Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_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: 5962497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 30
Found at i:3474666 original size:27 final size:25
Alignment explanation
Indices: 3474632--3474688 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
3474622 TTGACCCCCA
* *
3474632 TTTTTCT-TCTTTTTTCTTT-TTTC
1 TTTTTCTCTCTTTTTTTTTTCTTTT
3474655 TTTTTCTCTCTTTTTTTTTTCTTTT
1 TTTTTCTCTCTTTTTTTTTTCTTTT
3474680 TTTTTCTCT
1 TTTTTCTCT
3474689 TCAAGCATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.23
24 11 0.37
25 12 0.40
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (25 bp):
TTTTTCTCTCTTTTTTTTTTCTTTT
Found at i:3474684 original size:10 final size:10
Alignment explanation
Indices: 3474632--3474686 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
3474622 TTGACCCCCA
*
3474632 TTTTTCTTCT
1 TTTTTCTTTT
3474642 TTTTTC---T
1 TTTTTCTTTT
3474649 TTTTTCTTTT
1 TTTTTCTTTT
* *
3474659 TCTCTCTTTTT
1 TTTTTC-TTTT
3474670 TTTTTCTTTT
1 TTTTTCTTTT
3474680 TTTTTCT
1 TTTTTCT
3474687 CTTCAAGCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 7 0.19
10 22 0.59
11 8 0.22
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:3474689 original size:23 final size:24
Alignment explanation
Indices: 3474632--3474689 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 24
3474622 TTGACCCCCA
3474632 TTTTTCTTCTTTTTTCTTTTTTCTT
1 TTTTTC-TCTTTTTTCTTTTTTCTT
*
3474657 TTTCTCTCTTTTTT-TTTTCTT-TT
1 TTTTTCTCTTTTTTCTTTT-TTCTT
3474680 TTTTTCTCTT
1 TTTTTCTCTT
3474690 CAAGCATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 15 0.50
24 10 0.33
25 5 0.17
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTTCTCTTTTTTCTTTTTTCTT
Found at i:3478481 original size:26 final size:26
Alignment explanation
Indices: 3478449--3478501 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
3478439 TGATAAATAA
3478449 TCCATTCATAGCTTCTTCAACTATGT
1 TCCATTCATAGCTTCTTCAACTATGT
3478475 TCCATTCATAGCTTCTTCAACTATGT
1 TCCATTCATAGCTTCTTCAACTATGT
3478501 T
1 T
3478502 TTGATCTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.26, G:0.08, T:0.43
Consensus pattern (26 bp):
TCCATTCATAGCTTCTTCAACTATGT
Found at i:3481966 original size:15 final size:15
Alignment explanation
Indices: 3481943--3481974 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3481933 TGAAATGAAT
3481943 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
3481958 AATGCATGTATGCAA
1 AATGAATGTATGCAA
3481973 AA
1 AA
3481975 AGGTATTGAT
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:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:3487313 original size:3 final size:3
Alignment explanation
Indices: 3487305--3487367 Score: 99
Period size: 3 Copynumber: 21.0 Consensus size: 3
3487295 TTTAATATAT
* * *
3487305 TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3487353 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
3487368 ATAAATCAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3487337 original size:9 final size:9
Alignment explanation
Indices: 3487296--3487366 Score: 72
Period size: 9 Copynumber: 8.0 Consensus size: 9
3487286 TATTTTATAT
3487296 TTAAT-ATA
1 TTAATAATA
3487304 TTAATAATA
1 TTAATAATA
*
3487313 ATAATAATA
1 TTAATAATA
*
3487322 ATAATAATA
1 TTAATAATA
*
3487331 TTTATAATA
1 TTAATAATA
*
3487340 ATAATAATA
1 TTAATAATA
* *
3487349 ATAGTAATA
1 TTAATAATA
*
3487358 ATAATAATA
1 TTAATAATA
3487367 AATAAATCAA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
8 5 0.09
9 50 0.91
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (9 bp):
TTAATAATA
Found at i:3488677 original size:25 final size:24
Alignment explanation
Indices: 3488632--3488678 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3488622 CTATTGCTAG
**
3488632 AATTTTTAATATTTATTAATTAGA
1 AATTTTTAATATTTAGGAATTAGA
*
3488656 AATTTTTAATTTGTTAGGAATTA
1 AATTTTTAATAT-TTAGGAATTA
3488679 AGAGTTTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (24 bp):
AATTTTTAATATTTAGGAATTAGA
Found at i:3493341 original size:10 final size:9
Alignment explanation
Indices: 3493323--3493362 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
3493313 GCGTTTGAAG
3493323 AAGAAAAAA
1 AAGAAAAAA
*
3493332 AGGAAAAAA
1 AAGAAAAAA
3493341 AAGAAAAAGA
1 AAGAAAAA-A
3493351 AAGAAAAGAA
1 AAGAAAA-AA
3493361 AA
1 AA
3493363 AAATCCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
9 15 0.56
10 11 0.41
11 1 0.04
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:3493352 original size:15 final size:16
Alignment explanation
Indices: 3493328--3493363 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
3493318 TGAAGAAGAA
3493328 AAAAAGGAAAAAAAAG
1 AAAAAGGAAAAAAAAG
*
3493344 AAAAA-GAAAGAAAAG
1 AAAAAGGAAAAAAAAG
3493359 AAAAA
1 AAAAA
3493364 AATCCAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAGGAAAAAAAAG
Found at i:3493372 original size:24 final size:24
Alignment explanation
Indices: 3493323--3493399 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
3493313 GCGTTTGAAG
*
3493323 AAGAAAAAAAGGAAAAAAAAGAAA
1 AAGAAAAAAAGGAAAAAAAACAAA
*
3493347 AAGAAAGAAAA-GAAAAAAATCCAAA
1 AAGAAA-AAAAGGAAAAAAA-ACAAA
* * **
3493372 AA-ACAACAAGGAAAATCAA-AAA
1 AAGAAAAAAAGGAAAAAAAACAAA
3493394 AAGAAA
1 AAGAAA
3493400 TCAAGAAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
22 5 0.12
23 5 0.12
24 22 0.54
25 9 0.22
ACGTcount: A:0.78, C:0.06, G:0.13, T:0.03
Consensus pattern (24 bp):
AAGAAAAAAAGGAAAAAAAACAAA
Found at i:3497364 original size:2 final size:2
Alignment explanation
Indices: 3497357--3497393 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3497347 AAAGGGAAAG
3497357 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3497394 TAAGATATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3506977 original size:27 final size:26
Alignment explanation
Indices: 3506928--3506979 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
3506918 CATATGCAGT
3506928 TTTACTGCCTGTGAATAAATTGCACA
1 TTTACTGCCTGTGAATAAATTGCACA
* * *
3506954 TTTAGTGCCTTGTGAATCATTTGCAC
1 TTTACTGCC-TGTGAATAAATTGCAC
3506980 CATAGGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (26 bp):
TTTACTGCCTGTGAATAAATTGCACA
Found at i:3507959 original size:18 final size:17
Alignment explanation
Indices: 3507905--3507953 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3507895 TTGGACCCTT
* *
3507905 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
3507923 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
3507941 AGTGCATTCGATG
1 AGTGCA-TCGATG
3507954 TTTCAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:3508060 original size:66 final size:65
Alignment explanation
Indices: 3507925--3508086 Score: 195
Period size: 66 Copynumber: 2.5 Consensus size: 65
3507915 TGCACTAAGA
* * *
3507925 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAAATAGTCAGAGTGCATCAATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAACACTCA-AGTGCATCAATGCATGGCT
3507989 G
65 G
* * *
3507990 GTGCATCGATGCATCAAATGCATTTGATGTTTTCATTAAAACCCTC-AGTGCATCGATGCATGG-
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA--AAAACACTCAAGTGCATCAATGCATGGC
*
3508053 TAT
64 T-G
*
3508056 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
3508087 CAATTTATTC
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
65 28 0.33
66 50 0.60
68 6 0.07
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAACACTCAAGTGCATCAATGCATGGCTG
Found at i:3510801 original size:44 final size:42
Alignment explanation
Indices: 3510751--3510845 Score: 122
Period size: 42 Copynumber: 2.2 Consensus size: 42
3510741 GACCTTGTGC
*
3510751 ATCGATGCACATTCAATGCG-TGCATCGGTGCACCT-TCAAGGTGT
1 ATCGATGCACATTCAA-G-GATGCATCGATGCA-CTGT-AAGGTGT
*
3510795 ATCGATGCACATTCAAGGATGCATCGATGCACTGTTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCGATGCACTGTAAGGTGT
3510837 ATCGATGCA
1 ATCGATGCA
3510846 TTCAGCACAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
42 18 0.38
43 13 0.28
44 16 0.34
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.27
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCGATGCACTGTAAGGTGT
Found at i:3510803 original size:21 final size:21
Alignment explanation
Indices: 3510747--3510826 Score: 106
Period size: 21 Copynumber: 3.7 Consensus size: 21
3510737 GTATGACCTT
3510747 GTGCATCGATGCACATTCAATG
1 GTGCATCGATGCACATTCAA-G
* *
3510769 CGTGCATCGGTGCACCTTCAAG
1 -GTGCATCGATGCACATTCAAG
*
3510791 GTGTATCGATGCACATTCAAG
1 GTGCATCGATGCACATTCAAG
3510812 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
3510827 TGTTAGGTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
21 19 0.38
22 13 0.26
23 18 0.36
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCACATTCAAG
Found at i:3510842 original size:20 final size:21
Alignment explanation
Indices: 3510751--3510845 Score: 95
Period size: 21 Copynumber: 4.4 Consensus size: 21
3510741 GACCTTGTGC
*
3510751 ATCGATGCACATTCAATGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* *
3510774 ATCGGTGCACCTTCAAGGTGT
1 ATCGATGCACATTCAAGGTGT
*
3510795 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
3510817 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
3510837 ATCGATGCA
1 ATCGATGCA
3510846 TTCAGCACAA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
20 11 0.18
21 23 0.37
22 14 0.23
23 14 0.23
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.27
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:3519564 original size:20 final size:20
Alignment explanation
Indices: 3519539--3519599 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
3519529 TTTTGGTGCA
*
3519539 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
3519559 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
3519580 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATACCCCC
3519600 CACAGGGGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:3521288 original size:12 final size:12
Alignment explanation
Indices: 3521271--3521296 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3521261 TGAGCCTGAA
3521271 CAGCCCGAGGAG
1 CAGCCCGAGGAG
3521283 CAGCCCGAGGAG
1 CAGCCCGAGGAG
3521295 CA
1 CA
3521297 AGCACAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.35, G:0.38, T:0.00
Consensus pattern (12 bp):
CAGCCCGAGGAG
Found at i:3533022 original size:16 final size:16
Alignment explanation
Indices: 3533003--3533038 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
3532993 AGTTCTGTTT
3533003 TTTTTTACATAAAATA
1 TTTTTTACATAAAATA
*
3533019 TTTTTTACATTAAATA
1 TTTTTTACATAAAATA
3533035 TTTT
1 TTTT
3533039 AAAAAAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTTTACATAAAATA
Found at i:3533521 original size:24 final size:23
Alignment explanation
Indices: 3533490--3533571 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 23
3533480 TTAGTATTTA
*
3533490 ATATTAATATAATAATTTAATACT
1 ATATTAATATAATAATTTAA-AAT
* *
3533514 ATTTTAATA-AAGATATTTAAAAT
1 ATATTAATATAATA-ATTTAAAAT
*
3533537 ATATTAAT-TAATAATTTTTAAA-
1 ATATTAATATAATAA-TTTAAAAT
3533559 ATA-TAATATAATA
1 ATATTAATATAATA
3533572 CTATTACTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
21 4 0.08
22 9 0.19
23 21 0.44
24 14 0.29
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (23 bp):
ATATTAATATAATAATTTAAAAT
Found at i:3533869 original size:14 final size:14
Alignment explanation
Indices: 3533850--3533883 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3533840 AAATATAATT
3533850 TATTTTATAAAAAA
1 TATTTTATAAAAAA
* *
3533864 TATTTTTTGAAAAA
1 TATTTTATAAAAAA
3533878 TATTTT
1 TATTTT
3533884 CGGGGAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
TATTTTATAAAAAA
Found at i:3533968 original size:36 final size:36
Alignment explanation
Indices: 3533888--3533959 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
3533878 TATTTTCGGG
3533888 GAAATAAAATGACCCTTACTCTCTTTTCTATCATCA
1 GAAATAAAATGACCCTTACTCTCTTTTCTATCATCA
3533924 GAAATAAAATGACCCTTACTCTCTTTTCTATCATCA
1 GAAATAAAATGACCCTTACTCTCTTTTCTATCATCA
3533960 AAGTTAAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (36 bp):
GAAATAAAATGACCCTTACTCTCTTTTCTATCATCA
Found at i:3533977 original size:5 final size:5
Alignment explanation
Indices: 3533967--3534005 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
3533957 TCAAAGTTAA
3533967 AAGAG AAGAG AAGAG AAGAG AAGAG AAGAG AAGAG AAGA
1 AAGAG AAGAG AAGAG AAGAG AAGAG AAGAG AAGAG AAGA
3534006 ACCAACATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
AAGAG
Found at i:3535233 original size:93 final size:93
Alignment explanation
Indices: 3535090--3535271 Score: 249
Period size: 93 Copynumber: 2.0 Consensus size: 93
3535080 GCCTTTTAGA
* * * * *
3535090 TGCCTTATCCTTCTTTGGGTCGTGATCAGCATGTTCAGCTTGTTCGCCTTCTT-TTGGTTTCTCA
1 TGCCTGATCCTTCTTTGGGTCATGATCAGCATCTACAGCTTGCTCGCCTTCTTCTT-GTTTCTCA
*
3535154 TTGTTCTTCGATCTCCCAGGCTTTTCGGC
65 TTGTTCTTCGATCTCCCAGCCTTTTCGGC
* *
3535183 TGCCTGATCCTTCTTTGGGTCATGATGATCATCTACAGCTTGCTCGCCTTCTTCTTGTTTCTCAT
1 TGCCTGATCCTTCTTTGGGTCATGATCAGCATCTACAGCTTGCTCGCCTTCTTCTTGTTTCTCAT
* * *
3535248 TGTTGTTGGATTTCCCAGCCTTTT
66 TGTTCTTCGATCTCCCAGCCTTTT
3535272 TCTCTTTCTT
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
93 75 0.97
94 2 0.03
ACGTcount: A:0.10, C:0.26, G:0.19, T:0.45
Consensus pattern (93 bp):
TGCCTGATCCTTCTTTGGGTCATGATCAGCATCTACAGCTTGCTCGCCTTCTTCTTGTTTCTCAT
TGTTCTTCGATCTCCCAGCCTTTTCGGC
Found at i:3537867 original size:159 final size:160
Alignment explanation
Indices: 3537574--3537916 Score: 451
Period size: 159 Copynumber: 2.1 Consensus size: 160
3537564 TTTAAGTACA
* * *
3537574 TTTTTATCAAATTTGAACCACATACTCCTAAACCATAGGAGAATACAAGTGCACTTTCAATTCCT
1 TTTTTACCAAATTTGAACCACATACTCCTAAACCATAGGAAAATACAAGTACACTTTCAATTCCT
* * *
3537639 ATTTTTGAAAACAAAATTTTATTTTTTCAATTTAGTCCTTCAATTTTTCATAATATCTTTATTTA
66 ATTTTTGAAAACAAAATTTTATTTTTTAAATTTAGTCCTTCAATTTTTCATAATATCTATATTCA
*
3537704 TTCAATTCGTTATTTATTTTAAGT-CTTTG
131 TTCAATTCGTGATTTATTTTAAGTCCTTTG
* **
3537733 TTTTTACCAAATTT-AAGCCACATACTCCTAAACCATAGTAAAATACATTTACACTTTCAATTCC
1 TTTTTACCAAATTTGAA-CCACATACTCCTAAACCATAGGAAAATACAAGTACACTTTCAATTCC
* ** * * *
3537797 TCTTTTTGGTAAC-CAATTTTTTATTTTTAAATTTAGTCCTTCAATTTTTCATAATCTAC-ATAT
65 TATTTTTGAAAACAAAATTTTAT-TTTTTAAATTTAGTCCTTCAATTTTTCATAATAT-CTATAT
* * *
3537860 TCCTTCAATTTGTGATTTATTTTAAGTCCCTTTT
128 TCATTCAATTCGTGATTTATTTTAAGT-CCTTTG
3537894 TTTTTACCAAATTTGAACCACAT
1 TTTTTACCAAATTTGAACCACAT
3537917 GCTCATATAC
Statistics
Matches: 159, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
158 9 0.06
159 123 0.77
160 1 0.01
161 24 0.15
162 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.06, T:0.46
Consensus pattern (160 bp):
TTTTTACCAAATTTGAACCACATACTCCTAAACCATAGGAAAATACAAGTACACTTTCAATTCCT
ATTTTTGAAAACAAAATTTTATTTTTTAAATTTAGTCCTTCAATTTTTCATAATATCTATATTCA
TTCAATTCGTGATTTATTTTAAGTCCTTTG
Found at i:3539417 original size:22 final size:22
Alignment explanation
Indices: 3539391--3539437 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3539381 ATGTTTGAAA
*
3539391 AAACCTCTAAATACGATTTCTG
1 AAACCTCTAAATACGATTTCCG
* *
3539413 AAACCTCTCAGTACGATTTCCG
1 AAACCTCTAAATACGATTTCCG
3539435 AAA
1 AAA
3539438 GGCATGTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.28
Consensus pattern (22 bp):
AAACCTCTAAATACGATTTCCG
Found at i:3540619 original size:17 final size:17
Alignment explanation
Indices: 3540599--3540662 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
3540589 TATTTGATTT
3540599 TTTATTATTTTTAAATA
1 TTTATTATTTTTAAATA
*
3540616 TTTAATATTTATTAAAT-
1 TTTATTATTT-TTAAATA
* *
3540633 TTTA-TAATATTAAATA
1 TTTATTATTTTTAAATA
* *
3540649 TTTTTTAGTTTTAA
1 TTTATTATTTTTAA
3540663 TTTTTTAAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 6 0.16
16 6 0.16
17 20 0.53
18 6 0.16
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TTTATTATTTTTAAATA
Found at i:3542738 original size:6 final size:6
Alignment explanation
Indices: 3542727--3542770 Score: 70
Period size: 6 Copynumber: 7.2 Consensus size: 6
3542717 AAAGAAGGTT
*
3542727 GGGGGA GGGGGA GGGGGA GGGGGA GAGGGA GGGGGA GGGTGGA G
1 GGGGGA GGGGGA GGGGGA GGGGGA GGGGGA GGGGGA GGG-GGA G
3542771 AGAGCTTTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 31 0.89
7 4 0.11
ACGTcount: A:0.18, C:0.00, G:0.80, T:0.02
Consensus pattern (6 bp):
GGGGGA
Found at i:3543422 original size:39 final size:38
Alignment explanation
Indices: 3543379--3543490 Score: 111
Period size: 39 Copynumber: 2.9 Consensus size: 38
3543369 TTTATTATAG
* *
3543379 TAATATAGTATAATTTTTTGAAAATGTTTTTGAAAAATA
1 TAATATA-TATAGTTTTTTAAAAATGTTTTTGAAAAATA
** * *
3543418 TAATATATATAGTTTTCAAAAAATATTTTTTGAAATATA
1 TAATATATATAGTTTTTTAAAAAT-GTTTTTGAAAAATA
* * *
3543457 T-AT-TATATAGTTTTTTTAAAACGTTTTTAAAAAA
1 TAATATATATAGTTTTTTAAAAATGTTTTTGAAAAA
3543491 CTTATATCTT
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
36 9 0.15
37 15 0.25
38 15 0.25
39 20 0.34
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (38 bp):
TAATATATATAGTTTTTTAAAAATGTTTTTGAAAAATA
Found at i:3543484 original size:37 final size:39
Alignment explanation
Indices: 3543379--3543484 Score: 110
Period size: 37 Copynumber: 2.8 Consensus size: 39
3543369 TTTATTATAG
* *
3543379 TAATATAGTATAATTTTTTGAAAATG-TTTTTGAAAAATA
1 TAATATA-TATAGTTTTTTAAAAATGTTTTTTGAAAAATA
** * *
3543418 TAATATATATAGTTTTCAAAAAATATTTTTTGAAATATA
1 TAATATATATAGTTTTTTAAAAATGTTTTTTGAAAAATA
* *
3543457 T-AT-TATATAGTTTTTTTAAAACGTTTTT
1 TAATATATATAGTTTTTTAAAAATGTTTTT
3543485 AAAAAACTTA
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
37 20 0.36
38 15 0.27
39 20 0.36
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.50
Consensus pattern (39 bp):
TAATATATATAGTTTTTTAAAAATGTTTTTTGAAAAATA
Found at i:3543564 original size:35 final size:34
Alignment explanation
Indices: 3543508--3543724 Score: 159
Period size: 33 Copynumber: 6.4 Consensus size: 34
3543498 CTTATATACA
*
3543508 ATATATA-AGTTTT-AAAACATTTTGAAAATTAT
1 ATATATATAGTTTTAAAAACATTTTGAAAACTAT
* *
3543540 ATAGTATATAGTTTTGAAATCATTTTGAAAA-TAT
1 ATA-TATATAGTTTTAAAAACATTTTGAAAACTAT
*
3543574 A-ATATATAGTTTTTAAAAAACATTTTTGGAAAATTTATAT
1 ATATATATAG-TTTT-AAAAACA-TTTT-GAAAA---CTAT
* *
3543614 AATATATATAGTTTTAAAAAAATTTGGAAAACT-T
1 -ATATATATAGTTTTAAAAACATTTTGAAAACTAT
*
3543648 ATATA-AT-GTTTTTAAAATCATTTTTGAAAACTAT
1 ATATATATAG-TTTTAAAAACA-TTTTGAAAACTAT
* ** *
3543682 ATA-ATATAGTTTTGAAAATGTTTT-TAAA-TAT
1 ATATATATAGTTTTAAAAACATTTTGAAAACTAT
3543713 A-ATATATAGTTT
1 ATATATATAGTTT
3543725 ATTTTTTTTG
Statistics
Matches: 152, Mismatches: 14, Indels: 39
0.74 0.07 0.19
Matches are distributed among these distances:
30 1 0.01
31 14 0.09
32 24 0.16
33 29 0.19
34 29 0.19
35 20 0.13
36 5 0.03
38 5 0.03
39 3 0.02
40 9 0.06
41 5 0.03
42 8 0.05
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (34 bp):
ATATATATAGTTTTAAAAACATTTTGAAAACTAT
Found at i:3543640 original size:38 final size:41
Alignment explanation
Indices: 3543575--3543654 Score: 121
Period size: 38 Copynumber: 2.0 Consensus size: 41
3543565 TGAAAATATA
*
3543575 ATATATAGTTTTTAAAAAACATTTTTGGAAAATTTATATAAT
1 ATATATAGTTTTTAAAAAACA-TTTTGGAAAACTTATATAAT
3543617 ATATATAG-TTTTAAAAAA-A-TTTGGAAAACTTATATAAT
1 ATATATAGTTTTTAAAAAACATTTTGGAAAACTTATATAAT
3543655 GTTTTTAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
38 18 0.49
40 1 0.03
41 10 0.27
42 8 0.22
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (41 bp):
ATATATAGTTTTTAAAAAACATTTTGGAAAACTTATATAAT
Found at i:3543670 original size:72 final size:67
Alignment explanation
Indices: 3543507--3543689 Score: 187
Period size: 74 Copynumber: 2.7 Consensus size: 67
3543497 TCTTATATAC
* * ** *
3543507 AATATATAA-G-TTTTAAAACA-TTTTGAAAATTATAT-A-GTATATAGTTTTGAAATCATTTTG
1 AATATATAATGTTTTTAAAACATTTTTGAAAATTATATAATATATATAGTTTTAAAAAAATTTGG
3543567 AA
66 AA
3543569 AATATAATATATAGTTTTTAAAAAACATTTTTGGAAAATTTATATAATATATATAGTTTTAAAAA
1 AATAT-ATA-AT-GTTTTT--AAAACATTTTT-GAAAA-TTATATAATATATATAGTTTTAAAAA
3543634 AATTTGGAA
59 AATTTGGAA
*
3543643 AACTTATATAATGTTTTTAAAATCATTTTTGAAAACTATATAATATA
1 AA--TATATAATGTTTTTAAAA-CATTTTTGAAAATTATATAATATA
3543690 GTTTTGAAAA
Statistics
Matches: 100, Mismatches: 6, Indels: 22
0.78 0.05 0.17
Matches are distributed among these distances:
62 5 0.05
63 3 0.03
64 1 0.01
66 1 0.01
67 4 0.04
69 6 0.06
70 15 0.15
71 14 0.14
72 13 0.13
73 7 0.07
74 25 0.25
75 3 0.03
76 3 0.03
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (67 bp):
AATATATAATGTTTTTAAAACATTTTTGAAAATTATATAATATATATAGTTTTAAAAAAATTTGG
AA
Found at i:3543773 original size:6 final size:6
Alignment explanation
Indices: 3543757--3543786 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3543747 TATATAATCT
*
3543757 ATATTA TTATTA ATATTA ATATTA ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA
3543787 TTTTATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
ATATTA
Found at i:3543794 original size:5 final size:5
Alignment explanation
Indices: 3543784--3543813 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
3543774 AATATTAATA
3543784 TTATT TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT
3543814 AATTTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:3544049 original size:16 final size:15
Alignment explanation
Indices: 3544028--3544058 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
3544018 ACCGGTCGAA
3544028 CATCCCGGGACTGACC
1 CATCCCGGGA-TGACC
3544044 CATCCCGGGATGACC
1 CATCCCGGGATGACC
3544059 GGTCACACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.42, G:0.26, T:0.13
Consensus pattern (15 bp):
CATCCCGGGATGACC
Found at i:3544730 original size:31 final size:29
Alignment explanation
Indices: 3544663--3544729 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
3544653 GGAGAGAGCA
3544663 TTGAGAGAGCTAGGGAGCGTTTCTCTCAT
1 TTGAGAGAGCTAGGGAGCGTTTCTCTCAT
3544692 TTGAGAGAGCTAGGGAGCGTTTCTCTCAT
1 TTGAGAGAGCTAGGGAGCGTTTCTCTCAT
3544721 TTGAGAGAG
1 TTGAGAGAG
3544730 ATGATATCTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.22, C:0.15, G:0.33, T:0.30
Consensus pattern (29 bp):
TTGAGAGAGCTAGGGAGCGTTTCTCTCAT
Found at i:3545207 original size:2 final size:2
Alignment explanation
Indices: 3545202--3545234 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3545192 TTTGGGTCAT
3545202 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3545235 TTCCTCTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3545276 original size:13 final size:14
Alignment explanation
Indices: 3545252--3545280 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3545242 TGATTTACCA
3545252 TTTATTCATTTTAT
1 TTTATTCATTTTAT
3545266 TTTATTC-TTTTAT
1 TTTATTCATTTTAT
3545279 TT
1 TT
3545281 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTCATTTTAT
Found at i:3550830 original size:165 final size:165
Alignment explanation
Indices: 3550425--3551537 Score: 1310
Period size: 165 Copynumber: 6.7 Consensus size: 165
3550415 GCTCAAGGCA
* * * * * * *
3550425 AGAAGGGTTATTTACCAACAAAATACCTTTGAATTTGACTACGCTCAGCT-CAACGGCACATCAT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
* *
3550489 TTGCAACATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGC
65 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGC
* * * * ** *
3550554 TTCAAGGGCACATCATTTACAACATAACTCAAGGCT
130 TTCGAGGGCACATCATTTGCAGCATAACTTAAATCG
*
3550590 AGAA-GGTTATCTG-TAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * * * * * *
3550653 TGTAGTATAGCTTAAGTCGATAAGGGTTATCTGCCAAAGACCCCCGAGTTCAATTACATTAAGCT
66 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCT
3550718 TCGAGGGCACATCATTTGCAGCATAACTTAAATCG
131 TCGAGGGCACATCATTTGCAGCATAACTTAAATCG
* *
3550753 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTAAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * * *
3550818 TGCAGTATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCCCCAAGTTCGATTACATTCAGCT
66 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCT
3550883 TCGAGGGCACATCATTTGCAGCATAACTTAAATCG
131 TCGAGGGCACATCATTTGCAGCATAACTTAAATCG
*
3550918 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCGCATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
3550983 TGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCT
66 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCT
* * * ** *
3551048 TCGAGGGCATATCATTTACAGCATAACTCAAGGCT
131 TCGAGGGCACATCATTTGCAGCATAACTTAAATCG
* * *
3551083 AGAAGGGTTATCTGTC-ACCAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCAT
1 AGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* * * * * *
3551147 TTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCT
65 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTACACT
* * * * *
3551212 CAGC-TCCAAGGCGCATCATTTGCAGCATAGCTTAAGTCG
126 CAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAATCG
* ** * * * * *
3551251 AGAAGGGATATCTG----CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCAT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
* * * * * * * ** * *
3551312 TTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACATTCGAGTTCGACTACGCT
65 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CC-AAAGACCCTCGAGTTCGATTACACT
* * * **
3551377 CAGC-TCCAAGGCATATCATTTGCAATATAACTTAAATCG
126 CAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAATCG
*
3551416 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
** * *
3551481 TGCAATATAGATTAAGTCGAGAAGGGCTATCTGCCAAAGACTCTCGAGTTCGATTAC
66 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTAC
3551538 GTTCAGCTCA
Statistics
Matches: 823, Mismatches: 111, Indels: 29
0.85 0.12 0.03
Matches are distributed among these distances:
163 129 0.16
164 68 0.08
165 495 0.60
168 77 0.09
169 54 0.07
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (165 bp):
AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCT
TCGAGGGCACATCATTTGCAGCATAACTTAAATCG
Found at i:3550832 original size:84 final size:83
Alignment explanation
Indices: 3550325--3551546 Score: 1147
Period size: 84 Copynumber: 14.8 Consensus size: 83
3550315 ATAGCTTTTA
* * * * * * * * *
3550325 CAGCATAACTCAAGGCTAGAAAGGTTATCTGCCATCAAAGACCTTCAAGTTCAACCATGCTCAGC
1 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGC
*
3550390 TCTAAGGCACATCATTTG
66 TCCAAGGCACATCATTTG
* ** * * * * * * * * * * *
3550408 TAATATAGCTCAAGGCAAGAAGGGTTATTTACCAACAAAATACCTTTGAATTTGACTACGCTCAG
1 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACGCTCAG
3550473 CT-CAACGGCACATCATTTG
65 CTCCAA-GGCACATCATTTG
* * * ** * *
3550492 CAACATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGC
1 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGC
* *
3550554 TTCAAGGGCACATCATTTA
66 TCCAA-GGCACATCATTTG
* * * * **
3550573 CAACATAACTCAAGGCTAGAA-GGTTATCTGTAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
1 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGC
3550637 TCCAAGGCACATCATTTG
66 TCCAAGGCACATCATTTG
* * * * ** * * ** *
3550655 TAGTATAGCTTAAGTCGATAAGGGTTATCTG---CCAAAGACCCCCGAGTTCAATTACATTAAGC
1 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGC
* *
3550717 TTCGAGGGCACATCATTTG
66 -TCCAAGGCACATCATTTG
* * *
3550736 CAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTAAG
1 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACGCTCAG
3550801 CTCCAAGGCACATCATTTG
65 CTCCAAGGCACATCATTTG
* * * ** * * **
3550820 CAGTATAGCTTAAGTCGAGAAGGGCTATCT---ACCAAAGACCCCCAAGTTCGATTACATTCAGC
1 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGC
* *
3550882 TTCGAGGGCACATCATTTG
66 -TCCAAGGCACATCATTTG
*
3550901 CAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACGCTCAG
*
3550966 CTCCAAGGCGCATCATTTG
65 CTCCAAGGCACATCATTTG
* * * * * *
3550985 TAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCTCGAGTTCGATTACACTCAGC
1 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGC
* * * *
3551047 TTCGAGGGCATATCATTTA
66 -TCCAAGGCACATCATTTG
* * * * *
3551066 CAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTTGACTACGCTCAG
1 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGACTACGCTCAG
*
3551131 CTCCAAGGCATATCATTTG
65 CTCCAAGGCACATCATTTG
*
3551150 CAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACGCTCAG
*
3551215 CTCCAAGGCGCATCATTTG
65 CTCCAAGGCACATCATTTG
* * ** * *
3551234 CAGCATAGCTTAAGTCGAGAAGGGATATCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGC
1 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGC
* * * *
3551296 TTCGAGGGCATATCATTTA
66 -TCCAAGGCACATCATTTG
* * * * * *
3551315 CAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACATTCGAGTTCGACTACGCTCAG
1 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGACTACGCTCAG
*
3551380 CTCCAAGGCATATCATTTG
65 CTCCAAGGCACATCATTTG
** * *
3551399 CAATATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAG
1 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACGCTCAG
3551464 CTCCAAGGCACATCATTTG
65 CTCCAAGGCACATCATTTG
** * * *
3551483 CAATATAGA-TTAAGTCGAGAAGGGCTATCTG---CCAAAGA-CTCTCGAGTTCGATTACGTTCA
1 CAGCATA-ACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCT-TCGAGTTCGACTACGCTCA
3551543 GCTC
64 GCTC
3551547 AGAGGCAAAC
Statistics
Matches: 928, Mismatches: 180, Indels: 65
0.79 0.15 0.06
Matches are distributed among these distances:
79 2 0.00
80 161 0.17
81 192 0.21
82 25 0.03
83 67 0.07
84 375 0.40
85 106 0.11
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (83 bp):
CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGC
TCCAAGGCACATCATTTG
Found at i:3551019 original size:249 final size:248
Alignment explanation
Indices: 3550321--3551537 Score: 1434
Period size: 249 Copynumber: 4.9 Consensus size: 248
3550311 AAAGATAGCT
* * * * * * * *
3550321 TTTACAGCATAACTCAAGGCTAGAAAGGTTATCTGCCATC-AAAGACCTTCAAGTTCAACCATGC
1 TTTACAACATAACTCAAGGCTAGAAGGGTTATC-GTCACCAAAAGACCTTCGAGTTCGACTACGC
* * ** * * ** * * * * *
3550385 TCAGCTCTAAGGCACATCATTTGTAATATAGCTCAAGGCAAGAAGGGTTATTTACCAACAAAATA
65 TCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGA
* * * *
3550450 CCTTTGAATTTGACTACGCTCAGCT-CAACGGCACATCATTTGCAACATAGCTTAAGTCGAGAAG
130 CCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
3550514 GGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTT-CAAGGGCACATCA
194 GGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCCAA-GGCACATCA
*
3550569 TTTACAACATAACTCAAGGCTAGAA-GGTTATCTGTAACC-AAAGACCTTCGAGTTCGACTACGC
1 TTTACAACATAACTCAAGGCTAGAAGGGTTATC-GTCACCAAAAGACCTTCGAGTTCGACTACGC
* * * * *
3550632 TCAGCTCCAAGGCACATCATTTGTAGTATAGCTTAAGTCGATAAGGGTTATCTG----CCAAAGA
65 TCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGA
** * * ** * * * * *
3550693 CCCCCGAGTTCAATTACATTAAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAATCGAGAAG
130 CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
* *** * * *
3550758 GGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTAAGC-TCCAAGGCACATCA
194 GGCTATCTG----CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCCAAGGCACATCA
* ** * * * * * ** * * **
3550816 TTTGCAGTATAGCTTAAGTCGAGAAGGGCTATC-T-ACC-AAAGACCCCCAAGTTCGATTACATT
1 TTTACAACATAACTCAAGGCTAGAAGGGTTATCGTCACCAAAAGACCTTCGAGTTCGACTACGCT
* *
3550878 CAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGA
66 CAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGA
* *
3550943 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCGCATCATTTGTAGCATAGCTTAAGTCGAGAAGG
130 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
* * * *
3551008 GCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCA
195 GCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCCAAGGCACATCA
* *
3551062 TTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTTGACTACGC
1 TTTACAACATAACTCAAGGCTAGAAGGGTTATC-GTCACCAAAAGACCTTCGAGTTCGACTACGC
*
3551127 TCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGA
65 TCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGA
*
3551192 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGG
130 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
* * * *
3551257 GATATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCA
195 GCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCCAAGGCACATCA
*
3551311 TTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACATTCGAGTTCGACTACGC
1 TTTACAACATAACTCAAGGCTAGAAGGGTTATC-GTCACCAAAAGACCTTCGAGTTCGACTACGC
* **
3551376 TCAGCTCCAAGGCATATCATTTGCAATATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGA
65 TCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGA
* ** *
3551441 CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAATATAGATTAAGTCGAGAAGG
130 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
* *
3551506 GCTATCTGCCAAAGACTCTCGAGTTCGATTAC
195 GCTATCTGCCAAAGACCCCCGAGTTCGATTAC
3551538 GTTCAGCTCA
Statistics
Matches: 835, Mismatches: 116, Indels: 35
0.85 0.12 0.04
Matches are distributed among these distances:
243 19 0.02
244 41 0.05
245 53 0.06
246 80 0.10
247 105 0.13
248 59 0.07
249 432 0.52
250 46 0.06
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (248 bp):
TTTACAACATAACTCAAGGCTAGAAGGGTTATCGTCACCAAAAGACCTTCGAGTTCGACTACGCT
CAGCTCCAAGGCACATCATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGAC
CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGG
CTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCCAAGGCACATCA
Found at i:3552265 original size:37 final size:37
Alignment explanation
Indices: 3552195--3552266 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
3552185 TGTTTTTGAA
*
3552195 AAATATAATATATATAGTTTTCAAAAAATATTTTTTG
1 AAATATAATATATATAGTTTTCAAAAAACATTTTTTG
***
3552232 AAATAT-ATATTATATAGTTTTTTTAAAACATTTTT
1 AAATATAATA-TATATAGTTTTCAAAAAACATTTTT
3552267 AAAAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 3 0.10
37 27 0.90
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (37 bp):
AAATATAATATATATAGTTTTCAAAAAACATTTTTTG
Found at i:3555689 original size:22 final size:22
Alignment explanation
Indices: 3555661--3555707 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
3555651 GATATTACAT
3555661 TAATTAAAAATAATCAATAAAA
1 TAATTAAAAATAATCAATAAAA
**
3555683 TAATTAAAAATTCTCAATAAAA
1 TAATTAAAAATAATCAATAAAA
3555705 TAA
1 TAA
3555708 AATTCTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATTAAAAATAATCAATAAAA
Found at i:3558203 original size:41 final size:40
Alignment explanation
Indices: 3558158--3558234 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 40
3558148 ACTTGTCAAT
3558158 AGGGTAGTATCGATACCTGTTGAA-GA-GGTATCGATACTGTA
1 AGGGTAGTATCGATA-C--TTGAAGGATGGTATCGATACTGTA
3558199 AGGGTAGTATCGATACTTGAAGGATGGTATCGATAC
1 AGGGTAGTATCGATACTTGAAGGATGGTATCGATAC
3558235 CCTTAAAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
38 5 0.15
39 2 0.06
40 12 0.35
41 15 0.44
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.29
Consensus pattern (40 bp):
AGGGTAGTATCGATACTTGAAGGATGGTATCGATACTGTA
Found at i:3558208 original size:20 final size:21
Alignment explanation
Indices: 3558158--3558234 Score: 81
Period size: 20 Copynumber: 3.8 Consensus size: 21
3558148 ACTTGTCAAT
3558158 AGGGTAGTATCGATACCTGTTGA
1 AGGGTAGTATCGATA-CTG-TGA
*
3558181 AGAG--GTATCGATACTGT-A
1 AGGGTAGTATCGATACTGTGA
3558199 AGGGTAGTATCGATACT-TGA
1 AGGGTAGTATCGATACTGTGA
* *
3558219 AGGATGGTATCGATAC
1 AGGGTAGTATCGATAC
3558235 CCTTAAAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
18 4 0.09
19 2 0.04
20 29 0.62
21 9 0.19
23 3 0.06
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.29
Consensus pattern (21 bp):
AGGGTAGTATCGATACTGTGA
Found at i:3558316 original size:54 final size:53
Alignment explanation
Indices: 3558219--3558348 Score: 163
Period size: 54 Copynumber: 2.4 Consensus size: 53
3558209 CGATACTTGA
* * * * *
3558219 AGGATGGTATCGATACCCTTAAAACTCGAATGCCAGTTTGGTATCGGTTCCTTG
1 AGGA-GGTATCGATACCCTTGAAACTCAAATGCCAGTTTGGTATCCGTACCATG
* *
3558273 ATGAGGTATCGATACCCTTGAAACATCAAATGCTA-TTTCGGTATCCGTACCATG
1 AGGAGGTATCGATACCCTTGAAAC-TCAAATGCCAGTTT-GGTATCCGTACCATG
3558327 AGGAGGTATCGATACCCTTGAA
1 AGGAGGTATCGATACCCTTGAA
3558349 GGGATGTATC
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
53 22 0.33
54 44 0.67
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (53 bp):
AGGAGGTATCGATACCCTTGAAACTCAAATGCCAGTTTGGTATCCGTACCATG
Found at i:3558810 original size:21 final size:21
Alignment explanation
Indices: 3558741--3558812 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
3558731 ATGTTATGGA
* *
3558741 AATGTGGACTTTGAATAAGTA
1 AATGTGAACTTTGAATAAGTG
*
3558762 AATGTGGACTTTGAATAAGTG
1 AATGTGAACTTTGAATAAGTG
*
3558783 AATGTGAACTTTGAACAAGTG
1 AATGTGAACTTTGAATAAGTG
3558804 AATGTGAAC
1 AATGTGAAC
3558813 AAACTCTATG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.31
Consensus pattern (21 bp):
AATGTGAACTTTGAATAAGTG
Found at i:3573853 original size:14 final size:14
Alignment explanation
Indices: 3573834--3573860 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3573824 ATTGTGTATA
3573834 CTTGCACAGAATTG
1 CTTGCACAGAATTG
3573848 CTTGCACAGAATT
1 CTTGCACAGAATT
3573861 AAAGGATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (14 bp):
CTTGCACAGAATTG
Found at i:3576721 original size:20 final size:21
Alignment explanation
Indices: 3576669--3576748 Score: 87
Period size: 20 Copynumber: 3.9 Consensus size: 21
3576659 GGGAAATTAT
3576669 TAAGGGTAGTATCGATACCTG
1 TAAGGGTAGTATCGATACCTG
*
3576690 TTGAAGAG--GTATCGATA-CTG
1 -T-AAGGGTAGTATCGATACCTG
3576710 TAAGGGTAGTATCGATACCTG
1 TAAGGGTAGTATCGATACCTG
* *
3576731 -AAGGATGGTATCGATACC
1 TAAGGGTAGTATCGATACC
3576749 CTTAAAACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
18 4 0.08
19 1 0.02
20 28 0.56
21 12 0.24
22 1 0.02
23 4 0.08
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.28
Consensus pattern (21 bp):
TAAGGGTAGTATCGATACCTG
Found at i:3576829 original size:54 final size:52
Alignment explanation
Indices: 3576718--3576860 Score: 162
Period size: 54 Copynumber: 2.7 Consensus size: 52
3576708 TGTAAGGGTA
* *
3576718 GTATCGATACCTGAAGGATGGTATCGATACCCTTAAAACATTGAAACCAGTTTG
1 GTATCGATACCTG-AGGA-GGTATCGATACCCTTGAAACATCGAAACCAGTTTG
* *
3576772 GTATCGATACCTTGAGGAGGTATCGATACCCTTGAAACATCGAATGCTA-TTTCG
1 GTATCGATACC-TGAGGAGGTATCGATACCCTTGAAACATCGAA-ACCAGTTT-G
* * *
3576826 GTATTGGTACCATGAGGAGTTATCGATACCCTTGA
1 GTATCGATACC-TGAGGAGGTATCGATACCCTTGA
3576861 GGGGAGGTAT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
53 27 0.35
54 49 0.63
55 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (52 bp):
GTATCGATACCTGAGGAGGTATCGATACCCTTGAAACATCGAAACCAGTTTG
Found at i:3577280 original size:21 final size:21
Alignment explanation
Indices: 3577254--3577304 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 21
3577244 ATGTTATGGA
3577254 AATGTGAACTTTGAA-TAAGTG
1 AATGTGAACTTTGAACT-AGTG
3577275 AATGTGAACTTTGAACTAGTG
1 AATGTGAACTTTGAACTAGTG
3577296 AATGTGAAC
1 AATGTGAAC
3577305 AAACTCTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (21 bp):
AATGTGAACTTTGAACTAGTG
Found at i:3577464 original size:21 final size:21
Alignment explanation
Indices: 3577438--3577486 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
3577428 TCGAGGGTCT
3577438 TATGTGGTCCTTT-GGGATAAA
1 TATGTGGT-CTTTCGGGATAAA
3577459 TATGTGGTCTTTCGGGATAAA
1 TATGTGGTCTTTCGGGATAAA
3577480 TATGTGG
1 TATGTGG
3577487 CACTTCGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.22, C:0.08, G:0.31, T:0.39
Consensus pattern (21 bp):
TATGTGGTCTTTCGGGATAAA
Found at i:3577493 original size:21 final size:21
Alignment explanation
Indices: 3577438--3577494 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
3577428 TCGAGGGTCT
*
3577438 TATGTGGTCCTTTGGGATAAA
1 TATGTGGTCCTTCGGGATAAA
*
3577459 TATGTGGTCTTTCGGGATAAA
1 TATGTGGTCCTTCGGGATAAA
3577480 TATGTGG-CACTTCGG
1 TATGTGGTC-CTTCGG
3577495 TGCAAACCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.21, C:0.12, G:0.30, T:0.37
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGATAAA
Found at i:3577508 original size:12 final size:12
Alignment explanation
Indices: 3577491--3577515 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3577481 ATGTGGCACT
3577491 TCGGTGCAAACC
1 TCGGTGCAAACC
3577503 TCGGTGCAAACC
1 TCGGTGCAAACC
3577515 T
1 T
3577516 ATGTGGTCCT
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:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (12 bp):
TCGGTGCAAACC
Found at i:3591210 original size:18 final size:19
Alignment explanation
Indices: 3591175--3591215 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
3591165 ACACCTTGTG
*
3591175 CATTTGCATTTTCA-TTTT
1 CATTTGCATTCTCATTTTT
3591193 CATTTGCATTCT-AGTTTTT
1 CATTTGCATTCTCA-TTTTT
3591212 CATT
1 CATT
3591216 AATTCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 11 0.55
19 8 0.40
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.59
Consensus pattern (19 bp):
CATTTGCATTCTCATTTTT
Found at i:3594042 original size:16 final size:16
Alignment explanation
Indices: 3594021--3594134 Score: 85
Period size: 16 Copynumber: 6.9 Consensus size: 16
3594011 AAAAGATAGA
3594021 AAAAGAAGAAAAAAAG
1 AAAAGAAGAAAAAAAG
*
3594037 AAAAG-AGAAAAGATAG
1 AAAAGAAGAAAA-AAAG
*
3594053 AAAAG-AGAAAAGATAG
1 AAAAGAAGAAAA-AAAG
3594069 AAAAAGAAGAAAGGAAAAG
1 -AAAAGAAGAAA--AAAAG
*
3594088 AGAA-AAGATAGAAAAAG
1 AAAAGAAGA-A-AAAAAG
3594105 AAAAG-AGAAAAAAAAG
1 AAAAGAAG-AAAAAAAG
3594121 AGAAA-AAGAAAAAA
1 A-AAAGAAGAAAAAA
3594135 TGAGAAAAAA
Statistics
Matches: 83, Mismatches: 4, Indels: 22
0.76 0.04 0.20
Matches are distributed among these distances:
15 6 0.07
16 37 0.45
17 25 0.30
18 10 0.12
19 4 0.05
20 1 0.01
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (16 bp):
AAAAGAAGAAAAAAAG
Found at i:3594093 original size:46 final size:46
Alignment explanation
Indices: 3594011--3594132 Score: 167
Period size: 46 Copynumber: 2.6 Consensus size: 46
3594001 TAAATTCATA
3594011 AAAAGATAGAAAAAGAAGAAAAAAAGAAAAGAGAAAAGATAGAAAAGAG
1 AAAAGATAGAAAAAGAAG--AAAAAGAAAAGAGAAAAGATAGAAAA-AG
*
3594060 AAAAGATAGAAAAAGAAG-AAAGGAAAAGAGAAAAGATAGAAAAAG
1 AAAAGATAGAAAAAGAAGAAAAAGAAAAGAGAAAAGATAGAAAAAG
* *
3594105 AAAAGAGA-AAAAAAAGAGAAAAAGAAAA
1 AAAAGATAGAAAAAGA-AGAAAAAGAAAA
3594133 AATGAGAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
44 6 0.09
45 11 0.16
46 32 0.48
49 18 0.27
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (46 bp):
AAAAGATAGAAAAAGAAGAAAAAGAAAAGAGAAAAGATAGAAAAAG
Found at i:3594131 original size:30 final size:32
Alignment explanation
Indices: 3594012--3594134 Score: 59
Period size: 33 Copynumber: 3.8 Consensus size: 32
3594002 AAATTCATAA
3594012 AAAGATAGAAAAAGAAGAA-A-AAAAGAAAAGAG
1 AAAGATAGAAAAAGAA-AAGAGAAAA-AAAAGAG
* *
3594044 AAAAGATAGAAAAGAGAAAAGA-TAGAAAAAGAAG
1 -AAAGATAGAAAA-AGAAAAGAGAAAAAAAAG-AG
3594078 AAAG---GAAAAGAGAAAAGATAGAAAAAGAAAAGAG
1 AAAGATAGAAAA-AGAAAAG--AG-AAAA-AAAAGAG
*
3594112 AAA-A-A-AAAGAGAAAA-AGAAAAAA
1 AAAGATAGAAAAAGAAAAGAGAAAAAA
3594135 TGAGAAAAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 25
0.71 0.05 0.24
Matches are distributed among these distances:
28 2 0.03
29 4 0.05
30 15 0.20
32 1 0.01
33 29 0.39
34 19 0.25
35 5 0.07
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (32 bp):
AAAGATAGAAAAAGAAAAGAGAAAAAAAAGAG
Found at i:3596048 original size:62 final size:61
Alignment explanation
Indices: 3595974--3596120 Score: 174
Period size: 60 Copynumber: 2.4 Consensus size: 61
3595964 GGCTTCCTCG
* **
3595974 TGAAGAGAAGTCAACCTTTGTTATTCCTGACTCCCCAGCAGAGT-TGATCCTTGACTTTC-TAA
1 TGAA-AGAAGTCAATCTTTGTTATT-CTGACTCCCCAGCAGAGTCAAATCCTTGA-TTTCTTAA
* *
3596036 TGAACAGAAGTCAATCTTTGTTA-TCTGACTCCCCAGTAGAGTCAAATCCTTGATTTCTTCA
1 TGAA-AGAAGTCAATCTTTGTTATTCTGACTCCCCAGCAGAGTCAAATCCTTGATTTCTTAA
* *
3596097 TGAAAAAAGTCAATCTTTTTTATT
1 TGAAAGAAGTCAATCTTTGTTATT
3596121 TGATATTCAT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
60 37 0.50
61 16 0.22
62 21 0.28
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (61 bp):
TGAAAGAAGTCAATCTTTGTTATTCTGACTCCCCAGCAGAGTCAAATCCTTGATTTCTTAA
Found at i:3596949 original size:19 final size:19
Alignment explanation
Indices: 3596925--3596977 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
3596915 GGTTGACCTA
3596925 GTGTATCGGTACACTTGGG
1 GTGTATCGGTACACTTGGG
3596944 GTGTATCGGTACACTTGGG
1 GTGTATCGGTACACTTGGG
3596963 GTGTATCGGTACACT
1 GTGTATCGGTACACT
3596978 AATTACATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.34, T:0.32
Consensus pattern (19 bp):
GTGTATCGGTACACTTGGG
Found at i:3599691 original size:20 final size:20
Alignment explanation
Indices: 3599666--3599714 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
3599656 AAACCCGACA
* *
3599666 AGTGTATCGGTATACTGCAG
1 AGTGTATCGGTACAATGCAG
3599686 AGTGTATCGGTACAATGCAG
1 AGTGTATCGGTACAATGCAG
3599706 AGTGTATCG
1 AGTGTATCG
3599715 ATAAAAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.29
Consensus pattern (20 bp):
AGTGTATCGGTACAATGCAG
Found at i:3599771 original size:14 final size:15
Alignment explanation
Indices: 3599747--3599777 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3599737 AATACACTAT
3599747 CATAGTGTATCGATA
1 CATAGTGTATCGATA
3599762 CATA-TGTATCGATA
1 CATAGTGTATCGATA
3599776 CA
1 CA
3599778 CTGTGCACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (15 bp):
CATAGTGTATCGATA
Found at i:3603263 original size:17 final size:17
Alignment explanation
Indices: 3603241--3603279 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
3603231 TCCCCTTGGG
3603241 TATCCATTTGTGTAGGA
1 TATCCATTTGTGTAGGA
3603258 TATCCATTTGTGTAGGA
1 TATCCATTTGTGTAGGA
3603275 TATCC
1 TATCC
3603280 TTATCTTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (17 bp):
TATCCATTTGTGTAGGA
Found at i:3603646 original size:22 final size:21
Alignment explanation
Indices: 3603605--3603651 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3603595 GCGATTATTT
3603605 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
3603626 TCATTTTTGTATTTTGAAA-A
1 TCATTTTTCAATTTTGAAATA
3603646 T-ATTTT
1 TCATTTT
3603652 ATCATAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.21
20 2 0.08
21 17 0.71
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.57
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:3606328 original size:135 final size:135
Alignment explanation
Indices: 3605910--3606655 Score: 984
Period size: 136 Copynumber: 5.5 Consensus size: 135
3605900 ATGTTTTCAA
* ** *
3605910 CAAAAATTGATCTGACTACCCGAAAAAGAGAAACCGATCAAGGTC-GATCTCCCCTGAAAGAAGA
1 CAAAAATTGATCTGACTACCCGAAAAAGAGGAACAAATCAA-GTCTTATCT-CCCTGAAAGAAGA
* * *
3605974 GTTGAGCAGACATGTCTTCCAAAGATTTCTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCATA
64 GTGGAGCAGAC-CGTCTTCCAAAGATTTCTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGA
3606039 CTCGTTTT
128 CTCGTTTT
* * * *
3606047 -AAAAATTGATCTGACTACCTGAAAAA-AGGAACATATCAAGTCTTATCTTCCTAAAAGAAGAGT
1 CAAAAATTGATCTGACTACCCGAAAAAGAGGAACAAATCAAGTCTTATCTCCCTGAAAGAAGAGT
* * *
3606110 GGAGCAGACACGTATTCCAAATATTTCTTGAGTCTTATCTCCCTGAAAGGAGAGTGGAGCAGACT
66 GGAGCAGAC-CGTCTTCCAAAGATTTCTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACT
*
3606175 CATTTT
130 CGTTTT
*
3606181 CCAAAATTGATCTGACTACCCGAAAAAGAGGAACAAATCAAGTCTTATCTCCCTGAAAGAAGAGT
1 CAAAAATTGATCTGACTACCCGAAAAAGAGGAACAAATCAAGTCTTATCTCCCTGAAAGAAGAGT
* * * * * *
3606246 GGATCAGACCTGTCTTTCAAAGATTTCTCGAGTCTTATCTCCGT-AAAAAAGAGTGGAGTAGACT
66 GGAGCAGACC-GTCTTCCAAAGATTTCTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACT
3606310 CGTTTT
130 CGTTTT
* *
3606316 CCAAAATTGATCTGACTACCCG-AAAAGAGGAACAAATCAAGTCTTATCTCCCTGAAAGAAGAAT
1 CAAAAATTGATCTGACTACCCGAAAAAGAGGAACAAATCAAGTCTTATCTCCCTGAAAGAAGAGT
3606380 GGAGCAGACACGTCTTCCAAAGATTTCTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACT
66 GGAGCAGAC-CGTCTTCCAAAGATTTCTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACT
*
3606445 TGTTTT
130 CGTTTT
* * *
3606451 CTAAAATTGATCTGACTACCCGAAAAAGAGAAACATATCAAGTCTTATCTCCCTGAAAGAAGAGT
1 CAAAAATTGATCTGACTACCCGAAAAAGAGGAACAAATCAAGTCTTATCTCCCTGAAAGAAGAGT
* * * * * * * *
3606516 GGAGTAGACCCATCTTCCAAAGATTTCTCGAGTCTTATATCCCTGAAAGAATAGTGAAGCTGGCT
66 GGAGCAGA-CCGTCTTCCAAAGATTTCTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACT
*
3606581 CATTTT
130 CGTTTT
** * * *
3606587 CAAAAATTGAT-TGACTACCTAAAAAAGAGGAATAGATCAAGGTC-GATCTCCCCTGAAAGAAGA
1 CAAAAATTGATCTGACTACCCGAAAAAGAGGAACAAATCAA-GTCTTATCT-CCCTGAAAGAAGA
3606650 GTGGAG
64 GTGGAG
3606656 TGGATTTCCC
Statistics
Matches: 541, Mismatches: 58, Indels: 21
0.87 0.09 0.03
Matches are distributed among these distances:
134 159 0.29
135 156 0.29
136 225 0.42
137 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (135 bp):
CAAAAATTGATCTGACTACCCGAAAAAGAGGAACAAATCAAGTCTTATCTCCCTGAAAGAAGAGT
GGAGCAGACCGTCTTCCAAAGATTTCTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACTC
GTTTT
Found at i:3606400 original size:270 final size:271
Alignment explanation
Indices: 3605912--3606655 Score: 1025
Period size: 270 Copynumber: 2.7 Consensus size: 271
3605902 GTTTTCAACA
** *
3605912 AAAATTGATCTGACTACCCGAAAAAGAGAAACCGATCAAGGTC-GATCTCCCCTGAAAGAAGAGT
1 AAAATTGATCTGACTACCCGAAAAAGAGAAACAAATCAA-GTCTTATCT-CCCTGAAAGAAGAGT
* * * * * *
3605976 TGAGCAGACATGTCTTCCAAAGATTTCTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCATACT
64 GGATCAGACCTGTCTTCCAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGTAGACT
* * * * *
3606041 CGTTTT-AAAAATTGATCTGACTACCTGAAAAAAGGAACATATCAAGTCTTATCTTCCTAAAAGA
129 CGTTTTCAAAAATTGATCTGACTACCAGAAAAGAGGAACAAATCAAGTCTTATCTCCCTGAAAGA
* *
3606105 AGAGTGGAGCAGACACGTATTCCAAATATTTCTTGAGTCTTATCTCCCTGAAAGGAGAGTGGAGC
194 AGAGTGGAGCAGACACGTATTCCAAAGATTTCTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGC
3606170 AGACTCATTTTCC
259 AGACTCATTTTCC
*
3606183 AAAATTGATCTGACTACCCGAAAAAGAGGAACAAATCAAGTCTTATCTCCCTGAAAGAAGAGTGG
1 AAAATTGATCTGACTACCCGAAAAAGAGAAACAAATCAAGTCTTATCTCCCTGAAAGAAGAGTGG
* * *
3606248 ATCAGACCTGTCTTTCAAAGATTTCTCGAGTCTTATCTCCGT-AAAAAAGAGTGGAGTAGACTCG
66 ATCAGACCTGTCTTCCAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGTAGACTCG
* *
3606312 TTTTCCAAAATTGATCTGACTACCCGAAAAGAGGAACAAATCAAGTCTTATCTCCCTGAAAGAAG
131 TTTTCAAAAATTGATCTGACTACCAGAAAAGAGGAACAAATCAAGTCTTATCTCCCTGAAAGAAG
* *
3606377 AATGGAGCAGACACGTCTTCCAAAGATTTCTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAG
196 AGTGGAGCAGACACGTATTCCAAAGATTTCTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAG
** *
3606442 ACTTGTTTTCT
261 ACTCATTTTCC
*
3606453 AAAATTGATCTGACTACCCGAAAAAGAGAAACATATCAAGTCTTATCTCCCTGAAAGAAGAGTGG
1 AAAATTGATCTGACTACCCGAAAAAGAGAAACAAATCAAGTCTTATCTCCCTGAAAGAAGAGTGG
** * * * *
3606518 AGT-AGACCCATCTTCCAAAGATTTCTCGAGTCTTATATCCCTGAAAGAATAGTGAAGCT-GGCT
66 A-TCAGACCTGTCTTCCAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAG-TAGACT
* * * * *
3606581 CATTTTCAAAAATTGAT-TGACTACCTAAAAAAGAGGAATAGATCAAGGTC-GATCTCCCCTGAA
129 CGTTTTCAAAAATTGATCTGACTACC-AGAAAAGAGGAACAAATCAA-GTCTTATCT-CCCTGAA
3606644 AGAAGAGTGGAG
191 AGAAGAGTGGAG
3606656 TGGATTTCCC
Statistics
Matches: 420, Mismatches: 45, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
269 23 0.05
270 285 0.68
271 90 0.21
272 22 0.05
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (271 bp):
AAAATTGATCTGACTACCCGAAAAAGAGAAACAAATCAAGTCTTATCTCCCTGAAAGAAGAGTGG
ATCAGACCTGTCTTCCAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGTAGACTCG
TTTTCAAAAATTGATCTGACTACCAGAAAAGAGGAACAAATCAAGTCTTATCTCCCTGAAAGAAG
AGTGGAGCAGACACGTATTCCAAAGATTTCTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAG
ACTCATTTTCC
Found at i:3609236 original size:15 final size:17
Alignment explanation
Indices: 3609217--3609253 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3609207 AAATATCTTT
3609217 TAAAA-CAATTTTAAGA
1 TAAAATCAATTTTAAGA
*
3609233 -AAAATCATTTTTAAGA
1 TAAAATCAATTTTAAGA
3609249 TAAAA
1 TAAAA
3609254 ATTGGTCTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 4 0.22
16 10 0.56
17 4 0.22
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.32
Consensus pattern (17 bp):
TAAAATCAATTTTAAGA
Found at i:3609719 original size:2 final size:2
Alignment explanation
Indices: 3609712--3609737 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3609702 GCGTACATAG
3609712 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
3609738 GATTATAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3610298 original size:15 final size:16
Alignment explanation
Indices: 3610251--3610300 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
3610241 CAGACTTATT
* *
3610251 GAAAAATATATATATA
1 GAAAAATATAGATAAA
*
3610267 GATACAATATAGA-AAA
1 GA-AAAATATAGATAAA
3610283 GAAAAATATA-ATAAA
1 GAAAAATATAGATAAA
3610298 GAA
1 GAA
3610301 TACCAACGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
14 1 0.04
15 13 0.46
16 6 0.21
17 8 0.29
ACGTcount: A:0.66, C:0.02, G:0.10, T:0.22
Consensus pattern (16 bp):
GAAAAATATAGATAAA
Found at i:3612969 original size:3 final size:3
Alignment explanation
Indices: 3612961--3613113 Score: 242
Period size: 3 Copynumber: 51.0 Consensus size: 3
3612951 ACAGGGTTCT
3612961 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3613009 GAA GAA GAA GAA -AGA GAA GAA GAA GAAA GAA GAA -AGA GAA GAA -AA
1 GAA GAA GAA GAA GA-A GAA GAA GAA G-AA GAA GAA GA-A GAA GAA GAA
3613054 GAAA GAA GAA GAA GAA G-A GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3613099 GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA
3613114 AATAAAAGTA
Statistics
Matches: 142, Mismatches: 0, Indels: 16
0.90 0.00 0.10
Matches are distributed among these distances:
2 6 0.04
3 128 0.90
4 8 0.06
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3614269 original size:29 final size:30
Alignment explanation
Indices: 3614220--3614281 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
3614210 AATATAATAA
* *
3614220 TTATCTTTTTAAGTAAGAATTATTGATTTT
1 TTATCTTTTTAAATAAGAATTAGTGATTTT
*
3614250 TTAT-TTTTTAAATAATAATTAGTGATTTT
1 TTATCTTTTTAAATAAGAATTAGTGATTTT
3614279 TTA
1 TTA
3614282 AACTCATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (30 bp):
TTATCTTTTTAAATAAGAATTAGTGATTTT
Found at i:3615142 original size:3 final size:3
Alignment explanation
Indices: 3615125--3615178 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
3615115 ACTAATTTTT
* * *
3615125 TTA TTA CTA TAA TTA TTA TTA TTA TAA TTA TTA -TA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
3615170 TTA TTA TTA
1 TTA TTA TTA
3615179 AAAAATAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:3616805 original size:23 final size:24
Alignment explanation
Indices: 3616778--3616830 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
3616768 GTCATTTTGA
3616778 TATTTCTAAATA-A-ATAAATATTT
1 TATTTCTAAATATATATAAAT-TTT
*
3616801 TATTTATAAATATATATAAATTTT
1 TATTTCTAAATATATATAAATTTT
3616825 T-TTTCT
1 TATTTCT
3616831 TTTTTTTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 15 0.58
24 5 0.19
25 6 0.23
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTTCTAAATATATATAAATTTT
Found at i:3617362 original size:19 final size:18
Alignment explanation
Indices: 3617323--3617364 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
3617313 CTTTTCAAAT
3617323 TTTTTATATATACTTATTA
1 TTTTTATATATA-TTATTA
3617342 TTTTTATAGTAT-TTATATA
1 TTTTTATA-TATATTAT-TA
3617361 TTTT
1 TTTT
3617365 CTTATTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 4 0.19
19 14 0.67
20 3 0.14
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTTATATATATTATTA
Found at i:3620659 original size:15 final size:15
Alignment explanation
Indices: 3620639--3620670 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3620629 TCAATACCTT
3620639 TTTTGCATACATACA
1 TTTTGCATACATACA
*
3620654 TTTTGCATACATTCA
1 TTTTGCATACATACA
3620669 TT
1 TT
3620671 ATTCATTTCA
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:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:3627991 original size:13 final size:14
Alignment explanation
Indices: 3627973--3628010 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3627963 ATTATGCTTG
3627973 AAGAAAAGAAAG-A
1 AAGAAAAGAAAGAA
*
3627986 AAGAAAAAAAAGAA
1 AAGAAAAGAAAGAA
*
3628000 AAAAAAAGAAA
1 AAGAAAAGAAA
3628011 AAGGGGGTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAAAGAA
Found at i:3630328 original size:113 final size:113
Alignment explanation
Indices: 3629985--3630738 Score: 904
Period size: 113 Copynumber: 6.6 Consensus size: 113
3629975 GATTCAAATC
* *
3629985 CATCATTTGATGGATC-AGTATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAG
1 CATCATTTGATGGATCAACT-TTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAG
*
3630048 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
61 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* * * * * *
3630101 CATTATTTGATGGATTAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTAAAG-
1 CATCATTTGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGA
* *
3630164 A-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATT
62 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* * *
3630215 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGA
1 CATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
3630280 AGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
*
3630328 CATCATTTGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
3630393 AGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* * ** *
3630441 CATCATTTGATGAATTAAAATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGA
1 CATCATTTGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGA
* * * ** *
3630505 AGGAAGAGGAAATTCATAATGAGAAGAATTTGGTCAACCTTTTGCTCAAATC
62 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* * *
3630557 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
1 CATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
** *
3630622 AGAAGGAA-TTCATAATGAGAAGAATTTGTTCAAATTTTTGC-TCAATTT
66 AGAA-GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAA-TT
* * * *
3630670 CATCATTCGATGGATCAA-TATTGT-TAGA-AAGAGTTCATAATAAGAAGAACTCATCTAAAG-A
1 CATCATTTGATGGATCAACT-TT-TCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAA
3630731 GG-AGAAGA
63 GGAAGAAGA
3630739 GCTTATTCAA
Statistics
Matches: 563, Mismatches: 61, Indels: 34
0.86 0.09 0.05
Matches are distributed among these distances:
110 2 0.00
111 13 0.02
112 10 0.02
113 291 0.52
114 92 0.16
115 3 0.01
116 150 0.27
117 2 0.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (113 bp):
CATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
Found at i:3630588 original size:229 final size:227
Alignment explanation
Indices: 3629985--3630721 Score: 952
Period size: 229 Copynumber: 3.2 Consensus size: 227
3629975 GATTCAAATC
*
3629985 CATCATTTGATGGATCAGTATTTCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 CATCATTTGATGGATCAGAATTTCCAGGTAGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAA
* *
3630050 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATTATTTGATGGA
65 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGA
* * * * *
3630115 TTAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTAAAG-A-GAAGAAGAAATT
130 TCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAG-AATT
*
3630177 CATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATT
190 CATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* ** *
3630215 CATCACTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--CTCATCTGAAGAA
1 CATCATTTGATGGATCAGAATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCTCATCTGAAGAA
* *
3630277 TGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTTGAATTCATCATTTGATGGA
65 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGA
*
3630342 TCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
130 TCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA-TTCATA
* *
3630407 ATGAGAAGAATTTGTTTAACCTTTTGTTTGAATT
194 ATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* * *
3630441 CATCATTTGATGAATTAAAATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAA
1 CATCATTTGATGGATCAGAATTTCCAGGTAGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAA
* * * ** * *
3630506 GGAAGAGGAAATTCATAATGAGAAGAATTTGGTCAACCTTTTGCTCAAATCCATCACTTGATGGA
65 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGA
* *
3630571 TCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGGAATTCATA
130 TCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA-GAATTCATA
** *
3630636 ATGAGAAGAATTTGTTCAAATTTTTGC-TCAATTT
194 ATGAGAAGAATTTGTTCAACCTTTTGCTTGAA-TT
* * ** *
3630670 CATCATTCGATGGATCA-ATATTGT-TAGAAAGAGTTCATAATAAGAAGAACTC
1 CATCATTTGATGGATCAGA-ATT-TCCAGGTAGAGTTCATAATGAGAAGAACTC
3630722 ATCTAAAGAG
Statistics
Matches: 446, Mismatches: 48, Indels: 27
0.86 0.09 0.05
Matches are distributed among these distances:
224 9 0.02
225 5 0.01
226 84 0.19
227 101 0.23
228 7 0.02
229 192 0.43
230 47 0.11
231 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.31
Consensus pattern (227 bp):
CATCATTTGATGGATCAGAATTTCCAGGTAGAGTTCATAATGAGAAGAACTCTCATCTGAAGAAG
GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGAT
CAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAATTCATAAT
GAGAAGAATTTGTTCAACCTTTTGCTTGAATT
Found at i:3630990 original size:3 final size:3
Alignment explanation
Indices: 3630973--3631050 Score: 88
Period size: 3 Copynumber: 26.0 Consensus size: 3
3630963 ACTAATTTTT
* * * *
3630973 TTA TTA CTA TAA TTA TTA TTA TTA TAA TTA TTA TTA TAA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3631020 TATA TTA TTA -TA TATA TTA TTA TTA TTA TTA
1 T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
3631051 AAAAATAATT
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.06
3 53 0.84
4 6 0.10
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:3631231 original size:16 final size:16
Alignment explanation
Indices: 3631210--3631250 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
3631200 CCAGCAGGAA
3631210 ACCCTAGGGTTATGAT
1 ACCCTAGGGTTATGAT
3631226 ACCCTAGGGTTATGAT
1 ACCCTAGGGTTATGAT
3631242 ACCCTAGGG
1 ACCCTAGGG
3631251 ACTACGCCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (16 bp):
ACCCTAGGGTTATGAT
Found at i:3631527 original size:21 final size:21
Alignment explanation
Indices: 3631486--3631532 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
3631476 ACAGAGAGAC
*
3631486 AAACCGAGAGCAAAGATACAA
1 AAACCGAGAGCAAAGACACAA
*
3631507 AAACGGAGAGCAACA-ACACAA
1 AAACCGAGAGCAA-AGACACAA
*
3631528 CAACC
1 AAACC
3631533 AGCAAAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.55, C:0.26, G:0.17, T:0.02
Consensus pattern (21 bp):
AAACCGAGAGCAAAGACACAA
Found at i:3633873 original size:18 final size:18
Alignment explanation
Indices: 3633852--3633887 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3633842 CGGAGCTCTT
3633852 CCTCTTCCAAACGCTCGC
1 CCTCTTCCAAACGCTCGC
*
3633870 CCTCTTCCAAACGTTCGC
1 CCTCTTCCAAACGCTCGC
3633888 TTTCGTCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.11, T:0.25
Consensus pattern (18 bp):
CCTCTTCCAAACGCTCGC
Found at i:3634010 original size:2 final size:2
Alignment explanation
Indices: 3634003--3634033 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3633993 TTCGTGGTTT
3634003 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3634034 TGATTTGAAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3637160 original size:25 final size:25
Alignment explanation
Indices: 3637063--3637153 Score: 164
Period size: 25 Copynumber: 3.6 Consensus size: 25
3637053 ATATTTATAA
3637063 TAGACTTTCTTGCAAACAAAGTTAC
1 TAGACTTTCTTGCAAACAAAGTTAC
*
3637088 TAGACTTTCTTGCAAGCAAAGTTAC
1 TAGACTTTCTTGCAAACAAAGTTAC
*
3637113 TAGACTTTCTTGCAAGCAAAGTTAC
1 TAGACTTTCTTGCAAACAAAGTTAC
3637138 TAGACTTTCTTGCAAA
1 TAGACTTTCTTGCAAA
3637154 TAGAGTTTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 64 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (25 bp):
TAGACTTTCTTGCAAACAAAGTTAC
Found at i:3645731 original size:32 final size:32
Alignment explanation
Indices: 3645695--3645829 Score: 114
Period size: 32 Copynumber: 4.2 Consensus size: 32
3645685 TGTTGTATAC
3645695 CATGTCATCCAAAATGAAGATGTGACGTGTGT
1 CATGTCATCCAAAATGAAGATGTGACGTGTGT
* *
3645727 CATGTCA-CCTACAATGATAG-TGTGATGTGTGT
1 CATGTCATCC-AAAATGA-AGATGTGACGTGTGT
* * * * *
3645759 CATTTCACCCACAATGATGATGTGGA-GTGTGC
1 CATGTCATCCAAAATGAAGATGT-GACGTGTGT
* ** * *
3645791 CATGCCATTTAAAATGAAGATGTGGCGTGTAT
1 CATGTCATCCAAAATGAAGATGTGACGTGTGT
3645823 CATGTCA
1 CATGTCA
3645830 CTTAAGGAGA
Statistics
Matches: 81, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
31 4 0.05
32 71 0.88
33 6 0.07
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (32 bp):
CATGTCATCCAAAATGAAGATGTGACGTGTGT
Found at i:3647267 original size:37 final size:37
Alignment explanation
Indices: 3647219--3647312 Score: 145
Period size: 38 Copynumber: 2.5 Consensus size: 37
3647209 ACTTTATTTT
3647219 GTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCG
1 GTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCG
* *
3647256 GTTCGAGTCGGGTCAGGTTTTTTTAAGTGTGATATTCG
1 GTTCGGGTCGGGTC-GGGTTTTTTAAGTGTGATATTCG
3647294 GATT-GGGTCGGGTCGGGTT
1 G-TTCGGGTCGGGTCGGGTT
3647313 CAGGTTTAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
37 17 0.33
38 32 0.63
39 2 0.04
ACGTcount: A:0.12, C:0.11, G:0.38, T:0.39
Consensus pattern (37 bp):
GTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCG
Found at i:3647504 original size:261 final size:259
Alignment explanation
Indices: 3647038--3647531 Score: 782
Period size: 261 Copynumber: 1.9 Consensus size: 259
3647028 ATTCATATAT
* *
3647038 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACTGGACCAACCCGAAAATATATATAATTCAGGT
1 TCGGGTCGGGTTCAGGTTTAGGGTGAAAAAAACCGGACCAACCCGAAAATATATATAATTCAGGT
*
3647103 CGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTATTATTTTGGGTCGGGTCGA
66 CGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTATTATTTCGGGTCGGGTC--
*
3647168 GTTGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTC
129 G--GGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCAGGTCGGGTC
*
3647233 GGGTTTTTTAAGTGTGATATTCGGTTC-GAGTCGGGTCAGGTTTTTTTAAGTGTGATATTCGGAT
192 GGGTTTTTTAAGTGTGATATTCGGGTCAG-GTCGGGTCAGGTTTTTTTAAGTGTGATATTCGGAT
3647297 TGGG
256 TGGG
* *
3647301 TCGGGTCGGGTTCAGGTTTAGTGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGGGT
1 TCGGGTCGGGTTCAGGTTTAGGGTGAAAAAAACCGGACCAACCCGAAAATATATATAATTC----
*
3647366 TGGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATA-TTTTT-TTATTTCGGGTCGG
62 -AGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTATTATTTCGGGTCGG
3647429 GTC-GGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCAGGTCGGGT
126 GTCGGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCAGGTCGGGT
3647493 -GGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTCA
191 CGGG-TTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTCA
3647532 AGTTCGGGTT
Statistics
Matches: 216, Mismatches: 8, Indels: 16
0.90 0.03 0.07
Matches are distributed among these distances:
260 3 0.01
261 92 0.43
262 1 0.00
263 57 0.26
266 16 0.07
267 5 0.02
268 42 0.19
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (259 bp):
TCGGGTCGGGTTCAGGTTTAGGGTGAAAAAAACCGGACCAACCCGAAAATATATATAATTCAGGT
CGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTATTATTTCGGGTCGGGTCGG
GATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCAGGTCGGGTCGGGT
TTTTTAAGTGTGATATTCGGGTCAGGTCGGGTCAGGTTTTTTTAAGTGTGATATTCGGATTGGG
Found at i:3648134 original size:16 final size:18
Alignment explanation
Indices: 3648113--3648157 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
3648103 ATGGAATTAA
3648113 ATTCCAATTCC-T-ACAG
1 ATTCCAATTCCTTAACAG
*
3648129 ATTCCAATTCCTTAACAT
1 ATTCCAATTCCTTAACAG
3648147 ATTCCAATTCC
1 ATTCCAATTCC
3648158 CTCATAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 11 0.42
17 1 0.04
18 14 0.54
ACGTcount: A:0.31, C:0.31, G:0.02, T:0.36
Consensus pattern (18 bp):
ATTCCAATTCCTTAACAG
Found at i:3648306 original size:27 final size:27
Alignment explanation
Indices: 3648276--3648332 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
3648266 TAGAATCTTT
3648276 TATTTTAGTTACTTGTGTTTAATGATA
1 TATTTTAGTTACTTGTGTTTAATGATA
3648303 TATTTTAGTTACTTGTGTTTAATGATA
1 TATTTTAGTTACTTGTGTTTAATGATA
3648330 TAT
1 TAT
3648333 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.04, G:0.14, T:0.56
Consensus pattern (27 bp):
TATTTTAGTTACTTGTGTTTAATGATA
Found at i:3648334 original size:2 final size:2
Alignment explanation
Indices: 3648327--3648367 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3648317 GTGTTTAATG
3648327 AT AT AT AT AT 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 AT AT AT AT AT A
3648368 GAGTTTTCTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3649064 original size:7 final size:7
Alignment explanation
Indices: 3649052--3649085 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
3649042 TATATGCATA
3649052 TATAAAG
1 TATAAAG
3649059 TATAAAG
1 TATAAAG
3649066 TATATAAAG
1 --TATAAAG
3649075 TATAAAG
1 TATAAAG
3649082 TATA
1 TATA
3649086 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 18 0.72
9 7 0.28
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (7 bp):
TATAAAG
Found at i:3649071 original size:16 final size:16
Alignment explanation
Indices: 3649050--3649087 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
3649040 AATATATGCA
3649050 TATATAAAGTATAAAG
1 TATATAAAGTATAAAG
3649066 TATATAAAGTATAAAG
1 TATATAAAGTATAAAG
3649082 TATATA
1 TATATA
3649088 TATATATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (16 bp):
TATATAAAGTATAAAG
Found at i:3649746 original size:4 final size:4
Alignment explanation
Indices: 3649737--3650166 Score: 439
Period size: 4 Copynumber: 107.5 Consensus size: 4
3649727 GATAAGTGTA
*
3649737 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TACG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * *
3649785 TATG TATG TATA TACG TATG TATG TATG TACG TATG TATA TATA TACG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
3649833 TATG TATG TATG TATG TATG TATG TACG TATT TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * *
3649881 TACG CATA TATG TATG TACG TATG TATG TATG TACG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
3649929 TATG TATG TATG TACG TATG TATG TATG TACG TATG TATG TATG TACG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * *
3649977 TATG TATG TATG TACG TAGG TAGG TATG TACG TAGG TA-G ATATG TACG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG -TATG TATG
* * * * * * * * * **
3650025 TAGG TAGG TATG TACG TAGG TACG TATG TACG TAGG TACG TATA TACA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * ** * * *
3650073 TATG TACG TATG TACG TATG TATG TATG TACA TATA TACG TATG TACG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * *
3650121 TATG TACG TACG TATG TATA TATG TATG TATA TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
3650167 CTTATATTAA
Statistics
Matches: 354, Mismatches: 70, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
3 1 0.00
4 352 0.99
5 1 0.00
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.42
Consensus pattern (4 bp):
TATG
Found at i:3649758 original size:16 final size:16
Alignment explanation
Indices: 3649737--3650167 Score: 503
Period size: 16 Copynumber: 26.9 Consensus size: 16
3649727 GATAAGTGTA
*
3649737 TATGTATGTATGTATG
1 TATGTATGTATGTACG
*
3649753 TATGTATGTATGTATG
1 TATGTATGTATGTACG
3649769 TATGTATGTATGTACG
1 TATGTATGTATGTACG
*
3649785 TATGTATGTATATACG
1 TATGTATGTATGTACG
3649801 TATGTATGTATGTACG
1 TATGTATGTATGTACG
* *
3649817 TATGTATATATATACG
1 TATGTATGTATGTACG
*
3649833 TATGTATGTATGTATG
1 TATGTATGTATGTACG
* *
3649849 TATGTATGTACGTATTTATG
1 TATGTA--T--GTATGTACG
3649869 TATGTATGTATGTACG
1 TATGTATGTATGTACG
* *
3649885 CATATATGTATGTACG
1 TATGTATGTATGTACG
3649901 TATGTATGTATGTACG
1 TATGTATGTATGTACG
3649917 TATGTATGTA--T--G
1 TATGTATGTATGTACG
3649929 TATGTATGTATGTACG
1 TATGTATGTATGTACG
3649945 TATGTATGTATGTACG
1 TATGTATGTATGTACG
3649961 TATGTATGTATGTACG
1 TATGTATGTATGTACG
3649977 TATGTATGTATGTACG
1 TATGTATGTATGTACG
* *
3649993 TAGGTAGGTATGTACG
1 TATGTATGTATGTACG
*
3650009 TAGGTA-GATATGTACG
1 TATGTATG-TATGTACG
* *
3650025 TAGGTAGGTATGTACG
1 TATGTATGTATGTACG
* *
3650041 TAGGTACGTATGTACG
1 TATGTATGTATGTACG
* * * *
3650057 TAGGTACGTATATACA
1 TATGTATGTATGTACG
*
3650073 TATGTACGTATGTACG
1 TATGTATGTATGTACG
*
3650089 TATGTATGTATGTACA
1 TATGTATGTATGTACG
* *
3650105 TATATACGTATGTACG
1 TATGTATGTATGTACG
* * *
3650121 TATGTACGTACGTATG
1 TATGTATGTATGTACG
* **
3650137 TATATATGTATGTATA
1 TATGTATGTATGTACG
3650153 TATGTATGTATGTAC
1 TATGTATGTATGTAC
3650168 TTATATTAAT
Statistics
Matches: 368, Mismatches: 37, Indels: 20
0.87 0.09 0.05
Matches are distributed among these distances:
12 11 0.03
14 2 0.01
15 1 0.00
16 337 0.92
17 1 0.00
18 2 0.01
20 14 0.04
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.42
Consensus pattern (16 bp):
TATGTATGTATGTACG
Found at i:3658222 original size:2 final size:2
Alignment explanation
Indices: 3658217--3658332 Score: 89
Period size: 2 Copynumber: 57.5 Consensus size: 2
3658207 GCACACACAC
* * *
3658217 AT AT AT AT AT -T AT AGT TT AT AGT TT AT AT ACT AT AGT TT AT AT
1 AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT A-T AT A-T AT AT AT
* * *
3658260 AT TT AT ACT AT AT A- AT TT AT AT A- AT -T AT ACT TT AT AT -T AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
3658300 AT 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 AT A
3658333 AGTAGACTGG
Statistics
Matches: 91, Mismatches: 12, Indels: 22
0.73 0.10 0.18
Matches are distributed among these distances:
1 5 0.05
2 78 0.86
3 8 0.09
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3658273 original size:22 final size:21
Alignment explanation
Indices: 3658217--3658330 Score: 103
Period size: 22 Copynumber: 5.4 Consensus size: 21
3658207 GCACACACAC
3658217 ATATATATA-T-TATAGTTTAT
1 ATATATATACTATATA-TTTAT
* *
3658237 AGTTTATATACTATA-GTTTAT
1 A-TATATATACTATATATTTAT
*
3658258 ATATTTATACTATATAATTTAT
1 ATATATATACTATAT-ATTTAT
*
3658280 ATA-ATTATACTTTATATTATAT
1 ATATA-TATACTATATATT-TAT
*
3658302 ATATATATA-TATATATATAT
1 ATATATATACTATATATTTAT
3658322 ATATATATA
1 ATATATATA
3658331 TAAGTAGACT
Statistics
Matches: 77, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
20 24 0.31
21 22 0.29
22 28 0.36
23 3 0.04
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (21 bp):
ATATATATACTATATATTTAT
Found at i:3659325 original size:21 final size:21
Alignment explanation
Indices: 3659301--3659349 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3659291 CGTTTTGACT
3659301 TGAACTGACA-TCGATCCGAAC
1 TGAACTGACACT-GATCCGAAC
* *
3659322 TGAAATTACACTGATCCGAAC
1 TGAACTGACACTGATCCGAAC
3659343 TCGAACT
1 T-GAACT
3659350 TAATCTGATG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (21 bp):
TGAACTGACACTGATCCGAAC
Found at i:3659636 original size:32 final size:32
Alignment explanation
Indices: 3659595--3659657 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
3659585 GTCACATCAC
* *
3659595 CCAAGGTGATTATGTGTCTTGTGTAATGTCAT
1 CCAAGGTGATAATGTGTCTTATGTAATGTCAT
*
3659627 CCAAGGTGATAATGTGTCTTATGTTATGTCA
1 CCAAGGTGATAATGTGTCTTATGTAATGTCA
3659658 GTTAAAGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.40
Consensus pattern (32 bp):
CCAAGGTGATAATGTGTCTTATGTAATGTCAT
Found at i:3659668 original size:32 final size:32
Alignment explanation
Indices: 3659595--3659674 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
3659585 GTCACATCAC
* * *
3659595 CCAAGGTGATTATGTGTCTTGTGTAATGTCAT
1 CCAAAGTGATAATGTGTCTTATGTAATGTCAT
* *
3659627 CCAAGGTGATAATGTGTCTTATGTTATGTCAGT
1 CCAAAGTGATAATGTGTCTTATGTAATGTCA-T
* *
3659660 -TAAAGTGATGATGTG
1 CCAAAGTGATAATGTG
3659675 ACGTGCAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 40 0.98
33 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.26, T:0.39
Consensus pattern (32 bp):
CCAAAGTGATAATGTGTCTTATGTAATGTCAT
Found at i:3659823 original size:30 final size:31
Alignment explanation
Indices: 3659789--3659848 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
3659779 CACATCACCT
*
3659789 AAGGTGATAATGTGTCATGT-CATGTCATCC
1 AAGGTGATAATGTGTAATGTGCATGTCATCC
*
3659819 AAGGTGATGATGTGTAATGTGGCATGTCAT
1 AAGGTGATAATGTGTAATGT-GCATGTCAT
3659849 TCACATGCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 18 0.69
32 8 0.31
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (31 bp):
AAGGTGATAATGTGTAATGTGCATGTCATCC
Found at i:3660783 original size:24 final size:26
Alignment explanation
Indices: 3660719--3660785 Score: 93
Period size: 24 Copynumber: 2.7 Consensus size: 26
3660709 TTTTATAGAC
*
3660719 TAATAAAATAAAAATAAAAATATTTA
1 TAATTAAATAAAAATAAAAATATTTA
**
3660745 TAATTAAATTTAAATAAAAA-A-TTA
1 TAATTAAATAAAAATAAAAATATTTA
3660769 TAATTAAATAAAAATAA
1 TAATTAAATAAAAATAA
3660786 TTGTTGGTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
24 18 0.50
25 1 0.03
26 17 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
TAATTAAATAAAAATAAAAATATTTA
Found at i:3663389 original size:293 final size:293
Alignment explanation
Indices: 3662862--3663444 Score: 1040
Period size: 293 Copynumber: 2.0 Consensus size: 293
3662852 TATCAATTTT
*
3662862 CAGTTCCATTAAAATTCTTTGGTTAACTTTCTTCTCTTTTTTAAGTCATTTCTGAGTTATATAGG
1 CAGTTCCATTAAAATTCCTTGGTTAACTTTCTTCTCTTTTTTAAGTCATTTCTGAGTTATATAGG
3662927 TATATTGAGATGAAGTTGTTGAACCCATGCAAATAGGAAGCTCACTTTTACTCTGGCTTGGTTGG
66 TATATTGAGATGAAGTTGTTGAACCCATGCAAATAGGAAGCTCACTTTTACTCTGGCTTGGTTGG
* * * *
3662992 TTCATTGTTTTTCTGTTTGAGAATAATTGAAGTGCCTTACGGATTGGTGATCACATACTACCCTC
131 TTCATTGTTTTGCTGTTTGAGAAGAATTGAAGCGCCATACGGATTGGTGATCACATACTACCCTC
* *
3663057 GATTGGATTACCGTCCTCTTGTTCTCAACGGGGTGTAGCTGGGAATCCCCTCTGTCTGTTTCCTG
196 GATTGGATTACCGTCCTCTTGTTCTCAACAGGGTGTAGCTGGGAATCCCCTATGTCTGTTTCCTG
3663122 TTGCTGTTTGAGAAGGTTTGAATTGATTTAGGG
261 TTGCTGTTTGAGAAGGTTTGAATTGATTTAGGG
*
3663155 CAGTTCCATTGAAATTCCTTGGTTAACTTTCTTCTCTTTTTTAAGTCATTTCTGAGTTATATAGG
1 CAGTTCCATTAAAATTCCTTGGTTAACTTTCTTCTCTTTTTTAAGTCATTTCTGAGTTATATAGG
* **
3663220 TGTATTGAGATGAAGTTGTTGAACCCATGCAAATAGGAAGCTTGCTTTTACTCTGGCTTGGTTGG
66 TATATTGAGATGAAGTTGTTGAACCCATGCAAATAGGAAGCTCACTTTTACTCTGGCTTGGTTGG
3663285 TTCATTGTTTTGCTGTTTGAGAAGAATTGAAGCGCCATACGGATTGGTGATCACATACTACCCTC
131 TTCATTGTTTTGCTGTTTGAGAAGAATTGAAGCGCCATACGGATTGGTGATCACATACTACCCTC
* *
3663350 GATTGGATTACCTTCCTCTTGTTCTCATCAGGGTGTAGCTGGGAATCCCCTATGTCTGTTTCCTG
196 GATTGGATTACCGTCCTCTTGTTCTCAACAGGGTGTAGCTGGGAATCCCCTATGTCTGTTTCCTG
*
3663415 TTGCTGTTTGAGAAGGTTTGAATTTATTTA
261 TTGCTGTTTGAGAAGGTTTGAATTGATTTA
3663445 TGGTTCATTT
Statistics
Matches: 276, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
293 276 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (293 bp):
CAGTTCCATTAAAATTCCTTGGTTAACTTTCTTCTCTTTTTTAAGTCATTTCTGAGTTATATAGG
TATATTGAGATGAAGTTGTTGAACCCATGCAAATAGGAAGCTCACTTTTACTCTGGCTTGGTTGG
TTCATTGTTTTGCTGTTTGAGAAGAATTGAAGCGCCATACGGATTGGTGATCACATACTACCCTC
GATTGGATTACCGTCCTCTTGTTCTCAACAGGGTGTAGCTGGGAATCCCCTATGTCTGTTTCCTG
TTGCTGTTTGAGAAGGTTTGAATTGATTTAGGG
Found at i:3663587 original size:6 final size:6
Alignment explanation
Indices: 3663578--3663606 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3663568 GGGATGATAA
3663578 ACGGGG ACGGGG ACGGGG ACGGGG ACGGG
1 ACGGGG ACGGGG ACGGGG ACGGGG ACGGG
3663607 TTTGGTAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.66, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:3663646 original size:13 final size:13
Alignment explanation
Indices: 3663630--3663661 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
3663620 GCCCCGATTA
3663630 CCCGATTACCCGC
1 CCCGATTACCCGC
3663643 CCCGATTACCCGC
1 CCCGATTACCCGC
3663656 CCCGAT
1 CCCGAT
3663662 ACCGACCCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.53, G:0.16, T:0.16
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:3663733 original size:24 final size:26
Alignment explanation
Indices: 3663706--3663770 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 26
3663696 ATATATATAT
*
3663706 ATAATATTAATA-A-ATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
3663730 ATAA-A-AAATATATATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
*
3663754 ATATATATATATATATA
1 ATA-ATATAAATATATA
3663771 CCCGGCCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 4 0.12
23 2 0.06
24 18 0.53
25 1 0.03
26 1 0.03
27 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATAATATAAATATATATTTAATTTAA
Found at i:3663748 original size:19 final size:19
Alignment explanation
Indices: 3663724--3663763 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3663714 AATAAATTTA
3663724 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
3663743 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
3663762 AT
1 AT
3663764 ATATATACCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:3663783 original size:12 final size:12
Alignment explanation
Indices: 3663768--3663809 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
3663758 ATATATATAT
*
3663768 ATACCCGGCCCA
1 ATACCCGACCCA
3663780 ATA-CCGACCCA
1 ATACCCGACCCA
3663791 ATACCCGACCCA
1 ATACCCGACCCA
3663803 ATACCCG
1 ATACCCG
3663810 TTTAAATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.31, C:0.48, G:0.12, T:0.10
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:3671515 original size:20 final size:20
Alignment explanation
Indices: 3671490--3671528 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3671480 AATGAACCGA
*
3671490 CTGAAAACCGGTAGAATCGG
1 CTGAAAACCGGTAAAATCGG
*
3671510 CTGAAAATCGGTAAAATCG
1 CTGAAAACCGGTAAAATCG
3671529 TGGTGAACCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (20 bp):
CTGAAAACCGGTAAAATCGG
Found at i:3672855 original size:158 final size:158
Alignment explanation
Indices: 3672567--3672884 Score: 636
Period size: 158 Copynumber: 2.0 Consensus size: 158
3672557 GATCCTCGAT
3672567 TTGGGGCTCTTAACTTTGTTGTTGTTTCGTTGTTGTCCCCATGGTTAGTTTAAATTTGTATTTTA
1 TTGGGGCTCTTAACTTTGTTGTTGTTTCGTTGTTGTCCCCATGGTTAGTTTAAATTTGTATTTTA
3672632 TAGTTTTATGACCACTGTTTGGTTCATTTTAAATTCATTATATTATGCCCACTTCTTATGTAATG
66 TAGTTTTATGACCACTGTTTGGTTCATTTTAAATTCATTATATTATGCCCACTTCTTATGTAATG
3672697 CATACATGTGTTACCATATGCCCTATGC
131 CATACATGTGTTACCATATGCCCTATGC
3672725 TTGGGGCTCTTAACTTTGTTGTTGTTTCGTTGTTGTCCCCATGGTTAGTTTAAATTTGTATTTTA
1 TTGGGGCTCTTAACTTTGTTGTTGTTTCGTTGTTGTCCCCATGGTTAGTTTAAATTTGTATTTTA
3672790 TAGTTTTATGACCACTGTTTGGTTCATTTTAAATTCATTATATTATGCCCACTTCTTATGTAATG
66 TAGTTTTATGACCACTGTTTGGTTCATTTTAAATTCATTATATTATGCCCACTTCTTATGTAATG
3672855 CATACATGTGTTACCATATGCCCTATGC
131 CATACATGTGTTACCATATGCCCTATGC
3672883 TT
1 TT
3672885 CGTATTGCGT
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 160 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.47
Consensus pattern (158 bp):
TTGGGGCTCTTAACTTTGTTGTTGTTTCGTTGTTGTCCCCATGGTTAGTTTAAATTTGTATTTTA
TAGTTTTATGACCACTGTTTGGTTCATTTTAAATTCATTATATTATGCCCACTTCTTATGTAATG
CATACATGTGTTACCATATGCCCTATGC
Found at i:3674669 original size:14 final size:14
Alignment explanation
Indices: 3674650--3674687 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3674640 GTCCAGTTAC
3674650 TGAGTCAACTCGGT
1 TGAGTCAACTCGGT
**
3674664 TGAGTCAACT-TTT
1 TGAGTCAACTCGGT
3674677 TGAGTCAACTC
1 TGAGTCAACTC
3674688 ATTGACTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (14 bp):
TGAGTCAACTCGGT
Found at i:3674692 original size:13 final size:13
Alignment explanation
Indices: 3674650--3674692 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
3674640 GTCCAGTTAC
*
3674650 TGAGTCAACTCGGT
1 TGAGTCAACTC-AT
**
3674664 TGAGTCAACTTTT
1 TGAGTCAACTCAT
3674677 TGAGTCAACTCAT
1 TGAGTCAACTCAT
3674690 TGA
1 TGA
3674693 CTTTGACAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (13 bp):
TGAGTCAACTCAT
Found at i:3679920 original size:7 final size:7
Alignment explanation
Indices: 3679908--3679948 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
3679898 TGAGTCAACT
3679908 CGTTGAC
1 CGTTGAC
3679915 CGTTGAC
1 CGTTGAC
*
3679922 TGTTGAC
1 CGTTGAC
3679929 CGATCTGAC
1 CG-T-TGAC
3679938 CGTTGAC
1 CGTTGAC
3679945 CGTT
1 CGTT
3679949 AACTTTGACC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 22 0.73
8 2 0.07
9 6 0.20
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.32
Consensus pattern (7 bp):
CGTTGAC
Found at i:3679942 original size:16 final size:14
Alignment explanation
Indices: 3679908--3679948 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 14
3679898 TGAGTCAACT
3679908 CGTTGACCGTTGAC
1 CGTTGACCGTTGAC
*
3679922 TGTTGACCGATCTGAC
1 CGTTGACCG-T-TGAC
3679938 CGTTGACCGTT
1 CGTTGACCGTT
3679949 AACTTTGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.39
15 2 0.09
16 12 0.52
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.32
Consensus pattern (14 bp):
CGTTGACCGTTGAC
Found at i:3693294 original size:18 final size:17
Alignment explanation
Indices: 3693240--3693288 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3693230 TTGGACTCCT
* *
3693240 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
3693258 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
3693276 AGTGCATTCGATG
1 AGTGCA-TCGATG
3693289 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:3693390 original size:19 final size:19
Alignment explanation
Indices: 3693366--3693416 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
3693356 TAAATAAATC
3693366 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
3693385 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
3693404 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
3693417 TTTTAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:3693420 original size:64 final size:63
Alignment explanation
Indices: 3693240--3693449 Score: 212
Period size: 64 Copynumber: 3.3 Consensus size: 63
3693230 TTGGACTCCT
* * * *
3693240 AGTGCATCGGTGCACT-AAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAAA-AATAGCC
1 AGTGCATCGATGCA-TGGAGAGTGCATCGATGCATGAA-TGCATTCGATGTTTTAAATAA-A-TC
*
3693303 TG
62 AG
** *
3693305 -GTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAAATAAATCAG
1 AGTGCATCGATGCATGGAGAGTGCATCGATGCAT-GAATGCATTCGATGTTTTAAATAAATCAG
* * * *
3693368 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTTTAATTTATTCATT
1 AGTGCATCGATGCATGGAGAGTGCATCGATGCAT-GAATGCATTCGATGTTTTAAATAAATCA--
3693433 G
63 G
3693434 A-TGCATCGATGCATGG
1 AGTGCATCGATGCATGG
3693450 TATTGATGCA
Statistics
Matches: 123, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
63 3 0.02
64 99 0.80
65 19 0.15
66 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (63 bp):
AGTGCATCGATGCATGGAGAGTGCATCGATGCATGAATGCATTCGATGTTTTAAATAAATCAG
Found at i:3696048 original size:24 final size:23
Alignment explanation
Indices: 3695977--3696056 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
3695967 CATGATCTTG
* *
3695977 TGCATTGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
3696000 TGCATCGGTG--CA-TCATGCGGA
1 TGCATCGATGCACATTCAAG-GGA
3696021 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
3696045 TGCATCGATGCA
1 TGCATCGATGCA
3696057 TTGTTAAGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 13 0.28
23 10 0.22
24 17 0.37
25 2 0.04
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.24
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Done.