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 12 of 30
Found at i:2254433 original size:2 final size:2
Alignment explanation
Indices: 2254426--2254484 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
2254416 ATCAAATACA
2254426 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2254467 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
2254485 TATGGCTAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2263961 original size:25 final size:25
Alignment explanation
Indices: 2263925--2263973 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2263915 ATCAAAGGTA
*
2263925 CTGAAGCGTAAACATATAGTGATAC
1 CTGAAGCATAAACATATAGTGATAC
*
2263950 CTGAAGCATAAACATGTAGTGATA
1 CTGAAGCATAAACATATAGTGATA
2263974 TGGTGCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.24
Consensus pattern (25 bp):
CTGAAGCATAAACATATAGTGATAC
Found at i:2264483 original size:46 final size:46
Alignment explanation
Indices: 2264426--2264551 Score: 191
Period size: 46 Copynumber: 2.7 Consensus size: 46
2264416 AGAGTCGAGG
*
2264426 GTTCTATGTGGTCTTA-GGAGACATAGTGGTCCTACAGGACATATGT
1 GTTCTATGTGGTCCTACGG-GACATAGTGGTCCTACAGGACATATGT
* *
2264472 GTTCTACGTGGTCCTACGGGACATAGTGGTCCTACGGGACATATGT
1 GTTCTATGTGGTCCTACGGGACATAGTGGTCCTACAGGACATATGT
* *
2264518 GTTCTATGTGGTCCTATGGGATATAGTGGTCCTA
1 GTTCTATGTGGTCCTACGGGACATAGTGGTCCTA
2264552 TGGGAAAAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
46 71 0.97
47 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (46 bp):
GTTCTATGTGGTCCTACGGGACATAGTGGTCCTACAGGACATATGT
Found at i:2264502 original size:18 final size:18
Alignment explanation
Indices: 2264479--2264514 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2264469 TGTGTTCTAC
2264479 GTGGTCCTACGGGACATA
1 GTGGTCCTACGGGACATA
2264497 GTGGTCCTACGGGACATA
1 GTGGTCCTACGGGACATA
2264515 TGTGTTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.22
Consensus pattern (18 bp):
GTGGTCCTACGGGACATA
Found at i:2264506 original size:28 final size:28
Alignment explanation
Indices: 2264451--2264507 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
2264441 AGGAGACATA
*
2264451 GTGGTCCTACAGGACATATGTGTTCTAC
1 GTGGTCCTACAGGACATATGTGTCCTAC
*
2264479 GTGGTCCTACGGGACATA-GTGGTCCTAC
1 GTGGTCCTACAGGACATATGT-GTCCTAC
2264507 G
1 G
2264508 GGACATATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 24 0.92
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (28 bp):
GTGGTCCTACAGGACATATGTGTCCTAC
Found at i:2264552 original size:28 final size:28
Alignment explanation
Indices: 2264497--2264553 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
2264487 ACGGGACATA
*
2264497 GTGGTCCTACGGGACATATGTGTTCTAT
1 GTGGTCCTACGGGACATATGTGTCCTAT
* *
2264525 GTGGTCCTATGGGATATA-GTGGTCCTAT
1 GTGGTCCTACGGGACATATGT-GTCCTAT
2264553 G
1 G
2264554 GGAAAAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.35
Consensus pattern (28 bp):
GTGGTCCTACGGGACATATGTGTCCTAT
Found at i:2269682 original size:16 final size:17
Alignment explanation
Indices: 2269657--2269690 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2269647 CTGAGGTATC
2269657 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
2269673 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
2269690 A
1 A
2269691 GAATGGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:2270385 original size:21 final size:21
Alignment explanation
Indices: 2270353--2270406 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2270343 AGAATTTGTT
* *
2270353 CCGAAGGACCACATATATGTC
1 CCGAATGACCACATAGATGTC
*
2270374 CTGAATGACCACATAGATGTC
1 CCGAATGACCACATAGATGTC
2270395 CCGAATGACCAC
1 CCGAATGACCAC
2270407 TCCTTAAGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.30, G:0.19, T:0.19
Consensus pattern (21 bp):
CCGAATGACCACATAGATGTC
Found at i:2275923 original size:16 final size:16
Alignment explanation
Indices: 2275872--2275923 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
2275862 TTATGACATC
* *
2275872 CTAGTTGTTACTTATT
1 CTAGTTGTTAATGATT
*
2275888 CTAATTGTT-ATCGATT
1 CTAGTTGTTAAT-GATT
2275904 CTAGTTGTTAATGATT
1 CTAGTTGTTAATGATT
2275920 CTAG
1 CTAG
2275924 CTATTACTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 1 0.03
16 27 0.90
17 2 0.07
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (16 bp):
CTAGTTGTTAATGATT
Found at i:2276110 original size:28 final size:28
Alignment explanation
Indices: 2276078--2276133 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
2276068 GTATTTTAGT
*
2276078 TATTCAATGACTCTAGGGAAATCTCTAC
1 TATTCAATAACTCTAGGGAAATCTCTAC
** * *
2276106 TATTCTTTAACTTTGGGGAAATCTCTAC
1 TATTCAATAACTCTAGGGAAATCTCTAC
2276134 GCGATTTTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (28 bp):
TATTCAATAACTCTAGGGAAATCTCTAC
Found at i:2287117 original size:23 final size:23
Alignment explanation
Indices: 2287086--2287187 Score: 105
Period size: 23 Copynumber: 4.4 Consensus size: 23
2287076 TAATGAAGTG
*
2287086 CCACGTAGAAATATCCCAAAGGA
1 CCACGTAGAAATATCCCGAAGGA
* * *
2287109 CCACATAGATATGTCCCGAAGGA
1 CCACGTAGAAATATCCCGAAGGA
* * *
2287132 CCGCGTAGAAATGTCCCGAATGA
1 CCACGTAGAAATATCCCGAAGGA
* * *
2287155 CCACGTAGAATTATCTCGTAGGA
1 CCACGTAGAAATATCCCGAAGGA
*
2287178 CCGCGTAGAA
1 CCACGTAGAA
2287188 CCCTCGACTC
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (23 bp):
CCACGTAGAAATATCCCGAAGGA
Found at i:2287139 original size:46 final size:46
Alignment explanation
Indices: 2287089--2287187 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 46
2287079 TGAAGTGCCA
*
2287089 CGTAGAAATATCCCAAAGGACCACATAG-ATATGTCCCGAAGGACCG
1 CGTAGAAATATCCCAAAGGACCACATAGAAT-TATCCCGAAGGACCG
* * * * * *
2287135 CGTAGAAATGTCCCGAATGACCACGTAGAATTATCTCGTAGGACCG
1 CGTAGAAATATCCCAAAGGACCACATAGAATTATCCCGAAGGACCG
2287181 CGTAGAA
1 CGTAGAA
2287188 CCCTCGACTC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
46 43 0.96
47 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.18
Consensus pattern (46 bp):
CGTAGAAATATCCCAAAGGACCACATAGAATTATCCCGAAGGACCG
Found at i:2294673 original size:60 final size:59
Alignment explanation
Indices: 2294549--2294684 Score: 157
Period size: 60 Copynumber: 2.3 Consensus size: 59
2294539 AGGATAACTT
* * *
2294549 TATTAAAAGTTATAAAATAATCCTTCAATTATAAAGTATTATTTTATTAAATCTCTCGTT
1 TATTAAAAGTTAT-AAATAATCCTTCAATTATAAAGTATTACTTTATTAAATCCCTCGTC
* * * * * *
2294609 TATTAAAAATTAATAAATAATCCTTCAATTATAGAGTGTTACTTTGTTGAGTCCCTCAG-C
1 TATTAAAAGTT-ATAAATAATCCTTCAATTATAAAGTATTACTTTATTAAATCCCTC-GTC
2294669 TATTAAAAGTTATAAA
1 TATTAAAAGTTATAAA
2294685 ATGGTCACCA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
59 5 0.08
60 56 0.88
61 3 0.05
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (59 bp):
TATTAAAAGTTATAAATAATCCTTCAATTATAAAGTATTACTTTATTAAATCCCTCGTC
Found at i:2295043 original size:60 final size:60
Alignment explanation
Indices: 2294907--2295034 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 60
2294897 ATAGTCAGGC
** * **
2294907 GACCATTTTGTAACTTTTAATAGTCGAGGGACTTAATAAAACAACATTCTATAGTTGAAG
1 GACCATTTTACAACTTTTAATAGTCAAGGGACTTAATAAAACAACACCCTATAGTTGAAG
* * * **
2294967 GACTATTTTACAACTTTTAATAGTTAAGGGA-TTGAATAAAGCAACACCCTATAGTTGGGG
1 GACCATTTTACAACTTTTAATAGTCAAGGGACTT-AATAAAACAACACCCTATAGTTGAAG
2295027 GACCATTT
1 GACCATTT
2295035 ATATACTTTA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 2 0.04
60 54 0.96
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (60 bp):
GACCATTTTACAACTTTTAATAGTCAAGGGACTTAATAAAACAACACCCTATAGTTGAAG
Found at i:2295632 original size:15 final size:16
Alignment explanation
Indices: 2295593--2295658 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 16
2295583 TTTTATTTTA
2295593 ATTT-ATTTATTACAAT
1 ATTTAATTTATTA-AAT
*
2295609 -TTT-TTTTATTAAAT
1 ATTTAATTTATTAAAT
*
2295623 ATTTAA-TTATTTAAGT
1 ATTTAATTTA-TTAAAT
*
2295639 -TATAATTTATTAAAT
1 ATTTAATTTATTAAAT
2295654 ATTTA
1 ATTTA
2295659 TGTTTTATAC
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
14 3 0.08
15 25 0.64
16 11 0.28
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (16 bp):
ATTTAATTTATTAAAT
Found at i:2297739 original size:18 final size:18
Alignment explanation
Indices: 2297716--2297750 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2297706 CAATACAAAA
2297716 GAATTTACATC-AGAAATG
1 GAATTTA-ATCAAGAAATG
2297734 GAATTTAATCAAGAAAT
1 GAATTTAATCAAGAAAT
2297751 CAGATTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.29
Consensus pattern (18 bp):
GAATTTAATCAAGAAATG
Found at i:2301528 original size:7 final size:7
Alignment explanation
Indices: 2301516--2301576 Score: 122
Period size: 7 Copynumber: 8.7 Consensus size: 7
2301506 TCATTTGATT
2301516 GGATGAA
1 GGATGAA
2301523 GGATGAA
1 GGATGAA
2301530 GGATGAA
1 GGATGAA
2301537 GGATGAA
1 GGATGAA
2301544 GGATGAA
1 GGATGAA
2301551 GGATGAA
1 GGATGAA
2301558 GGATGAA
1 GGATGAA
2301565 GGATGAA
1 GGATGAA
2301572 GGATG
1 GGATG
2301577 GGATTTCCCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 54 1.00
ACGTcount: A:0.41, C:0.00, G:0.44, T:0.15
Consensus pattern (7 bp):
GGATGAA
Found at i:2302653 original size:21 final size:21
Alignment explanation
Indices: 2302616--2302668 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
2302606 TGTTGAAGAG
*
2302616 GTATCGATA-CTATAAGGGATA
1 GTATCGATACCTAGAA-GGATA
*
2302637 GTATCGATACCT-GAAGGATG
1 GTATCGATACCTAGAAGGATA
2302657 GTATCGATACCT
1 GTATCGATACCT
2302669 TGAAACATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 16 0.55
21 11 0.38
22 2 0.07
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (21 bp):
GTATCGATACCTAGAAGGATA
Found at i:2302660 original size:41 final size:39
Alignment explanation
Indices: 2302588--2302666 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 39
2302578 GAGTATTTGG
2302588 AAGGGTAGTATCGATACCTGTTGAAGAGGTATCGATACTAT
1 AAGGGTAGTATCGATACC--TTGAAGAGGTATCGATACTAT
2302629 AAGGGATAGTATCGATACC-TGAAGGATGGTATCGATAC
1 AAGGG-TAGTATCGATACCTTGAA-GA-GGTATCGATAC
2302667 CTTGAAACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
39 4 0.11
40 2 0.06
41 16 0.46
42 13 0.37
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.27
Consensus pattern (39 bp):
AAGGGTAGTATCGATACCTTGAAGAGGTATCGATACTAT
Found at i:2302672 original size:21 final size:21
Alignment explanation
Indices: 2302595--2302672 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
2302585 TGGAAGGGTA
2302595 GTATCGATACCTGTTGAA-GA-G
1 GTATCGATACC--TTGAAGGATG
*
2302616 GTATCGATA-CTAT-AAGGGATA
1 GTATCGATACCT-TGAA-GGATG
2302637 GTATCGATACC-TGAAGGATG
1 GTATCGATACCTTGAAGGATG
2302657 GTATCGATACCTTGAA
1 GTATCGATACCTTGAA
2302673 ACATCGAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
18 3 0.06
19 1 0.02
20 19 0.40
21 24 0.50
22 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (21 bp):
GTATCGATACCTTGAAGGATG
Found at i:2304492 original size:22 final size:22
Alignment explanation
Indices: 2304461--2304512 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
2304451 TGATCCTTCA
*
2304461 GGACATATACAGAGGTCATTCG
1 GGACAAATACAGAGGTCATTCG
* *
2304483 GGACAAATACATAGGTCCTTCG
1 GGACAAATACAGAGGTCATTCG
2304505 GGACAAAT
1 GGACAAAT
2304513 TTCATATGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
GGACAAATACAGAGGTCATTCG
Found at i:2306057 original size:21 final size:23
Alignment explanation
Indices: 2306033--2306076 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
2306023 TGAATTGTGT
*
2306033 AATTGTATAAGAA-AT-TATATG
1 AATTATATAAGAACATATATATG
*
2306054 AATTATATGAGAACATATATATG
1 AATTATATAAGAACATATATATG
2306077 TGAATATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 2 0.11
23 6 0.32
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (23 bp):
AATTATATAAGAACATATATATG
Found at i:2312517 original size:14 final size:14
Alignment explanation
Indices: 2312450--2312517 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
2312440 AGTTTGAAAT
*
2312450 AAAATGCAATTATGCA
1 AAAATGCAA--ATGTA
*
2312466 AAGATGCAAATGTA
1 AAAATGCAAATGTA
* *
2312480 AAAATGAAAATATA
1 AAAATGCAAATGTA
2312494 AATAA---AAATGTA
1 AA-AATGCAAATGTA
2312506 AAAATGCAAATG
1 AAAATGCAAATG
2312518 CAAATATGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
11 2 0.05
12 8 0.19
14 22 0.52
15 2 0.05
16 8 0.19
ACGTcount: A:0.59, C:0.06, G:0.13, T:0.22
Consensus pattern (14 bp):
AAAATGCAAATGTA
Found at i:2312522 original size:26 final size:26
Alignment explanation
Indices: 2312473--2312523 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2312463 GCAAAGATGC
*
2312473 AAATGTAAAAATGAAAATATAAATAA
1 AAATGTAAAAATGAAAATACAAATAA
* *
2312499 AAATGTAAAAATGCAAATGCAAATA
1 AAATGTAAAAATGAAAATACAAATA
2312524 TGTAAATATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.65, C:0.04, G:0.10, T:0.22
Consensus pattern (26 bp):
AAATGTAAAAATGAAAATACAAATAA
Found at i:2312598 original size:7 final size:7
Alignment explanation
Indices: 2312588--2312625 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
2312578 CATAAAAGTA
2312588 AAAATGC
1 AAAATGC
2312595 AAAATG-
1 AAAATGC
2312601 AAAATGC
1 AAAATGC
*
2312608 AAAGATGT
1 AAA-ATGC
2312616 AAAATGC
1 AAAATGC
2312623 AAA
1 AAA
2312626 TGTATGTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 6 0.22
7 15 0.56
8 6 0.22
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (7 bp):
AAAATGC
Found at i:2312628 original size:13 final size:14
Alignment explanation
Indices: 2312588--2312629 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
2312578 CATAAAAGTA
2312588 AAAATGCAAAATG-
1 AAAATGCAAAATGT
2312601 AAAATGCAAAGATGT
1 AAAATGCAAA-ATGT
2312616 AAAATGC-AAATGT
1 AAAATGCAAAATGT
2312629 A
1 A
2312630 TGTATGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 15 0.56
14 5 0.19
15 7 0.26
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.19
Consensus pattern (14 bp):
AAAATGCAAAATGT
Found at i:2312776 original size:43 final size:44
Alignment explanation
Indices: 2312704--2312790 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
2312694 ACGTGCATCA
* * *
2312704 AACAAAACTTTTACATGTATGGGACAACTTTCAGTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
* *
2312748 AACAAAAC-TTTACATATAGGGGATAACTTTCCCTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
2312791 TCTAAAGCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
43 30 0.79
44 8 0.21
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.31
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
Found at i:2314640 original size:2 final size:2
Alignment explanation
Indices: 2314627--2314666 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
2314617 TTTTAAGAAA
2314627 AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2314666 A
1 A
2314667 AATAAGATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2316503 original size:3 final size:3
Alignment explanation
Indices: 2316483--2316525 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
2316473 AATATTTATT
*
2316483 TAA TAA AAA TAGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2316526 ACAAAACGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:2316949 original size:3 final size:3
Alignment explanation
Indices: 2316943--2317004 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
2316933 TCATTTAAAT
* *
2316943 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTAA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
2316989 TTA TTA GTA -TA TTA TT
1 TTA TTA TTA TTA TTA TT
2317005 TTTAAATAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
2 3 0.06
3 44 0.88
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2316960 original size:18 final size:18
Alignment explanation
Indices: 2316937--2316994 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
2316927 TTTTTTTCAT
2316937 TTAAATTTATTATTATTA
1 TTAAATTTATTATTATTA
2316955 TTAAATTTATTATTATTA
1 TTAAATTTATTATTATTA
* * *
2316973 TTATTATTAAATATTATTA
1 TTA-AATTTATTATTATTA
2316992 TTA
1 TTA
2316995 GTATATTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
18 21 0.58
19 15 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAAATTTATTATTATTA
Found at i:2316970 original size:24 final size:25
Alignment explanation
Indices: 2316943--2317019 Score: 111
Period size: 24 Copynumber: 3.0 Consensus size: 25
2316933 TCATTTAAAT
2316943 TTATTATTATTATTAAAT-TTATTA
1 TTATTATTATTATTAAATATTATTA
2316967 TTATTATTATTATTAAATATTATTA
1 TTATTATTATTATTAAATATTATTA
*
2316992 TTAGTATATTATTTTTAAATAGTTATTA
1 TTA-T-TATTATTATTAAATA-TTATTA
2317020 CAAACCCATT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
24 18 0.38
25 9 0.19
26 1 0.02
27 14 0.29
28 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (25 bp):
TTATTATTATTATTAAATATTATTA
Found at i:2317017 original size:14 final size:13
Alignment explanation
Indices: 2316947--2317019 Score: 87
Period size: 12 Copynumber: 5.6 Consensus size: 13
2316937 TTAAATTTAT
2316947 TATTATTATTAAA
1 TATTATTATTAAA
*
2316960 T-TTATTATT-AT
1 TATTATTATTAAA
2316971 TATTATTATTAAA
1 TATTATTATTAAA
*
2316984 TATTATTATTAGTA
1 TATTATTATTA-AA
*
2316998 TATTATTTTTAAA
1 TATTATTATTAAA
2317011 TAGTTATTA
1 TA-TTATTA
2317020 CAAACCCATT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
11 2 0.04
12 16 0.32
13 16 0.32
14 16 0.32
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TATTATTATTAAA
Found at i:2317405 original size:11 final size:12
Alignment explanation
Indices: 2317383--2317409 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2317373 CAGAGAACAG
2317383 AAAACAGAAAAA
1 AAAACAGAAAAA
2317395 AAAACAGAAAAA
1 AAAACAGAAAAA
2317407 AAA
1 AAA
2317410 GAACAGAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.07, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAACAGAAAAA
Found at i:2318335 original size:20 final size:21
Alignment explanation
Indices: 2318289--2318335 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
2318279 CTGCTTTTAA
*
2318289 ATATATCGTTCTAATTGTATT
1 ATATATTGTTCTAATTGTATT
* *
2318310 -TTTATTGTTTTAATTGT-TT
1 ATATATTGTTCTAATTGTATT
2318329 ATATATT
1 ATATATT
2318336 TAAATATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.62
Consensus pattern (21 bp):
ATATATTGTTCTAATTGTATT
Found at i:2323811 original size:12 final size:11
Alignment explanation
Indices: 2323793--2323819 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2323783 AAAGAAAGAA
2323793 GAAAAAAAAAG
1 GAAAAAAAAAG
2323804 GAAAAAAAAAG
1 GAAAAAAAAAG
2323815 GAAAA
1 GAAAA
2323820 TTGAATCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAG
Found at i:2326253 original size:114 final size:114
Alignment explanation
Indices: 2326053--2326281 Score: 377
Period size: 114 Copynumber: 2.0 Consensus size: 114
2326043 AGCAAGTGCC
*
2326053 ATTTGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATTTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
* * * *
2326118 ATCTGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGA
66 ATCTGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGA
*
2326167 ATTTGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATTTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
* * *
2326232 ATCTGATTCGGTAGGAACCCCATAACCGATCATTGGAATTGAAAGATGA
66 ATCTGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGA
2326281 A
1 A
2326282 CTGCATGATC
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 106 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (114 bp):
ATTTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
ATCTGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGA
Found at i:2327323 original size:45 final size:45
Alignment explanation
Indices: 2327273--2327362 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
2327263 AGCAATATGA
*
2327273 ATATTTGAGTATTTTTGGGGGCTCATCTCAACAAGAAGTAATGTT
1 ATATTTGAGTATTTTTGGAGGCTCATCTCAACAAGAAGTAATGTT
2327318 ATATTTGAGTATTTTTGGAGGCTCATCTCAACAAGAAGTAATGTT
1 ATATTTGAGTATTTTTGGAGGCTCATCTCAACAAGAAGTAATGTT
2327363 GAACACACTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (45 bp):
ATATTTGAGTATTTTTGGAGGCTCATCTCAACAAGAAGTAATGTT
Found at i:2328497 original size:54 final size:54
Alignment explanation
Indices: 2328432--2328586 Score: 247
Period size: 54 Copynumber: 2.9 Consensus size: 54
2328422 GAAATCTTGG
*
2328432 CAGAAGCCACAGTAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
1 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
* *
2328486 CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAG
1 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
*** *
2328540 CAGAAGCCACAGGAAAGGATGAATGCACTGTCAAATGTTTTAAGAAC
1 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
2328587 CTGCTATTCT
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 93 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (54 bp):
CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
Found at i:2328966 original size:22 final size:22
Alignment explanation
Indices: 2328937--2328991 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
2328927 ATCTACACTC
*
2328937 TTCAAAGATGATAGGTTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
2328959 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2328981 TTCAAAGATGA
1 TTCAAAGATGA
2328992 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:2329779 original size:76 final size:76
Alignment explanation
Indices: 2329653--2330826 Score: 2260
Period size: 76 Copynumber: 15.5 Consensus size: 76
2329643 CTATTTCTCA
2329653 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2329718 AGCCTTCGGGT
66 AGCCTTCGGGT
2329729 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2329794 AGCCTTCGGGT
66 AGCCTTCGGGT
2329805 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2329870 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2329881 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2329946 AGCCTTCGGGT
66 AGCCTTCGGGT
2329957 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2330022 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2330033 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2330098 AGCCTTCGGGT
66 AGCCTTCGGGT
2330109 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2330174 AGCCTTCGAGT
66 AGCCTTCGGGT
*
2330185 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2330250 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2330261 CATCTGTAAGCCCTTTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2330326 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2330337 CATCTGTAAGCCCTTCAGTGCATAATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2330402 AGCCTTCGGGT
66 AGCCTTCGGGT
2330413 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2330477 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2330488 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2330553 AGCCTTCGGGT
66 AGCCTTCGGGT
2330564 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2330629 AGCCTTCGGGT
66 AGCCTTCGGGT
2330640 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2330705 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2330716 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2330781 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2330792 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAA
2330827 CATTTCCATC
Statistics
Matches: 1081, Mismatches: 16, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
75 74 0.07
76 1007 0.93
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:2330974 original size:18 final size:18
Alignment explanation
Indices: 2330951--2331008 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
2330941 TTTTTTTCAT
2330951 TTAAATTTATTATTATTA
1 TTAAATTTATTATTATTA
2330969 TTAAATTTATTATTATTA
1 TTAAATTTATTATTATTA
* * *
2330987 TTATTATTAAATATTATTA
1 TTA-AATTTATTATTATTA
2331006 TTA
1 TTA
2331009 GTATATTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
18 21 0.58
19 15 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAAATTTATTATTATTA
Found at i:2330984 original size:24 final size:24
Alignment explanation
Indices: 2330957--2331033 Score: 102
Period size: 24 Copynumber: 3.1 Consensus size: 24
2330947 TCATTTAAAT
2330957 TTATTATTATTATTAAATTTATTA
1 TTATTATTATTATTAAATTTATTA
2330981 TTATTATTATTATTAAATATTATTA
1 TTATTATTATTATTAAAT-TTATTA
* *
2331006 TTAGTATATTATTTTTAAA-TAATTA
1 TTA-T-TATTATTATTAAATTTATTA
2331031 TTA
1 TTA
2331034 CAAACCCATT
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.38
25 17 0.35
26 1 0.02
27 12 0.25
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (24 bp):
TTATTATTATTATTAAATTTATTA
Found at i:2331030 original size:14 final size:14
Alignment explanation
Indices: 2330962--2331033 Score: 66
Period size: 12 Copynumber: 5.5 Consensus size: 14
2330952 TAAATTTATT
2330962 ATTATTATTAAAT-
1 ATTATTATTAAATA
*
2330975 -TTATTATT--ATT
1 ATTATTATTAAATA
2330986 ATTATTATTAAAT-
1 ATTATTATTAAATA
*
2330999 ATTATTATT-AGTA
1 ATTATTATTAAATA
*
2331012 TATTATTTTTAAATA
1 -ATTATTATTAAATA
2331027 ATTATTA
1 ATTATTA
2331034 CAAACCCATT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
10 2 0.04
12 18 0.38
13 9 0.19
14 16 0.33
15 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (14 bp):
ATTATTATTAAATA
Found at i:2331033 original size:3 final size:3
Alignment explanation
Indices: 2330957--2331018 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
2330947 TCATTTAAAT
* *
2330957 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTAA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
2331003 TTA TTA GTA -TA TTA TT
1 TTA TTA TTA TTA TTA TT
2331019 TTTAAATAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
2 3 0.06
3 44 0.88
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2331415 original size:13 final size:13
Alignment explanation
Indices: 2331397--2331431 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
2331387 CAGAGAACAG
2331397 AAAACAGAAAAAA
1 AAAACAGAAAAAA
2331410 AAAACAGAAAAAA
1 AAAACAGAAAAAA
2331423 AAGAACAGA
1 AA-AACAGA
2331432 GAGGAAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAACAGAAAAAA
Found at i:2331421 original size:14 final size:14
Alignment explanation
Indices: 2331397--2331431 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2331387 CAGAGAACAG
2331397 AAAACAG-AAAAAA
1 AAAACAGAAAAAAA
2331410 AAAACAGAAAAAAA
1 AAAACAGAAAAAAA
*
2331424 AGAACAGA
1 AAAACAGA
2331432 GAGGAAGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAACAGAAAAAAA
Found at i:2332349 original size:20 final size:21
Alignment explanation
Indices: 2332303--2332349 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
2332293 CTGCTTTTAA
*
2332303 ATATATCGTTCTAATTGTATT
1 ATATATTGTTCTAATTGTATT
* *
2332324 -TTTATTGTTTTAATTGT-TT
1 ATATATTGTTCTAATTGTATT
2332343 ATATATT
1 ATATATT
2332350 TAAATATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.62
Consensus pattern (21 bp):
ATATATTGTTCTAATTGTATT
Found at i:2335522 original size:15 final size:15
Alignment explanation
Indices: 2335502--2335532 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2335492 TCCGTAGGAT
2335502 CGGGCAGCCCTTGAA
1 CGGGCAGCCCTTGAA
2335517 CGGGCAGCCCTTGAA
1 CGGGCAGCCCTTGAA
2335532 C
1 C
2335533 CTGCAATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.35, G:0.32, T:0.13
Consensus pattern (15 bp):
CGGGCAGCCCTTGAA
Found at i:2338678 original size:43 final size:43
Alignment explanation
Indices: 2338570--2338681 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 43
2338560 ATTTTTTTAT
* * *
2338570 ATTTTAAA-ATACAAA-AATTATA-TTTATAATTATTTACTAT
1 ATTTTAAATATTCAAATAATTATATTTTATAATAATTTACTAC
* * **
2338610 ATATTAAATAATTAAAAT-AGCATATTTTATAATAATTTACTAC
1 ATTTTAAAT-ATTCAAATAATTATATTTTATAATAATTTACTAC
2338653 ATTTTAAATATTCAAATAATTATATTTTA
1 ATTTTAAATATTCAAATAATTATATTTTA
2338682 ATATTACAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
40 7 0.12
42 16 0.29
43 33 0.59
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.46
Consensus pattern (43 bp):
ATTTTAAATATTCAAATAATTATATTTTATAATAATTTACTAC
Found at i:2343381 original size:23 final size:23
Alignment explanation
Indices: 2343355--2343399 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2343345 CACCACAGCT
*
2343355 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
2343378 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
2343400 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:2344056 original size:19 final size:20
Alignment explanation
Indices: 2344019--2344056 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2344009 TTTTTTTATA
*
2344019 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
2344039 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
2344057 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:2344107 original size:21 final size:21
Alignment explanation
Indices: 2344083--2344125 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2344073 TTCATATTCG
* *
2344083 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2344104 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2344125 T
1 T
2344126 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2350187 original size:23 final size:23
Alignment explanation
Indices: 2350161--2350205 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2350151 CACCACAGCT
2350161 CGTATAAA-TGCACCGAAGTGCCG
1 CGTA-AAATTGCACCGAAGTGCCG
*
2350184 CGTAAAATTGCACCGTAGTGCC
1 CGTAAAATTGCACCGAAGTGCC
2350206 ATATAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAAAATTGCACCGAAGTGCCG
Found at i:2350865 original size:19 final size:20
Alignment explanation
Indices: 2350828--2350865 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2350818 TTTTTTTATA
*
2350828 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
2350848 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
2350866 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:2353324 original size:179 final size:182
Alignment explanation
Indices: 2353021--2353402 Score: 569
Period size: 179 Copynumber: 2.1 Consensus size: 182
2353011 ATTTCTAATT
* * * *
2353021 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATAATT
1 TATATAATATATTTAATATTTTCTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATAATT
* *
2353085 ATAAAATAAAAATTTCAGATTAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTG
66 AT-AAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTATAAAAGTTATTG
* *
2353150 GATCTTAAATTATTAATTAGGTTTTAAATGGTTTGAGCTGAGCCTATATGTTA
130 AATCTTAAATTATTAATTAGGTTTTAAATGGTTTGAGCTGAGCCCATATGTTA
*
2353203 TATATAATATATTTAATATTTTCTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTCTAATTCAAAAAAAAGTTTACAATTAATTTAAAT-A-ATATAA
* *
2353267 TTAT-AA-AAAAA-TT-ATATAAATTTTTTAATTAATTAATATTGATTTATGTATAAAAGTTATT
64 TTATAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTATAAAAGTTATT
* *
2353328 GAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
129 GAATCTTAAATTATTAATTAGGTTTTAAATGGTTTGAGCTGAGCCCATATGTTA
*
2353382 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
2353403 AAAATTTAAT
Statistics
Matches: 183, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
179 114 0.62
180 2 0.01
181 5 0.03
182 34 0.19
183 18 0.10
184 10 0.05
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (182 bp):
TATATAATATATTTAATATTTTCTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATAATT
ATAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTATAAAAGTTATTGA
ATCTTAAATTATTAATTAGGTTTTAAATGGTTTGAGCTGAGCCCATATGTTA
Found at i:2355007 original size:35 final size:35
Alignment explanation
Indices: 2354961--2355030 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
2354951 CAGAACCTTA
2354961 TTTTCCGAGAAGAGCTATACAGCCCTTACCAGCTC
1 TTTTCCGAGAAGAGCTATACAGCCCTTACCAGCTC
2354996 TTTTCCGAGAAGAGCTATACAGCCCTTACCAGCTC
1 TTTTCCGAGAAGAGCTATACAGCCCTTACCAGCTC
2355031 ATATGATAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (35 bp):
TTTTCCGAGAAGAGCTATACAGCCCTTACCAGCTC
Found at i:2357121 original size:21 final size:21
Alignment explanation
Indices: 2357048--2357245 Score: 74
Period size: 20 Copynumber: 9.6 Consensus size: 21
2357038 CAGTTTCCAG
* * * *
2357048 ATTCGCAACGCGATTATGACT
1 ATTCGCAATGCGATTTTCACA
2357069 A-TCGCAATGCGATTTTC-CA
1 ATTCGCAATGCGATTTTCACA
**
2357088 ATTTCGCGTTGCGATTTTCACA
1 A-TTCGCAATGCGATTTTCACA
**
2357110 ATTCGCAATGCGAATAAGT-A-A
1 ATTCGCAATGCG-AT-TTTCACA
**
2357131 A-TCGCAATGCGAATTTGGA-A
1 ATTCGCAATGCG-ATTTTCACA
* ** * *
2357151 AATCGCAATGCGATACTGACT
1 ATTCGCAATGCGATTTTCACA
*
2357172 A-TCGCAATGCAATTTTC-CTA
1 ATTCGCAATGCGATTTTCAC-A
* * *
2357192 ATTCACATTGCGA-TTT-ACGT
1 ATTCGCAATGCGATTTTCAC-A
** *
2357212 ATTCGCGTTGCGATTTTCATA
1 ATTCGCAATGCGATTTTCACA
2357233 ATTCGCAATGCGA
1 ATTCGCAATGCGA
2357246 ATACGTAAAT
Statistics
Matches: 131, Mismatches: 33, Indels: 26
0.69 0.17 0.14
Matches are distributed among these distances:
19 3 0.02
20 61 0.47
21 59 0.45
22 7 0.05
23 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (21 bp):
ATTCGCAATGCGATTTTCACA
Found at i:2357137 original size:20 final size:21
Alignment explanation
Indices: 2357112--2357163 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2357102 TTTTCACAAT
*
2357112 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
2357132 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2357153 TCGCAATGCGA
1 TCGCAATGCGA
2357164 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2357142 original size:41 final size:40
Alignment explanation
Indices: 2357097--2357306 Score: 124
Period size: 41 Copynumber: 5.1 Consensus size: 40
2357087 AATTTCGCGT
2357097 TGCGATTTTCACAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCA-AATTCGCAATGCGAATAAGTAAATCGCAA
** * * *
2357138 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCG-ATTTTCAAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * * * **
2357179 TGCAATTTTCCTAATTCACATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTT-CAAATTCGCAATGCGA-ATAAGTAAATCGCAA
*
2357220 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCA-AATTCGCAATGCGAATAAGTAAATCGCAA
* * * *
2357261 CGTGATTAAGT-AAA-TCGCAATGCGAATTAAGAAAATCGCAA
1 TGCGATT--TTCAAATTCGCAATGCGAA-TAAGTAAATCGCAA
2357302 TGCGA
1 TGCGA
2357307 ATACGTAAAT
Statistics
Matches: 123, Mismatches: 34, Indels: 24
0.68 0.19 0.13
Matches are distributed among these distances:
39 2 0.02
40 25 0.20
41 87 0.71
42 6 0.05
43 2 0.02
44 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (40 bp):
TGCGATTTTCAAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:2357260 original size:20 final size:20
Alignment explanation
Indices: 2357235--2357346 Score: 127
Period size: 20 Copynumber: 5.5 Consensus size: 20
2357225 TTTTCATAAT
2357235 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * * *
2357255 TCGCAACGTGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2357275 TCGCAATGCGAATTAAGAAAA
1 TCGCAATGCGAA-TACGTAAA
2357296 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2357316 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
2357336 TCGCAATGCGA
1 TCGCAATGCGA
2357347 TTTACATAGC
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
19 3 0.04
20 56 0.72
21 19 0.24
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2357315 original size:41 final size:41
Alignment explanation
Indices: 2357235--2357328 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
2357225 TTTTCATAAT
* * * *
2357235 TCGCAATGCGAA-TACGTAAATCGCAACGTGATTAAGTAAA
1 TCGCAATGCGAATTAAGAAAATCGCAACGCGAATAAGTAAA
* *
2357275 TCGCAATGCGAATTAAGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTAAGAAAATCGCAACGCGAATAAGTAAA
2357316 TCGCAATGCGAAT
1 TCGCAATGCGAAT
2357329 CTTACTATCG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 12 0.26
41 35 0.74
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.21
Consensus pattern (41 bp):
TCGCAATGCGAATTAAGAAAATCGCAACGCGAATAAGTAAA
Found at i:2357921 original size:19 final size:20
Alignment explanation
Indices: 2357872--2357925 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
2357862 TAGTTTCGAG
**
2357872 AATGAAAATCGCAATGCGAA
1 AATGAAAATCGCAACACGAA
*
2357892 AAT-AACTATCGCAACACG-A
1 AATGAA-AATCGCAACACGAA
2357911 AATGAAAATCGCAAC
1 AATGAAAATCGCAAC
2357926 GAGATAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.50, C:0.20, G:0.15, T:0.15
Consensus pattern (20 bp):
AATGAAAATCGCAACACGAA
Found at i:2357994 original size:33 final size:34
Alignment explanation
Indices: 2357952--2358015 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 34
2357942 GAAACCAAAA
*
2357952 TCGTTGCGATAGTCATTT-CGCGTTGCGATTCTC
1 TCGTTGCGATAGTCATTTCCGCGTTACGATTCTC
2357985 TCGTTGCGATAGTCATTTCCGCGTTACGATT
1 TCGTTGCGATAGTCATTTCCGCGTTACGATT
2358016 TTCATTATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 18 0.62
34 11 0.38
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.39
Consensus pattern (34 bp):
TCGTTGCGATAGTCATTTCCGCGTTACGATTCTC
Found at i:2358020 original size:20 final size:20
Alignment explanation
Indices: 2357997--2358043 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2357987 GTTGCGATAG
2357997 TCATTTCCGCGTTACGATTT
1 TCATTTCCGCGTTACGATTT
* *
2358017 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTACGATTT
2358037 TCATTTC
1 TCATTTC
2358044 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.15, C:0.23, G:0.13, T:0.49
Consensus pattern (20 bp):
TCATTTCCGCGTTACGATTT
Found at i:2359875 original size:15 final size:15
Alignment explanation
Indices: 2359855--2359887 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2359845 GAACACATAT
2359855 TTTA-TTATTTTATTA
1 TTTATTTATTTT-TTA
2359870 TTTATTTATTTTTTA
1 TTTATTTATTTTTTA
2359885 TTT
1 TTT
2359888 CATGTTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATTTATTTTTTA
Found at i:2361213 original size:3 final size:3
Alignment explanation
Indices: 2361207--2361264 Score: 68
Period size: 3 Copynumber: 19.3 Consensus size: 3
2361197 ATTCTTCTCT
2361207 TTA TTA TTA TT- TATA TTA TTA TTA TT- TATA TTA TTA TTA -TA TATA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-TA
2361252 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
2361265 ATATATTACT
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
2 4 0.08
3 40 0.82
4 5 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2361225 original size:15 final size:15
Alignment explanation
Indices: 2361207--2361272 Score: 107
Period size: 15 Copynumber: 4.4 Consensus size: 15
2361197 ATTCTTCTCT
2361207 TTATTATTATTTATA
1 TTATTATTATTTATA
2361222 TTATTATTATTTATA
1 TTATTATTATTTATA
*
2361237 TTATTATTATATATA
1 TTATTATTATTTATA
2361252 TTATTATTA-TTATA
1 TTATTATTATTTATA
2361266 TATATTA
1 T-TATTA
2361273 CTAACCAAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.10
15 43 0.90
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTATTATTTATA
Found at i:2361773 original size:24 final size:25
Alignment explanation
Indices: 2361712--2361789 Score: 72
Period size: 28 Copynumber: 3.0 Consensus size: 25
2361702 TCACTTAATC
2361712 CTTTTTATTTTCTTTATCTTTTTATCT
1 CTTTTTATTTTCTTTA--TTTTTATCT
*
2361739 CTGTATTATTTTCTTTA-TTTTAT-T
1 CT-TTTTATTTTCTTTATTTTTATCT
2361763 CGTTTTTATTTTCTCATT-TTTTTATCT
1 C-TTTTTATTTTCT--TTATTTTTATCT
2361790 AACACTTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
24 12 0.28
25 7 0.16
26 8 0.19
27 3 0.07
28 13 0.30
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.72
Consensus pattern (25 bp):
CTTTTTATTTTCTTTATTTTTATCT
Found at i:2362733 original size:15 final size:16
Alignment explanation
Indices: 2362708--2362738 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2362698 TCCTTTACCA
2362708 TTTATTTTTTATTTTT
1 TTTATTTTTTATTTTT
2362724 TTTA-TTTTTATTTTT
1 TTTATTTTTTATTTTT
2362739 CTATTTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTATTTTTTATTTTT
Found at i:2372183 original size:1 final size:1
Alignment explanation
Indices: 2372177--2372242 Score: 60
Period size: 1 Copynumber: 66.0 Consensus size: 1
2372167 CCTAAGTTGC
* * * * * * * *
2372177 AAAAAAAAAAACAAAAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2372242 A
1 A
2372243 GAACGTTTAG
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2372187 original size:5 final size:5
Alignment explanation
Indices: 2372179--2372242 Score: 84
Period size: 5 Copynumber: 13.8 Consensus size: 5
2372169 TAAGTTGCAA
*
2372179 AAAAA AAAAC -AAA- AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
2372227 AAAA- AAAA- AAAA- AAAA
1 AAAAC AAAAC AAAAC AAAA
2372243 GAACGTTTAG
Statistics
Matches: 56, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
4 18 0.32
5 38 0.68
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:2373326 original size:105 final size:105
Alignment explanation
Indices: 2373058--2374151 Score: 1864
Period size: 105 Copynumber: 10.4 Consensus size: 105
2373048 AGGTTTTACC
2373058 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
2373123 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTC-AATTT
* *
2373164 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
2373229 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
2373269 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
2373334 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
2373374 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
2373439 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
2373479 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
2373544 ACGAAGGGACCGCTGGTTGTCAATAAATATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
2373584 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
2373649 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
2373689 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
2373754 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
2373794 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
2373859 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* **
2373899 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAATACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
** ** *
2373964 ACGAAGGGACCGCTGACTGTCAACCGACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * * * *
2374005 CAAGAGCCAATTTCAAATTCACAACGAATGATACTGGACTCCGGACAACACAAGTTCAACTTCAC
1 C-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* * * *
2374070 GACGAAGGGACCGTTAGTTGTCAACAAACAATTTCCCAATTC
65 GACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * * *
2374112 CAGAACCAGTTTCAACTTCACAGCGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
2374152 GGAGCAATAC
Statistics
Matches: 941, Mismatches: 45, Indels: 4
0.95 0.05 0.00
Matches are distributed among these distances:
105 708 0.75
106 142 0.15
107 91 0.10
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:2374677 original size:15 final size:15
Alignment explanation
Indices: 2374657--2374689 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2374647 GAACACATAT
2374657 TTTA-TTATTTTATTA
1 TTTATTTATTTT-TTA
2374672 TTTATTTATTTTTTA
1 TTTATTTATTTTTTA
2374687 TTT
1 TTT
2374690 CATGTTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATTTATTTTTTA
Found at i:2376016 original size:3 final size:3
Alignment explanation
Indices: 2376010--2376067 Score: 68
Period size: 3 Copynumber: 19.3 Consensus size: 3
2376000 ATTCTTCTCT
2376010 TTA TTA TTA TT- TATA TTA TTA TTA TT- TATA TTA TTA TTA -TA TATA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-TA
2376055 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
2376068 ATATATTACT
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
2 4 0.08
3 40 0.82
4 5 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2376028 original size:15 final size:15
Alignment explanation
Indices: 2376010--2376075 Score: 107
Period size: 15 Copynumber: 4.4 Consensus size: 15
2376000 ATTCTTCTCT
2376010 TTATTATTATTTATA
1 TTATTATTATTTATA
2376025 TTATTATTATTTATA
1 TTATTATTATTTATA
*
2376040 TTATTATTATATATA
1 TTATTATTATTTATA
2376055 TTATTATTA-TTATA
1 TTATTATTATTTATA
2376069 TATATTA
1 T-TATTA
2376076 CTAACCAAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.10
15 43 0.90
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTATTATTTATA
Found at i:2376576 original size:24 final size:25
Alignment explanation
Indices: 2376515--2376592 Score: 72
Period size: 28 Copynumber: 3.0 Consensus size: 25
2376505 TCACTTAATC
2376515 CTTTTTATTTTCTTTATCTTTTTATCT
1 CTTTTTATTTTCTTTA--TTTTTATCT
*
2376542 CTGTATTATTTTCTTTA-TTTTAT-T
1 CT-TTTTATTTTCTTTATTTTTATCT
2376566 CGTTTTTATTTTCTCATT-TTTTTATCT
1 C-TTTTTATTTTCT--TTATTTTTATCT
2376593 AACACTTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
24 12 0.28
25 7 0.16
26 8 0.19
27 3 0.07
28 13 0.30
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.72
Consensus pattern (25 bp):
CTTTTTATTTTCTTTATTTTTATCT
Found at i:2377357 original size:21 final size:21
Alignment explanation
Indices: 2377333--2377399 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2377323 TCATTCCTCG
2377333 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2377354 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2377375 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2377396 AGAG
1 AGAG
2377400 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2377357 original size:42 final size:42
Alignment explanation
Indices: 2377281--2377399 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
2377271 CACTAGCCTG
* * * *
2377281 TCATCCCTC-AAGA-GTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCAT-CCTCGAAGAGGTCC-CTCCCACCATTCAAGAGGCCACTA
* *
2377323 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTCGAAGAGGT-CCCTCCCACCATTCAAGAGGCCACTA
* *
2377365 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAG
2377400 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
41 4 0.06
42 54 0.86
43 5 0.08
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAGGCCACTA
Found at i:2378770 original size:14 final size:14
Alignment explanation
Indices: 2378751--2378786 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2378741 ATTGTTTAAT
2378751 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2378765 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2378779 TGATTTGT
1 TGATTTGT
2378787 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2378915 original size:19 final size:17
Alignment explanation
Indices: 2378902--2378987 Score: 58
Period size: 14 Copynumber: 5.2 Consensus size: 17
2378892 TATCGCAATG
*
2378902 CGAAATGAAAATCGTAA
1 CGAAATGAAAATCGCAA
*
2378919 CG--A-GAGAATCGCAACA
1 CGAAATGAAAATCGC-A-A
2378935 CGAAATGAAAATCGCAA
1 CGAAATGAAAATCGCAA
*
2378952 CG--A-GAGAATCGCAA
1 CGAAATGAAAATCGCAA
*
2378966 TGCGAAATGAAAATTGCAA
1 --CGAAATGAAAATCGCAA
2378985 CGA
1 CGA
2378988 CAAAATCACA
Statistics
Matches: 53, Mismatches: 6, Indels: 20
0.67 0.08 0.25
Matches are distributed among these distances:
14 17 0.32
15 3 0.06
16 5 0.09
17 8 0.15
18 3 0.06
19 17 0.32
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (17 bp):
CGAAATGAAAATCGCAA
Found at i:2378939 original size:33 final size:33
Alignment explanation
Indices: 2378893--2378987 Score: 154
Period size: 33 Copynumber: 2.9 Consensus size: 33
2378883 AAAAATGACT
*
2378893 ATCGCAATGCGAAATGAAAATCGTAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
2378926 ATCGCAACACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2378959 ATCGCAATGCGAAATGAAAATTGCAACGA
1 ATCGCAATGCGAAATGAAAATCGCAACGA
2378988 CAAAATCACA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2379039 original size:19 final size:19
Alignment explanation
Indices: 2379011--2379108 Score: 99
Period size: 19 Copynumber: 5.7 Consensus size: 19
2379001 CAAAACTAAA
*
2379011 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
2379030 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
2379046 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
2379063 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
2379079 ATCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
2379096 TTCGCATTGCGAT
1 TTCGCATTGCGAT
2379109 AGTAATTTCC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 12 0.19
16 14 0.22
17 14 0.22
19 24 0.38
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:2379057 original size:33 final size:33
Alignment explanation
Indices: 2379015--2379108 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
2379005 ACTAAATTCG
*
2379015 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTAT
2379048 CGTTGCGATTTTCATTTCGCATTGCGATTCTAT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTAT
2379081 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2379109 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTAT
Found at i:2379419 original size:20 final size:20
Alignment explanation
Indices: 2379365--2379419 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
2379355 GATTTTAAAG
* *
2379365 ATGAAAATCGCAACACGAAA
1 ATGACAATCGCAACGCGAAA
*
2379385 ATGACAATCGCAACGCGAAT
1 ATGACAATCGCAACGCGAAA
* *
2379405 TTGACTATCGCAACG
1 ATGACAATCGCAACG
2379420 AGAGAATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
ATGACAATCGCAACGCGAAA
Found at i:2379695 original size:22 final size:22
Alignment explanation
Indices: 2379668--2379711 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2379658 GATGGAGATA
2379668 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2379690 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2379712 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2379928 original size:20 final size:20
Alignment explanation
Indices: 2379898--2380004 Score: 117
Period size: 20 Copynumber: 5.3 Consensus size: 20
2379888 GATTATGTAT
*
2379898 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * *
2379918 TATTGCGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
2379938 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
2379958 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
2379979 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
2379999 TATCGC
1 TATCGC
2380005 AACGTGATTT
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.04
20 53 0.74
21 14 0.19
22 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:2379948 original size:40 final size:41
Alignment explanation
Indices: 2379898--2380004 Score: 144
Period size: 40 Copynumber: 2.6 Consensus size: 41
2379888 GATTATGTAT
* *
2379898 TATCTCGTTGCGAAAGTCAGTATTGCGTTGCGAAATT-AAG
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAATTGAAG
** * *
2379938 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAATTGAAG
*
2379979 TATCGCGTTGCGATAGTCAGTATCGC
1 TATCGCGTTGCGAAAGTCAGTATCGC
2380005 AACGTGATTT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
40 33 0.56
41 26 0.44
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (41 bp):
TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAATTGAAG
Found at i:2379997 original size:41 final size:41
Alignment explanation
Indices: 2379878--2380004 Score: 166
Period size: 41 Copynumber: 3.1 Consensus size: 41
2379868 CGCTTTGAAA
* * *
2379878 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** * *
2379919 ATTGCGTTGCGAAATT-AAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
2379959 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
2380000 ATCGC
1 ATCGC
2380005 AACGTGATTT
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 34 0.48
41 37 0.52
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:2380034 original size:21 final size:21
Alignment explanation
Indices: 2380010--2380094 Score: 118
Period size: 21 Copynumber: 4.1 Consensus size: 21
2380000 ATCGCAACGT
2380010 GATTTTCCAAATTCGCATTGC
1 GATTTTCCAAATTCGCATTGC
* *
2380031 GATTTTCTAAATTCACATTGC
1 GATTTTCCAAATTCGCATTGC
2380052 GATTTTCCAAATTCGCATTGC
1 GATTTTCCAAATTCGCATTGC
* **
2380073 GA-TTTACTTATTCGCATTGC
1 GATTTTCCAAATTCGCATTGC
2380093 GA
1 GA
2380095 ATTGTGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
20 17 0.30
21 40 0.70
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (21 bp):
GATTTTCCAAATTCGCATTGC
Found at i:2380058 original size:42 final size:41
Alignment explanation
Indices: 2380010--2380094 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 41
2380000 ATCGCAACGT
*
2380010 GATTTTCCAAATTCGCATTGCGATTTTCTAAATTCACATTGC
1 GATTTTCCAAATTCGCATTGCGATTTACT-AATTCACATTGC
* *
2380052 GATTTTCCAAATTCGCATTGCGATTTACTTATTCGCATTGC
1 GATTTTCCAAATTCGCATTGCGATTTACTAATTCACATTGC
2380093 GA
1 GA
2380095 ATTGTGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 12 0.30
42 28 0.70
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (41 bp):
GATTTTCCAAATTCGCATTGCGATTTACTAATTCACATTGC
Found at i:2380109 original size:41 final size:42
Alignment explanation
Indices: 2380010--2380109 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
2380000 ATCGCAACGT
* * *
2380010 GATTTTCCAAATTCGCATTGCGATTTTCTAAATTCACATTGC
1 GATTGTCCAAAATCGCATTGCGATTTACTAAATTCACATTGC
* * * *
2380052 GATTTTCCAAATTCGCATTGCGATTTACT-TATTCGCATTGC
1 GATTGTCCAAAATCGCATTGCGATTTACTAAATTCACATTGC
*
2380093 GAATTGT-GAAAATCGCA
1 G-ATTGTCCAAAATCGCA
2380110 ACGCGAAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 19 0.37
42 32 0.63
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (42 bp):
GATTGTCCAAAATCGCATTGCGATTTACTAAATTCACATTGC
Found at i:2380136 original size:21 final size:22
Alignment explanation
Indices: 2380084--2380136 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
2380074 ATTTACTTAT
2380084 TCGCATTGCG-AATTGTGAAAA
1 TCGCATTGCGAAATTGTGAAAA
**
2380105 TCGCAACGCGAAATTG-GAAAA
1 TCGCATTGCGAAATTGTGAAAA
2380126 TCGCATTGCGA
1 TCGCATTGCGA
2380137 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGTGAAAA
Found at i:2381252 original size:14 final size:14
Alignment explanation
Indices: 2381233--2381272 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2381223 CCCTTCCTCC
2381233 TTTAAAATTAAAT-T
1 TTTAAAA-TAAATAT
2381247 TTTAAAATAAATAT
1 TTTAAAATAAATAT
*
2381261 TTTAAAAAAAAT
1 TTTAAAATAAAT
2381273 TATAATAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTTAAAATAAATAT
Found at i:2381771 original size:32 final size:31
Alignment explanation
Indices: 2381686--2381771 Score: 84
Period size: 37 Copynumber: 2.6 Consensus size: 31
2381676 TTGTATAATA
2381686 TTAC-AAATTATAAAATATTTATATATTTTCT
1 TTACAAAATTA-AAAATATTTATATATTTTCT
* *
2381717 TTAAAAAATTAAATTCATAATATTTATATAATTTTTT
1 TTACAAAATT-AA---A-AATATTTATAT-ATTTTCT
2381754 TTACAAAATTAAAAATAT
1 TTACAAAATTAAAAATAT
2381772 AAAAAAAGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
31 3 0.07
32 11 0.24
33 2 0.04
35 1 0.02
36 13 0.29
37 15 0.33
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (31 bp):
TTACAAAATTAAAAATATTTATATATTTTCT
Found at i:2385734 original size:3 final size:3
Alignment explanation
Indices: 2385726--2385826 Score: 148
Period size: 3 Copynumber: 33.7 Consensus size: 3
2385716 TTTTTATCCA
* * *
2385726 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAA TAT TAT TAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** *
2385774 TAT TAT TAT TAT TGC TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2385822 TAT TA
1 TAT TA
2385827 ATTTATATTA
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:2385737 original size:15 final size:14
Alignment explanation
Indices: 2385725--2385845 Score: 110
Period size: 15 Copynumber: 8.6 Consensus size: 14
2385715 ATTTTTATCC
2385725 ATATTATTATTATTA
1 ATATTATTATTA-TA
2385740 ATATTATTATTATTA
1 ATATTATTATTA-TA
2385755 ATATTATTATTATTA
1 ATATTATTATTA-TA
2385770 ATATTATTATTAT-
1 ATATTATTATTATA
**
2385783 -TATTGCTATTATCA
1 ATATTATTATTAT-A
*
2385797 TTATTATTATTATTA
1 ATATTATTATTA-TA
*
2385812 TTATTATTATTATTA
1 ATATTATTATTA-TA
2385827 AT-TTA-TATTA-A
1 ATATTATTATTATA
2385838 ATA-TATTA
1 ATATTATTA
2385846 AATACATAAT
Statistics
Matches: 95, Mismatches: 5, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
11 5 0.05
12 12 0.13
13 5 0.05
14 4 0.04
15 68 0.72
16 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.60
Consensus pattern (14 bp):
ATATTATTATTATA
Found at i:2387449 original size:17 final size:18
Alignment explanation
Indices: 2387424--2387476 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
2387414 GGATATTTTT
2387424 AAATAAATATAATTTTGA
1 AAATAAATATAATTTTGA
* *
2387442 AAAT-AATAGAATTAT-A
1 AAATAAATATAATTTTGA
* *
2387458 AATTAAATATATTTTTGA
1 AAATAAATATAATTTTGA
2387476 A
1 A
2387477 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 4 0.15
17 17 0.63
18 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
AAATAAATATAATTTTGA
Found at i:2399829 original size:52 final size:52
Alignment explanation
Indices: 2399751--2400151 Score: 793
Period size: 52 Copynumber: 7.7 Consensus size: 52
2399741 GAATATGCCA
2399751 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
2399803 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
2399855 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
2399907 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
2399959 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
2400011 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
2400063 ATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
2400115 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
2400152 TGGACAGAAT
Statistics
Matches: 347, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 347 1.00
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:2400296 original size:130 final size:130
Alignment explanation
Indices: 2400063--2400360 Score: 569
Period size: 130 Copynumber: 2.3 Consensus size: 130
2400053 TGGACAGAAC
*
2400063 ATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
2400128 GAAGTGTTCTTTGAGTTATCTGATTGGACAGAATCAAGCATTGAATTTAGAATATGAATTTGCCA
66 GAAGTGTTCTTTGAGTTATCTGATTGGACAGAATCAAGCATTGAATTTAGAATATGAATTTGCCA
2400193 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
*
2400258 GAAGTGTTCTTTGAGTTATCTGATTGGACAGGATCAAGCATTGAATTTAGAATATGAATTTGCCA
66 GAAGTGTTCTTTGAGTTATCTGATTGGACAGAATCAAGCATTGAATTTAGAATATGAATTTGCCA
*
2400323 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
2400361 CGAAGAAGTG
Statistics
Matches: 165, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 165 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (130 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
GAAGTGTTCTTTGAGTTATCTGATTGGACAGAATCAAGCATTGAATTTAGAATATGAATTTGCCA
Found at i:2400298 original size:47 final size:48
Alignment explanation
Indices: 2400193--2400288 Score: 149
Period size: 52 Copynumber: 1.9 Consensus size: 48
2400183 GAATTTGCCA
2400193 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA----GTTGGACAGAAC
2400245 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA-TTGGACAG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAGTTGGACAG
2400289 GATCAAGCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
47 8 0.18
52 36 0.82
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.38
Consensus pattern (48 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAGTTGGACAGAAC
Found at i:2401350 original size:112 final size:113
Alignment explanation
Indices: 2400918--2401689 Score: 1219
Period size: 112 Copynumber: 6.8 Consensus size: 113
2400908 AGCAAAGATT
* * *
2400918 TGAATCCATCATTTGATGGAACAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
*
2400983 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
* * * * *
2401031 TGAATCCGTCATTTGATGGATCAGCTTTTTTCAGAGAAGGTTTATAATGAGAAGAACTCATCTGA
1 TGAATCCATCATTTGATGGATCATC-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * ***
2401096 AGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTT
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
* * * * *
2401145 TAAATCCGTCATTTGATGGATCAGCTTTTTTCAGAGAAGGTTCATAATGAGAAGAACTCATCTGA
1 TGAATCCATCATTTGATGGATCATC-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
2401210 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
2401259 TGAATCCATCATTTGATGGATCATCTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
2401323 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
*
2401371 TAAATCCATCATTTGATGGATCATCTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
*
2401435 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GC
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
* * * * *
2401482 TCAAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 T-GAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
2401547 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
*
2401596 TGAATCCATCATTTGATGGATCATCTTTTCCAGAG-AAGTTCATAATGAGAAGAATTCATCTGAA
1 TGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* *
2401660 GAAGAAAGAAAAAGTTCATAATGAGAAGAA
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAA
2401690 CTCATCAAGA
Statistics
Matches: 618, Mismatches: 37, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
111 2 0.00
112 270 0.44
113 135 0.22
114 211 0.34
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
TGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
Found at i:2401602 original size:337 final size:339
Alignment explanation
Indices: 2400918--2401689 Score: 1280
Period size: 337 Copynumber: 2.3 Consensus size: 339
2400908 AGCAAAGATT
* * *
2400918 TGAATCCATCATTTGATGGAACAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGATGGATCATCTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAA
* * *
2400983 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCGTCATTTGAT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTAAATCCATCATTTGAT
* * *
2401048 GGATCAGCTTTTTTCAGAGAAGGTTTATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTT
130 GGATCAGCTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTT
* * * * *
2401113 CATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATCCGTCATTTGATGGATCAGCTTTTTTCA
195 CATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA-CTTTTTTCA
*
2401178 GAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATT
259 GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATT
2401243 TGTTCAACCTTTTACC
324 TGTTCAACCTTTTACC
2401259 TGAATCCATCATTTGATGGATCATCTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 TGAATCCATCATTTGATGGATCATCTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAG
2401324 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTAAATCCATCATTTGATG
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTAAATCCATCATTTGATG
* *
2401389 GATCATC-TTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
131 GATCAGCTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTC
* * *
2401452 ATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTA-TTTTTTCCAG
196 ATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCACTTTTTT-CAG
2401516 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
260 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
2401581 GTTCAACCTTTTACC
325 GTTCAACCTTTTACC
* *
2401596 TGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAGTTCATAATGAGAAGAATTCATCTGAAG
1 TGAATCCATCATTTGATGGATCATCTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
2401661 AAGAAAGAAAAAGTTCATAATGAGAAGAA
66 AAGGAAGAAGAAGTTCATAATGAGAAGAA
2401690 CTCATCAAGA
Statistics
Matches: 406, Mismatches: 24, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
336 6 0.01
337 172 0.42
338 90 0.22
339 8 0.02
340 98 0.24
341 32 0.08
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (339 bp):
TGAATCCATCATTTGATGGATCATCTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTAAATCCATCATTTGATG
GATCAGCTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCACTTTTTTCAGA
GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
TTCAACCTTTTACC
Found at i:2401608 original size:225 final size:226
Alignment explanation
Indices: 2400920--2401689 Score: 1226
Period size: 225 Copynumber: 3.4 Consensus size: 226
2400910 CAAAGATTTG
* *
2400920 AATCCATCATTTGATGGAACAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
2400985 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCGTCATTTGATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTCGAATCCATCATTTGATGG
* * *
2401050 ATCAGCTTTTTT-CAGAGAAGGTTTATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTC
131 ATCA--TTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
* * ***
2401114 ATAATGAGAAGAACTTGTTCAACTTTTTGTTTA
194 ATAATGAGAAGAATTTGTTCAACCTTTTACCTA
* * *
2401147 AATCCGTCATTTGATGGATCAGCTTTTTTCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATCAGC-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
2401212 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC-CTGAATCCATCATTTGAT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTC-GAATCCATCATTTGAT
*
2401276 GGATCATCTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
129 GGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
2401340 ATAATGAGAAGAATTTGTTCAACCTTTTACCTA
194 ATAATGAGAAGAATTTGTTCAACCTTTTACCTA
*
2401373 AATCCATCATTTGATGGATCATCTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
2401437 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTCGAATCCATCATTTGATGG
*
2401502 ATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
131 ATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
2401567 AATGAGAAGAATTTGTTCAACCTTTTACCTG
196 AATGAGAAGAATTTGTTCAACCTTTTACCTA
* *
2401598 AATCCATCATTTGATGGATCATCTTTTCCAGAG-AAGTTCATAATGAGAAGAATTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
2401662 AGAAAGAAAAAGTTCATAATGAGAAGAA
66 AGGAAGAAGAAGTTCATAATGAGAAGAA
2401690 CTCATCAAGA
Statistics
Matches: 509, Mismatches: 28, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
224 103 0.20
225 176 0.35
226 98 0.19
227 25 0.05
228 107 0.21
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (226 bp):
AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTCGAATCCATCATTTGATGG
ATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAATTTGTTCAACCTTTTACCTA
Found at i:2401947 original size:3 final size:3
Alignment explanation
Indices: 2401939--2402030 Score: 139
Period size: 3 Copynumber: 30.7 Consensus size: 3
2401929 TTTTTATCCA
* *
2401939 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** *
2401987 TAT TAT TGC TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2402031 ATTTATATTA
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2403653 original size:17 final size:18
Alignment explanation
Indices: 2403628--2403680 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
2403618 GGATATTTTT
2403628 AAATAAATATAATTTTGA
1 AAATAAATATAATTTTGA
* *
2403646 AAAT-AATAGAATTAT-A
1 AAATAAATATAATTTTGA
* *
2403662 AATTAAATATATTTTTGA
1 AAATAAATATAATTTTGA
2403680 A
1 A
2403681 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 4 0.15
17 17 0.63
18 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
AAATAAATATAATTTTGA
Found at i:2405702 original size:2 final size:2
Alignment explanation
Indices: 2405695--2405719 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2405685 TTTCGTAATA
2405695 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 A
2405720 ATTTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2409224 original size:20 final size:19
Alignment explanation
Indices: 2409174--2409229 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
2409164 AACCAATAAT
2409174 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
*
2409193 GATGAAAA-AAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
2409213 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
2409230 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 15 0.48
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:2409633 original size:25 final size:25
Alignment explanation
Indices: 2409583--2409634 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
2409573 AAATAATAAT
*
2409583 ATAATATATATATAATAATAGGAAA
1 ATAATATATATATAATAATAGAAAA
2409608 ATAATATA-ATATAACGTAA-AGAAAA
1 ATAATATATATATAA--TAATAGAAAA
2409633 AT
1 AT
2409635 GAAAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 6 0.25
25 15 0.62
26 3 0.12
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.29
Consensus pattern (25 bp):
ATAATATATATATAATAATAGAAAA
Found at i:2409927 original size:37 final size:37
Alignment explanation
Indices: 2409886--2409970 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 37
2409876 GGATCCTATC
** *
2409886 TTTAGGAGTTTAAATAATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTAAATAATAACAAAACTCTATCATATT
* ** * *
2409923 TTTAGGAGTTTGAATCCTAACAAAATTCTATCCTATT
1 TTTAGGAGTTTAAATAATAACAAAACTCTATCATATT
2409960 TTTAGGAGTTT
1 TTTAGGAGTTT
2409971 GAATCCTAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAACAAAACTCTATCATATT
Found at i:2410916 original size:106 final size:106
Alignment explanation
Indices: 2410731--2411901 Score: 1842
Period size: 106 Copynumber: 11.0 Consensus size: 106
2410721 AGCATTGTTC
* * * *
2410731 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
2410796 ACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
2410837 CGAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
2410902 ACCAGCGGTTCCTTCGTCATGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
2410943 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
2411008 ACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
2411049 GGAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
2411114 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* **
2411155 GGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCCT-AAATTGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT-CTGAAATTGGGAAATTGTTTGTTGAC
2411219 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * **
2411261 AGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCAAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
2411326 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
** * *
2411367 CGAGTCCAATATTTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAAA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
2411432 ACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
2411473 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGTCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
2411538 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
2411579 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
2411644 ACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
2411685 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAATTGTTTATTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
2411750 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * * *
2411791 GGAATCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTAGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * * *
2411856 ATCAGCCGTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
2411897 CGAGT
1 CGAGT
2411902 GGCACGATAT
Statistics
Matches: 995, Mismatches: 67, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
105 2 0.00
106 991 1.00
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:2412933 original size:21 final size:21
Alignment explanation
Indices: 2412882--2412934 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2412872 ATTATGACTA
2412882 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
***
2412903 TCGTGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
2412924 TCGCAATGCGA
1 TCGCAATGCGA
2412935 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:2412993 original size:21 final size:21
Alignment explanation
Indices: 2412941--2412996 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
2412931 GCGAATAAGT
*
2412941 AAATCGCAACACGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
2412962 AAATCGCAACGCGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
2412983 AAATCGCAACGCGA
1 AAATCGCAACGCGA
2412997 TAATACAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTTGGA
Found at i:2413032 original size:20 final size:20
Alignment explanation
Indices: 2413007--2413059 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
2412997 TAATACAAAA
2413007 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
2413027 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
2413047 TCGCAACGAGATA
1 TCGCAACGCGATA
2413060 ATACATAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:2413073 original size:21 final size:21
Alignment explanation
Indices: 2412984--2413079 Score: 83
Period size: 20 Copynumber: 4.7 Consensus size: 21
2412974 GAATTTGGAA
*
2412984 AATCGCAACGCGATAAT-ACAA
1 AATCGCAACGCGATAATGAC-T
*
2413005 AATCGCAACGCGATACTGACT
1 AATCGCAACGCGATAATGACT
* *
2413026 -TTCGCAACGCGATACTGACT
1 AATCGCAACGCGATAATGACT
* *
2413046 -TTCGCAACGAGATAAT-ACAT
1 AATCGCAACGCGATAATGAC-T
*
2413066 AATCGCAATGCGAT
1 AATCGCAACGCGAT
2413080 TTTCAAAGCG
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.03
20 34 0.53
21 26 0.41
22 2 0.03
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (21 bp):
AATCGCAACGCGATAATGACT
Found at i:2413274 original size:22 final size:22
Alignment explanation
Indices: 2413246--2413289 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2413236 CACTCTCTCA
2413246 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
2413268 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2413290 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2413601 original size:20 final size:20
Alignment explanation
Indices: 2413552--2413610 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2413542 TTTATTCTCT
* **
2413552 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
2413572 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
2413592 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
2413611 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:2413801 original size:25 final size:24
Alignment explanation
Indices: 2413747--2413801 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
2413737 TGTTTATTAT
* *
2413747 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
2413771 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
2413797 TGTTT
1 TGTTT
2413802 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:2414949 original size:18 final size:18
Alignment explanation
Indices: 2414928--2414975 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
2414918 TTTACTTCGG
2414928 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
2414946 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2414964 GAGCCATCACCT
1 GAGCCATCACCT
2414976 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2415511 original size:20 final size:20
Alignment explanation
Indices: 2415486--2415531 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2415476 TAGTTTACTT
2415486 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
2415506 TCGCAATGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
2415526 TCGCAA
1 TCGCAA
2415532 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Done.