Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000389.1 Hibiscus syriacus cultivar Beakdansim tig00000715_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: 2672246
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 15
Found at i:2400025 original size:25 final size:25
Alignment explanation
Indices: 2399997--2400046 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2399987 CATTATTTTC
*
2399997 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
*
2400022 CAAATAATGTGCCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2400047 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:2400157 original size:20 final size:20
Alignment explanation
Indices: 2400125--2400172 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2400115 TTTCGCAACG
*
2400125 CTTA-TTTCGCGTTGCGAAT
1 CTTACTTTCACGTTGCGAAT
2400144 CTTACTTTCACGTTGCGAAT
1 CTTACTTTCACGTTGCGAAT
2400164 -TTGACTTTC
1 CTT-ACTTTC
2400173 GCATTGATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.44
Consensus pattern (20 bp):
CTTACTTTCACGTTGCGAAT
Found at i:2402950 original size:12 final size:12
Alignment explanation
Indices: 2402929--2402962 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2402919 GGTTGTGGGT
*
2402929 TTTGAGATTGTG
1 TTTGATATTGTG
2402941 TTTGATATTGTG
1 TTTGATATTGTG
*
2402953 TTTGGTATTG
1 TTTGATATTG
2402963 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:2403946 original size:20 final size:20
Alignment explanation
Indices: 2403923--2404018 Score: 104
Period size: 20 Copynumber: 4.8 Consensus size: 20
2403913 TGCAATTTTC
*
2403923 CAAATTCGCAACGCGAAAGG
1 CAAATTCGCAACGCGAAAGT
* *
2403943 CAAACTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
* *
2403963 CAAATTTGCAACACGAAAGT
1 CAAATTCGCAACGCGAAAGT
* * **
2403983 CAAATTTGCAAC-TGAATTT
1 CAAATTCGCAACGCGAAAGT
2404002 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
2404019 TTTAATTTTG
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
19 15 0.24
20 48 0.76
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:2404006 original size:19 final size:20
Alignment explanation
Indices: 2403962--2404033 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 20
2403952 AACGCGATAG
**
2403962 TCAAATTTGCAACACGAAAG
1 TCAAATTTGCAACACGAATT
*
2403982 TCAAATTTGCAAC-TGAATT
1 TCAAATTTGCAACACGAATT
* *
2404001 TCAAATTCGCAACGCGAATT
1 TCAAATTTGCAACACGAATT
*
2404021 T-AATTTTGCAACA
1 TCAAATTTGCAACA
2404034 GGTTTTAGTT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
19 24 0.56
20 19 0.44
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.29
Consensus pattern (20 bp):
TCAAATTTGCAACACGAATT
Found at i:2404021 original size:20 final size:20
Alignment explanation
Indices: 2403823--2404021 Score: 99
Period size: 20 Copynumber: 10.0 Consensus size: 20
2403813 AAATGACCAA
*
2403823 CAAATTCGCAACGC-AATCT
1 CAAATTCGCAACGCGAATTT
* *
2403842 CAAATTCGCAACACGGA-TT
1 CAAATTCGCAACGCGAATTT
* * *
2403861 CTAATTTCGCAAC-CCAGTTT
1 C-AAATTCGCAACGCGAATTT
*
2403881 CCAATTTCGCAACGCGAATATGT
1 -CAAATTCGCAACGCGAAT-T-T
**
2403904 -AAA-TCGCATTGC-AATTTT
1 CAAATTCGCAACGCGAA-TTT
***
2403922 CCAAATTCGCAACGCGAAAGG
1 -CAAATTCGCAACGCGAATTT
* *
2403943 CAAACTCGCAACGCG-ATAGT
1 CAAATTCGCAACGCGAAT-TT
* * **
2403963 CAAATTTGCAACACGAAAGT
1 CAAATTCGCAACGCGAATTT
* *
2403983 CAAATTTGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
2404002 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
2404022 AATTTTGCAA
Statistics
Matches: 136, Mismatches: 29, Indels: 29
0.70 0.15 0.15
Matches are distributed among these distances:
18 1 0.01
19 35 0.26
20 82 0.60
21 14 0.10
22 3 0.02
23 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:2404798 original size:12 final size:12
Alignment explanation
Indices: 2404777--2404810 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2404767 ACCACATTTC
*
2404777 CAATACCAAACA
1 CAATATCAAACA
2404789 CAATATCAAACA
1 CAATATCAAACA
*
2404801 CAATCTCAAA
1 CAATATCAAA
2404811 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:2404975 original size:24 final size:24
Alignment explanation
Indices: 2404939--2404988 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
2404929 TCGAAATTTT
*
2404939 ATCTTGGTAAATACCCAGACTTTG
1 ATCTTGGTAAATACACAGACTTTG
* *
2404963 ATCTTGGTCAATACACAGATTTTG
1 ATCTTGGTAAATACACAGACTTTG
2404987 AT
1 AT
2404989 GATATAATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (24 bp):
ATCTTGGTAAATACACAGACTTTG
Found at i:2407534 original size:20 final size:20
Alignment explanation
Indices: 2407509--2407558 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2407499 ATGTTGCGAT
*
2407509 CAACGCGAAA-ATCAAATTTG
1 CAACGCGAAAGA-CAAATTCG
2407529 CAACGCGAAAGACAAATTCG
1 CAACGCGAAAGACAAATTCG
2407549 CAACGCGAAA
1 CAACGCGAAA
2407559 TAAGCGTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.46, C:0.24, G:0.18, T:0.12
Consensus pattern (20 bp):
CAACGCGAAAGACAAATTCG
Found at i:2407804 original size:25 final size:25
Alignment explanation
Indices: 2407766--2407815 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2407756 TAATCAATTA
*
2407766 AACATTGTTGTGGGTATATTATTTG
1 AACATTGTTATGGGTATATTATTTG
2407791 AACATTGTTATGGGTATATTATTTG
1 AACATTGTTATGGGTATATTATTTG
2407816 GAAAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.22, T:0.48
Consensus pattern (25 bp):
AACATTGTTATGGGTATATTATTTG
Found at i:2408222 original size:18 final size:18
Alignment explanation
Indices: 2408201--2408237 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2408191 GTAATTGGAG
2408201 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
2408219 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
2408237 T
1 T
2408238 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:2408244 original size:24 final size:24
Alignment explanation
Indices: 2408193--2408245 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2408183 ATTTATATGT
* * *
2408193 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
2408217 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
2408241 AATTT
1 AATTT
2408246 CGGCTCCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:2408586 original size:39 final size:39
Alignment explanation
Indices: 2408543--2408627 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
2408533 TCCGATGCTC
2408543 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
2408582 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
2408621 ATAAAAA
1 ATCAAAA
2408628 ATCTACAACT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.49, C:0.19, G:0.15, T:0.16
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:2408867 original size:20 final size:20
Alignment explanation
Indices: 2408844--2408889 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
2408834 AATAAGCGTT
*
2408844 GCGATAGTCAAATTCGCAAA
1 GCGAAAGTCAAATTCGCAAA
2408864 GCGAAAGTCAAATTCGCAAA
1 GCGAAAGTCAAATTCGCAAA
*
2408884 CCGAAA
1 GCGAAA
2408890 ATCGCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAA
Found at i:2408951 original size:20 final size:20
Alignment explanation
Indices: 2408923--2408960 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2408913 GCAACGCTTA
2408923 TTTCACGTTGCGAATTTGAC
1 TTTCACGTTGCGAATTTGAC
*
2408943 TTTCGCGTTGCGAATTTG
1 TTTCACGTTGCGAATTTG
2408961 TACCTTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (20 bp):
TTTCACGTTGCGAATTTGAC
Found at i:2410549 original size:21 final size:21
Alignment explanation
Indices: 2410525--2410623 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
2410515 GCGGGCGGGA
*
2410525 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
2410546 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
2410567 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGAGAGGGG
*
2410588 CCTCTTGAACGAT-AGGAGGCG
1 CCTCTTGAACGATGA-GAGGGG
*
2410609 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
2410624 TAGGTGCATC
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
20 2 0.03
21 59 0.94
22 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:2410606 original size:42 final size:42
Alignment explanation
Indices: 2410525--2410623 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
2410515 GCGGGCGGGA
* * * *
2410525 CCTCTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCG
* *
2410567 CTTCTTCG-ATGATGAGAGGGGCCTCTTGAACGATAGGAGGCG
1 CCTCTT-GAATGATGACAGGGGCCTCTTGAACGATAGGAGGCG
2410609 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
2410624 TAGGTGCATC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.02
42 46 0.96
43 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.23
Consensus pattern (42 bp):
CCTCTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCG
Found at i:2412837 original size:13 final size:13
Alignment explanation
Indices: 2412819--2412843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2412809 TTTCTTCAAC
2412819 AAAAAGACAAAAT
1 AAAAAGACAAAAT
2412832 AAAAAGACAAAA
1 AAAAAGACAAAA
2412844 CAAAGACAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.08, G:0.08, T:0.04
Consensus pattern (13 bp):
AAAAAGACAAAAT
Found at i:2413082 original size:22 final size:22
Alignment explanation
Indices: 2413054--2413100 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2413044 GATGGAGATA
2413054 GACGGATTTCGTCGAAAATGGG
1 GACGGATTTCGTCGAAAATGGG
* *
2413076 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGAAAATGGG
2413098 GAC
1 GAC
2413101 AGATGTCGCC
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:0.23, C:0.15, G:0.40, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGTCGAAAATGGG
Found at i:2413360 original size:20 final size:20
Alignment explanation
Indices: 2413309--2413364 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
2413299 ATTTACATAT
*
2413309 TCGCGTTACGAAATTGGAAA
1 TCGCGTTACGAAATTTGAAA
* * *
2413329 TTGGGTTACGAAATTTGAGA
1 TCGCGTTACGAAATTTGAAA
*
2413349 TCGCGTTGCG-AATTTG
1 TCGCGTTACGAAATTTG
2413365 TTGGTCATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.32
Consensus pattern (20 bp):
TCGCGTTACGAAATTTGAAA
Found at i:2413936 original size:2 final size:2
Alignment explanation
Indices: 2413929--2413955 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2413919 CATGATACAA
2413929 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2413956 ATTCTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2426098 original size:21 final size:21
Alignment explanation
Indices: 2426016--2426099 Score: 64
Period size: 21 Copynumber: 3.9 Consensus size: 21
2426006 CAGAACCCCA
*
2426016 GGGGGGTATCGATTCCC-C-T
1 GGGGGGGATCGATTCCCTCAT
* *
2426035 GTGGGGGGAATCGGTTCCCCTTCAA
1 G-GGGGGG-ATCGATT-CCC-TCAT
* * *
2426060 AGGGGGAATCGGTTCCCTCAT
1 GGGGGGGATCGATTCCCTCAT
2426081 GGGGGGGATCGATTCCCTC
1 GGGGGGGATCGATTCCCTC
2426100 TGCACCAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
19 1 0.02
20 5 0.10
21 25 0.50
22 6 0.12
23 7 0.14
24 6 0.12
ACGTcount: A:0.14, C:0.25, G:0.37, T:0.24
Consensus pattern (21 bp):
GGGGGGGATCGATTCCCTCAT
Found at i:2437756 original size:29 final size:26
Alignment explanation
Indices: 2437692--2437768 Score: 66
Period size: 29 Copynumber: 2.8 Consensus size: 26
2437682 TTGAAAACGT
*
2437692 TTTTTGGAAA-TATATATATTATATA
1 TTTTTGGAAATTATATATATAATATA
* **
2437717 GTTTTAAAAATGTATACTATATAATTATA
1 TTTTTGGAAAT-TATA-TATATAA-TATA
2437746 TTTTTGGAAATATATATTATATA
1 TTTTTGGAAAT-TATA-TATATA
2437769 GTTTTAAAAC
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
25 7 0.18
27 4 0.10
28 6 0.15
29 22 0.56
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.49
Consensus pattern (26 bp):
TTTTTGGAAATTATATATATAATATA
Found at i:2437792 original size:35 final size:36
Alignment explanation
Indices: 2437745--2437851 Score: 126
Period size: 35 Copynumber: 2.9 Consensus size: 36
2437735 ATATAATTAT
*
2437745 ATTTTTGGAAATATATATTATATAGTTTTAAAA-CA
1 ATTTTTGAAAATATATATTATATAGTTTTAAAATCA
* *
2437780 ATTTTTGAAAATATATATTATGTGGTTTTGAAAATCA
1 ATTTTTGAAAATATATATTATATAGTTTT-AAAATCA
* * *
2437817 TTTTTTTAAAGCATATATAATATATAGTTTTAAAA
1 ATTTTTGAAA--ATATATATTATATAGTTTTAAAA
2437852 ATGTTTTTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
35 26 0.43
36 4 0.07
37 10 0.17
38 4 0.07
39 16 0.27
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (36 bp):
ATTTTTGAAAATATATATTATATAGTTTTAAAATCA
Found at i:2437880 original size:20 final size:20
Alignment explanation
Indices: 2437855--2437899 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2437845 TTTAAAAATG
2437855 TTTTTTA-TTATATATTAATA
1 TTTTTTAGTTATATA-TAATA
* *
2437875 TTTTTTAGTTTTATATATTA
1 TTTTTTAGTTATATATAATA
2437895 TTTTT
1 TTTTT
2437900 ATTTATTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTTAGTTATATATAATA
Found at i:2437904 original size:17 final size:17
Alignment explanation
Indices: 2437856--2437916 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 17
2437846 TTAAAAATGT
*
2437856 TTTTTATTATATATTAATA
1 TTTTTATT-TATA-TATTA
2437875 TTTTTTAGTTTTATATATTA
1 -TTTTTA--TTTATATATTA
2437895 TTTTTATTTAT-TACTTA
1 TTTTTATTTATATA-TTA
2437912 TTTTT
1 TTTTT
2437917 TTCCTTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
16 2 0.05
17 13 0.35
19 6 0.16
20 10 0.27
21 4 0.11
22 2 0.05
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTTTATTTATATATTA
Found at i:2438307 original size:25 final size:27
Alignment explanation
Indices: 2438269--2438327 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
2438259 TCAATCGAAC
* *
2438269 CAAAAAAACAATACCAATC-AAAAAAA
1 CAAAACAACAATACAAATCGAAAAAAA
*
2438295 CAAAACAAC-ATACAAATCGAACAAAA
1 CAAAACAACAATACAAATCGAAAAAAA
2438321 -AAAACAA
1 CAAAACAA
2438328 TCCCAAATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 15 0.52
26 14 0.48
ACGTcount: A:0.71, C:0.20, G:0.02, T:0.07
Consensus pattern (27 bp):
CAAAACAACAATACAAATCGAAAAAAA
Found at i:2439015 original size:8 final size:9
Alignment explanation
Indices: 2438994--2439018 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2438984 GGAATAAATT
2438994 TTTTTTCTA
1 TTTTTTCTA
2439003 TTTTTTCTA
1 TTTTTTCTA
2439012 TTTTTTC
1 TTTTTTC
2439019 CCTTGACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTCTA
Found at i:2439451 original size:29 final size:30
Alignment explanation
Indices: 2439418--2439478 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
2439408 ATGCACGTTT
*
2439418 TTCCAGTTTAGTGA-CTAATGTTT-ATTTCG
1 TTCCAGTTTAGT-ATCTAATGTTTCATTCCG
*
2439447 TTCCAGTTTGGTATCTAATGTTTCATTCCG
1 TTCCAGTTTAGTATCTAATGTTTCATTCCG
2439477 TT
1 TT
2439479 ACTCAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 1 0.04
29 20 0.71
30 7 0.25
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.49
Consensus pattern (30 bp):
TTCCAGTTTAGTATCTAATGTTTCATTCCG
Found at i:2440008 original size:24 final size:27
Alignment explanation
Indices: 2439959--2440008 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
2439949 ATGTGTTTTC
*
2439959 TTTTTTAATATATATATATAATTTTAT
1 TTTTTTAATATATATATATAAATTTAT
2439986 TTTTTTAAT-TATATA-A-AAATTTA
1 TTTTTTAATATATATATATAAATTTA
2440009 AAACTATCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 1 0.05
26 6 0.27
27 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TTTTTTAATATATATATATAAATTTAT
Found at i:2440142 original size:29 final size:30
Alignment explanation
Indices: 2440086--2440143 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
2440076 TTTGAGTAAC
*
2440086 GAAATGAAACGTTAGATACCAAAATGAAAT
1 GAAATGAAACGTTAGACACCAAAATGAAAT
* *
2440116 GAAAT-AAACGTTAGACACTAAACTGAAA
1 GAAATGAAACGTTAGACACCAAAATGAAA
2440144 AATGGGCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.53, C:0.12, G:0.16, T:0.19
Consensus pattern (30 bp):
GAAATGAAACGTTAGACACCAAAATGAAAT
Found at i:2440247 original size:2 final size:2
Alignment explanation
Indices: 2440240--2440334 Score: 167
Period size: 2 Copynumber: 48.5 Consensus size: 2
2440230 ATTTTAAATT
2440240 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2440282 TA TA TA TA TA TA TA TA TC TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2440323 TA TA TA -A TA TA T
1 TA TA TA TA TA TA T
2440335 TAAAGGTGAT
Statistics
Matches: 89, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
1 2 0.02
2 87 0.98
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2440366 original size:27 final size:27
Alignment explanation
Indices: 2440334--2440389 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
2440324 ATATAATATA
2440334 TTAAAGGTGATTAAAAAGTAATACATG
1 TTAAAGGTGATTAAAAAGTAATACATG
2440361 TTAAAGGTGATTAAAAAGTAATACATG
1 TTAAAGGTGATTAAAAAGTAATACATG
2440388 TT
1 TT
2440390 CTAAGTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.46, C:0.04, G:0.18, T:0.32
Consensus pattern (27 bp):
TTAAAGGTGATTAAAAAGTAATACATG
Found at i:2441771 original size:2 final size:2
Alignment explanation
Indices: 2441766--2441801 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2441756 TTCTTTTTTA
2441766 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2441802 ATTTTATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2447024 original size:34 final size:35
Alignment explanation
Indices: 2446981--2447050 Score: 115
Period size: 34 Copynumber: 2.0 Consensus size: 35
2446971 TTCATTTAGG
2446981 GGGGAATCGATACCCCCCA-GGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
*
2447015 GGGGAATCGATACCCCCTAGGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCA-GGGGGAATCTGTTCCC
2447051 CCTGGACATA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 18 0.55
36 15 0.45
ACGTcount: A:0.20, C:0.30, G:0.31, T:0.19
Consensus pattern (35 bp):
GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
Found at i:2451343 original size:35 final size:35
Alignment explanation
Indices: 2451295--2451364 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
2451285 TTCATTTAGG
*
2451295 GGGGAATCGATACCCCCCAGGGAG-AATCTGTTCCC
1 GGGGAATCAATA-CCCCCAGGGAGAAATCTGTTCCC
*
2451330 GGGGAATCAATACCCCCAGGGGGAAATCTGTTCCC
1 GGGGAATCAATACCCCCAGGGAGAAATCTGTTCCC
2451365 CCTGCACATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 10 0.31
35 22 0.69
ACGTcount: A:0.24, C:0.30, G:0.29, T:0.17
Consensus pattern (35 bp):
GGGGAATCAATACCCCCAGGGAGAAATCTGTTCCC
Found at i:2468213 original size:5 final size:5
Alignment explanation
Indices: 2468057--2468216 Score: 167
Period size: 5 Copynumber: 30.6 Consensus size: 5
2468047 CGTATTACCA
* *
2468057 CGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACA CGACA
1 CGACC -CGACC -CGACC -CGACC -CGACC -CGACC -CGACC -CGACC CGACC
* * * * * * * *
2468109 CGACA CGACA CGACA CGACA CGACA CGACA CGACA CGACA CGACC CGACC
1 CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGACC
2468159 CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGACC
1 CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGACC
2468209 CGACC CGA
1 CGACC CGA
2468217 GACGGGACGG
Statistics
Matches: 152, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
5 112 0.74
6 40 0.26
ACGTcount: A:0.30, C:0.51, G:0.19, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:2468531 original size:19 final size:19
Alignment explanation
Indices: 2468508--2468678 Score: 153
Period size: 19 Copynumber: 8.2 Consensus size: 19
2468498 TATTTTGGAT
* *
2468508 TTTTCACTATCGCAACACT
1 TTTTAACTATCGCAACACA
*
2468527 TTTTCACTATCGCAACAACA
1 TTTTAACTATCGCAAC-ACA
*
2468547 CGTTTTTCAAACTCTCGCAACACA
1 ---TTTT--AACTATCGCAACACA
2468571 TTTTAACTATCGCAACAACACA
1 TTTTAACTATCG---CAACACA
2468593 TTTTAACTATCGTAACAACACA
1 TTTTAACTATCG---CAACACA
*
2468615 TTTTTCAAACTCTCGCAACACA
1 -TTTT--AACTATCGCAACACA
2468637 TTTTAACTATCGCAACACA
1 TTTTAACTATCGCAACACA
*
2468656 TTTTAACTATCGCAACATA
1 TTTTAACTATCGCAACACA
2468675 TTTT
1 TTTT
2468679 TCAAAATCGC
Statistics
Matches: 132, Mismatches: 8, Indels: 24
0.80 0.05 0.15
Matches are distributed among these distances:
19 59 0.45
20 2 0.02
21 8 0.06
22 35 0.27
23 8 0.06
24 3 0.02
25 17 0.13
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.33
Consensus pattern (19 bp):
TTTTAACTATCGCAACACA
Found at i:2468603 original size:66 final size:63
Alignment explanation
Indices: 2468508--2468672 Score: 258
Period size: 66 Copynumber: 2.6 Consensus size: 63
2468498 TATTTTGGAT
* * * *
2468508 TTTTCACTATCGCAACACTTTTTCACTATCGCAACAACACGTTTTTCAAACTCTCGCAACACA
1 TTTTAACTATCGCAACACATTTTAACTATCGCAACAACACATTTTTCAAACTCTCGCAACACA
*
2468571 TTTTAACTATCGCAACAACACATTTTAACTATCGTAACAACACATTTTTCAAACTCTCGCAACAC
1 TTTTAACTATCG---CAACACATTTTAACTATCGCAACAACACATTTTTCAAACTCTCGCAACAC
2468636 A
63 A
2468637 TTTTAACTATCGCAACACATTTTAACTATCGCAACA
1 TTTTAACTATCGCAACACATTTTAACTATCGCAACA
2468673 TATTTTTCAA
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
63 34 0.37
66 59 0.63
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (63 bp):
TTTTAACTATCGCAACACATTTTAACTATCGCAACAACACATTTTTCAAACTCTCGCAACACA
Found at i:2468612 original size:44 final size:41
Alignment explanation
Indices: 2468508--2468672 Score: 174
Period size: 44 Copynumber: 3.9 Consensus size: 41
2468498 TATTTTGGAT
* * * *
2468508 TTTTCACTATCGCAACACTTTTTCACTATCGCAACAACACGT
1 TTTTAACTATCGCAACACATTTTAACTATCGCAACAACAC-A
*
2468550 TTTTCAAACTCTCGCAACACATTTTAACTATCGCAACAACACA
1 TTTT--AACTATCGCAACACATTTTAACTATCGCAACAACACA
*
2468593 TTTTAACTATCGTAACAACACATTTTTCAAACTCTCG---CAACACA
1 TTTTAACTATCG---CAACACA-TTTT--AACTATCGCAACAACACA
2468637 TTTTAACTATCGCAACACATTTTAACTATCGCAACA
1 TTTTAACTATCGCAACACATTTTAACTATCGCAACA
2468673 TATTTTTCAA
Statistics
Matches: 104, Mismatches: 8, Indels: 23
0.77 0.06 0.17
Matches are distributed among these distances:
38 7 0.07
40 4 0.04
41 16 0.15
42 4 0.04
43 4 0.04
44 58 0.56
45 4 0.04
47 7 0.07
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (41 bp):
TTTTAACTATCGCAACACATTTTAACTATCGCAACAACACA
Found at i:2473249 original size:17 final size:18
Alignment explanation
Indices: 2473212--2473250 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2473202 ATATTATGTA
2473212 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
*
2473230 TTTATTTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
2473247 TTTA
1 TTTA
2473251 CTAATATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:2477908 original size:20 final size:20
Alignment explanation
Indices: 2477864--2478091 Score: 164
Period size: 20 Copynumber: 11.2 Consensus size: 20
2477854 AATGACCAAC
**
2477864 AAAATCGCAACGCGA-TATC
1 AAAATCGCAACGCGATTAAG
*
2477883 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
2477903 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
2477923 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
2477943 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
2477964 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
2477985 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
2478006 AAGAATCGCAATGCGATTCAA-
1 AA-AATCGCAACGCGATT-AAG
2478027 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
2478049 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
* *
2478067 AAAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTAAG
2478087 AAAAT
1 AAAAT
2478092 GAGTAAATTC
Statistics
Matches: 168, Mismatches: 26, Indels: 29
0.75 0.12 0.13
Matches are distributed among these distances:
18 4 0.02
19 15 0.09
20 106 0.63
21 16 0.10
22 27 0.16
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:2477991 original size:42 final size:42
Alignment explanation
Indices: 2477940--2478082 Score: 220
Period size: 42 Copynumber: 3.5 Consensus size: 42
2477930 CAACGGTCAA
2477940 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
* *
2477982 AAGAGAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
*
2478024 CAA-AAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATT
1 -AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
*
2478064 AAGAAAATCGCAATGCGAT
1 AAGAAAATCGCAACGCGAT
2478083 TCAGAAAATG
Statistics
Matches: 91, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
39 2 0.02
40 34 0.37
42 53 0.58
43 2 0.02
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (42 bp):
AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
Found at i:2478033 original size:62 final size:60
Alignment explanation
Indices: 2477866--2478091 Score: 169
Period size: 62 Copynumber: 3.7 Consensus size: 60
2477856 TGACCAACAA
* * * * *
2477866 AATCGCAACGCGA-TATCAAAATCGCAACGCGATTTAGAAAATCGCAA--CG-TTGAAAAG
1 AATCGCAACGCGATTAACAAAATCGCAATGCGATTCAAAAAATCGCAACGCGATT-CAAAG
* * * * * *
2477923 AAAATCGCAACG-G-TCAAAAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT-AAG
1 --AATCGCAACGCGAT--TAACAAAATCGCAATGCG--ATTCAAAAAATCGCAACGCGATTCAA-
2477985 AG
59 AG
** *
2477987 AATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAAAAAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGAT-TAACAA-AATCGCAATGCGATTCAAAAAATCGCAACGCGATTCAAAG
* *
2478049 AATCGCAACGCGATTAAGAAAATCGCAATGCGATTCAGAAAAT
1 AATCGCAACGCGATTAACAAAATCGCAATGCGATTCAAAAAAT
2478092 GAGTAAATTC
Statistics
Matches: 133, Mismatches: 21, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
58 1 0.01
59 10 0.08
60 37 0.28
61 3 0.02
62 58 0.44
63 6 0.05
64 16 0.12
65 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (60 bp):
AATCGCAACGCGATTAACAAAATCGCAATGCGATTCAAAAAATCGCAACGCGATTCAAAG
Found at i:2478062 original size:40 final size:40
Alignment explanation
Indices: 2477864--2478084 Score: 220
Period size: 40 Copynumber: 5.5 Consensus size: 40
2477854 AATGACCAAC
*
2477864 AAAATCGCAACGCGATAT-CAA-AATCGCAACGCGATTTAG
1 AAAATCGCAACGCGAT-TCCAAGAATCGCAACGCGATTAAG
* **** *
2477903 AAAATCGCAACGTTGAAAAGAA-AATCGCAACG-G-TCAAAAG
1 AAAATCGCAACG-CGATTCCAAGAATCGCAACGCGAT--TAAG
*
2477943 AAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATTAAG
* *
2477985 AGAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAA-
1 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATT-AAG
2478027 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
*
2478067 AAAATCGCAATGCGATTC
1 AAAATCGCAACGCGATTC
2478085 AGAAAATGAG
Statistics
Matches: 152, Mismatches: 17, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
38 1 0.01
39 16 0.11
40 67 0.44
41 3 0.02
42 61 0.40
43 3 0.02
44 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (40 bp):
AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
Found at i:2478719 original size:6 final size:6
Alignment explanation
Indices: 2478708--2478752 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
2478698 TCTCGTCTCG
2478708 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
2478753 AATACGTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:2478880 original size:20 final size:20
Alignment explanation
Indices: 2478855--2479099 Score: 205
Period size: 20 Copynumber: 11.8 Consensus size: 20
2478845 CTCATTTTCT
*
2478855 GAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
** * *
2478875 GAATCGTATTGCGATTTTTTTTCT
1 GAATCGCGTTGCGA---TTCTT-G
*
2478899 GAATCACGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
2478920 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
2478939 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
2478960 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
2478979 GAAGATCGCGTTGCGATTCTTA
1 G-A-ATCGCGTTGCGATTCTTG
*
2479001 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
*
2479021 GAATCGCGTTGCGATTTTTG
1 GAATCGCGTTGCGATTCTTG
*
2479041 GAAGATCGCGTTGCGATT-TTAT
1 G-A-ATCGCGTTGCGATTCTT-G
*
2479063 GAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
2479083 GAAGATCGCGTTGCGAT
1 G-A-ATCGCGTTGCGAT
2479100 CTTCTTTTCA
Statistics
Matches: 190, Mismatches: 15, Indels: 38
0.78 0.06 0.16
Matches are distributed among these distances:
18 10 0.05
19 2 0.01
20 96 0.51
21 11 0.06
22 50 0.26
23 10 0.05
24 11 0.06
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:2479006 original size:42 final size:40
Alignment explanation
Indices: 2478920--2479099 Score: 202
Period size: 42 Copynumber: 4.3 Consensus size: 40
2478910 CGATTTTCTT
***
2478920 AATCGCGTTGCGATTCTTGGAATCGCGTTGCGATT-TTCTT
1 AATCGCGTTGCGATT-TTGGAATCGCGTTGCGATTCTTGGA
*
2478960 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTAG-
1 AATCGCGTTGCGATT-TTGG-A-ATCGCGTTGCGATTCTTGGA
* *
2479002 AATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTTGGA
1 AATCGCGTTGCGATTTT-GGAATCGCGTTGCGATTCTTGGA
* *
2479043 AGATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTGGA
1 A-ATCGCGTTGCGATTTT-GGAATCGCGTTGCGATTCTTGGA
2479085 AGATCGCGTTGCGAT
1 A-ATCGCGTTGCGAT
2479100 CTTCTTTTCA
Statistics
Matches: 126, Mismatches: 8, Indels: 10
0.88 0.06 0.07
Matches are distributed among these distances:
40 37 0.29
41 5 0.04
42 82 0.65
43 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.36
Consensus pattern (40 bp):
AATCGCGTTGCGATTTTGGAATCGCGTTGCGATTCTTGGA
Found at i:2479008 original size:62 final size:62
Alignment explanation
Indices: 2478857--2479078 Score: 270
Period size: 62 Copynumber: 3.5 Consensus size: 62
2478847 CATTTTCTGA
* * ** * ***
2478857 ATCGCATTGCGATTCTTGGAATCGTATTGCGATTTTTTTTCTGAATCACGTTGCGATT-TTCTTA
1 ATCGCGTTGCGATTCTTAGAATCGCGTTGCGA----TTTTCTGAATCGCGTTGCGATTCTTGGAA
2478921 -
62 G
* *
2478921 ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTTAGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
*
2478983 ATCGCGTTGCGATTCTTAGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTTGGAAG
1 ATCGCGTTGCGATTCTTAGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
*
2479045 ATCGCGTTGCGATT-TTATGAATCGCATTGCGATT
1 ATCGCGTTGCGATTCTTA-GAATCGCGTTGCGATT
2479079 CTTGGAAGAT
Statistics
Matches: 143, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
60 20 0.14
61 6 0.04
62 88 0.62
64 29 0.20
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (62 bp):
ATCGCGTTGCGATTCTTAGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
Found at i:2479115 original size:104 final size:102
Alignment explanation
Indices: 2478848--2479161 Score: 352
Period size: 104 Copynumber: 3.0 Consensus size: 102
2478838 GAATTTACTC
** *
2478848 ATTTTCTGAATCGCATTGCGATTCTTGG-A-ATCGTATTGCGAT-TTTTTTTCTGAATCACGTTG
1 ATTTTCTGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATCTTATTTTC---A--ACGTTG
* *
2478910 CGATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
61 CGATTTTCTAAATCGCGTTGCGATTTTTGGAATCGCGTTGCG
* * *** *
2478952 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTAGAATC-GCGTTGCGAT
1 ATTTTCTGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGA-TCTTATTTTCAACGTTGCGAT
*
2479016 TTTCTGAATCGCGTTGCGATTTTTGGAAGATCGCGTTGCG
65 TTTCTAAATCGCGTTGCGATTTTTGG-A-ATCGCGTTGCG
* * *
2479056 ATTTTATGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATCTTCTTTTCAACGTTGCGCTT
1 ATTTTCTGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATCTTATTTTCAACGTTGCGATT
*
2479121 TTCTAAATCGCGTTGCG-GTTTT-GATATCGCGTTGCG
66 TTCTAAATCGCGTTGCGATTTTTGGA-ATCGCGTTGCG
*
2479157 GTTTT
1 ATTTT
2479162 GTTGATCATT
Statistics
Matches: 179, Mismatches: 24, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
101 16 0.09
102 34 0.19
103 11 0.06
104 102 0.57
105 1 0.01
106 10 0.06
107 1 0.01
108 4 0.02
ACGTcount: A:0.17, C:0.18, G:0.24, T:0.40
Consensus pattern (102 bp):
ATTTTCTGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATCTTATTTTCAACGTTGCGATT
TTCTAAATCGCGTTGCGATTTTTGGAATCGCGTTGCG
Found at i:2479117 original size:42 final size:41
Alignment explanation
Indices: 2478987--2479117 Score: 119
Period size: 42 Copynumber: 3.2 Consensus size: 41
2478977 TGGAAGATCG
* * *
2478987 CGTTGCGATTCTTAG-A-ATCGCGTTGCGATTTTCTGAATC-G
1 CGTTGCGATTCTTGGAAGATCGCGTTGCGA-TTTCT-TATCAA
* *
2479027 CGTTGCGATTTTTGGAAGATCGCGTTGCGA-TT-TTATGAA
1 CGTTGCGATTCTTGGAAGATCGCGTTGCGATTTCTTATCAA
*
2479066 TCGCATTGCGATTCTTGGAAGATCGCGTTGCGATCTTCTTTTCAA
1 -CG--TTGCGATTCTTGGAAGATCGCGTTGCGAT-TTCTTATCAA
2479111 CGTTGCG
1 CGTTGCG
2479118 CTTTTCTAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
38 2 0.03
39 1 0.01
40 17 0.23
41 1 0.01
42 44 0.59
44 4 0.05
45 5 0.07
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTCTTGGAAGATCGCGTTGCGATTTCTTATCAA
Found at i:2479134 original size:20 final size:20
Alignment explanation
Indices: 2478893--2479161 Score: 197
Period size: 20 Copynumber: 13.2 Consensus size: 20
2478883 TTGCGATTTT
* *
2478893 TTTTCTGAATCACGTTGCGA
1 TTTTCTAAATCGCGTTGCGA
*
2478913 TTTTCTTAATCGCGTTGCGA
1 TTTTCTAAATCGCGTTGCGA
**
2478933 TTCTT-GGAATCGCGTTGCGA
1 TT-TTCTAAATCGCGTTGCGA
*
2478953 TTTTCTTAATCGCGTTGCGA
1 TTTTCTAAATCGCGTTGCGA
**
2478973 TTCTTGGAAGATCGCGTTGCGA
1 TT-TTCTAA-ATCGCGTTGCGA
*
2478995 TTCT-TAGAATCGCGTTGCGA
1 TTTTCTA-AATCGCGTTGCGA
*
2479015 TTTTCTGAATCGCGTTGCGA
1 TTTTCTAAATCGCGTTGCGA
2479035 TTTT-TGGAAGATCGCGTTGCGA
1 TTTTCT--AA-ATCGCGTTGCGA
* * *
2479057 TTTTATGAATCGCATTGCGA
1 TTTTCTAAATCGCGTTGCGA
**
2479077 TTCTTGGAAGATCGCGTTGCGA
1 TT-TTCTAA-ATCGCGTTGCGA
* ** * *
2479099 TCTTCT-TTTCAACGTTGCGC
1 TTTTCTAAATC-GCGTTGCGA
*
2479119 TTTTCTAAATCGCGTTGCGG
1 TTTTCTAAATCGCGTTGCGA
* * *
2479139 TTTT-GATATCGCGTTGCGG
1 TTTTCTAAATCGCGTTGCGA
2479158 TTTT
1 TTTT
2479162 GTTGATCATT
Statistics
Matches: 201, Mismatches: 34, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
19 22 0.11
20 119 0.59
21 17 0.08
22 42 0.21
23 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.40
Consensus pattern (20 bp):
TTTTCTAAATCGCGTTGCGA
Found at i:2481191 original size:16 final size:15
Alignment explanation
Indices: 2481158--2481204 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
2481148 TTGAATACTT
2481158 AAAAATACATTTT-AA
1 AAAAATA-ATTTTAAA
2481173 AAAAATAATTTTAAGA
1 AAAAATAATTTTAA-A
2481189 AAAAATAATTTTAAA
1 AAAAATAATTTTAAA
2481204 A
1 A
2481205 GATAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.17
15 10 0.33
16 15 0.50
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
AAAAATAATTTTAAA
Found at i:2483352 original size:45 final size:45
Alignment explanation
Indices: 2483319--2483412 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 45
2483309 TTCAAGGAAG
2483319 ACAACACTGAAATATTGACTCCTCTACACGAGAAAGTCAAGAATA
1 ACAACACTGAAATATTGACTCCTCTACACGAGAAAGTCAAGAATA
* * * * * * *
2483364 ATAATACTGAGATATTGACTTCTCTTCACGAGGAAGTCGAGAATA
1 ACAACACTGAAATATTGACTCCTCTACACGAGAAAGTCAAGAATA
2483409 ACAA
1 ACAA
2483413 AGATTGACTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.23
Consensus pattern (45 bp):
ACAACACTGAAATATTGACTCCTCTACACGAGAAAGTCAAGAATA
Found at i:2483419 original size:38 final size:38
Alignment explanation
Indices: 2483377--2483724 Score: 449
Period size: 38 Copynumber: 9.2 Consensus size: 38
2483367 ATACTGAGAT
2483377 ATTGACTTCTCTTCACGAGGAAGTC-GAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAG-GAATAACAAAG
*
2483415 ATTGACTTCTTTTCACGAGGAAGTC-GAGAATAAC-AAG
1 ATTGACTTCTCTTCACGAGGAAGTCAG-GAATAACAAAG
**
2483452 ATTGAC-TCATCTT-TGGAGG-AGTCAGGAATAACAAAG
1 ATTGACTTC-TCTTCACGAGGAAGTCAGGAATAACAAAG
* * * *
2483488 ATTGACTTCTCTTCACGAGGAAGTTAAGAATAAAAAAT
1 ATTGACTTCTCTTCACGAGGAAGTCAGGAATAACAAAG
*
2483526 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAGGAATAACAAAG
* *
2483564 ATTGAC-TCATCTTCGCGAGGGAGTCAGGAATAACAAAG
1 ATTGACTTC-TCTTCACGAGGAAGTCAGGAATAACAAAG
* * *
2483602 ATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAGGAATAACAAAG
* * *
2483640 ATTGACTTCTCTTCGCGAGGGAGTCATGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAGGAATAACAAAG
* *
2483678 ATTGACTTCTCTTCACGAGGAAGTCATGAATAACAGAG
1 ATTGACTTCTCTTCACGAGGAAGTCAGGAATAACAAAG
2483716 ATTGACTTC
1 ATTGACTTC
2483725 CTCGTGACAA
Statistics
Matches: 280, Mismatches: 22, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
35 11 0.04
36 20 0.07
37 20 0.07
38 228 0.81
39 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (38 bp):
ATTGACTTCTCTTCACGAGGAAGTCAGGAATAACAAAG
Found at i:2483861 original size:169 final size:172
Alignment explanation
Indices: 2483573--2484082 Score: 492
Period size: 189 Copynumber: 2.9 Consensus size: 172
2483563 GATTGACTCA
* * * * *
2483573 TCTTCGCGAGGGAGTCAGGAATAACAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAA
1 TCTTCACGAGGAAGTCAAGAATAAC-AAGATTGAATCATCTTCGCGAGGGAGTCAGGAATAACAA
* * * *
2483638 AGATTGACTTCTCTTCGCGAGGGAGTCATGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTC
65 AGATTAACTCCTCTTCACGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTC
* *
2483703 ATGAATAACAGAGATTGACTTCCTCGTGACAAAGACTAACTTC
130 AAGAATAACAAAGATTGACTTCCTCGTGACAAAGACTAACTTC
*
2483746 TCTTCACGAGGAAGTCAAGAATAAC-AGATTGAATCATTTTCGCGAGGGAGTCA-GAATAACAAA
1 TCTTCACGAGGAAGTCAAGAATAACAAGATTGAATCATCTTCGCGAGGGAGTCAGGAATAACAAA
* *
2483809 GATTAACTCCTCTTCACGA-TGAGTCAGGAGTAACAAAGATTGACTTCTCTTCACGAGGAAGTCA
66 GATTAACTCCTCTTCACGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCA
* * *
2483873 AGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCGAGAATAACAAAGATTGACTCC
131 AGAATAACAAAGATTGACTTC-C-T--C------GT---G----ACAAAGACTAACTTC
* * * * * * *
2483932 TTTTTACGAGGGAGTCAGGAATAACAAAGATT-AACTTC-TCTTCACGAGGAAGTCAAGAATAAC
1 TCTTCACGAGGAAGTCAAGAATAAC-AAGATTGAA--TCATCTTCGCGAGGGAGTCAGGAATAAC
* * * * * * * *
2483995 AAAGACTGACTTCTC-TCACGAGGAAGTCATGAATAACAAATATTGACTTCTCTTCATGAGTAAG
63 AAAGATTAACTCCTCTTCACGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAG
*
2484059 TTAAGAATAACAAAGATTGACTTC
128 TCAAGAATAACAAAGATTGACTTC
2484083 TCTTCACGAG
Statistics
Matches: 279, Mismatches: 35, Indels: 30
0.81 0.10 0.09
Matches are distributed among these distances:
169 61 0.22
170 27 0.10
171 26 0.09
173 23 0.08
179 2 0.01
182 1 0.00
186 33 0.12
187 2 0.01
188 25 0.09
189 79 0.28
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25
Consensus pattern (172 bp):
TCTTCACGAGGAAGTCAAGAATAACAAGATTGAATCATCTTCGCGAGGGAGTCAGGAATAACAAA
GATTAACTCCTCTTCACGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCA
AGAATAACAAAGATTGACTTCCTCGTGACAAAGACTAACTTC
Found at i:2483881 original size:38 final size:38
Alignment explanation
Indices: 2483731--2484101 Score: 475
Period size: 38 Copynumber: 9.9 Consensus size: 38
2483721 CTTCCTCGTG
* *
2483731 ACAAAGACTAACTTCTCTTCACGAGGAAGTCAAGAATA
1 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATA
* * * *
2483769 AC--AGATTGA-ATCATTTTCGCGAGGGAGTC-AGAATA
1 ACAAAGATTGACTTC-TCTTCACGAGGAAGTCAAGAATA
* * * * *
2483804 ACAAAGATTAACTCCTCTTCACGATG-AGTCAGGAGTA
1 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATA
2483841 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATA
1 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATA
*
2483879 ACAAAGATTGACTTCTCTTCACGAGGAAGTCGAGAATA
1 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATA
* * * * *
2483917 ACAAAGATTGACTCCTTTTTACGAGGGAGTCAGGAATA
1 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATA
*
2483955 ACAAAGATTAACTTCTCTTCACGAGGAAGTCAAGAATA
1 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATA
* *
2483993 ACAAAGACTGACTTCTC-TCACGAGGAAGTCATGAATA
1 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATA
* * * *
2484030 ACAAATATTGACTTCTCTTCATGAGTAAGTTAAGAATA
1 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATA
2484068 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAG
1 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAG
2484102 TTGAAGTTTC
Statistics
Matches: 281, Mismatches: 45, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
35 10 0.04
36 22 0.08
37 75 0.27
38 174 0.62
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (38 bp):
ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATA
Found at i:2483889 original size:207 final size:210
Alignment explanation
Indices: 2483530--2484101 Score: 681
Period size: 207 Copynumber: 2.7 Consensus size: 210
2483520 AAAAATATTG
*
2483530 ACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTCATCTTCGCGAGGGAGTCAGGAAT
1 ACTTCTCTTCACGAGGAAGTCAAGAATAAC-AAGATTGAATCATCTTCGCGAGGGAGTCAGGAAT
* * *
2483595 AACAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCGCGAGG
65 AACAAAGATTAACTCCTCTTCACGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGG
* * *
2483660 GAGTCATGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTC-ATGAATAACAGAGATTGACTT
130 AAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCGA-GAATAACAAAGATTGACTT
2483724 CCTCGTGACAAAGACTA
194 CCTCGTGACAAAGACTA
*
2483741 ACTTCTCTTCACGAGGAAGTCAAGAATAAC-AGATTGAATCATTTTCGCGAGGGAGTCA-GAATA
1 ACTTCTCTTCACGAGGAAGTCAAGAATAACAAGATTGAATCATCTTCGCGAGGGAGTCAGGAATA
* *
2483804 ACAAAGATTAACTCCTCTTCACGA-TGAGTCAGGAGTAACAAAGATTGACTTCTCTTCACGAGGA
66 ACAAAGATTAACTCCTCTTCACGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGA
2483868 AGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCGAGAATAACAAAGATTGAC-TCC
131 AGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCGAGAATAACAAAGATTGACTTCC
*
2483932 TTTTTACGAGGGAGTCAGGAATAACAAAGATTA
196 ----T-C------GT---G----ACAAAGACTA
* * * * *
2483965 ACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGACTG-A-CTTCTCTCACGAGGAAGTCATGAA
1 ACTTCTCTTCACGAGGAAGTCAAGAATAAC-AAGATTGAATCATCT-TCGCGAGGGAGTCAGGAA
* * * * ** * *
2484028 TAACAAATATTGACTTCTCTTCATGAGTAAGTTAAGAATAACAAAGATTGACTTCTCTTCACGAG
64 TAACAAAGATTAACTCCTCTTCACGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAG
2484093 GAAGTCAAG
129 GAAGTCAAG
2484102 TTGAAGTTTC
Statistics
Matches: 313, Mismatches: 24, Indels: 32
0.85 0.07 0.09
Matches are distributed among these distances:
206 3 0.01
207 93 0.30
208 28 0.09
209 26 0.08
210 1 0.00
211 31 0.10
217 2 0.01
220 1 0.00
224 42 0.13
225 13 0.04
226 30 0.10
227 43 0.14
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (210 bp):
ACTTCTCTTCACGAGGAAGTCAAGAATAACAAGATTGAATCATCTTCGCGAGGGAGTCAGGAATA
ACAAAGATTAACTCCTCTTCACGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGA
AGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCGAGAATAACAAAGATTGACTTCC
TCGTGACAAAGACTA
Found at i:2484018 original size:151 final size:150
Alignment explanation
Indices: 2483731--2484099 Score: 519
Period size: 151 Copynumber: 2.5 Consensus size: 150
2483721 CTTCCTCGTG
* * * * *
2483731 ACAAAGACTAACTTCTCTTCACGAGGAAGTCAAGAATAAC--AGATTGAATCATTTTCGCGAGGG
1 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTCCTTTTCACGAGGG
* * * *
2483794 AGTCAGAATAACAAAGATTAACTCCTCTTCACGATGAGTCAGGAGTAACAAAGATTGACTTCTCT
66 AGTCAGAATAACAAAGATTAACTCCTCTTCACGAGGAGTCAAGAATAACAAAGACTGACTTCTCT
2483859 TCACGAGGAAGTCAAGAATA
131 TCACGAGGAAGTCAAGAATA
* *
2483879 ACAAAGATTGACTTCTCTTCACGAGGAAGTCGAGAATAACAAAGATTGACTCCTTTTTACGAGGG
1 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTCCTTTTCACGAGGG
*
2483944 AGTCAGGAATAACAAAGATTAACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGACTGACTTCT
66 AGTCA-GAATAACAAAGATTAACTCCTCTTCACGAGG-AGTCAAGAATAACAAAGACTGACTTCT
*
2484009 C-TCACGAGGAAGTCATGAATA
129 CTTCACGAGGAAGTCAAGAATA
* * * * * * *
2484030 ACAAATATTGACTTCTCTTCATGAGTAAGTTAAGAATAACAAAGATTGACTTCTCTTCACGAGGA
1 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTCCTTTTCACGAGGG
2484095 AGTCA
66 AGTCA
2484100 AGTTGAAGTT
Statistics
Matches: 195, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
148 37 0.19
150 24 0.12
151 109 0.56
152 25 0.13
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (150 bp):
ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTCCTTTTCACGAGGG
AGTCAGAATAACAAAGATTAACTCCTCTTCACGAGGAGTCAAGAATAACAAAGACTGACTTCTCT
TCACGAGGAAGTCAAGAATA
Found at i:2484082 original size:113 final size:112
Alignment explanation
Indices: 2483731--2484101 Score: 500
Period size: 113 Copynumber: 3.3 Consensus size: 112
2483721 CTTCCTCGTG
* *
2483731 ACAAAGACTAACTTCTCTTCACGAGGAAGTCAAGAATAAC--AGATTGAATCATT-T-TCGCGAG
1 ACAAAGATTAACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTG-A-C-TTCTCTCACGAG
* * *
2483792 GGAGTCAGAATAACAAAGATTAACTCCTCTTCACGA-TGAGTCAGGAGTA
63 GAAGTCAGAATAACAAAGATTGACTCCTCTTCACGAGTGAGTCAGGAATA
*
2483841 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGA
1 ACAAAGATTAACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTC-TCACGAGGA
* * *
2483906 AGTCGAGAATAACAAAGATTGACTCCTTTTTACGAGGGAGTCAGGAATA
65 AGTC-AGAATAACAAAGATTGACTCCTCTTCACGAGTGAGTCAGGAATA
*
2483955 ACAAAGATTAACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGACTGACTTCTCTCACGAGGAA
1 ACAAAGATTAACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTCACGAGGAA
* * * * * *
2484020 GTCATGAATAACAAATATTGACTTCTCTTCATGAGTAAGTTAAGAATA
66 GTCA-GAATAACAAAGATTGACTCCTCTTCACGAGTGAGTCAGGAATA
*
2484068 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAG
1 ACAAAGATTAACTTCTCTTCACGAGGAAGTCAAG
2484102 TTGAAGTTTC
Statistics
Matches: 232, Mismatches: 21, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
109 2 0.01
110 40 0.17
111 1 0.00
112 18 0.08
113 107 0.46
114 64 0.28
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (112 bp):
ACAAAGATTAACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTCACGAGGAA
GTCAGAATAACAAAGATTGACTCCTCTTCACGAGTGAGTCAGGAATA
Found at i:2493815 original size:22 final size:21
Alignment explanation
Indices: 2493785--2493825 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2493775 GATGAAGCTG
*
2493785 AAAAGATATATTAAAATAAAAT
1 AAAAAATATA-TAAAATAAAAT
*
2493807 AAAAAATATATATAATAAA
1 AAAAAATATATAAAATAAA
2493826 TATTATAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAAAATATATAAAATAAAAT
Found at i:2494634 original size:68 final size:68
Alignment explanation
Indices: 2494508--2494634 Score: 179
Period size: 68 Copynumber: 1.9 Consensus size: 68
2494498 TAAAACATCT
*
2494508 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAAAAATAATAATATAATA
1 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCAAAAAAAATAATAATATAATA
2494573 TTC
66 TTC
* *
2494576 TAAATCTTAATTAAAATAC-TAAAACCTATTTAAACTAAAATA-CAAAGATAAAAT-ATAAT
1 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCAAA-A-AAAATAATAAT
2494635 GTTTAAAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
67 8 0.15
68 40 0.75
69 5 0.09
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.31
Consensus pattern (68 bp):
TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCAAAAAAAATAATAATATAATA
TTC
Found at i:2496141 original size:36 final size:36
Alignment explanation
Indices: 2496100--2496179 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
2496090 AATCGAATTA
* *
2496100 AACGGGGATAGG-GAAAAATTATTTATGCTAAACGGG
1 AACGGGGAT-GGAGAAAAATCATTTATACTAAACGGG
* * *
2496136 GACGGGGATGGAGAAAAATCGTTTATATTAAACGGG
1 AACGGGGATGGAGAAAAATCATTTATACTAAACGGG
2496172 AACGGGGA
1 AACGGGGA
2496180 CAAGTTTAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
35 2 0.05
36 35 0.95
ACGTcount: A:0.38, C:0.09, G:0.34, T:0.20
Consensus pattern (36 bp):
AACGGGGATGGAGAAAAATCATTTATACTAAACGGG
Found at i:2500110 original size:14 final size:14
Alignment explanation
Indices: 2500091--2500128 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2500081 TGAGGTATTT
2500091 TGTTTAGGGTTTAG
1 TGTTTAGGGTTTAG
*
2500105 TGTTTAGAGTTTAG
1 TGTTTAGGGTTTAG
2500119 -GATTTAGGGT
1 TG-TTTAGGGT
2500129 GTGTTCCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 1 0.05
14 20 0.95
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.47
Consensus pattern (14 bp):
TGTTTAGGGTTTAG
Found at i:2500697 original size:2 final size:2
Alignment explanation
Indices: 2500690--2500731 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2500680 TTTATTCTAT
2500690 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2500732 CGTGTGTGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2504983 original size:22 final size:21
Alignment explanation
Indices: 2504958--2505002 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2504948 AGACAATCCC
2504958 TTATCATAATTAATGAGATGTT
1 TTATC-TAATTAATGAGATGTT
* *
2504980 TTATCTCATTAATTAGATGTT
1 TTATCTAATTAATGAGATGTT
2505001 TT
1 TT
2505003 CTGGTCGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.51
Consensus pattern (21 bp):
TTATCTAATTAATGAGATGTT
Found at i:2505223 original size:76 final size:77
Alignment explanation
Indices: 2505092--2505246 Score: 267
Period size: 76 Copynumber: 2.0 Consensus size: 77
2505082 TCTGTCACGA
*
2505092 ATCAAGTGATCTTTATAATAAAATAATAATTATTATTTTTTGAGGACTTAAGTTCGAGCACAATA
1 ATCAAGTGATCTTTATAATAAAAGAATAATTATTATTTTTTGAGGACTTAAGTTCGAGCACAATA
*
2505157 GATGACAGTGGT
66 GATGACAGGGGT
**
2505169 ATCAAGTGATCTTTATAAT-AAAGAATTGTTATTATTTTTTGAGGACTTAAGTTCGAGCACAATA
1 ATCAAGTGATCTTTATAATAAAAGAATAATTATTATTTTTTGAGGACTTAAGTTCGAGCACAATA
2505233 GATGACAGGGGT
66 GATGACAGGGGT
2505245 AT
1 AT
2505247 GAGCGTTCAA
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
76 55 0.74
77 19 0.26
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (77 bp):
ATCAAGTGATCTTTATAATAAAAGAATAATTATTATTTTTTGAGGACTTAAGTTCGAGCACAATA
GATGACAGGGGT
Found at i:2511985 original size:28 final size:28
Alignment explanation
Indices: 2511945--2512003 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
2511935 CGATGGTAGA
2511945 ATTCAAACTTAACCTTA-ACATTTCAACC
1 ATTCAAACTTAACCTTAGA-ATTTCAACC
2511973 ATTCAAACTTAACCTTAGAATTTCAACC
1 ATTCAAACTTAACCTTAGAATTTCAACC
2512001 ATT
1 ATT
2512004 TGTGCCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.34
Consensus pattern (28 bp):
ATTCAAACTTAACCTTAGAATTTCAACC
Found at i:2513700 original size:3 final size:3
Alignment explanation
Indices: 2513692--2513728 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
2513682 ATTTTTTCAG
2513692 ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2513729 AAATTAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2517237 original size:16 final size:14
Alignment explanation
Indices: 2517208--2517236 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2517198 TCCAAAAAAC
2517208 TCAAAATTTATATA
1 TCAAAATTTATATA
2517222 TCAAAATTTATATA
1 TCAAAATTTATATA
2517236 T
1 T
2517237 AGATATTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (14 bp):
TCAAAATTTATATA
Found at i:2523405 original size:2 final size:2
Alignment explanation
Indices: 2523398--2523457 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
2523388 TGGGTAGTTG
2523398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2523440 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
2523458 GTTTCGACAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2526599 original size:75 final size:75
Alignment explanation
Indices: 2526509--2526757 Score: 337
Period size: 75 Copynumber: 3.4 Consensus size: 75
2526499 AACTTAATCG
** * *
2526509 GTTAAAATAAAATAGGCGCTACCTATTATATTAAACTACCTACTGATTTGTTTGAAGGTTACTAA
1 GTTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGGTTTGTTTAAAGGTTACTAA
2526574 TAATGTAAAC
66 TAATGTAAAC
* * * * *
2526584 GTTAAAACATAATAGGTGCTA---ATTACGTTAAAATATCTA-TCGGTTTGTTTAAAGGTTACTA
1 GTTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACT-GGTTTGTTTAAAGGTTACTA
2526645 ATAATGTAAAC
65 ATAATGTAAAC
* * *
2526656 GGTAAAATAAAATAGGCACTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAA
1 GTTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGGTTTGTTTAAAGGTTACTAA
2526721 TAATGTAAAC
66 TAATGTAAAC
2526731 AG-TAAAATAAAATAGGCGCTACCTATT
1 -GTTAAAATAAAATAGGCGCTACCTATT
2526758 GTTGAAAACA
Statistics
Matches: 150, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
71 1 0.01
72 59 0.39
75 89 0.59
76 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (75 bp):
GTTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGGTTTGTTTAAAGGTTACTAA
TAATGTAAAC
Found at i:2533067 original size:20 final size:20
Alignment explanation
Indices: 2533041--2533090 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
2533031 CTGCTAGCAT
2533041 CATTAAAATCGTGCAAACAA
1 CATTAAAATCGTGCAAACAA
*
2533061 TATTAAAATCGTGCAAACAA
1 CATTAAAATCGTGCAAACAA
*
2533081 CATCAAAATC
1 CATTAAAATC
2533091 CACTCAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.50, C:0.20, G:0.08, T:0.22
Consensus pattern (20 bp):
CATTAAAATCGTGCAAACAA
Found at i:2536708 original size:154 final size:154
Alignment explanation
Indices: 2536429--2536895 Score: 697
Period size: 154 Copynumber: 3.0 Consensus size: 154
2536419 AGGTTAATAA
* * * *
2536429 TAATGTAAACGGTAAAATATATACAATTTGATCGTTTGAAATA-ATTTTTTAAAATTCGAAAGTA
1 TAATGTAAACGGTAAAATATATACAACTTAATAGTTTGAAATATTTTTTTTAAAATTCGAAAGTA
* *
2536493 TGGATACTTACTCTAAAAGTATGGATACTCTAAAGTTTGATAATAATGTATCCATACTTACTCTA
66 TGGATACTTACTCTAAAAGTATGGATACTCTAAAGTTTAATAATAATGTATCTATACTTACTCTA
*
2536558 AAAGTATGGATATTGTTTCGACAG
131 AAAGTATGAATATTGTTTCGACAG
2536582 TAATGTAAACGGTAAAATATATACAACTTAATAGTTTGAAATATTTTTTTTAAAATTCGAAAGTA
1 TAATGTAAACGGTAAAATATATACAACTTAATAGTTTGAAATATTTTTTTTAAAATTCGAAAGTA
* * * *
2536647 TGGATATTTACTCTAAAAGTATGAATACTTTAAAATTTAATAATAATGTATCTATACTTACTCTA
66 TGGATACTTACTCTAAAAGTATGGATACTCTAAAGTTTAATAATAATGTATCTATACTTACTCTA
2536712 AAAGTATGAATATTGTTTCGACAG
131 AAAGTATGAATATTGTTTCGACAG
* * * * *
2536736 TAATTTTAAACGGTAAAATATATACAAGTTAACCA-TTTGAAATCTTTTTTTTTTTAAATTCGAA
1 TAA-TGTAAACGGTAAAATATATACAACTTAA-TAGTTTGAAA--TATTTTTTTTAAAATTCGAA
*
2536800 AGTATGGATACTTACTCTAAAAGTATGGATACTCTAAAGGTTAATAATAATGTAT-TCATACTTA
62 AGTATGGATACTTACTCTAAAAGTATGGATACTCTAAAGTTTAATAATAATGTATCT-ATACTTA
* *
2536864 CTCCAAAAGTATGAATAATGTTTCGACAG
126 CTCTAAAAGTATGAATATTGTTTCGACAG
2536893 TAA
1 TAA
2536896 GTTATGTCCA
Statistics
Matches: 285, Mismatches: 23, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
153 40 0.14
154 105 0.37
155 33 0.12
156 2 0.01
157 105 0.37
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (154 bp):
TAATGTAAACGGTAAAATATATACAACTTAATAGTTTGAAATATTTTTTTTAAAATTCGAAAGTA
TGGATACTTACTCTAAAAGTATGGATACTCTAAAGTTTAATAATAATGTATCTATACTTACTCTA
AAAGTATGAATATTGTTTCGACAG
Found at i:2537270 original size:118 final size:118
Alignment explanation
Indices: 2537060--2537304 Score: 330
Period size: 118 Copynumber: 2.1 Consensus size: 118
2537050 AAAAAAATCA
** * * *
2537060 AGTAATTAACCTATTTTGTTATCGTCGGCTTTCTAAGGCCCCATCAACTTTAAACATGCGCTATC
1 AGTAATTAACCTATTTTGTTATCGTCGAATTTATAAGGCCCCATCAACTTTAAAAATGCACTATC
* * *
2537125 TATTACATTAAATAAGTATTACTTGTTATGTTATTATGGTTAATAATGTTTCC
66 TATTACATTAAATAAGCACTACCTGTTATGTTATTATGGTTAATAATGTTTCC
* * *
2537178 AGTAATTAACCTATTTTGTTATCGTCGAATTTATAATGCTCCATCAGCTTTAAAAATGCACTA-C
1 AGTAATTAACCTATTTTGTTATCGTCGAATTTATAAGGCCCCATCAACTTTAAAAATGCACTATC
* * * *
2537242 TTATTACGTTACATAAGCGCTACCTGTTATGTTATTATGGTTGATAATGTTTCC
66 -TATTACATTAAATAAGCACTACCTGTTATGTTATTATGGTTAATAATGTTTCC
*
2537296 AATAATTAA
1 AGTAATTAA
2537305 TCGGTTATGT
Statistics
Matches: 110, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
117 1 0.01
118 109 0.99
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (118 bp):
AGTAATTAACCTATTTTGTTATCGTCGAATTTATAAGGCCCCATCAACTTTAAAAATGCACTATC
TATTACATTAAATAAGCACTACCTGTTATGTTATTATGGTTAATAATGTTTCC
Found at i:2547086 original size:50 final size:50
Alignment explanation
Indices: 2547011--2547128 Score: 182
Period size: 50 Copynumber: 2.4 Consensus size: 50
2547001 TTTTATAGTA
* *
2547011 TTATTGGAAATCGTCACGTTAATATGAAGAGTTTAAATAAAAATATTTTT
1 TTATTCGAAATCGTCACGTCAATATGAAGAGTTTAAATAAAAATATTTTT
* * *
2547061 TTATTCGAATTCGTCACGTCGATATGATGAGTTTAAATAAAAATATTTTT
1 TTATTCGAAATCGTCACGTCAATATGAAGAGTTTAAATAAAAATATTTTT
*
2547111 TTATTCGAACTCGTCACG
1 TTATTCGAAATCGTCACG
2547129 CTGAGGTGAC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (50 bp):
TTATTCGAAATCGTCACGTCAATATGAAGAGTTTAAATAAAAATATTTTT
Found at i:2547143 original size:50 final size:50
Alignment explanation
Indices: 2547011--2547149 Score: 163
Period size: 50 Copynumber: 2.8 Consensus size: 50
2547001 TTTTATAGTA
* * ** * *
2547011 TTATTGGAAATCGTCACGTTAATATGAAGAGTTTAAATAAAAATATTTTT
1 TTATTCGAACTCGTCACGTCGAGATGACGAGTTTAAATAAAAATATTTTT
* * *
2547061 TTATTCGAATTCGTCACGTCGATATGATGAGTTTAAATAAAAATATTTTT
1 TTATTCGAACTCGTCACGTCGAGATGACGAGTTTAAATAAAAATATTTTT
* *
2547111 TTATTCGAACTCGTCACG-CTGAGGTGACGAGTTTGAATA
1 TTATTCGAACTCGTCACGTC-GAGATGACGAGTTTAAATA
2547150 GAATATAATG
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
49 1 0.01
50 77 0.99
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (50 bp):
TTATTCGAACTCGTCACGTCGAGATGACGAGTTTAAATAAAAATATTTTT
Found at i:2558298 original size:20 final size:20
Alignment explanation
Indices: 2558269--2558326 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
2558259 GGATGCACTG
*
2558269 ATGCACCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
2558289 ATGCATCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
2558309 ATGCATCGATGCACCAAT
1 ATGCATCGATGCACCAAT
2558327 GAATAAATTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.31, C:0.34, G:0.16, T:0.19
Consensus pattern (20 bp):
ATGCATCGATGCACCAATCC
Found at i:2564188 original size:21 final size:22
Alignment explanation
Indices: 2564159--2564216 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
2564149 TGCATCCCTT
2564159 TGAATGTGCATCGATACAC-CA
1 TGAATGTGCATCGATACACTCA
* * * * *
2564180 TGAAGGTGCACCAATGCACTCT
1 TGAATGTGCATCGATACACTCA
2564202 TGAATGTGCATCGAT
1 TGAATGTGCATCGAT
2564217 GCACAAGGAC
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (22 bp):
TGAATGTGCATCGATACACTCA
Found at i:2564210 original size:22 final size:21
Alignment explanation
Indices: 2564140--2564220 Score: 81
Period size: 22 Copynumber: 3.7 Consensus size: 21
2564130 ACACTTAACA
2564140 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCA--CC-TTGAAT
* * *
2564164 GTGCATCGATACACCATGAAG
1 GTGCATCGATGCACCTTGAAT
* *
2564185 GTGCACCAATGCACTCTTGAAT
1 GTGCATCGATGCAC-CTTGAAT
2564207 GTGCATCGATGCAC
1 GTGCATCGATGCAC
2564221 AAGGACATGC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
21 15 0.33
22 19 0.41
24 12 0.26
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (21 bp):
GTGCATCGATGCACCTTGAAT
Found at i:2566873 original size:20 final size:20
Alignment explanation
Indices: 2566844--2566881 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2566834 TTTCAAAGGG
*
2566844 ATGCACCGATGCATCAATCC
1 ATGCACCGATGCACCAATCC
*
2566864 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
2566882 GAATAAATTG
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:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:2566968 original size:65 final size:64
Alignment explanation
Indices: 2566892--2567071 Score: 206
Period size: 65 Copynumber: 2.8 Consensus size: 64
2566882 GAATAAATTG
* *
2566892 AACATCGAATGCAATTTATGCATTGATGTACTCTCCATGCATCGATGCACTCAGG-T-TTTAATG
1 AACATCGAATGCAATTTATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGCTATTT--TG
2566955 AA
64 -A
** *
2566957 AACATCGAATGC-ATTTGATGCATCGATGCACAATCCATGCATCGATGAACTCAGGCTATTTTGA
1 AACATCGAATGCAATTT-ATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGCTATTTTGA
* * * *
2567021 AACATCGAATGCACTTCATGCATCGATGCACTCT-TAGTGCACCGATGCACT
1 AACATCGAATGCAATTTATGCATCGATGCACTCTCCA-TGCATCGATGCACT
2567072 AAGGGTCCAA
Statistics
Matches: 98, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
63 1 0.01
64 44 0.45
65 49 0.50
66 1 0.01
67 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCAATTTATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGCTATTTTGA
Found at i:2567049 original size:64 final size:63
Alignment explanation
Indices: 2566844--2567051 Score: 206
Period size: 65 Copynumber: 3.2 Consensus size: 63
2566834 TTTCAAAGGG
* * **
2566844 ATGCACCGATGCATCAATCCATGCATCGATGCAC-CAATGAATAAATTG-AACATCGAATGCAAT
1 ATGCATCGATGCA-CAATCCATGCATCGATGCACTC-A-G-GTATTTTGAAACATCGAATGCAAT
*
2566907 TT
62 TC
* * ** *
2566909 ATGCATTGATGTACTCTCCATGCATCGATGCACTCAGGT-TTTAATGAAAACATCGAATGCATTT
1 ATGCATCGATGCACAATCCATGCATCGATGCACTCAGGTATTT--TG-AAACATCGAATGCAATT
*
2566973 G
63 C
* *
2566974 ATGCATCGATGCACAATCCATGCATCGATGAACTCAGGCTATTTTGAAACATCGAATGCACTTC
1 ATGCATCGATGCACAATCCATGCATCGATGCACTCAGG-TATTTTGAAACATCGAATGCAATTC
2567038 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2567052 TCTTAGTGCA
Statistics
Matches: 119, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
63 3 0.03
64 49 0.41
65 61 0.51
66 1 0.01
67 3 0.03
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (63 bp):
ATGCATCGATGCACAATCCATGCATCGATGCACTCAGGTATTTTGAAACATCGAATGCAATTC
Found at i:2567051 original size:17 final size:19
Alignment explanation
Indices: 2567023--2567071 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2567013 TATTTTGAAA
2567023 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
2567041 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
2567060 CACCGATGCACT
1 CATCGATGCACT
2567072 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:2568159 original size:29 final size:28
Alignment explanation
Indices: 2568122--2568263 Score: 185
Period size: 29 Copynumber: 4.9 Consensus size: 28
2568112 GTTGACTGAA
2568122 TGATATTTTCGTAATTATTTTTAAAATGG
1 TGATATTTTCGTAATTATTTTTAAAA-GG
* *
2568151 TGCTATTTTTGTAATTATTTTTAAAAGGG
1 TGATATTTTCGTAATTATTTTTAAAA-GG
*
2568180 TGATATTTTTCATAATTATTTTTAAAAGG
1 TGATA-TTTTCGTAATTATTTTTAAAAGG
* * *
2568209 TGATAGTTTCGTAATTATATTTAAAAGA
1 TGATATTTTCGTAATTATTTTTAAAAGG
*
2568237 TGATATTTTCGTAAATATTTCTTAAAA
1 TGATATTTTCGTAATTATTT-TTAAAA
2568264 AAAAGGTGAT
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
28 36 0.37
29 43 0.44
30 19 0.19
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (28 bp):
TGATATTTTCGTAATTATTTTTAAAAGG
Found at i:2576626 original size:12 final size:12
Alignment explanation
Indices: 2576609--2576633 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2576599 ACAAAGCACC
2576609 ATTTGGTGCCTA
1 ATTTGGTGCCTA
2576621 ATTTGGTGCCTA
1 ATTTGGTGCCTA
2576633 A
1 A
2576634 ATTATTTGAC
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:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:2582271 original size:43 final size:43
Alignment explanation
Indices: 2582197--2582287 Score: 146
Period size: 43 Copynumber: 2.1 Consensus size: 43
2582187 TCAATAAAAG
2582197 ATTGAAAGTGGGAAAATGAGTTGCTGCATTGAAACTAAAGGTT
1 ATTGAAAGTGGGAAAATGAGTTGCTGCATTGAAACTAAAGGTT
* * * *
2582240 ATTGAAAGTGGGAAAATGTGTTGTTGTATTGAAGCTAAAGGTT
1 ATTGAAAGTGGGAAAATGAGTTGCTGCATTGAAACTAAAGGTT
2582283 ATTGA
1 ATTGA
2582288 GATTAGTGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (43 bp):
ATTGAAAGTGGGAAAATGAGTTGCTGCATTGAAACTAAAGGTT
Found at i:2587562 original size:36 final size:35
Alignment explanation
Indices: 2587515--2587586 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
2587505 AAGGAATTTT
*
2587515 AAGGGTACCGATACCTTGAAGAACAATATCGATACC
1 AAGGGTACCGATACCTTAAAGAA-AATATCGATACC
**
2587551 AAGGGTACCGATACCTTAAAGAAGGTATCGATACC
1 AAGGGTACCGATACCTTAAAGAAAATATCGATACC
2587586 A
1 A
2587587 TCTTTGAACG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.33
36 22 0.67
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (35 bp):
AAGGGTACCGATACCTTAAAGAAAATATCGATACC
Found at i:2589160 original size:21 final size:21
Alignment explanation
Indices: 2589134--2589178 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2589124 GAGTTCTGGG
* *
2589134 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2589155 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2589176 CAA
1 CAA
2589179 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2590070 original size:31 final size:31
Alignment explanation
Indices: 2590032--2590156 Score: 180
Period size: 31 Copynumber: 4.0 Consensus size: 31
2590022 AGGGTCGAGG
*
2590032 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
2590063 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
2590094 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
2590125 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
2590156 G
1 G
2590157 GTCCTTCGGG
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
31 83 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:2591189 original size:2 final size:2
Alignment explanation
Indices: 2591182--2591212 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2591172 TGTAACCATA
2591182 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2591213 AATAAATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2591723 original size:36 final size:35
Alignment explanation
Indices: 2591658--2591727 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
2591648 TGTTCAAAGA
2591658 TGGTATCGATAGCTTCCTTAAGGTATCAGTACCCT
1 TGGTATCGATAGCTTCCTTAAGGTATCAGTACCCT
*
2591693 TGGTATCGATA-CTGTTCTTCAAGGTATCAGTACCC
1 TGGTATCGATAGCT-TCCTT-AAGGTATCAGTACCC
2591728 CTTAAATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 2 0.06
35 15 0.47
36 15 0.47
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (35 bp):
TGGTATCGATAGCTTCCTTAAGGTATCAGTACCCT
Found at i:2592839 original size:35 final size:36
Alignment explanation
Indices: 2592793--2592862 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 36
2592783 CCTTCAAAGA
2592793 TGGTATCGATACCT-TCCTT-AAGGTATCGGTACCCT
1 TGGTATCGATA-CTGTCCTTCAAGGTATCGGTACCCT
*
2592828 TGGTATCGATACTGTTCTTCAAGGTATCGGTACCC
1 TGGTATCGATACTGTCCTTCAAGGTATCGGTACCC
2592863 CTTAAATTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 2 0.06
35 15 0.47
36 15 0.47
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.34
Consensus pattern (36 bp):
TGGTATCGATACTGTCCTTCAAGGTATCGGTACCCT
Found at i:2606898 original size:19 final size:19
Alignment explanation
Indices: 2606870--2606909 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2606860 ATAATTCATG
*
2606870 TTTTGATTCAACTTTCTCT
1 TTTTGATTCAACTTTCACT
*
2606889 TTTTGCTTCAACTTTCACT
1 TTTTGATTCAACTTTCACT
2606908 TT
1 TT
2606910 CTTCAATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTTGATTCAACTTTCACT
Found at i:2617019 original size:13 final size:13
Alignment explanation
Indices: 2616997--2617037 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
2616987 AATTTTTGTA
2616997 TGGATTATATATG
1 TGGATTATATATG
*
2617010 TGGTTTATATATG
1 TGGATTATATATG
2617023 TGGATTATATATG
1 TGGATTATATATG
2617036 TG
1 TG
2617038 TTTTCAGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (13 bp):
TGGATTATATATG
Found at i:2620687 original size:15 final size:15
Alignment explanation
Indices: 2620667--2620695 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2620657 TTAATATTAT
2620667 ATAAAATAAACCTAC
1 ATAAAATAAACCTAC
2620682 ATAAAATAAACCTA
1 ATAAAATAAACCTA
2620696 AACTAGTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (15 bp):
ATAAAATAAACCTAC
Found at i:2630894 original size:62 final size:63
Alignment explanation
Indices: 2630818--2630938 Score: 190
Period size: 64 Copynumber: 1.9 Consensus size: 63
2630808 GAAATTATTT
* *
2630818 AGTGTATCGATGCACCCCTT-AAATGAAAACATTGAATGTAATTTGTGTATCGATGCACAGGA
1 AGTGTATCGATGCACCCATTAAAATGAAAACATCGAATGTAATTTGTGTATCGATGCACAGGA
* *
2630880 AGTGTATCGATGCACCCATTAAAAATGGAAACATCGAATGTGATTTGTGTATCGATGCA
1 AGTGTATCGATGCACCCATT-AAAATGAAAACATCGAATGTAATTTGTGTATCGATGCA
2630939 TAGTTAGTGC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 19 0.36
64 34 0.64
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (63 bp):
AGTGTATCGATGCACCCATTAAAATGAAAACATCGAATGTAATTTGTGTATCGATGCACAGGA
Found at i:2630953 original size:64 final size:62
Alignment explanation
Indices: 2630816--2630954 Score: 188
Period size: 64 Copynumber: 2.2 Consensus size: 62
2630806 CAGAAATTAT
* *
2630816 TTAGTGTATCGATGCACCCCTTAAATGAAAACATTGAATGTAATTTGTGTATCGATGCACAG
1 TTAGTGTATCGATGCACCCATTAAATGAAAACATCGAATGTAATTTGTGTATCGATGCACAG
** * * *
2630878 GAAGTGTATCGATGCACCCATTAAAAATGGAAACATCGAATGTGATTTGTGTATCGATGCATAG
1 TTAGTGTATCGATGCACCCATT--AAATGAAAACATCGAATGTAATTTGTGTATCGATGCACAG
*
2630942 TTAGTGCATCGAT
1 TTAGTGTATCGAT
2630955 TCACAAGTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 19 0.29
64 46 0.71
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (62 bp):
TTAGTGTATCGATGCACCCATTAAATGAAAACATCGAATGTAATTTGTGTATCGATGCACAG
Found at i:2631405 original size:24 final size:22
Alignment explanation
Indices: 2631375--2631429 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
2631365 TGGTTATTGC
*
2631375 ATATGTTATACAATATATGTGAAT
1 ATATGTTAT--AATACATGTGAAT
**
2631399 ATATGTTATGGTACATGTGAAT
1 ATATGTTATAATACATGTGAAT
2631421 ATATGTTAT
1 ATATGTTAT
2631430 GGTAAATGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 19 0.68
24 9 0.32
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (22 bp):
ATATGTTATAATACATGTGAAT
Found at i:2631416 original size:22 final size:22
Alignment explanation
Indices: 2631391--2631442 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
2631381 TATACAATAT
*
2631391 ATGTGAATATATGTTATGGTAC
1 ATGTGAATATATGTTATGGTAA
2631413 ATGTGAATATATGTTATGGTAA
1 ATGTGAATATATGTTATGGTAA
2631435 ATGTGAAT
1 ATGTGAAT
2631443 GAGTATAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.40
Consensus pattern (22 bp):
ATGTGAATATATGTTATGGTAA
Found at i:2633169 original size:23 final size:23
Alignment explanation
Indices: 2633135--2633220 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 23
2633125 GGGCATATTA
*
2633135 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
2633158 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* * *
2633181 AGATC-CTTCAGGAT-AAATTCTACG
1 TG-GCACTTC-GG-TGCAATTCTACG
*
2633205 TGGCACTTTGGTGCAA
1 TGGCACTTCGGTGCAA
2633221 ATTTATAAGA
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
22 1 0.02
23 31 0.65
24 15 0.31
25 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:2633804 original size:22 final size:22
Alignment explanation
Indices: 2633779--2633823 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2633769 GTAGCAGTAT
2633779 TGTAGCAGGGGAATCAGTTCCC
1 TGTAGCAGGGGAATCAGTTCCC
*
2633801 TGTAGCAGGGGAATCGGTTCCC
1 TGTAGCAGGGGAATCAGTTCCC
2633823 T
1 T
2633824 ATTTGCAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.22, G:0.33, T:0.24
Consensus pattern (22 bp):
TGTAGCAGGGGAATCAGTTCCC
Found at i:2638083 original size:19 final size:20
Alignment explanation
Indices: 2638061--2638103 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
2638051 GAGAAAAGGT
2638061 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
*
2638080 AAAA-TTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
2638099 AAAAG
1 AAAAG
2638104 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:2642265 original size:17 final size:17
Alignment explanation
Indices: 2642243--2642282 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2642233 TTAGTTTATA
*
2642243 ATTCCATTTCTGTTAAC
1 ATTCCATTTCTATTAAC
2642260 ATTCCATTTCTATTAAC
1 ATTCCATTTCTATTAAC
2642277 ATTCCA
1 ATTCCA
2642283 AGTAATGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.25, G:0.03, T:0.45
Consensus pattern (17 bp):
ATTCCATTTCTATTAAC
Found at i:2649458 original size:20 final size:21
Alignment explanation
Indices: 2649433--2649486 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
2649423 AATCCCTACT
2649433 ATTATTACTATAT-TTTTGTG
1 ATTATTACTATATATTTTGTG
* *
2649453 ATTATTATTTTATATTTTGTG
1 ATTATTACTATATATTTTGTG
*
2649474 -TAATTA-TATATAT
1 ATTATTACTATATAT
2649487 ATATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 6 0.21
20 16 0.55
21 7 0.24
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (21 bp):
ATTATTACTATATATTTTGTG
Found at i:2649487 original size:21 final size:21
Alignment explanation
Indices: 2649433--2649488 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
2649423 AATCCCTACT
*
2649433 ATTATTACTATATTTTTGTGATT
1 ATTATTA-TATA-TTTTGTGATA
*
2649456 ATTATTTTATATTTTGTG-TA
1 ATTATTATATATTTTGTGATA
2649476 ATTATATATATAT
1 ATTAT-TATATAT
2649489 ATATATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 6 0.21
21 13 0.45
22 4 0.14
23 6 0.21
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (21 bp):
ATTATTATATATTTTGTGATA
Found at i:2649489 original size:23 final size:22
Alignment explanation
Indices: 2649432--2649492 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
2649422 TAATCCCTAC
*
2649432 TATTATTACTATATTTTTGTGAT
1 TATTATTA-TATATTTTTGTAAT
*
2649455 TATTATTTTATATTTTGTGTAAT
1 TATTATTATATATTTT-TGTAAT
2649478 TATATATATATATAT
1 TAT-TAT-TATATAT
2649493 ATATATATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 8 0.25
23 15 0.47
24 3 0.09
25 6 0.19
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.61
Consensus pattern (22 bp):
TATTATTATATATTTTTGTAAT
Found at i:2649810 original size:14 final size:14
Alignment explanation
Indices: 2649779--2649823 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2649769 CTATATTTTC
2649779 TTTATT-TATTTA-
1 TTTATTCTATTTAT
2649791 TTTATTACT-TTTAT
1 TTTATT-CTATTTAT
*
2649805 TTTATTTTATTTAT
1 TTTATTCTATTTAT
2649819 TTTAT
1 TTTAT
2649824 CCATCTTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 6 0.21
13 5 0.18
14 17 0.61
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTCTATTTAT
Found at i:2649817 original size:9 final size:9
Alignment explanation
Indices: 2649772--2649823 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
2649762 AGATTATCTA
*
2649772 TATTTTCTT
1 TATTTTATT
2649781 TA-TTTATT
1 TATTTTATT
2649789 TA-TTTA-T
1 TATTTTATT
2649796 TACTTTTATTT
1 TA-TTTTA-TT
2649807 TATTTTATT
1 TATTTTATT
2649816 TATTTTAT
1 TATTTTAT
2649824 CCATCTTTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
7 3 0.08
8 11 0.29
9 16 0.42
10 5 0.13
11 3 0.08
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (9 bp):
TATTTTATT
Found at i:2653730 original size:95 final size:89
Alignment explanation
Indices: 2653615--2653854 Score: 296
Period size: 95 Copynumber: 2.7 Consensus size: 89
2653605 ATAATATTTA
*
2653615 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAT
1 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAG
* *
2653680 ATTCAGGTAGCCTGATAAAAGTGATTAT
66 ATTCAGCTAACCTGAT-AAAG-G--TAT
*
2653708 ACTATACAATAAAGCTTGAGTTGTCCCTCTA-AGGCAAATGGTTAAACGCCCCGGCTTTATGGAT
1 --TATACAATAAAGCTTGAGTTGTCCCTCTAGA-GCAATTGGTTAAACGCCCCGGCTTTATGGAT
2653772 AAGATTCAGCTAACCTGATAAAGGTAT
63 AAGATTCAGCTAACCTGATAAAGGTAT
* * * *
2653799 T-TAC-AT--A--TTGAGATATCCCTCTAGAGCAATTGGTAAAACGCCTCGGCTTTATGGAT
1 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGAT
2653855 CCAGCTAGCC
Statistics
Matches: 134, Mismatches: 9, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
83 42 0.31
84 1 0.01
85 1 0.01
87 2 0.01
88 3 0.02
89 1 0.01
91 3 0.02
93 1 0.01
94 5 0.04
95 75 0.56
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (89 bp):
TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAG
ATTCAGCTAACCTGATAAAGGTAT
Found at i:2654577 original size:19 final size:17
Alignment explanation
Indices: 2654536--2654586 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
2654526 ATTATCTATA
*
2654536 TTTTCTTTA-TTTATTT
1 TTTTATTTATTTTATTT
2654552 TTTTA-TTACTTTTATTT
1 TTTTATTTA-TTTTATTT
2654569 TACTTTATTTATTTTATT
1 T--TTTATTTATTTTATT
2654587 CACATTTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 3 0.10
16 4 0.14
17 8 0.28
19 11 0.38
20 3 0.10
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTATTTTATTT
Found at i:2654601 original size:31 final size:26
Alignment explanation
Indices: 2654541--2654610 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 26
2654531 CTATATTTTC
2654541 TTTATTTATTTTTTTATTACTTTTAT
1 TTTATTTATTTTTTTATTACTTTTAT
*
2654567 TTTACTTTATTTATTTTATTCACATTTCTTT
1 TTTA-TTTATTT-TTTTATT-AC-TTT-TAT
2654598 TTTATCTTATTTT
1 TTTAT-TTATTTT
2654611 CCTTTGCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
26 4 0.11
27 7 0.19
28 7 0.19
29 2 0.05
30 5 0.14
31 12 0.32
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTATTTATTTTTTTATTACTTTTAT
Found at i:2656022 original size:22 final size:22
Alignment explanation
Indices: 2655997--2656043 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2655987 ATCAATATTC
2655997 TTATCAT-TTATATCTTATAATT
1 TTATCATCTTATATC-TATAATT
* *
2656019 TTATCCTCTTATATCTATTATT
1 TTATCATCTTATATCTATAATT
2656041 TTA
1 TTA
2656044 CTCAACATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.28, C:0.13, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATCATCTTATATCTATAATT
Found at i:2656375 original size:23 final size:23
Alignment explanation
Indices: 2656349--2656394 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2656339 CACCACAGCT
*
2656349 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
2656372 CGTAGAATTGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2656395 TATAAAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2659595 original size:9 final size:10
Alignment explanation
Indices: 2659574--2659606 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2659564 TTTTTTAAAA
2659574 AAAATGCAAT
1 AAAATGCAAT
2659584 AAAATG-AAT
1 AAAATGCAAT
*
2659593 AAAATTCAAT
1 AAAATGCAAT
2659603 AAAA
1 AAAA
2659607 ATATAATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (10 bp):
AAAATGCAAT
Found at i:2660741 original size:14 final size:14
Alignment explanation
Indices: 2660722--2660752 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2660712 GGATCAAATG
2660722 AATTATTATTTATT
1 AATTATTATTTATT
*
2660736 AATTATTATTTTTT
1 AATTATTATTTATT
2660750 AAT
1 AAT
2660753 AACAGTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
AATTATTATTTATT
Found at i:2665077 original size:8 final size:8
Alignment explanation
Indices: 2665053--2665099 Score: 51
Period size: 9 Copynumber: 5.5 Consensus size: 8
2665043 TATTTTTTAA
2665053 TTAAAATTT
1 TTAAAA-TT
2665062 TCTAAAATT
1 T-TAAAATT
2665071 TTAAAA-T
1 TTAAAATT
2665078 TTAATAATT
1 TTAA-AATT
2665087 TTAATAATT
1 TTAA-AATT
2665096 TTAA
1 TTAA
2665100 TCAAATTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 5 0.14
8 7 0.20
9 18 0.51
10 5 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (8 bp):
TTAAAATT
Found at i:2665091 original size:9 final size:9
Alignment explanation
Indices: 2665067--2665115 Score: 59
Period size: 9 Copynumber: 5.7 Consensus size: 9
2665057 AATTTTCTAA
2665067 AATTTTAA-
1 AATTTTAAT
2665075 AA-TTTAAT
1 AATTTTAAT
2665083 AATTTTAAT
1 AATTTTAAT
2665092 AATTTTAAT
1 AATTTTAAT
*
2665101 CAAATTTAAT
1 -AATTTTAAT
2665111 -ATTTT
1 AATTTT
2665116 TTAAAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
7 5 0.14
8 8 0.22
9 15 0.42
10 8 0.22
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (9 bp):
AATTTTAAT
Found at i:2665116 original size:19 final size:18
Alignment explanation
Indices: 2665077--2665181 Score: 55
Period size: 18 Copynumber: 6.1 Consensus size: 18
2665067 AATTTTAAAA
*
2665077 TTTAATAATTTTAATAAT
1 TTTAATAAATTTAATAAT
2665095 TTTAATCAAATTTAAT-AT
1 TTTAAT-AAATTTAATAAT
* *
2665113 TTT-TTAAA-AT-A-AAT
1 TTTAATAAATTTAATAAT
***
2665127 TTCCTTAAACTTTAA-AA-
1 TTTAATAAA-TTTAATAAT
*
2665144 TCTAATAAATTTAATAAT
1 TTTAATAAATTTAATAAT
*
2665162 TTAAATCAAA-TTAATAAT
1 TTTAAT-AAATTTAATAAT
2665180 TT
1 TT
2665182 ATCATTTTAG
Statistics
Matches: 67, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
14 5 0.07
15 6 0.09
16 8 0.12
17 9 0.13
18 28 0.42
19 11 0.16
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTAATAAATTTAATAAT
Found at i:2665127 original size:67 final size:66
Alignment explanation
Indices: 2665043--2665177 Score: 182
Period size: 67 Copynumber: 2.0 Consensus size: 66
2665033 ATTAATCTTT
* * * * * *
2665043 TATTTTTTAATTAAAATTTTCTAAAATTTTAAAATTTAATAATTTTAATAATTTTAATCAAATTT
1 TATTTTTTAAATAAAATTTCCTAAAACTTTAAAATCTAATAAATTTAATAATTTAAATCAAA-TT
2665108 AA
65 AA
*
2665110 TATTTTTTAAA-ATAAATTTCCTTAAACTTTAAAATCTAATAAATTTAATAATTTAAATCAAATT
1 TATTTTTTAAATA-AAATTTCCTAAAACTTTAAAATCTAATAAATTTAATAATTTAAATCAAATT
2665174 AA
65 AA
2665176 TA
1 TA
2665178 ATTTATCATT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
66 7 0.12
67 53 0.88
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (66 bp):
TATTTTTTAAATAAAATTTCCTAAAACTTTAAAATCTAATAAATTTAATAATTTAAATCAAATTA
A
Done.