923563 ACATATTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (30 bp):
TGCATCCCATCCACAACAATAGATAGTACA
Found at i:5928312 original size:10 final size:10
Alignment explanation
Indices: 5928284--5928338 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
5928274 GATGGTTGTA
**
5928284 AAAAAAAAAA
1 AAAAAAAACC
5928294 AAAAAAAACC
1 AAAAAAAACC
5928304 AAAAAAAACC
1 AAAAAAAACC
*
5928314 --TAAAAACC
1 AAAAAAAACC
* *
5928322 TAAAAAAACT
1 AAAAAAAACC
5928332 AAAAAAA
1 AAAAAAA
5928339 TGAAAATGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
8 7 0.19
10 30 0.81
ACGTcount: A:0.82, C:0.13, G:0.00, T:0.05
Consensus pattern (10 bp):
AAAAAAAACC
Found at i:5928318 original size:18 final size:17
Alignment explanation
Indices: 5928287--5928336 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
5928277 GGTTGTAAAA
**
5928287 AAAAAAAAAAAAAAACC
1 AAAAAAAACTAAAAACC
5928304 AAAAAAAACCTAAAAACC
1 AAAAAAAA-CTAAAAACC
*
5928322 TAAAAAAACTAAAAA
1 AAAAAAAACTAAAAA
5928337 AATGAAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.80, C:0.14, G:0.00, T:0.06
Consensus pattern (17 bp):
AAAAAAAACTAAAAACC
Found at i:5928337 original size:18 final size:19
Alignment explanation
Indices: 5928296--5928337 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
5928286 AAAAAAAAAA
5928296 AAAAAACCAAAAAAAACCT
1 AAAAAACCAAAAAAAACCT
*
5928315 -AAAAACCTAAAAAAA-CT
1 AAAAAACCAAAAAAAACCT
5928332 AAAAAA
1 AAAAAA
5928338 ATGAAAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.76, C:0.17, G:0.00, T:0.07
Consensus pattern (19 bp):
AAAAAACCAAAAAAAACCT
Found at i:5928338 original size:9 final size:10
Alignment explanation
Indices: 5928295--5928338 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
5928285 AAAAAAAAAA
*
5928295 AAAAAAACCA
1 AAAAAAACCT
5928305 AAAAAAACCT
1 AAAAAAACCT
5928315 --AAAAACCT
1 AAAAAAACCT
5928323 AAAAAAA-CT
1 AAAAAAACCT
5928332 AAAAAAA
1 AAAAAAA
5928339 TGAAAATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
8 8 0.26
9 9 0.29
10 14 0.45
ACGTcount: A:0.77, C:0.16, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAACCT
Found at i:5928344 original size:18 final size:18
Alignment explanation
Indices: 5928287--5928338 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
5928277 GGTTGTAAAA
* *
5928287 AAAAAAAAAAAAAAACCA
1 AAAAAAATAAAAAAACCT
***
5928305 AAAAAAACCTAAAAACCT
1 AAAAAAATAAAAAAACCT
5928323 AAAAAAACTAAAAAAA
1 AAAAAAA-TAAAAAAA
5928339 TGAAAATGAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.81, C:0.13, G:0.00, T:0.06
Consensus pattern (18 bp):
AAAAAAATAAAAAAACCT
Found at i:5930288 original size:126 final size:127
Alignment explanation
Indices: 5930147--5930383 Score: 320
Period size: 126 Copynumber: 1.9 Consensus size: 127
5930137 AATAAAAATA
* * ** * *
5930147 AAAAAAAGACATTTGCATTTGCATCACTCATATTTGTACTTACAT-A-TGCATCATGAGAAAAAT
1 AAAAAAAGACATTTGCATTCGCATCACTCACATTCATACTT--ATGAGTGCATCATGAAAAAAAC
* * *
5930210 ATTTGCATTCACA-TCTGCATCACAAAAAAGATATTTGCATTTGCATCATTTACATCTGCATCAT
64 ATTTACATTCA-ATTCTACATCACAAAAAAGACATTTGCATTTGCATCATTTACATCTGCATCAT
*
5930274 AAAAAAAG-CATTTGCATTCGTATCACTCACATTCATACTTATGAGTGCATCATGAAAAAAACAT
1 AAAAAAAGACATTTGCATTCGCATCACTCACATTCATACTTATGAGTGCATCATGAAAAAAACAT
*
5930338 TTACATTCAATTCTACATCACAAAAAAGACATTTGTATTTGCATCA
66 TTACATTCAATTCTACATCACAAAAAAGACATTTGCATTTGCATCA
5930384 CTCACATTCG
Statistics
Matches: 96, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
124 2 0.02
125 2 0.02
126 84 0.88
127 8 0.08
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (127 bp):
AAAAAAAGACATTTGCATTCGCATCACTCACATTCATACTTATGAGTGCATCATGAAAAAAACAT
TTACATTCAATTCTACATCACAAAAAAGACATTTGCATTTGCATCATTTACATCTGCATCAT
Found at i:5930364 original size:85 final size:85
Alignment explanation
Indices: 5930275--5930429 Score: 231
Period size: 85 Copynumber: 1.8 Consensus size: 85
5930265 CTGCATCATA
*
5930275 AAAAAAG-CATTTGCATTCGTATCACTCACATTCATACTTATGAGTGCATCATGAAAAAAACATT
1 AAAAAAGACATTTGCATTCGCATCACTCACATTCATACTTATGAGTGCATCATGAAAAAAACATT
5930339 TACATTCAATTCTACATCAC
66 TACATTCAATTCTACATCAC
* * * * * *
5930359 AAAAAAGACATTTGTATTTGCATCACTCACATTCGTACTTATTAGTGTATCATGAAAAAGACATT
1 AAAAAAGACATTTGCATTCGCATCACTCACATTCATACTTATGAGTGCATCATGAAAAAAACATT
*
5930424 TGCATT
66 TACATT
5930430 TGCGTCACTT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
84 7 0.11
85 55 0.89
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (85 bp):
AAAAAAGACATTTGCATTCGCATCACTCACATTCATACTTATGAGTGCATCATGAAAAAAACATT
TACATTCAATTCTACATCAC
Found at i:5930700 original size:24 final size:28
Alignment explanation
Indices: 5930645--5930701 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 28
5930635 AAATGTATTT
*
5930645 GCATCAAGCATTTGCATTCTTGCATTTA
1 GCATCAAGCATTTGCATTCTTGCATTCA
5930673 -CATCAA-CATTTGCA-T-TTGCA-TCA
1 GCATCAAGCATTTGCATTCTTGCATTCA
5930696 GCATCA
1 GCATCA
5930702 TTTGATGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 2 0.07
24 10 0.37
25 1 0.04
26 8 0.30
27 6 0.22
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (28 bp):
GCATCAAGCATTTGCATTCTTGCATTCA
Found at i:5931143 original size:83 final size:83
Alignment explanation
Indices: 5930997--5931158 Score: 216
Period size: 83 Copynumber: 2.0 Consensus size: 83
5930987 CAGATATATT
* * * * * * * *
5930997 TCCAAGACCTCCGGGTAAAATATTTTAATTTTTTAAAGTTTTAACACCTTTATTACGAGGAGCAT
1 TCCAAGACCTCCGAGCAAAACATTTTAAATTTTCAAAGTTTCAACACCTCTATTACAAGGAGCAT
5931062 TCAAAGATTTTTTAGATC
66 TCAAAGATTTTTTAGATC
* ** *
5931080 TCCAGGACCTCCGAGCAAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTATTACAATGAGCAT
1 TCCAAGACCTCCGAGCAAAACATTTTAAATTTTCAAAGTTTCAACACCTCTATTACAAGGAGCAT
5931145 TCAAAGATTTTTTA
66 TCAAAGATTTTTTA
5931159 AGACTTTCAG
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
83 67 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (83 bp):
TCCAAGACCTCCGAGCAAAACATTTTAAATTTTCAAAGTTTCAACACCTCTATTACAAGGAGCAT
TCAAAGATTTTTTAGATC
Found at i:5931429 original size:105 final size:106
Alignment explanation
Indices: 5931167--5931531 Score: 436
Period size: 105 Copynumber: 3.5 Consensus size: 106
5931157 TAAGACTTTC
* * * * * *
5931167 AGGCATAATTTCCAAGACC-TATGGGTAAAACATTTTAAATTTTCAAAGTTTCAACACCTCTAAT
1 AGGCATAATTTCTAAGACCTTCTAGGCAAAACATTTTAAATTTTCAAAGTTTCAACGCCTCTATT
* *
5931231 ATGAGGAGCATTCAAAGAATTTTTAGATTTCTAAAACCTCT
66 ATGAAGAGCATTCAAAGATTTTTTAGATTTCTAAAACCTCT
*
5931272 -GGCATAATTTCTAATA-CTTCTAGGCAAAACATTTTAAATTTTCAAAGTTTCAACGCCTCTATT
1 AGGCATAATTTCTAAGACCTTCTAGGCAAAACATTTTAAATTTTCAAAGTTTCAACGCCTCTATT
** *
5931335 ACAAAGAACATTCAAAGATTTTTTAGATTTCTAAAACCTCT
66 ATGAAGAGCATTCAAAGATTTTTTAGATTTCTAAAACCTCT
* * *** * *
5931376 AGGCATAATTTCTAATACCTT-TAGGCTAAACATTTTAAACAATCAAAGCTTCAATGCCTCTATT
1 AGGCATAATTTCTAAGACCTTCTAGGCAAAACATTTTAAATTTTCAAAGTTTCAACGCCTCTATT
* * * * * *
5931440 ATGATGAGTATTCAAAGATTTTTGAGATTTCTAAGACCCCC
66 ATGAAGAGCATTCAAAGATTTTTTAGATTTCTAAAACCTCT
* *
5931481 AGAG-ATAATTTCTAAGACCTTCCA-GCAAAACATTTTAACTTTTCAAAGTTT
1 AG-GCATAATTTCTAAGACCTTCTAGGCAAAACATTTTAAATTTTCAAAGTTT
5931532 TAAACATTTT
Statistics
Matches: 220, Mismatches: 35, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
103 1 0.00
104 90 0.41
105 124 0.56
106 5 0.02
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (106 bp):
AGGCATAATTTCTAAGACCTTCTAGGCAAAACATTTTAAATTTTCAAAGTTTCAACGCCTCTATT
ATGAAGAGCATTCAAAGATTTTTTAGATTTCTAAAACCTCT
Found at i:5931945 original size:12 final size:12
Alignment explanation
Indices: 5931928--5931967 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
5931918 TAATTCACAA
5931928 AAAAAAAAAAAC
1 AAAAAAAAAAAC
*
5931940 AAAAAACAAAAC
1 AAAAAAAAAAAC
5931952 AAAAACAAAAAA-
1 AAAAA-AAAAAAC
5931964 AAAA
1 AAAA
5931968 CTTTCAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 20 0.80
13 5 0.20
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:5932622 original size:143 final size:147
Alignment explanation
Indices: 5932444--5932773 Score: 391
Period size: 145 Copynumber: 2.3 Consensus size: 147
5932434 TAGGAAGTAC
*
5932444 AAAATTATTAAAAT-GCCCT-TAGAGGGTATTTTCGTAATTTGACCCTTC-CAAGCTCAG-ATTT
1 AAAATTACTAAAATAGCCCTATAGAGGGTATTTTCGTAATTTGACCCTTCTCAAGCT-AGAATTT
*
5932505 TT-T-AAAACTTTTTAAATCTTAATTTC-TAATATTTCATGATTTTTTAG-GCATTTGAAATCAC
65 TTATGAAAA-TTTTTAAATCTTAATTTCATAATATTTCAT-AATTTTTAGTGCATTTGAAATCAC
5932566 AAG-AATA-CCTCGAAAAATAT
128 -AGCAATACCCT-GAAAAATAT
* * * *
5932586 AAAATTACCAAAATAGCCCTATA-AGGGTATTTTCGTAATTT-ACCTTTCTCGAGCTTGAATTTT
1 AAAATTACTAAAATAGCCCTATAGAGGGTATTTTCGTAATTTGACCCTTCTCAAGCTAGAATTTT
* *
5932649 TATGAAAATTTTTAGATCTTAATTTCATAATATTTCATAATTTTTGGTGCATTTGAAATCACAGC
66 TATGAAAATTTTTAAATCTTAATTTCATAATATTTCATAATTTTTAGTGCATTTGAAATCACAGC
* * *
5932714 AGTACCCTGAAAAGTGT
131 AATACCCTGAAAAATAT
* *
5932731 GAAATTACTAAAATA-CCCATATAG-GAGTATTTTCGTAATTTGA
1 AAAATTACTAAAATAGCCC-TATAGAGGGTATTTTCGTAATTTGA
5932774 TATTTTCAAA
Statistics
Matches: 161, Mismatches: 14, Indels: 22
0.82 0.07 0.11
Matches are distributed among these distances:
142 19 0.12
143 34 0.21
144 32 0.20
145 72 0.45
146 4 0.02
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (147 bp):
AAAATTACTAAAATAGCCCTATAGAGGGTATTTTCGTAATTTGACCCTTCTCAAGCTAGAATTTT
TATGAAAATTTTTAAATCTTAATTTCATAATATTTCATAATTTTTAGTGCATTTGAAATCACAGC
AATACCCTGAAAAATAT
Found at i:5933882 original size:21 final size:21
Alignment explanation
Indices: 5933843--5933886 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5933833 ACTATTTGCT
*
5933843 TGTTATTTTAATTTAGTTTCA
1 TGTTATTTTAATATAGTTTCA
* *
5933864 TGTTATTTTACTATGGTTTCA
1 TGTTATTTTAATATAGTTTCA
5933885 TG
1 TG
5933887 ATAGTTTAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.07, G:0.14, T:0.59
Consensus pattern (21 bp):
TGTTATTTTAATATAGTTTCA
Found at i:5941210 original size:18 final size:18
Alignment explanation
Indices: 5941184--5941223 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5941174 TATAAACCTA
* * *
5941184 AAAATTAAAAATTAAAGT
1 AAAAGTAAAAATAAAAAT
5941202 AAAAGTAAAAATAAAAAT
1 AAAAGTAAAAATAAAAAT
5941220 AAAA
1 AAAA
5941224 TAATGGGCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (18 bp):
AAAAGTAAAAATAAAAAT
Found at i:5946820 original size:67 final size:67
Alignment explanation
Indices: 5946741--5946880 Score: 226
Period size: 67 Copynumber: 2.1 Consensus size: 67
5946731 AGAAAAGATG
* **
5946741 AATGCACCAGGATGTAACTTAGAATAAAAGAAAGGGAAAATAATGCATGTTTAACATTAATGGTT
1 AATGCACCAGGATGCAACTTAGAATAAAAGAAAGGGAAAATAACCCATGTTTAACATTAATGGTT
5946806 GA
66 GA
* * *
5946808 AATGCATCAGGATGCACCTTAGAATAAAAGAAAGGGAAAATAACCCCTGTTTAACATTAATGGTT
1 AATGCACCAGGATGCAACTTAGAATAAAAGAAAGGGAAAATAACCCATGTTTAACATTAATGGTT
5946873 GA
66 GA
5946875 AATGCA
1 AATGCA
5946881 AGAGCTTTGA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (67 bp):
AATGCACCAGGATGCAACTTAGAATAAAAGAAAGGGAAAATAACCCATGTTTAACATTAATGGTT
GA
Found at i:5950868 original size:2 final size:2
Alignment explanation
Indices: 5950861--5950896 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5950851 CTCCAATACA
5950861 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5950897 CAAGTGTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5954832 original size:25 final size:25
Alignment explanation
Indices: 5954804--5954857 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 25
5954794 TTTTGGAACC
5954804 TTTTTT-AGA-TTTTTTTAAAATTT
1 TTTTTTGAGATTTTTTTTAAAATTT
5954827 TATTTTTGAGATTTTTTTTAAAATTT
1 T-TTTTTGAGATTTTTTTTAAAATTT
5954853 TTTTT
1 TTTTT
5954858 ATTATTGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 1 0.04
24 5 0.18
25 7 0.25
26 15 0.54
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (25 bp):
TTTTTTGAGATTTTTTTTAAAATTT
Found at i:5954858 original size:12 final size:12
Alignment explanation
Indices: 5954813--5954858 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
5954803 CTTTTTTAGA
5954813 TTTTTTTAAAATT
1 TTTTTTTAAAA-T
* *
5954826 TTATTTTTGAGAT
1 TT-TTTTTAAAAT
5954839 TTTTTTTAAAAT
1 TTTTTTTAAAAT
5954851 TTTTTTTA
1 TTTTTTTA
5954859 TTATTGATGG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 16 0.57
13 5 0.18
14 7 0.25
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (12 bp):
TTTTTTTAAAAT
Found at i:5955585 original size:18 final size:19
Alignment explanation
Indices: 5955549--5955588 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5955539 AATTAATTCT
5955549 AATTTAAATATATATTTAA
1 AATTTAAATATATATTTAA
5955568 AATTT-AATATGATA-TTAA
1 AATTTAAATAT-ATATTTAA
5955586 AAT
1 AAT
5955589 AAGCATTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
AATTTAAATATATATTTAA
Found at i:5956453 original size:13 final size:14
Alignment explanation
Indices: 5956420--5956458 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
5956410 CAATATATGG
5956420 TAGTAAATAGAAGA
1 TAGTAAATAGAAGA
*
5956434 TAG-AAATATAA-A
1 TAGTAAATAGAAGA
5956446 TAGTAAATAGAAG
1 TAGTAAATAGAAG
5956459 TTGTGATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 4 0.19
13 14 0.67
14 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.23
Consensus pattern (14 bp):
TAGTAAATAGAAGA
Found at i:5956613 original size:19 final size:17
Alignment explanation
Indices: 5956575--5956621 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
5956565 TATAAAATAT
5956575 AATTTAAATTTTTATTA
1 AATTTAAATTTTTATTA
*
5956592 AATTTATATATTTTATTAA
1 AATTTAAAT-TTTTATT-A
5956611 AATTTTAAATT
1 AA-TTTAAATT
5956622 ATTTTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 8 0.32
18 7 0.28
19 4 0.16
20 6 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTTAAATTTTTATTA
Found at i:5962571 original size:24 final size:24
Alignment explanation
Indices: 5962544--5962592 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
5962534 TAGCAGTATG
5962544 AAAAAATTAGCTTACGTGATTGTC
1 AAAAAATTAGCTTACGTGATTGTC
5962568 AAAAAATTAGCTTACGTGATTGTC
1 AAAAAATTAGCTTACGTGATTGTC
5962592 A
1 A
5962593 CTTTGGCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (24 bp):
AAAAAATTAGCTTACGTGATTGTC
Found at i:5974297 original size:178 final size:178
Alignment explanation
Indices: 5973996--5974356 Score: 544
Period size: 178 Copynumber: 2.0 Consensus size: 178
5973986 GGTATGCATA
* * * **
5973996 TTTTATTAGATTGCAACCTGAAACCCACGTAAATCGTTTCTGCCCTGCTTCTTATATCCCACCTT
1 TTTTATTAGATTGCAACCTAAAACCCACGTAAACCGTTTCTACCCCACTTCTTATATCCCACCTT
5974061 AAGCCAAGCTACATAGAAGCTGAGTCATCCAAGCCAAGCCACTTTAGTTGCCTTTTGTACCTAAA
66 AAGCCAAGCTACATAGAAGCTGAGTCATCCAAGCCAAGCCACTTTAGTTGCCTTTTGTACCTAAA
** * *
5974126 GCCAAGCCGTGCAACCCAGTCACATAGTCGAGCCAACTTCAGGTATTT
131 GCCAAGCCGCACAACCCAGCCACATAGTCGAGCCAACTTCAAGTATTT
* * *
5974174 TTTTATTAGATTGCCACCTAAAACCCACTTAAACCGTTTTTACCCCACTT-TCTATATCCCACCT
1 TTTTATTAGATTGCAACCTAAAACCCACGTAAACCGTTTCTACCCCACTTCT-TATATCCCACCT
* * *
5974238 TAAGTCAAGCTACATAGAAGTTGAGTCATCCAAGCCAAGCCACTTTAGTTGCTTTTTGTACCTAA
65 TAAGCCAAGCTACATAGAAGCTGAGTCATCCAAGCCAAGCCACTTTAGTTGCCTTTTGTACCTAA
* * *
5974303 AGCCAAGCCGCACAATCCAGCCACATAGTCGAGCCAATTTCAAGTTTTT
130 AGCCAAGCCGCACAACCCAGCCACATAGTCGAGCCAACTTCAAGTATTT
5974352 TTTTA
1 TTTTA
5974357 AATTTTATTG
Statistics
Matches: 164, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
177 1 0.01
178 163 0.99
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (178 bp):
TTTTATTAGATTGCAACCTAAAACCCACGTAAACCGTTTCTACCCCACTTCTTATATCCCACCTT
AAGCCAAGCTACATAGAAGCTGAGTCATCCAAGCCAAGCCACTTTAGTTGCCTTTTGTACCTAAA
GCCAAGCCGCACAACCCAGCCACATAGTCGAGCCAACTTCAAGTATTT
Found at i:5975272 original size:19 final size:17
Alignment explanation
Indices: 5975228--5975272 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
5975218 TATGACAATA
5975228 AAAAAATGAAAAGAAA-
1 AAAAAATGAAAAGAAAT
5975244 AAAAAA--AAAAGAGAAT
1 AAAAAATGAAAAGA-AAT
5975260 ACAAAAATGAAAA
1 A-AAAAATGAAAA
5975273 ATGAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 6 0.25
15 2 0.08
16 7 0.29
17 5 0.21
19 4 0.17
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (17 bp):
AAAAAATGAAAAGAAAT
Found at i:5975429 original size:21 final size:20
Alignment explanation
Indices: 5975401--5975443 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
5975391 TTAAAAAACT
*
5975401 AATTATTTCCCAAAAAAGTA
1 AATTATTTCCCAAAAAAATA
**
5975421 AATTAATTTTTCAAAAAAATA
1 AATT-ATTTCCCAAAAAAATA
5975442 AA
1 AA
5975444 AATGAGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (20 bp):
AATTATTTCCCAAAAAAATA
Found at i:5976010 original size:19 final size:20
Alignment explanation
Indices: 5975986--5976026 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
5975976 TCATCTTTTC
5975986 TTTCTTTCTTTCTTTTC-TT
1 TTTCTTTCTTTCTTTTCATT
* *
5976005 TTTCTTTTTTTTTTTTCATT
1 TTTCTTTCTTTCTTTTCATT
5976025 TT
1 TT
5976027 AGATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTCTTTCTTTCTTTTCATT
Found at i:5976019 original size:13 final size:13
Alignment explanation
Indices: 5975979--5976026 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
5975969 ATAAAGTTCA
* *
5975979 TCTTTTCTTTCTT
1 TCTTTTTTTTTTT
5975992 TCTTTCTTTTCTTTT
1 TCTTT-TTTT-TTTT
5976007 TCTTTTTTTTTTT
1 TCTTTTTTTTTTT
5976020 TCATTTT
1 TC-TTTT
5976027 AGATAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 11 0.37
14 11 0.37
15 8 0.27
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (13 bp):
TCTTTTTTTTTTT
Found at i:5979810 original size:13 final size:12
Alignment explanation
Indices: 5979791--5979834 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
5979781 TGTTCAATAA
5979791 TATAATATTATT
1 TATAATATTATT
5979803 TATGAATA-TA-T
1 TAT-AATATTATT
5979814 TATAATATTATT
1 TATAATATTATT
5979826 TATTAATAT
1 TA-TAATAT
5979835 AATACTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.14
11 6 0.21
12 8 0.29
13 10 0.36
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATAATATTATT
Found at i:5979810 original size:18 final size:19
Alignment explanation
Indices: 5979789--5979845 Score: 53
Period size: 23 Copynumber: 2.8 Consensus size: 19
5979779 ATTGTTCAAT
5979789 AATATAATATTATTTATGAA
1 AATATAATATTATTTATG-A
*
5979809 TATATTATAATATTATTTAT-T
1 -A-A-TATAATATTATTTATGA
*
5979830 AATATAATACTATTTA
1 AATATAATATTATTTA
5979846 AAAATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 13 0.41
19 1 0.03
20 1 0.03
21 1 0.03
22 1 0.03
23 15 0.47
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
AATATAATATTATTTATGA
Found at i:5979821 original size:23 final size:23
Alignment explanation
Indices: 5979791--5979835 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
5979781 TGTTCAATAA
5979791 TATAATATTATTTATGAATATAT
1 TATAATATTATTTATGAATATAT
*
5979814 TATAATATTATTTATTAATATA
1 TATAATATTATTTATGAATATA
5979836 ATACTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATAATATTATTTATGAATATAT
Found at i:5979951 original size:20 final size:19
Alignment explanation
Indices: 5979889--5979951 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
5979879 AATTCTACTT
*
5979889 ATAAATAATTTTTTTGAAAA
1 ATAAATAA-TTTTTTAAAAA
* * ***
5979909 ATATATATTTTTTTAATTT
1 ATAAATAATTTTTTAAAAA
5979928 ATAAGATAATTTTTTAAAAA
1 ATAA-ATAATTTTTTAAAAA
5979948 ATAA
1 ATAA
5979952 TTTTATTTTT
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
19 10 0.32
20 21 0.68
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
ATAAATAATTTTTTAAAAA
Found at i:5979961 original size:39 final size:39
Alignment explanation
Indices: 5979887--5979983 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
5979877 ATAATTCTAC
*
5979887 TTATAAATAATTTTTTTGAAAAATATATATTTTTTTAAT
1 TTATAAATAATTTTTTTAAAAAATATATATTTTTTTAAT
* *
5979926 TTATAAGATAA-TTTTTTAAAAAATA-ATTTTATTTTTTAT
1 TTATAA-ATAATTTTTTTAAAAAATATATATT-TTTTTAAT
* *
5979965 TAATAAAAAATATTTTTTA
1 TTATAAATAAT-TTTTTTA
5979984 TTGATCAACT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
38 7 0.14
39 31 0.63
40 11 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (39 bp):
TTATAAATAATTTTTTTAAAAAATATATATTTTTTTAAT
Found at i:5980703 original size:34 final size:34
Alignment explanation
Indices: 5980595--5980701 Score: 205
Period size: 34 Copynumber: 3.1 Consensus size: 34
5980585 AGAAAGATAC
5980595 AGTTGAAGCCTATCACTGGAGTGGTTTAAATGAA
1 AGTTGAAGCCTATCACTGGAGTGGTTTAAATGAA
5980629 AGTTGAAGCCTATCACTGGAGTGGTTTAAATGAA
1 AGTTGAAGCCTATCACTGGAGTGGTTTAAATGAA
*
5980663 AGTTGTAGCCTATCACTGGAGTGGTTTAAATGAA
1 AGTTGAAGCCTATCACTGGAGTGGTTTAAATGAA
5980697 AGTTG
1 AGTTG
5980702 TATTTCATAC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 72 1.00
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (34 bp):
AGTTGAAGCCTATCACTGGAGTGGTTTAAATGAA
Found at i:5981203 original size:26 final size:25
Alignment explanation
Indices: 5981165--5981213 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
5981155 ATTTATGATT
5981165 AAAATATGAAAAATAAATTATTATAA
1 AAAATATGAAAAAT-AATTATTATAA
** *
5981191 AAAATATTTAAAATATTTATTAT
1 AAAATATGAAAAATAATTATTAT
5981214 CAAATTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (25 bp):
AAAATATGAAAAATAATTATTATAA
Found at i:5981244 original size:22 final size:22
Alignment explanation
Indices: 5981216--5981262 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5981206 TTTATTATCA
*
5981216 AATTATTTACAATATTAAT-TTT
1 AATTATTT-CAATAATAATATTT
*
5981238 AATTATTTTAATAATAATATTT
1 AATTATTTCAATAATAATATTT
5981260 AAT
1 AAT
5981263 AATAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTATTTCAATAATAATATTT
Found at i:5981260 original size:13 final size:13
Alignment explanation
Indices: 5981244--5981282 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
5981234 TTTTAATTAT
5981244 TTTAATAATAATA
1 TTTAATAATAATA
*
5981257 TTTAATAATAAAA
1 TTTAATAATAATA
*
5981270 TTT-ATATTAATA
1 TTTAATAATAATA
5981282 T
1 T
5981283 ACTTGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTTAATAATAATA
Found at i:5983426 original size:97 final size:97
Alignment explanation
Indices: 5983319--5983505 Score: 266
Period size: 97 Copynumber: 1.9 Consensus size: 97
5983309 TAATTTCTAA
*
5983319 AAGATCATTAAACATTCTAACAGTTAGGTAAGATTTAATTTTAAGATTTAAATTCTTCAATAGTT
1 AAGATCATTAAACATTCTAACAGTTAGGTAAGATTTAATTTTAAGATTTAAATCCTTCAATAGTT
*
5983384 CGATAGGATTAATTTAAAAAAATTTATTTTTT
66 CGATACGATTAATTTAAAAAAATTTATTTTTT
* * * * * * *
5983416 AAGATCATTAAACCTTTTAATAGTTTGTTAATATTTAATTTTACGATTTAAATCCTTCAATAGTT
1 AAGATCATTAAACATTCTAACAGTTAGGTAAGATTTAATTTTAAGATTTAAATCCTTCAATAGTT
* * *
5983481 TGATACTATTAATTTAAAAATATTT
66 CGATACGATTAATTTAAAAAAATTT
5983506 TTAATTAAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
97 78 1.00
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (97 bp):
AAGATCATTAAACATTCTAACAGTTAGGTAAGATTTAATTTTAAGATTTAAATCCTTCAATAGTT
CGATACGATTAATTTAAAAAAATTTATTTTTT
Found at i:5983677 original size:22 final size:22
Alignment explanation
Indices: 5983633--5983677 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5983623 AATTTTATAT
* *
5983633 AAAAATTTAATTTAAATAAAAA
1 AAAAATTAAATTTAAAGAAAAA
*
5983655 AAAAATTAAATTTAAAGATAAA
1 AAAAATTAAATTTAAAGAAAAA
5983677 A
1 A
5983678 TTACTAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAAATTAAATTTAAAGAAAAA
Found at i:5984754 original size:22 final size:22
Alignment explanation
Indices: 5984729--5984812 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 22
5984719 TCATTATTAC
5984729 AAATTCAAAGATTCACAATTTG
1 AAATTCAAAGATTCACAATTTG
* *
5984751 AAATT-AACAAATTCGA-AACTTG
1 AAATTCAA-AGATTC-ACAATTTG
* * ** *
5984773 AAATTTAAAGGTTTTCAATATG
1 AAATTCAAAGATTCACAATTTG
5984795 AAATTCAAAGATTCACAA
1 AAATTCAAAGATTCACAA
5984813 CTACAATTTC
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
21 2 0.04
22 41 0.89
23 3 0.07
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (22 bp):
AAATTCAAAGATTCACAATTTG
Found at i:5985015 original size:19 final size:19
Alignment explanation
Indices: 5984866--5985071 Score: 147
Period size: 19 Copynumber: 10.9 Consensus size: 19
5984856 AATTCCAAAA
*
5984866 TTTGCAGAAGATTCAAA-G
1 TTTGCAAAAGATTCAAAGG
* *
5984884 TTTGCAAAAGACTT-TAAGA
1 TTTGCAAAAGA-TTCAAAGG
* *
5984903 TTTGTAAAAGATTCAAATAG
1 TTTGCAAAAGATTCAAA-GG
* *
5984923 -TTGTAAAAG-TCTCAAAGA
1 TTTGCAAAAGAT-TCAAAGG
*
5984941 TTTTCAAAAGAATT-AAAGG
1 TTTGCAAAAG-ATTCAAAGG
*
5984960 TTTGCAAAAGATTCAAAGA
1 TTTGCAAAAGATTCAAAGG
*
5984979 TTTGCAAAAAATTCAAAGG
1 TTTGCAAAAGATTCAAAGG
* *
5984998 TTCGCAAAAGATTGAAAGG
1 TTTGCAAAAGATTCAAAGG
* * * *
5985017 -TTGATAAAAAATTGAAAGA
1 TTTG-CAAAAGATTCAAAGG
*
5985036 TTCT-CAAAAGTTTCAAAGG
1 TT-TGCAAAAGATTCAAAGG
*
5985055 TTTGCAAAATATTCAAA
1 TTTGCAAAAGATTCAAA
5985072 AACCTCACTA
Statistics
Matches: 145, Mismatches: 30, Indels: 25
0.73 0.15 0.12
Matches are distributed among these distances:
18 21 0.14
19 120 0.83
20 2 0.01
21 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (19 bp):
TTTGCAAAAGATTCAAAGG
Found at i:5985122 original size:20 final size:20
Alignment explanation
Indices: 5985085--5985165 Score: 56
Period size: 20 Copynumber: 4.0 Consensus size: 20
5985075 CTCACTAATA
* *
5985085 AATTTTAAATATTCACAAAT
1 AATTTCAAAGATTCACAAAT
*
5985105 AATTTCAAAGATTTACAAAT
1 AATTTCAAAGATTCACAAAT
* * *
5985125 GAAACTAT-AGAGATTCGCAAAT
1 --AA-TTTCAAAGATTCACAAAT
* *
5985147 AATTTTAAAGGTTCACAAA
1 AATTTCAAAGATTCACAAA
5985166 AGAAATTTCA
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
19 2 0.04
20 29 0.63
22 13 0.28
23 2 0.04
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (20 bp):
AATTTCAAAGATTCACAAAT
Found at i:5985252 original size:22 final size:22
Alignment explanation
Indices: 5985224--5985312 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 22
5985214 AAATACAAAG
5985224 ATTCAAAAGTTCACATCTAAAA
1 ATTCAAAAGTTCACATCTAAAA
*
5985246 ATTC-AAAGCTTCACATTTAAAAA
1 ATTCAAAAG-TTCACATCT-AAAA
* *
5985269 ATTTAGAAA-TTCACATC-CAAA
1 ATTCA-AAAGTTCACATCTAAAA
* * *
5985290 ATTCAAAAATTTACATTTAAAA
1 ATTCAAAAGTTCACATCTAAAA
5985312 A
1 A
5985313 GTTTATGATT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
20 3 0.06
21 17 0.32
22 16 0.30
23 14 0.26
25 3 0.06
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (22 bp):
ATTCAAAAGTTCACATCTAAAA
Found at i:5985306 original size:44 final size:45
Alignment explanation
Indices: 5985233--5985317 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 45
5985223 GATTCAAAAG
**
5985233 TTCACATCTAAAAATTCAAAGCTTCACATTTAAAAAATTTAGAAA
1 TTCACATCTAAAAATTCAAAAATTCACATTTAAAAAATTTAGAAA
* * *
5985278 TTCACATC-CAAAATTCAAAAATTTACATTTAAAAAGTTTA
1 TTCACATCTAAAAATTCAAAAATTCACATTTAAAAAATTTA
5985318 TGATTTAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 27 0.77
45 8 0.23
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (45 bp):
TTCACATCTAAAAATTCAAAAATTCACATTTAAAAAATTTAGAAA
Found at i:5985370 original size:75 final size:74
Alignment explanation
Indices: 5985250--5985392 Score: 198
Period size: 75 Copynumber: 1.9 Consensus size: 74
5985240 CTAAAAATTC
* * *
5985250 AAAGCTTCACATTTAAAAAATTTAGAAATTCACATCCAAAATTCAAAAATTTACA-TTTAAAAAG
1 AAAGCTTCACATTCAAAAAATTTAGAAATTCAAATACAAAATTCAAAAATTTACATTTTAAAAA-
5985314 TTTATGATTT
65 TTTATGATTT
* * * *
5985324 AAAGGTTCACATTCAAAAAATTCTAGAGATTCAAATATAAAATTCAAAGATTTACATTTTAAAAA
1 AAAGCTTCACATTCAAAAAATT-TAGAAATTCAAATACAAAATTCAAAAATTTACATTTTAAAAA
5985389 TTTA
65 TTTA
5985393 GAGATTCACA
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
74 20 0.33
75 32 0.53
76 8 0.13
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.34
Consensus pattern (74 bp):
AAAGCTTCACATTCAAAAAATTTAGAAATTCAAATACAAAATTCAAAAATTTACATTTTAAAAAT
TTATGATTT
Found at i:5985403 original size:23 final size:23
Alignment explanation
Indices: 5985320--5985408 Score: 67
Period size: 23 Copynumber: 3.9 Consensus size: 23
5985310 AAAGTTTATG
*
5985320 ATTTAAAGGTTCACATTCA-AAAA
1 ATTTAAAGATTCACATT-ATAAAA
* *
5985343 ATTCTAGAGATTCA-AATAT-AAA
1 ATT-TAAAGATTCACATTATAAAA
* * *
5985365 ATTCAAAGATTTACATTTTAAAA
1 ATTTAAAGATTCACATTATAAAA
*
5985388 ATTTAGAGATTCACATCTATA
1 ATTTAAAGATTCACAT-TATA
5985409 TTCAAATATT
Statistics
Matches: 49, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
21 7 0.14
22 10 0.20
23 21 0.43
24 11 0.22
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (23 bp):
ATTTAAAGATTCACATTATAAAA
Found at i:5985424 original size:43 final size:45
Alignment explanation
Indices: 5985324--5985428 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 45
5985314 TTTATGATTT
* *
5985324 AAAGGTTCACATTCAAAAAATTCTAGAGATTCAAATATAAAATTC
1 AAAGATTCACATTTAAAAAATTCTAGAGATTCAAATATAAAATTC
* * * * *
5985369 AAAGATTTACATTTTAAAAATT-TAGAGATTCACATCT-ATATTC
1 AAAGATTCACATTTAAAAAATTCTAGAGATTCAAATATAAAATTC
*
5985412 AAATATTCACATTTAAA
1 AAAGATTCACATTTAAA
5985429 GCTCAAATAT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 19 0.38
44 13 0.26
45 18 0.36
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (45 bp):
AAAGATTCACATTTAAAAAATTCTAGAGATTCAAATATAAAATTC
Found at i:5985436 original size:21 final size:21
Alignment explanation
Indices: 5985410--5985449 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5985400 ACATCTATAT
5985410 TCAAATATTCACATTTAAAGC
1 TCAAATATTCACATTTAAAGC
**
5985431 TCAAATATTTTCATTTAAA
1 TCAAATATTCACATTTAAA
5985450 ATTTAAAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (21 bp):
TCAAATATTCACATTTAAAGC
Found at i:5985674 original size:32 final size:34
Alignment explanation
Indices: 5985638--5985723 Score: 104
Period size: 32 Copynumber: 2.6 Consensus size: 34
5985628 TCAAAGTTTG
** *
5985638 AAAATGAAATGACTTGGACTAA-ATGAAATC-TA
1 AAAATGAAATGACTTGGACTAAGACAAAATCACA
* *
5985670 AAAATAAAATGACTTGGACTAAGCCAAAATCACA
1 AAAATGAAATGACTTGGACTAAGACAAAATCACA
*
5985704 AAAATGAAATGACATGGACT
1 AAAATGAAATGACTTGGACT
5985724 TAGCCAAGGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 21 0.47
33 5 0.11
34 19 0.42
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (34 bp):
AAAATGAAATGACTTGGACTAAGACAAAATCACA
Found at i:5985714 original size:34 final size:33
Alignment explanation
Indices: 5985638--5985730 Score: 107
Period size: 34 Copynumber: 2.8 Consensus size: 33
5985628 TCAAAGTTTG
*** *
5985638 AAAATGAAATGACTTGGACTAA-ATGAAATCTA
1 AAAATGAAATGACTTGGACTAAGCCAAAATCCA
*
5985670 AAAATAAAATGACTTGGACTAAGCCAAAATCACA
1 AAAATGAAATGACTTGGACTAAGCCAAAATC-CA
* *
5985704 AAAATGAAATGACATGGACTTAGCCAA
1 AAAATGAAATGACTTGGACTAAGCCAA
5985731 GGTCAAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 21 0.41
33 5 0.10
34 25 0.49
ACGTcount: A:0.51, C:0.14, G:0.15, T:0.20
Consensus pattern (33 bp):
AAAATGAAATGACTTGGACTAAGCCAAAATCCA
Found at i:5987093 original size:17 final size:17
Alignment explanation
Indices: 5987071--5987103 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5987061 TTTCACCATA
5987071 AAAATAACAA-AAAAAAT
1 AAAATAA-AAGAAAAAAT
5987088 AAAATAAAAGAAAAAA
1 AAAATAAAAGAAAAAA
5987104 AATTAACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.85, C:0.03, G:0.03, T:0.09
Consensus pattern (17 bp):
AAAATAAAAGAAAAAAT
Found at i:5987329 original size:33 final size:33
Alignment explanation
Indices: 5987285--5987350 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
5987275 GGTTCAGAGA
*
5987285 ATCGAAGGGAGTGTTTCAAGCTTTTTTGGGATT
1 ATCGAAAGGAGTGTTTCAAGCTTTTTTGGGATT
5987318 ATCGAAAGGAGTGTTTCAAGCTTTTTTGGGATT
1 ATCGAAAGGAGTGTTTCAAGCTTTTTTGGGATT
5987351 TTTTTATAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.23, C:0.09, G:0.29, T:0.39
Consensus pattern (33 bp):
ATCGAAAGGAGTGTTTCAAGCTTTTTTGGGATT
Found at i:5998212 original size:18 final size:17
Alignment explanation
Indices: 5998171--5998212 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
5998161 TTATATATAC
*
5998171 AAAAATTAATTTAAATA
1 AAAAATTAAATTAAATA
5998188 AACAAATTAAATTAAATTA
1 AA-AAATTAAATTAAA-TA
5998207 AAAAAT
1 AAAAAT
5998213 AAAAATTACC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 16 0.73
19 4 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAATTAAATTAAATA
Found at i:6001383 original size:2 final size:2
Alignment explanation
Indices: 6001365--6001413 Score: 71
Period size: 2 Copynumber: 24.0 Consensus size: 2
6001355 AAAGTCTTGT
* *
6001365 TA TA TGA TA TT TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6001408 TA TA TA
1 TA TA TA
6001414 AAGGCTCAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6001602 original size:40 final size:40
Alignment explanation
Indices: 6001539--6001632 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
6001529 TTGTACATGG
* * * *
6001539 ATTTAATTAT-TTAATTATGTTATAATTTATTAATTGATT
1 ATTTAATTATCATAATTATGTTATAATATAATAATTAATT
*
6001578 GTTTAATTATCATAATTTAT-TTATAATATAATAATTAATT
1 ATTTAATTATCATAA-TTATGTTATAATATAATAATTAATT
6001618 ATTTAATTAATCATA
1 ATTTAATT-ATCATA
6001633 TAAATTTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 9 0.20
40 27 0.59
41 10 0.22
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.54
Consensus pattern (40 bp):
ATTTAATTATCATAATTATGTTATAATATAATAATTAATT
Found at i:6004396 original size:8 final size:8
Alignment explanation
Indices: 6004385--6004410 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
6004375 TTATATAAGA
6004385 ATTTAATT
1 ATTTAATT
6004393 ATTTAATT
1 ATTTAATT
6004401 ATTTAATT
1 ATTTAATT
6004409 AT
1 AT
6004411 GTTTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTTAATT
Found at i:6006455 original size:38 final size:38
Alignment explanation
Indices: 6006404--6006480 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
6006394 GCATGCCCAG
*
6006404 AAAATAACTTCAAGTATATGTGCATAGATAGCTATATA
1 AAAATAACTTCAAGTATATATGCATAGATAGCTATATA
6006442 AAAATAACTTCAAGTATATATGCATAGATAGCTATATA
1 AAAATAACTTCAAGTATATATGCATAGATAGCTATATA
6006480 A
1 A
6006481 CTTTTACAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (38 bp):
AAAATAACTTCAAGTATATATGCATAGATAGCTATATA
Found at i:6007949 original size:1 final size:1
Alignment explanation
Indices: 6007943--6007986 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
6007933 TCTGCAATGC
* * * *
6007943 AAAAAAAAAAAAAAAAAAGAAAAAAAAAAGAAAAGAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6007987 GTTATGATAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Done.